Biomedical subjects

Peter M W Gill

Publications and source records attributed to Peter M W Gill.

11 recordsLinked to original sources

PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗

PubMed2006

SG-0: a small standard grid for DFT quadrature on large systems.

We report the development of a new standard quadrature grid for DFT calculations. Standard Grid 0 (SG-0) is designed to be approximately half as large as, and to provide approximately half the accuracy of, the established SG-1 grid. It is based on MultiExp and Lebedev quadrature for radial and angular coordinates, respectively. We find that SG-0 is typically 50% faster than SG-1 for energy, gradient, and hessian calculations for the exchange-correlation energy. This leads to a 35-38% speedup in the total gradient and hessian computations, and we particularly recommend its use for preliminary calculations on moderately large biochemical systems. It has been implemented as the default grid for DFT calculations in the Q-Chem 3.0 package.

Journal Article↗

PubMed2005

Transformation of alpha-tocopherol (vitamin E) and related chromanol model compounds into their phenoxonium ions by chemical oxidation with the nitrosonium cation.

[reaction: see text] Alpha-tocopherol (alpha-TOH), the main oil component making up vitamin E, and its nonnatural solid 6-hydroxy-2,2,5,7,8-pentamethylchroman and 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid structurally related analogues were oxidized quantitatively with 2 mol equiv of NO+ SbF6(-) in CH3CN at 233 K to form phenoxonium cations (alpha-TO+ SbF6(-)) in a chemically reversible two-electron/one-proton process. Solution-phase infrared spectroscopy, 1H and 13C NMR spectroscopy, and corresponding theoretical calculations of the spectroscopic data using density-based and wave-function-based models support the identity of the remarkably stable phenoxonium cations. The presence of an oxygen atom in the para position to the hydroxyl group and the chromanol ring structure appear to be important factors in stabilization of the phenoxonium ions, which raises the interesting possibility that the cations play a crucial role in the mode of action of vitamin E in biological systems. Although the phenoxonium cations are reactive toward nucleophiles such as water, they may be moderately stable in the hydrophobic (lipophilic) environment where vitamin E is known to occur naturally.

Antioxidants↗

PubMed2005

A family of intracules, a conjecture and the electron correlation problem.

We present a radical approach to the calculation of electron correlation energies. Unlike conventional methods based on Hartree-Fock or density functional theory, it is based on the two-electron phase-space information in the Omega intracule, a three-dimensional function derived from the Wigner distribution. Our formula for the correlation energy is isomorphic to the Hartree-Fock energy expression but requires a new type of four-index integral. Preliminary results, obtained using a model that is based on the known correlation energies of small atoms, are encouraging.

Electrons↗

PubMed2005

Auxiliary basis expansions for large-scale electronic structure calculations.

One way to reduce the computational cost of electronic structure calculations is to use auxiliary basis expansions to approximate four-center integrals in terms of two- and three-center integrals, usually by using the variationally optimum Coulomb metric to determine the expansion coefficients. However, the long-range decay behavior of the auxiliary basis expansion coefficients has not been characterized. We find that this decay can be surprisingly slow. Numerical experiments on linear alkanes and a toy model both show that the decay can be as slow as 1/r in the distance between the auxiliary function and the fitted charge distribution. The Coulomb metric fitting equations also involve divergent matrix elements for extended systems treated with periodic boundary conditions. An attenuated Coulomb metric that is short-range can eliminate these oddities without substantially degrading calculated relative energies. The sparsity of the fit coefficients is assessed on simple hydrocarbon molecules and shows quite early onset of linear growth in the number of significant coefficients with system size using the attenuated Coulomb metric. Hence it is possible to design linear scaling auxiliary basis methods without additional approximations to treat large systems.

Alkanes↗

PubMed2005

Finite jellium models. I. Restricted Hartree-Fock calculations.

Restricted Hartree-Fock calculations have been performed on the Fermi configurations of n electrons confined within a cube. The self-consistent-field orbitals have been expanded in a basis of N particle-in-a-box wave functions. The difficult one- and two-electron integrals have been reduced to a small set of canonical integrals that are calculated accurately using quadrature. The total energy and exchange energy per particle converge smoothly toward their limiting values as n increases; the highest occupied molecular orbital-lowest unoccupied molecular orbital gap and Dirac coefficient converge erratically. However, the convergence in all cases is slow.

Journal Article↗

PubMed2004

Extracting atoms from molecular electron densities via integral equations.

The observation that a molecular electron density is close to the superposition of its constituent atoms leads naturally to the idea of modeling a density by a sum of nuclear-centered, spherically symmetric functions. The functions that are optimal in a least-squares sense are known as Stewart atoms. Previous attempts to construct Stewart atoms by expanding them in an auxiliary basis have been thwarted by slow convergence with respect to the size of the auxiliary basis used. We present a method for constructing Stewart atoms via convolution integrals which bypasses the need for an auxiliary basis, and is able to produce highly accurate approximations to Stewart atoms.

Journal Article↗

PubMed2004

Atomic and molecular intracules for excited states.

Intracules in position space, momentum space and phase space have been calculated for low-lying excited states of the He atom, Be atom, formaldehyde and butadiene. The phase-space intracules (Wigner intracules) provide significantly more information than the position- and momentum-space intracules, particularly for the Be atom. Exchange effects are investigated through the differences between corresponding singlet and triplet states.

Journal Article↗

PubMed2003

Stereoselective association of binuclear metallacycles in coordination polymers.

A series of structurally related binuclear metallacycles [Cd(NO(3))(2)L](2), where L is an angular exo-bidentate ligand, have been synthesized. Each metallacycle contains two coordinatively unsaturated, chiral metal centers within a single molecule, and the assembly of these metallacycles into polymeric framework structures has been studied systematically for the first time. Stereoselective homochiral association of [Cd(NO(3))(2)L](2) leads to the formation of helical coordination polymers, whereas meso type association results in nonhelical chain structures. The type of stereoselective aggregation depends on the conditions of self-assembly as well as on ligand functionality. Both helical and nonhelical polymeric complexes have been isolated for the metallacycle [Cd(NO(3))(2)(2,4'-pyacph)](2) (2,4'-pyacph = 2,4'-(4-ethynylphenyl)bipyridyl). Homochiral association results in the formation of helical [Cd(NO(3))]( infinity ) chains which link the binuclear [Cd(NO(3))(2)(2,4'-pyacph)](2) metallacycles into racemic two-dimensional sheets which contain both P and M [Cd(NO(3))]( infinity ) helices. In contrast, meso-association leads to the formation of nonhelical one-dimensional chains. It is shown that the product of homochiral association is predominately formed at room temperature and that of meso-association is generated at elevated temperatures. Thus, it may be concluded that the homochiral association appears to be energetically less favorable than the meso-association, a conclusion that has been confirmed by theoretical calculations of the crystal lattice energy. Several high-yield syntheses of bipyridyl-type ligands used for metallacyclic assembly are also reported.

Journal Article↗

PubMed2003

Radial quadrature for multiexponential integrands.

We introduce a Gaussian quadrature, based on the polynomials that are orthogonal with respect to the weight function ln(2)x on the interval [0, 1], which is suitable for the evaluation of radial integrals. The quadrature is exact if the non-Jacobian part of the integrand is a linear combination of a geometric sequence of exponential functions. We find that the new scheme is a useful alternative to existing approaches, particularly for integrands that exhibit multiexponential behavior.

Journal Article↗

PubMed2002

Probing the reactivity of photoinitiators for free radical polymerization: time-resolved infrared spectroscopic study of benzoyl radicals.

A series of substituted benzoyl radicals has been generated by laser flash photolysis of alpha-hydroxy ketones, alpha-amino ketones, and acyl and bis(acyl)phosphine oxides, all of which are used commercially as photoinitiators in free radical polymerizations. The benzoyl radicals have been studied by fast time-resolved infrared spectroscopy. The absolute rate constants for their reaction with n-butylacrylate, thiophenol, bromotrichloromethane and oxygen were measured in acetonitrile solution. The rate constants of benzoyl radical addition to n-butylacrylate range from 1.3 x 10(5) to 5.5 x 10(5) M(-1) s(-1) and are about 2 orders of magnitude lower than for the n-butylacrylate addition to the counterradicals that are produced by alpha-cleavage of the investigated ketones. Density functional theoretical calculations have been performed in order to rationalize the observed reactivities of the initiating radicals. Calculations of the phosphorus-centered radicals generated by photolysis of an acyl and bis(acyl)phosphine oxide suggest that P atom Mulliken spin populations are an indicator of the relative reactivities of the phosphorus-centered radicals. The alpha-cleavage of (2,4,6-trimethylbenzoyl)phosphine oxide was studied by picosecond pump-probe and nanosecond step-scan time-resolved infrared spectroscopy. The results support a mechanism in which the alpha-cleavage occurs from the triplet excited state that has a lifetime less than or equal to the singlet excited state.

Journal Article↗