Biomedical subjects

K N Houk

Publications and source records attributed to K N Houk.

At least 73 records · Page 4Linked to original sources

PubMed2004

Origins of selectivities in proline-catalyzed alpha-aminoxylations.

The mechanisms, transition structures, regioselectivity, and stereoselectivity of proline-catalyzed alpha-aminoxylation reactions were studied with density functional theory (B3LYP/6-31G(d)). The most favorable transition structure involves the nucleophilic attack of the (E)-proline enamine to the oxygen of the nitrosobenzene with proton transfer from the carboxylic acid to the nitrogen. Enamine attack to the oxygen is favored over the attack on the nitrogen due to the greater basicity of the nitrogen. Previously proposed zwitterionic enaminium pathways are highly disfavored due to the energetic penalty associated with charge separations.

Aldehydes↗

PubMed2004

Equilibrium isotope effects as a probe of nonbonding attractions.

The equilibrium isotope effects (EIEs) in the capsule complex (12 + p-xylene + CCl4) were computed with two simple models that mimic two types of contacts, -CH3.Ar and -CH3.CCl4. By using the MP2/6-311++G(d,p) method, the calculated equilibrium constants are consistent with the reported experimental data. Harmonic frequency analyses indicate that vibrational frequency changes caused by nonbonding attractions lead to the observed EIE.

Benzene↗

PubMed2004

Theoretical study of the stereoselective additions of chiral alcohols to ketenes.

In 1989, Larsen et al. at Merck discovered that the addition of chiral alcohols to ketenes provided enantiomerically enriched aryl propionic acids, compounds valued for their therapeutic antiinflammatory properties. The high 1,4-asymmetric induction observed (>99:1 dr in the addition, and up to 99% ee after hydrolysis to the acid) is rare. A quantitative model based on B3LYP density functional theory calculations accounts for the stereoselectivity in the addition of (S)-methyl lactate, (S)-3-methyl-2-butanol, and (S)-pantolactone to methylphenylketene. The conformational processes of the intermediates can impact the stereoselectivity of the process, and either the addition step, or the protonation of the enolate intermediate, may be stereoselectivity determining.

Alcohols↗

PubMed2004

Antibody-catalyzed oxy-cope rearrangement: mechanism and origins of catalysis and stereoselectivity from DFT quantum mechanics and flexible docking.

Density functional theory using B3LYP and flexible ligand docking methods were used to investigate the complete potential surface for the uncatalyzed and the AZ28 antibody-catalyzed oxy-Cope reaction of 2,5-diaryl-1,5-hexadien-3-ol derivatives. The reaction mechanism is stepwise, involving a cyclohexane diyl intermediate. Theoretical deuterium isotope effects match well with those from experiment. Gas-phase transition structures show mixed preferences for the axial vs equatorial hydroxyl group, while solvation favors the axial isomer. Specific phenyl group conformations are shown to be critical to transition-state stabilization (by up to 15 kcal/mol), and the effective conformation is not that found in the hapten used to generate the germline and affinity-matured AZ28 catalytic antibodies. Docking studies support greater transition-state binding than reactant binding. Docking studies also predict the S stereoselectivity of mature AZ28 and suggest that binding modes quite different from those of the hapten might play a role in catalysis, with specific focus on ligand hydrogen bonding to Asp(H101).

Alcohols↗

PubMed2004

On the mechanism of [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) reactions between vinylcyclopropanes and alkynes.

DFT calculations have been applied to investigate the reaction mechanism of rhodium dimer, [Rh(CO)2Cl]2, catalyzed intermolecular (5 + 2) reactions between vinylcyclopropanes and alkynes. The catalytic species is Rh(CO)Cl and the catalytic cycle is through the sequential reactions of cyclopropyl cleavage of vinylcyclopropane, alkyne insertion (rate-determining step), and a migratory reductive elimination.

Journal Article↗

PubMed2004

Steric retardation of SN2 reactions in the gas phase and solution.

The gas-phase S(N)2 reactions of chloride with ethyl and neopentyl chlorides and their alpha-cyano derivatives have been explored with B3LYP, CBS-QB3, and PDDG/PM3 calculations. Calculations predict that the steric effect of the tert-butyl group raises the activation energy by about 6 kcal/mol relative to methyl in both cases. Solvent effects have been computed with QM/MM Monte Carlo simulations for DMSO, methanol, and water, as well as with a polarizable continuum model, CPCM. Solvents cause a large increase in the activation energies of these reactions but have a very small differential effect on the ethyl and neopentyl substrates and their cyano derivatives. The theoretical results contrast with previous conclusions that were based upon gas-phase rate measurements.

Journal Article↗

PubMed2004

Nonspecific medium effects versus specific group positioning in the antibody and albumin catalysis of the base-promoted ring-opening reactions of benzisoxazoles.

The mechanisms by which solvents, antibodies, and albumins influence the rates of base-catalyzed reactions of benzisoxazoles have been explored theoretically. New experimental data on substituent effects and rates of reactions in several solvents, in an antibody, and in an albumin are reported. Quantum mechanical calculations were carried out for the reactions in water and acetonitrile, and docking of the transition state into a homology model of antibody 34E4 and an X-ray structure of human serum albumin was accomplished. A microenvironment made up of catalytic polar groups (glutamate in antibody 34E4 and lysine in human serum albumin) surrounded by relatively nonpolar groups is present in both catalytic proteins.

Antibodies, Catalytic↗

PubMed2004

Oligoacenes: theoretical prediction of open-shell singlet diradical ground states.

A series of oligoacenes from benzene to decacene were studied computationally with DFT and CASSCF methods. In contrast to the common view that acenes are closed-shell systems or may have a triplet ground state, these results offer the first theoretical predictions for the singlet ground state and diradical character for oligoacenes. The nature of the ground states of these molecules arises from the disjoint nature of the NBMOs that are singly occupied in the diradical.

Journal Article↗

PubMed2004

Theoretical investigation of the origins of catalysis of a retro-Diels-Alder reaction by antibody 10F11.

The antibody 10F11 catalyzes a retro-Diels-Alder reaction that forms HNO. Deductions about the mechanism of catalysis were made by Reymond, Baumann et al. from X-ray crystal structures and from kinetic measurements for mutated antibodies. We report a study of these reactions with quantum mechanical methods and a study of the substrate and transition state binding to the active site of the antibody 10F11 using density functional theory and empirical docking methods. We have quantitated the likely contributions to catalysis of three residues identified as possible causes of catalysis: Trp H104, Phe H101, and Ser H100. Trp H104 can make a significant contribution to catalysis through dispersive interactions (pi-stacking aromatic-aromatic stabilization). On its own, Phe H101 makes only a small contribution to catalysis. When both aromatic residues are present, they act cooperatively and can make greater contributions to catalysis than expected for each residue alone. Ser H100 and the backbone NH of Phe H101 are expected to act through hydrogen bonding to speed up the reaction, but our calculations suggest that they make only a small contribution to catalysis. Reymond's studies suggest that the hydrogen-bonding network may be mediated through a water molecule in the binding site.

Antibodies, Catalytic↗

PubMed2004

Mechanisms of HNO and NO production from Angeli's salt: density functional and CBS-QB3 theory predictions.

The mechanism of decomposition of Angeli's salt, Na(2)N(2)O(3), was explored with B3LYP and CBS-QB3 computational methods. Angeli's salt produces both nitroxyl (HNO) and nitric oxide (NO), depending upon the pH of the solution. These calculations show that protonation on N(2), while less favorable than O protonation, leads spontaneously to HNO production, while diprotonation at O(3) leads to NO generation. K(a) values for protonation at different centers and rate constants have been found which reproduce experimental data satisfactorily.

Models, Chemical↗

PubMed2004

Theoretical evidence for oxygenated intermediates in the reductive cyclization of nitrobenzenes.

Deoxygenation of nitroaromatics is a classic synthetic method for the construction of nitrogen heterocycles. The generally accepted mechanism involves exhaustive deoxygenation to a singlet nitrene. We present theoretical evidence for an alternative, 6pi-electron 5-atom electrocyclization of nitroso-styrenes, -stilbenes, and -biphenyls to nitronates. A downstream 1,5-H shift and tautomerization leads to N-hydroxy heterocycles. [reaction: see text]

Journal Article↗

PubMed2004

Demonstrating the synergy of synthetic, mechanistic, and computational studies in a regioselective aniline synthesis.

Tri- and tetrasubstituted anilines are formed in good to excellent yields by the addition of ketones to vinamidinium salts (up to 98%). The reaction proceeds via the formation of dienone intermediates, which react to form an enamine with the liberated amine. In the case of a nitro, or dimethylaminomethylene substituent, the enamines undergo a facile electrocyclic ring closure to form a cyclohexadiene, which goes on to form anilines with a high degree of selectivity (up to 50:1) with a minor competing pathway proceeding via the enol providing phenols. Competition experiments using isotopic substitution reveal that the rate determining step en route to dienone is enol/enolate addition to the vinamidinium salt, which is characterized by an inverse secondary isotope effect (k(H/D) 0.7-0.9). Computational studies have been used to provide a framework for understanding the reaction pathway. The original proposal for a [1,5]-H shift was ruled out on the basis of the calculations, which did not locate a thermally accessible transition state. The minimum energy conformation of the enamine is such that a facile electrocyclic ring closure is ensured, which is corroborated by the experimental studies. A framework for understanding the reaction pathway is presented.

Journal Article↗

PubMed2004

The mechanism of NO formation from the decomposition of dialkylamino diazeniumdiolates: density functional theory and CBS-QB3 predictions.

The mechanism of decomposition of dialkylamino diazeniumdiolate salts, R(2)N[NONO](-)M(+), to form nitric oxide, NO, was explored using theoretical methods. B3LYP/6-311+G(d) density functional theory calculations gave the optimized geometries, and energetics were further evaluated with the high accuracy CBS-QB3 method, when feasible. Relative pK(a) values were estimated using the PCM model for aqueous solvation. The terminal oxygen is the most basic site, followed closely by the internal oxygen. Protonation of these sites does not lead to decomposition. However, protonation of the weakly basic amino nitrogen leads to very rapid decomposition and NO generation.

Algorithms↗

PubMed2004

Origins of enantioselectivity in reductions of ketones on cinchona alkaloid modified platinum.

A model to explain the stereoselectivities of reductions of activated ketones on cinchona alkaloid modified platinum is proposed and is supported by calculations by density functional and force field methods. The model involves nucleophilic catalysis by the cinchona alkaloid. The zwitterionic adduct between a cinchona alkaloid and ketone is adsorbed on Pt through the quinoline ring and two heteroatoms and is subsequently reduced with inversion. The model rationalizes the observed stereoselectivities for hydrogenation of carbonyl compounds.

Cinchona Alkaloids↗

PubMed2004

Theory of asymmetric organocatalysis of Aldol and related reactions: rationalizations and predictions.

Computational studies have led to models to understand some classic and contemporary asymmetric reactions involving organocatalysts. The Hajos-Parrish-Eder-Sauer-Wiechert reaction and intermolecular aldol reactions as well as Mannich reactions and oxyaminations catalyzed by proline and other amino acids, and Diels-Alder reactions catalyzed by MacMillan's chiral amine organocatalysts have been studied with density functional theory. Quantitative predictions for several new catalysts and reactions are provided.

Journal Article↗

PubMed2003

Intramolecular cycloadditions of cyclobutadiene with dienes: experimental and computational studies of the competing (2 + 2) and (4 + 2) modes of reaction.

Highly functionalized, cyclobutene-containing adducts are afforded through intramolecular cycloadditions between cyclobutadiene and tethered dienes. The cycloaddition displays the following reactivity trend: cyclobutadiene serves as a dienophile in intramolecular reactions when it is connected to the diene through a four-atom tether. In cases where a three-atom linker separates the two reaction partners, the cyclobutadiene can function as both a diene and dienophile, affording a mixture of vinylcyclobutane (2 + 2) and cyclohexene-containing cycloadducts (4 + 2). Theoretical studies provide insight into the factors influencing the various pericyclic pathways operative in this system. In cases where cyclobutadiene functions as a diene to generate vinylcyclobutanes, these (2 + 2) adducts can be converted into the corresponding (4 + 2) cyclohexenyl products through a [3,3]-sigmatropic rearrangement.

Bridged Bicyclo Compounds↗

PubMed2003

Dimerizations of nitrile oxides to furoxans are stepwise via dinitrosoalkene diradicals: a density functional theory study.

Density functional theory calculations at the B3LYP/6-31G* level on the dimerization reactions of acetonitrile oxide and para-chlorobenzonitrile oxide to form furoxans indicate that these processes are stepwise involving dinitrosoalkene intermediates that have considerable diradical character. The rate-determining steps for these two reactions correspond to C-C bond formation. The retardation of dimerization in aromatic nitrile oxides arises from the interruption of conjugation between the nitrile oxide and aryl groups in the C-C bond formation step. The present study also suggests that the isomerization of single-ring furoxans occurs via a diradical intermediate mechanism.

Journal Article↗

PubMed2003

Mechanism of the glutathione transferase-catalyzed conversion of antitumor 2-crotonyloxymethyl-2-cycloalkenones to GSH adducts.

Human glutathione (GSH) transferase (hGSTP1-1) processes with similar kinetic efficiencies the antitumor agents 2-crotonyloxymethyl-2-cyclohexenone (COMC-6), 2-crotonyloxymethyl-2-cycloheptenone (COMC-7), and 2-crotonyloxymethyl-2-cyclopentenone (COMC-5) to 2-glutathionylmethyl-2-cyclohexenone, 2-glutathionylmethyl-3-glutathionyl-2-cycloheptenone, and 2-glutathionylmethyl-2-cyclopentenone, respectively. This process likely involves initial enzyme-catalyzed Michael addition of GSH to the COMC derivative to give a glutathionylated enol(ate), which undergoes nonstereospecific ketonization, either while bound to the active site or free in solution, to a glutathionylated exocyclic enone. Free in solution, GSH reacts at the exomethylene carbon of the exocyclic enone, displacing the first GSH to give the final product. This mechanism is supported by the observation of multiphasic kinetics in the presence of high concentrations of hGSTP1-1 and the ability to trap kinetically competent exocyclic enones in aqueous acid using COMC-6 and COMC-7 as substrates. That the exocyclic enone is formed by nonstereospecific ketonization of an enol(ate) species is indicated by the observation that COMC-6 (chirally labeled with deuterium at the exomethylene carbon) gives stereorandomly labeled exocyclic enone. The isozymes hGSTP1-1, hGSTA1-1, hGSTA4-4, and hGSTM2-2 catalyze the conversion of COMC-6 to final product with similar efficiencies (K(m) = 0.08-0.34 mM, k(cat) = 1.5-6.1 s(-)(1)); no activity was detected with the rat rGSTT2-2 isozyme. Molecular docking studies indicate that in hGSTP1-1, the hydroxyl group of Tyr108 might serve as a general acid catalyst during substrate turnover. The possible significance of these observations with respect to the metabolism of COMC derivatives in multidrug resistant tumors is discussed.

Antineoplastic Agents↗