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Biomedical subjects

K N Houk

Publications and source records attributed to K N Houk.

At least 55 records · Page 3Linked to original sources
PubMed2005

Theoretical evidence for enhanced NO dimerization in aromatic hosts: implications for the role of the electrophile (NO)(2) in nitric oxide chemistry.

Nitric oxide dimerization in gas phase and aromatic hosts (benzene) has been investigated with ab initio quantum mechanics. Using the (RO)MP2-aug-cc-pVDZ method, the computed bond dissociation energy (ON...NO) and geometry of (NO)2 in the gas phase are consistent with the reported spectroscopic data. A relatively strong interaction (-5.4 kcal/mol) between (NO)2 and benzene indicates that aromatic surrounding enhances the NO dimerization. Calculations on reactions of phosphine and methanethiol with NO and (NO)2 show that the dimer is much more reactive. This explains reactions of NO with phosphines and thiols.

Benzene↗
PubMed2005

The three corrugated surfaces of 1,4-divinyltetramethylene diradical intermediates and their connections to 1,2-divinylcyclobutane, 4-vinylcyclohexene, 1,5-cyclooctadiene, and two butadienes.

The three potential energy surfaces of the trans-trans, cis-trans, and cis-cis divinyltetramethylene diradicals have been located with DFT calculations at the BPW91/6-311+G levels. The three surfaces account well for the experimental results reported for the thermolysis of optically active trans-1,2-divinylcyclobutane and optically active and deuterated 4-vinylcyclohexene. The surfaces account also for the outcome of the dimerization of butadiene and the thermolysis of cis,cis-1,5-cyclooctadiene. The three diradical intermediates are connected to the cyclization and dissociation products through conformations that are explored fully here.

Journal Article↗
PubMed2005

Electronic structures and properties of twisted polyacenes.

The effects of twisting on the electronic structures and properties of polyacenes were studied computationally using DFT methods. Singlet-triplet and HOMO-LUMO gaps and vertical S0-S1 transition energies are marginally affected as a function of end-to-end twist angle. The large twist induced by the phenyl substituents in 9,10,11,20,21,22-hexaphenyltetrabenzo[a,c,l,n]pentacene has little influence on its electronic structure.

Journal Article↗
PubMed2005

Dienophile twisting and substituent effects influence reaction rates of intramolecular Diels-Alder cycloadditions: a DFT study.

Intramolecular cycloadditions of 5-vinyl-1,3-cyclohexadienes were studied with B3LYP/6-31G(d) density functional calculations. The one-atom tether dictates that the Z substituent becomes exo and the E substituent becomes endo in the TS. The geometry of the cycloaddition TS is typical of a pericyclic transformation except unusual twisting of the dienophile places the endo substituent in a relatively steric-free position and the exo substituent in a highly crowded position. The experimental rate differences between isomeric pairs of vinylcyclohexadienes can be explained by comparing reactant destabilization when a bulky group occupies the Z position of the starting alkene and transition state stabilization when a bulky group is endo in the cycloaddition TS.

Cyclohexanes↗
PubMed2005

The mechanism of the self-initiated thermal polymerization of styrene. Theoretical solution of a classic problem.

The Mayo and Flory mechanisms for the self-initiation of styrene polymerization were explored with B3LYP and BPW91 density functional calculations. The Diels-Alder dimer (AH) is the key intermediate, and the lowest energy pathway for AH formation is a stepwise mechanism via a gauche/sickle (*M2*Gs) or gauche/U-shaped (*M2*Gu) diradical. Ring closure of the 1,4-diradical to diphenylcyclobutane (DCB) is predicted to have a lower barrier than ring closure to AH. Dynamic effects are likely to play an important role in determining the rate of AH versus DCB formation. Hydrogen transfer from AH to styrene to generate two monoradical species is predicted to be a reasonable process that initiates monoradical polymerization.

Journal Article↗
PubMed2005

Mechanism of aerobic decomposition of Angeli's salt (sodium trioxodinitrate) at physiological pH.

The recent determination that Angeli's salt may have clinical application as a nitrogen oxide donor for treatment of cardiovascular diseases such as heart failure has led to renewed interest in the mechanism and products of thermal decomposition of Angeli's salt under physiological conditions. In this report, several mechanisms are evaluated experimentally and by quantum mechanical calculations to determine whether HNO is in fact released from Angeli's salt in neutral, aerobic solution. The mechanism of product autoxidation is also considered.

Hydrogen-Ion Concentration↗
PubMed2005

Origin of selectivity in the antibody 20F10-catalyzed Yang cyclization.

The first antibody-catalyzed Yang (Norrish type II) cyclization has been achieved with antibodies that were elicited against cis- and trans-2,3-diaryloxetanes. The photocyclization of 1,4-diarylbutan-1-one produced a single stereoisomer of cis-1,2-diarylcyclobutanol with very high enantioselectivity. The background photochemical reaction in the absence of the antibody yielded only fragmentation products. The antibody 20F10-catalyzed reaction was studied in detail, exploring its selectivity, substituent effects, substrate and hapten binding, kinetic parameters and irradiation wavelength dependence. Quantum mechanical calculations suggest that the activation enthalpy of fragmentation pathway is favored by 7.9 kcal/mol over cyclization pathway. Hapten, substrate, and transition state docking studies on a homology based modeled antibody binding site indicate that the trans hapten, substrate and the cyclization transition state have similar binding modes. By contrast, the fragmentation transition state is bound in a different way, not easily accessible within the lifetime of the bound substrate excited state. Several side chain residues were identified that can act as local sensitizers to enhance the cyclization process.

Amino Acid Sequence↗
PubMed2005

Quantum mechanical determinations of reaction mechanisms, acid base, and redox properties of nitrogen oxides and their donors.

This chapter reviews computational methods based on quantum mechanics and commonly used commercial programs for the exploration of chemical phenomena, particularly in the field of nitrogen oxides. Examples from the literature are then used to demonstrate the application of these methods to the chemistry and biochemistry of various nitrogen oxides. These examples include determining reaction mechanisms using computed reaction energies, predicting rates of reactions using transition state theory, and determining chemical properties such as hydration equilibria, pKa's, and reduction potentials.

Acids↗
PubMed2005

Why enzymes are proficient catalysts: beyond the Pauling paradigm.

Pauling proposed that "enzymes are molecules that are complementary in structure to the activated complexes of the reactions that they catalyze, ..., [rather than] entering into reactions". This paradigm has dominated thinking in the field. While complementarity of the type proposed by Pauling can account for acceleration up to 11 orders of magnitude, most enzymes exceed that proficiency. Enzymes with proficiencies ((k(cat)/K(M))/k(uncat)) > 10(11) M(-1) achieve over 15 kcal/mol of "transition state binding" not merely by a concatenation of noncovalent effects but by covalent bond formation between enzyme or cofactor and transition state, involving a change in mechanism from that in aqueous solution. Enzymes enter into reactions with substrates and do not merely complement the transition states of the uncatalyzed reactions.

Animals↗
PubMed2004

Synthesis and relative stability of 3,5-diacyl-4,5-dihydro-1H-pyrazoles prepared by dipolar cycloaddition of enones and alpha-diazoketones.

An unusual reaction process that produced unexpected heterocyclic systems by a fragmentation-recombination mechanism is described. Thus treatment of the triketone, 3-acetyl-2,6-heptanedione, 1, with methanesulfonyl azide gave, in addition to the expected alpha-diazo ketone 3a, the dihydropyrazole 3c and its oxidation product, the pyrazole 3d. We propose that the initially formed alpha-diazo ketone 3a fragments into the simple alpha-diazomethyl ketone and methyl vinyl ketone which then undergo an intermolecular [2,3]-dipolar cycloaddition. Analogous treatment of the trifluoromethyl trione 2 again afforded a pyrazole 4c. Further experiments were carried out to lend evidence to our mechanistic hypothesis. Thus alpha-diazoacetophenone 5 and MVK underwent a [2,3]-dipolar cycloaddition under mild conditions to give the two regioisomeric dihydropyrazoles 6a and 6b. Interestingly these were formed in a 2:1 ratio, which suggested that 6a was more stable than 6b. The structures of 6a and 6b were optimized by using the B3LYP density functional method and the 6-31G* basis set and isomer 6a was predicted to be 1.5 kcal/mol more stable than isomer 6b. This energy difference could be rationalized by the greater capacity of the acetyl group than the benzoyl group to conjugate with the hydrazone. This difference in conjugation is reflected by key bond length differences. Thus we have discovered a novel fragmentation-cycloaddition process. We have also presented evidence for the mechanism of the formation of the dihydropyrazoles and carried out calculations to support these findings.

Journal Article↗
PubMed2004

How large is the conjugative stabilization of diynes?

The conjugation stabilization energies of dienes and diynes are considerably larger than estimates based on heat of hydrogenation differences between 1,3-butadiyne and 1-butyne as well as between 1,3-butadiene and 1-butene. Such comparisons do not take into account the counterbalancing hyperconjugative stabilization of the partially hydrogenated products by their ethyl groups. When alkyl hyperconjugation is considered, the conjugation stabilization of diynes ( approximately 9.3 kcal/mol) is found by two methods (involving isomerization of nonconjugated into conjugated isomers and heats of hydrogenation) to be larger than that of dienes ( approximately 8.2 kcal/mol).

Journal Article↗
PubMed2004

Crankshaft motion in a highly congested bis(triarylmethyl)peroxide.

Crankshaft motion has been proposed in the solid state for molecular fragments consisting of three or more rotors linked by single bonds, whereby the two terminal rotors are static and the internal rotors experience circular motion. Bis-[tri-(3,5-di-tert-butyl)phenylmethyl]-peroxide 2 was tested as a model in search of crankshaft motion at the molecular level. In the case of peroxide 2, the bulky trityl groups may be viewed as the external static rotors, while the two peroxide oxygens can undergo the sought after internal rotation. Evidence for this process in the case of peroxide 2 was obtained from conformational dynamics determined by variable-temperature (13)C and (1)H NMR between 190 and 375 K in toluene-d(8). Detailed spectral assignments for the interpretation of two coalescence processes were based on a correlation between NMR spectra obtained in solution at low temperature, in the solid state by (13)C CPMAS NMR, and by GIAO calculations based on a B3LYP/6-31G structure of 2 obtained from its X-ray coordinates as the input. Evidence supporting crankshaft rotation rather than slippage of the trityl groups was obtained from molecular mechanics calculations.

Journal Article↗
PubMed2004

Computational studies on the electrocyclizations of 1-amino-1,3,5-hexatrienes.

Electrocyclizations of 1,3,5-hexatrienes containing up to four electron-donating and/or electron withdrawing substituents have been studied computationally using the hybrid density functional, B3LYP. Electron donating substituents at positions C-1 and C-5 decrease activation barriers by 0.3 to 2.3 kcal/mol. Introducing of an electron-withdrawing group, CO(2)Me, at C-4 further decreases the activation energy by 7 kcal/mol. Electron-withdrawing groups (NO(2), SO(2)Ph and C=N(+)Me(2)) at C-2 have a profound effect of 17-25 kcal/mol on the activation energy.

Journal Article↗