Biomedical subjects

Ryan M Olson

Publications and source records attributed to Ryan M Olson.

6 recordsLinked to original sources

PubMed2006

The structure of the Si9H12 cluster: A coupled cluster and multi-reference perturbation theory study.

Full geometry optimizations using both singles and doubles coupled cluster theory with perturbative triple excitations, CCSD(T), and second order multi-reference perturbation theory, MRMP2, have been employed to predict the structure of Si9H12, a cluster commonly used in calculations to represent the Si(100) surface. Both levels of theory predict the structure of this cluster to be symmetric (not buckled), and no evidence for a buckled (asymmetric) structure is found at either level of theory.

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PubMed2006

Parallel coupled perturbed CASSCF equations and analytic CASSCF second derivatives.

A parallel algorithm for solving the coupled-perturbed MCSCF (CPMCSCF) equations and analytic nuclear second derivatives of CASSCF wave functions is presented. A parallel scheme for evaluating derivative integrals and their subsequent use in constructing other derivative quantities is described. The task of solving the CPMCSCF equations is approached using a parallelization scheme that partitions the electronic hessian matrix over all processors as opposed to simple partitioning of the 3 N solution vectors among the processors. The scalability of the current algorithm, up to 128 processors, is demonstrated. Using three test cases, results indicate that the parallelization of derivative integral evaluation through a simple scheme is highly effective regardless of the size of the basis set employed in the CASSCF energy calculation. Parallelization of the construction of the MCSCF electronic hessian during solution of the CPMCSCF equations varies quantitatively depending on the nature of the hessian itself, but is highly scalable in all cases.

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PubMed2005

Where does the planar-to-nonplanar turnover occur in small gold clusters?

Several levels of theory, including both Gaussian-based and plane wave density functional theory (DFT), second-order perturbation theory (MP2), and coupled cluster methods (CCSD(T)), are employed to study Au6 and Au8 clusters. All methods predict that the lowest energy isomer of Au6 is planar. For Au8, both DFT methods predict that the two lowest isomers are planar. In contrast, both MP2 and CCSD(T) predict the lowest Au8 isomers to be nonplanar.

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PubMed2004

A new hierarchical parallelization scheme: generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO).

A two-level hierarchical scheme, generalized distributed data interface (GDDI), implemented into GAMESS is presented. Parallelization is accomplished first at the upper level by assigning computational tasks to groups. Then each group does parallelization at the lower level, by dividing its task into smaller work loads. The types of computations that can be used with this scheme are limited to those for which nearly independent tasks and subtasks can be assigned. Typical examples implemented, tested, and analyzed in this work are numeric derivatives and the fragment molecular orbital method (FMO) that is used to compute large molecules quantum mechanically by dividing them into fragments. Numeric derivatives can be used for algorithms based on them, such as geometry optimizations, saddle-point searches, frequency analyses, etc. This new hierarchical scheme is found to be a flexible tool easily utilizing network topology and delivering excellent performance even on slow networks. In one of the typical tests, on 16 nodes the scalability of GDDI is 1.7 times better than that of the standard parallelization scheme DDI and on 128 nodes GDDI is 93 times faster than DDI (on a multihub Fast Ethernet network). FMO delivered scalability of 80-90% on 128 nodes, depending on the molecular system (water clusters and a protein). A numerical gradient calculation for a water cluster achieved a scalability of 70% on 128 nodes. It is expected that GDDI will become a preferred tool on massively parallel computers for appropriate computational tasks.

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PubMed2004

A study of the reactions of molecular hydrogen with small gold clusters.

This work presents a study of reactions between neutral and negatively charged Au(n) clusters (n=2,3) and molecular hydrogen. The binding energies of the first and second hydrogen molecule to the gold clusters were determined using density functional theory (DFT), second order perturbation theory (MP2) and coupled cluster (CCSD(T)) methods. It is found that molecular hydrogen easily binds to neutral Au(2) and Au(3) clusters with binding energies of 0.55 eV and 0.71 eV, respectively. The barriers to H(2) dissociation on these clusters with respect to Au(n)H(2) complexes are 1.10 eV and 0.59 eV for n=2 and 3. Although negatively charged Au(n) (-) clusters do not bind molecular hydrogen, H(2) dissociation can occur with energy barriers of 0.93 eV for Au(2) (-) and 1.39 eV for Au(3) (-). The energies of the Au(2)H(2) (-) and Au(3)H(2) (-) complexes with dissociated hydrogen molecules are lower than the energies of Au(2) (-)+H(2) and Au(3) (-)+H(2) by 0.49 eV and 0.96 eV, respectively. There is satisfactory agreement between the DFT and CCSD(T) results for binding energies, but the agreement is not as good for barrier heights.

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PubMed2004

Enthalpies of formation of gas-phase N3, N3-, N5+, and N5- from Ab initio molecular orbital theory, stability predictions for N5(+)N3(-) and N5(+)N5(-), and experimental evidence for the instability of N5(+)N3(-).

Ab initio molecular orbital theory has been used to calculate accurate enthalpies of formation and adiabatic electron affinities or ionization potentials for N3, N3-, N5+, and N5- from total atomization energies. The calculated heats of formation of the gas-phase molecules/ions at 0 K are DeltaHf(N3(2Pi)) = 109.2, DeltaHf(N3-(1sigma+)) = 47.4, DeltaHf(N5-(1A1')) = 62.3, and DeltaHf(N5+(1A1)) = 353.3 kcal/mol with an estimated error bar of +/-1 kcal/mol. For comparison purposes, the error in the calculated bond energy for N2 is 0.72 kcal/mol. Born-Haber cycle calculations, using estimated lattice energies and the adiabatic ionization potentials of the anions and electron affinities of the cations, enable reliable stability predictions for the hypothetical N5(+)N3(-) and N5(+)N5(-) salts. The calculations show that neither salt can be stabilized and that both should decompose spontaneously into N3 radicals and N2. This conclusion was experimentally confirmed for the N5(+)N3(-) salt by low-temperature metathetical reactions between N5SbF6 and alkali metal azides in different solvents, resulting in violent reactions with spontaneous nitrogen evolution. It is emphasized that one needs to use adiabatic ionization potentials and electron affinities instead of vertical potentials and affinities for salt stability predictions when the formed radicals are not vibrationally stable. This is the case for the N5 radicals where the energy difference between vertical and adiabatic potentials amounts to about 100 kcal/mol per N5.

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