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Energy Expression (energy + expression)
Selected AbstractsUsing an interval branch-and-bound algorithm in the Hartree,Fock methodINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Carlile C. Lavor Abstract The Hartree,Fock (HF) method is widely used to obtain atomic and molecular electronic wave functions, based on the minimization of a functional of the energy. We propose to use a deterministic global optimization algorithm, based on a branch-and-bound method, that applies techniques of interval arithmetic. This algorithm is applied directly to the minimization of the energy expression derived from the HF method. The proposed approach was successfully applied to the ground state of He and Be atoms. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environmentJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2005Robert J. Deeth The ligand field molecular mechanics (LFMM) model, which incorporates the ligand field stabilization energy (LFSE) directly into the potential energy expression of molecular mechanics (MM), has been implemented in the "chemically aware" molecular operating environment (MOE) software package. The new program, christened DommiMOE, is derived from our original in-house code that has been linked to MOE via its applications programming interface and a number of other routines written in MOE's native scientific vector language (SVL). DommiMOE automates the assignment of atom types and their associated parameters and popular force fields available in MOE such as MMFF94, AMBER, and CHARMM can be easily extended to provide a transition metal simulation capability. Some of the unique features of the LFMM are illustrated using MMFF94 and some simple [MCl4]2, and [Ni(NH3)n]2+ species. These studies also demonstrate how density functional theory calculations, especially on experimentally inaccessible systems, provide important data for designing improved LFMM parameters. DommiMOE treats Jahn,Teller distortions automatically, and can compute the relative energies of different spin states for Ni(II) complexes using a single set of LFMM parameters. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 123,130, 2005 [source] Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2004Bernd Kuhn Abstract The prediction of pKa shifts of ionizable groups in proteins is of great relevance for a number of important biological phenomena. We present an implementation of the MM-GBSA approach, which combines molecular mechanical (MM) and generalized Born (GB) continuum solvent energy terms, to the calculation of pKa values of a panel of nine proteins, including 69 individual comparisons with experiment. While applied so far mainly to the calculation of biomolecular binding free energies, we show that this method can also be used for the estimation of protein pKa shifts, with an accuracy around 1 pKa unit, even for strongly shifted residues. Our analysis reveals that the nonelectrostatic terms that are part of the MM-GBSA free energy expression are important contributors to improved prediction accuracy. This suggests that most of the previous approaches that focus only on electrostatic interactions could be improved by adding other nonpolar energy terms to their free energy expression. Interestingly, our method yields best accuracy at protein dielectric constants of ,int = 2,4, which is in contrast to previous approaches that peak at higher ,int , 8. An important component of our procedure is an intermediate minimization step of each protonation state involving different rotamers and tautomers as a way to explicitly model protein relaxation upon (de)protonation. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1865,1872, 2004 [source] Quasiparticle approximations and electron propagator theoryINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2003J. V. Ortiz Abstract A comparison of quasiparticle concepts arising from the Dyson equation of electron propagator theory and from orbital functional theory shows close relationships between self,energy expressions in the former to correlation potentials in the latter. Detailed formulae are presented for second-order theories with general occupation numbers. Limitations of the Dyson and Landau quasiparticle concepts in the context of perturbative correlation formulae are discussed. Numerical results on N2, H2O, and their valence ionization energies are presented. Comparisons are made between total energy differences, orbital energies, and transition operator results. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003 [source] Atom,atom partitioning of total (super)molecular energy: The hidden terms of classical force fieldsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2007M. Rafat Abstract Classical force fields describe the interaction between atoms that are bonded or nonbonded via simple potential energy expressions. Their parameters are often determined by fitting to ab initio energies and electrostatic potentials. A direct quantum chemical guide to constructing a force field would be the atom,atom partitioning of the energy of molecules and van der Waals complexes relevant to the force field. The authors used the theory of quantum chemical topology to partition the energy of five systems [H2, CO, H2O, (H2O)2, and (HF)2] in terms of kinetic, Coulomb, and exchange intra-atomic and interatomic contributions. The authors monitored the variation of these contributions with changing bond length or angle. Current force fields focus only on interatomic interaction energies and assume that these purely potential energy terms are the only ones that govern structure and dynamics in atomistic simulations. Here the authors highlight the importance of self-energy terms (kinetic and intra-atomic Coulomb and exchange). © 2006 Wiley Periodicals, Inc. J Comput Chem 2007 [source] Glass forming ability and nanocrystallization kinetics of Fe65Nb10B25 metallic glassesPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 5 2010J. Torrens-Serra Abstract In this work the mechanisms controlling the nanocrystallization kinetics of the Fe65Nb10B25 metallic glasses have been determined by the combination of the analysis microstructural data from XRD and TEM, and the kinetic analysis performed using the Master Curve method of the continuous heating and isothermal calorimetric curves. The results show that the transformation starts by the nucleation and interface controlled growth of the Fe23B6 -type phase that changes to diffusion controlled growth as the transformation advances until is stopped by the soft-impingement effect. The transformation is modeled in the framework of the Kolmogorov,Johnson,Mehl,Avrami (KJMA) theory using constant activation energy expressions for the nucleation frequency and interface-controlled growth and taking into account the reduction of those quantities with the transformed fraction due to the change in the matrix composition using a mean-field approximation. The parameters of the modeling are determined from the coupling between the isothermal and constant heating rate calorimetric analysis and from the quantitative analysis of microstructural data. This is the outset for the determination of the viscosity, driving force for crystallization, and interfacial energy when replacing the constant activation energy expressions by the classical nucleation and growth ones. Both the glass forming ability in Fe,Nb,B based bulk metallic glasses and the temperature dependence of the interfacial energy are discussed in terms of the influence of the minor alloying elements. [source] | ||||||||||