Biomedical subjects

Nicholas A Besley

Publications and source records attributed to Nicholas A Besley.

11 recordsLinked to original sources

PubMed2006

Application of Wigner and Husimi intracule based electron correlation models to excited states.

A new approach to the electron correlation problem based on phase space intracules derived from the Wigner distribution is applied to excited states. The computed electron correlation energy reduces the mean absolute error in the prediction of the excitation energies of 55 atomic excited states from 0.65 eV for unrestricted Hartree-Fock to 0.32 eV. This compares favorably to a mean absolute deviation of 0.52 eV for second order Moller-Plesset perturbation theory and 0.35 eV for the Lee-Yang-Parr functional. An analogous correlation model based on the Husimi distribution is developed. Predicted correlation energies and excitation energies from this model are significantly worse than for the Wigner intracule based model. Alternative correlation kernels may be more suitable for the Husimi intracule based approach.

Journal Article↗

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

Electronic excited states of Si(100) and organic molecules adsorbed on Si(100).

The electronically excited states of the Si(100) surface and acetylene, benzene, and 9,10-phenanthrenequinone adsorbed on Si(100) are studied with time-dependent density functional theory. The computational cost of these calculations can be reduced through truncation of the single excitation space. This allows larger cluster models of the surface in conjunction with large adsorbates to be studied. On clean Si(100), the low-lying excitations correspond to transitions between the pi orbitals of the silicon-silicon dimers. These excitations are predicted to occur in the range 0.4-2 eV. When organic molecules are adsorbed on the surface, surface --> molecule, molecule --> surface, and electronic excitations localized within the adsorbate are also observed at higher energies. For acetylene and benzene, the remaining pipi* excitations are found to lie at lower energies than in the corresponding gas-phase species. Even though the aromaticity of 9,10-phenanthrenequinone is retained, significant shifts in the pipi* excitations of the aromatic rings are predicted. This is in part due to structural changes that occur upon adsorption.

Journal Article↗

PubMed2005

Theoretical study of the 13C NMR spectroscopy of single-walled carbon nanotubes.

The 13C NMR spectroscopy of armchair and zigzag single-walled carbon nanotubes has been investigated theoretically. Spectra for (4,4), (5,5), (6,6), (6,0), (9,0), and (10,0) nanotubes have been simulated based on ab initio calculations of model systems. The calculations predict a dominant band arising from the carbon atoms in the "tube" with smaller peaks at higher chemical shifts arising from the carbon atoms of the caps. The dominant band lies in the range of 128 and 138 ppm. Its position depends weakly on the length, width, and chirality of the tubes. The calculations demonstrate how structural information may be gleaned from relatively low-resolution nanotube 13C NMR spectra.

Journal Article↗

PubMed2005

Modeling the absorption spectrum of tryptophan in proteins.

We have applied time-dependent density functional theory (TDDFT) to study the valence pi-pi* excited states of the tryptophan chromophore in the environment of the proteins barnase and human serum albumin. The chromophore is represented by indole. Due to the approximate nature of TDDFT, in the gas phase the calculated vertical transition energies to the 1L valence states are reordered with respect to experiment. The 1L(a) state responds more than the 1L(b) state to the local environment, described fully at the TDDFT level, and to bulk environment, described by a set of point charges. Nevertheless, the vertical transitions are readily identified. For human serum albumin, our calculations predict distinct spectral characteristics between structures with different tryptophan side chain torsion angles. The computational tractability of TDDFT relative to more accurate ab initio methods allows a large part of the surrounding protein environment (up to 100 atoms) to be explicitly included in the TDDFT calculations.

Bacillus↗

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

A systematic shift in the electronic spectra of substituted benzene molecules trapped in helium nanodroplets.

Electronic spectra (S1<--S0) have been recorded from five separate substituted benzene derivatives trapped in helium nanodroplets. Each member of the series is found to exhibit a blueshift with respect to the equivalent transition in the gas phase. Taken together with previous results for benzene, the observed shifts show a remarkably good correlation with changes in electron density that occur within each of the aromatic rings as a result of electronic excitation.

Journal Article↗

PubMed2005

Theoretical study of the electronic spectroscopy of CO adsorbed on Pt(111).

The excited states of CO adsorbed on the Pt(111) surface are studied using a time-dependent density functional theory formalism. To reduce the computational cost, electronic excitations are computed within a reduced single excitation space. Using cluster models of the surface, excitation energies are computed for CO in the on-top, threefold, and bridge binding sites. On adsorption, there is a lowering of the 5sigma orbital energy. This leads to a large blueshift in the 5sigma- -> pi(CO*) excitation energy for all adsorption sites. The 1pi and 4sigma orbital energies are lowered to a lesser extent, and smaller shifts in the corresponding excitation energies are predicted. For the larger clusters, pi* excitations at lower energies are observed. These transitions correspond to excitations to virtual orbitals of pi* character which lie below the pi* orbitals of gas phase CO. These orbitals are associated predominantly with the metal atoms of the cluster. The excitation energies are also found to be sensitive to changes in the adsorption geometry. The electronic spectrum of CO on Pt(111) is simulated and the assignment of the bands observed in experimental electron energy loss spectroscopy discussed.

Journal Article↗

PubMed2004

A sequential molecular mechanics/quantum mechanics study of the electronic spectra of amides.

We report gas-phase electronic spectra of formamide, N-methyformamide, acetamide, and N-methylacetamide at 300 K calculated using a combination of classical molecular dynamics and time-dependent density functional theory (TDDFT). In comparison to excitation energies computed using the global minima structures, the valence npi* and pi(nb)pi* states show a significant red-shift of 0.1-0.35 eV, while smaller shifts are found for the n3s and pi(nb)3s Rydberg states. In this work, we have identified the physical origin of these shifts arising from variations of the molecular structure. We present simple relationships between key geometrical parameters and spectral shifts. Consequently, electronic spectra can be generated directly from ground-state structures, without additional quantum chemical calculations. The electronic spectrum of formamide in aqueous solution is computed using TDDFT using an explicit solvent model. This provides a quantitative determination of the condensed-phase spectrum. In general, this study shows that temperature effects can change the predicted excitation energies significantly and demonstrates how electronic spectra at elevated temperatures can be computed in a computationally efficient way.

Amides↗

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↗

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↗