Questions and Answers of Organic Chemistry 6th

(a) What is the α-carbon configuration of L-cysteine in the R,S system?(b) Explain why L-cysteine and L-serine have different configurations in the R,S system.
(a) How might the structure of the resin in Eq. 27.9 be altered to make the resin an anion exchanger (that is, an anion-binding resin)?(b) Predict the order of elution of the following peptides from
(a) Estimate the isoelectric point of each of the following peptides.A-K-V-I-M G-D-G-L-F (b) Draw the structures of these peptides, indicating the predominant ionization state of each at
Indicate which of the methods in this section can be used to prepare each of the following amino acids. For each method that can be used, give an equation. For each case in which a method would not
If the hydrochloride salt of glycine methyl ester is neutralized and allowed to stand in solution, a polymer forms. If the hydrochloride itself is allowed to stand, the polymerization reaction does
Calculate the average yield of each of the 369 steps in the synthesis of ribonuclease by the solid-phase method discussed, assuming the reported overall yield of 17%.
(a) Arrange the following esters in order of increasing reactivity toward glycinamide (the amide of the amino acid glycine), least reactive first, and explain your choice.(b) Give the product of the
What average yield per amino acid would be required to synthesize a protein containing 100 amino acids in 50% overall yield?
In some tRNAs the anticodon contains an inosine. The heterocyclic base in inosine is hypoxanthine.Inosine can form hydrogen-bonded base pairs with A, U, or C. This means that the inosine in tRNA can
AQC-tryptophan is not shown in Fig. 27.5 because the indole ring does not survive the acid hydrolysis. In what general region of the chromatogram would you expect to find AQC-Trp if it were present?
(a) Notice in peptide P (see previous discussion) that Asn and Asp are not distinguished by amino acid analysis. Explain.(b) What other pair of amino acids are not differentiated by amino acid
The amino acids Lys and Cys, after “tagging” with AQC, are each found to contain two AQC groups. Explain; your explanation should involve the structures of the AQC-amino acids.
Using the curved-arrow notation, write in detail the mechanisms for the reactions in(a) Eq. 27.42a (b) Eq. 27.42b (c) Eq. 27.42c O Ph N C S + H₂N-CH-C-NH- Pep phenyl isothiocyanate (Edman
Give the curved-arrow mechanism for the formation of each of the following fragment ions in Fig. 27.7 from an M + 1 ion.(a) The fragment at m/z = 551.94.(b) The fragment ion at m/z = 710.97(c) The
When a peptide Q with the amino acid analysis (A,F,G2,I,K,N,P,R,S,Y) is treated with trypsin, three new peptides are formed (amino acid analysis in parentheses): T1(A,F,R,S); T2(G,I,K); and
(a) Give the m/z values of the fragment ions expected from b-type fragmentation of an M + 1 ion of the peptide N-F-E-S-G-K.(b) Give the m/z values of the fragment ions expected from y-type
Some peptides found in nature have an amino-terminal acetyl group (red):(a) Can these peptides undergo the Edman degradation? Explain.(b) Does N-acylation have any adverse effect on sequencing by MS
(a) Draw the structure of a phosphotyrosine residue.(b) Would the equilibrium constant for formation of a phosphotyrosine residue from ATP (by a reaction analogous to the one shown in Eq. 27.43) be
(a) Draw a resonance structure for the carbocation intermediate in Eq. 27.48.(b) All of the enzyme-catalyzed glycosylations require Mn2+, a divalent cation. Suggest a role for the metal ion in the
Draw a curved-arrow mechanism for the Amadori rearrangement in Eq. 27.50. Let H3O+ and H2O be the acid–base pair, present as necessary.
Using abbreviated structures, draw the structure of an N-acetylgalactosamine conjugate with a threonine residue of an acceptor protein formed with inversion of configuration at the anomeric carbon.
It is possible to envision an Amadori rearrangement of an N-glycoside formed at an asparagine amide-NH2 group. In fact, this does not occur because the imine required for the rearrangement does not
Referring to Table 27.1, identify the amino acid(s) that satisfy each of the following criteria.(a) The most acidic amino acid(b) The most basic amino acid(c) The amino acids that can exist as
When the formation of HbA1c reverses, not only glucose, but also mannose, is formed. Explain the origin of the mannose.
Aeruginosin-B is a recently discovered natural product that inhibits trypsin.Postulate one structural reason that aeruginosin-B binds to trypsin. Explain. H orig HH
What would you expect to happen when hemoglobin is treated with a denaturant such as 8 M urea? Explain.
Give the structures of the products expected when (1) valine and (2) proline (or other compounds indicated) react with each of the following reagents: (a) ethanol (solvent), H₂SO4 catalyst (b)
The scientists who developed Norvir stated that one of the significant interactions of the inhibitor with the enzyme is hydrogen bonding of a thiazole nitrogen (the thiazole on the right side of the
Show all of the potential hydrogen-bonding sites of Darunavir; explain whether they are acceptor or donor sites.
According to its amino acid composition (Fig. 27.6), lysozyme has an isoelectric point that is (choose one and explain):(1) >6 residue number from the amino
Consider the following two peptides, which may have been isolated from the floor of a Big Ten basketball arena circa 2000:A: K-E-A-D-Y B: K-N-I-G-H-T(a) Which peptide is more basic (has the higher
An amino acid A, isolated from the acid-catalyzed hydrolysis of a peptide antibiotic, gave a positive test with ninhydrin and had a specific optical rotation (HCl solution) of 137.5° mL g–1
In repeated attempts to synthesize the dipeptide Val-Leu, aspiring peptide chemist Polly Styreen performs each of the following operations. Explain what, if anything, is wrong with each procedure.(a)
Which of the following statements would correctly describe the isoelectric point of cysteic acid, an oxidation product of cysteine? Explain your answer.(1) Lower than that of aspartic acid(2) About
A peptide was subjected to one cycle of the Edman degradation, and the following compound was obtained. What is the amino-terminal residue of the peptide? Ph. S= N -C ZH O N Η S CH(CH,)NH–C-NH—Ph
A peptide Q has the following composition by amino acid analysis:Treatment of Q once with the Edman reagent followed by anhydrous acid gives a new peptide R with the following composition by amino
A peptide C was found to have a molecular mass of about 1000. Amino acid analysis of C revealed its composition to be (Ala2,Arg,Gly,Ile). The peptide was unchanged on treatment with the Edman
(a) What reagent would be used to convert the corresponding chloromethyl polystyrene resin into the following resin?(b) To a column containing this resin suspended in a pH 6 buffer is added a mixture
Explain each of the following observations. (a) The optical rotations of alanine are different in water, 1 M HCl, and 1 M NaOH. (b) Two mono-N-acetyl derivatives of lysine are known. (c) The peptide
When a mixture of the amino acids Phe and Gly is subjected to chromatography in a pH 6 buffer on the ion-exchange resin shown in Eq. 27.9, the Phe emerges from the column much later than the Gly,
When either Norvir or Crixivan bind to the active site of HIV protease, the —OH group in the middle of each molecule is found by X-ray crystallography to displace the tightly bound water present in
One posttranslational side-chain modification of proteins is the methylation of aspartic acid residues to give a sidechain Asp-methyl ester. Draw the structure of this residue, and indicate what
Sometimes preparations of chymotrypsin are contaminated with small amounts of trypsin. This can be a problem if the specific hydrolysis of peptides with only chymotrypsin is desired. How could
Following is a ribbon diagram for one type of opioid receptor, a family of proteins that bind morphine and other opioids and initiate their physiological effects. The opioid receptor consists mostly
Complete the reactions given in Fig. P27.75 by giving the structure of the major organic product(s). (a) ethylamine + Ph-N-C=S (b) (d) PhCH=O + KCN + CH3NH, NaOH (1
Complete the reactions given in Fig. P27.70 assuming the amino acid residue is part of a peptide in aqueous solution and is at neither the amino nor the carboxy terminus. (a) lysine residue + H₂C=O
Poly-l-lysine (a peptide containing only lysine residues) exists entirely in an a-helical conformation at pH > 11. Below pH 10, however, the peptide becomes a random coil. Poly-l-glutamic acid, on
(a) For many years it was difficult to determine the X-ray structures of proteins that are imbedded in membranes because, when they are extracted into an aqueous buffer, they denature. Explain why
Identify each of the compounds A–D in the reaction scheme shown in Fig. P27.76. Explain your answers. i || || H3C-C-NH-CH-C-OEt I CH(CH3)2 Figure P27.76 HN–NH, B A HC1,
Draw a curved-arrow mechanism for each of the reactions given in Fig. P27.77. (a) (b) (c) (d) CH=O CH=0 o-phthalaldehyde CH 0 I CH₂Cl + NH3 + Na+ SH + acetone H + H₂N-CH-CO2 +
In 2007, scientists in New Zealand isolated a peptide P from enzymatic digests of the pili of gram-positive bacteria.(A pilus is a fibrous appendage that a bacterium uses, among other things, to bind
Predict the stereochemistry of the thermal electrocyclic ring closure of (2E,4Z,6E)-2,4,6-octatriene to 5,6-dimethyl-1,3-cyclohexadiene. H H₂C H C H H H
Classify each of the following pericyclic reactions as an electrocyclic, cycloaddition, or sigmatropic reaction. Give the curved-arrow notation for each reaction, and tell how many electrons are
(a) Explain why two monomethyl esters of N-acetyl-laspartic acid are known. Draw their structures.(b) Explain why a mixture of these two compounds can be separated by cation-exchange chromatography
Classify the following sigmatropic reaction by giving its bracketed-number designation and its stereochemistry with respect to the plane of the π-electron system. CH3 CH3 H S configuration
Answer the following questions for the 2,4,6-heptatrienyl cation.(a) Which MO is nonbonding?(b) Classify each MO as symmetric or antisymmetric.(c) To which carbon atoms in this cation is the positive
Which one of the following electrocyclic reactions should occur readily by a concerted mechanism? Reaction 1: Reaction 2: heat H H 0-$ heat H H
Answer the following questions for 1,3,5-hexatriene, the conjugated triene containing six carbons.(a) How many π MOs are there?(b) Classify each MO as symmetric or antisymmetric.(c) Which MOs are
In the thermal ring opening of trans-3,4-dimethylcyclobutene, two products could be formed by a conrotatory mechanism, but only one is observed. Give the two possible products. Which one is observed
Give the product of the following reaction, which involves an [8s + 2s] cycloaddition: + EtO₂C-C=C-CO₂Et
Show that using the HOMO from the 2π-electron component and the LUMO from the 4π-electron component also gives bonding overlap in a [4s + 2s] cycloaddition.
(a) Refer to Study Problem 28.2 and, assuming an antarafacial migration, give the structure of a starting material that would give a stereoisomer of the product with the R configuration at the
Classify the following sigmatropic reactions with bracketed numbers. (a) D. (b) (c) Ph Ö:- I D. S Ph
Explain why the hydrogen migration shown in reaction (1) occurs readily and why the very similar migration shown in (2) does not take place even under forcing conditions. (The asterisked carbons
(a) What allowed and reasonable sigmatropic reaction(s) can account for the following transformation?(b) What product(s) are expected from a similar reaction of 2,3-dimethyl-1,3- cyclopentadiene?
(a) Aliphatic allylic vinylic ethers undergo the Claisen rearrangement. Complete the following reaction:(b) What starting material would give the following compound in an aliphatic Claisen
Show how the transition state for a [3,3] sigmatropic reaction can be analyzed as the interaction of two allylic radicals, and that the same stereochemical outcome is predicted.
When previtamin D2 (which is identical to previtamin D3, except for the R-group) is isolated and irradiated, ergosterol is obtained along with a stereoisomer, lumi sterol. Explain mechanistically the
What do the pericyclic selection rules have to say about the position of equilibrium in each of the reactions given in Fig. P28.30? Which side of each equilibrium is favored and why? (a) Ph (b)
Heptafulvalene undergoes a thermal reaction with tetracyanoethylene (TCNE) to give the adduct shown in Fig. P28.36. What is the stereochemistry of this adduct? Explain. heptafulvalene Figure
(a) Explain why the following equilibrium lies far to the right.(b) Chemists had always assumed that this reaction would be so fast that compound A could never be isolated. However, this compound was
Classify the following sigmatropic reaction, give the curved- arrow notation, and show that the stereochemistry is that expected for a thermal concerted reaction. (This reaction, discovered by Prof.
When 1,3,5-cyclooctatriene, A, is heated to 80–100°C, it comes to equilibrium with an isomeric compound B. Treatment of the mixture of A and B with CH3O2C—C≡C—CO2CH3 gives a compound C,
The reaction in Fig. P28.41 occurs as a sequence of two pericyclic reactions. Identify the intermediate A, and describe the two reactions. CH3 +BO_i_c_c_i_OF EtO-C- a-phellandrene Figure
Certain black bugs of the order Hemiptera, generally observed in the tropical regions of India immediately after the rainy season, give off a characteristic nauseating smell whenever they are
When each of the compounds shown in Fig. P28.43 is heated in the presence of maleic anhydride, an intermediate is trapped as a Diels–Alder adduct. What is the intermediate formed in each reaction,
A compound A (C11H14O3) is insoluble in base and gives an isomeric compound B when heated strongly. Compound B gives a sodium salt when treated with NaOH.Treatment of the sodium salt of B with
An all-suprafacial [3,3] sigmatropic rearrangement could in principle take place through either a chair-like or a boat-like transition state:(a) According to the following results, which of these two
Each of the following reactions involves a sequence of two pericyclic reactions. Identify the intermediate X or Y involved in each reaction, and describe the pericyclic reactions involved.
(a) The transformation shown in Fig. P28.50, which involves a sequence of two pericyclic reactions, was used as a key step in a synthesis of the sex hormone estrone. Identify the unstable
Ions as well as neutral molecules undergo pericyclic reactions. Classify the pericyclic reactions of the cation involved in the trans formation shown in Fig. P28.49. Tell whether the methyl groups
In 1985, two researchers at the University of California, Riverside, carried out the reaction given in Fig. P28.51.The equilibrium mixture contained compound A (22%), a single stereoisomer of B
An interesting heterocyclic compound C was prepared and trapped by the sequence of reactions given in Fig. P28.52.Give the structure of all missing compounds, and explain what happens in each
Anticipating the isolation of the potentially aromatic hydrocarbon B, a group of chemists irradiated compound A with ultraviolet light. Compound C was obtained as a product instead of B.(a) Explain
(a) Identify the hydrocarbon B and the intermediate A (both with the formulas C11H10) in the following reaction sequence. Compound B is formed spontaneously from A in a pericyclic reaction.(b) The
Draw condensed structures for each of the following:(a) A phenylalanine residue in a large protein(b) A serine residue in an enzyme
Draw three valid line-and-wedge general structures for naturally occurring a-amino acids in addition to the ones shown in this section.
(a) L-Isoleucine has two asymmetric carbons and has the 2S,3S configuration. Complete the following line-and-wedge structure for l-isoleucine.(b) Alloisoleucine is the diastereomer of isoleucine.
The Negishi reaction is a Pd(0)-catalyzed cross-coupling reaction of organozinc compounds and aryl or vinylic iodides, as in the example shown in Fig. P18.79.(a) Outline a mechanism of this coupling
In 1991, chemists at the University of Iowa were able to prepare trifluoromethylcopper(I), F3C—Cu. This compound could be used to prepare trifluoromethyl-substituted aromatic compounds by reactions
Propose a synthesis of 2-butanol by the reaction of a Grignard reagent with an aldehyde or ketone.
Arrange the compounds within each set in order of increasing acidity, and explain your reasoning.(a) Cyclohexyl mercaptan, cyclohexanol, benzenethiol (b) Cyclohexanol, phenol, benzyl alcohol (c)
Give the products formed in the reaction of 1-hexene with each of the following compounds in the presence of the Grubbs G2 catalyst.(a) An excess of allyl alcohol (2-propen-1-ol)(b) An excess of
Although enols are unstable compounds (Sec. 14.5A), suppose that the acidity of an enol could be measured. Which would be more acidic: enol A or alcohol B? Why? OH OH I H3C-C=CH₂ H3C-CH-CH3 A B
Enols, like phenols, have pKa values of ~10–11. However, the pKa of warfarin, a widely used anticoagulant, is 5.0.(a) Give the structure of the conjugate base of warfarin.(b) Use resonance
Identify compounds A, B, and C from the following information.(a) Compound A, C8H10O, is insoluble in water but soluble in aqueous NaOH solution, and yields 3,5-dimethylcyclohexanol when hydrogenated
Choose the one compound within each set (see Fig. P18.54)that meets the indicated criterion, and explain your choice.(a) The compound that reacts with alcoholic KOH to liberate fluoride ion.(b) The
Contrast the reactivities of cyclohexanol and phenol with each of the following reagents, and explain.(a) Aqueous NaOH solution(b) NaH in THF(c) Triflic anhydride in pyridine, 0° 8C(d) Concentrated
The UV spectrum of p-nitrophenol in aqueous solution is shown in Fig. P18.59 (spectrum A). When a few drops of concentrated NaOH are added, the solution turns yellow and the spectrum changes
Phenols, like alcohols, are Brønsted bases.(a) Write the reaction in which the oxygen of phenol reacts as a base with the acid H2SO4.(b) On the basis of resonance and polar effects, decide whether

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