Biomedical subjects

Mark S Gordon

Publications and source records attributed to Mark S Gordon.

At least 19 recordsLinked to original sources

PubMed2007

Electrostatic energy in the effective fragment potential method: theory and application to benzene dimer.

Evaluation of the electrostatic energy within the effective fragment potential (EFP) method is presented. The performance of two variants of the distributed multipole analysis (DMA) together with two different models for estimating the charge penetration energies was studied using six homonuclear dimers. The importance of damping the higher order multipole terms, i.e. charge dipole, was also investigated. Damping corrections recover more than 70% of the charge penetration energy in all dimers, whereas higher order damping introduces only minor improvement. Electrostatic energies calculated by the numerical DMA are less accurate than those calculated by the analytic DMA. Analysis of bonding in the benzene dimer shows that EFP with inclusion of the electrostatic damping term performs very well compared to the high-level coupled cluster singles, doubles, and perturbative triples method. The largest error of 0.4 kcal/mol occurs for the sandwich dimer configuration. This error is about half the size of the corresponding error in second order perturbation theory. Thus, EFP in the current implementation is an accurate and computationally inexpensive method for calculating interaction energies in weakly bonded molecular complexes.

Algorithms↗

PubMed2006

Exploring the effect of anharmonicity of molecular vibrations on thermodynamic properties.

Thermodynamic properties of selected small and medium size molecules were calculated using harmonic and anharmonic vibrational frequencies. Harmonic vibrational frequencies were obtained by normal mode analysis, whereas anharmonic ones were calculated using the vibrational self-consistent field (VSCF) method. The calculated and available experimental thermodynamic data for zero point energy, enthalpy, entropy, and heat capacity are compared. It is found that the anharmonicity and coupling of molecular vibrations can play a significant role in predicting accurate thermodynamic quantities. Limitations of the current VSCF method for low frequency modes have been partially removed by following normal mode displacements in internal, rather than Cartesian, coordinates.

Journal Article↗

PubMed2006

Gradients of the polarization energy in the effective fragment potential method.

The effective fragment potential (EFP) method is an ab initio based polarizable classical method in which the intermolecular interaction parameters are obtained from preparative ab initio calculations on isolated molecules. The polarization energy in the EFP method is modeled with asymmetric anisotropic dipole polarizability tensors located at the centroids of localized bond and lone pair orbitals of the molecules. Analytic expressions for the translational and rotational gradients (forces and torques) of the EFP polarization energy have been derived and implemented. Periodic boundary conditions (the minimum image convention) and switching functions have also been implemented for the polarization energy, as well as for other EFP interaction terms. With these improvements, molecular dynamics simulations can be performed with the EFP method for various chemical systems.

Journal Article↗

PubMed2006

Incremental solvation of nonionized and zwitterionic glycine.

Microsolvation and combined microsolvation-continuum approaches are employed in order to examine the structures and relative energies of nonionized (N) and zwitterionic (Z) glycine clusters. Bridging structures are predicted to be the global minima after 3-5 discrete water molecules are included in the calculations. Calculations incorporating electron correlation stabilize the zwitterionic structures by about 7-9 kcal/mol relative to the N structures regardless of the number of discrete water molecules considered. Continuum calculations stabilize the Z structures relative to N structures; this effect decreases as the number of discrete water molecules is increased. Eight water molecules do not appear to fully solvate glycine.

Glycine↗

PubMed2006

Methanol-water mixtures: a microsolvation study using the effective fragment potential method.

The formation process of methanol-water mixtures, (MeOH/H2O)n, n = 2, 3,..., 8 is studied at the molecular level using the general effective fragment potential (EFP2) method and second-order perturbation theory (MP2). Extensive Monte Carlo/simulated annealing global optimizations were used to locate global minimum structures for each n, for both homo and hetero clusters. Mixing at the microscopic level was investigated, and some general conclusions about the microsolvation behavior of these mixtures are presented. For all of these clusters, incomplete mixing is observed at the molecular level. Low-energy (MeOH/H2O)n clusters retain much of their initial structure in the global minima of the mixed clusters.

Computer Simulation↗

PubMed2006

Electronic structure studies of tetrazolium-based ionic liquids.

New energetic ionic liquids are investigated as potential high energy density materials. Ionic liquids are composed of large, charge-diffuse cations, coupled with various (usually oxygen containing) anions. In this work, calculations have been performed on the tetrazolium cation with a variety of substituents. Density functional theory (DFT) with the B3LYP functional, using the 6-311G(d,p) basis set was used to optimize geometries. Improved treatment of dynamic electron correlation was obtained using second-order perturbation theory (MP2). Heats of formation of the cation with different substituent groups were calculated using isodesmic reactions and Gaussian-2 calculations on the reactants. The cation was paired with oxygen rich anions ClO4-, NO3-, or N(NO2)2- and those structures were optimized using both DFT and MP2. The reaction pathway for proton transfer from the cation to the anion was investigated.

Journal Article↗

PubMed2006

Charge transfer interaction in the effective fragment potential method.

An approximate formula is derived and implemented in the general effective fragment potential (EFP2) method to model the intermolecular charge transfer interaction. This formula is based on second order intermolecular perturbation theory and utilizes canonical molecular orbitals and Fock matrices obtained with preparative self-consistent field calculations. It predicts charge transfer energies that are in reasonable agreement with the reduced variational space energy decomposition analysis. The formulas for the charge transfer gradients with respect to EFP translational and rotational displacements are also derived and implemented.

Chemistry, Physical↗

PubMed2006

Growing multiconfigurational potential energy surfaces with applications to X + H2 (X = C,N,O) reactions.

A previously developed method, based on a Shepard interpolation procedure to automatically construct a quantum mechanical potential energy surface (PES), is extended to the construction of multiple potential energy surfaces using multiconfigurational wave functions. These calculations are accomplished with the interface of the PES-building program, GROW, and the GAMESS suite of electronic structure programs. The efficient computation of multiconfigurational self-consistent field surfaces is illustrated with the C + H2, N + H2, and O + H2 reactions.

Journal Article↗

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.

Journal Article↗

PubMed2006

Dissociation potential curves of low-lying states in transition metal hydrides. 3. Hydrides of groups 6 and 7.

The dissociation curves of low-lying spin-mixed states in monohydrides of groups 6 and 7 were calculated by using an effective core potential (ECP) approach. This approach is based on the multiconfiguration self-consistent field (MCSCF) method, followed by first-order configuration interaction (FOCI) calculations, in which the method employs an ECP basis set proposed by Stevens and co-workers (SBKJC) augmented by a set of polarization functions. Spin-orbit coupling (SOC) effects are estimated within the one-electron approximation by using effective nuclear charges, since SOC splittings obtained with the full Breit-Pauli Hamitonian are underestimated when ECP basis sets are used. The ground states of group 6 hydrides have Omega = (1)/(2)(X(6)Sigma(+)(1/2)), where Omega is the z component of the total angular momentum quantum number. Although the ground states of group 7 hydrides have Omega = 0(+), their main adiabatic components are different; the ground state in MnH originates from the lowest (7)Sigma(+), while in TcH and ReH the main component of the ground state is the lowest (5)Sigma(+). The present paper reports a comprehensive set of theoretical results including the dissociation energies, equilibrium distances, electronic transition energies, harmonic frequencies, anharmonicities, and rotational constants for several low-lying spin-mixed states in these hydrides. Transition dipole moments were also computed among the spin-mixed states and large peak positions of electronic transitions are suggested theoretically for these hydrides. The periodic trends of physical properties of metal hydrides are discussed, based on the results reported in this and other recent studies.

Journal Article↗

PubMed2006

A systematic multireference perturbation-theory study of the low-lying states of SiC3.

The three known lowest-energy isomers of SiC(3), two cyclic singlets (2s and 3s) and a linear triplet (1t), have been reinvestigated using multireference second-order perturbation theory (MRPT2). The dependence of the relative energies of the isomers upon the quality of the basis sets and the sizes of the reference active spaces is explored. When using a complete-active-space self-consistent-field reference wave function with 12 electrons in 11 orbitals [CASSCF (12, 11)] together with basis sets that increase in size up to the correlation-consistent polarized core-valence quadruple zeta basis set (cc-pCVQZ), the MRPT2 method consistently predicts the linear triplet to be the most stable isomer. A new parallel direct determinant MRPT2 code has been used to systematically explore reference spaces that vary in size from CASSCF (8,8) to full optimized reaction space [FORS or CASSCF (16,16)] with the cc-pCVQZ basis. It is found that the relative energies of the isomers change substantially as the active space is increased. At the best level of theory, MRPT2 with a full valence FORS reference, the 2s isomer is predicted to be more stable than 3s and 1t by 4.7 and 2.2 kcal/mol, respectively.

Carbon Compounds, Inorganic↗

PubMed2006

Modeling styrene-styrene interactions.

This study is the first step in the systematic investigation of substituted (carboxyl) polystyrene nanoparticles. Understanding the fundamental interactions between the p-carboxyl styrene monomers, where an ethyl group is used instead of a vinyl group (referenced, for convenience, as "p-carboxyl styrene"), provides the basic information needed to construct potentials for nanoparticles composed of these monomers. In this work, low-energy isomers of p-carboxyl styrene dimer were studied. The dimer structures and their relative and binding energies were determined using both Møller-Plesset second-order perturbation theory (MP2) and the general effective fragment potential (EFP2) method. Sections of the intermolecular potential energy surface (PES) of the p-carboxylated styrene dimer in its global minimum orientation were also determined. As expected, double hydrogen bonding between the two carboxylic groups provides the strongest interaction in this system, followed by isomers with a single H-bond and strong benzene ring-benzene ring (pi-pi) type interactions. Generally, the EFP2 method reproduces the MP2 geometries and relative energies with good accuracy, so it appears to be an efficient alternative to the correlated ab initio methods, which are too computationally demanding to be routinely used in the study of the more-complex polymeric systems of interest.

Journal Article↗

PubMed2006

Scalable implementation of analytic gradients for second-order Z-averaged perturbation theory using the distributed data interface.

The analytic gradient expression for second-order Z-averaged perturbation theory is revised and its parallel implementation is described in detail. The distributed data interface is used to access molecular-orbital integral arrays stored in distributed memory. The algorithm is designed to maximize the use of local data and reduce communication costs. The iterative solution and the preconditioner used to induce the convergence of the coupled-perturbed Hartree-Fock equations are presented. Several illustrative timing examples are discussed.

Journal Article↗

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.

Journal Article↗

PubMed2006

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO).

The polarizable continuum model (PCM) for the description of solvent effects is combined with the fragment molecular orbital (FMO) method at several levels of theory, using a many-body expansion of the electron density and the corresponding electrostatic potential, thereby determining solute (FMO)-solvent (PCM) interactions. The resulting method, denoted FMO/PCM, is applied to a set of model systems, including alpha-helices and beta-strands of alanine consisting of 10, 20, and 40 residues and their mutants to charged arginine and glutamate residues. The FMO/PCM error in reproducing the PCM solvation energy for a full system is found to be below 1 kcal/mol in all cases if a two-body expansion of the electron density is used in the PCM potential calculation and two residues are assigned to each fragment. The scaling of the FMO/PCM method is demonstrated to be nearly linear at all levels for polyalanine systems. A study of the relative stabilities of alpha-helices and beta-strands is performed, and the magnitude of the contributing factors is determined. The method is applied to three proteins consisting of 20, 129, and 245 residues, and the solvation energy and computational efficiency are discussed.

Journal Article↗

PubMed2005

Influence of multi-atom bridging ligands on the electronic structure and magnetic properties of homodinuclear titanium molecules.

The electronic structure and magnetic properties of homodinuclear titanium(III) molecules with bridging ligands from groups 14, 15, and 16 are examined. Single- and multireference methods with triple-zeta plus polarization basis sets are employed. Dynamic electron correlation effects are included via second-order multireference perturbation theory. Isotropic interaction parameters are calculated, and two of the complexes studied are predicted to be ferromagnetic based on multireference second-order perturbation (MRMP2) theory, using the TZVP(fg) basis set. Zero-field splitting parameters are determined using spin-orbit coupling obtained from complete active space (CAS) self-consistent field (SCF) and multiconfigurational quasi-degenerate perturbation theory (MCQDPT) wave functions. Three Breit-Pauli-based spin coupling methods were employed: full Breit-Pauli (HSO2), the partial two-electron method (P2E), and the semiempirical one-electron method (HSO1).

Computer Simulation↗

PubMed2005

Infrared spectra and ab initio calculations for the Cl--(CH4)n (n = 1-10) anion clusters.

In an effort to elucidate their structures, mass-selected Cl--(CH4)n (n = 1-10) clusters are probed using infrared spectroscopy in the CH stretch region (2800-3100 cm(-1)). Accompanying ab initio calculations at the MP2/6-311++G(2df,2p) level for the n = 1-3 clusters suggest that methane molecules prefer to attach to the chloride anion by single linear H-bonds and sit adjacent to one another. These conclusions are supported by the agreement between experimental and calculated vibrational band frequencies and intensities. Infrared spectra in the CH stretch region for Cl--(CH4)n clusters containing up to ten CH4 ligands are remarkably simple, each being dominated by a single narrow peak associated with stretching motion of hydrogen-bonded CH groups. The observations are consistent with cluster structures in which at least ten equivalent methane molecules can be accommodated in the first solvation shell about a chloride anion.

Journal Article↗

PubMed2005

Theoretical study of the solvation of fluorine and chlorine anions by water.

The solvation of fluoride and chloride anions (F(-) and Cl(-), respectively) by water has been studied using effective fragment potentials (EFPs) for the water molecules and ab initio quantum mechanics for the anions. In particular, the number of water molecules required to fully surround each anion has been investigated. Monte Carlo calculations have been used in an attempt to find the solvated system X(-)(H(2)O)(n) (X = F, Cl) with the lowest energy for each value of n. It is predicted that 18 water molecules are required to form a complete solvation shell around a Cl(-) anion, where "complete solvation" is interpreted as an ion that is completely surrounded by solvent molecules. Although fewer water molecules may fully solvate the Cl(-) anion, such structures are higher in energy than partially solvated molecules, up to n > or = 18. Calculations on the F(-) anion suggest that 15 water molecules are required for a complete solvation shell. The EFP predictions are in good agreement with the relative energies predicted by ab initio energy calculations at the EFP geometries.

Journal Article↗