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Molecular Energy (molecular + energy)
Selected AbstractsComparison of the numerical stability of methods for anharmonic calculations of vibrational molecular energiesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2007Petr Dan Abstract On model examples, we compare the performance of the vibrational self-consistent field, variational, and four perturbational schemes used for computations of vibrational energies of semi-rigid molecules, with emphasis on the numerical stability. Although the accuracy of the energies is primarily dependent on the quality of the potential energy surface, approximate approaches to the anharmonic vibrational problem often do not converge to the same results due to the approximations involved. For furan, the sensitivity to variations of the anharmonic potential was systematically investigated by adding random noise to the cubic and quartic constants. The self-consistent field methods proved to be the most resistant to the potential variations. The second order perturbational techniques are sensitive to random degeneracies and provided the least stable results. However, their stability could be significantly improved by a simple generalization of the perturbational formula. The variational configuration interaction is practically limited by the size of the matrix that can be diagonalized for larger molecules; however, relatively fewer states need to be involved than for smaller ones, in favor of the computing. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Topochemically controlled solid-state methyl rearrangement in thiocyanuratesACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001Mark Greenberg 4,6-Dimethoxy-3-methyl-1,3,5-triazine-2(3H)-thione crystallizes in two polymorphic forms, needles and plates. In the needle-shaped crystals (9a) the molecules occupy the crystallographic mirror plane, thus the layers are stacked along the b axis. The molecules of the other polymorph [plate-shape crystals, (9b)] are packed in a herringbone packing mode. Upon heating, (9b) undergoes a phase transition to form (9a). At 378,K the needles undergo O , S topochemically controlled methyl transfer in the solid state to produce 1-methyl-4-methoxy-6-methylthio-1,3,5-triazine-2(1H)-one in 75% yield. The enthalpy of the rearrangement is estimated to be ,39.1,kJ,mol,1. 1-Methyl-6-methoxy-4-methylthio-1,3,5-triazine-2(1H)-thione crystallizes in space group P21 with two crystallographically independent molecules in the asymmetric unit. Compound (9b) undergoes O , S methyl transfer in the solid state at 373,K. The rearrangement is topochemically assisted and the product, 1-methyl-2,4-bismethylthio-1,3,5-triazine-6(1H)-one, is obtained in quantitative yield. The enthalpy of the rearrangement is estimated to be ,58.8,kJ,mol,1. The crystal structures of the compounds as well as their DSC thermographs are described and discussed. Energy calculation by ab initio methods shows that the driving force for the reactions is the difference between the molecular energies of the pre-rearranged compounds and their products, 54.2 and 59.3,kJ,mol,1 in the two cases, respectively. [source] A generalized higher order kernel energy approximation methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Stewart N. Weiss Abstract We present a general mathematical model that can be used to improve almost all fragment-based methods for ab initio calculation of total molecular energy. Fragment-based methods of computing total molecular energy mathematically decompose a molecule into smaller fragments, quantum-mechanically compute the energies of single and multiple fragments, and then combine the computed fragment energies in some particular way to compute the total molecular energy. Because the kernel energy method (KEM) is a fragment-based method that has been used with much success on many biological molecules, our model is presented in the context of the KEM in particular. In this generalized model, the total energy is not based on sums of all possible double-, triple-, and quadruple-kernel interactions, but on the interactions of precisely those combinations of kernels that are connected in the mathematical graph that represents the fragmented molecule. This makes it possible to estimate total molecular energy with high accuracy and no superfluous computation and greatly extends the utility of the KEM and other fragment-based methods. We demonstrate the practicality and effectiveness of our model by presenting how it has been used on the yeast initiator tRNA molecule, ytRN (1YFG in the Protein Data Bank), with kernel computations using the Hartree-Fock equations with a limited basis of Gaussian STO-3G type. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [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] Structure, magnetizability, and nuclear magnetic shielding tensors of bis-heteropentalenes.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2006Abstract The geometry of the heteropentalenes formed by two phosphole units has been determined at the DFT level. The magnetic susceptibility and the nuclear magnetic shielding at the nuclei of these systems have also been calculated using gauge-including atomic orbitals and a large Gaussian basis set to achieve near Hartree,Fock estimates. A comparative study of the various isomers, of their flattened analogs, and of the parent phosphole molecule, shows that the [3,4-c] isomer is the most aromatic system in the set considered, assuming diatropicity and degree of planarity as indicators, even if it is the less stable in terms of total molecular energy. Plots of magnetic field-induced current densities confirm diatropicity of P-containing bis-heteropentalenenes, showing, however, significant differences from the analogous systems with distinct heteroatoms. The maps give evidence of spiral flow nearby CC bonds, compatible with prevalent distortive behavior of , electrons exalted by pyramidalization at P, and competing against the , electron compression, which would favor planar structure. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 344,351, 2006 [source] A Novel Method for Fixed-node Quantum Monte CarloCHINESE JOURNAL OF CHEMISTRY, Issue 10 2001Hong-Xin Huang Abstract In this paper, a novel method for fixed-node quantum Monte Carlo is given. By comparing this method with the traditional fixed-node one, this novel method can be applied to calculate molecular energy more exactly. An expansion of the eigenvalue of the energy for a system has been derived. It is proved that the value of the energy calculated using the traditional fixed-node method is only the zeroth order approximation of the eigenvalue of the energy. But when using this novel method, in the case of only increasing less computing amounts ( < 1%), the first order approximation, the second order approximation, and so on can be obtained conveniently with the detailed equations and steps in the practical calculation to calculate the values of the zeroth, first and second approximation of the energies of 1 1A, state of CH2, 1A2(C4h, acet) state of C8 and the ground-states of H2, LiH, Li2, and H2O The results indicate that for these states it needs only the second order approximation to obtain over 97% of electronic correlation energy, which demonstrates that this novel method is very excellent in both the computing accuracy and the amount of calculation required. [source] | ||||||||||