Dependence of the Intermolecular Electrostatic Interaction Energy on the Level of Theory and the Basis Set

Volkov, Anatoliy; King, Harry F.; Coppens, Philip

doi:10.1021/ct050216x

Cited by 42 publications

(53 citation statements)

References 62 publications

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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%

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.

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152

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%

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.

Self Cite

152

175

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“…The MP2 calculations were performed with the Gaussian 03 package 27 using augmented correlation-consistent polarized valence basis sets of double ζ quality (aug-cc-pVDZ). 28 This basis set has been shown to yield accurate molecular electrostatic interaction energies 29 and charge transfer estimates compared with experiment. 30 The total energy was converged to a precision of 10 -8 Hartrees.…”

Section: B Electronic Structure Calculationsmentioning

confidence: 99%

“…32 We chose the aug-cc-pvdz basis set 28 for both efficiency and high quality results. 29,30 There exists a variety of methods available for estimating atomic charges and dipoles from the electron density. One approach is to obtain effective charges from the Electrostatic Potential (ESP) by fitting charges (and perhaps point dipoles) to match the ESP computed at the quantum level; points within the van der Waals radii of the atoms in the molecule or cluster are excluded from the fit.…”

Section: B Electronic Structure Calculationsmentioning

confidence: 99%

Polarization and charge transfer in the hydration of chloride ions

Zhao

Rogers

Beck

2010

The Journal of Chemical Physics

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A theoretical study of the structural and electronic properties of the chloride ion and water molecules in the first hydration shell is presented. The calculations are performed on an ensemble of configurations obtained from molecular dynamics simulations of a single chloride ion in bulk water. The simulations utilize the polarizable AMOEBA force field for trajectory generation, and MP2-level calculations are performed to examine the electronic structure properties of the ions and surrounding waters in the external field of more distant waters. The ChelpG method is employed to explore the effective charges and dipoles on the chloride ions and first-shell waters. The Quantum Theory of Atoms in Molecules (QTAIM) is further utilized to examine charge transfer from the anion to surrounding water molecules. The clusters extracted from the AMOEBA simulations exhibit high probabilities of anisotropic solvation for chloride ions in bulk water. From the QTAIM analysis, 0.2 elementary charges are transferred from the ion to the first-shell water molecules. The default AMOEBA model overestimates the average dipole moment magnitude of the ion compared with the estimated quantum mechanical value. The average magnitude of the dipole moment of the water molecules in the first shell treated at the MP2 level, with the more distant waters handled with an AMOEBA effective charge model, is 2.67 D. This value is close to the AMOEBA result for first-shell waters (2.72 D) and is slightly reduced from the bulk AMOEBA value (2.78 D). The magnitude of the dipole moment of the water molecules in the first solvation shell is most strongly affected by the local water-water interactions and hydrogen bonds with the second solvation shell, rather than by interactions with the ion.

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“…No cerne da química atômico--molecular, as interações consideradas fracas com características puramente eletrostáticas são as mais importantes, pois os sistemas são interpretados como sendo ligados 6,7 e não covalentes, 8,9 e nestas circunstâncias átomos formam as ligações químicas 10 e moléculas atingem condições eletrônicas propícias para formarem estruturas intermoleculares estáveis. 11 Na natureza há uma imensidade de sistemas estabilizados intermolecularmente, destes aqueles contendo regiões com altas densidades eletrônicas (pares de elétrons não compartilhados, [12][13][14] elétrons π, [15][16][17] ou hidretos [18][19][20][21] representados por Y -δ na ligação X-Y -δ ) são atraídos por espécies doadoras de prótons (ácidos de Lewis 22,23 simbolizados por H …”

Section: Introductionunclassified

SAPT: ligação de hidrogênio ou interação de van der Waals?

Oliveira¹,

Araújo²

2012

Quím. Nova

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Recebido em 24/11/11; aceito em 27/6/12; publicado na web em 17/9/12 SAPT: HYDROGEN BOND OR van der WAALS INTERACTION? It is through the application of an electronic partition approach called Symmetry-Adapted Perturbation Theory (SAPT) that the nature of hydrogen bonds and van der Waals interactions can be unveiled according to the contribution of electrostatic, charge transfer, exchange repulsion, polarization, and dispersion terms. Among these, electrostatic partition governs the formation of the hydrogen bonds, whose energies are arguably high. However, the weakness of the interaction strength is caused by dispersion forces, whose contribution decisively lead to the stabilization of complexes formed via van der Waals interactions. Keywords: hydrogen bonds; van der Waals interactions; SAPT. INTRODUÇÃOFisicamente, as interações fortes, fracas, eletromagnéticas e gravitacionais governam o contato entre as partículas.1 Destas, é bem estabelecido pela cromodinâmica quântica que as interações fortes ocorrem entre prótons e nêutrons através da ação dos quarks e glúons, 2 cujo resultado é a formação do núcleo atômico denso e compacto. Presente em nível nuclear, as interações fracas são 10 13 menos intensas e são caracterizadas pelas manifestações dos bósons W (Weak nuclear force) e Z (Zero).3 Interações eletromagnéticas são típicas de partículas elementares carregadas 4 e são 10 2 mais fracas em relação às interações fortes. Por fim, a geometrodinâmica estabelece que as interações gravitacionais são 10 42 mais amenas e estão presentes em sistemas com massas macroscopicamente mensuráveis, 5 como estrelas, galáxias e todo o universo. No cerne da química atômico--molecular, as interações consideradas fracas com características puramente eletrostáticas são as mais importantes, pois os sistemas são interpretados como sendo ligados 6,7 e não covalentes, 8,9 e nestas circunstâncias átomos formam as ligações químicas 10 e moléculas atingem condições eletrônicas propícias para formarem estruturas intermoleculares estáveis. As interações intituladas de van der Waals foram assim concebidas em reconhecimento ao físico neerlândes Johannes Diederik van der Waals pelos seus estudos com substâncias gasosas e líquidas, em uma proposta que objetivava a otimização dos modelos de Boyle e Charles 54 através da descrição do tamanho molecular e a força intermolecular atuante, a qual é composta pelas contribuições de Keesom (interação entre dipolo permanente--dipolo permanente), 55 Debye (interação entre dipolo permanente--dipolo induzido) 56 e London (interação entre dipolo induzido-dipolo induzido). 57 As interações de van der Waals têm sido foco de muitos pesquisas, principalmente no aprimoramento de alguns métodos que falham na captura dos efeitos provenientes das forças de dispersão. 58As ligações de hidrogênio ou interações de van der Waals são, de fato, alicerces de suma importância para a Biologia, Medicina, Química, Engenharia, Física 59 e áreas correlatas. Entretanto, dentro da comunidade científica ainda persiste um intenso deba...

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Dependence of the Intermolecular Electrostatic Interaction Energy on the Level of Theory and the Basis Set

Cited by 42 publications

References 62 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

Polarization and charge transfer in the hydration of chloride ions

SAPT: ligação de hidrogênio ou interação de van der Waals?

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