Biomedical subjects

Garth A Jones

Publications and source records attributed to Garth A Jones.

5 recordsLinked to original sources

PubMed2006

Intramolecular Diels-Alder reactions of ester linked 1,3,9-decatrienes: cis/trans selectivity in thermal and Lewis acid promoted reactions of ethylene-tethered and benzo-tethered systems.

High cis (i.e., endo) diastereoselectivities are witnessed in heat-promoted intramolecular Diels-Alder (IMDA) reactions of ethylene-tethered hexadienyl acrylates. The cis stereoselectivity is improved by promotion with Et2AlCl. The first examples of Et2AlCl catalyzed intramolecular Diels-Alder reactions of ester-activated dienophiles are reported. In contrast, the corresponding benzo-tethered hexadienyl acrylates undergo moderately trans (i.e., exo) selective IMDA reactions. Very high trans stereoselection is obtained upon promotion with ATPH. The outcomes of these reactions are essentially insensitive to dienophile (C10) geometry and substitution. DFT (B3LYP/6-31+G(d)) computed cis/trans product distributions-based on Boltzmann transition structure populations-are in good agreement with the experimental results. These computational investigations provide useful insights into the origins of stereoselection in these systems. The stereoselectivity exhibited by the ethylene-tethered hexadienyl acrylates is ascribed to stabilizing secondary orbital interactions at play in the cis-transition structures (TSs). In the benzo-tethered series, this effect is overridden by stabilizing pi-conjugative interactions, between the benzo moiety and the 1,3-diene component, which are stronger in trans TSs, compared to the cis TSs. The computed TS geometries generally exhibit advanced peripheral bond forming asynchronicity, with the tether carbonyl group in conjugation with the dienophile. Such TS features significantly weaken the stereodirecting influence of terminal dienophile substituents.

Acids↗

PubMed2006

Classical polarization in hybrid QM/MM methods.

We have presented a method for modeling polarization in hybrid QM/MM calculations. The method, which expresses the induced dipoles as a set of "induced" charges, is based on the induced dipole approach and methodology for calculating potential-derived point charges from distributed multipole series. The method has the advantage that the same methodology can be used to determine the induced charges and the potential derived charges and so both sets of charges are rigorously defined within the same framework. This underlying link with the wave function makes the method particularly suitable for use in hybrid QM/MM calculations. Here we assess the importance of explicit polarization in the classical part of a QM/MM system with regard to improving the classical description and the consequent effects on the quantum description. The main advantages of the induced charge approach are that the method is readily interfaced with quantum mechanical methods and that induced charges are more readily interpreted than induced dipoles. The ease of interpretation is illustrated by analysis of the charges involved in dimeric and trimeric hydrogen bonded systems. The method for treating the MM polarization has been validated by a regression analysis of the charges induced in both the QM and MM systems against those derived from full quantum mechanical calculations. The method has also been validated using two energy decomposition approaches, which show that MM polarization makes a significant and reliable contribution to the QM - MM interaction energy in a hybrid system. The distance dependency of the induced charges is investigated in calculations on methylsuccinyl-Ala-Ala-Pro-Ala chlormethyl ketone interacting with human neutrophil elastase and propranolol interacting with asparagine residues in a model of the beta(2)-adrenergic receptor.

Algorithms↗

PubMed2006

Mono- and bichromatic electron dynamics: LiH, a test case.

This paper describes an electron dynamics method where the time dependence of an external oscillating electric field is the perturbing part of the Hamiltonian. Application of the electric field induces charge movement inside the molecule and electronic transitions between the molecular orbitals. The test system is the neutral LiH molecule. The method is applied to wave functions calculated using the B3LYP (hybrid) density functional, with the STO-3G and the 6-31+G basis sets. The molecule undergoes full population inversion between the HOMO and the LUMO when the electric field is in resonance with the HOMO-LUMO energy gap. The magnitude of the electric field directly affects the rate at which electronic transitions occur and the rate at which charges move between lithium and hydrogen atoms. The method is used to model both monochromatic and bichromatic multiphoton effects in LiH. Monochromatic one-, two- and three-photon transitions occur between the HOMO, LUMO and two other virtual orbitals. There is evidence of both [1+2] direct and [1+1+1] stepwise multiphoton transitions. Bichromatically, two "laser" pulses are applied at different frequencies. Electronic transitions can be fine-tuned to occur via pre-specified pathways of virtual molecular orbitals.

Journal Article↗

PubMed2005

On the origin of cis/trans stereoselectivity in intramolecular Diels-Alder reactions of substituted pentadienyl acrylates: a comprehensive density functional study.

[structures: see text] A gas-phase B3LYP/6-31+G(d) study of substituent effects on the stereochemistry of both intramolecular Diels-Alder (IMDA) reactions of 9-E- and 9-Z-substituted pentadienyl acrylates and intermolecular Diels-Alder (DA) reactions between butadiene and monosubstituted alkenes and 3-substituted acrylates is reported and involves the calculation of 230 transition structures. It was found that, although exo ("anti-Alder") addition of monosubstituted ethenes to butadiene is the norm, Alder endo selectivity is more widely predicted for 3-substituted methyl acrylate dienophiles, and this was explained in terms of secondary orbital interactions (SOIs). Whereas cis/trans selectivity for IMDA reactions involving 9-E-substituted pentadienyl acrylates generally follows the normal pattern found for the corresponding intermolecular DA reactions, the 9-Z-substituted stereoisomers generally displayed trans selectivity that was much stronger than can be attributed to effects of the isolated substituent. This is strikingly so with unsaturated electron-withdrawing substituents whose endo selectivities, displayed in intermolecular DA reactions, are reversed in the IMDA reactions of pentadienyl acrylates. The origin of this anomalous Z-effect is explained in terms of the twist-mode asynchronicity concept of Brown and Houk. These ideas are used to explain the stereochemical outcomes of IMDA reactions of other triene systems.

Journal Article↗

PubMed2002

On the endo/exo stereoselectivity of intramolecular Diels-Alder reactions of hexadienylacrylates: an interesting failure of density functional theory.

[formula: see text] A combined experimental and computational study of endo/exo stereoselectivity in a series of IMDA reactions of hexadienylacrylates has found that DFT makes erroneous predictions when the endo and exo transition states possess differing degrees of conjugation. These problems are overcome by carrying out calculations at the MP2 level of theory, which gives remarkably accurate Boltzmann distributions of products. These findings are used to predict ways to obtain either endo- or exo-cycloadducts exclusively.

Journal Article↗