Determination of net atomic charges using a modified partial equalization of orbital electronegativity method.  1.  Application to neutral molecules as models for polypeptides

No, Kyoung Tai; Grant, Jennifer; Scheraga, Harold A.

doi:10.1021/j100374a066

Cited by 117 publications

(107 citation statements)

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“…21 The model uses the concept of electronegativity equalization. [85][86][87][88][89][90][91] The TIP4P-FQ model uses the geometry of the TIP4P water model and includes Lennard-Jones interactions between oxygen sites and three charge sites: two on the hydrogen atoms and one on the M site 0.15Å from the oxygen atom. 66 The FQ model has additional interactions between charge sites on the same molecule.…”

Section: Methodsmentioning

confidence: 99%

Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model

Rick

2001

The Journal of Chemical Physics

178

159

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Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model The temperature dependence of the thermodynamic and dynamical properties of liquid water using the polarizable fluctuating charge ͑FQ͒ model is presented. The properties of ice Ih, both for a perfect lattice with no thermal disorder and at a temperature of 273 K, are also presented. In contrast to nonpolarizable models, the FQ model has a density maximum of water near 277 K. For ice, the model has a dipole moment of the perfect lattice of 3.05 Debye, in good agreement with a recent induction model calculation. The simulations at 273 K and the correct density find that thermal motion decreases the average dipole moment to 2.96 D. The liquid state dipole moment is less than the ice value and decreases with temperature.

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Section: Methodsmentioning

confidence: 99%

Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model

Rick

2001

The Journal of Chemical Physics

178

159

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“…Parameters and topologies of PMX-B and LPS as well as partial charges of PMX-B for GROMACS were established based on data from the PRODRG server (32) and the GROMOS 53a6 force field (33). Partial charges of LPS were assigned for a protonation state corresponding to experimental conditions of pH by the MPEOP method (34,35). Parameters for DPC were derived from values for dipalmitoylphosphatidylcholine from the GROMOS force field library.…”

Section: Production Ofmentioning

confidence: 99%

Interactions of Lipopolysaccharide and Polymyxin Studied by NMR Spectroscopy

Mareš

Kumaran

Gobbo

et al. 2009

Journal of Biological Chemistry

103

111

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In the light of occurrence of bacterial strains with multiple resistances against most antibiotics, antimicrobial peptides that interact with the outer layer of Gram-negative bacteria, such as polymyxin (PMX), have recently received increased attention. Here we present a study of the interactions of PMX-B, -E, and -M with lipopolysaccharide (LPS) from a deep rough mutant strain of Escherichia coli. A method for efficient purification of biosynthetically produced LPS using reversed-phase high-performance liquid chromatography in combination with ternary solvent mixtures was developed. LPS was incorporated into a membrane model, dodecylphosphocholine micelles, and its interaction with polymyxins was studied by heteronuclear NMR spectroscopy. Data from chemical shift mapping using isotopelabeled LPS or labeled polymyxin, as well as from isotope-filtered nuclear Overhauser effect spectroscopy experiments, reveal the mode of interaction of LPS with polymyxins. Using molecular dynamics calculations the complex of LPS with PMX-B in the presence of dodecylphosphocholine micelles was modeled using restraints derived from chemical shift mapping data and intermolecular nuclear Overhauser effects. In the modeled complex the macrocycle of PMX is centered around the phosphate group at GlcN-B, and additional contacts from polar side chains are formed to GlcN-A and Kdo-C, whereas hydrophobic side chains penetrate the acyl-chain region.

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“…r ik is the distance between the ith atom and the kth surface fragment. The net atomic charge q i and the effective atomic polarizability α i of the ith atom of the solute were calculated by using the modified partial equalization of orbital electronegativity and the charge dependent effective atomic polarizability methods, respectively (51)(52)(53)(54)(55). The cavity surface of a solute is defined by the union of the SAS of atoms in the solute (Fig.…”

Section: Theorymentioning

confidence: 99%

A generalized G-SFED continuum solvation free energy calculation model

Lee

Cho

Kang

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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An empirical continuum solvation model, solvation free energy density (SFED), has been developed to calculate solvation free energies of a molecule in the most frequently used solvents. A generalized version of the SFED model, generalized-SFED (G-SFED), is proposed here to calculate molecular solvation free energies in virtually any solvent. G-SFED provides an accurate and fast generalized framework without a complicated description of a solution. In the model, the solvation free energy of a solute is represented as a linear combination of empirical functions of the solute properties representing the effects of solute on various solute-solvent interactions, and the complementary solvent effects on these interactions were reflected in the linear expansion coefficients with a few solvent properties. G-SFED works well for a wide range of sizes and polarities of solute molecules in various solvents as shown by a set of 5,753 solvation free energies of diverse combinations of 103 solvents and 890 solutes. Octanol-water partition coefficients of small organic compounds and peptides were calculated with G-SFED with accuracy within 0.4 log unit for each group. The G-SFED computation time depends linearly on the number of nonhydrogen atoms (n) in a molecule, O(n).implicit solvent | macromolecules | linear time A n accurate description of the effect of solvent on solvation is crucial for understanding chemical and biological phenomena. Because many peptide and protein drugs are currently being developed (1, 2), computational efficiency as well as accuracy are very important. Among the different approaches that have been used, continuum solvation models are appealing because of the simplified yet accurate description of the solvent effect (3-8).Continuum solvent models have been developed based on the early work of Born (9), Bell (10), Kirkwood (11), and Onsanger (12). They focus primarily on the description of the solute either at the quantum mechanical level or as a classical collection of point charges and try to represent the influence of the solvent based on an approximate treatment as a dielectric continuum medium. The charge distribution of the solute induces electric polarization of the surrounding solvent, and the electric field generated by the polarized solvent, the reaction field, in turn perturbs the solute, leading to a modification of the charge distribution of the solute. This electrostatic problem of the mutual polarization between solute and solvent can be recast by using boundary conditions at the cavity surface, leading to significant simplifications in the associated equations.In the classical approaches, most work is concerned with describing the electrostatic contribution to the solvation in terms of the Poisson-Boltzmann equation (PBE) (13). Several different computational techniques for solving the PBE have been developed, for example, finite difference methods in which the dielectric property of the solvent is described in terms of a 3D grid around the solute (14-17) and boundary element methods i...

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Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. 1. Application to neutral molecules as models for polypeptides

Cited by 117 publications

References 0 publications

Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model

Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model

Interactions of Lipopolysaccharide and Polymyxin Studied by NMR Spectroscopy

A generalized G-SFED continuum solvation free energy calculation model

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