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G A Worth

Publications and source records attributed to G A Worth.

5 recordsLinked to original sources

A novel algorithm for non-adiabatic direct dynamics using variational Gaussian wavepackets.

In a recent paper (G. Worth, P. Hunt and M. Robb, J. Phys. Chem. A, 2003, 107, 621), we used surface hopping direct dynamics calculations to study the molecular dynamics of the butatriene radical cation in the X/A manifold, which is coupled by a conical intersection. Here, we present the first direct dynamics calculations using a novel algorithm, again using this ideal test system. The algorithm, which is based on the powerful multi-configuration time-dependent Hartree (MCTDH) wavepacket propagation method, uses a variational basis of coupled frozen Gaussian functions that optimally represent the evolving nuclear wavepacket at all times. Each Gaussian function follows a "quantum trajectory", along which the potential surface is evaluated by quantum chemistry calculations. As far fewer Gaussian functions are needed than classical trajectories in a semi-classical method, the number of quantum chemical calculations is drastically reduced. A crucial point in direct dynamics. To validate the method, initial calculations have been made using an analytic model Hamiltonian, where it is shown to reproduce the main features of the state population transfer with 8-16 basis functions per state. Coupled to the GAUSSIAN quantum chemistry program, the method is then shown to provide a feasible direct dynamics algorithm for the description of this non-adiabatic process.

Journal Article↗

Local interactions of aromatic residues in short peptides in aqueous solution: a combined database and energetic analysis.

Although short peptides are usually structurally disordered in aqueous solution, particular peptide sequences display local structure. We performed database and conformational searches, along with molecular dynamics simulations, to study two local interactions detected by 1H-NMR in tetrapeptides excised from bovine pancreatic trypsin inhibitor: aromatic-(i+2)amide and (i-1)cisproline-aromatic. For both types of interaction, at least two major and distinct peptide conformations are identified in the folded state. The aromatic-(i+2)amide interaction can have parallel and perpendicular arrangements of the N-H bond and the aromatic ring. The (i-1)cisproline-aromatic interaction can have close packing of the aromatic ring to the (i-2)C alpha H or the (i-1)C gamma H but not both simultaneously. Although these local aromatic interactions are weak, they may influence folding and binding properties. The combination of search and simulation techniques provides a useful route towards obtaining an atomic-detail description of peptides exhibiting these interactions.

Amides↗

TRAJAN: a tool for analyzing trajectories from molecular simulations.

Molecular dynamics simulations of biological systems are notoriously difficult to analyze because of the complexity of the information that contain. We describe a new method for analyzing trajectories from simulations in order to extract important features of the motion. The trajectory of each atom is partitioned into conformation wells, in each of which its motion is assumed to be predominantly harmonic oscillation around an average position. Thus each atom moves anharmonically through a sequence of wells during the trajectory. The movement of atoms between wells, their ellipsoids of motion within each well, and correlations in the motion of atoms are quantified and can be visualized with molecular graphics. The TRAJAN analysis procedure is applicable to trajectories from equilibrium and nonequilibrium simulations and is not restricted to molecular dynamics simulations. Its application is demonstrated for a range of model systems.

Algorithms↗

Histamine tautomerism and its mode of action.

An established combination of quantum mechanical calculations and molecular dynamics simulations (Worth, C.A., King, P.M. and Richards, W.G. (1989) Biochim. Biophys. Acta 993, 134-136; Cieplak, P., Singh, U.C. and Kollman, P.A. (1987) Int. J. Quant. Chem. QBS14, 65-74; Reynolds, C.A., King, P.M. and Richards, W.G. (1988) Nature 334, 80-82) has been used to calculate the tautomer ratios of histamine species in aqueous solution. The results are in good agreement with experiment and provide a bridge between experimental data and earlier theoretical calculations.

Calorimetry↗