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Selected AbstractsAn analysis of the dynamic , polarization in the V state of etheneINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Celestino Angeli Abstract The importance of the dynamic , polarization (absent in methods where the , skeleton is treated at a mean-field level) for the correct description of the V state of the ethene molecule has been recognized by many authors in the past. In this article, this physical effect is analyzed and it is seen as arising from the sum of two contributions: the polarization of the , CC bond and of the , CH bonds. In both cases it is described in a valence bond scheme and the types of excitations needed in a molecular orbital frame to introduce such effects are identified. The effect of the dynamic , polarization on the spatial extent of the V state (,x2,) is described. The analysis here reported has been used in a recent article (Angeli, J Comp Chem 2009, 30, 1319) for the accurate calculation of the V state and of its vertical excitation energy. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2436,2447, 2010 [source] Charge parameterization of the metal centers in cytochrome c oxidaseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2008Mikael P. Johansson Abstract Reliable atomic point charges are of key importance for a correct description of the electrostatic interactions when performing classical, force field based simulations. Here, we present a systematic procedure for point charge derivation, based on quantum mechanical methodology suited for the systems at hand. A notable difference to previous procedures is to include an outer region around the actual system of interest. At the cost of increasing the system sizes, here up to 265 atoms, including the surroundings achieves near-neutrality for the systems as well as structural stability, important factors for reliable charge distributions. In addition, the common problem of converting between CH bonds and CC bonds at the border vanishes. We apply the procedure to the four redox-active metal centers of cytochrome c oxidase: CuA, haem a, haem a3, and CuB. Several relevant charge and ligand states are considered. Charges for two different force fields, CHARMM and AMBER, are presented. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Spin states in polynuclear clusters: The [Fe2O2] core of the methane monooxygenase active siteJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2006Carmen Herrmann Abstract The ability to provide a correct description of different spin states of mono- and polynuclear transition metal complexes is essential for a detailed investigation of reactions that are catalyzed by such complexes. We study the energetics of different total and local spin states of a dinuclear oxygen-bridged iron(IV) model for the intermediate Q of the hydroxylase component of methane monooxygenase by means of spin-unrestricted Kohn,Sham density functional theory. Because it is known that the spin state total energies depend systematically on the density functional, and that this dependence is intimately connected to the exact exchange admixture of present-day hybdrid functionals, we compare total energies, local and total spin values, and Heisenberg coupling constants calculated with the established functionals BP86 and B3LYP as well as with a modified B3LYP version with an exact exchange admixture ranging from 0 to 24%. It is found that exact exchange enhances local spin polarization. As the exact exchange admixture increases, the high-spin state is energetically favored, although the Broken-Symmetry state always is the ground state. Instead of the strict linear variation of the energy splittings observed for mononuclear complexes, a slightly nonlinear dependence is found. The Heisenberg coupling constants JFe1Fe2,evaluated according to three different proposals from the literature,are found to vary from ,129 to ,494cm,1 accordingly. The experimental finding that intermediate Q has an antiferromagnetic ground state is thus confirmed. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1223,1239, 2006 [source] Study of electronic spectra of free-base porphin and Mg-porphin: Comprehensive comparison of variety of ab initio, DFT, and semiempirical methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2005Josef Abstract SAC (symmetry adapted cluster)/SAC-CI and CASPT2 (multiconfigurational second-order perturbation theory) electron excitation spectra of free-base porphin and magnesium-porphin were determined using basis set functions augmented by both the polarization and diffuse functions,6-31+G(d). Such basis is recommended for correct description of the spectra because diffuse functions play fundamental roles in the formation of Rydberg MOs. The obtained results indicated that already the lowest roots in Au, B1u, B2g, and B3g irreducible representations display Rydberg character. The calculated spectra are in a good agreement with both experimental and recently calculated electronic transitions. It is concluded that the SAC/SAC-CI level spectral lines are significantly affected by configuration selection when energy thresholds 5.0 × 10,6 and 5.0 × 10,7 a.u. are used for the determination of ground and excited state properties. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 294,303, 2005 [source] Specific force field parameters determination for the hybrid ab initio QM/MM LSCF methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2002Nicolas Ferré Abstract The pure quantum mechanics method, called Local Self-Consistent Field (LSCF), that allows to optimize a wave function within the constraint that some predefined spinorbitals are kept frozen, is discussed. These spinorbitals can be of any shape, and their occupation numbers can be 0 or 1. Any post-Hartree,Fock method, based on the restricted or unrestricted Hartree,Fock Slater determinant, and Kohn,Sham-based DFT method are available. The LSCF method is easily applied to hybrid quantum mechanics/molecular mechanics (QM/MM) procedure where the quantum and the classical parts are covalently bonded. The complete methodology of our hybrid QM/MM scheme is detailed for studies of macromolecular systems. Not only the energy but also the gradients are derived; thus, the full geometry optimization of the whole system is feasible. We show that only specific force field parameters are needed for a correct description of the molecule, they are given for some general chemical bonds. A careful analysis of the errors induced by the use of molecular mechanics in hybrid computation show that a general procedure can be derived to obtain accurate results at low computation effort. The methodology is applied to the structure determination of the crambin protein and to Menshutkin reactions between primary amines and chloromethane. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 610,624, 2002 [source] Grafted Polymer Chains Interacting with Substrates: Computer Simulations and ScalingMACROMOLECULAR THEORY AND SIMULATIONS, Issue 9 2008Radu Descas Abstract We review scaling methods and computer simulations used in the study of the static and dynamic properties of polymer chains tethered to adsorbing surfaces under good solvent conditions. By varying both the grafting density and the monomer/surface interactions a variety of phases can form. In particular, for attractive interactions between the chains and the surface the classical mushroom-brush transition known for repulsive substrates splits up into an overlap transition and a saturation transition which enclose a region of semidilute surface states. At high grafting densities oversaturation effects and a transition to a brush state can occur. We emphasize the role of the critical adsorption parameters for a correct description and understanding of such polymer adsorption phenomena. [source] Optical response in multi-quantum wells under Bragg conditionsPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 6 2004L. Pilozzi Abstract A microscopic description of matter polarization and electromagnetic field is used to study the linear optical response of N quantum wells under Bragg condition at the resonant wavelength. In this system the radiative interaction among induced polarizations plays an essential role and the inclusion of this effect leads to a correct description of the size and internal structure dependence of the optical response. The spectral evolution of reflectivity and absorbance with increasing N from the super,radiance regime to the 1D photonic crystal limit (N , ,) is shown. Polaritonic dispersion curves are calculated for the infinite system and compared with the photonic dispersion curves due to the background dielectric function modulation. A decomposition of the polaritonic matrix of interaction is proposed in order to separate different contributions in the optical response and to achieve a comparison with the response of a cluster of non-interacting units. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Analysis of the influence of coupled diffusion on transport in protein crystal growth for different gravity levelsACTA CRYSTALLOGRAPHICA SECTION D, Issue 10-1 2002D. Castagnolo Diffusion has a central role in protein crystal growth both in microgravity conditions and on ground. Recently several reports have been focused on the importance to use the generalized Fick's equations in n -component systems where crystals grow. In these equations the total flux of each component is produced by the own concentration gradient (main flow) and by the concentration gradient of the other components (cross-flow) present in the system. However in literature the latter effect is often neglected, and the so-called pseudo-binary approximation is used. Lin et al. (1995) proposed a mathematical model to evaluate the concentration profile of the species present around a growing protein crystal. Although the model is reliable, it suffers of the pseudo-binary approximation (neglecting cross term diffusion coefficients and using binary diffusion coefficients), probably because of the lack of multicomponent diffusion data. The present model is based on the experimental set-up proposed by Lin et al. (1995). Nevertheless we have included the coupled diffusion effects, according to the correct description of the matter transport through the generalized Fick's equations. The crystal growth rate is calculated for different gravity levels. The model has been applied to the ternary lysozyme-NaCl-water and quaternary lysozyme-poly(ethylene glycol) (PEG)-NaCl-water systems using recent diffusion data. [source] Interpreting Experimental Data by Using Molecular Simulation Instead of Model BuildingCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2009Zrinka Gattin Abstract A proper description of the conformational equilibrium of polypeptides or proteins is essential for a correct description of their function. The conformational ensembles from 16 molecular dynamic simulations of two ,- heptapeptides were used to interpret the primary NMR data, which were also compared to a set of NMR model structures (see graphic). One of the most used spectroscopic techniques for resolving the structure of a biomolecule, such as a protein or peptide, is NMR spectroscopy. Because only NMR signal intensities and frequencies are measured in the experiment, a conformational interpretation of the primary data, that is, measured data, is not straightforward, especially for flexible molecules. It is hampered by the occurrence of conformational and/or time-averaging, by insufficient number of experimental data and by insufficient accuracy of experimental data. All three problematic aspects of structure refinement based on NMR nuclear Overhauser effect (NOE) intensities and 3J coupling data are illustrated by using two ,-heptapeptides in methanol as an example. We have performed 16 molecular dynamics (MD) simulations between 20 to 100,ns in length of unrestrained and NOE distance-restrained cases (instantaneous and time-averaged) of two ,-heptapeptides with a central ,-HAla(,-OH) amino acid in methanol at two different temperatures using two different GROMOS force-field parameter sets, 45,A3 and 53,A6. The created conformational ensembles were used to interpret the primary NMR data on these molecules. They also were compared to a set of NMR model structures derived by single-structure refinement in vacuo by using standard techniques. It is shown that the conformational interpretation of measured experimental data can be significantly improved by using unrestrained, instantaneous and time-averaged restrained MD simulations of the peptides by using a thermodynamically calibrated force field and by explicitly including solvent degrees of freedom. [source] | ||||||||||