Biomedical subjects

Mark S Gordon

Publications and source records attributed to Mark S Gordon.

At least 37 records · Page 2Linked to original sources

PubMed2005

Triazolium-based energetic ionic liquids.

The energetic ionic liquids formed by the 1,2,4-triazolium cation family and dinitramide anion are investigated by ab initio quantum chemistry calculations, to address the following questions: How does substitution at the triazolium ring's nitrogen atoms affect its heat of formation, and its charge delocalization? What kind of ion dimer structures might exist? And, do deprotonation reactions occur, as a possible first step in the decomposition of these materials?

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PubMed2005

Potential energy surfaces of SimOn cluster formation and isomerization.

The reaction paths for formation and isomerization of a set of silica SimOn (m = 2,3, n = 1-5) nanoclusters have been investigated using second-order perturbation theory (MP2) with the 6-31G(d) basis set. The MP2/6-31G(d) calculations have predicted singlet ground states for all clusters excluding Si3O2. The total energies of the most important points on the potential energy surfaces (PES) have been determined using the completely renormalized (CR) singles and doubles coupled cluster method including perturbative triples, CR-CCSD(T) with the cc-pVTZ basis set. Although transition states have been located for many isomerization reactions, only for Si3O3 and Si3O4 have some transition states been found for the formation of a cluster from the separated reactants. In all other cases, the process of formation of SimOn clusters appears to proceed without potential energy barriers.

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PubMed2005

Time-resolved gas-phase kinetic and quantum chemical studies of the reaction of silylene with oxygen.

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reaction with O(2). The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF(6) bath gas, at five temperatures in the range 297-600 K. The second order rate constants at 10 Torr were fitted to the Arrhenius equation: [see text] The decrease in rate constant values with increasing temperature, although systematic is very small. The rate constants showed slight increases in value with pressure at each temperature, but this was scarcely beyond experimental uncertainty. From estimates of Lennard-Jones collision rates, this reaction is occurring at ca. 1 in 20 collisions, almost independent of pressure and temperature. Ab initio calculations at the G3 level backed further by multi-configurational (MC) SCF calculations, augmented by second order perturbation theory (MRMP2), support a mechanism in which the initial adduct, H(2)SiOO, formed in the triplet state (T), undergoes intersystem crossing to the more stable singlet state (S) prior to further low energy isomerisation processes leading, via a sequence of steps, ultimately to dissociation products of which the lowest energy pair are H2O+SiO. The decomposition of the intermediate cyclo-siladioxirane, via O-O bond fission, plays an important role in the overall process. The bottleneck for the overall process appears to be the T-->S process in H2SiOO. This process has a small spin-orbit coupling matrix element, consistent with an estimate of its rate constant of 1x10(9) s-1 obtained with the aid of RRKM theory. This interpretation preserves the idea that, as in its reactions in general, SiH2 initially reacts at the encounter rate with O2. The low values for the secondary reaction barriers on the potential energy surface account for the lack of an observed pressure dependence. Some comparisons are drawn with the reactions of CH2+O2 and SiCl2+O2.

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PubMed2005

Exploring the mechanism for the synthesis of silsesquioxanes. 4. The synthesis of T8.

In an attempt to explore the mechanism for the synthesis of silsesquioxanes (POSS), the entire reaction processes from HSi(OH)3 to T8, one of the most common and stable POSS was investigated with electronic structure theory calculations, including electron correlation effects. In addition, the effect of some controlling factors, which play important roles in the reaction mechanism, is discussed.

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PubMed2005

Cycloaddition isomerizations of adsorbed 1,3-cyclohexadiene on Si(100)-2x1 surface: first neighbor interactions.

The initial and subsequent surface reaction mechanisms of 1,3-cyclohexadiene on the Si(100)-2x1 surface were theoretically explored, focusing on the possible first-neighbor interactions. Five different initial reaction channels leading to nine different surface products were identified, confirming previous experimental reports of inter-dimer structures. Among the nine identified products, five of these surface products are new species that have not previously been reported. Potential energy surface studies reveal that the net reaction barriers within a given channel are very small, indicating that the final product distributions within that channel are determined by thermodynamics. On the other hand, thermal isomerizations between different channels are not expected to occur easily. Therefore, the surface product distributions among the five different channels are more likely to be determined by kinetics. As a result, understanding the relationships among the available reaction channels both kinetically and thermodynamically is essential for properly interpreting the experimental results. The current study shows that the subsequent surface chemical reactions of unsaturated initial surface products are strongly coupled with the first-neighbor interactions.

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PubMed2005

Comparative study of surface cycloadditions of ethylene and 2-butene on the Si(100)-2 x 1 surface.

Multireference wave functions were used to study the ethylene and 2-butene surface reactions on Si(100) in their lowest energy singlet states. In addition to the diradical pathway, a pi-complex pathway on the ethylene surface was found. The net barrier for the latter process is 4.5 kcal/mol higher than that for the former, making the pi-complex pathway kinetically less accessible. Therefore, although there is a competition between the two initial channels, the diradical path is slightly favored, and rotational isomerization is possible. However, since the initial potential energy surfaces of the two channels are different, depending on experimental conditions, the branching ratio between the two channels may change. Consequently, the combined effects that would favor one channel over the other may not derive directly from the initial reaction barrier. This provides an explanation of the experimental controversy. As a result, the final distributions of surface products may depend on the experimental kinetic environment, especially when the population change due to the rotational isomerization is expected to be very small. A significantly different reaction channel is found in the 2-butene surface reaction on Si(100), in which a methyl hydrogen easily transfers to the surface yielding a new type of surface product other than the expected [2 + 2] cycloaddition product, with a comparatively small activation barrier. Consequently, the overall surface reactions of ethylene and 2-butene may be quite different. Therefore, direct comparisons between ethylene and 2-butene experimental results would be very useful.

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PubMed2005

Cycloaddition of benzene on Si(100) and its surface conversions.

A comprehensive ab initio study of the adsorption of benzene on the silicon(100) surface is presented. Five potential candidates ([2+2] adduct, [4+2] adduct, two tetra-sigma-bonded structures, and one radical-like structure) for the reaction product are examined to determine the lowest energy adsorption configuration. A [4+2] butterfly structure is determined to be the global minimum (-29.0 kcal/mol), although one of the two tetra-sigma-bonded structures (-26.7 kcal/mol) is similar in energy to it. Multireference perturbation theory suggests that the [4+2] addition mechanism of benzene on Si(100) is very similar to the usual Diels-Alder reaction (i.e., small or zero activation barrier), even though benzene adsorption entails the loss of benzene aromaticity during the reaction. On the other hand, the [2+2] cycloaddition mechanism is shown to require a relatively high activation barrier (17.8 kcal/mol), in which the initial step is to form a (relatively strongly bound) van der Waals complex (-8.9 kcal/mol). However, the net activation barrier relative to reactants is only 8.9 kcal/mol. Careful examination of the interconversion reactions among the reaction products indicates that the two tetra-sigma-bonded structures (that are energetically comparable to the [4+2] product) can be derived from the [2+2] adduct with activation barriers of 15.5 and 21.4 kcal/mol. However, unlike the previous theoretical predictions, it is found that the conversion of the [4+2] product to the tetra-sigma-bonded structures entails huge barriers (>37.0 kcal/mol) and is unlikely to occur. This suggests that the [4+2] product is not only thermodynamically the most stable configuration (lowest energy product) but also kinetically very stable (large barriers with respect to the isomerization to other products).

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PubMed2005

Solvent effects on the S(N)2 reaction: Application of the density functional theory-based effective fragment potential method.

The performance of the density functional theory (DFT)-based effective fragment potential (EFP) method is assessed using the S(N)2 reaction: Cl- + nH2O + CH3Br = CH3Cl + Br- + nH2O. The effect of the systematic addition of water molecules on the structures and relative energies of all species involved in the reaction has been studied. The EFP1 method is compared with second-order perturbation theory (MP2) and DFT results for n = 1, 2, and 3, and EFP1 results are also presented for four water molecules. The incremental hydration effects on the barrier height are the same for all methods. However, only full MP2 or MP2 with EFP1 solvent molecules are able to provide an accurate treatment of the transition state (TS) and hence the central barriers. Full DFT and DFT with EFP1 solvent molecules both predict central barriers that are too small. The results illustrate that the EFP1-based DFT method gives reliable results when combined with an accurate quantum mechanical (QM) method, so it may be used as an efficient alternative to fully QM methods in the treatment of larger microsolvated systems.

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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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PubMed2005

Multireference second-order perturbation theory: how size consistent is "almost size consistent".

A systematic study of the deviation from size consistency of the multireference second-order Moller-Plesset perturbation theory (MRMP2) method is presented. The size-consistency error is shown to depend on the number of monomers in a supermolecule calculation, size of basis set, number of correlated valence electrons, and size of active space. HF, F(2), and N(2) are used as test cases, with stretched bonds, to include simple, well-defined multireference character. This is essential in ensuring that MRMP2 is being tested as a multireference method. It is concluded that the MRMP2 and other multireference perturbation theory methods can exhibit significant size-consistency errors, and that the size of the error depends on the manner in which the perturbation theory is implemented.

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PubMed2004

Fast fragments: the development of a parallel effective fragment potential method.

The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute plus some number of solvent molecules, if desired, and an "effective fragment" region that contains the remaining solvent molecules. Interactions introduced with this fragment region (for example, Coulomb and polarization interactions) are added as one-electron terms to the total system Hamiltonian. As larger systems and dynamics are just starting to be studied with the EFP method, more needs to be done to decrease the calculation time of the method. This article considers parallelization of both the EFP fragment-fragment and mixed quantum mechanics (QM)-EFP interaction energy and gradient computation within the GAMESS suite of programs. The iteratively self-consistent polarization term is treated with a new algorithm that makes use of nonblocking communication to obtain better scalability. Results show that reasonable speedup is achieved with a variety of sizes of water clusters and number of processors.

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PubMed2004

Binding of propene on small gold clusters and on Au(111): simple rules for binding sites and relative binding energies.

We use density functional theory (DFT) to investigate the bonding of propene to small gas-phase gold clusters and to a Au(111) surface. The desorption energy trends and the geometry of the binding sites are consistent with the following set of rules. (1) The bond of propene to gold is formed by donation of electron density from the highest occupied molecular orbital (HOMO) of propene to one of the low-lying empty orbitals [denoted by LUMO1, LUMO2, em leader (LUMO-lowest unoccupied molecular orbital)] of the gold cluster. (2) Propene binds to a site on the Au cluster where one of the low-lying LUMOs protrudes in the vacuum. Different isomers (same cluster, but different binding sites for propene) correspond to sites where different low-lying LUMOs protrude in space. (3) The desorption energy of the lowest energy isomer correlates with the energy of the lowest empty orbital of the cluster; the lower the energy of that LUMO, the higher the desorption energy. (4) If the lowest-lying LUMO protrudes into space at two nonequivalent sites at the edge of a cluster, propene binds more strongly to the site with the lowest coordination. These rules are consistent with the calculated bond energies and geometries for [Au(n)(C(3)H(6))](q), for n=1-5 and n=8 and q=-1, 0, +1. Based on them we have made a number of predictions that have been confirmed by DFT calculations. The bond of propene to gold is strengthened as the net charge of the cluster varies from -1, to zero, to +1. Compared to a gas-phase cluster, a cluster on a support binds propene more strongly if the support takes electron density from the cluster (e.g., a Au cluster on a gold surface) and more weakly if the support donates electron density to the cluster (e.g., a Au cluster on an oxygen vacancy on an oxide surface).

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PubMed2004

The effective fragment potential: small clusters and radial distribution functions.

The effective fragment potential (EFP) method for treating solvent effects provides relative energies and structures that are in excellent agreement with the analogous fully quantum [i.e., Hartree-Fock (HF), density functional theory (DFT), and second order perturbation theory (MP2)] results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. The resulting radial distribution functions (RDF) suggest that as the underlying quantum method is improved from HF to DFT to MP2, the agreement with the experimental RDF also improves. The MP2-based EFP method yields a RDF that is in excellent agreement with experiment.

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PubMed2004

Ab initio vibrational state calculations with a quartic force field: applications to H2CO, C2H4, CH3OH, CH3CCH, and C6H6.

For polyatomic molecules, n-mode coupling representations of the quartic force field (nMR-QFF) are presented, which include terms up to n normal coordinate couplings in a fourth-order polynomial potential energy function. The computational scheme to evaluate third-and fourth-order derivatives by finite differentiations of the energy is fully described. The code to generate the nMR-QFF has been implemented into GAMESS program package and interfaced with the vibrational self-consistent field (VSCF) and correlation corrected VSCF (cc-VSCF) methods. As a demonstration, fundamental frequencies have been calculated by the cc-VSCF method based on 2MR-QFF for formaldehyde, ethylene, methanol, propyne, and benzene. The applications show that 2MR-QFF is a highly accurate potential energy function, with errors of 1.0-1.9% relative to the experimental value in fundamental frequencies. This approach will help quantitative evaluations of vibrational energies of a general molecule with a reasonable computational cost.

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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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PubMed2004

Predicting shielding constants in solution using gauge invariant atomic orbital theory and the effective fragment potential method.

A method to approximate ab initio shielding constants is presented, in which the ab initio density matrix is replaced in the gauge invariant atomic orbital formalism with the density matrix resulting from an effective fragment potential calculation. The resulting first-order density matrix is then iterated to self-consistency. The method is compared with fully ab initio gauge invariant atomic orbital restricted Hartree-Fock calculations on hydrogen chloride, water, and ammonia solutes with up to nine solvent water molecules using the 6-31G, 6-31G(d,p), and 6-31+G(d,p) basis sets. Using the 6-31G(d,p) basis sets, the average of the average absolute deviations for the three environments tested is 0.34 ppm. This is sufficiently accurate to allow for the identification of specific (1)H nuclei in a solvated molecule when the chemical shift between nuclei is not less than 1 ppm. The success of the method at this level of approximation is due to a cancellation of errors between the paramagnetic and diamagnetic terms of the shielding constant: the diamagnetic term is underestimated by roughly the same amount that the paramagnetic term is overestimated.

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