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Potential Energy Function (potential + energy_function)
Selected AbstractsTheoretical investigations on analytical potential energy function and spectroscopic parameters for the state b3,u of dimer 7Li2INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2007De-Heng Shi Abstract The SAC-CI (symmetry-adapted-cluster configuration-interaction) method presented in Gaussian 03 program package is applied to investigate the adiabatic potential energy curves (PECs) of 7Li2(b3,u). These calculations are performed at numbers of basis sets, such as 6-311++G(3df,3pd), 6-311++G(2df,2pd), 6-311++G(df,pd), D95V++, D95(3df,3pd), D95(d,p), cc-PVTZ, 6-311++G and 6-311++G(d,p). All the ab initio calculated points are fitted to the analytic Murrell-Sorbie functions and then used to compute the spectroscopic parameters. The analytic potential energy function (APEF) for this b3,u state is reported. By comparison, the spectroscopic parameters reproduced by the APEF attained at 6-311++G(2df,2pd) are found to be very close to the latest experimental findings. With the APEF obtained at the SAC-CI/6-311++G(2df,2pd) level of theory, a total of 62 vibrational states is found when J = 0. The complete vibrational levels, classical turning points, inertial rotation and centrifugal distortion constants for these vibrational states are also reported. The reasonable dissociation limit for this state is deduced using the calculated results at present. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Coarse-grained model of nucleic acid basesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Maciej Maciejczyk Abstract Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3,5) interaction centers. van der Waals interactions are modeled by Lennard-Jones spheres with a 12,6 potential energy function. The charge distribution is modeled by a set of electric dipole moments located at the centers of the Lennard-Jones spheres. The method for computing the Lennard-Jones parameters, electric dipole moments (their magnitude and orientation) and positions of the interaction centers is described. Several models with different numbers of interaction centers were tested. The model with three-center cytosine, four-center guanine, four-center thymine, and five-center adenine satisfactorily reproduces the canonical Watson,Crick hydrogen bonding and stacking interaction energies of the all-atom AMBER model. The computation time with the coarse-grained model is reduced seven times compared with that of the all-atom model. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] New angle-dependent potential energy function for backbone,backbone hydrogen bond in protein,protein interactionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2010Hwanho Choi Abstract Backbone,backbone hydrogen bonds (BBHBs) are one of the most abundant interactions at the interface of protein,protein complex. Here, we propose an angle-dependent potential energy function for BBHB based on density functional theory (DFT) calculations and the operation of a genetic algorithm to find the optimal parameters in the potential energy function. The angular part of the energy funtion is assumed to be the product of the power series of sine and cosine functions with respect to the two angles associated with BBHB. Two radial functions are taken into account in this study: Morse and Leonard-Jones 12-10 potential functions. Of these two functions under consideration, the former is found to be more accurate than the latter in terms of predicting the binding energies obtained from DFT calculations. The new HB potential function also compares well with the knowledge-based potential derived by applying Boltzmann statistics for a variety of protein,protein complexes in protein data bank. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] High-level ab initio calculations on HGeCl and the equilibrium geometry of the Ã1A, state derived from Franck-Condon analysis of the single-vibronic-level emission spectra of HGeCl and DGeClJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2010Daniel K. W. Mok Abstract CCSD(T) and/or CASSCF/MRCI calculations have been carried out on the X,1A, and Ã1A, states of HGeCl. The fully relativistic effective core potential, ECP10MDF, and associated standard valence basis sets of up to the aug-cc-pV5Z quality were employed for Ge. Contributions from core correlation and extrapolation to the complete basis set limit were included in determining the computed equilibrium geometrical parameters and relative electronic energy of these two states of HGeCl. Based on the currently, most systematic CCSD(T) calculations performed in this study, the best theoretical geometrical parameters of the X,1A, state are re(HGe) = 1.580 ± 0.001 Å, ,e = 93.88 ± 0.01° and re(GeCl) = 2.170 ± 0.001 Å. In addition, Franck-Condon factors including allowance for anharmonicity and Duschinsky rotation between these two states of HGeCl and DGeCl were calculated employing CCSD(T) and CASSCF/MRCI potential energy functions, and were used to simulate Ã1A, , X,1A, SVL emission spectra of HGeCl and DGeCl. The iterative Franck-Condon analysis (IFCA) procedure was carried out to determine the equilibrium geometrical parameters of the Ã1A, state of HGeCl by matching the simulated, and available experimental SVL emission spectra of HGeCl and DGeCl of Tackett et al., J Chem Phys 2006, 124, 124320, using the available, estimated experimental equilibrium (r) structure for the X,1A, state, while varying the equilibrium geometrical parameters of the Ã1A, state systematically. Employing the derived IFCA geometry of re(HGe) = 1.590 Å, re(GeCl) = 2.155 Å and ,e(HGeCl) = 112.7° for the Ã1A, state of HGeCl in the spectral simulation, the simulated absorption and SVL emission spectra of HGeCl and DGeCl agree very well with the available experimental LIF and SVL emission spectra, respectively. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] CHARMM: The biomolecular simulation programJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2009B. R. Brooks Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2009. [source] A combined ab initio and Franck-Condon factor simulation study on the photodetachment spectrum of ScO2,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2009Edmond P. F. Lee Abstract Restricted-spin coupled-cluster single-double plus perturbative triple excitation {RCCSD(T)} potential energy functions (PEFs) of the 2B2 state of ScO2 and the 1A1 state of ScO2, were computed, employing the augmented correlation-consistent polarized-weighted core-valence quadruple-zeta (aug-cc-pwCVQZ) basis set for Sc and augmented correlation-consistent polarized valence quadruple-zeta (aug-cc-pVQZ) basis set for O, and with the outer core Sc 3s23p6 electrons being explicitly correlated. Franck-Condon factors, which include allowance for Duschinsky rotation and anharmonicity, were calculated using the computed RCCSD(T) PEFs, and were used to simulate the first photodetachment band of ScO2,. The simulated spectrum matches well with the corresponding experimental 355 nm photodetachment spectrum of Wu and Wang, J Phys Chem A 1998, 102, 9129, confirming the assignment of the photodetachment spectrum and the reliability of the RCCSD(T) PEFs used. Further calculations on low-lying electronic states of ScO2 gave adiabatic relative electronic energies (Te's) of, and vertical excitation energies (Tv's) to, the 2A1, 2B1, and 2A2 states of ScO2 (from the 2B2 state of ScO2), as well as electron affinities (EAs) and vertical detachment energies (VDEs) to these neutral states from the 1A1 state of ScO2,. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] | ||||||||||