Distributed multipole analysis, or how to describe a molecular charge distribution

Stone, Anthony J.

doi:10.1016/0009-2614(81)85452-8

Cited by 1,019 publications

(590 citation statements)

References 8 publications

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“…The geometries with the lowest total energy are reported here. Electron distributions were calculated using a Distributed Multipole Analysis (DMA) [17] Mulliken populations [18] are employed to consider the bond-strengths.…”

Section: Computational Detailsmentioning

confidence: 99%

Ab initio calculations on various sialic acids provide valuable information about sialic acid-specific enzymes

Lenthe

Boer

Havenith

et al. 2004

Journal of Molecular Structure: THEOCHEM

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This study presents ab initio calculations on six sialic acid derivatives (N-acetylneuraminic acid, 2-deoxy-2,3-didehydro-Nacetylneuraminic acid, N-acetyl-4-O-acetylneuraminic acid, N-glycolylneuraminic acid, N-glycolyl-4-O-acetylneuraminic acid and N-acetyl-9-O-acetylneuraminic acid). The calculations were carried out using the GAMESS-UK-Program. Since the charge distribution of a ligand has an essential impact on the specific interaction with an enzyme or a receptor, the precise results of ab initio calculations lead to significant information concerning possible roles of the different functional groups occurring on sialic acids. In correlation to this, valuable conclusions about the activities of different sialic acid-specific enzymes, such as sialidases, trans-sialidases, lyases and O-acetyl-or O-methyltransferases can be drawn, since these activities strongly depend on the presence or absence of the various functional groups. q 2004 Published by Elsevier B.V.

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Section: Computational Detailsmentioning

confidence: 99%

Ab initio calculations on various sialic acids provide valuable information about sialic acid-specific enzymes

Lenthe

Boer

Havenith

et al. 2004

Journal of Molecular Structure: THEOCHEM

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“…The generation of the first library of fragment multicentered multipolar expansions are done using an adapted version of the DMA method 59,60 implemented in the GAMESS package. 68 The fragment input files to the GAMESS program are generated automatically manner by a program written by us, using as input the atomic coordinates of the refined protein structure in a PDB file format.…”

Section: Electrostatics In the Papain Catalytic Sitementioning

confidence: 99%

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25 (؊) …His159 (؉) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG3(His159)-ND1 direction; (ii) the electrostatic profile has a saddlepoint character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E SG3 ND1 attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator. Proteins 2003;52:236 -253.

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“…The electrostatic energy is calculated using the distributed multipolar expansion introduced by Stone [39,40], with the expansion carried out through octopoles. The expansion centers are taken to be the atom centers and the bond midpoints.…”

Section: Effective Fragment Potential Methodsmentioning

confidence: 99%

Coarse-Grained Intermolecular Potentials Derived From The Effective Fragment Potential: Application To Water, Benzene, And Carbon Tetrachloride

Pranami

Slipchenko

Lamm

et al. 2009

Challenges and Advances in Computational Chemistry and Physics

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Abstract:A force matching technique based on previous work by Voth and co-workers is developed and employed to coarse grain intermolecular potentials for three common solvents: carbon tetrachloride, benzene, and water. The accuracy of the force-matching approach is tested by comparing radial distribution functions (RDF) obtained from simulations using the atomistic and coarse-grained potentials. Atomistic molecular dynamics simulations were performed using the effective fragment potential method (EFP). The RDFs obtained from molecular dynamics simulations of EFPs for carbon tetrachloride, benzene and water are in a good agreement with the corresponding experimental data. The coarse-grained potentials reproduce the EFP molecular dynamics center-of-mass RDFs with reasonable accuracy. The biggest discrepancies are observed for benzene, while the coarse-graining of water and spherically symmetric carbon tetrachloride is of better quality

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Distributed multipole analysis, or how to describe a molecular charge distribution

Cited by 1,019 publications

References 8 publications

Ab initio calculations on various sialic acids provide valuable information about sialic acid-specific enzymes

Ab initio calculations on various sialic acids provide valuable information about sialic acid-specific enzymes

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

Coarse-Grained Intermolecular Potentials Derived From The Effective Fragment Potential: Application To Water, Benzene, And Carbon Tetrachloride

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