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Electrostatic Energy (electrostatic + energy)
Selected AbstractsElectrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2005Robert J. Petrella Abstract A rapid method for the calculation of the electrostatic energy of a system without a cutoff is described in which the computational time grows linearly with the number of particles or charges. The inverse of the distance is approximated as a polynomial, which is then transformed into a function whose terms involve individual particles, instead of particle pairs, by a partitioning of the double sum. In this way, the electrostatic energy that is determined by the interparticle interactions is obtained without explicit calculation of these interactions. For systems of positive charges positioned on a face-centered cubic lattice, the calculation of the energy by the new method is shown to be faster than the calculation of the exact energy, in many cases by an order of magnitude, and to be accurate to within 1,2%. The application of this method to increase the accuracy of conventional truncation-based calculations in condensed-phase systems is also demonstrated by combining the approximated long-range electrostatic interactions with the exact short-range interactions in a "hybrid" calculation. For a 20-Å sphere of water molecules, the forces are shown to be six times as accurate using this hybrid method as those calculated with conventional truncation of the electrostatic energy function at 12 Å. This is accomplished with a slight increase in speed, and with a sevenfold increase in speed relative to the exact all-pair calculation. Structures minimized with the hybrid function are shown to be closer to structures minimized with an exact all-pair electrostatic energy function than are those minimized with a conventional 13-Å cutoff-based electrostatic energy function. Comparison of the energies and forces calculated with the exact method illustrate that the absolute errors obtained with standard truncation can be very large. The extension of the current method to other pairwise functions as well as to multibody functions, is described. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 755,787, 2005 [source] Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme,substrate complex: influenza neuraminidase inhibitionACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2009Paulina M. Dominiak Although electrostatic interactions contribute only a part of the interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In the reported study, a wide range of complexes of influenza neuraminidases with inhibitor molecules (sialic acid derivatives and others) have been analyzed using charge densities from a transferable aspherical-atom data bank. The strongest interactions of the residues are with the acidic group at the C2 position of the inhibitor (,,300,kJ,mol,1 for ,COO, in non-aromatic inhibitors, ,,120,210,kJ,mol,1 for ,COO, in aromatic inhibitors and ,,450,kJ,mol,1 for ,PO32,) and with the amino and guanidine groups at C4 (,,250,kJ,mol,1). Other groups contribute less than ,100,kJ,mol,1. Residues Glu119, Asp151, Glu227, Glu276 and Arg371 show the largest variation in electrostatic energies of interaction with different groups of inhibitors, which points to their important role in the inhibitor recognition. The Arg292,Lys mutation reduces the electrostatic interactions of the enzyme with the acidic group at C2 for all inhibitors that have been studied (SIA, DAN, 4AM, ZMR, G20, G28, G39 and BCZ), but enhances the interactions with the glycerol group at C6 for inhibitors that contain it. This is in agreement with the lower level of resistance of the mutated virus to glycerol-containing inhibitors compared with the more hydrophobic derivatives. [source] Progress in the Understanding of Drug,Receptor Interactions, Part,2: Experimental and Theoretical Electrostatic Moments and Interaction Energies of an Angiotensin II Receptor Antagonist (C30H30N6O3S)CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2007Raffaella Soave Dr. Abstract A combined experimental and theoretical charge density study of an angiotensin II receptor antagonist (1) is presented focusing on electrostatic properties such as atomic charges, molecular electric moments up to the fourth rank and energies of the intermolecular interactions, to gain an insight into the physical nature of the drug,receptor interaction. Electrostatic properties were derived from both the experimental electron density (multipole refinement of X-ray data collected at T=17,K) and the ab initio wavefunction (single molecule and fully periodic calculations at the DFT level). The relevance of S,,,O and S,,,N intramolecular interactions on the activity of 1 is highlighted by using both the crystal and gas-phase geometries and their electrostatic nature is documented by means of QTAIM atomic charges. The derived electrostatic properties are consistent with a nearly spherical electron density distribution, characterised by an intermingling of electropositive and -negative zones rather than by a unique electrophilic region opposed to a nucleophilic area. This makes the first molecular moment scarcely significant and ill-determined, whereas the second moment is large, significant and highly reliable. A comparison between experimental and theoretical components of the third electric moment shows a few discrepancies, whereas the agreement for the fourth electric moment is excellent. The most favourable intermolecular bond is show to be an NH,,,N hydrogen bond with an energy of about 50,kJ,mol,1. Key pharmacophoric features responsible for attractive electrostatic interactions include CH,,,X hydrogen bonds. It is shown that methyl and methylene groups, known to be essential for the biological activity of the drug, provide a significant energetic contribution to the total binding energy. Dispersive interactions are important at the thiophene and at both the phenyl fragments. The experimental estimates of the electrostatic contribution to the intermolecular interaction energies of six molecular pairs, obtained by a new model proposed by Spackman, predict the correct relative electrostatic energies with no exceptions. [source] Theory of Ion Transport in Electrochemically Switchable Nanoporous Metallized MembranesCHEMPHYSCHEM, Issue 1 2009Christian Amatore Dr. Abstract A physicomathematical model of ion transport through a synthetic electrochemically switchable membrane with nanometric metal-plated pores is presented. Due to the extremely small size of the cylindrical pores, electrical double layers formed inside overlap, and thus, strong electrostatic fields whose intensities vary across the cross-sections of the nanopores are created. Based on the proposed model a relationship between the relative electrostatic energies experienced by ions in the nanopores and the potential applied to the membrane is established. This allows the prediction of transference numbers and explains quantitatively the ion-transport switching capability of such synthetic membranes. The predictions of this model agree satisfactorily with previous experimental data obtained for this type of devices by Martin and co-workers. [source] Electrostatic analysis of charge interactions in proteinsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2010G. P. Tsironis Abstract We model proteins as continuous electrostatic media immersed in water to investigate charge mediated processes in their interior. We use a Green's function formalism and find analytical expressions for the electrostatic energy in the vicinity of the protein surfaces. We find that due to image charges generated by the protein dielectric medium embedded in water, the effective electrostatic interaction between the two charges in the interior of the protein has an energy larger than the thermal energy. We focus specifically on kinesin to asses the strength of the electrostatic interaction between ATP and ADP molecules. It is known experimentally that ADP expulsion is correlated to ATP kinesin binding while both processes are essential for the kinesin walk. We estimate that the Bjerrum length in the interior of the kinesin dimer protein is of the order of 4 nm and that the pure electrostatic ATP,ADP interaction is of the order of 3,5 kBT. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [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] A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contributionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2005Jean-Philip Piquemal Abstract Intermolecular interaction energy decompositions using the Constrained Space Orbital Variation (CSOV) method are carried out at the Hartree,Fock level on the one hand and using DFT with usual GGA functionals on the other for a number of model complexes to analyze the role of electron correlation in the intermolecular stabilization energy. In addition to the overall stabilization, the results provide information on the variation, with respect to the computational level, of the different contributions to the interaction energy. The complexes studied are the water linear dimer, the N -methylformamide dimer, the nucleic acid base pairs, the benzene,methane and benzene-N2 van der Waals complexes, [Cu+ -(ImH)3]2, where "ImH" stands for the Imidazole ligand, and ImH-Zn++. The variation of the frozen core energy (the sum of the intermolecular electrostatic energy and the Pauli repulsion energy) calculated from the unperturbed orbitals of the interacting entities indicates that the intramolecular correlation contributions can be stabilizing as well as destabilizing, and that general trends can be derived from the results obtained using usual density functionals. The most important difference between the values obtained from HF and DFT computations concerns the charge transfer contribution, which, in most cases, undergoes the largest increase. The physical meaning of these results is discussed. The present work gives reference calculations that might be used to parametrize new correlated molecular mechanics potentials. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1052,1062, 2005 [source] Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2005Robert J. Petrella Abstract A rapid method for the calculation of the electrostatic energy of a system without a cutoff is described in which the computational time grows linearly with the number of particles or charges. The inverse of the distance is approximated as a polynomial, which is then transformed into a function whose terms involve individual particles, instead of particle pairs, by a partitioning of the double sum. In this way, the electrostatic energy that is determined by the interparticle interactions is obtained without explicit calculation of these interactions. For systems of positive charges positioned on a face-centered cubic lattice, the calculation of the energy by the new method is shown to be faster than the calculation of the exact energy, in many cases by an order of magnitude, and to be accurate to within 1,2%. The application of this method to increase the accuracy of conventional truncation-based calculations in condensed-phase systems is also demonstrated by combining the approximated long-range electrostatic interactions with the exact short-range interactions in a "hybrid" calculation. For a 20-Å sphere of water molecules, the forces are shown to be six times as accurate using this hybrid method as those calculated with conventional truncation of the electrostatic energy function at 12 Å. This is accomplished with a slight increase in speed, and with a sevenfold increase in speed relative to the exact all-pair calculation. Structures minimized with the hybrid function are shown to be closer to structures minimized with an exact all-pair electrostatic energy function than are those minimized with a conventional 13-Å cutoff-based electrostatic energy function. Comparison of the energies and forces calculated with the exact method illustrate that the absolute errors obtained with standard truncation can be very large. The extension of the current method to other pairwise functions as well as to multibody functions, is described. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 755,787, 2005 [source] Collagen structure: The molecular source of the tendon magic angle effectJOURNAL OF MAGNETIC RESONANCE IMAGING, Issue 2 2007Gary D. Fullerton PhD Abstract This review of tendon/collagen structure shows that the orientational variation in MRI signals from tendon, which is referred to as the "magic angle" (MA) effect, is caused by irreducible separation of charges on the main chain of the collagen molecule. These charges are held apart in a vacuum by stereotactic restriction of protein folding due in large part to a high concentration of hydroxyproline ring residues in the amino acids of mammalian collagen. The elevated protein electrostatic energy is reduced in water by the large dielectric constant of the highly polar solvent (, , 80). The water molecules serve as dielectric molecules that are bound by an energy that is nearly equivalent to the electrostatic energy between the neighboring positive and negative charge pairs in a vacuum. These highly immobilized water molecules and secondary molecules in the hydrogen-bonded water network are confined to the transverse plane of the tendon. Orientational restriction causes residual dipole coupling, which is directly responsible for the frequency and phase shifts observed in orientational MRI (OMRI) described by the MA effect. Reference to a wide range of biophysical measurements shows that native hydration is a monolayer on collagen hm = 1.6 g/g, which divides into two components consisting of primary hydration on polar surfaces hpp = 0.8 g/g and secondary hydration hs = 0.8 g/g bridging over hydrophobic surface regions. Primary hydration further divides into side-chain hydration hpsc = 0.54 g/g and main-chain hydration hpmc = 0.263 g/g. The main-chain fraction consists of water that bridges between charges on the main chain and is responsible for almost all of the enthalpy of melting ,H = 70 J/g-dry mass. Main-chain water bridges consist of one extremely immobilized Ramachandran water bridge per tripeptide hRa = 0.0658 g/g and one double water bridge per tripeptide hdwb = 0.1974 g/g, with three water molecules that are sufficiently slowed to act as the spin-lattice relaxation sink for the entire tendon. J. Magn. Reson. Imaging 2007. © 2007 Wiley-Liss, Inc. [source] | ||||||||||