Combination of the exact potential and multipole methods (EP/MM) for evaluation of intermolecular electrostatic interaction energies with pseudoatom representation of molecular electron densities

Volkov, and Anatoliy V.

doi:10.1016/s0009-2614(04)00667-0

Cited by 3 publications

(5 citation statements)

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“…Electrostatic interactions are evaluated with the exact potential/multipole moment (EPMM) method of Volkov et al 2,45 implemented in the XDPROP module of the XD package. The EPMM method combines numerical evaluation of the exact Coulomb integral for the short-range interactions between atoms within a certain limiting distance (here, taken as 4.5 Å) with the Buckinghamtype multipole approximation for the long-range interatomic interactions between atoms for which no charge density overlap occurs.…”

Section: Resultsmentioning

confidence: 99%

“…It was shown that the databank allows calculation of the electrostatic interaction energies of amino acid dimers with an accuracy of ∼3 kJ per mole. 2 Its merits relative to the experimental databank pioneered by Pichon-Pesme et al 3 have been the subject of a previous discussion. 4,5 In a more recent article, the databank has been used to evaluate the electrostatic component of the interaction between fragments of the antibiotic vancomycin and substrate molecules, with the nonelectrostatic contribution evaluated with perturbationtheory-based pairwise atom-atom potentials.…”

Section: Introductionmentioning

confidence: 99%

“…Usually, only element type and hybridization are taken into account to characterize any neighboring atom, except for neighboring sp 3 (2), where the number in parentheses represents the number of neighbors of the nitrogen atom. Hybridization states of neighboring atoms are derived solely from the number of attached atoms and, in the case of nitrogens, planarity of the group.…”

Section: Introductionmentioning

confidence: 99%

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A Theoretical Databank of Transferable Aspherical Atoms and Its Application to Electrostatic Interaction Energy Calculations of Macromolecules

Dominiak

Volkov

et al. 2006

J. Chem. Theory Comput.

151

175

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Abstract:A comprehensive version of the theoretical databank of transferable aspherical pseudoatoms is described, and its first application to protein-ligand interaction energies is discussed. The databank contains all atom types present in natural amino acid residues and other biologically relevant molecules. Each atom type results from averaging over a family of chemically unique pseudoatoms, taking into account both first and second neighbors. The spawning procedure is used to ensure that close transferability is obeyed. The databank is applied to the syntenin PDZ2 domain complexed with four-residue peptides and to the PDZ2 dimer. Analysis of the electrostatic interactions energies calculated by the exact-potential/multipolemoment-databank method stresses the importance of the P 0 and P -2 residues of the peptide in establishing the interaction, whereas the P -1 residue is shown to play a much smaller role. Unexpectedly, the charged P -3 residue contributes significantly to the interaction. The class I and II peptides are bound with the same strength by the syntenin PDZ2 domain, though the electrostatic interaction energy of the P -2 residue is smaller for class I peptides. There is no difference between the interaction energies of the peptides with PDZ2 domains from singledomain protein fragments and those from PDZ1-PDZ2 tandems.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A Theoretical Databank of Transferable Aspherical Atoms and Its Application to Electrostatic Interaction Energy Calculations of Macromolecules

Dominiak

Volkov

et al. 2006

J. Chem. Theory Comput.

151

175

View full text Add to dashboard Cite

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“…To obtain the electrostatic interaction energy ( E el ) between drug and receptor, the exact potential and multipole model (EPMM) [ 65 ] was applied, which allowed computation of E el between two molecular charge distributions represented within the Hansen–Coppens electron-density formalism [ 66 ]. It combines a numerical evaluation of the exact Coulomb integral for short-range interatomic interactions (less than 4.5 Å) with a Buckingham type multipole approximation for the long-range contacts.…”

Section: Methodsmentioning

confidence: 99%

Experimental and Computational Studies on Structure and Energetic Properties of Halogen Derivatives of 2-Deoxy-D-Glucose

Ziemniak

Zawadzka‐Kazimierczuk

Pawlędzio

et al. 2021

IJMS

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The results of structural studies on a series of halogen-substituted derivatives of 2-deoxy-D-glucose (2-DG) are reported. 2-DG is an inhibitor of glycolysis, a metabolic pathway crucial for cancer cell proliferation and viral replication in host cells, and interferes with D-glucose and D-mannose metabolism. Thus, 2-DG and its derivatives are considered as potential anticancer and antiviral drugs. X-ray crystallography shows that a halogen atom present at the C2 position in the pyranose ring does not significantly affect its conformation. However, it has a noticeable effect on the crystal structure. Fluorine derivatives exist as a dense 3D framework isostructural with the parent compound, while Cl- and I-derivatives form layered structures. Analysis of the Hirshfeld surface shows formation of hydrogen bonds involving the halogen, yet no indication for the existence of halogen bonds. Density functional theory (DFT) periodic calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings. NMR studies in the solution show that most of the compounds do not display significant differences in their anomeric equilibria, and that pyranose ring puckering is similar to the crystalline state. For 2-deoxy-2-fluoro-D-glucose (2-FG), electrostatic interaction energies between the ligand and protein for several existing structures of pyranose 2-oxidase were also computed. These interactions mostly involve acidic residues of the protein; single amino-acid substitutions have only a minor impact on binding. These studies provide a better understanding of the structural chemistry of halogen-substituted carbohydrates as well as their intermolecular interactions with proteins determining their distinct biological activity.

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“…Spackman recognized this [115], but the model was lacking the most important part of the penetration as later recognized [116]. Volkov [117] and Gavezzotti [118] proposed volume integration of the electron densities for the evaluation of the exact electrical potential. A combination of exact-potential at short atom-atom distances and multipole model at large atom-atom distances [119] has now become the standard.…”

Section: Fine and Coarse Grain Approaches For The Intermolecular Intementioning

confidence: 99%

Modern charge density studies: the entanglement of experiment and theory

Macchi

2013

Crystallography Reviews

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This tutorial review article is intended to provide a general guidance to a reader interested to learn about the methodologies to obtain accurate electron density mapping in molecules and crystalline solids, from theory or from experiment, and to carry out a sensible interpretation of the results, for chemical, biochemical or materials science applications. The review mainly focuses on X-ray diffraction techniques and refinement of experimental models, in particular multipolar models. Neutron diffraction, which was widely used in the past to fix accurate positions of atoms, is now used for more specific purposes. The review illustrates three principal analyses of the experimental or theoretical electron density, based on quantum chemical, semi-empirical or empirical interpretation schemes, such as the Quantum Theory of Atoms in Molecules, the semi-classical evaluation of interaction energies and the Hirshfeld analysis. In particular, it is shown that a simple topological analysis based on a partition of the electron density cannot alone reveal the whole nature of chemical bonding. More information based on the pair density is necessary. A connection between quantum mechanics and observable quantities is given in order to provide the physical grounds to explain the observations and to justify the interpretations.

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Combination of the exact potential and multipole methods (EP/MM) for evaluation of intermolecular electrostatic interaction energies with pseudoatom representation of molecular electron densities

Cited by 3 publications

References 0 publications

A Theoretical Databank of Transferable Aspherical Atoms and Its Application to Electrostatic Interaction Energy Calculations of Macromolecules

A Theoretical Databank of Transferable Aspherical Atoms and Its Application to Electrostatic Interaction Energy Calculations of Macromolecules

Experimental and Computational Studies on Structure and Energetic Properties of Halogen Derivatives of 2-Deoxy-D-Glucose

Modern charge density studies: the entanglement of experiment and theory

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