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Molecular Dipole Moment (molecular + dipole_moment)
Selected AbstractsStudy of peptide conformation in terms of the ABEEM/MM methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2006Zhong-Zhi Yang Abstract The ABEEM/MM model (atom-bond electronegativity equalization method fused into molecular mechanics) is applied to study of the polypeptide conformations. The Lennard,Jones and torsional parameters were optimized to be consistent with the ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic fitting function. Molecular dipole moments, dimerization energies, and hydrogen bond lengths of complexes are reasonably achieved by our model, compared to ab initio results. The ABEEM/MM fluctuating charge model reproduces both the peptide conformational energies and structures with satisfactory accuracy with low computer cost. The transferability is tested by applying the parameters of our model to the tetrapeptide of alanine and another four dipeptides. The overall RMS deviations in conformational energies and key dihedral angles for four di- or tetrapeptide, is 0.39 kcal/mol and 7.7°. The current results agree well with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results make us believe that our fluctuating charge model can obtain more promising results in protein and macromolecular modeling with good accuracy but less computer cost. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 1,10, 2006 [source] Range and strength of intermolecular forces for van der Waals complexes of the type H2Xn -Rg, with X = O, S and n = 1,2INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2010Patrícia R. P. Barreto Abstract This study is intended as a continuation of previous experimental and theoretical works on the systems H2O-Rg, H2S-Rg, H2O2 -Rg, and H2S2 -Rg, where Rg = He, Ne, Ar, Kr, Xe. For the H2O-Rg and H2S-Rg systems, molecular and atomic polarizabilities have been calculated and from them, using phenomenological correlation formulas modeling the dispersion-repulsion (van der Waals) forces, the isotropic interaction parameters have been determined and compared with experimental data from this laboratory. For the H2O2 -Rg and H2S2 -Rg systems, the molecular polarizabilities have been calculated and used in correlation formulas to predict well depths and positions of van der Waals forces and a comparison made with the corresponding potential energy surfaces calculated in previous works. The approach correctly predicts the interaction parameters, except for H2O and H2O2 with the heavier rare gases. The correlation formulas have been then extended to include an attractive induction contribution accounting for the interaction between the permanent molecular dipole moment and the instantaneous induced atomic dipole moment, to improve the predicted parameters for H2O and H2O2 -Ar, Kr and Xe. The agreement with experimental and theoretical data is improved but the predicted data still underestimate the interaction. This is probably due to the presence of a significant non van der Waals contribution to the interaction for the heavier gases, as suggested by analogy with the previously studied water-Rg case. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] QSAR study of ,-lactam antibiotic efflux by the bacterial multidrug resistance pump AcrB,JOURNAL OF CHEMOMETRICS, Issue 5 2004Márcia M. C. Ferreira Abstract AcrAB-TolC is the most important efflux pump system of Gram-negative bacteria, responsible for their resistance to lipophilic and amphilic drugs. In this work, HCA,PCA studies were performed to investigate the relationship between efflux activities (negative logarithm of minial inhibitor concentration, pMIC) of three strains of S. thypimurium with respect to ,-lactams, and to analyze the relationship between lipophilicity parameters calculated by different methods. The analyses demonstrate that pMICs strongly depend on properties of both bacterial strains and drug molecules, and that lipophilicity parameters do not necessarily contain the same information about the drugs. QSAR studies have shown that the calculated lipophilicities, in some cases, are non linearly related to the pMICs originated by active AcrAB-TolC bacterial pumps, due to the existence of ,-lactams with nitrogen- and sulfur-rich substituents. Among the most important ,-lactam molecular properties quantitatively related to pMICs are lipophilicity and electronic and hydrogen,bonding properties. Parameters describing these properties were included in the QSAR study to obtain parsimonius regression models for MICs. ,-Lactams were classified as good, moderately good and poor AcrAB-TolC substrates. Their stereoelectronic molecular properties, especially the Y-component of the molecular dipole moment and hydrogen binding properties, reflected this classification. Copyright © 2004 John Wiley & Sons, Ltd. [source] Dipole Moment Enhancement in Molecular Crystals from X-ray Diffraction DataCHEMPHYSCHEM, Issue 14 2007Mark A. Spackman Prof. Abstract Although reliable determination of the molecular dipole moment from experimental charge density analyses on molecular crystals is a challenging undertaking, these values are becoming increasingly common experimental results. We collate all known experimental determinations and use this database to identify broad trends in the dipole moment enhancements implied by these measurements as well as outliers for which enhancements are pronounced. Compelling evidence emerges that molecular dipole moments from X-ray diffraction data can provide a wealth of information on the change in the molecular charge distribution that results from crystal formation. Most importantly, these experiments are unrivalled in their potential to provide this information in such detail and deserve to be exploited to a much greater extent. The considerable number of experimental determinations now available has enabled us to pinpoint those studies that merit further attention, either because they point unequivocally to a considerable enhancement in the crystal (of 50,% or more), or because the experimental determinations suggest enhancements of 100,% or more,much larger than independent theoretical estimates. In both cases further detailed experimental and theoretical studies are indicated. [source] Electronic Structure of Self-Assembled Monolayers on Au(111) Surfaces: The Impact of Backbone PolarizabilityADVANCED FUNCTIONAL MATERIALS, Issue 23 2009LinJun Wang Abstract Modifying metal electrodes with self-assembled monolayers (SAMs) has promising applications in organic and molecular electronics. The two key electronic parameters are the modification of the electrode work function because of SAM adsorption and the alignment of the SAM conducting states relative to the metal Fermi level. Through a comprehensive density-functional-theory study on a series of organic thiols self-assembled on Au(111), relationships between the electronic structure of the individual molecules (especially the backbone polarizability and its response to donor/acceptor substitutions) and the properties of the corresponding SAMs are described. The molecular backbone is found to significantly impacts the level alignment; for molecules with small ionization potentials, even Fermi-level pinning is observed. Nevertheless, independent of the backbone, polar head-group substitutions have no effect on the level alignment. For the work-function modification, the larger molecular dipole moments achieved when attaching donor/acceptor substituents to more polarizable backbones are largely compensated by increased depolarization in the SAMs. The main impact of the backbone on the work-function modification thus arises from its influence on the molecular orientation on the surface. This study provides a solid theoretical basis for the fundamental understanding of SAMs and significantly advances the understanding of structure,property relationships needed for the future development of functional organic interfaces. [source] CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2004Sandeep Patel Abstract A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 Ĺ r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1,0.2 Debye in keeping with previously reported work. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 1,15, 2004 [source] Dipole Moment Enhancement in Molecular Crystals from X-ray Diffraction DataCHEMPHYSCHEM, Issue 14 2007Mark A. Spackman Prof. Abstract Although reliable determination of the molecular dipole moment from experimental charge density analyses on molecular crystals is a challenging undertaking, these values are becoming increasingly common experimental results. We collate all known experimental determinations and use this database to identify broad trends in the dipole moment enhancements implied by these measurements as well as outliers for which enhancements are pronounced. Compelling evidence emerges that molecular dipole moments from X-ray diffraction data can provide a wealth of information on the change in the molecular charge distribution that results from crystal formation. Most importantly, these experiments are unrivalled in their potential to provide this information in such detail and deserve to be exploited to a much greater extent. The considerable number of experimental determinations now available has enabled us to pinpoint those studies that merit further attention, either because they point unequivocally to a considerable enhancement in the crystal (of 50,% or more), or because the experimental determinations suggest enhancements of 100,% or more,much larger than independent theoretical estimates. In both cases further detailed experimental and theoretical studies are indicated. [source] | ||||||||||