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Long-range Electrostatic Interactions (long-range + electrostatic_interaction)
Selected AbstractsComputational alanine scanning of the 1:1 human growth hormone,receptor complexJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2002Shuanghong Huo Abstract The MM-PBSA (Molecular Mechanics,Poisson,Boltzmann surface area) method was applied to the human Growth Hormone (hGH) complexed with its receptor to assess both the validity and the limitations of the computational alanine scanning approach. A 400-ps dynamical trajectory of the fully solvated complex was simulated at 300 K in a 101 Å×81 Å×107 Å water box using periodic boundary conditions. Long-range electrostatic interactions were treated with the particle mesh Ewald (PME) summation method. Equally spaced snapshots along the trajectory were chosen to compute the binding free energy using a continuum solvation model to calculate the electrostatic desolvation free energy and a solvent-accessible surface area approach to treat the nonpolar solvation free energy. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in the structural epitope of the hormone and the receptor to alanine and recomputing the ,Gbinding. To further investigate a particular structure, a 200-ps dynamical trajectory of an R43A hormone,receptor complex was simulated. By postprocessing a single trajectory of the wild-type complex, the average unsigned error of our calculated ,,Gbinding is ,1 kcal/mol for the alanine mutations of hydrophobic residues and polar/charged residues without buried salt bridges. When residues involved in buried salt bridges are mutated to alanine, it is demonstrated that a separate trajectory of the alanine mutant complex can lead to reasonable agreement with experimental results. Our approach can be extended to rapid screening of a variety of possible modifications to binding sites. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 15,27, 2002 [source] Adiabatic decoupling of the reaction coordinateINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2008J. C. Lorquet Abstract When the dynamics is constrained by adiabatic invariance, a reactive process can be described as a one-dimensional motion along the reaction coordinate in an effective potential. This simplification is often valid for central potentials and for the curved harmonic valley studied in the reaction path Hamiltonian model. For an ion,molecule reaction, the action integral ,P,, = (1/2,),P,d, is an adiabatic invariant. The Poisson bracket of ,P,,2 with Hamiltonians corresponding to a great variety of long-range electrostatic interactions is found to decrease with the separation coordinate r, faster than the corresponding potential. This indicates that the validity of the adiabatic approximation is not directly related to the shape of the potential energy surface. The leading role played by the translational momentum is accounted for by Jacobi's form of the least action principle. However, although the identification of adiabatic regions by this procedure is limited to a specific range of coordinate configurations, equivalent constraints must persist all along the reaction coordinate and must operate during the entire reaction, as a result of entropy conservation. The study of the translational kinetic energy released on the fragments is particularly appropriate to detect restrictions on energy exchange between the reaction coordinate and the bath of internal degrees of freedom. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Charge transport in stacking metal and metal-free phthalocyanine iodides.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2009Effects of packing, central metals, core modification, dopants, external electric field, substitutions Abstract The charge-transport properties of the one-dimensional stacking metal phthalocyanine iodides (M(Pc)I, M = Fe, Co, Ni, Cu) and metal-free phthalocyanine iodide (H2(Pc)I) have been theoretically investigated. On the basis of the tight-binding approximation and two-state theory, both the site-energy corrected energy splitting in dimer and Fock-matrix-based methods are used to calculate the transfer integral. The intermolecular motions, including interplanar translation, rotation, slip, and tilt, exert remarkable impacts on the transfer integral. The order/disorder of the dopant stack and the long-range electrostatic interactions are also demonstrated to be crucial factors for modulation of charge-transport properties. The transfer integral undergoes slight changes under an applied electric field along the stacking direction in the range of 106 , 107 V cm,1. The change of central metals in MPc has little effect on the transfer integrals, but significantly affects the reorganization energies. The extension of the ,-conjugation in macrocyclic ligand brings about considerable influence on the transfer integrals. Peripheral substitutions by animo, hydroxyl, and methyl lead to deviations from planarity of macromolecular rings, and hence affect the valence bands significantly. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [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] One-Armed Artificial Receptors for the Binding of Polar Tetrapeptides in Water: Probing the Substrate Selectivity of a Combinatorial Receptor LibraryCHEMISTRY - A EUROPEAN JOURNAL, Issue 5 2006Carsten Schmuck Prof. Dr. Abstract We have recently developed a new class of one-armed artificial receptors 1 for the binding of the polar tetrapeptide N -Ac- D -Glu- L -Lys- D -Ala- D -Ala-OH (EKAA) 2 in water using a combined combinatorial and statistical approach. We have now further probed the substrate selectivity of this receptor library 1 by screening a second tetrapeptide substrate (3) with the inverse sequence N -Ac- D -Ala- D -Ala- L -Lys- D -Glu-OH (AAKE). This "inverse" substrate is also efficiently bound by our receptors, with Kass ,6000,m,1 for the best receptors, as determined both by a quantitative on-bead binding assay and by UV and fluorescence titration studies in free solution. Hence, the inverse tetrapeptide 3 is in general bound two to three times less efficiently than the "normal" peptide 2 (Kass ,17,000,m,1), even though the complexation mainly involves long-range electrostatic interactions and both the receptor and substrate are rather flexible. Molecular modeling and ab initio calculations have been used to rationalize the observed substrate selectivity and to analyze the various binding interactions within the complex. [source] | ||||||||||