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216 Cards in this Set
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What are structural formulas for molecules involving H, C, N, O, F, S, P, Si, Cl?
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Structural formulas show every atom and every bond, as well as the unshared electron pairs found in a molecule. Atoms are represented by their atomic symbol. Bonds are represented by solid black lines. A single black line or dash represents 2 shared electrons in a single covalent bond. Two black lines represent 4 shared electrons in a double covalent bond. Three black lines represent 6 shared electrons in a triple covalent bond. An unshared electron pair is represented by two dots paired together adjacent to the atomic symbol.
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What kinds of molecules are H and C bonds found in?
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What types of molecules are N atoms found in?
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What types of molecules are O atoms found in?
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What types of molecules are F atoms found in?
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What types of molecules are S atoms found in?
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What types of molecules are P atoms found in?
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What types of molecules are Si atoms found in?
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What types of molecules are Cl atoms found in?
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Explain the concept of delocalized electrons and resonance in ions and molecules.
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Resonance structures result from electrons not being fixed in position (that's why you "push" electrons when drawing resonance structures).
When electrons are not fixed in position, they are delocalized electrons. For all practical purposes, resonance and electron delocalization mean the same thing. In ions, resonance and electron delocalization occurs to "distribute" the charge around. In molecules, resonance and electron delocalization occurs in aromatic rings and conjugated double bonds. Resonance of molecules distributes the electrons around to produce a hybrid structure. The electron and charge delocalization described by resonance enhances the stability of the molecules or ions. No atoms change their positions within the common structural framework. Only electrons are moved. The better resonance structure is that which has the least amount of formal charge. Just with electrostatics, like charges repel, so they like to be spread out as much as possible - this lowers the potential energy of the molecule. |
Huckel's rule: aromatic is planar monocyclic rings with 4n + 2 pi electrons (where n is any integer, including zero).
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How does multiple bonding affect bond length and bond energy?
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Multiple bonding decreases bond length.
Multiple bonding increases bond energy. Covalent bonds are strong and are usually permanent. Ionic bonds are stronger than covalent bonds. Disulfide bonds are covalent bonds that occur between 2 cysteine amino acids. Hydrogen bonds are weaker intermolecular interactions than covalent bonds. London dispersion forces are the weakest of the interactions. |
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How does multiple bonding affect rigidity in molecular structure?
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Multiple bonding increases rigidity in molecular structure.
Single bonds can rotate, but double and triple bonds can't. Even partial double bonds like those found in the peptide bond prevents free rotation. A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water (H2O). This is a dehydration synthesis reaction (the condensation reaction part is when the 2 molecules combine into 1), and usually occurs between amino acids. The resulting C(O)NH bond is called a peptide bond, and the resulting molecule is an amide. The amide group has two resonance forms and the resonance suggests that the amide group has a partial double bond character. |
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What are isomers?
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Same molecular formula, different structural formula.
"Same in writing, different in drawing..." |
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What are constitutional isomers?
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Constitutional isomerism in accordance with IUPAC, is a form of isomerism in which molecules with the same molecular formula have atoms bonded together in different orders, as opposed to stereoisomerism. Constitutional isomers are also called structural isomers, and they have the same molecular formula, but different connectivity.
Position isomers: structural isomers that have the same functional groups, but they are positioned differently. Functional group isomers: structural isomers that have the same molecular formula, but different functional groups. |
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What are geometric isomers?
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Geometric isomers have the same molecular formula, same connectivity, but have different orientation across a double bond. When both sides of the double bond contains the SAME 2 groups, then cis and trans is used. Cis = same side, Trans = opposite sides. When DIFFERENT groups are attached to either side of a double bone, Z and E is used.
Z is when the higher priority groups (ranked according to the Cahn-Ingold-Prelog rules) are orientated on the same side across the double bond. Zusammen is the German word for together. In the picture CH3 and Cl are the higher priority groups. Even if you have a double bond in the middle of the chain and it is difficult to see what side the groups are on, first look for the highest priority group period, like halogens, then compare that to the groups on the other side of the bond, which could be the carbon chain itself. E is when the higher priority groups are orientated on different sides across the double bond. Entgegen is the German word for opposed. For 1,2 substitution on a cyclohexane ring, axial and equitorial positions is a cis relationship. For a 1,2 substitution on a cyclohexane ring, axial and axial positions (opposite directions) as well as equitorial and equitorial positions (opposite directions) are trans configuraitons. The most stable configuration occurs when the largest groups are in the equitorial position. Even if it's a 1,2 substituted cyclohexane ring and the 2 groups are appear to have more steric hindrance in equitorial/equitorial than if it would if they were in axial/axial positions, equitorial positions are more stable..period! |
Geometric isomers have different physical properties. Cis molecules have a dipole moment while trans molecules do not. Due to their dipole moment, cis molecules have stronger intermolecular forces leading to higher boiling points (harder to boil to gas because of interactions). Due to their lower symmetry, however, cis molecules do NOT form crystals as readily, and thus have lower melting/freezing points (makes it harder to freeze/easier to melt, stays longer as a fluid). The substituent groups in the cis position may crowd each other; a condition known as steric hindrance. Steric hindrance in cis molecules produces higher energy levels resulting in higher heats of combustion.
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What are meso compounds?
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Meso compounds may have chiral centers, but as a molecule, they are achiral and optically inactive.
Meso compounds reduce the total number of stereoisomers. |
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What are stereoisomers and chiral centers?
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Stereoisomers have the same molecular formula, same connectivity, but have different 3-D arrangements across one or more asymmetric (chiral) centers. Stereoisomers are diastereomers, enantiomers, and cis/trans isomers (Geometric isomers). Chiral center is any atom with 4 different entities attached to it. You can't have stereoisomers if you don't have a chiral center. Enantiomers have the same chemical and physical properties (unless reactions with other chila compounds or reactions with polarized light). Geometric isomers have the same chemical properties, different physical properties. Diastereomers have different chemical and physical properties. The maximum number of optically active isomers that a single compound can have is equal to 2^(# of chiral centers). Two chiral centers in a single molecule may offset each other creating an optically inactive molecule. Such compounds are called meso compounds. Meso compounds have a plane of symmetry through their centers which divides them into two halves that are mirror images to each other. Meso compounds are achiral and therefore optically inactive.
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What are enantiomers?
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Enantiomers are mirror images of each other. That means ALL chiral centers in one enantiomer is reversed in the other. So if one enantiomer is R, the other is S. If two chiral centers if 1 enantiomer is R and S, the other is S and R.
Enantiomers have the same physical properties and chemical properties except for 2 cases: 1) reactions with ohter chiral compounds and 2) reactions with polarized light. |
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What are diastereomers?
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Diastereomers - more than one chiral center, inversion of stereochemistry on some but not all of its chiral centers. For examples, diastereomers would have stereochemistries of (R)-(R) vs (R)-(S). Another example of diastereomers would be (R)-(R)-(S)-(R) vs (R)-(R)-(R)-(R). Note: in biological molecules, people use D and L for R and S, respectively. Caution: D and L (absolute configurations) are NOT the same as d and l (relative configuration). The letters d and l are used for plane polarized light. Diastereomers have different physical properties and the same chemical properties. The absolute stereo configuration of the amino acids at the alpha carbon is typically referred to using the D/L notation with reference to the absolute configuration of Glyceraldehyde rather than the more modern R/S designation. Geometric isomers (cis/trans and E/Z) are diastereomers.
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What are cis and trans isomers?
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In rings, it is easier to assign stereoisomers as cis/trans rather than R or S. Cis is having the same groups on the same side of the ring. Trans is having the same groups on different sides of the ring. If there are two hydrogen groups on one end of the double bond, it cannot have geometric isomers.
Hydrogenation, when H2 adds to a double or triple bond, results in syn-addition, in which the 2 hydrogens add to the same face of the double bond - a cis molecule results. Or the result could be an alkane. The 2 hydrogens add to the same face of the double bond because hydrogenation must occur with a metal catalyst (Pt, Pd, Ni etc) and the 2 hydrogens are bound to the catalyst together when they approach the molecule. The metal catalyst increases the reaction rate by lowering the activation energy. High temperature aren't needed. The double bonds in benzene is even less reactive than regular alkenes because hydrogenation ruins the aromaticity of the molecule. Also, in order for benzene rings to maintain aromaticity, they undergo substitution reactions instead of addition reactions (a proton is substituted for something else). Also, if an alkene is reacted with an acid in a reaction, the alkene is the electrophile because it gets protonated by the acid and becomes a carbocation. |
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What are conformational isomers?
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Conformational isomers have the same molecular formula, same connectivity, same stereochemistry, but can rotate about a single bond to switch between different conformations.
Technically, conformational isomers are not really isomers because you don't have to break any bonds to convert from one conformation to another. They are more accurately called conformers. |
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What are staggered and eclipsed conformations?
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Conformers about a single bond
Eclipsed Syn-periplanar: highest torsional strain, most unstable, bulky groups eclipse each other. Anticlinal eclipsed: high torsional strain, unstable, bulky groups eclipse hydrogens. Staggered Gauche: low torsional strain, stable, bulky groups 60° staggered. Anti: lowest torsional strain, most stable, bulky groups 180° staggered. Single bonds will rotate such that it achieves the most stable conformation. |
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What are chair, twisted boat, and boat conformations?
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Conformers of cyclohexose
Chair: most stable, everything is staggered. Twist boat: less stable, things are not completely eclipsed. Boat: least stable, everything is eclipsed. Hexose rings will twist and turn to achieve the most stable conformation. |
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What are axial and equatorial conformations?
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Torsional strain: the strain due to eclipsing of groups across a single bond.
Steric interactions Axial: most unstable because the axial groups are orientated with a high degree of clashing. Equatorial: most stable because the equatorial groups are orientated away from one another. Bulky groups like to be in the equatorial position. Most stable conformation: completely staggered (chair), with bulky groups in the equatorial position. Least stable conformation: completely eclipsed (boat), with bulky groups in the axial position. |
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What is the polarization of light?
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Light is an electromagnetic wave.
Electromagnetic waves are waves of electric and magnetic fields (in phase, but perpendicular to each other and also to the direction of propagation). Normal light has the EM fields in all directions (in a 360° circle perpendicular to the direction of propagation). Polarized light has EM fields all in one direction. |
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What is specific rotation?
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Specific rotation: chiral molecules containing a single enantiomer will rotate polarized light (to varying degrees) either to the left or to the right. This is why chiral molecules are said to be "optically active".
Left rotation: (-) or l or levorotatory. Right rotation: (+) or d or dextrorotatory. Caution: (+) or (-) does NOT correspond to R/S configurations. Caution: d and l is NOT the same as D and L. The upper case letters denote absolute configurations in sugars. |
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What are the Cahn-Ingold-Prelog rules for assigning priority?
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Start with the atoms directly bonded to the chiral carbon.
The atom with the higher MW has greater priority. It is assigned the number 1. The lowest priority is assigned the number 4. The movement goes from 1 to 2 to 3, and if it is counterclockwise, it's S, if it's clockwise it's R. If atoms are the same, look at the group of atoms attached to the atoms that are the same. The group with the higher MW has greater priority or the group with more bonds to the high MW species wins. For example, -CHO will have higher priority than -CH2OH because the carbon has a double bond to oxygen. Double bonds are counted twice in groups and triple bonds are counted three times in groups. Another example is, -CH(OH)2 will have higher priority than -CH2OH because the diol has 2 oxygens while the alcohol only has 1. What about -CH(OH)2 vs. CH2F? Ans: It doesn't matter how many oxygens there are, because fluorine has greater molecular weight. So fluorine has higher priority. |
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What are the Steps in assigning (R) and (S)?
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Steps in assigning (R) and (S):
a. Is the carbon center chiral? For our molecule, the answer is yes because 4 different groups are attached to the carbon atom. b. Assign priorities according to the Cahn-Ingold-Prelog rules c. Turn the molecule such that the lowest priority group at the back. d. Rotate from the 1st to 2nd to 3rd priority group like a steering wheel. It's (R) if you end up turning right, and it's (S) if you end up turning left. note: if the highest priority group is shifted to the back, assign the R or S, but then switch it! The lowest priority group has to be facing the back, not the highest. So watch out for where the highest priority group is facing. |
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What is absolute configuration?
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Absolute configuration is the (R) or (S) that's labeled on the chiral centers.
Make sure that the lowest priority is oriented away from the observer (pointed back). If the lowest priority is pointed toward the observer, then preliminarily assign the R/S configuration with the lowest priority pointing forward, then choose the opposite of that configuration to ultimately get the answer. |
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What is relative configuration?
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Relative configuration is always defined in relationship to another chiral center. The direction that a molecule rotates plane-polarized light is the prime example of relative configuration.
Before the mid-1800s, people did not have an understanding of the tetrahedral carbon atom, so they did not have absolute configurations. Instead, they used the relative configurations of which way a compound rotates plane-polarized light. The definition for relative configuration can be very broad. For example, you may arbitrarily assign one chiral center to be R* (even though it may or may not actually be R) as long as it is of opposite configuration to S* (which may or may not actually be S). Additionally, the cis or trans configuration that describes how one group is orientated relative to another group is also an example of relative configuration. Reactions can also proceed via retention or inversion, which describes the stereochemistry in relationship with the original reactant. |
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What are the conventions for writing R and S forms?
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If only 1 chiral center
(R/S)-molecule, where R/S is the absolute configuration and molecule is the name of the compound. For example, (R)-2-hydroxyl-propanal. If more than 1 chiral center (#R/S, #R/S)-molecule, where # is the carbon number (in ascending order), R/S is the absolute configuration, and molecule is the name of the compound. For example, (2R,3S)-2,3,4-hydroxyl-butanal. |
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What are the conventions for writing E and Z forms?
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If only 1 double bond
(E/Z)-molecule, where E/Z is the geometric configuration across the double bond, and molecule is the name of the compound. For example, (Z)-2-chloro-2-butene. (see geometric isomer figure) If more than 1 double bond (#E/Z, #E/Z)-molecule, where # is the carbon number (the smaller number in the double bond, in ascending order), and molecule is the name of the compound. By the smaller number in the double bond, we would use the carbon with the number 2 and not the carbon with the number 3 of the double bond. So the name of the molecule would be 2E,4Z instead of 3E,5Z. |
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What are racemic mixtures?
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Racemic mixtures contain equal amounts of both enantiomers. Another name for racemic mixtures is racemate.
Racemic mixtures do not rotate polarized light, so they are optically inactive. |
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How do you separate enantiomers?
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The separation of enantiomers is called resolution. Convert enantiomers to diastereomers. -Separation of diastereomers. Convert diastereomers back to enantiomers. Separation of enantiomers by biological means: Enzymes are highly specific and can differentiate between enantiomers. For example, if an enzyme digests or modifies all L-amino acids, then you'd be able to use that enzyme to separate a D/L racemic mixture. In nature, all proteins are made up of L-amino acids. All of the amino acids used in proteins (except for glycine which is not optically active) are of L configuration. The resolution of racemates is the separation of an equimolar mixture of enantiomers (racemate) by physical or chemical methods. Usually, the separation is carried out after a preceding conversion of the enantiomers into diastereomers, because, as a result of their practically identical chemical and physical properties, enantiomers cannot be separated directly.
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What are intramolecular vibrations and rotations?
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Vibrations: bonds can stretch, compress and bend like a spring. It is this vibration that is measured in IR-spec.
Rotations: molecules can rotate. Rotations produce waves mainly in the microwave region. However, part of the rotation spectra does overlap with the vibration spectra. |
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What is infrared spectroscopy?
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Infrared spectra plots transmittance vs. wavenumbers (cm-1). Wavenumber = 1 / wavelength in centimeters. This is also considered the frequency scale. It's located at the bottom of the chart is given in units of reciprocal centimeters (cm-1) rather than Hz, because the numbers are more manageable. The reciprocal centimeter is the number of wave cycles in one centimeter; whereas, frequency in cycles per second or Hz. Photon energies associated with this part of the infrared are not large enough to excite electrons, but may induce vibrational excitation of covalently bonded atoms and groups. The covalent bonds in molecules are not rigid sticks or rods, such as found in molecular model kits, but are more like stiff springs that can be stretched and bent. The mobile nature of organic molecules was noted in the chapter concerning conformational isomers. We must now recognize that, in addition to the facile rotation of groups about single bonds, molecules experience a wide variety of vibrational motions, characteristic of their component atoms. Consequently, virtually all organic compounds will absorb infrared radiation that corresponds in energy to these vibrations. Transmittance is the fraction of incident light at a specified wavelength that passes through a sample.
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What are the common characteristic group absorptions?
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Anything around 3000 cm-1 involves a hydrogen atom, be it O-H, N-H, or C-H.
Anything around 2000 cm-1 and below does not involve hydrogen, be it C=O, C=C, C-C, or C-O. With the same atoms, the higher the bond order, the faster it vibrates, and so the higher the wavenumber. 1700 cm-1 is for the carbonyl group. Remember this. 3300 cm-1 can be O-H, N-H, or alkyne C-H. OH is the broadest, N-H slightly sharper, alkyne C-H is very sharp. Broad peaks are due to hydrogen bonding (OH and NH). |
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What is the fingerprint region?
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Absorptions in the IR spectroscopy between 1300 and 909 cm-1, the fingerprint region, are primarily due to more complex vibrational motions. Patterns in the fingerprint region are unique for each compound just like a fingerprint is unique for each person. It is much more difficult to pick out individual bonds in this region than it is in the "cleaner" region at higher wavenumbers. The importance of the fingerprint region is that each different compound produces a different pattern of troughs in this part of the spectrum.
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Explain how the absorption in visible region yields complementary color.
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Absorption in visible region gives complementary color (e.g., carotene). There are primary colors of light and primary colors of pigment. Complementary color is the color that's on the opposite side of the color wheel. For example, the complementary of red is cyan. The absence of (when you absorb) a primary color of light, you end up with its complementary color. The primary colors of pigments is exactly the complementary colors of the primary colors of light. This is because pigments absorb a certain color of light and reflect the rest back into your eyes. Carotene absorbs blue light and reflect the others into your eyes. The absence of blue produces yellow, the complementary color of blue. Ultraviolet-visible spectroscopy refers to absorption spectroscopy in the UV-visible spectral region. This means it uses light in the visible and adjacent (near-UV and near-infrared (NIR)) ranges. The absorption in the visible range directly affects the perceived color of the chemicals involved. In this region of the electromagnetic spectrum, molecules undergo electronic transitions. Visible wavelengths cover a range from approximately 400 to 800 nm. The longest visible wavelength is red and the shortest is violet. Other common colors of the spectrum, in order of decreasing wavelength, may be remembered by the mnemonic: ROY G BIV.
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Explain the effect of structural changes on absorption.
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Effect of structural changes on absorption (e.g., indicators). Changes to chemical structure can lead to changes in absorption. H-indicator <--> H+ + Indicator- . H-indicator absorbs at a certain wavelength and is of one color. Indicator- absorbs at a different wavelength so is of a different color.
At low pH, high [H+], H-indicator and its color will predominate. At high pH, low [H+], indicator- and its color will predominate. At neutral pH, both H-indicator and indicator- will co-exist in an equilibrium, so the color will be a mixture of the two. Phenolphthalein is another example of the effect of molecular shape on delocalization of pi electrons. Phenolphthalein molecule is colorless in acid solution and its pi system is nonplanar. The electrons in the double bonds are "localized. The excitation energy is large and in the ultraviolet range. The molecule loses protons in basic solutions and forms a minus 2 anion. This negative ion is flat and the pi system is conjugated. In the planar ion the pi electrons in the eleven double bonds can delocalize over the 3 rings, the COO-1 carboxyl group and the oxygens. The anion imparts a color to solutions because the energy separation between the pi and pi antibonding levels is smaller and matches light in the visible range. |
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What are the universal indicators?
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Red: very acidic
Orange: acidic Yellow: weakly acidic Green: neutral Blue: basic Purple: very basic |
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Explain the pi-electron and nonbonding electron transitions in the ultraviolet region.
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Every time you have a bond, the atoms in a bond have their atomic orbitals merged together to form molecular orbitals. These valence electrons are not in their regular shells (s, p, d, f). They are in a new molecular bonding orbital, a special orbital for electrons between bonded atoms. Every time you have a molecular orbitals, you get bonding molecular orbitals and non-bonding (where the lone pairs are) and/or anti-bonding orbitals (higher energy state of the electrons). Normally, electrons sit in their bonding orbitals because it is the most stable there. If bonding orbitals are full, then non-bonding orbitals are occupied. Given enough energy (as in absorption), the electrons transition from the bonding or non-bonding orbitals to the anti-bonding orbitals.For UV absorption, we're interested in the pi-electrons of double and triple bonds because their molecular orbital transitions result in UV absorption. Double and triple bonds absorb UV because the pi electrons transition from the bonding and non-bonding molecular orbitals to the anti-bonding orbitals. Molecular orbital theory provides a model for the way electromagnetic radiation interacts with molecules. For example, an electron in the pi bonding molecular orbital (MO) of an alkene can be excited to a pi antibonding MO. This is described as a pi to pi* transition. For an isolated pi bond the energy separation, E, between the pi bonding and pi antibonding MO's is large; ultraviolet light with its large energy and short wavelength is needed to excite the pi electron. The large amount of energy that is needed to excite the pi electron can be accomplished by UV light because it has a lot of energy.
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What are conjugated systems?
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Conjugated systems decreases the energy of electromagnetic radiation that is absorbed.
The more conjugated double bonds there are, the longer the wavelengths of absorbed radiation. If there are enough conjugated double bonds, the molecule will start to absorb in the visible region. |
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What is mass spectroscopy?
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Mass spec is when you bombard a molecule with electrons. When electrons smash into your molecule, it is fragments into ions. What if the electrons "miss" your molecule? Ans: Your molecule is neither fragmented nor ionized. Uncharged molecules are not detected and are not included in the mass spectra. What if the electrons do not break apart your molecule, but merely ionizes it? Ans: this "molecular ion" will be detected as the parent peak, also called the molecular ion peak. What if the electrons not only ionize but also fragment your molecule? Ans: all the fragmented ions will be detected and plotted in the mass spectra. The faster (higher energy) the bombarding electron, the more fragmentation. The more fragmentation, the smaller the molecular ion peak. The x-axis of this bar graph is the increasing m/z ratio. The y-axis is the relative abundance of each ion, which is related to the number of times an ion of that m/z ratio strikes the detector. Assignment of relative abundance begins by assigning the most abundant ion a relative abundance of 100% (base peak). All other ions are shown as a percentage of that most abundant ion. Relative abundance is a way to directly compare spectra produced at different times or using different instruments.
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What is mass to charge ratio?
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Mass-to-charge ratio (m/e) or m/z. The mass-to-charge ratio is a physical quantity and shows that two particles with the same mass-to-charge ratio move in the same path in a vacuum when subjected to the same electric and magnetic fields. When electrons smash into your molecule, it is fragments into ions. These ions have a characteristic mass to charge ratio (m/e). A magnetic field resolves (separates) the different m/e ions so they can be individually detected and plotted on a spectrum. The resulting spectrum plots Relative abundance vs. the m/e ratio. It's important to realise that the pattern of lines in the mass spectrum of an organic compound tells you something quite different from the pattern of lines in the mass spectrum of an element. With an element, each line represents a different isotope of that element. With a compound, each line represents a different fragment produced when the molecular ion breaks up.
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What is the Molecular ion peak?
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The parent peak, or the molecular ion peak, is the peak that depicts the ion of the molecule without fragmentation. It has the highest m/z ratio.
Peaks clustered really close to one another depicts isotopes. The base peak is the tallest peak (most abundant species). |
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What is mass spectroscopy useful for?
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Mass spec is useful for: Measuring the molecular weight of a molecule. Identify the molecule by fragmentation patterns. Identity heteroatoms by their characteristic isotope ratios. Probably the most useful information you should be able to obtain from a MS spectrum is the molecular weight of the sample. This will often be the heaviest ion observed from the sample provided this ion is stable enough to be observed. The molecular ion (M+) is the molecular weight of the molecule. For most molecules the M+ peak is seen on the mass spectrum but it is not seen if formation of a stable cation is possible (it won't be seen if there is no positive charge on it). The base peak is caused by the most stable cation. The base peak is usually given an arbitrary height of 100, and the height of everything else is measured relative to this. The base peak is the tallest peak because it represents the commonest fragment ion to be formed - either because there are several ways in which it could be produced during fragmentation of the parent ion, or because it is a particularly stable ion.
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Explain the concept of Protons in a magnetic field in H NMR Spectroscopy.
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Protons have spins of up or down (+½ or -½, counterclockwise or clockwise. With an even number of protons, the spins pair up and the up and down spins of all the protons cancel each other out. With an odd number of protons, there is a net spin of up or down. Normally, both up or down spins are equal in energy (they are degenerate). So, either way goes. In the presence of a magnetic field, the spin that lines up with the magnetic field gets the lower energy. If the external magnetic field is up, then you better spin up. If the magnetic field is down, then you better spin down.
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What are resonance frequencies in NMR Spectroscopy?
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If we were to give the protons some energy (by radio wave absorption), then the protons can be promoted (flipped) to the higher energy spin, which is opposite to the direction of the external magnetic field. This absorption is called resonance. The resonance frequency is the frequency of the radio wave that's needed to cause a flip in spin.
The resonance frequency (or energy or field strength) of absorption is called the chemical shift. Different protons have different resonance frequencies. Equivalent protons have the same resonance frequencies. You can substitute X at any of the equivalent protons, and you should end up with the same new compound. If not, then they're not equivalent protons. What makes protons have different resonance frequencies depends on what atom they're close to. NMR measures the chemical shift relative to a standard called TMS (tetramethylsilane) in unit of ppm. The more "different" two protons are, the farther their chemical shifts. Resonance frequencies are sometimes referred to as frequencies and rf. |
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Explain electron shielding and deshielding in NMR Spectroscopy.
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What makes protons "different" is the degree of electron shielding or deshielding. Next to stuff like carbon, hydrogen is shielded by electrons because carbon is not so electronegative. The hydrogen has a higher electron density near things like carbon and is shielded from the magnetic field. Next to stuff like oxygen, hydrogen is deshielded because oxygen is very electronegative. The hydrogen near things like oxygen has a lower electron density and is deshielded from the magnetic field. When things are shielded, the magnetic field is smaller and they have small chemical shifts and appear upfield (to the right). When things are deshielded, the magnetic field is larger and they have large chemical shifts and appear downfield (to the left). Since the magnetic field strength dictates the energy separation of the spin states and hence the radio frequency of the resonance, the structural factors mean that different types of proton will occur at different chemical shifts. This is what makes NMR so useful for structure determination, otherwise all protons would have the same chemical shift. The electrons around the proton create a magnetic field that opposes the applied field. Since this reduces the field experienced at the nucleus, the electrons are said to shield the proton. So those elements that have more electrons surrounding them (more electronegative) they are more shielded. If the electron density about a proton nucleus is relatively high, the induced field due to electron motions will be stronger than if the electron density is relatively low. The shielding effect in such high electron density cases will therefore be larger, and a higher external field (Bo) will be needed for the rf energy to excite the nuclear spin. The ranges are from 0 ppm to 12ppm and the higher numbers indicate the the deshielded (downfield) end and the lower numbers indicate the shielded (upfield) end.
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How do equivalent protons produce signals in NMR spectroscopy?
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NMR is nuclear magnetic resonance because the nuclear stands for protons; magnetic stands for the external magnetic field; the resonance stands for the absorption of radio waves.
Signals by n equivalent protons add up to produce one signal the height n times the signal for a single proton. The 1H NMR spectrum of an organic compound provides information concerning: 1) the # of different types of hydrogens present in the molecule 2) the relative #'s of the different types of hydrogens 3) the electronic environment of the different types of hydrogens 4) the number of hydrogen "neighbor" a hydrogen has. Nuclear magnetic resonance is an effect that occurs when the nucleus of an atom is placed in a magnetic field. The spinning nucleus in a constant magnetic field wobbles just like a spinning top. If in addition to the constant magnetic field, there is another magnetic field that varies at the same frequency as the nucleus wobbles, the nucleus will flip back and forth so that the nucleus effectively alternates the direction in which it spins. As the nucleus flips its spin direction, it either absorbs or emits low energy radio waves. Studying these radio waves allows physicists to deduce various properties of the atomic nuclei undergoing NMR. |
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What is extraction?
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Extraction (Distribution of Solute Between Two Immiscible Solvents). Liquid-liquid extraction is a method to separate compounds based on their relative solubilities in two different immiscible liquids, usually water and an organic solvent. It is an extraction of a substance from one liquid phase into another liquid phase. The liquids must be immiscible: this means that they will form two layers when mixed together, like oil and vinegar do in dressing. Some compounds are more soluble in the organic layer (the "oil") and some compounds are more soluble in the aqueous layer (the "vinegar"). The aim is to to extract a compound of interest that is present in very small amounts in an aqueous solution. The compound is not soluble in the aqueous solution. With the help of an organic liquid in which that compound is highly soluble, the compound of interest gets extracted out the aqueous solution and into the organic solution in which it is soluble. We are extracting the liquid with the compound of interest, not the compound itself. This method is based on the relative solubility of the compounds in organic solvents versus aqueous medium. The organic liquid in which the compound is more soluble is generally called the 'solvent'. The solvent chosen should satisfy the following conditions: 1) The solvent should be immiscible with water. 2) The compound initially present in aqueous solution should be highly soluble in the solvent.
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What is the process for extraction?
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The aqueous solution of the compound (to be extracted) is taken in a separating funnel. A small quantity of a suitable organic solvent is added to this. The separating funnel is stoppered and the contents are shaken for some time. The funnel is then allowed to stand undisturbed on a tripod stand for some time. The liquids in the flask separate into two layers. These two layers are collected separately in two beakers/flasks. The aqueous layer is again transferred to the separating funnel and the process is repeated with the fresh organic solvent. Once the extractino process is completed, drying agents can now be used and the product can be isolated from the organic solvent. Differential extraction becomes more effective if the process is repeated a number of times using a small volume of the organic solvent each time, than by using the whole solvent in one lot, i.e. multiple extraction is more efficient than single extraction. For example, iodine (I2) can be extracted from its dilute aqueous solution (solubility of iodine in water in very small) by differential extraction method using carbon tetrachloride (CCl4). This is because iodine is much more soluble in carbon tetrachloride than in water, and carbon tetrachloride is immiscible with water. Carbon tetrachloride is heavier than water. So, the solution of iodine in CCl4 forms the lower layer. If you are given a question that says a compound has a water solubility of 5.5% by volume, and the solution is made with 5ml of the compound mixed with 95 ml of water, then the solution would be homogenous because there is 5% of the compound present, so less of the 5.5% solubility threshold means the compound will be completely soluble, while more than 5.5% of the threshold means the compound will not be soluble. Solubility is the property of a solid, liquid, or gaseous chemical substance called solute to dissolve in a liquid solvent to form a homogeneous solution of the solute in the solvent.
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What is distillation?
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Separates liquids based on boiling point. The stuff with the lower boiling point is boiled off and collected; the higher boiling point stuff remains behind. Simple distillation = done with a normal column = can separate two liquids if the difference in boiling point is large. Fractional distillation = done with a fractionating column = can separate two liquids with smaller differences in boiling point. Vacuum distillation = done under lower pressure (vacuum) = lowers the boiling point for all liquid components so you don't have to crank up the temperature so high (chemical might decompose). Vacuum distillation is distillation at a reduced pressure. Since the boiling point of a compound is lower at a lower external pressure, the compound will not have to be heated to as high a temperature in order for it to boil. Vacuum distillation is used to distill compounds that have a high boiling point or any compound which might undergo decomposition on heating at atmospheric pressure.
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What is chromatography?
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The solute refers to the sample components in partition chromatography.
The solvent refers to any substance capable of solubilizing other substance, and especially the liquid mobile phase in LC. Chromatography is the collective term for a set of laboratory techniques for the separation of mixtures. It involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture based on differential partitioning between the mobile and stationary phases. The analyte is the substance that is to be separated during chromatography. |
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What is the mobile phase of chromatography?
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The mobile phase is the phase which moves in a definite direction. It may be a liquid (LC and CEC), a gas (GC), or a supercritical fluid (supercritical-fluid chromatography, SFC). The mobile phase consists of the sample being separated/analyzed and the solvent that moves the sample through the column. In the case of HPLC the mobile phase consists of a non-polar solvent(s) such as hexane in normal phase or polar solvents in reverse phase chromotagraphy and the sample being separated. The mobile phase moves through the chromatography column (the stationary phase) where the sample interacts with the stationary phase and is separated.
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What is the stationary phase of chromatography?
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The stationary phase is the substance which is fixed in place for the chromatography procedure. Examples include the silica layer in thin layer chromatography
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What is Gas–liquid chromatography?
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Gas chromatography (GC), is a common type of chromatography used in analytic chemistry for separating and analyzing compounds that can be vaporized without decomposition. Good if analyte can be promoted to gas phase. Gas-liquid chromatography (GLC) is the same thing as gas chromatography (GC). The gas part is the mobile phase, the liquid part is the stationary phase coated to the inside walls of the column. Substrate equilibrates between mobile (gas) and stationary (liquid coat) phase. Those with greater affinity for the stationary phase comes out of the column slower. Polar substrate has more affinity for polar stationary phase, and hydrophobic substrate has more affinity for hydrophobic stationary phase. Gas chromatography is also similar to fractional distillation, since both processes separate the components of a mixture primarily based on boiling point (or vapor pressure) differences. However, fractional distillation is typically used to separate components of a mixture on a large scale, whereas GC can be used on a much smaller scale (i.e. microscale). The gaseous compounds being analyzed interact with the walls of the column, which is coated with different stationary phases. This causes each compound to elute at a different time, known as the retention time of the compound. The comparison of retention times is what gives GC its analytical usefulness.
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What is elution?
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Elution is a term used in analytical and organic chemistry to describe the emergence of chemicals from the column of a chromatograph. As they elute, the chemicals typically flow into a detector. Predicting and controlling the order of elution is a key aspect of column chromatographic methods.
The material emerging from the column is known as the eluate or mobile phase. The eluent is the carrier that moves the chemicals through the column. in gas chromatography, it is the carrier gas.[1] The mobile phase specifically includes the analytes/solutes passing through the column, while the eluent is only the carrier. The elution time of a solute is the time between the start of the separation (the time at which the solute enters the column) and the time at which the solute elutes. In the same way, the elution volume is the volume of eluent required to cause elution. Under standard conditions for a known mix of solutes in a certain technique, the elution volume may be enough information to identify solutes. |
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What is paper chromatography?
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Paper chromatography is an analytical chemistry technique for separating and identifying mixtures that are or can be coloured, especially pigments. Classically used to separate pigments in dyes. Solvent = mobile phase. Paper = stationary phase. Pigments in dyes stick to paper, solvent tries to wash them along, those with greater affinity to paper stays behind, those with greater affinity to solvent gets washed along. Rf value = distance traveled by pigment / distance of solvent front. Rf = 0 means that pigment has not moved. Rf = 1 means that pigment moved as far as the solvent front. The paper is composed of cellulose, a polar substance, so polar compounds have a high affinity for the paper.
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What is the technique for paper chromatography?
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A small concentrated spot of solution that contains the sample of the solute is applied to a strip of chromatography paper about two centimeters away from the base of the plate, usually using a capillary tube for maximum precision. This sample is absorbed onto the paper and may form interactions with it. Any substance that reacts or bonds with the paper cannot be measured using this technique. The paper is then dipped into a suitable solvent, such as ethanol or water, taking care that the spot is above the surface of the solvent, and placed in a sealed container. The solvent moves up the paper by capillary action, which occurs as a result of the attraction of the solvent molecules to the paper; this can also be explained as differential adsorption of the solute components into the solvent. As the solvent rises through the paper it meets and dissolves the sample mixture, which will then travel up the paper with the solvent solute sample. Different compounds in the sample mixture travel at different rates due to differences in solubility in the solvent, and due to differences in their attraction to the fibers in the paper. The more soluble the component the further it goes. Since paper is composed of cellulose, a polar substance, polar substances have a high affinity for the paper. Paper chromatography takes anywhere from several minutes to several hours. In some cases, paper chromatography does not separate pigments completely; this occurs when two substances appear to have the same values in a particular solvent.
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What is Thin-layer chromatography?
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Thin-layer chromatography = advanced paper chromatography. Thin layer chromatography (TLC) is a chromatography technique used to separate mixtures.
Instead of paper, you have a plate coated with a specific stationary phase of your choosing. Rf value used in the same way as paper chromatography. Thin layer chromatography is performed on a sheet of glass, plastic, or aluminum foil, which is coated with a thin layer of adsorbent material, usually silica gel, aluminium oxide, or cellulose. This kind of adsorbent material is polar. This layer of adsorbent is known as the stationary phase. Thus, if you have a non-polar solvent, non-polar compounds will move farther than more polar compounds because polar compounds bond more strongly to the polar chromatography paper (or sheet). After the sample has been applied on the plate, a solvent or solvent mixture (known as the mobile phase) is drawn up the plate via capillary action. Because different analytes ascend the TLC plate at different rates, separation is achieved. |
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What is adsorption?
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Adsorption is the adhesion of molecules of gas, liquid, or dissolved solids to a surface. This process creates a film of the adsorbate (the molecules or atoms being accumulated) on the surface of the adsorbent. It differs from absorption, in which a fluid permeates or is dissolved by a liquid or solid. The term sorption encompasses both processes, while desorption is the reverse of adsorption.
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What is recrystallization?
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Recrystalization (Solvent Choice from Solubility Data). Recrystalization = barely dissolving your compound, then let it recrystalize out of solution = compound ends up being more pure. Barely dissolving = use just enough to fully dissolve your compound under warm temperature = saturated solution. Recrystalize = solution cools, solubility decreases, compound comes out of solution. Solvent choice = choose a solvent in which your compound is soluble in at warm temperature, but not at cool temperature. Also, choose a solvent in which impurities are highly soluble. Impurities should remain dissolved in the solvent even your compound recrystalizes out. In chemistry, recrystallization is a procedure for purifying compounds. The most typical situation is that a desired "compound A" is contaminated by a small amount of "impurity B". Typically, the mixture of "compound A" and "impurity B" are dissolved in the smallest amount of solvent to fully dissolve the mixture, thus making a saturated solution. Normally the solvent is warmed before use, increasing solubility. The solution is then allowed to cool. As the solution cools the solubility of compounds in solution drops. This results in the desired compound dropping (recrystallizing) from solution. The slower the rate of cooling, the bigger the crystals formed.
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What is the nomenclature for hydrocarbons?
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After Decane, there is Undecane (11), Dodecane (12), Tridecane (13), Tetradecane (14), and so forth for eleven membered alkanes upwards.
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What are the physical properties of hydrocarbons (alkanes)?
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Hydrophobic. London Dispersion Forces present only. Lower boiling points than compounds the same size but with functional groups. Very long alkanes can have very high boiling points due to the sum of all the dispersion forces. A useful reference is that heptane, the 7 membered alkane, has the same boiling point as water. Molecules which strongly interact or bond with each other through a variety of intermolecular forces can not move easily or rapidly and therefore, do not achieve the kinetic energy necessary to escape the liquid state. This is a consequence of the increased kinetic energy needed to break the intermolecular bonds so that individual molecules may escape the liquid as gases. Therefore, molecules with strong intermolecular forces will have higher boiling points, and these forces result in a more polar molecules. The dispersion forces are instantaneous dipoles, so the stronger these dipoles are, the more polar the molecule. The boiling point can be a rough measure of the amount of energy necessary to separate a liquid molecule from its nearest neighbors and to form a gas molecule. As the chain length (numbers of carbons) increases the melting and boiling points of the alkanes gradually increase for these compounds. The reason that longer chain molecules have higher boiling points is that longer chain molecules become wrapped around and enmeshed in each other much like the strands of spaghetti. More energy is needed to separate them than short chain molecules which have only weak forces of attraction for each other. Alkanes in general have low reactivity. Even though they are used as fuel in combustion reactions, they are generally stable compounds. The activation energy required to ignite alkanes is quite high, and below such temperatures the compounds are stable. They are also abundant on earth and do not react naturally react with oxygen or other compounds. Alkanes are nonpolar because the electronegativity of H is 2.1 and the electronegativity of C is 2.5 - so there is not a big difference between their electronegativities and they share the electrons between them equally (for the most part - that's why there are some temporary dipoles from london dispersion forces).
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Melting points of UNBRANCHED alkanes tend to increase with increasing molecular weights like boiling points, though not as smoothly. This is because intermolecular forces within a crystal depend upon shape as well as size. Alkanes have the lowest density of all groups of organic compounds. Density increases with molecular weight. Think of an oil spill where alkanes float on water. As branching increases, the boiling point decreases, and the melting point can increase if the branching causes the compounds to be harder to melt because they are more bound together.
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What is combustion?
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Complete combustion of alkanes: (alkane or cycloalkane) + O2 → CO2 + H2O + heat. Complete combustion of anything: fuel + oxygen → carbon dioxide + water + heat. The combustion of carbon compounds, especially hydrocarbons, has been the most important source of heat energy for human civilizations throughout recorded history. Every covalent bond in the reactants is been broken and an entirely new set of covalent bonds are formed in the products. Since all the covalent bonds in the reactant molecules are broken, the quantity of heat evolved in this reaction is related to the strength of these bonds (and, of course, the strength of the bonds formed in the products). The O2 is from the air. The relative heat of combustion can be used to judge the stability of alkanes. If you have branched and unbranched alkanes, and they have the same number of carbons, the more branched alkane will have the lower heat of combustion, because branched alkane is more stable. Also, the heat of combustion of a ketone is lower than an aldehyde, because the ketone is more branched, and therefore more stable. The relatively low heat of combustion of benzene tells you how stable benzene is. Benzene is stable because it is aromatic (satisfies the 2n + 2 rule).
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Combustion is a radical reaction. Heat of Combustion is a change in enthalpy of a combustion reaction. Combustion of isomeric hydrocarbons requires equal amounts of O2 and produces equal amounts of CO2 and H2O. Therefore, heats of combustion can be used to compare relative stabilities of isomers. The higher the heat of combustion, the higher the energy level of the molecule, the less stable the molecule. For cycloalkanes, comparisons can be made of different size rings on a "per CH2" basis to reveal relative stabilities. Although the molar heat of combustion for cyclohexane is nearly twice that of cyclopropane, the "per CH2" group heat of combustion is greater for cyclopropane due to ring strain.
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Explain the stability of free radicals for alkanes.
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The more substituted the radical, the more stable it is. Stability: 3° > 2° > 1° > methyl. Substitution will occur preferentially at the more substituted carbon atom. The more substituted carbon atom requires the least amount of energy to break because it forms the most stable radical product. The order from most reactive to least reactive for the halogen radicals is: F>Cl>Br>I. F is the most reactive and I is the least reactive. F is the most reactive because it is the most electronegative atom and wants to form a bond quick! In fact, once it does for the bond, it is chemically and thermodynamically the most stable bonds of the carbon-halogen bonds. The strength of the carbon-halogen bonds are C-F>C-Cl>C-Br>C-I. That is why as anions, they have the same pattern of reactivity. Also, the opposite reason is why I- is a great leaving group. Acid strength of H-F,H-Cl,H-Br, and H-I increase from H-F<HCl < HBr < HI so I is the most stable ion and F is the least stable ion, so I is a great leaving group and F is a bad leaving group. Although F is the strongest electronegative and "should" be a stable anion, it doesn't like to dissociate - H-F is the strongest covalent carbon-halogen bond and it's hard to break. In the same way, Also, nucleophilicity increases from top to bottom (it increases with size), so I>Br>Cl>F as well. In most hydrocarbons more than one possible product exists depending on which hydrogen is replaced. Butane (CH3-CH2-CH2-CH3), for example, can be chlorinated at the "1" position to give 1-chlorobutane (CH3-CH2-CH2-CH2Cl) or at the "2" position to give 2-chlorobutane (CH3-CH2-CHCl-CH3). The product distribution depends on relative reaction rates: in this case the "2" position of butane reacts faster and 2-chlorobutane is the major product. So primary, secondary, and tertiary carbons can be possible products for halogenation, but it depends on the halogen to determine the selectivity. Chlorination is generally less selective than bromination and will react with different carbons. Fluorination is the least selective. Iodine reactions are not common. Either way, the more substituted carbon atom will be the highest yield.
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What are radical initiators?
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In chemistry, radical initiators are substances that can produce radical species under mild conditions and promote radical polymerization reactions. These substances generally possess weak bonds—bonds that have small bond dissociation energies. Radical initiators are utilized in industrial processes such as polymer synthesis. Typical examples are halogen molecules, azo compounds, and organic peroxides. Like all diatomic molecules, halogens can generate two free radicals resulting from the homolysis of the bond, but halogens undergo the homolytic fission relatively easily. Chlorine, for example, gives two chlorine radicals (Cl•) by irradiation with ultraviolet light. This process is used for chlorination of alkanes.
Azo compounds (R-N=N-R') can be the precursor of two carbon-centered radicals (R• and R'•). Organic peroxides each have a peroxide bond (-O-O-), which is readily cleaved to give two oxygen-centered radicals. The oxyl radicals are rather unstable and believed to be transformed into relatively stable carbon-centered radicals. Radical initiators, especially azo compounds and organic peroxides, are inherently unstable. If you are working with radicals, the initial step of breaking the bond requires a small amount of reactant. Afterward, the free radicals are recycled and are re-formed. So initial amount of reactant is a catalytic amount of reactant. |
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Explain chain reaction mechanism (free radical reaction) of hydrocarbons.
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1. Initiation: Splitting or homolysis of a chlorine molecule to form two chlorine atoms, initiated by ultraviolet radiation. A chlorine atom has an unpaired electron and acts as a free radical. The splitting is called a homolytic cleavage by heat or light - formation of two radicals from a single bond. Only the initiation step has the homolytic cleavage.
2. chain propagation (two steps): a hydrogen atom is pulled off from methane. The methyl radical then pulls a Cl· from Cl2. This results in the desired product plus another chlorine radical. This radical will then go on to take part in another propagation reaction causing a chain reaction. If there is sufficient chlorine, other products such as CH2Cl2 may be formed. 3. chain termination: recombination of two free radicals. |
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Explain the concept of ring strain in cyclic compounds.
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Cyclopropane has the highest ring strain.
Cyclobutane has the second highest ring strain. Cyclohexane has the lowest ring strain. Any ring with greater or equal to 14 carbon atoms has the next lowest ring strain. Stick with the above rule and you can answer any questions comparing ring strain. The MCAT will not require you to make weird ring strain comparisions, for example between cyclopropane and cycloheptane. |
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What kinds of strain does ring strain consist of?
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Ring strain consists of Angle (Baeyer) strain and Torsional strain. Angle (Baeyer) strain is caused by deviation from the ideal sp3 tetrahedral bond angle of 109.5°. As an example of angle strain, take cyclic alkanes, in which each carbon is equally bonded two carbons and two hydrogens. Since each of the four bonds of a carbon is equivalent, it is sp3 hybridized and ideally should have cos−1(−1/3) ≈ 109.5° (the angle that maximizes the distance between atoms) bond angles. Due to the limitations of cyclic structure, however, the ideal angle is only achieved in a six carbon ring - cyclohexane, and only when it is in its chair conformation. For other cyclic alkanes, the bond angles deviate from ideal. In cyclopropanes (3 carbons) and cyclobutanes (4 carbons) the C-C bonds will be 60° and ~90° respectively. Torsional strain is caused by the molecule having eclipsed conformations instead of staggered ones. Cyclopropane has both angle (Baeyer) strain and torsional strain. Cyclohexane, in the chair conformation, has no angle (Baeyer) or torsional strain. You'll frequently see people write Bayer strain instead of Baeyer strain. They mean the same thing.
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What are bicyclic molecules?
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Bicyclic molecules have more ring strain than monocyclic molecules. Except for spiro bicyclics, which have similar ring strain as their monocyclic counterparts.
A bicyclic molecule is a molecule that features two fused rings. Fusion of the rings can occur in three ways: Across a bond between two atoms - has a C-C bond shared between two cyclohexane rings; Across a sequence of atoms (bridgehead) - can be viewed as a pair of cyclopentane rings that share three of the five carbon atoms; or At a single atom (spirocyclic, forming a spiro compound) Singly fused rings are the most common, and spiro rings are the least common. |
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What is the nomenclature for alcohols?
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Prefix: hydroxyl, hydroxy. Suffix: -ol, alcohol. In SN1 reactions with alcohols - a carbocation intermediate is formed, it is unimolecular (only depends on 1 molecule to react), and the mechanism has two steps. The rate of the SN1 reaction depends on the concentration of the ELECTROPHILE only, not the nucleophile. The nucleophile (could be a halogen) attacks the electrophile (the carbocation with the alcohol attached). For SN2 reactions, the rate determining step is bimolecular (meaninig it depends on two reactants to react) and the reaction occurs in 1 step. SN2 reactions depend on the concentration of both the electrophile (what's being substituted), and the nucleophile (the alcohol). Good nucleophiles are electron-rich, so molecules with a negative charge are usually good nucleophiles. SN1 reactions require acid catalysts like ZnCl2, H2SO4, and HCl because the OH makes a very poor leaving group without heating the alcohol in the presence of concentrated aqueous acid, thus protonating the OH group to OH2+. OH2+ is a great leaving group! The SN2 reaction with an optically active alcohol proceeds with inversion of configuration whereas the SN1 reaction produces racemization. In an SN1, the nucleophile attacks the planar carbocation. Since there is an equally probability of attack on each face there will be a loss of stereochemistry at the reactive center as both products will be observed. Alcohols react with hydrogen halides by nucleophilic substitution. The OH group is replaced by a halogen; water is the byproduct. In the reaction mechanism, the first step involves formation of an oxonium ion by the Lewis acid-base reaction of the hydrogen ion of the hydrogen halide and alcohol oxygen. The rest of the reaction occurs by one of the nucleophilic substitution mechanisms depending on structure of the alcohol. Tertiary and secondary alcohols react by the SN1 mechanism because they can form relatively stable intermediate carbocations; primary alcohols react by the SN2 mechanism that does not require a carbocation. The relative rates of reaction are 3'>2'>1'.
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What are the physical properties of alcohols?
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Alcohol has Hydrogen bonding. Higher boiling point than the same compound without the alcohol group because of the hydrogen bonding. Water soluble as long as molecule does not contain a long hydrophobic region. Infrared absorption of OH group: 3300 cm-1 and broad due to hydrogen bonding. Alcohols are among the most polar organiccompounds because the hydroxyl OH group is strongly polar and (because the H atom is bonded to the highly electronegative O atom) can easily participate in hydrogen bonding. Thus, the simplest alcohols are completely miscible in water. Two opposing solubility trends in alcohols are: the tendency of the polar OH to promote solubility in water, and of the carbon chain to resist it and thus limit the solubility in water. Thus, methanol, ethanol, and propanol are miscible in water because the hydroxyl group wins out over the short carbon chain. Butanol, with a four-carbon chain, is moderately soluble because of a balance between the two trends. Alcohols of five or more carbons (pentanol and higher) are effectively insoluble because of the hydrocarbon chain's dominance.Alcohols, like water, can show either acidic or basic properties at the OH group. Due to potential cleavage of the O-H bond, alcohols can behave as Lewis acids by losing a proton. Meanwhile the oxygen O atom has lone pairs of non-bonding electrons that render it weakly basic in the presence of strong acids such as sulfuric acid.
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What factors do SN1 and SN2 substitution reactions depend on for alcohols?
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One method of making alkyl halides is by the reaction of alcohols with hydrogen halides via nucleophilic substitution. Factors that favor SN1: stable carbocation, tertiary carbon center (from tertiary alcohol), protic solvent, and steric hindrance. Protic solvents are solvents which can donate H+, whereas aprotic solvents cannot donate H+. Factors that favor SN2: unstable carbocation, primary carbon center (from primary alcohol), aprotic (but polar) solvent, and the least steric hindrance. All substitution reactions need a good leaving group. SN1 = unimolecular reaction, intermediate carbocation formed. Occurs in two steps. SN2 = bimolecular reaction, passes through transition state. Occurs in one step. The oxygen atom of an alcohol is nucleophilic and is therefore prone to attack by electrophiles. The resulting intermediate then loses a proton to a base, giving the substitution product. The SN1 reaction is a substitution reaction in organic chemistry. "SN" stands for nucleophilic substitution and the "1" represents the fact that the rate-determining step is unimolecular. The reaction involves a carbocation intermediate and is commonly seen in reactions of secondary or tertiary alkyl halides or, under strongly acidic conditions, with secondary or tertiary alcohols. With primary alkyl halides, the alternative SN2 reaction occurs. The SN2 reaction (also known as bimolecular nucleophilic substitution or as backside attack) is a type of nucleophilic substitution, where a lone pair from a nucleophile attacks an electron deficient electrophilic center and bonds to it, expelling another group called a leaving group. Thus the incoming group replaces the leaving group in one step. Since two reacting species are involved in the slow, rate-determining step of the reaction, this leads to the name bimolecular nucleophilic substitution, or SN2. SN1 and E1 reactions occur under the same conditions, similar to SN2 and E2 reactions, it's just that instead of a substitution, the E1 and E2 reactions eliminate the OH and create a double bond. Protic solvent's don't work for SN2 substitutions because the nucleophile is already surrounded by protons, so it doesn't need to attack and it's stabilized. Protic solvents facilitate carbocation formation because it stabilizes the leaving group in SN1 substitution. Aprotic solvents are polar, but they don't do hydrogen bonding. Aprotic solvents stabilize the transition state, but they don't stabilize the leaving group or nucleophile where carbocations would be formed.
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How are alcohols oxidized?
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KMnO4, Na2Cr2O7, H2Cr2O7, and CrO3 will oxidize primary alcohols to carboxylic acids and secondary alcohols to ketones, but PCC will only oxidize a primary alcohol to the aldehyde. Tertiary alcohols do not oxidize. The oxidation of an alcohol involves the loss of one or more (alpha) hydrogens from the carbon-bearing OH group. The type product formed depends upon how many of these (alpha) hydrogens the alcohol contains -- that is, whether the alcohol is primary, secondary, or tertiary. A primary alcohol contains two (alpha) hydrogens, and can lose one of them to form an aldehyde or both of them to form a carboxylic acid. A secondary alcohol can lose its only (alpha) hydrogen to form a ketone. A tertiary alcohol contains no (alpha) hydrogens and is not oxidized. PCC is also C5H5NH(+)CrO3Cl(–), as shown in the diagram.
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Alcohols can also be oxidized by the addition of halogens (X2). Br2 is an oxidizing agent. Alcohols can be reduced by the loss of halogens (X2).
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What is pinacol rearrangement in polyhydroxyalcohols and what are the synthetic uses?
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The pinacol rearrangement is a method for converting a 1,2-diol to a carbonyl compound in organic chemistry. This rearrangement takes place under acidic conditions. Basically, it produces ketones (a carbonyl). In the course of this organic reaction, protonation of one of the -OH groups occurs and a carbocation is formed. If both the -OH groups are not alike, then the one which yields a more stable carbocation participates in the reaction. Subsequently, an alkyl group from the adjacent carbon migrates to the carbocation center. The driving force for this rearrangement step is believed to be the relative stability of the resultant ion. The migration of alkyl groups in this reaction occurs in accordance with their usual migratory aptitude, Ph- > tertiary > secondary > methyl .
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What is the mechanism of the pinacol rearrangement?
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In the course of this organic reaction, protonation of one of the -OH groups occurs and a carbocation is formed. If both the -OH groups are not alike, then the one which yields a more stable carbocation participates in the reaction. Subsequently, an alkyl group from the adjacent carbon migrates to the carbocation center. The driving force for this rearrangement step is believed to be the relative stability of the resultant oxonium ion, which has complete octet configuration at all centers (as opposed to the preceding carbocation). The migration of alkyl groups in this reaction occurs in accordance with their usual migratory aptitude, i.e. hydride > Ph- > tertiary > secondary > methyl . The oxonium ion in chemistry is any oxygen cation with three bonds. The simplest oxonium ion is the hydronium ion H3O+.
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What are the protecting groups for alcohols?
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Protection of alcohols: the best protecting group for alcohol is the trimethylsilyl group.
To protect, add Cl-SiMe3 to R-OH. The alcohol gets "capped" into R-O-SiMe3. To deprotect and convert back to alcohol, add F- or acid. A protecting group or protective group is introduced into a molecule by chemical modification of a functional group in order to obtain chemoselectivity in a subsequent chemical reaction. It plays an important role in multistep organic synthesis. |
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What are the reactions of alcohol with SOCl2 and PBr3?
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R-OH + SOCl2 --> R-Cl (by products: SO2 + HCl)
R-OH + PBr3 --> R-Br (by products: H3PO3, R3PO3, HBr) |
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How can mesylates and tosylates be prepared?
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Sulfonates R-SO3- are good leaving groups.
The R can be: Methane, which makes methanesulfonate. Toluene, which makes tosylate. Trifluoromethane, which makes triflate. Mesylates can be prepared by reacting an alcohol (R-OH) with mesyl chloride (MsCl). Tosylates can be prepared by reacthing an alcohol (R-OH) with tosyl chloride (TsCl). |
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What is esterification?
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esterification: carboxylic acid + alcohol = ester
An ester can be synthesized by an acid-catalyzed reaction between an alcohol and a carboxylic acid. When an ester is hydrolyzed in a base, then acidified, it produces an alcohol and carboxylic acid. Functional class name = alkyl alkanoate. Substituent suffix = -oate. Esters are name from two groups, the alcohol group and the carboxylic acid group. For example, if the alcohol component is methanol, the the alkyl = methyl. If the carboxylic acid component is propanoic acid, the second component is propanoate. Put them together and you get methyl propanoate. The oxygen in the alcohol is nucleophilic and attacks the carbonyl carbon of the carboxylic acid. The oxygen of the hydroxyl group of the carboxylic acid leaves as water. Because ester formation is an acid-catalyzed reaction, the acid protonates the oxygen of the hydroxyl group of the carboxylic acid and converts it to water. Water is a great leaving group! The acid also activates the carboxylic acid as an electrophile by protonating the carbonyl oxygen of the carboxylic acid, which makes the carbonyl carbon more electron deficient and subjects it to nucleophilic attack by the alcohol. |
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What are inorganic esters?
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inorganic esters: replace the carbon of esters with a different atom. In the diagram, the Carbon gets replaces with phosporus and sulfur.
Organic compounds are those which contain carbon bonds in which at least one carbon atom is covalently linked to an atom of another type (commonly hydrogen, oxygen or nitrogen). |
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What is the mechanism involving the formation of inorganic esters?
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Formation of mesylates and tosylates are also reactions that create inorganic esters. In biochemistry DNA/RNA polymerization, the 3'-OH alcohol group attacks the 5'-phosphate to form an inorganic ester linkage (phosphodiester linkage of DNA/RNA backbone) - the phosphorus replaces the carbon to create an inorganic ester.
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What does hydrogen bonding in alcohols do?
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hydrogen bonding: hydrogen bonding in alcohols give them a higher boiling point than their corresponding alkanes.
There are two things that increase the boiling point - the strength of the intermolecular force and the molecular mass. If you have the same kind of intermolecular forces, and if you increase the mass, then the boiling point will increase. Or if you have same size of molecule, but you go from like ethane to methanol- which you have about the same molecular mass, the methanol has a much stronger intermolecular force, so it is liquid at room temperature. |
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What is the effect of chain branching on physical properties on alcohols?
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effect of chain branching on physical properties: more branching = molecules can not pack as well = more fluidity = harder to freeze = lower freezing. By the freezing point being lower, the melting point as a result is lower. Also, impurities in molecular samples lowers the melting point of the sample and broadens the temperature range of the sample - colligative property of freezing point lowering (freezing point and melting point are related in this way). Also, shorter chains lower the melting point because the surface area is smaller. Double bonds (like unsaturated molecules like fatty acid chains like oil) have an affect on whether substances are solid or liquid at room temperature. Oil is a liquid at room temperature because there is not as much access between each of the fatty acid chains for a strong intermolecular force due to the double bonds. The average kinetic energy at room temperature for oil is only great enough for it to move from the solid state to the liquid state. It's double bonds allow it to be disordered just enough to be a liquid (there is just enough movement for it to be a liquid). While with saturated fat (molecules with just single bonds like margarine), the chains are relatively straight, so there is a lot of access for the intermolecular force to take over, so there is a deeper potential energy well between these bonds. So the temperature of the room is not enough for the substance to be melted, because the substance has a substantially bigger intermolecular force. Whereas, for the oil, they don't have as much potential energy to overcome because there is not as much attraction between the molecules due to the steric hindrance - the double bonds are not straight and there is less access for bonding. The more the molecules can bond, the stronger the intermolecular force, the more the substance will be a solid. The less the molecules can bond, the smaller the intermolecular force, the more the substance will be a liquid, or a gas. The stronger the intermolecular force for a given mass, the higher the melting point, the higher the boiling point. The stronger the force, the more work it takes to separate the mutual attraction. Without an intermolecular force, there would never be a condensed state - but this is not possible - at cold temperatures, or absolute zero - everything condenses. Also, the longer the chain, the higher the melting point.
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Think of melting point and freezing point at the perspective of the solid or liquid. If you have a liquid, by looking at the freezing point, you are looking how low the temperature needs to be to freeze it. If it doesn't pack well enough to be a solid (due to double bonds), the freezing point will need to be lower than things that do pack well enough to be solids. If you have a substance that has long chains (no double/triple bonds), those chains will engage in intermolecular forces that will pack well, so that increases the melting point, because it will want to stay as a solid longer and will raise the temperature to make it a liquid. So the melting point is increased, and therefore, the freezing point has increased. Solids made of molecules with kinks (double bonds) or branching melts sooner than molecules that do pack well, and that is why they have lower melting points.
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What is the acidity of alcohols compared to other classes of oxygen-containing compounds?
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In general, lower pKa = more acidic. pKa = -logKa. The bigger Ka is, the more acidic. Alcohols, like water, can show either acidic or basic properties at the O-H group. With a pKa of around 16-19 they are generally slightly weaker acids than water, but they are still able to react with strong bases such as sodium hydride or reactive metals such as sodium. The salts that result are called alkoxides, with the general formula RO- M+. Meanwhile the oxygen atom has lone pairs of nonbonded electrons that render it weakly basic in the presence of strong acids such as sulfuric acid.
Phenols (and their acidic protons) are more acidic than straight chain alcohols because phenol has resonance stabilization of the negative charge. The more stable the conjugate base is, the more acidic the acid is. However, benzyl alcohols - alcohols that aren't directly attached to the benzene and are instead attached to a carbon that is attached to the benzene ring, behave more like aliphatic alcohols than phenols because the negative charge isn't stabilized on the benzene ring like it is with phenols. Because of the resonance stabilization phenols are more acidic than aliphatic alcohols and therefore benzyl alcohols. Phenols, because they are more acidic, are soluble in strong bases and aliphatic alcohols and benzyl alcohols, since they aren't acidic, aren't soluble in bases (they are soluble in acids). Short-chain (with fewer than 5 carbons) alcohols are water soluble, but longer chained alcohols like benzyl alcohol are not water-soluble. Phenols are still weak acids, though aliphatic and benzyl alcohols are weaker acids, so none of them are soluble in bases like NaHCO3. Acidic phenols have the ability to dissolve in aqueous sodium hydroxide (a strong base), but not in aqueous sodium bicarbonate (a weak base) because although phenols are acidic, it is still weak, so it takes a strong base to dissolve it instead of a weak base. Acids dissolve in bases and bases dissolve in acids. |
The acidity of alcohols decreases while going from primary to secondary to tertiary. This decrease in acidity is due to two factors: an increase of electron density on the oxygen atom of the more highly-substituted alcohol, and steric hindrance (because of the alkyl groups, which inhibit solvation of the resulting alkoxide ion). Both of these situations increase the activation energy for proton removal. The basicity of alkoxide ions increases while going from primary to tertiary.
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What is the nomenclature of aldehydes and ketones?
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Aldehyde suffix: -al, -aldehyde. Ketone prefix: keto- and oxo. Ketone suffix: -one, ketone. In other cases, such as when a -CHO group is attached to a ring, the suffix -carbaldehyde may be used. Thus, C6H11CHO is known as cyclohexanecarbaldehyde. If the presence of another functional group demands the use of a suffix, the aldehyde group is named with the prefix formyl-. If the compound is a natural product or a carboxylic acid, the prefix oxo- may be used (like with ketones) to indicate which carbon atom is part of the aldehyde group; for example, CHOCH2COOH is named 3-oxopropanoic acid.
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What are the physical properties of aldehydes and ketones?
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C=O bond is polar, with the carbon partially positive and oxygen partially negative.
Dipole-dipole interactions give these molecules higher boiling points than their corresponding alkanes, but not as high as the corresponding alcohols or carboxylic acids. The dipole-dipole interactions arise from the carbonyl being polar, and this increases the boiling point. infrared absorption of C=O bond: 1700 cm-1. Infrared absorption of the =C-H bond of the aldehyde is 2800 cm-1. All carbonyls (C=O, ketones and aldehydes) is 1700 cm-1. The carboxylic acid's carbonyl is around 1700 cm-1. Aldehydes are less polar than alcohols, and alcohols are less polar than COOH. |
Whenever you see a carbonyl, think about 2 things: 1) planar stereochemistry and 2) partial negative charge on oxygen and partial positive charge on carbon. The planar stereochemistry of a carbonyl leaves open space above and below, making it susceptible to chemical attack. The partial positive charge on the carbon means that any attack on the carbonyl will be from a nucleophile.
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What is the nucleophilic addition reactions at C=O bond for acetals and hemiacetals?
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Aldehydes and ketones react with 1 equivalent of alcohols to make hemiacetals. ACID CATALYST is needed. Aldehydes and ketones react with 2 equivalent of alcohols to make acetals. Hemiketal and ketal are the same as acetals except the starting compound must be a ketone and not an aldehyde. The reaction is acid catalyzed. In ketal and acetal reactions, both of the oxygens come from the alcohols, not the carbonyls. The carbonyl oxygens leave as water. Basically, the carbonyl oxygen gets protonated by the acid, then the carbonyl carbon becomes an electrophile. The alcohol is the nucleophile and attackes the carbonyl carbonyl electrophile and adds its oxygen and alkyl to it. Then, it initially forms a hemiacetal or hemiketal, but then a water (containing the oxygen of the carbonyl) leaves. Now we have an ether, but there is still a positive charge on both the oxygen of the either and the tertiary carbon (both structures are at equilibrium). So, a second amount of alcohols come in and finish the job by acting as nucleophiles. The alcohol attacks the oxygen with the positive charge and adds its oxygen and alkyl to it. Any extra protons leave and we are left with the acetal or ketal.
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What are the nucleophilic addition reactions at C=O bond for imine and enamines?
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Primary amine + aldehyde or ketone = imine.
Secondary amine + aldehyde or ketone = enamine. An imine is a functional group containing a carbon–nitrogen double bond, with the nitrogen attached to a hydrogen atom (H) or hydrocarbon (R group). An enamine is a compound derived from the reaction of an aldehyde or ketone with a secondary amine followed by loss of H2O. An enamine produces a C single bonded to the N, with the N attached to H or R groups. With imine and enamines, the oxygen group is gone. All is left is the Nitrogen bonded to carbon. With imine, there is a double bond between Nitrogen and carbon. With enamine, there is a single bond between nitrogen and carbon - but the carbon is double bonded to another akyl group. The word "enamine" is derived from the affix en-, used as the suffix of alkene, and the root amine. This can be compared with enol, which is a functional group containing both alkene (en-) and alcohol (-ol). |
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What are haloform reactions?
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The haloform reaction is a reaction at the adjacent position. Ketones + halogen = halogenation of the alpha position (carbon adjacent to the C=O group). Methyl ketone + halogen = haloform + carboxylate. Trihalogenated methyl = good leaving group. The haloform reaction is a chemical reaction where a haloform (CHX3, where X is a halogen) is produced by the exhaustive halogenation of a methyl ketone (a molecule containing the R-CO-CH3 group) in the presence of a base. R may be H, alkyl or aryl (aryl refers to any functional group derived from a simple aromatic ring). The reaction can be used to produce CHCl3 (chloroform), CHBr3 (bromoform) or CHI3 (iodoform). Substrates which successfully undergo the haloform reaction are methyl ketones and secondary alcohols oxidizable to methyl ketones. The halogen used may be chlorine, bromine, and iodine. carboxylate anion, RCO2−, is an ion with negative charge that contains the group -COO−. It is the conjugate base of a carboxylic acid.
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A strong base is needed during the haloform reaction to neutralize the strong acid that is formed during the reaction.
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What is the difference between aldol self-condensation reactions and intramolecular aldol reactions?
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Aldol self condensation reactions involve 2 identical molecules, 2 moles of 1 molecule, that combine to form a beta-hydroxy ketone, which then undergoes condensation to get rid of the OH group and form a carbon-carbon double bond. Aldol intramolecular reactions involve 1 molecule with 2 carbonyls on it, that react within the molecule to form an aldol product. The product would turn into a ring as a result. A dimer is a chemical or biological entity consisting of two structurally similar subunits called monomers, which are joined by bonds, which can be strong or weak. Molecular dimers are often formed by the reaction of two identical compounds e.g.: 2A → A-A. In this example, monomer "A" is said to dimerise to give the dimer "A-A". Say you have this question: What is the molecular weight of a compound that undergoes an aldol self-condensation reaction to result in a beta-hydroxy ketone with a molecular weight of 144? First, note that the question says "a" compound undergoes an aldol self-condensation - really there are 2 moles of an identical compound. Second, note that the product still has the hydroxy, so no condensation happened yet. Because the aldol (addition) product is a dimer of the starting compound (of which there were 2 moles), the product has a molecular mass that is twice the starting compound (because it is a dimer A-A, while the starting compound was just A). So the molecular weight of the starting compound is 144/2 = 72 g/mol.
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How can aldol condensation be catalyzed by an acid or base?
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For either base-catalyzed or acid-catalyzed aldol condensations, the carbonyl that is base catalyzed (meaning a base took an alpha hydrogen of the carbonyl, making the carbonyl an enolate) or acid-catalyzed (meaning the acid protonated the oxygen of the carbonyl, making the carbonyl turn into an enolate) - either way makes the carbonyl an enolate, and by doing so, it is the nucleophile. The carbonyl that it attacks is the electrophile. If acetone is the enolate, the removal of either alpha hydrogen produces a single enolate ion. Carbonyls that do not have alpha protons cannot form an enolate ion. Tautomerization can racemize optically active ketones and aldehydes. Those carbonyls that are mono-substituted at the alpha carbon will lose it's chirality because the chiral carbon is the alpha carbon. The alpha carbon will lose the alpha hydrogen in the process of becoming an enol (the tautomerization) and a double bond will take the place, while the oxygen gets the H. The double bond is why the carbonyl loses it's chirality.
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What are aldol condensation reactions?
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Occurs because of the acidic alpha proton of carbonyl compound that becomes the enolate nucleophile. It's a useful carbon-carbon bond-forming reaction. In its usual form, it involves the nucleophilic addition of a ketone enolate (nucleophile) to an aldehyde to form a β-hydroxy ketone (or aldehyde, both are electrophiles). Dehydration will get rid of alcohol and yield a conjugated enone (an unsaturated consisting of a conjugated system of an alkene and a ketone). Traditionally, it is the acid- or base-catalyzed condensation of one carbonyl compounds with the enolate/enol of another, which may or may not be the same, to generate a β-hydroxy carbonyl compound—an aldol. It is reversible in nature. The reaction may occur between two molecules of aldehyde, two molecules of ketones or one molecule of aldehyde and a molecule of ketone. When two different carbonyl compounds react, it is known as mixed aldol/ Crossed aldol condensation. Ethanal and propanal can react together and form 4 different products because ethanal can react with itself or propanal and act as the nucleophile or ethanal can react with itself and propanal while propanal acts as the nucelophile. Aldol condensation involves the following steps in the mechanism: 1. Addition phase: (a) Formation of an enol or enolate anion. (b) Nucleophilic addition (c) Proton transfer 2. Dehydration phase (lose H20) and OH group becomes a double bond (If strong base/acid or some heat is applied). Some Important Facts: 1. The reaction involves an enolate reacting with another molecule of the aldehyde. 2. Remember enolates are good nucleophiles and carbonyl C is electrophiles. 3. The products of these reactions are βhydroxyaldehydes or aldehyde-alcohols = aldols (this is aldol addition, not condensation). 4. The simplest aldol reaction is the condensation of ethanal. Acid-based aldol addition is when the acid protonates the oxygen of a carbonyl, making the carbon carbonyl electrophilic and susceptible to nucleophilic attack by the enolate (also formed by protonation of acid), while the base-catatlyzed reaction is when the base deprotonates one of the carbonyls, making the enolate, which attacks another carbonyl. To prevent crossed aldol reaction (to prevent multiple products), pick a carbonyl with no alpha hydrogens, because if it doesn't have alpha hydrogens, then it can't be deprotonated and made into an enol.
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What are the oxidation reactions of aldehydes and ketones?
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Oxidation: aldehydes oxidize to carboxylic acids. Ketones do not oxidize further.
The diagram shows common oxidants. K2Cr2O7 oxidizes secondary alcohols to ketones and primary alcohols to carboxylic acids. K2Cr2O7 and Na2Cr2O7 oxidizes aldehydes to carboxylic acids. |
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What are 1,3-dicarbonyl compounds and what is internal hydrogen bonding?
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1,3-dicarbonyls have 2 carbonyl groups with a carbon atom with an acidic proton in the middle of them.
Also referred to as active methylene compounds. Tautomerism causes one of the carbonyls to switch to its enol form, which contains an -OH group that hydrogen bonds with the other carbonyl C=O group on the same molecule. This is called intramolecular (internal) hydrogen bonding. |
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What is keto–enol tautomerism?
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Enol form is the one with the alcohol. Keto form is the one with the ketone. Keto form is more stable, it is the predominant form. Carbonyl compounds with a hydrogen on the α-carbon (carbon next to the carbonyl) rapidly equilibrate between the keto form (carbonyl) and the enol form (C=C bond with OH). This process formally involves the movement of a proton from the α-carbon to the oxygen and the π-bond from C-O to C-C. Note, that this is not resonance since an atom is moving. This type of isomerization is called tautomerization, which is any rapid equilibrium that involves movement of one or more atoms (usually protons). The α-carbon of an enol is nucleophilic. The α-position will react with electrophiles to give α-substituted carbonyl derivatives. Tautomers are structural isomers. Resonance forms are representations of contributors to a single structure and the only thing shifting around are electrons. Here, hydrogens are shifting around. So if you have a question about resonance structures, only pick those structures that shift charges. Resonance is the appearance of delocalized electrons within certain molecules or polyatomic ions, so that the bonding cannot be expressed by one single Lewis formula. A molecule or ion with such delocalized electrons is represented by several resonance structures. Enol ends with an "ol" so it has an alcohol group. Keto is a ketone group.
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What are organometallic reagents?
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Organometallic reagents makes R-, which attacks C=O to make R-C-OH. The purpose of organometallic reagents is to add an R group to the molecule through the formation of a new carbon-carbon bond. Organometallic reagents like Grignard reagents, are nucleophilic because they attack the electrophilic carbon of a carbonyl. R-X + Li -> R-Li (byproduct: LiX). R-X + BuLi -> R-Li (byproduct: Bu-X).
R-Li + C=O -> R-C-OH. Compounds that contain a metal-carbon bond, R-M, are known as "organometallic" compounds. Organometallic compounds of Li, Mg (Grignard reagents) are amongst some of the most important organic reagents. Vinyl groups (formula −CH=CH2) are derivatives of ethene, CH2=CH2, with one hydrogen atom replaced with some other group. Organometallic reagents include organolithium reagents (Li-R) and organomagnesium reagents, called Grignard reagents (RMgX). A Grignard reagant or organolithium reagent can add to the "front" or "back" face of a ketone or aldehyde because the carbonyl group is planar (sp2 hybridized) and it yields a racemic mixture (not optically active). |
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What is the Wolff–Kishner reaction?
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This reaction reduces C=O to -CH2- .
C=O + NH2NH2 -> -CH2- + N2 The Wolff-Kishner reduction is a chemical reaction that fully reduces a ketone (or aldehyde) to an alkane. It involves the formation of a hydrazone and diazene. Diazene is a compound having the formula (NH)2. Methylene is a chemical species in which a carbon atom is bonded to two hydrogen atoms. A hydrazone is a class of organic compounds with the structure R1R2C=NNH2. They are related to ketones and aldehydes by the replacement of the oxygen with the NNH2 functional group. They are formed usually by the action of hydrazine on ketones or aldehydes. Hydrazine is an inorganic chemical compound with the formula N2H4. |
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What are Grignard reagents?
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Grignard reagents are just like organometallic reagents, they produce R-. They add at least 1 more carbon atom. R-X + Mg -> R-Mg-X This is the grignard reagent. R-Mg-X + C=O -> R-C-OH. It ultimately reduces the carbonyl to the alcohol. A Grignard reagent has a formula RMgX where X is a halogen, and R is an alkyl or aryl (based on a benzene ring) group. A secondary alcohol has two alkyl groups (the same or different) attached to the carbon with the -OH group on it. A tertiary alcohol has three alkyl groups attached to the carbon with the -OH attached. A primary alcohol has only one alkyl group attached to the carbon atom with the -OH group on it. The R groups around the carbonyl determine whether the resulting alcohol will be primary, secondary, or tertiary. In general, carbonyl compounds are electrophilic and in reactions, they are the electrophile. Oxygen is more electronegative than carbon, and thus pulls electron density away from carbon to increase the bond's polarity. Therefore, the carbonyl carbon becomes electrophilic, and thus more reactive with nucleophiles. The only time the electronegative oxygen reacts with an electrophile is with a proton in an acidic solution or other Lewis Acid. When the oxygen of an alcohol reacts with the electrophile in an SN2 reaction, the oxygen becomes protonated and turns into a good leaving group. Or, the oxygen could become protonated and draw more electron density away from the carbon carbonyl, making the carbon more positive and susceptible to nucleophilic attack. Mostly think of the carbonyl compounds as electrophiles. Grignard reagents need solvents that don't have acidic protons like ethers because they behave as bases (they are nucleophiles) and they attack protons. In excess, grignard reagents can reduce carbonyls to alcohols, and then to alkanes, because grignard reagents can also reduce alcohols to alkanes.
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Organometallic reagents possess a highly polarized carbon-metal bond. The carbon is more electronegative than the metal, so the carbon takes on a strnog partial negative charge. The polarized carbon-metal bond and the partial negative charge on the carbon atom makes the carbon a strong nucleophile and base. So this carbon is the reason for the nucleophilic attack on a carbonyl carbon, which after an acid bath, produces an alcohol. Grignard reagents extend the carbon skeleton.
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What is the effect of substituents on reactivity of C=O and the effects of steric hindrance?
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Bulky groups on either side of C=O blocks access to the electrophilic carbon, so reactivity goes down.
More steric hindrance on carbonyl carbon means slower nucleophilic attack. If there is more steric hindrance, elimination is more likely to occur because the nucleophile can't reach the carbocation, and instead just plucks a proton. Also, hindered bases favor elimination. Small, unhindered nucleophiles favor substitution. Steric hindrance could prevent a stable carbocation formation with SN1 reactions because the partially positive carbon has so many attached groups around it that the nucleophile has a difficult time gaining access to the carbon. So instead it just takes a proton off and calls it a day. |
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Explain the acidity of α hydrogens for aldehydes and ketones.
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Alpha proton is acidic because the resulting carbanion is stabilized by resonance. Treatment of ketones or aldehydes with at least one proton on an α-carbon with a halogen (Cl2, Br2, or I2) under acidic conditions results in halogenation of the α-position. The mechanism involves acid-catalyzed formation of an enol. The enol then acts as a nucleophile and attacks the halogen. Deprotonation of the carbonyl gives the halogenated carbonyl. The α-C-H bonds are more acidic because of the electron-withdrawing effect of the carbonyl group. Deprotonation gives a carbanion that is known as an enolate. The carbanion is stabilized by resonance electron-withdrawal by the carbonyl. The alternate resonance structure with a C=C bond and an oxygen anion is relatively stable (hence the name enolate). If a carbon is α to two carbonyl groups it's protons are considerably more acidic. However, these acidic alpha protons are less acidic if 1 of the protons is replaced with an alkyl group (called a monoalkylated product). If one of the alpha protons shares the alpha carbon with an alkyl group, then it is less acidic than if there were 2 acidic alpha protons. It's less acidic because it is less reactive because the alkyl group is in the way. A stronger base is needed (the nucleophile) to attack the proton because the alkyl is in the way. If there is considerable steric hindrance from the alkylated group, a smaller base (but still strong) is needed to abstract the proton. Also, this monoalkylated product is less soluble because of the increase in hydrocarbons. Alcohols also have acidic protons due to the higher electronegativity of the oxygen atom which helps stabilize the negative charge of the conjugate base of the alcohol. more stable conjugate base means a stronger acid. Ethers do not have acidic protons because they cannot share the negative charge - the bond would be broken and the molecule would split into two.
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What is the significance of α,beta−unsaturated carbonyl compounds and what are their resonance structures?
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α,β-unsaturated carbonyl + nucleophile -> addition of the nucleophile at the β position. Alpha-beta unsaturated carbonyls are carbonyls with a double bond at the alpha/beta position. Nucleophiles attack the beta position because the resonance structure reveals that the beta carbon is an electrophile and is deficient of electrons because the carbonyl forms an enol and draws the electrons to it. Nucleophile attacks the beta hydrogen, pushing the α,β-unsaturated carbonyl into the enol form, which tautomerizes to the original carbonyl.
Michael addition is the nucleophilic addition of a carbanion or another nucleophile to an alpha, beta unsaturated carbonyl compound. This is one of the most useful methods for the mild formation of C-C bonds. In the diagram, the nucleophile was OH-, but it can be any nucleophile, the that nucleophile may have R groups. α,β-Unsaturated carbonyl compounds are an important class of carbonyl compounds with the general structure Cβ=Cα−C=O−. In these compounds the carbonyl group is conjugated with an alkene (hence the adjective unsaturated). |
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What is the nomenclature of carboxylic acids?
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Suffix: -oic acid, carboxylic acid, -dioic acid.
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What are the physical properties and solubility of carboxylic acids?
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High boiling point due to hydrogen bonding.
Soluble in water and base infrared absorption C=O at 1700 cm-1 -OH at 3300 cm-1 Carboxylic acids are soluble in base (e.g. 5% NaOH) |
Carboxylic acids and its derivatives prefer nucleophilic substitution while aldehydes and ketones prefer nucleophilic addition.
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What reactions involve nucleophilic attack of carboxyl groups?
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Nucleophilic attack occurs on the electrophilic carbon of C=O.
Nucleophilic attack occurs by the nucleophilic oxygen of COOH. Elimination (E1, E2) act in the same conditions as SN1 and SN2, respectively. Elimination is when a double bond is created. E1 forms a carbocation like SN1. Bases for E1 are not strong, but bases are strong for E2 reactions. E1 reactions favor tertiary and secondary molecules. E1 and SN1 compete with each other. E2 and SN2 compete, but if there is a strong base, E2 will happen. Hindered strong bases acting as nucleophiles will also cause an elimination reaction because all they do is pluck the proton, then the molecule forms a double bond. E2 reactions favor tertiary hindered carbons because even though the carbon is tertiary and can form a carbocation, it is hindered, so a nucleophile can only pluck the hydrogen. Basically, E2, SN1 and E1 reactions all favor tertiary carbons, but if the solvent is not a base, then SN1 and E1 will compete. If the solvent is a strong base, then E2 will take over. E2 reactions will also happen with primary and secondary carbons. E1 reactions will only happen with tertiary carbons, and compete with SN1 to do it. E1 reactions occur with tertiary HINDERED compounds like tert-butyl chloride because first, the nucleophile can't access the carbon to make a carbocation (what is created for SN1 and E1), and instead, the nucleophile plucks off a proton of one of the adjacent carbons, the primary carbon (because that's easiest), and makes a carbanion. At the same time, the leaving group leaves and a double bond is created. So with this reaction, no carbocation is made. The intermediate primary carbanion is so unstable that it uses the electrons to create a double bond and bump the leaving group off. With SN1 and E1 reactions, an intermediate carbocation is made. With SN1 and E1 reactions, the leaving group comes off FIRST, that's the rate determining step, then the nucleophile comes in or the double bond is created. Here, with E2, the nucleophile takes off a proton (cuz it's easy to do and it's a strong base), and then the leaving group leaves. No carbocation is made with E2 and SN2. |
The strength of the nucleophile is unimportant for an SN1 reaction but important for an SN2 reaction. A base is always a stronger nucleophile than its conjugate acid, but basicity is not the same thing as nucleophicity. If a nucleophile behaves as a base, elimination results. To avoid this, we use a less bulky nucleophile. A negative charge and polarizability add to nucleophilicity. Electronegativity reduces nucleophilicity. In general, nucleophilicity decreases going up and to the right on the periodic table. Nucleophilic strength relates to how easility a compound can donate an electron pair. The more electronegative an atom, the less nucleophilic because the electrons are held together more tightly. Nucleophilicity increases as you go down a group because the electrons are not held as tightly as size increases.
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What reduction reaction are COOH involved in?
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■LiAlH4 + COOH -> alcohol.
Carboxylic acid gets reduced to primary alcohol with lithium aluminum hydride. First it gets reduced to the aldehyde, but it is unstable, then gets reduced to the primary alcohol. Lithium aluminum hydride is a reducing agent that will reduce the carboxylic acid and the ketone to alcohols. A diol is a chemical compound containing two hydroxyl groups (-OH groups). A geminal diol has two hydroxyl groups bonded to the same atom. A vicinal diol is a diol with two hydroxyl groups in vicinal positions, that is, attached to adjacent atoms. Geminal diols and vicinal diols are a subclass of the diols, which in turn are a special class of alcohols. The two hydroxyls in a geminal diol are easily converted to a carbonyl or keto group C=O by loss of one water molecule, thus turning the diol into a ketone. Conversely, ketones tend to combine with water to form the corresponding geminal diols. LiAlH4 and NaBH4 are both reducing agents. They both reduce aldehydes to primary alcohols and ketones to secondary alcohols. NaBH4 CAN'T be used with carboxylic acids. The sodium tetrahydridoborate isn't reactive enough to reduce carboxylic acids. |
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When does decarboxylation occur for COOH?
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Decarboxylation: occurs for beta-keto acids. Decarboxylation is a chemical reaction which releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids.
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What is the esterification reaction of COOH?
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◦esterification: COOH + ROH under acidic conditions = ester.
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What is the mechanism of the halogenation reaction at α position of carboxylic acids?
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Halogenation: RCOOH + X2 -> halogenation at the alpha carbon (2 position). Reagents most commonly : Br2 and either PCl3, PBr3. Carboxylic acids can be halogenated at the C adjacent to the carboxyl group. This reaction depends on the enol type character of carbonyl compounds. The product of the reaction, an a-bromocarboxylic acid can be converted via substitution reactions to a-hydroxy- or a-amino carboxylic acids. Acyl or acid halides are derivatives of carboxylic acids. They have the general formula RCOX. The CO is a carbonyl (C=O). The mechanism involves the formation of acid bromide with the PBr3. Because the acid bromide is much more electrophilic than a carboxylic acid, the enol form is formed more easily. The enol then reacts with bromine to give the α-brominated acid bromide. Treatment with water gives the α-bromoacid. Note that any nucleophile could be used to react with the acid bromide (i.e. an alcohol to give an ester or an amine to give an amide).
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What are the general principles of H bonding of COOH molecules?
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•H bonding: COOH has high boiling point because of H bonding.
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Explain how COOH molecules dimerize.
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•dimerization: Hydrogen bonding causes dimerization of carboxylic acids.
Carboxylic acids are polar. Because they are both hydrogen-bond acceptors (the carbonyl) and hydrogen-bond donors (the hydroxyl), they also participate in hydrogen bonding. Together the hydroxyl and carbonyl group forms the functional group carboxyl. Carboxylic acids usually exist as dimeric pairs in nonpolar media due to their tendency to “self-associate.” Smaller carboxylic acids (1 to 5 carbons) are soluble with water, whereas higher carboxylic acids are less soluble due to the increasing hydrophobic nature of the alkyl chain. These longer chain acids tend to be rather soluble in less-polar solvents such as ethers and alcohols. The diagram shows a COOH dimer pair. |
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Explain the acidity of the carboxyl group.
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•acidity of the carboxyl group: pKa of COOH is about 5. pKa of H+ is 0 while the pKa of water is 16. So, COOH can be classified as a weak acid. Vinegar is dilute acetic acid, which is CH3COOH.
Carboxylic acids are typically weak acids, meaning that they only partially dissociate into H+ cations and RCOO– anions in neutral aqueous solution. Carboxylic acids are Brønsted-Lowry acids — they are proton donors. Salts and anions of carboxylic acids are called carboxylates. When its carboxyl group is deprotonated, the conjugate base is resonance stabilized increasing its stability. This causes carboxylic acids to be more acidic than alcohols. Alcohols are slightly acidic, comparable to water, because the anion of the alcohol has the negative charge on the oxygen. However, overall, carboxylic acids and alcohols are both weak acids (acetic acid, as an example of COOH is weak), but COOH is a stronger acid than oxygen because of resonance stability of the anion. COOH is a weak acid because the hydrogen atom of the carboxyl group can dissociate (detach as H+) only to a very small extent, behavior that classifies carboxylic acids as weak acids. Alcohol partially dissociates as well, so it's a weak acid. |
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Explain the inductive effect of substituents on COOH molecules.
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◦electron withdrawing groups attached to positions close to the COOH helps to distribute the charge of the COO- and stabilize it.
◦A more stabilized carboxylate ion makes a stronger acid. Electronegative substituents give stronger acids. If loss of a proton places a negative charge (or more generally an extra lone pair) on a more electronegative atom than that proton will be more acidic. Secondly, if loss of a proton allows a pair of electrons to be delocalized by resonance this increases the acidity of that proton. |
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Explain the resonance stability of carboxylate anion.
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•resonance stability of carboxylate anion: the reason why COOH is a good acid is because the conjugate base (carboxylate ion) is stabilized by resonance. Deprotonation of a carboxylic acid gives a carboxylate anion, which is resonance stabilized because the negative charge is shared (delocalized) between the two oxygen atoms increasing its stability. Each of the carbon-oxygen bonds in a carboxylate anion has partial double-bond character.
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What is the nomenclature for acid derivatives?
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What are the physical properties of acid derivatives?
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C=O bond is polar, so there are dipole-dipole interactions. No hydrogen bond exists in acid chlorides, anhydrides, or esters unless there is an -OH group somewhere. Amides can hydrogen bond because of the N-H group. In fact, hydrogen bonding involving the amide backbone of polypeptides form the secondary structure of proteins. Amides have higher boiling points than the other acid derivatives because of the H bonding. Acid derivatives have high boiling points than alkanes because of the C=O dipole interactions. Acid derivatives can all be prepared from the "parent" carboxylic acid and on hydrolysis, they all convert back to the parent carboxylic acid. Reactivity order : acyl chloride > anhydride > ester = carboxylic acid > amide > carboxylate. Amides have high melting points - melting points increase with increasing numbers of N-H bonds. Acid chlorides are subject to nucleophilic attack because of the carbonyl carbon - the chloride simply withdraws more electrons and makes the carbon more electron deficient.
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What is the infrared absorption of acid derivatives?
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◦Acid chloride: the C=O will show up at greater than 1700 cm^-1, pretty close to 1800 cm^-1
◦Anhydride: the double C=O doesn't show up as a single band. Instead, 2 bands shows up between 1700^-1 and 1800 cm^-1. ◦Amide: the N-H shows up around 3300^-1, the C=O shows up at 1700^-1 ◦Ester: C=O group shows up at 1700^-1. The C-O ether stretch shows up around 1200^-1 |
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How do you prepare acid derivatives?
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◦Carboxylic acid + SOCl2 → Acid chloride.
◦Carboxylic acid + carboxylic acid + HEAT → Anhydride. ◦Acid chloride + carboxylic acid + base → Anhydride. ◦Acid chloride + alcohol + base → Ester. ◦Acid chloride + amine → Amide. ◦Acid chloride + water → Carboxylic acid. Forming anhydride from 2 carboxylic acids requires heat. It is an acidification. |
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What is Hofmann rearrangement?
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Hofmann rearrangement converts an amide, with the loss of one carbon, into an amine. Beginning with the amide, strong base, and halogen, the strong base ionizes the amide to form an amide anion. Amide anions have certain characteristics in common with the enolate anions, and halogenation occurs in manner similar to the alpha-halogenation of aldehydes and ketones. Halogenation enhances the acidity of the remaining hydrogen, which the base removes easily. To assist the task of retaining in memory the formidable Hofmann rearrangement mechanism, imagine the point of view of nitrogen atom at this point. In the bromoamide anion, nitrogen has one bond to a carbonyl carbon, which has the strong electronegative pull of oxygen working across it, and another bond to bromine, which also pulls tenaciously on electrons. From the point of view of nitrogen, these are two greedy neighbors. Intramolecular electron pair migrations occur to stabilize the entire system as an alkyl shift occurs from the carbonyl carbon onto nitrogen and the departure of halide ion. Isocyanate results, which contains a very electropositive carbon that draws the approach of a nucleophilic water molecule. This leads to N-alkylcarbamic acid, which is still unstable. Decarboxylization occurs as the last major step, releasing carbon dioxide to leave the final amine, with a new carbon-nitrogen bond.
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What is transesterification?
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•transesterification: Ester + alcohol → new ester
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What is the hydrolysis of fats and glycerides?
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•hydrolysis of fats and glycerides (saponification): saponification is basically the hydrolysis of an ester in base.Saponification is the hydrolysis of an ester under basic conditions to form an alcohol and the salt of a carboxylic acid (carboxylates). Saponification is commonly used to refer to the reaction of a metallic alkali (base) with a fat or oil to form soap. Saponification is the hydrolysis of an ester using aqueous hydroxide. A base that could be used for saponification is NaOH. The saponification product is a carboxylate salt. This carboxylate salt can be acidified into the carboxylic acid.
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What is the relative reactivity of acid derivatives?
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•relative reactivity of acid derivatives: Acid chloride > Anhydride > Esters > Amides. Acid halides are the most reactive derivatives because halides are very good leaving groups. Amides are the most stable derivatives because NR2- is a terrible leaving group. Also, the C-N bond has a partial double bond characteristic. Proteins are made of peptide bonds (carboxyl group and amine group forming an amide), and they are very stable. Carboxylic acid derivatives react tend to react via Nucleophilic Acyl substitution where the group on the acyl unit, R-C=O undergoes substitution. Note that unlike aldehydes and ketones, this reactivity of carboxylic acids retains the carbonyl group, C=O. A heteroatom is any atom that is not a carbon or hydrogen. It is typically, but not exclusively, nitrogen, oxygen, sulfur, phosphorus, boron, chlorine, bromine, or iodine.
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What are the electronic effects of acid derivatives?
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•electronic effects: groups that can redistribute and stabilize negative charges are good leaving groups. For example, the anhydride has a good leaving group - the carboxylate ion - because the COO- can redistribute the negative charge to both oxygens via resonance. The reactivity of carboxylic acid derivatives follows the trend: amide < carboxylic acid = ester < anhydride < acid chloride. This order can be predicted based on the electronic effect of the various substituents on the electrophilic nature of the carbonyl carbon. The nitrogen of amide is a strong resonance donor and weak inductive withdrawing group, so it makes the carbonyl carbon less electrophilic. Chloride is a weak resonance donor and strong inductive withdrawing group so it makes the carbon more electrophilic. We can also think about the reactivity in terms of the leaving group ability of the substituent. Chloride is a good leaving group, while NH2– is a very poor leaving group.
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What kinds of strain can occur with acid derivatives?
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Beta-lactams is an example of ring strain. β-Lactam (beta-lactam) is an amide contained within a four-membered ring. The antibiotic activity of penicillins and cephalosporins is due β-lactam ring strain. Beta-lactamases are enzymes produced by some bacteria and are responsible for their resistance to beta-lactam antibiotics like penicillins, cephalosporins. These antibiotics have a common element in their molecular structure: a four-atom ring known as a beta-lactam. The lactamase enzyme breaks that ring open, deactivating the molecule's antibacterial properties. Amides have a double bond characteristic between the carbon and nitrogen. This means that the C-N bond can not rotate. Normally, the sigma bonds in a ring rotate as to achieve the most stable conformation, but this can't occur for the C-N bond if the ring contains an amide. Because of C-N bond in an amide can not rotate, rings that contain amides have higher strain. An example of this is the beta-lactam, which is basically a 4 membered ring with 1 amide in it. The amide group has two resonance forms and it stabilizes the group, making it less reactive than the other acid derivatives. The resonance suggests that the amide group has a partial double bond character.
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What is the nomenclature of keto-acids and esters?
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•α-keto acid = 2-oxo acid. For example: α-ketopropanoic acid = 2-oxopropanoic acid
•β-keto acid = 3-oxo acid. •α-keto ester = 2-oxo ester. •β-keto ester = 3-oxo ester. For example: methyl β-ketobutanoate = methyl 3-oxobutanoate Keto acids (or oxo acids) are organic acids containing a ketone functional group and a carboxylic acid group. Common types of keto acids include: Alpha-keto acid, or 2-oxo acids, have the keto group adjacent to the carboxylic acid Beta-keto acids, or 3-oxo acids, have the ketone group at the second carbon from the carboxylic acid Gamma-keto acids, or 4-oxo acids, have the ketone group at the third carbon from the carboxylic acid |
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What kinds of decarboxylation reaction occurs with keto acids and esters?
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◦beta-keto esters → beta-keto acids → enols → ketones Decarboxylation of beta-keto acids is easy because the reaction intermediate, the enol, is stabilized, and is a tautomer of the ketone.
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What is acetoacetic ester synthesis?
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◦Acetoacetic ester is synthesized by Claisen condensation of ethyl acetate in a process called acetoacetic ester condensation
■2 x ethylacetate → ethyl acetoacetate ■acetoacetic ester = β-keto ester ◦"Acetoacetic ester synthesis" is a reaction where acetoacetic ester is used to synthesize a new ketone. 1.Acidic alpha proton comes off, resulting carbanion attacks new R group. 2.Hydrolysis of ester turns it into a β-keto carboxylic acid. 3.β-keto acids undergo decarboxylation because the β-keto group stabilizes the resulting carbanion via enol formation. Enol converts back to keto form, and the net result of this reaction is that an R group is made to attach to the α carbon of acetone. Acetoacetic ester synthesis is a chemical reaction where acetoacetate is alkylated at the α-carbon to both carbonyl groups and then converted into a ketone, or more specifically an α-substituted acetone. |
Acetoacetic ester synthesis is the production of a keton from acetoacetic ester due to the strongly acidic properties of the alpha hydrogen.
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Explain the acidity of α hydrogens in beta−keto esters.
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◦Any hydrogen alpha to (adjacent to) a carbonyl group is more acidic than a regular hydrogen. The alpha hydrogen of a beta-keto ester is even more acidic because it's adjacent to 2 carbonyl groups.
◦The reason for the acidity is the stabilization of the deprotonated species by the enolate ion resonance structures. |
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What is the nomenclature of amines?
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When N is in the front of the name for amines, it is saying that the group is on the methyl. For instance, N-methylaniline means that the methyl group is on the amine. The amine itself is attached to the phenyl. But the methyl is not attached to the phenyl.
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What is the stereochemistry of amines?
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■3° amines are not optically active and always racemic because of spontaneous inversions from their lone pair of electrons
■4° amines can be optically active because they don't undergo inversion - they don't have lone pairs of electrons. ◦infrared absorption ■primary amines = R-NH2 = 2 N-H bonds = 2 peaks around 3300 cm-1. ■secondary amines = R2-NH = 1 N-H bonds = 1 peak around 3300 cm-1. ■tertiary amines = R3-N = no N-H bonds = 0 peak around 3300 cm-1. |
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How are amides formed?
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■Amine + acid derivative with a good leaving group → amide
■Usually the acide derivative is acyl chloride with chlorine as the leaving group. However, any other good leaving group will work. ■An important biological amide formation is the peptide bond formation in protein synthesis. Here amine + carboxylic acid → amide. The leaving group is water (not OH-). Amides are not soluble in dilute acid or base. |
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What is the mechanism of an amine with nitrous acid?
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A diazo is formed during this reaction N2+. With aromatic amines like phenylamine (aniline) the diazonium ion formed is much more stable.
In general, phenyl rings stabilize charges. |
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Explain why the nitrogen in nitrous acid can be attacked.
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What is alkylation of amines?
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■multiple products formed from polyalkylation.
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Explain the significance of the basicity of amines.
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■Amines are basic. They like to gain a proton (like Bronsted bases). R-NH2 → R-NH3+ . Most amines are Brønsted and Lewis bases.
■It is very difficult for neutral amines to lose a proton. ■An amide, however, can lose a proton much more easily. This is because the carbonyl group next to the nitrogen contributes to a resonance structure that places the negative charge on the oxygen. Thus, the negative charge of the conjugate base is distributed over both nitrogen and oxygen. Amines have acidic protons because the nitrogen is an electronegative atom that shares the negative charge. |
Because amines like to gain protons like bases, instead of lose protons (like acids), the general trend of amine basicity from highest to lowest when the functinoal groups are electron donating: 2°>1°>ammonia. Electron withdrawing groups decrease the basicity of an amine whereas electron donating groups increase the basicity of an amine. Steric hindrance created by bulky functional groups tends to hinder the ability of an amine to donate its lone pair, thus decreasing its basicity.
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Explain the concept of the stabilization of adjacent carbocations of amines.
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■The nitrogen of the amine donates its lone electron pair to the adjacent carbonium ion (carbocation). Therefore adjacent carbocations are stabilized by amines.
Even without amines, alkyl groups are somewhat electron donating - that is why carbocations are relatively stable. |
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What is the effect of substituents on basicity of aromatic amines?
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■Aromatic amines are weaker bases than aliphatic amines. This is because the amine donates its electron density to the aromatic ring. Also, the amine forms stable resonance structures with the aromatic ring, which is absent once the amine becomes protonated. Electron donating groups on the aromatic amine increase the basicity of aromatic amines by donating their lone pairs of electrons to the ring. This is because the electron donating groups contribute to the electron density on the nitrogen. These groups make it easier for the aromatic amine to donate electrons and generally, bases donate electrons. Electron withdrawing groups on the aromatic amine decrease the basicity of aromatic amines. This is because the electron withdrawing groups steal electron density from the nitrogen. These groups make it harder for the amines to donate electrons and make the amines want to accept electrons. Acids accept electrons. Anything ortho to the amine, no matter whether it is electron donating or withdrawing, will decrease the basicity of the aromatic amine. This is because of the ortho effect, which is basically sterics. The protonated amine will have a greater steric interaction with the ortho group, so it will be less stable. Some examples of electron donating groups are OH, OR, NH2, NR2, Alkyl, and they direct ortho/para. They are activating because the benzene ring’s electrons are already acting as the nucleophile and they donate electrons. Some examples of electron withdrawing groups are Ester (COOR), Acid (COOH), Aldehyde (CHO), Nitro (NO2), Ketone (or acyl, COR), Cyano (CN) Acid Halide (COCl) and they direct meta. Halogens are also electron withdrawing groups, but they direct ortho/para. Meta directing and ortho/para directing means the group ON THE RING, directs the halogen where to go. The halogen that is reacting with the ring does not direct itself. When the halogen adds to the ring, it will only be 1 halogen, not two. If you start with a phenol and react it with a nitro group, the phenol will direct the nitro group on the ortho and para positions, with more para products than ortho products due to steric hindrance. Always look at what's on the ring for the position direction, not what's adding to the ring.
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To deactivate the ring simply means to make it less reactive.
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What is the nomenclature of carbohydrates?
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■Carbohydrate = Sugars, monosaccharides, disaccharides, polysaccharides. Prefix: 1) Deoxy = it has an -H in place of an -OH 2) D/L = absolute configuration = chirality of the carbon atom furthest from the carbonyl group. 3) α/β = anomeric configuration. Anomeric configuration means the sugar only differs in its configuration at the hemiacetal or hemiketal carbon, and is also called the anomeric carbon. Suffix: all sugars end in -ose. Monosaccharides- Sugars that cannot be hydrolyzed into simpler sugars that consist of 3 to 7 carbons and exist either as aldoses or ketoses. Disaccharides are composed of 2 monosaccharides. Polysaccharides are long chains of monosaccharides. Carbohydrate size is represented by the appropriate numeric prefix: for ex., triose (3-C monosaccharide) and tetrose (4-C monosaccharide). Functionality is represented by the appropriate prefix: Keto or aldo: for ex., aldotriose (3-C monosaccharide with an aldehyde group) and ketotriose (3-C monosaccharide with a ketone group). Denoting D or L refers to the configuration of the highest numbered asymmetric carbon (farthest from aldehyde or ketone groups): D is used if the hydroxyl group on the highest number asymmetric carbon is on the right of the model, L is used if the hydroxyl is on the left. D-form monosaccharides prevail in nature (like L-amino acids). Diastereomer sugars- sugars that differ at more than one chiral carbon. Epimer sugars- sugars that differ at one chiral carbon
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What is the classification of carbohydrates?
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Aldose = sugars with an aldehyde group. Ketose = sugars with a ketone group. Pyranose = sugars in a 6 membered ring structure = hexagon shaped. For example, glucopyranose = glucose in a 6 membered ring. Furanose = sugars in a 5 membered ring structure = pentagon shaped. For example, fructofuranose = fructose in a 5 membered ring. #ose = sugar with # carbon atoms. For example, hexose = sugar with 6 carbons. Another example: aldopentose = a five-carbon sugar with an aldehyde group. Aldoses cyclize to produce cyclic hemiacetals -forming a pyranose sugar. Ketose cyclize to produce cyclic hemiketals - forming a furanose sugar. In order to be classified as a carbohydrate, a molecule must have: 1) at least a 3 carbon backbone. 2) an aldehyde or ketone group. 3) at least 2 hydroxyl groups. All monosaccharides have the ability to cyclize and form ringed structures
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What are the smallest carbohydrates?
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■The simplest, smallest carbohydrates are glyceraldehyde and dihydroxyacetone.
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What are the 3 most common carbohydrates?
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■The 3 common monosaccharides are glucose, fructose, and galactose. Glucose is our blood sugar and the product of photosynthesis. Fructose is the sugar in fruits, and it is sweeter than glucose. Galactose is one of the monomers that make up lactose, which is the sugar in milk; it is less sweet than glucose.
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What is the sugar that makes up RNA and DNA?
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■The sugar that make up RNA is ribose, and for DNA it is deoxyribose (More precisely it's 2'-deoxyribose because the difference is at the 2 carbon). Deoxy sugars are sugars that have had a hydroxyl group replaced with a hydrogen.
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What is sucrose?
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■Sucrose is a disaccharide made from α-glucose and α-fructose joined at the hydroxyl groups on the anomeric carbons (making acetals). Sucrose is table sugar, the sugar we buy in stores.
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What is lactose?
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■Lactose is a disaccharide made from β-galactose and α-glucose or β-glucose joined by a 1-4 linkage.
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What is starch?
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■Starch = glucose molecules joined by α1-4 linkage.
Cellulose are glucose molecules joined by Beta 1-4 linkage, amylose are glucose molecules joined by α1-4 linkage. Amylopectin are glucose molecules joined by α1-4 linkages, which branches of α1-6 linkages every 12-30 residues. Glycogen are are glucose molecules joined by α1-4 linkages, which branches of α1-6 linkages every 8-12 residues. Maltose is made of 2 glucose molecules. |
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What is glycogen?
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■Glycogen = same as starch, but with additional α1-6 linkages for branching.
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What are the absolute configurations of carbohydrates?
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◦The chiral carbon furthest from the carbonyl group determines the absolute configuration L or D of the sugar.
◦If in the fischer projection, the OH group on the chiral carbon furthest from the carbonyl is pointing left, then it's L. If it's pointing right, then it's D. ◦Note: L and D are enantiomers, not epimers. So, every chiral carbon center inverts. It's just that you assign L and D based on the chiral carbon furthest from the carbonyl. |
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Explain the cyclic structure of hexoses.
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◦Glucose forms a pyranose when carbon 5 attacks the carbonyl carbon.
◦Convert a Fischer projection to Haworth (cyclic) form ■-OH groups that are pointing Left on the Fischer becomes Up on the Haworth. ■-OH groups that are pointing Right on the Fischer becomes Down on the Haworth. ■The -OH group on the anomeric carbon (the Fischer carbonyl) can be either up (BETA) or down (ALPHA). Think "Bup" ■The CH2OH group on the absolute configuration carbon (carbon 5) points up for D, and down for L. Pyranose is a 6 membered ring, furanose is a 5 membered ring. |
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What are the conformations of hexose?
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◦In the planar conformation, everything is eclipsed.
◦In the chair conformation, everything is staggered. ◦All the conformations in between are partially eclipsed. ◦The Boat conformation has Flagpole interactions because axial groups attached to the head and tail of the boat clash. ◦The Twist-boat conformation lessens these Flagpole interactions in addition to reducing the number of eclipsed interactions. Flagpole interactions is due to steric strain resulting from the two axial 1,4-hydrogen atoms and results in higher energy. |
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What are epimers and anomers and how are they different from enantiomers?
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◦Epimers = different configuration in just one chiral carbon. Anomers = different configuration in the chiral, anomeric carbon when the molecule is in the cyclic form. Anomers are simply a special type of epimers. Epimers are simply a special type of diastereomers. Don't confuse with enantiomers (D/L configuration), in which everything changes configuration.
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What is the hydrolysis of the glycoside linkage?
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•Glycoside linkage = acetal linkage = linkage involving the hydroxyl group of the anomeric carbon. Glycoside linkage can also mean the linkage between the sugar and the base in nucleotides. Examples of glycosidic linkages = starch, glycogen, nucleotide. Hydrolysis of the glycosidic bond has the same mechanism as hydrolysis of the acetal bond. Glycoside + H2O + catalyst → hemiacetal of one compound and hydroxyl group of other compound. Catalysts include: Amylase for starch and glycosylase for nucleotide. Hydrolysis of the glycosidic bond breaks the bond apart with water. A large molecule is split into smaller sections by breaking a bond, adding -H to one section and -OH to the other. Basically, glycosidic bonds can bond monosaccarides to create disaccharides and polysaccharides and hydrolysis of the glycosidic bonds between them can break these sugars up into the individual monosaccharides. Glycosidic bonds are cyclic monosaccharide hemiacetals and hemiketals that react with alcohols to form acetals and ketals, referred to as glycosides.
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What is the absolute configuration at the alpha position for amino acids?
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A rule of thumb for determining the d/l isomeric form of an amino acid is the "CORN" rule. The groups:
COOH, R, NH2 and H (where R is a variant carbon chain) are arranged around the chiral center carbon atom. Sighting with the hydrogen atom away from the viewer, if these groups are arranged clockwise around the carbon atom, then it is the d-form. If counter-clockwise, it is the l-form. ◦L-amino acids are the more common in nature, and are the type found in proteins. D-amino acids are less common in nature, and are never found in proteins. The amino acids found in the body are all alpha amino acids. There are no amine groups that are beta or beyond the carboxylic acid. |
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Explain why amino acids are classified as dipolar ions?
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◦At low pH, amino acids exist in the cationic form. At high pH, amino acids exist in the anionic form. At pH = pI (isoelectric point), amino acids exist in the zwitterion form, which is overall neutral. A zwitterion is a chemical compound that carries a total net charge of 0 and is thus electrically neutral, but carries formal charges on different atoms. The chemistry of amino acids is complicated by the fact that the -NH2 group is a base and the -CO2H group is an acid. In aqueous solution, an H+ ion is therefore transferred from one end of the molecule to the other to form a zwitterion. At a certain pH known as the isoelectric point an amino acid has no overall charge, since the number of protonated ammonium groups (positive charges) and deprotonated carboxylate groups (negative charges) are equal. The amino acids all have different isoelectric points. The ions produced at the isoelectric point have both positive and negative charges and are known as a zwitterion.
Essential amino acids are amino acids that cannot be synthesized by the body. There are 8 essential amino acids. Base treatment of an amino acid increases the rate of a nucleophilic reaction of the free amino group because the nitrogen of the free amino group has its lone pairs and is able tto act as a nucleophile. |
Of an amino acid, the better base (proton acceptor) is the amino group (-NH2) and not the carboxyl group (COOH). The carboxyl group is the carboxylic acid and the amino group is the basic group. Bases accept PROTONS and acids donate PROTONS. Bases donate ELECTRONS and acids accept ELECTRONS.
The point in a titration when 50% of the amino acid exists as a zwitterion is the half-equivalence point. The isoelectric point is where 100% of the amino acid exists as a zwitterion. The isoelectric point occurs at the first equivalence point. |
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What is the classification of amino acids?
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■If the R group contains carboxylic acid, then it's an acidic amino acid. There are two acidic amino acids, aspartic acid and glutamic acid. If the R group contains an amine group, then it's a basic amino acid. There are thre basic amino acids, lysine, histidine, and arginine. If the R group contains only hydrocarbons, then it's hydrophobic. If the R group contains heteroatoms, then it's hydrophilic. If the side chain contains an acid functional group, the whole amino acid produces an acidic solution. Normally, an amino acid produces a nearly neutral solution since the acid group and the basic amine group on the root amino acid neutralize each other in the zwitterion. If the amino acid structure contains two acid groups and one amine group, there is a net acid producing effect. If the side chain contains an amine functional group, the amino acid produces a basic solution because the extra amine group is not neutralized by the acid group. Amino acids with an amide on the side chain do not produce basic solutions i.e. asparagine and glutamine. Amino acid with amides are neutral. Amino acids are amphoteric - meaning that they can act as acids or bases. They can either donate or accept a proton because of their carboxylic acid and amine group. Self-ionizable compounds such as water and ammonia are also amphoteric because they can donate or accept protons.
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The carboxylate anions and salts of glutamic acid (deprotonated glutamic acids) are known as glutamates. The carboxylate anion of aspartic acid (deprotonated aspartic acid) is known as aspartate. For our purposes, histidine, lysine, and arginine are considered basic, even though histidine technically has a pka of 6.
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What is a peptide linkage reaction?
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◦Peptide bond = amide bond.
◦The peptide bond is formed by the amine group attacking the carbonyl carbon. When determining whether a protein is a dipeptide, tripeptide, etc, count the number of peptide bonds, then add 1. So a dipeptide will have 1 peptide bond, a tripeptide will have 2 peptide bonds. When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. |
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What is the hydrolysis reaction of amino acids?
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◦The peptide bond (or amide bond) is very slow to hydrolyze on its own. It requires a strong base, a strong acid, or a biological enzyme. In an aqueous base, hydroxyl ions are better nucleophiles than dipoles such as water. In acid, the carbonyl group becomes protonated, and this leads to a much easier nucleophilic attack. The peptide bonds in proteins will break spontaneously in the presence of water releasing free energy, but this process is extremely slow. In living organisms, the process is facilitated by enzymes. Protein turnover is an important process in living systems. Proteins that have served their purpose must be degraded so that their constituent amino acids can be recycled for the synthesis of new proteins. Proteases cleave proteins by a hydrolysis reaction—the addition of a molecule of water to a peptide bond. Although the hydrolysis of peptide bonds is thermodynamically favored, such hydrolysis reactions are extremely slow. In the absence of a catalyst, the half-life for the hydrolysis of a typical peptide at neutral pH is estimated to be between 10 and 1000 years. Yet, peptide bonds must be hydrolyzed within milliseconds in some biochemical processes. The chemical bonding in peptide bonds is responsible for their kinetic stability. Specifically, the resonance structure that accounts for the planarity of a peptide bond also makes such bonds resistant to hydrolysis. This resonance structure endows the peptide bond with partial double-bond character. The carbon-nitrogen bond is strengthened by its double-bond character, and the carbonyl carbon atom is less electrophilic and less susceptible to nucleophilic attack. Consequently, to promote peptide-bond cleavage, an enzyme must facilitate nucleophilic attack at a normally unreactive carbonyl group.
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What is the primary structure of proteins?
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◦Primary structure = sequence of amino acids. The primary structure of proteins (the counting of amino acids) is read from the N-terminus to the C-terminus of the protein. The N-terminus of a peptide/protein is the end with it's alpha-amine NOT involved in a peptide bond. The C-terminus is the end with its carboxylic acid NOT involved in a peptide bond. In order to function properly, peptides and proteins must have the correct sequence of amino acids. Since there are only 20 amino acids, they are in multiple combinations to create proteins. If you are asked to figure out how many different tripeptides may exist that contain 3 amino acids, you use a factorial formula. The formula for the number of possible peptides that containn one of each of n amino acids is n! (n factorial). For n = 3 (a tripeptide, since a tripeptide contains 3 amino acids), n! = 3! = 3*2*1 = 6. Or, for tripeptide ABC (where A, B, and C are the individual amino acids), the following combinations are possible: ABC, ACB, BAC, BCA, CAB, CBA, or 6 combinations.
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What is the secondary structure of proteins?
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◦Secondary structure = one or more stretches of amino acids that take on a characteristic structure due to backbone interactions. Backbone interactions = hydrogen bonding between the NH and C=O. The two most common secondary structures are α helices and β pleated sheets. The α helix is right-handed, with the R groups sticking outward. In β sheets, R groups stick out above and below the sheet. The secondary structure of a segment of polypeptide chain is the local spatial arrangement of its main-chain atoms. The alpha-helix and beta-structure conformations for polypeptide chains are generally the most thermodynamically stable of the regular secondary structures. With the alpha helix, the C=O (or N-H) of one turn is hydrogen bonded to N-H (or C=O) of the neighboring turn. Hydrogen bonds play a role in stabilizing the a helix conformation. With the alpha helix: 1) the R groups of the amino acids all extend to the outside 2) The helix is right-handed; it twists in a clockwise direction 3)The carbonyl group (-C=O) of each peptide bond extends parallel to the axis of the helix and points directly at the -N-H group of the peptide bond 4 amino acids below it in the helix. A hydrogen bond forms between them [-N-H·····O=C-] . 4) every 3.6 residues make one turn. A beta sheet is a protein structure formed by the association of parallel beta strands 1) consists of pairs of chains lying side-by-side and 2) stabilized by hydrogen bonds between the carbonyl oxygen atom on one chain and the -NH group on the adjacent chain.
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What are steroids?
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◦Steroids are made from the cyclization of squalene, which is a terpene. A steroid is a type of organic compound that contains a specific arrangement of four rings that are joined to each other. Examples of steroids include cholesterol, the sex hormones estradiol and testosterone, and the anti-inflammatory drug dexamethasone. Steroids are important hormones and structural components of cell membranes. Terpenes are hydrocarbon chains of alternating double and single bonded carbon atoms. Steroids are built of simple three carbon terpene units called isoprene units. Squalene is a hydrocarbon and a triterpene, and is a natural and vital part of the synthesis of cholesterol, steroid hormones, and vitamin D in the human body.
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What are terpenes?
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◦Terpenes are made from the polymerization of isoprene. Terpenes contain double bonds, which gives the molecule the ability to undergo cyclization. Squalene, the precursor of steroids, is a terpene that consists of 6 isoprene subunits. A complex self-cyclization reaction converts squalene to make steroids. Squalene is classified as a triterpene. Triterpene = 6 isoprene subunits. Diterpene = 4 units. Monoterpene = 2 units. Isoprene has the molecular formula C5H8. The basic molecular formulae of terpenes are multiples of that, (C5H8)n where n is the number of linked isoprene units. This is called the isoprene rule or the C5 rule. The isoprene units may be linked together "head to tail" to form linear chains or they may be arranged to form rings. One can consider the isoprene unit as one of nature's common building blocks. Isoprene itself does not undergo the building process, but rather activated forms, isopentenyl pyrophosphate (IPP or also isopentenyl diphosphate) and dimethylallyl pyrophosphate (DMAPP or also dimethylallyl diphosphate), are the components in the biosynthetic pathway. In the diagram, OPP is just short hand for the O-P-O-P-O part of the bond.
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How do you number terpenes?
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Terpenes are derived biosynthetically from units of isoprene, which has the molecular formula C5H8. The basic molecular formulae of terpenes are multiples of that, (C5H8)n where n is the number of linked isoprene units. This is called the isoprene rule or the C5 rule. As chains of isoprene units are built up, the resulting terpenes are classified sequentially by size as hemiterpenes, monoterpenes, sesquiterpenes, diterpenes, sesterterpenes, triterpenes, and tetraterpenes. Terpenes may be classified by the number of terpene units in the molecule; a prefix in the name indicates the number of terpene units needed to assemble the molecule. Hemiterpenes consist of a single isoprene unit. Isoprene itself is considered the only hemiterpene. Monoterpenes consist of two isoprene units and have the molecular formula C10H16. Sesquiterpenes consist of three isoprene units and have the molecular formula C15H24. Diterpenes are composed for four isoprene units and have the molecular formula C20H32. Sesterterpenes, terpenes having 25 carbons and five isoprene units, are rare relative to the other sizes. Triterpenes consist of six isoprene units and have the molecular formula C30H48. Squalene is a triterpene. Tetraterpenes contain eight isoprene units and have the molecular formula C40H64. Polyterpenes consist of long chains of many isoprene units.
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What are triacyl glycerols?
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◦Glycerol + 3 Fatty acids → Triacyl Glycerol. The reverse of triacyl glycerol synthesis is saponification. Triglyceride (triacylglycerol, TAG or triacylglyceride) is an ester composed of a glycerol bound to three fatty acids. Glycerol is an organic compound with three hydrophilic hydroxyl groups that are responsible for its solubility in water and is a central component of many lipids. a fatty acid is a carboxylic acid with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated. Fatty acids are produced by the hydrolysis of the ester linkages in a fat or biological oil (both of which are triglycerides), with the removal of glycerol. Fatty acids are aliphatic monocarboxylic acids derived from, or contained in esterified form in, an animal or vegetable fat, oil, or wax.
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What is the structure of phosphoric acids?
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Phosphoric acids are anhydrides and esters. Pyrophosphate is the simplest phosphoric acid anhydride. ◦Phosphoric acid = H3PO4 . Phosphoric acid is a mineral (inorganic) acid having the chemical formula H3PO4. The -OH groups in phosphoric acids can also condense with the hydroxyl groups of alcohols to form phosphate esters. Since phosphoric acid as three -OH groups, it can esterify with one, two, or three alcohol molecules to form a mono-, di-, or triester.
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In a living cell at a pH of about 7, triphosphates exist as negatively charged ions, making them less susceptible to nucleophilic attack and relatively stable. ATP is an example of an important triphophate.
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What is a phosphodiester?
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◦Phosphodiester bonds link together the DNA and RNA backbone.
◦Phosphoester bonds link the phosphates to the sugar in ATP. |
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What are the rules of precedence for Cahn-Ingold-Prelog?
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Ligands of the higher atomic number precede those with lower ones, e.g. Br precedes Cl (Br>Cl).
For ligands with the same type of atoms linked to the center C, the precedence is determined based on the atomic numbers of ligands in the next sphere, e.g. ligand with C-O sequence precedes C-C. If no difference is detected, the determination is based on the distinction in the next spheres, and search is continued until the difference is detected. The coordination number of non-hydrogen atoms is assumed to be 4, i.e. atoms bonded with multiple bonds are considered to be bonded to multiple atoms, e.g. carbonyl carbon is treated as if it was bonded to two oxygen atoms, and carboxyl carbon as if it was bonded to three oxygens (these are then called phantom atoms). |
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What is absorption spectroscopy?
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Absorption spectroscopy refers to spectroscopic techniques that measure the absorption of radiation, as a function of frequency or wavelength, due to its interaction with a sample. The sample absorbs energy, i.e., photons, from the radiating field. The intensity of the absorption varies as a function of frequency, and this variation is the absorption spectrum. Absorption spectroscopy is performed across the electromagnetic spectrum. Absorption spectroscopy is employed as an analytical chemistry tool to determine the presence of a particular substance in a sample and, in many cases, to quantify the amount of the substance present. Infrared and ultraviolet-visible spectroscopy are particularly common in analytical applications. Infrared spectroscopy (IR spectroscopy) is the subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum. It covers a range of techniques, the most common being a form of absorption spectroscopy. As with all spectroscopic techniques, it can be used to identify compounds and investigate sample composition. A common laboratory instrument that uses this technique is an infrared spectrophotometer. A material's absorption spectrum is the fraction of incident radiation absorbed by the material over a range of frequencies. The absorption spectrum is primarily determined by the atomic and molecular composition of the material. The frequencies where absorption lines occur, as well as their relative intensities, primarily depend on the electronic and molecular structure of the molecule.
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How do you read infrared spectroscopy graphs?
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Transmittance increases as you go up the y-axis. Where transmittance dips down, that's a region of absorbance. Infrared spectroscopy exploits the fact that molecules absorb specific frequencies that are characteristic of their structure. These absorptions are resonant frequencies, i.e. the frequency of the absorbed radiation matches the frequency of the bond or group that vibrates. Wavenumbers decrease from left to right. Wavenumbers are correlated to frequency. Wavenumber is basically frequency, but in units of cm^-1 instead of cycles/seconds. Peaks toward the left have higher frequency of vibration (or wavenumber). Significant for the identification of the source of an absorption band are intensity (weak, medium or strong), shape (broad or sharp), and position (cm-1) in the spectrum. Each trough is caused because energy is being absorbed from that particular frequency of infra-red radiation to excite bonds in the molecule to a higher state of vibration - either stretching or bending.
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What is anti-bonding?
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A simple covalent bond between two atoms forms from half-filled atomic orbitals on each atom overlapping in space to form a new orbital (a molecular orbital) containing both electrons. Molecular orbital theory demands that if you start with two atomic orbitals, you must end up with two molecular orbitals - and we seem to be only producing one. A second molecular orbital is formed, but in most cases (including the hydrogen molecule) it is left empty of electrons. It is described as an anti-bonding orbital. The anti-bonding orbital has a quite different shape and energy from the bonding orbital.
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What happens when light is absorbed by molecules?
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When light passes through the compound, energy from the light is used to promote an electron from a bonding or non-bonding orbital into one of the empty anti-bonding orbitals.
The possible electron jumps that light might cause are shown in the diagram. In each possible case, an electron is excited from a full orbital into an empty anti-bonding orbital. Each jump takes energy from the light, and a big jump obviously needs more energy than a small one. Each wavelength of light has a particular energy associated with it. If that particular amount of energy is just right for making one of these energy jumps, then that wavelength will be absorbed - its energy will have been used in promoting an electron. The energy of light E = hv, Planck's constant h and the frequency of light v. You can see that if you want a high energy jump, you will have to absorb light of a higher frequency. The greater the frequency, the greater the energy. That's easy - but unfortunately UV-visible absorption spectra are always given using wavelengths of light rather than frequency. That means that you need to know the relationship between wavelength and frequency. Wavelength (lamda) = c/v. c is the speed of light and v is frequency. You can see from this that the higher the frequency is, the lower the wavelength is. So . . . If you have a bigger energy jump, you will absorb light with a higher frequency - which is the same as saying that you will absorb light with a lower wavelength. The larger the energy jump, the lower the wavelength of the light absorbed. |
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What does UV-visible spectroscopy look like?
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How does conjugation and delocalization affect absorption?
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It takes less energy to excite an electron in the buta-1,3-diene case than with ethene. In the hexa-1,3,5-triene case, it is less still. The highest occupied molecular orbital is often referred to as the HOMO - in these cases, it is a pi bonding orbital. The lowest unoccupied molecular orbital (the LUMO) is a pi anti-bonding orbital. If you extend this to compounds with really massive delocalisation, the wavelength absorbed will eventually be high enough to be in the visible region of the spectrum, and the compound will then be seen as coloured. A good example of this is the orange plant pigment, beta-carotene - present in carrots, for example. The more delocalisation there is, the smaller the gap between the highest energy pi bonding orbital and the lowest energy pi anti-bonding orbital. To promote an electron therefore takes less energy in beta-carotene than in the cases we've looked at so far - because the gap between the levels is less.
Remember that less energy means a lower frequency of light gets absorbed - and that's equivalent to a longer wavelength. Beta-carotene absorbs throughout the ultra-violet region into the violet - but particularly strongly in the visible region between about 400 and 500 nm with a peak about 470 nm. The longer the conjugated pi system (alternating double and single bonds), the lower the energy and longer wavelength, so it gets absorbed more |
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How is absorption or emission of ultraviolet or visible light by a molecule similar to absorption or emission of electromagnetic radiation by an atom?
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Absorption or emission of ultraviolet or visible light by a molecule depends on electron transitions between molecular orbital energy levels, just as absorption or emission of electromagnetic radiation by an atom is determined by electron transitions between different energy levels in the atom and the Es for those transitions. Molecular spectra follow rules analogous to the rules for atomic spectra: energy is absorbed only when the amount of energy provided matches the difference in energy, E, of 2 energy levels. When an electron goes from a higher to a lower energy state, a photon of definite wavelength and frequency is emitted. Every atom or molecule has a characteristic electronic spectrum depending on its characteristic Es. Because of a molecule's greater complexity, we can often construct a molecule that will give a particular spectrum, rather than having to just accept the spectra available as we do with atoms. This possibility arises because of the interdependence of molecular orbital energy level values for the molecule, molecular shape, bonding, and distribution of electron density within the molecule. Energy transitions in phenolphthalein indicator, plant pigments, and isolated pi systems demonstrate this.
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What is the procedure for mass spectroscopy?
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Mass spectrometry (MS) is an analytical technique for the determination of the elemental composition of a sample or molecule. It is also used for elucidating the chemical structures of molecules, such as peptides and other chemical compounds. The MS principle consists of ionizing chemical compounds to generate charged molecules or molecule fragments and measurement of their mass-to-charge ratios. In a typical MS procedure: 1. a sample is loaded onto the MS instrument, and undergoes vaporization (goes from liquid to gas). 2. the components of the sample are ionized by one of a variety of methods (e.g., by impacting them with an electron beam), which results in the formation of charged particles (ions) 3. the positive ions are then accelerated by an electric field 4. computation of the mass-to-charge ratio (m/z) of the particles based on the details of motion of the ions as they transit through electromagnetic fields, and 5. detection of the ions, which in step 4 were sorted according to m/z. MS instruments consist of three modules: an ion source, which can convert gas phase sample molecules into ions (or, in the case of electrospray ionization, move ions that exist in solution into the gas phase); a mass analyzer, which sorts the ions by their masses by applying electromagnetic fields; and a detector, which measures the value of an indicator quantity and thus provides data for calculating the abundances of each ion present. The whole point of using ionization for mass spectroscopy is to make the cation (molecular ion).
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What is NMR spectroscopy?
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Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy, is the name given to a technique which exploits the magnetic properties of certain nuclei. The most important applications for the organic chemist are proton NMR and carbon-13 NMR spectroscopy. In principle, NMR is applicable to any nucleus possessing spin. Many types of information can be obtained from an NMR spectrum. Much like using infrared spectroscopy (IR) to identify functional groups, analysis of a NMR spectrum provides information on the number and type of chemical entities in a molecule. However, NMR provides much more information than IR. The impact of NMR spectroscopy on the natural sciences has been substantial. It can, among other things, be used to study mixtures of analytes, to understand dynamic effects such as change in temperature and reaction mechanisms, and is an invaluable tool in understanding protein and nucleic acid structure and function. It can be applied to a wide variety of samples, both in the solution and the solid state. When placed in a magnetic field, NMR active nuclei (such as 1H or 13C) absorb at a frequency characteristic of the isotope. The resonant frequency, energy of the absorption and the intensity of the signal are proportional to the strength of the magnetic field.
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What is the chemical shift of NMR spectroscopy?
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Depending on the local chemical environment, different protons in a molecule resonate at slightly different frequencies. Since both this frequency shift and the fundamental resonant frequency are directly proportional to the strength of the magnetic field, the shift is converted into a field-independent dimensionless value known as the chemical shift. The chemical shift is reported as a relative measure from some reference resonance frequency. (For the nuclei 1H, 13C, and 29Si, TMS (tetramethylsilane) is commonly used as a reference.) This difference between the frequency of the signal and the frequency of the reference is divided by frequency of the reference signal to give the chemical shift. The frequency shifts are extremely small in comparison to the fundamental NMR frequency. A typical frequency shift might be 100 Hz, compared to a fundamental NMR frequency of 100 MHz, so the chemical shift is generally expressed in parts per million (ppm). By understanding different chemical environments, the chemical shift can be used to obtain some structural information about the molecule in a sample. The conversion of the raw data to this information is called assigning the spectrum. For example, for the 1H-NMR spectrum for ethanol (CH3CH2OH), one would expect three specific signals at three specific chemical shifts: one for the CH3 group, one for the CH2 group and one for the OH group. A typical CH3 group has a shift around 1 ppm, a CH2 attached to an OH has a shift of around 4 ppm and an OH has a shift around 2–3 ppm depending on the solvent used. Because of molecular motion at room temperature, the three methyl protons average out during the course of the NMR experiment (which typically requires a few ms). These protons become degenerate and form a peak at the same chemical shift. The shape and size of peaks are indicators of chemical structure too. In the example above—the proton spectrum of ethanol—the CH3 peak would be three times as large as the OH. Similarly the CH2 peak would be twice the size of the OH peak but only 2/3 the size of the CH3 peak.
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The units for chemical shift of hydrogens in a NMR spectrum is ppm (parts per million). Wavenumbers are used for IR spectroscopy for how functional groups absorb infrared radiation.
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What is the magnetic property of nuclei?
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Nuclear magnetic resonance (NMR) is a property that magnetic nuclei have in a magnetic field and applied electromagnetic (EM) pulse or pulses, which cause the nuclei to absorb energy from the electromagnetic pulse and radiate this energy back out. The energy radiated back out is at a specific resonance frequency which depends on the strength of the magnetic field and other factors. This allows the observation of specific quantum mechanical magnetic properties of an atomic nucleus. Many scientific techniques exploit NMR phenomena to study molecular physics, crystals and non-crystalline materials through NMR spectroscopy. NMR is also routinely used in advanced medical imaging techniques, such as in magnetic resonance imaging (MRI). All stable nuclides that contain an odd number of protons and/or of neutrons (see Isotope) have an intrinsic magnetic moment and angular momentum, in other words a nonzero spin, while all nuclides with even numbers of both have spin 0. The most commonly studied nuclei are 1H (the most NMR-sensitive isotope after the radioactive 3H) and 13C, although nuclei from isotopes of many other elements are studied by high-field NMR spectroscopy as well. A key feature of NMR is that the resonance frequency of a particular substance is directly proportional to the strength of the applied magnetic field. It is this feature that is exploited in imaging techniques; if a sample is placed in a non-uniform magnetic field then the resonance frequencies of the sample's nuclei depend on where in the field they are located.
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What is Spin–spin splitting in H NMR Spectroscopy?
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Magnetic fields produced by neighboring protons cause spin-spin splitting. Spin-spin splitting are also called J coupling. Neighboring is defined as 3 bonds away, which is the same thing as hydrogens attached to adjacent atoms. Things are split into n+1 peaks, where n is the number of neighboring protons. Aromatic protons can split over 3 bonds, which is why the NMR spectra for the aromatic region is a mess. The J value defines how far apart things get split. Protons across single and aromatic bonds get split approximately the same. Protons across double bonds get split farther apart. The figure shows the NMR spectrum for chloroethane. Protons on a carbon atom can feel the effects of other protons on adjacent carbon atoms. The signal for a particular proton will be split by protons on adjacent carbons into n+1 peaks (n being the number of adjacent protons). The figure shows the splitting for chloroethane. Notice that there are two signals (for the two different types of protons) each split according to the number of adjacent protons.
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How does NMR help us understand the different compounds?
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Alkanes and alkane-like (saturated) groups will give upfield peaks in NMR: absorption by sp3-hybridized carbons and the protons attached to them. Aromatics will show downfield absorption in NMR. Hydrogens of alkenes are deshielded similar to hydrogens of aromatics, but aromatics are more downfield than alkenes. Alkynes, with triply bonded sp-hybridized carbons, are more upfield. Electronegative atoms - halogen, oxygen, nitrogen - will shift peaks downfield in NMR, but not usually outside the region where we expect to see them. Precise molecular structures can only be elucidated using the number of signals and their splitting. Alcohols and Ethers. NMR absorption by a hydroxylic proton (O-H) is shifted downfield by hydrogen bonding. The chemical shift that is observed depends, therefore, on the degree of hydrogen bonding, which in turn depends on temperature, concentration and the nature of the solvent. Thus, a signal can appear anywhere in the range 1 - 5 ppm. It may be hidden among the peaks due to alkyl protons, although its presence there is often revealed through proton counting. A hydroxyl proton ordinarily gives rise to a singlet in the NMR spectrum. its signal is not split by nearby protons, nor does it split their signals. Proton exchange between two identical molecules of alcohol is so fast that the proton - now in one molecule and the next instant in another - cannot see nearby protons in their various combinations of spin alignments, but in a single average alignment. Presumably through its inductive effect, the oxygen of an alcohol causes a downfield shift for nearby protons. This shift is of about the same size as other electronegative atoms.
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What is chromatography?
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Chromatography is the collective term for a set of laboratory techniques for the separation of mixtures. It involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture. Chromatography may be preparative or analytical. The purpose of preparative chromatography is to separate the components of a mixture for further use (and is thus a form of purification). Analytical chromatography is done normally with smaller amounts of material and is for measuring the relative proportions of analytes in a mixture. The two are not mutually exclusive.
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What is halogenation of alkanes?
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Substitution reactions with halogens or halogenation. Alkane + halogen + free radical initiator → alkyl halide. CH4 + Cl2 + energy ——> CH3Cl + HCl. Free radical initiators = hν (UV light) or peroxides. Substitution occurs via a free radical mechanism. Halogenation is the replacement of one or more hydrogen atoms in an organic compound by a halogen (fluorine, chlorine, bromine or iodine). Unlike the complex transformations of combustion, the halogenation of an alkane appears to be a simple substitution reaction in which a C-H bond is broken and a new C-X bond is formed. The reactivity of the halogens decreases in the following order: F2 > Cl2 > Br2 > I2. Energy input in the form of heat or light is necessary to initiate these halogenations. Halogenation reactions may be conducted in either the gaseous or liquid phase. In liquid phase halogenations radical initiators such as peroxides facilitate the reaction. The most plausible mechanism for halogenation is a chain reaction involving neutral intermediates such as free radicals or atoms. A radical is an atomic or molecular species having an unpaired, or odd, electron. Between chlorination and bromination, the bromine is more selective than the chlorine. Bromination is more endothermic because it is more selective.
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Halogenation is an exothermic process. Alkyl radicals exhibit trigonal planer geometry. The stability of the alkyl radical follows the same order as carbocation stability: 3°>2°>1°>methyl. Keep in mind that if there are more primary hydrogens to react with than tertiary hydrogens, the radicals may react with a primary carbon instead of what we would usually predict: a tertiary carbon.
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How are free radical reactions inhibited?
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The free radical chain reaction is dependent on the presence of free radicals. Therefore, anything that inhibits free radicals will inhibit this reaction. One example is antioxidants, which eats up free radicals and therefore inhibits the free radical chain reaction. There are many kinds of inhibitors, but the most common are phenols with bulky groups ortho to the OH group. Most commercial monomers are packaged with traces of inhibitor to prevent premature polymerization. The inhibitor can be removed prior to polymerization by distillation, chromatography, or extraction. In many cases, it is simply left alone, and additional initiator is used to overwhelm the inhibitor. Inhibitors are added in minute quantities to many other chemicals (e.g., ether, THF) to interupt radical chain reactions that lead to decomposition. They are also used in foods to slow oxidation that leads to spoilage. Oxygen can also inhibit the radical chain reaction mechanism in the gas phase.
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What are the substitution reactions of COOH?
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◦substitution reactions: RCOOH + E+ -> substitution at the alpha carbon (2 position).
1.Carboxylic acid converted to Acyl Halide, which can enolize. 2.Acyl Halide tautomerizes to its enol form by abstraction of acidic alpha hydrogen. 3.Halogen (or some other E+) gets attacked by alpha position. 4.Revert back to carboxylic acid. The net effect is that the alpha H get substituted by an electrophile. The α-carbon of an enol is nucleophilic. If we consider an alternate resonance structure where the OH donates a pair of electrons to generate a C=O double bond and place a negative charge on the α-carbon. The α-position will react with electrophiles to give α-substituted carbonyl derivatives. |
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How do you assign R and S configuration in a Fischer projection?
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Just pay attention to whether the lowest priority group is on the vertical line or horizontal line. If it's on the horizontal line, it's pointing towards us, so we have to switch the assignment. If it's on the vertical line, it's where it needs to be.
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What is nucleophilic substitution of acid derivatives?
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•nucleophilic substitution: Nucleophile attacks the carbon center of the C=O group. This is probably the single most important reaction of carboxylic acid derivatives. It is nucleophilic substitution at an acyl group (RCO). Different carboxylic acid derivatives have very different reactivities, acyl chlorides and bromides being the most reactive and amides the least reactive. acylation reactions generally take place by an addition-elimination process in which a nucleophilic reactant bonds to the electrophilic carbonyl carbon atom to create a tetrahedral intermediate. This tetrahedral intermediate then undergoes an elimination to yield the products. In this two-stage mechanism bond formation occurs before bond cleavage, and the carbonyl carbon atom undergoes a hybridization change from sp2 to sp3 and back again. The facility with which nucleophilic reagents add to a carbonyl group was noted earlier for aldehydes and ketones. The mechanism for acyl substitution is different from SN1 and SN2 reactions. In any SN1 and SN2 substitution reaction two things must happen: the bond from the substrate to the leaving group must be broken, and a bond to the replacement group must be formed. Also, with SN1 and SN2 reactions, halogens bonded to sp2 or sp hybridized carbon atoms do not usually undergo substitution reactions with nucleophilic reagents (but this is not the case with acyl substitution reactions).
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What are good leaving groups?
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A leaving group , LG, is an atom (or a group of atoms) that is displaced as stable species taking with it the bonding electrons. Typically the leaving group is an anion (e.g. Cl-) or a neutral molecule (e.g. H2O). The better the leaving group, the more likely it is to depart. A "good" leaving group can be recognized as being the conjugate base of a strong acid. For acidity, the more stable A- is, then the more the equilibrium will favour dissociation, and release of protons meaning that HA is more acidic. For the leaving group, the more stable LG- is, the more it favours "leaving". If you have an alkyl halide, and it is reacted with sodium hydroxide, the alkyl with the best leaving group will react the fastest. Since I- is one of the best leaving groups, t-butyl iodide will react faster than t-butyl chloride, t-butyl fluoride, and t-butyl bromide. This is different from the reactivity of halogens in halogenation, in which fluoride reacts the fastest. The difference is that the halogens are LEAVING the alkyl in the reaction with sodium hydroxide, where as the halogens are substituted to the molecule. SN1 and SN2 reactions with alcohols work great in acidic solutions because the acid protonates the OH group and make it an OH2+ group, which makes it a great leaving group.
I>Br>Cl in terms of leaving groups. The better the leaving group, the stronger the conjugate acid (I- versus Br- and Cl-). |
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What is the reaction of hydrolysis of amides?
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Hydrolysis of amides: the leaving group is not NR2-, it is the neutral amine. Amides hydrolyse to the parent carboxylic acid and the appropriate amine. The mechanisms are similar to those of esters. Reagents : Strong acid (e.g. H2SO4) / heat (preferred) or strong base (e.g. NaOH) / heat. It is a nucleophilic acyl substitution reaction. Hydrolysis of amides is the same thing as the hydrolysis of a peptide bond. In the hydrolysis of an amide into a carboxylic acid and an amine or ammonia, the carboxylic acid has a hydroxyl group derived from a water molecule and the amine (or ammonia) gains the hydrogen ion. Water (or OH-) is the nucleophile in hydrolysis reactions because the oxygen has 2 lone pairs. However, water alone usually needs a catalyst because water is a dipole and has positive charges; but hydroxyl ions (OH-) work fine. Where water (or OH-) substitutes for the leaving group, it is called hydrolysis.
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What are the steric effects of acid derivatives?
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•steric effects: bulky groups around the C=O group helps protect the carbon center from nucleophilic attack
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What are the common groups of IR Spectroscopy?
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One way to begin analyzing an IR spectrum is to start at the high wavenumber end of the spectrum (typically 4000 cm-1) and look for the presence and absence of characteristic absorptions as you move toward lower wavenumbers. The intensity of an absorption in the IR spectrum is related to the change in dipole that occurs during the vibration. Consequently, vibrations that produce a large change in dipole (e.g. C=O stretch) result in a more intense absorption than those that result in a relatively modest change in dipole (e.g. C=C). Vibrations that do not result in a change in dipole moment (e.g., a symmetrical alkyne C triple bond C stretch) will show little or no absorption for this vibration.
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What are the trends of wavenumbers for IR spectroscopy?
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How is the spin-spin splitting different between 1-1-dichloroethane and 1-2-dichloroethane?
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What does a doublet, triplet,a and quartet look like for spin-spin splitting?
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The splitting patterns shown display the ideal or "First-Order" arrangement of lines. This is usually observed if the spin-coupled nuclei have very different chemical shifts (the change in resonance frequency is large compared to the coupling constant).
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What if the protons have similar chemical shifts in a NMR?
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What causes this signal splitting, and what useful information can be obtained from it ?
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Basically, you add the hydrogen of interest plus any of the hydrogens near the hydrogen of interest to get the total number of spins (doublet, triplet, quartet, etc). If the hydrogens aren't near any other hydrogens, then it will only be 1 signal. It might be a tall signal if there are 3 hydrogens, or 2 hydrogens (because these are equivalent protons and they are additive), but there will still be only 1 signal.
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What are the important requirements and characteristics for spin 1/2 nuclei?
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What are the physical properties of amines?
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Hydrogen bonding significantly influences the properties of primary and secondary amines, but the boiling points are generally lower than those of the corresponding alcohols (because N-H bonds are weaker than O-H bonds). Also reflecting their ability to form hydrogen bonds, most aliphatic amines display some solubility in water. Solubility decreases with the increase in the number of carbon atoms. Aliphatic (compound containing hydrogen and carbon and no aromatic rings) amines display significant solubility in organic solvents, especially polar organic solvents. Primary amines react with ketones such as acetone, and most amines are incompatible with chloroform and carbon tetrachloride (because chloroform and carbon tetrachloride are non-polar). Just because a solvent is organic solvents doesn't mean that it's non-polar, ian organic solvent is just a solvent that contains carbon atoms. It can be non-polar or polar. The aromatic amines, such as aniline, have their lone pair electrons conjugated into the benzene ring, thus their tendency to engage in hydrogen bonding is diminished, but they can still hydrogen bond. Their boiling points are increased because of the hydrogen bonding and their solubility in water low because they have more carbons (6 or more). Primary and secondary amines can H-bond with themselves (other primary and secondary amines), so have relatively high boiling points.However, because the N-H bond is less polar than the O-H bond, amines have lower boiling points than alcohols. Primary and secondary amines have boiling points similar to aldehydes and ketones. Tertiary amines can’t H-bond with themselves (other tertiary amines), and so have boiling points near those of ethers and hydrocarbons. However, tertiary amines can hydrogen bond in general because of the lone pair of electrons on the nitrogen. Smaller amines (less than 5 carbons) are soluble in water - primary and secondary amines are more soluble than tertiary because they have more H-bonding with water. Amines are soluble in dilute acid (e.g 5% HCl)
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Why do primary amine have high boiling points?
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It is useful to compare the boiling point of methylamine, CH3NH2, with that of ethane, CH3CH3. Both molecules contain the same number of electrons and have, as near as makes no difference, the same shape. However, the boiling point of methylamine is -6.3°C, whereas ethane's boiling point is much lower at -88.6°C. The reason for the higher boiling points of the primary amines is that they can form hydrogen bonds with each other as well as van der Waals dispersion forces and dipole-dipole interactions. The CH3 of the amines in the molecule don't participate in H bonding because are not near an electronegative atom that would make them slightly positive. They are experiencing an equal share of electrons. The H in C-H bonds aren't slightly positive.
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Why do secondary amines have a boiling point that's lower than primary amines?
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For a fair comparison you would have to compare the boiling point of dimethylamine with that of ethylamine. They are isomers of each other - each contains exactly the same number of the same atoms. The boiling point of the secondary amine is a little lower than the corresponding primary amine with the same number of carbon atoms. Secondary amines still form hydrogen bonds, but having the nitrogen atom in the middle of the chain rather than at the end makes the permanent dipole on the molecule slightly less. The lower boiling point is due to the lower dipole-dipole attractions in the dimethylamine compared with ethylamine.
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Why do tertiary amines have the lowest boiling point of all the amines?
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This time to make a fair comparison you would have to compare trimethylamine with its isomer 1-aminopropane. If you look back at the table further up the page, you will see that the trimethylamine has a much lower boiling point (3.5°C) than 1-aminopropane (48.6°C). In a tertiary amine there aren't any hydrogen atoms attached directly to the nitrogen. That means that hydrogen bonding BETWEEN tertiary amine molecules is impossible. That's why the boiling point is much lower. However, in general, tertiary amines can hydrogen bond with another molecule that can donate a hydrogen to it. But in general, when answering questions, tertiary amines do not hydrogen bond.
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What is Hofmann elimination of amines?
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Hofmann elimination (also known as exhaustive methylation) is a process where an amine is reacted to create a tertiary amine and an alkene by treatment with excess methyl iodide. After the first step, a quaternary ammonium iodide salt is created. After replacement of iodine by an hydroxyl anion, an elimination reaction takes place to the alkene.
With unsymmetrical amines, the major alkene product is the least substituted and generally the least stable, an observation known as the Hofmann rule. ■amine + methyl iodide → exhaustive methylation of the amine → elimination with the methylated amine as leaving group. Hofmann elimination forms the less substituted double bond (Hofmann). |
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How do you assign alpha and beta to sugars?
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The Beta position is defined as the -OH being on the same side of the ring as the C # 6. In the Haworth structure this results in an upward projection.
The Alpha position is defined as the -OH being on the opposite side of the ring as the C # 6. In the Haworth structure this also results in a downward projection. |
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What is the difference between hemiacetals and hemiketals?
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Each cyclization process can produce 2 isomers based on position of hydroxy of 1st carbon. Anomers- isomers that differ by hydroxyl position of anomeric carbon (C-1). 1) alpha anomer- when the hydroxyl on the anomeric carbon is the same side as the oxygen on the highest numbered asymmetric carbon. (Fischer)-the hydroxyl on the anomeric is opposite the C-6 in the Haworth. 2) beta-anomer- when the hydroxyl on the anomeric carbon is on the opposite side as the oxygen on the highest numbered asymmetric carbon. The hydroxyl on the anomeric is on the same side as C-6 in the Haworth. Fischer to Haworth- Right is down, left is up. Mutarotation- interconversions of the a & b forms of a sugar.
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What is Tollen's reagent for monosaccharides?
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Tollens' reagent is an oxidizing agent, which is itself reduced to silver metal. This feature is used as a test for aldehydes, which are oxidized to carboxylic acids. It's also known as the the silver mirror test. Tollens' reagent contains the diamminesilver(I) ion, [Ag(NH3)2]+. This is made from silver(I) nitrate solution. To carry out the test, you add a few drops of the aldehyde or ketone to the freshly prepared reagent. If it's a ketone, no change in colorless solution. If it's an aldehyde, the colorless solution produces a grey precipitate of silver because the aldehyde reduced the diamminesilver(I) ion to metallic silver.
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What are reactions with monosaccharides?
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•Hemiacetal formation = -OH attacks carbonyl group = produces ring form. •Acetal formation = another -OH attack on the same carbonyl group = produces polysaccharides if the -OH is from another monosaccharide. •Mutarotation = equilibrium between the α and β anomers. •Strong oxidation turns aldehyde and terminal hydroxyls to carboxylic acids, and other hydroxyls to ketones. The strongest kind of oxidation turns everything to CO2, and this occurs in cellular respiration. •Mild oxidation is more selective. Tollens agent (the test for aldoses, silver precipitant forms if aldehyde is present) oxidizes only the aldehyde to carboxylic acid. Nitric acid oxidizes both the aldehyde and the terminal hydroxyl to carboxylic acids, but leaves the other hydroxyls alone. •Reduction turns monosaccharides into sugar alcohols called alditols. Reduction involves the carbonyl groups at the ends of the monosaccharides and they become alcohols. Esterification of the OH groups of monosaccharides with COOH groups of other compounds is another reaction and this reaction forms lipids.
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What are free fatty acids?
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Free fatty acids are unesterified fatty acids. In animals, much of the dietary lipid is hydrolysed to form free acids before it is absorbed and utilized for lipid synthesis. Intact lipids in tissues can be hydrolysed to free acids by a variety of lipolytic enzymes (e.g. lipoprotein lipase, hormone-sensitive lipase, phospholipase A), before being metabolized in various ways including oxidation, desaturation, elongation or re-esterification. Monomeric fatty acids in the free state have very low solubilities in aqueous media. In serum, they are transported between tissues bound to the protein albumin, which has up to six strong binding sites and a large number of weak binding sites where non-polar interactions are possible between the fatty acid hydrocarbon chains and uncharged amino acid side chains. In this way, the concentration of a long-chain fatty acid in serum can be increased by as much as 500 times above its normal maximum. Fatty acids may be found in scarce amounts in free form but, in general they are combined in more complex molecules through ester or amide bonds. When fatty acids are combined in more complex molecules such as acylglycerols, cholesterol esters, waxes and glycosphingolipids, they can be obtained free by saponification. a fatty acid is a carboxylic acid with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated. A saturated compound has no double or triple bonds. Unsaturated is used when any carbon structure contains double or occasionally triple bonds. The compound is saturated with hydrogens if it's a saturated compound. Saponification is the hydrolysis of an ester or amide under basic conditions to form an alcohol (or amine) and the salt of a carboxylic acid (carboxylates). Fatty acid (and steroids) are synthesized in the cytosol.
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What are Wittig reactions?
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The Wittig Reaction converts a ketone or aldehyde to an alkene. A phosphorus ylide is used. An ylide is a neutral molecule with a negatively charged carbanion. The R group of the ylide is added to the ketone or aldehyde, then a double bond is created.
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What is the mechanism of lithium aluminum hydride reduction?
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The aluminum hydride, similar to sodium borohydride, have nucleophilic hydrides that attack the carbonyl carbon and add a hydrogen to it, reducing it. Then, the oxygen of the carbonyl carbon takes on a negative charge because the double bond that it had with the carbonyl is broken and the electrons add to the oxygen. So, the oxygen picks up another hydrogen from either the ethanol that is reacted with the sodium borohydride or the water that is reacted with the lithium aluminum hydride. The water and the ethanol then lose a hydrogen and the oxygen of those reactants take on a negative charge.
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Hydrides do not extend the carbon skeleton, like grignard reagents. Both NaBH4 and LiAlH4 will reduce aldehydes and ketones, but only LiAlH4 is strong enough to reduce esters and acetates.
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What is an imide?
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In organic chemistry, an imide is a functional group consisting of two carbonyl groups bound to nitrogen. These compounds are structurally related to acid anhydrides. The relationship between esters and amides and between imides and anhydrides are analogous, the amine-derived groups are less reactive. The organic functional group called an imide contains two acyl groups are attached to NH or NR. Most imides are derived from dicarboxylic acids and their names reflect the parent acid.
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What is the index of hydrogen deficiency?
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What are gem-dihalides, vic-dihalides, hydrazines, hydrazones, nitrosos, and oximes?
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What are 6 things to remember about SN1 versus SN2?
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How can alkyl halides be created from alcohols?
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Why are ethers useful solvents?
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What is gel electrophoresis?
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Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or protein molecules using an electric field applied to a gel matrix. Basically, a battery is used to drive the oxidation at the anode and the reduction at the cathode. What is important to think about is the direction of the electrons and the molecules, like proteins or DNA, that you are separating. Since oxidation is taking place at the anode, the electrons are leaving and travelling to the cathode, where reduction takes place. So negatively charged PROTEINS are not going to want to travel where the negatively charged ELECTRONS are going - they aren't going to travel to the cathode, they are going to travel where the electrons are leaving, which is the anode. The same for positively charged proteins, they are going to go to where the electrons are travelling to - the cathode. I can still think of the anode as negatively charged, if you think of it as the ELECTRONS leaving, and the cathode as positive as the ELECTRONS going to the positive cathode.
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