Exam 6: Organic Chemistry

Passage The cryptophycins, isolated from cyanobacteria, are a family of macrocyclic molecules.  Researchers have studied the biological activity of these compounds and found that many of them are active against multi-drug-resistant tumor cells.Cryptophycin-52, an analogue of the natural cryptophycins, has been tested in clinical trials for its efficacy against cancer cells, but the studies were suspended due to neurotoxic side effects.  Nevertheless, the synthesis of similar analogues continues to be of interest in cancer research.  A key step in the synthesis of cryptophycin-52 is the stereospecific formation of an epoxide from an alkene and oxone (Figure 1), which can be facilitated by the Shi catalyst.  The Shi catalyst (Figure 2) is derived from the carbohydrate D-fructose and is known among organic chemists for its ability to form epoxides in hydrocarbons in a stereospecific manner. Figure 1  Shi epoxidation of compound 1 Figure 2  Structure of the Shi catalystThe epoxidation of compound 1 was monitored by thin-layer chromatography (TLC).  When the reaction was completed, high-performance liquid chromatography (HPLC) was used to analyze the epoxide product.  A chiral column that had an affinity for the desired epoxide was used.  A standard of the desired epoxide was obtained to optimize the conditions and determine the retention time of the epoxide.  The HPLC chromatogram of the epoxide standard is shown in Figure 3. Figure 3  HPLC of epoxide standard Adapted from Weiß C, Bogner T, Sammet B, Sewald N. Total synthesis and biological evaluation of fluorinated cryptophycins. Beilstein J Org Chem. 2012. -Which of the following functional groups will be reduced when LiAlH₄ is added to Compound 1, the substrate for the Shi epoxidation described in the passage?

Passage The β-lactam scaffold is an important feature in a class of broad-spectrum antibiotics that includes the penicillins, cephalosporins, and monobactams.  These antibiotics are used to treat a variety of diseases caused by bacteria.  The penicillins work by inhibiting a step in the synthesis of peptidoglycan.  However, the development of antibiotic resistance in the form of enzymes such as β-lactamase is an ongoing problem.An aromatic ring linked to the β-lactam ring has been reported to participate in hydrophobic interactions with β-lactamase active sites, and an aromatic ring bonded to the nitrogen of the β-lactam has shown to be beneficial to biological activity.  With this in mind, researchers synthesized a group of penicillanic acid analogues with substituted aromatic rings bonded to the β-lactam ring in an effort to overcome the challenge of antibiotic resistance.  The substituents on the aromatic rings were varied, including -OCH₃ and -NO₂, to make several analogues.  A key step in the synthesis of these analogues was the coupling of Compounds 1 and 2 to form a compound with two β-lactam rings (Reaction 1). Reaction 1The researchers studied the analogues' structure-activity relationship and antimicrobial activity against the gram-negative bacteria Escherichia coli and the gram-positive bacteria Staphylococcus aureus.  Ampicillin, a penicillin derivative used to treat illnesses brought about by gram-positive and gram-negative bacteria, was used as a control.  The minimal inhibitory concentrations are shown in Table 1.Table 1  Minimal Inhibitory Concentration (MIC) The penicillanic acid analogues were tested for their effect on mammalian cell viability because toxicity to cells is also an important factor to consider for potential drug candidates.  The general acceptable level of cell viability for a drug candidate is 70%.  These results are shown in Figure 1. Figure 1  Cell viability assay results Adapted from De rosa M, Vigliotta G, Palma G, Saturnino C, Soriente A. Novel Penicillin-Type Analogues Bearing a Variable Substituted 2-Azetidinone Ring at Position 6: Synthesis and Biological Evaluation. Molecules. 2015. -Which conclusion about the bioactivity of Compounds 3-6 is best supported by the data in Table 1 and Figure 1?

A wax is made up of a long-chain fatty acid and a long-chain alcohol joined by:

Passage Malaria is caused by the parasite Plasmodium falciparum and is transmitted through a female mosquito bite.  Although there are antimalarial treatments available, P. falciparum has become resistant to many of these drugs.  P. falciparum cells contain a respiratory organelle called the apicoplast that is necessary for the parasite's survival but is not found in humans.  Therefore, a new drug that targets this organelle could be useful in the treatment of malaria.A portion of the apicoplast protein ferredoxin (PfFd) is shown in Figure 1, with certain amino acid residues labeled.  In the apicoplast, ferredoxin NADP⁺ reductase (PfFNR) interacts electrostatically with PfFd and catalyzes an electron transfer reaction.  A compound that selectively inhibits this interaction could be a beneficial antimalarial agent. Figure 1  Structure of a portion of PfFdChalcone (Compound 3) is a compound that interacts with PfFd and exhibits antimalarial properties.  A series of chalcone derivatives (Compounds 4-8) were synthesized via the aldol condensation shown in Scheme 1, where nucleophilic addition of Compound 1 to Compound 2 is followed by elimination to yield α,β-unsaturated carbonyl molecules, Compounds 3-8. Scheme 1An inhibition assay was performed to compare chalcone (Compound 3) and its derivatives by determining the extent to which these compounds inhibited electron transfer between PfFNR and PfFd (Table 1).Table 1  Inhibition of electron transfer assay results Adapted from H. Suwito et al. "Design and synthesis of chalcone derivatives as inhibitors of the ferredoxin - ferredoxin-NADP+ reductase interaction of Plasmodium falciparum: pursuing new antimalarial agents." Molecules. ©2014 MDPI. -The aldol condensation is an important carbon-carbon bond-forming reaction that requires a compound with an α-H. Given that an enolate is formed in the first step of the aldol condensation, which site will be deprotonated by a base?

Which structure is the product of the reaction of 4-tert-butyl-2-octanone and NaCN?

Passage High blood pressure, or hypertension, is a prevalent condition in the United States.  One in three adults has hypertension, and approximately 20% do not know that they have it.  If left untreated, high blood pressure can lead to major health issues, including stroke, heart attack, and kidney disease or failure.  A number of drugs can help control hypertension, including those shown in Table 1.  These drugs can be classified into different groups based on their mechanism of action.Table 1  Drugs Used to Treat High Blood Pressure Labetalol (Figure 1) exists as four stereoisomers and is administered as a mixture of all four.  This drug can be classified as a pseudohybrid drug because two of the isomers, (R,R) and (S,R), exhibit biological activity; the other two isomers, (S,S) and (R,S), are not active.  The (R,R) isomer acts as a nonselective β-adrenergic receptor blocker, and the (S,R) isomer acts as a selective α-adrenergic receptor blocker. Figure 1  Structure of (±)-labetalol and l-epinephrinel-epinephrine (Figure 1) is the agonist of the α- and β-adrenergic receptors.  The structural motifs that allow l-epinephrine to bind to the adrenergic receptors include an amine separated from an aromatic ring by two carbon units, a hydroxyl group at a chiral center beta to the amine, and two hydroxyl groups on the aromatic ring in the meta and para positions.  With a few structural modifications, the agonist l-epinephrine can be converted into the antagonist labetalol.  Substitution of a hydroxyl on the aromatic ring with an amide group and extension of the methyl group on the amine transforms l-epinephrine into labetalol.  These substitutions keep a majority of the structural motifs necessary for labetalol to mimic l-epinephrine and bind to the adrenergic receptors. -Below is the structure of valsartan.  All of the following are structural isomers of valsartan EXCEPT:

All of the following can be described as an aromatic heterocycle EXCEPT:

Passage Fluorescent amino acids are useful for labeling proteins because they can be visualized spectroscopically, facilitating the study of protein structure and interactions.  The noncanonical amino acid dansylalanine, a fluorescent amino acid that is sensitive to the hydrophobicity of its environment, is a good candidate to be incorporated into proteins because of its small size and fluorescent capabilities.  Dansyl chloride and Compound 1 were used to synthesize dansylalanine, as shown in Reaction 1.  Dansylalanine absorbs maximally at 340 nm and emits at approximately 540 nm. Reaction 1  Synthesis of dansylalanineA leucyl-tRNA synthetase from Escherichia coli was engineered to aminoacylate bacterial tRNAs containing a CUA anticodon with dansylalanine.  After verifying that the tRNA/synthetase pair does not interact with endogenous amino acids or tRNAs, it was transfected into the yeast Saccharomyces cerevisiae along with a plasmid encoding a mutated human superoxide dismutase (hSOD).  Using this system, dansylalanine was genetically incorporated into hSOD in place of either Gln-16 or Trp-33, and expressed in S. cerevisiae.Position 16 is located on the surface of hSOD at the N-terminus of a β-strand, and position 33 lies in the center of a strand within a β-barrel.  To probe changes in the structure of hSOD, researchers exposed the purified protein to guanidinium chloride (GdmCl) to denature the protein at concentrations ranging 0-4.5 M.  The experiment was conducted in a 35 mM sodium phosphate buffer at pH 7.2.  The fluorescence of hSOD with dansylalanine at either position 16 or 33 was monitored at each GdmCl concentration, and the results of the unfolding experiment are shown in Figure 1. Figure 1  Plot of dansylalanine fluorescence at different concentrations of GdmCl Adapted from Summerer D, Chen S, Wu N, Deiters A, Chin JW, Schultz PG. A genetically encoded fluorescent amino acid. Proc Natl Acad Sci USA. 2006. -Of the positions where dansylalanine was incorporated, which one most likely experiences the greatest environmental change upon unfolding of the protein?

If Staphylococcus aureus V8 protease is specific for acidic amino acids, which of the following residues would be cleaved by this protease?

In the ultraviolet (UV) range, pyrimidine has maximum absorptions at 240 nm and 280 nm, and the absorption at 280 nm is due to nonbonding electron excitation.  The nonbonding electrons on nitrogen in pyrimidine undergo which of the following transitions when absorbing UV light?

Passage The N-terminus of an amino acid must be protected with 9-fluorenylmethoxycarbonyl (Fmoc) during solid state peptide synthesis to avoid side reactions (Scheme I). Scheme IThe Fmoc protecting group is typically removed with piperidine (Scheme II), a heterocyclic secondary amine. Scheme IIBecause the use of piperidine is restricted, structurally similar amines were examined as possible replacements.  To determine whether piperidine analogues were suitable alternatives for Fmoc removal, deprotection of Compound 2 was carried out with several amine bases (Scheme III). Scheme IIICompound 2 was prepared from L-tryptophan and Fmoc-Cl, and the reaction was monitored by thin-layer chromatography (TLC) and visualized by ultraviolet light.  The deprotections were done with piperidine and each analogue using a microwave set to 155 watts at 75 °C for 15 seconds.  The products of the deprotections were analyzed by high-performance liquid chromatography (HPLC) and mass spectrometry; the retention times of the products were compared to tryptophan and Compound 2 standards. Adapted from O.P. Luna et al, "Deprotection Reagents in Fmoc Solid Phase Peptide Synthesis: Moving Away from Piperidine?." Molecules. ©2016 MDPI. -Which of the following statements provides the most plausible explanation for why UV light was used to visualize the thin-layer chromatography plate?

Which of the following statements correctly describes the peaks displayed in a mass spectrum?

Passage A limited number of cellular functions exist for D-amino acids, such as the structural role of D-alanine and D-glutamate in bacterial cell walls.  Because genetically encoded amino acids are synthesized in the L form, production of D-amino acids depends on enzymes called racemases.  With the exception of cysteine, conversion of an L-amino acid to a D-amino acid corresponds to the conversion of an S stereoisomer to an R stereoisomer.  The mechanism of conversion requires the formation of a high-energy carbanion intermediate.  Although pyridoxal phosphate (PLP)-dependent amino acid racemases such as glutamate racemase use PLP as a coenzyme to stabilize this intermediate, the reaction catalyzed by PLP-independent racemases such as alanine racemase proceeds through the enolate intermediate shown in Figure 1. Figure 1  PLP-independent amino acid racemase reactionThe first step in most PLP-dependent reactions is the condensation of an aldehyde group on the coenzyme PLP.  This forms a Schiff base linking PLP to a lysine side chain on the enzyme's active site.  The lysine is then substituted with the amino acid to be converted from L to D configuration (Figure 2). Figure 2  Formation of an amino acid-PLP adductThe next step in PLP-dependent reactions is the removal of the amino acid's α-hydrogen by a base in the enzyme's active site.  A quinonoid intermediate and two additional intermediates are formed, as shown in Figure 3.  The final step includes the rebonding of PLP to the enzyme's active site and the release of the D-amino acid. Figure 3  Intermediates of a PLP-dependent amino acid racemase-catalyzed reactionOther PLP-dependent enzymes participate in the decarboxylation of amino acids via a similar mechanism.  Such enzymes break the bond between the carboxylate carbon and α-carbon in an amino acid by forming a quinonoid intermediate, which helps stabilize the carbanion intermediate of the reaction. Adapted from Cava F, Lam H, De pedro MA, Waldor MK. Emerging knowledge of regulatory roles of D-amino acids in bacteria. Cell Mol Life Sci. 2011. -Compared to the enolate intermediate shown in Figure 1, the quinonoid intermediate in Figure 3 is:

Passage The drug paracetamol, also known as acetaminophen, is used to relieve pain and fever, and is a metabolite of the antipyretic drug phenacetin (Figure 1).  These two drugs have similar medicinal properties, but phenacetin has been shown to be carcinogenic and cause kidney damage.  Acetaminophen is a safer alternative to phenacetin when taken in therapeutic doses. Figure 1  Structure of phenacetinA student synthesizes acetaminophen in a laboratory from phenol according to the reactions shown.  The synthesis begins with the nitration of phenol by sodium nitrate (NaNO₃) to produce the mixture of the isomers 2-nitrophenol and 4-nitrophenol (Reaction 1).  These isomers can be easily separated by steam distillation to isolate the desired product, 4-nitrophenol.  Reduction of the nitro group with sodium borohydride (NaBH₄) (Reaction 2) is followed by acetylation of the amine with acetic anhydride (Reaction 3) to afford the final product, acetaminophen. Reaction 1 Reaction 2 Reaction 3 - The compound 4-nitrophenol shown contains all of the following signals in its infrared spectrum EXCEPT:

Consider the reaction below. Which of the following observations would indicate the reaction product is pure?

Passage Fatty acids (FAs) are lipids that play important roles in cellular function, including energy storage and membrane structure.  Most polyunsaturated fatty acids (PUFAs) are made in the body; however, omega-3 alpha-linolenic acid and omega-6 linoleic acid must be obtained from the diet.  These two PUFAs are precursors to other omega-3 and omega-6 long-chain FAs that are necessary for physiological processes such as neurological development, normal growth, and immune response.  Insufficient omega-3 and omega-6 long-chain FAs can lead to an increase in omega-9 fatty acids such as mead acid, and to essential fatty acid deficiency (EFAD), which can cause infertility, decreased growth, and increased susceptibility to infection.Total FA levels in plasma and serum can be used to diagnose EFAD.  Plasma and serum samples from several individuals were hydrolyzed to release FAs from triacylglycerols and phospholipids.  Once isolated, the free FAs were converted to pentafluorobenzyl (PFB) derivatives and separated by gas chromatography (GC).  Total levels of each type of fatty acid were quantified by negative chemical ionization-mass spectrometry (NCI-MS) immediately after GC.  NCI is an ionization technique that creates negatively charged ions with little to no fragmentation.  The NCI-MS revealed that two of the peaks from GC had the same m/z ratio (Figure 1).  They were both confirmed to be forms of an unsaturated, unbranched 22-carbon FA called omega-9 docosenoic acid. Figure 1  Selected ion chromatogram of docosenoic acidResearchers have proposed that an elevated ratio of the triene omega-9 mead acid to the tetraene omega-6 arachidonic acid, known as the triene/tetraene (TT) ratio, can signify EFAD.  Using GC and NCI-MS, they measured the TT ratio, concentration of mead acid, and individual concentrations of omega-3 and omega-6 FAs in plasma and serum samples from three patients and compared their results to normal ranges.  An increased TT ratio and mead acid concentration and decreased omega-3 and omega-6 FA concentrations were observed in the patient samples compared to normal ranges. Adapted from E. Kish-Trier et al., "Quantitation of total fatty acids in plasma and serum by GC-NCI-MS." Clinical Mass Spectrometry. ©2016 Elsevier. -Researchers separated fatty acid sodium salts from glycerol by adding HCl and then extracting with hexanes.  Which statement correctly describes the extraction process?

Which of the following statements accurately describes the stereochemical outcome of the Strecker synthesis of alanine?

Passage The cryptophycins, isolated from cyanobacteria, are a family of macrocyclic molecules.  Researchers have studied the biological activity of these compounds and found that many of them are active against multi-drug-resistant tumor cells.Cryptophycin-52, an analogue of the natural cryptophycins, has been tested in clinical trials for its efficacy against cancer cells, but the studies were suspended due to neurotoxic side effects.  Nevertheless, the synthesis of similar analogues continues to be of interest in cancer research.  A key step in the synthesis of cryptophycin-52 is the stereospecific formation of an epoxide from an alkene and oxone (Figure 1), which can be facilitated by the Shi catalyst.  The Shi catalyst (Figure 2) is derived from the carbohydrate D-fructose and is known among organic chemists for its ability to form epoxides in hydrocarbons in a stereospecific manner. Figure 1  Shi epoxidation of compound 1 Figure 2  Structure of the Shi catalystThe epoxidation of compound 1 was monitored by thin-layer chromatography (TLC).  When the reaction was completed, high-performance liquid chromatography (HPLC) was used to analyze the epoxide product.  A chiral column that had an affinity for the desired epoxide was used.  A standard of the desired epoxide was obtained to optimize the conditions and determine the retention time of the epoxide.  The HPLC chromatogram of the epoxide standard is shown in Figure 3. Figure 3  HPLC of epoxide standard Adapted from Weiß C, Bogner T, Sammet B, Sewald N. Total synthesis and biological evaluation of fluorinated cryptophycins. Beilstein J Org Chem. 2012. -Fructose for the synthesis of the Shi catalyst can be obtained by cleaving sucrose.  What type of reaction occurs when sucrose is cleaved?

Passage A limited number of cellular functions exist for D-amino acids, such as the structural role of D-alanine and D-glutamate in bacterial cell walls.  Because genetically encoded amino acids are synthesized in the L form, production of D-amino acids depends on enzymes called racemases.  With the exception of cysteine, conversion of an L-amino acid to a D-amino acid corresponds to the conversion of an S stereoisomer to an R stereoisomer.  The mechanism of conversion requires the formation of a high-energy carbanion intermediate.  Although pyridoxal phosphate (PLP)-dependent amino acid racemases such as glutamate racemase use PLP as a coenzyme to stabilize this intermediate, the reaction catalyzed by PLP-independent racemases such as alanine racemase proceeds through the enolate intermediate shown in Figure 1. Figure 1  PLP-independent amino acid racemase reactionThe first step in most PLP-dependent reactions is the condensation of an aldehyde group on the coenzyme PLP.  This forms a Schiff base linking PLP to a lysine side chain on the enzyme's active site.  The lysine is then substituted with the amino acid to be converted from L to D configuration (Figure 2). Figure 2  Formation of an amino acid-PLP adductThe next step in PLP-dependent reactions is the removal of the amino acid's α-hydrogen by a base in the enzyme's active site.  A quinonoid intermediate and two additional intermediates are formed, as shown in Figure 3.  The final step includes the rebonding of PLP to the enzyme's active site and the release of the D-amino acid. Figure 3  Intermediates of a PLP-dependent amino acid racemase-catalyzed reactionOther PLP-dependent enzymes participate in the decarboxylation of amino acids via a similar mechanism.  Such enzymes break the bond between the carboxylate carbon and α-carbon in an amino acid by forming a quinonoid intermediate, which helps stabilize the carbanion intermediate of the reaction. Adapted from Cava F, Lam H, De pedro MA, Waldor MK. Emerging knowledge of regulatory roles of D-amino acids in bacteria. Cell Mol Life Sci. 2011. -Which of the following structures can result from the PLP-dependent decarboxylation of an α-amino acid?

The glycosidic bond in a disaccharide composed of N-acetylmuramic acid (Mur2Ac) and N-acetylglucosamine (GlcNAc) is cleaved by lysozyme.  The first step of the mechanism is shown below. In the second step, Glu35 creates a good nucleophile for the cleavage of the glycosidic bond between Mur2Ac and Asp52 by removing a proton from which of the following molecules?