Biomedical subjects

Ryan P Steele

Publications and source records attributed to Ryan P Steele.

4 recordsLinked to original sources

PubMed2007

An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: application to alanine tetrapeptide conformational analysis.

We present a new algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory (RI-MP2) and thoroughly assess its computational performance and chemical accuracy. This algorithm addresses the potential I/O bottlenecks associated with disk-based storage and access of the RI-MP2 t-amplitudes by utilizing a semi-direct batching approach and yields computational speed-ups of approximately 2-3 over the best conventional MP2 analytical gradient algorithms. In addition, we attempt to provide a straightforward guide to performing reliable and cost-efficient geometry optimizations at the RI-MP2 level of theory. By computing relative atomization energies for the G3/99 set and optimizing a test set of 136 equilibrium molecular structures, we demonstrate that satisfactory relative accuracy and significant computational savings can be obtained using Pople-style atomic orbital basis sets with the existing auxiliary basis expansions for RI-MP2 computations. We also show that RI-MP2 geometry optimizations reproduce molecular equilibrium structures with no significant deviations (>0.1 pm) from the predictions of conventional MP2 theory. As a chemical application, we computed the extended-globular conformational energy gap in alanine tetrapeptide at the extrapolated RI-MP2/cc-pV(TQ)Z level as 2.884, 4.414, and 4.994 kcal/mol for structures optimized using the HF, DFT (B3LYP), and RI-MP2 methodologies and the cc-pVTZ basis set, respectively. These marked energetic discrepancies originate from differential intramolecular hydrogen bonding present in the globular conformation optimized at these levels of theory and clearly demonstrate the importance of long-range correlation effects in polypeptide conformational analysis.

Alanine↗

PubMed2006

Dual-basis analytic gradients. 1. Self-consistent field theory.

Analytic gradients of dual-basis Hartree-Fock and density functional theory energies have been derived and implemented, which provide the opportunity for capturing large basis-set gradient effects at reduced cost. Suggested pairings for gradient calculations are 6-31G/6-31G**, dual[-f,-d]/cc-pVTZ, and 6-311G*/6-311 + +G(3df,3pd). Equilibrium geometries are produced within 0.0005 A of large-basis results for the latter two pairings. Though a single, iterative SCF response equation must be solved (unlike standard SCF gradients), it may be obtained in the smaller basis set, and integral screening further reduces the cost for well-chosen subsets. Total nuclear force calculations exhibit up to 75% savings, relative to large-basis calculations.

Journal Article↗

PubMed2006

Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations.

The resolution-of-the-identity (RI) approximation has placed the onus of the cost of a second-order Moller-Plesset (MP2) calculation on the underlying self-consistent field (SCF) calculation for many moderately sized molecules. A dual-basis approach to the SCF calculation, based on previous methods demonstrated for density functional theory, is combined with RI-MP2 calculations, and small basis subsets for cc-pVTZ, cc-pVQZ, and 6-311++G(3df,3pd) are presented. These subsets provide time savings of greater than 90%, with negligible errors in absolute and relative energies, compared to the associated full-basis counterpart. The method is tested with a series of rotational barriers, relative conformational energies of alanine tetrapeptides, as well as the full G3/99 molecular set. RI-MP2 calculations on alanine octapeptides (40 heavy atoms, 3460 basis functions), using cc-pVQZ, are presented. Results improve upon previous methods that diagonalize the virtual space separately.

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↗