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Point Charges (point + charge)
Selected AbstractsRational determination of charge distributions for free energy calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2003Christophe Chipot Abstract Point charges derived from RHF/6-31G* electrostatic potentials are attractive because they tend to exaggerate the polarity of solvated molecules, thereby compensating in an average fashion missing induction effects. In the context of free energy calculations, wherein the molecule is transferred from a polar environment to a nonpolar one, we propose a more rational approach based on a self-consistent reaction field computation at a higher level of theory, supplemented by an estimation of the corresponding distortion energy to account for the change of polarity of the surroundings. Application of this method to the test cases acetamide, acetic acid, methyl acetate and phenol, using multinanosecond molecular dynamics/"umbrella sampling" simulations, yields consistent hydration free energies in reasonably good agreement with experiment. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 409,415, 2003 [source] X-ray atomic orbital analysis.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2008The scattering unit of X-ray crystal structure analysis is changed from atoms to the subshell electrons by X-ray atomic orbital analysis (XAO). All the atoms in the unit cell are divided into groups of subshell electrons in the XAO analysis. Each subshell is treated as an independent pseudo-atom, which enables the atomic orbitals (AO's) and the electron population of each AO expressed as a linear combination of s/p/d/f orbitals in each subshell to be determined. When the environmental condition of the sample is varied, the electron transfer among the AO's in the crystal can be traced with XAO. It is applicable mainly to analyses of the electron-density distribution in ionic solids including those with a nonstoichiometric structure. The expansion coefficients of each AO are calculated with the perturbation theory putting a point charge on each atom in the unit cell. This automatically makes the perturbation potential have the point-group symmetry of the atom in the crystal field. Then the coefficients of each AO are refined to fit to the observed structure factors keeping the orthonormal relationships among the AO's. Complex basis functions with , or , spin as well as real ones are employed for heavy atoms and the relationships among the coefficients for the AO's of an electron in the crystal fields of the 32 point-group symmetries are derived for p, d and f orbitals. The AO's thus derived can be applicable to an anti-symmetrized multi-electron system, although X-ray diffraction cannot specify the atomic terms occupied when the crystal symmetry permits the atom to have many terms. [source] The embedded ion method: A new approach to the electrostatic description of crystal lattice effects in chemical shielding calculationsCONCEPTS IN MAGNETIC RESONANCE, Issue 5 2006Dirk Stueber Abstract The nuclear magnetic shielding anisotropy of NMR active nuclei is highly sensitive to the nuclear electronic environment. Hence, measurements of the nuclear magnetic shielding anisotropy represent a powerful tool in the elucidation of molecular structure for a wide variety of materials. Quantum mechanical ab initio nuclear magnetic shielding calculations effectively complement the experimental NMR data by revealing additional structural information. The accuracy and capacity of these calculations has been improved considerably in recent years. However, the inherent problem of the limitation in the size of the systems that may be studied due to the relatively demanding computational requirements largely remains. Accordingly, ab initio shielding calculations have been performed predominantly on isolated molecules, neglecting the molecular environment. This approach is sufficient for neutral nonpolar systems, but leads to serious errors in the shielding calculations on polar and ionic systems. Conducting ab initio shielding calculations on clusters of molecules (i.e., including the nearest neighbor interactions) has improved the accuracy of the calculations in many cases. Other methods of simulating crystal lattice effects in shielding calculations that have been developed include the electrostatic representation of the crystal lattice using point charge arrays, full ab initio methods, ab initio methods under periodic boundary conditions, and hybrid ab initio/molecular dynamics methods. The embedded ion method (EIM) discussed here follows the electrostatic approach. The method mimics the intermolecular and interionic interactions experienced by a subject molecule or cluster in a given crystal in quantum mechanical shielding calculations with a large finite, periodic, and self-consistent array of point charges. The point charge arrays in the EIM are generated using the Ewald summation method and embed the molecule or ion of interest for which the ab initio shielding calculations are performed. The accuracy with which the EIM reproduces experimental nuclear magnetic shift tensor principal values, the sensitivity of the EIM to the parameters defining the point charge arrays, as well as the strengths and limitations of the EIM in comparison with other methods that include crystal lattice effects in chemical shielding calculations, are presented. © 2006 Wiley Periodicals, Inc. Concepts Magn Reson Part A 28A: 347,368, 2006 [source] Theoretical studies on effects of hydrogen bonds attaching to cysteine ligands on 4Fe-4S clustersINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2008Y. Kitagawa Abstract The effect of hydrogen bonds attaching to sulfur atoms of cysteine ligands on 4Fe-4S cluster is examined by using UB3LYP method. Calculated results indicate that an existence of the hydrogen bonds scarcely changes SOMO-SUMO gap, shapes of Kohn-Sham orbitals, and magnetic interactions between Fe ions, although it stabilizes Kohn-Sham orbital energies of SOMO and SUMO about 1.0 eV. And they also make a reduced state stable in comparison with an oxidized state. In addition, the point charges of +0.1e (e: elementary electric charge) at the position of the hydrogen atoms give almost same results to the hydrogen bonds quantitatively. The results suggest that a positive environment from the hydrogen bonds around the clusters is important for a redox potential of 4Fe-4S clusters. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Molecular dynamics simulations of polarizable DNA in crystal environmentINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2006Volodymyr Babin Abstract We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the "right" distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Sergio A. Hassan Abstract Biological macromolecules and other polymers belong to the class of mesoscopic systems, with characteristic length scale of the order of a nanometer. Although microscopic models would be the preferred choice in theoretical calculations, their use in computer simulations becomes prohibitive for large systems or long simulation times. On the other hand, the use of purely macroscopic models in the mesoscopic domain may introduce artifacts, with effects that are difficult to assess and that may compromise the reliability of the calculations. Here is proposed an approach with the aim of minimizing the empirical nature of continuum approximations of solvent effects within the scope of molecular mechanics (MM) approximations in mesoscopic systems. Using quantum chemical methods, the potential generated by the molecular electron density is first decomposed in a multicenter-multipole expansion around predetermined centers. The monopole and dipole terms of the expansion at each site create electric fields that polarize the surrounding aqueous medium whose dielectric properties can be described by the classical theory of polar liquids. Debye's theory allows a derivation of the dielectric profiles created around isolated point charges and dipoles that can incorporate Onsager reaction field corrections. A superposition of screened Coulomb potentials obtained from this theory makes possible a simple derivation of a formal expression for the total electrostatic energy and the polar component of the solvation energy of the system. A discussion is presented on the physical meaning of the model parameters, their transferability, and their convergence to calculable quantities in the limit of simple systems. The performance of this continuum approximation in computer calculations of amino acids in the context of an atomistic force field is discussed. Applications of a continuum model based on screened Coulomb potentials in multinanosecond simulations of peptides and proteins are briefly reviewed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [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] A combined electronegativity equalization and electrostatic potential fit method for the determination of atomic point chargesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2007Imre Berente Abstract We report an approach for the determination of atomic monopoles of macromolecular systems using connectivity and geometry parameters alone. The method is appropriate also for the calculation of charge distributions based on the quantum mechanically determined wave function and does not suffer from the mathematical instability of other electrostatic potential fit methods. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Electric field-derived point charges to mimic the electrostatics in molecular crystalsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2006Andrew E. Whitten Abstract Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree,Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1063,1070, 2006 [source] A molecular mechanics force field for biologically important sterolsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Zoe Cournia Abstract A parameterization has been performed of the biologically important sterols cholesterol, ergosterol, and lanosterol for the CHARMM27 all-atom molecular mechanics force field. An automated parameterization method was used that involves fitting the potential to vibrational frequencies and eigenvectors derived from quantum-chemical calculations. The partial charges were derived by fitting point charges to quantum-chemically calculated electrostatic potentials. To model the dynamics of the hydroxyl groups of the sterols correctly, the parameter set was refined to reproduce the energy barrier for the rotation of the hydroxyl group around the carbon connected to the hydroxyl of each sterol. The frequency-matching plots show good agreement between the CHARMM and quantum chemical normal modes. The parameters are tested in a molecular dynamics simulation of the cholesterol crystal structure. The experimental geometry and cell dimensions are well reproduced. The force field derived here is also useful for simulating other sterols such as the phytosterols sigmasterol, and campesterol, and a variety of steroids. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1383,1399, 2005 [source] Electrostatic effects on inertial particle transport in bifurcated tubesAICHE JOURNAL, Issue 6 2009Fong Yew Leong Abstract Most aerosols found naturally in the ambient environment or those dispersed from artificial devices such as dry powder inhalers, are electrically charged. It is known that a strong electrostatic charge on aerosols can result in transport behavior dramatically different from that of uncharged aerosols, even in the absence of an external electric field. In the present work, we study pneumatic transport of corona-charged particles in bifurcated tubes. This is accomplished by tracking the motion of discrete particles numerically under the influence of drag, gravitational, and electrostatic forces. The model aerosol is fly ash powder, whose size and charge distributions have been determined experimentally. The electrical mobility of the charged particle cloud is modeled through coulombic interactions between discrete point charges. For the case of polydispersed particles electrically charged across a distribution, the deposition efficiency was found to be greater than what is indicated by the mean charge and size. In particular, use of negatively charged fly ash powder of mean size of 2 ,m and mean charge of ,1.5 C/kg led to significant increase in deposition efficiency (,29%) compared with uncharged fly ash powder of the same size distribution (,8%). Analysis of particle residence times suggests significant interaction between electrical and drag forces. These findings could have implications for pneumatic powder conveying or pulmonary drug delivery applications. © 2009 American Institute of Chemical Engineers AIChE J, 2009 [source] | ||||||||||