Biomedical subjects
Publications and source records attributed to K N Houk.
[reaction: see text] The stereoselectivity of the key epoxidation step in the synthesis of guanacastepene A is shown to be controlled by torsional steering. In this particular epoxidation reaction, the transition structure energetic difference is enhanced by the great asynchronicity of the forming C-O bonds that intensifies the torsional interactions.
B3LYP/6-31G(d) density functional theory has been used to study Diels-Alder reactions of cyclopentadiene with alpha,beta-unsaturated aldehydes and ketones organocatalyzed by MacMillan's chiral imidazolidinones. Preferred conformations of transition structures and reaction intermediates have been located. The dramatically different reactivities and enantioselectivities exhibited by two similar chiral imidazolidinones are rationalized.
Isopropylamine diazeniumdiolate, IPA/NO, the product of the reaction of isopropylamine and nitric oxide, NO, decomposes in a pH-dependent manner to afford nitroxyl, HNO, in the pH range of 13 to above 5, and NO below pH 7. Theoretical studies using B3LYP/6-311+G(d) density functional theory, the polarizable continuum and conductor-like polarizable continuum solvation models, and the high-accuracy CBS-QB3 method on the simplified model compound methylamine diazeniumdiolate predict a mechanism involving HNO production via decomposition of the unstable tautomer MeNN+(O-)NHO-. The production of NO at lower pH is predicted to result from fragmentation of the amide/NO adduct upon protonation of the amine nitrogen.
Mannich reactions between aldehydes and N-p-methoxyphenyl-protected alpha-imino ethyl glyoxylate have been performed using (S)-pipecolic acid as catalyst. The reactions give both syn- and anti-products (dr=1.4-2:1) with high enantioselectivities (>98% ee). In contrast, (S)-proline-catalyzed reactions give mainly syn-products with high enantioselectivities. Computational studies reveal that the energetic preference between the transition structures involving the s-cis-enamine and the s-trans-enamine is smaller for the pipecolic acid as compared to proline, yielding the (2S,3R)-anti and the (2S,3S)-syn Mannich product in nearly equal amounts.
Nitric oxide (NO) plays important roles in many biological processes. S-Nitrosothiols have long been believed to have significant roles in NO biochemistry. The modified cysteine residue of hemoglobin was previously identified as a distorted S-nitrosothiol (RSNO) or an S-hydroxyamino radical (RSN*OH). Here we show that a thionitroxide (RSNHO*, S-aminyloxyl radical) is likely the observed species. Computational studies show that the thionitroxide is the only structure consistent with the electron density in the hemoglobin Cysbeta93-SNO structure previously reported. Although a metastable adduct, the thionitroxide in a hydrogen-bonding environment can form readily and release NO upon exposure to an aqueous environment. The thionitroxides could be responsible for the biological effects attributed to S-nitrosothiols or could serve as precursors to S-nitrosothiols in oxidative conditions.
The activation enthalpies for the reactions of cyclopentadiene with ethylene, acrylonitrile, fumaronitrile, maleonitrile, vinylidene cyanide, tricyanoethylene, and tetracyanoethylene have been computed with the Hartree-Fock quantum mechanical method and a variety of density functionals (B3LYP, BPW91, and MPW1K) and compared to classic experimental data obtained by Sauer, Wiest, and Mielert (Chem. Ber. 1964, 97, 3183). Some significant errors in B3LYP activation enthalpies involving cyano groups, especially 3 or 4 cyano groups, have been identified, whereas HF and MPW1K reproduce substituent effects quite accurately.
The development of catalysts for Mannich-type reactions that afford anti-products with excellent diastereo- and enantioselectivities under mild conditions and low catalyst loadings (1-5 mol %) is reported. Based on principles gained from the study of (S)-proline-catalyzed Mannich-type reactions that afford enantiomerically enriched syn-products, (3R,5R)-5-methyl-3-pyrrolidinecarboxylic acid (RR35) has been designed to catalyze the direct enantioselective anti-selective Mannich-type reactions. Computational studies of the above reaction using HF/6-31G* level of theory suggested that this design would be highly effective. The catalyst was subsequently synthesized and studied in organocatalytic Mannich-type reactions between unmodified aldehydes and N-PMP-protected alpha-imino esters. In accord with the design principles and in quantitative agreement with the theoretical predictions, reactions catalyzed by this catalyst afforded anti-products in good yields with excellent diastereo- and enantioselectivities (anti:syn 94:6 to 98:2, >97 to >99% ee).
Quasiclassical direct dynamics simulations are applied to a 4-fold degenerate rearrangement which yields a nonstatistical product distribution. The simulated product ratio agrees with experiment and is found to be entirely dynamically determined. Trajectory lifetimes are on the order of a low-frequency vibrational period. The interaction of reaction momentum with the geometric features of the potential surface produces selectivity despite a common energy barrier. A geometric model is described for qualitatively estimating much of the dynamically determined product ratio independently of trajectory calculations. The characteristics of this reaction are expected also to apply to others involving modestly stabilized diradical intermediates.
[graph: see text] The vinylcyclobutane-cyclohexene rearrangement has been studied computationally with density functional theory and complete active space SCF calculations. The rearrangement proceeds through a diradical that exists on a very flat potential energy surface. Transition structures for conformational processes, only slightly higher in energy than the minimum energy reaction path, account for the stereochemistries of products observed in the thermal rearrangements of vinylcyclobutane derivatives. The connection of this rearrangement to the Diels-Alder reaction of butadiene with ethylene is discussed.
Diazeniumdiolates, more commonly referred to as NONOates, have been extremely useful in the investigation of the biological effects of nitric oxide (NO) and related nitrogen oxides. The NONOate Angeli's salt (Na(2)N(2)O(3)) releases nitroxyl (HNO) under physiological conditions and exhibits unique cardiovascular features (i.e., positive inotropy/lusitropy) that may have relevance for pharmacological treatment of heart failure. In the search for new, organic-based compounds that release HNO, we examined isopropylamine NONOate (IPA/NO; Na[(CH(3))(2)CHNH(N(O)NO]), which is an adduct of NO and a primary amine. The chemical and pharmacological properties of IPA/NO were compared to those of Angeli's salt and a NO-producing NONOate, DEA/NO (Na[Et(2)NN(O)NO]), which is a secondary amine adduct. Under physiological conditions IPA/NO exhibited all the markers of HNO production (e.g., reductive nitrosylation, thiol reactivity, positive inotropy). These data suggest that primary amine NONOates may be useful as HNO donors in complement to the existing series of secondary amine NONOates, which are well-characterized NO donors.
[reaction: see text] The mechanism of aldol reactions in pure water has been studied with density functional calculations (B3LYP/6-311++G(3d,3p)//B3LYP/6-31G(d)). The reaction is a three-step process that involves: (1) water autoionization generates catalytic hydroxide and hydronium ions, (2) hydroxide and hydronium ions rapidly convert donor aldehyde or ketone into enol, and (3) C-C bond formation and proton transfer occur to give the aldol product. This study provides a general basis for understanding acid/base catalysis by pure water.
[Figure: see text]. A series of donor-acceptor pretzelanes has been synthesized, using self-assembly and template-directed protocols, and the dynamic processes that these pretzelanes undergo have been investigated in solution. These compounds exist as libraries of diastereoisomers as a result of their multiple stereoelements, which are dynamically interconverted by several different, in some cases competing, processes. Altering the structure of the pretzelanes changes the rates and mechanisms by which these diastereoisomers equilibrate. Additionally, inserting an element of fixed chirality allows the equilibrium to be biased, while maintaining the barrier to the equilibration processes. These results bode well for the future construction of molecular devices based on switchable diastereoisomerism involving metastable states.
Activation barriers and reaction energetics for the three main classes of 1,3-dipolar cycloadditions, including nine different reactions, were evaluated with the MPW1K and B3LYP density functional methods, MP2, and the multicomponent CBS-QB3 method. The CBS-QB3 values were used as standards for 1,3-dipolar cycloaddition activation barriers and reaction energetics, and the density functional theory (DFT) and MP2 methods were benchmarked against these values. The MPW1K/6-31G* method and basis set performs best for activation barriers, with a mean absolute deviation (MAD) value of 1.1 kcal/mol. The B3LYP/6-31G* method and basis set performs best for reaction enthalpies, with a MAD value of 2.4 kcal/mol, while the MPW1K method shows large errors for reaction energetics. The MP2 method gives the expected systematic underestimation of barriers. Concerted and nearly synchronous transition structures are predicted by all DFT and MP2 methods. Also reported are revised estimated 0 K experimental activation enthalpies for a standard set of hydrocarbon pericyclic reactions and updated comparisons to experiment for DFT, ab initio, and multicomponent methods. B3LYP and MPW1K methods with MAD values of 1.5 and 2.1 kcal/mol, respectively, fortuitously outperform the multicomponent CBS-QB3 method, which has a MAD value of 2.3. The MAD value of the O3LYP functional improves to 2.4 kcal/mol from the previously reported 3.0 kcal/mol.
[reaction: see text] The stereochemistries of [3,3] sigmatropic Johnson-Claisen (J-C) rearrangements of six intermediates studied in the synthesis of gelsemine were modeled using DFT methodology. The possible origins of the rearrangement stereoselectivity are explored and compared with the experimentally suggested rationalizations by Danishefsky et al. (J. Am. Chem. Soc. 2002, 124, 9812-9824). In the intermediate used for the J-C rearrangement in the Danishefsky synthesis (3), the closure is inhibited by the repulsive interactions between the enolate terminus and the carbon atoms of the double bond as well as with the hydrogen on C7. The closure is favored by stabilizing interactions between the enolate terminus and the H's of the oxetane ring.
The effects of different amino acid catalysts and substrate substituents on the stereoselectivity of the title reactions have been studied with the aid of density functional theory methods. Experimental data available in the literature have been compiled. B3LYP/6-31G(d) calculations match the general experimental trends and provide useful insights into the origins of the variations in stereoselectivities. Acyclic primary amino acids allow a greater conformational flexibility in the aldol transition states compared with proline. This makes them poorer enantioselective catalysts with triketone substrates with a methyl ketone side chain. The steric repulsion upon substitution at the terminal methyl group increases the energy difference between anti- and syn-chairs with primary amino acid catalysts and, consequently, the stereoselectivities. Proline, in contrast, is a poor catalyst for the latter reactions because the substituent's steric bulkiness raises the activation energy of the favored C-C bond-forming pathway.
The decomposition of S-nitrosothiols (RSNO) in solution under oxidative conditions is significantly faster than can be accounted for by homolysis of the S-N bond. Here we propose a cationic chain mechanism in which nitrosation of nitrosothiol produces a nitrosated cation that, in turn, reacts with a second nitrosothiol to produce nitrosated disulfide and the NO dimer. The nitrosated disulfide acts as a source of nitrosonium for nitrosothiol nitrosation, completing the catalytic cycle. The mechanism accounts for several unexplained facets of nitrosothiol chemistry in solution, including the observation that the decomposition of an RSNO is accelerated by O(2), mixtures of O(2) and NO, and other oxidants, that decomposition is inhibited by thiols and other antioxidants, that decomposition is dependent on sulfur substitution, and that decomposition often shows nonintegral kinetic orders.
The rates of deuterium transfer in the photoenolization of triplet 1,4-dimethyl-10H-anthracen-9-one (1) with varying degrees of deuterium label in their methyl groups (1-d3, 1-d2, and 1-d) have been investigated as a function of temperature between 5 and 77 K. Measurable rate constants in the case of 1-d3 and 1-d2 were used to construct Arrhenius plots which illustrate the expected curvature and leveling off of rate constant versus temperature. The difference in tunneling rate constants of 1-d3 and 1-d2 yields a tunneling isotope effect, TIE = 2.4, which is attributed to the secondary alpha isotopic substitution. Density functional theory (DFT, B3LYP/6-31G*) calculations were carried out to obtain structural and energetic information for the H(D) transfer along the triplet state zero-point energy levels. The temperature dependence of the rate constants for each isotopologue was simulated with a model that considers the frequency of the C-D stretching mode and the quantum mechanical permeability determined from calculated energy parameters. The model suggests that a difference in barrier width of only 0.015 A between 1-d3 and 1-d2 leads to the observed 2-fold difference between tunneling rates.
The introduction of a stereogenic center by a stereospecific synthesis into an optically active, donor-acceptor pretzelane, that exhibits helicity as well as fixed chirality, leads to a marked preference for one conformational diastereoisomer over the other in both acetone and dimethylsulfoxide that can be understood from computational models.