Intermolecular interactions: Elaboration on an additive procedure including an explicit charge‐transfer contribution

Gresh, Nohad; Claverie, P.; Pullman, Alberte

doi:10.1002/qua.560290110

Cited by 100 publications

(129 citation statements)

References 26 publications

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“…This is analogous to the charge-transfer interaction first described by Murrel, 146 which was later modeled empirically with force fields, 147 and which is now also one of the contributions in the SIBFA model. 148 When the dissociated fragments are not neutral, a trivial Coulomb term is also present.…”

Section: Dissociation In Acks2mentioning

confidence: 70%

ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order

Verstraelen

Ayers

Speybroeck

et al. 2013

The Journal of Chemical Physics

135

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Section: Dissociation In Acks2mentioning

confidence: 70%

ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order

Verstraelen

Ayers

Speybroeck

et al. 2013

The Journal of Chemical Physics

135

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“…However, even considering a single static configuration, our results cannot be considered as quantitative ones because our methodological approach does not include inter-fragment polarization effects (only a local correction is introduced by the OME reassociation method in the important peptide junction region). A methodology that incorporates inter-fragment polarization effects 69,[81][82][83] and a correction for the charge penetration effect 84 is under development. These improvements are especially important to avoid significant errors when evaluating the internal ion pair energy and also when evaluating the ion pair interaction with the surrounding protein residues and water molecules.…”

Section: Discussionmentioning

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 proposed proportionality of the intermolecular induction energy is inspired by the exponentially decaying nature of charge transfer. 23,32,[69][70][71][72][73] More specifically, the proportionality between exchange-repulsion and the charge-transfer interaction has been demonstrated in the context of SAPT. 74 We expect that this assumption will work fairly well for dispersion-dominated complexes, where the induction energy is dominated by contributions from charge-transfer effects because classical polarization plays a minor role in such complexes.…”

Section: Inductionmentioning

confidence: 98%

The Monomer Electron Density Force Field (MEDFF): A Physically Inspired Model for Noncovalent Interactions

Vandenbrande

Waroquier

Speybroeck

et al. 2016

J. Chem. Theory Comput.

112

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We propose a methodology to derive pairwise-additive non-covalent force fields from monomer electron densities without any empirical input. Energy expressions are based on the Symmetry-Adapted Perturbation Theory (SAPT) decomposition of interaction energies. This ensures a physically motivated force field featuring an electrostatic, exchange-repulsion, dispersion and induction contribution, which contain two types of parameters. First, each contribution depends on several fixed atomic parameters, resulting from a partitioning of the monomer electron density. Second, each of the last three contributions (exchange-repulsion, dispersion and induction) contains exactly one linear fitting parameter. These three so-called interaction parameters in the model, are initially estimated separately using SAPT reference calculations for the S66x8 database of non-covalent dimers. In a second step, the three interaction parameters are further refined simultaneously to reproduce CCSD(T)/CBS interaction energies for the same database. The limited number of parameters that are fitted to 1 dimer interaction energies (only three), avoids ill-conditioned fits that plague conventional parameter optimizations.For the exchange-repulsion and dispersion component, good results are obtained for all dimers in the S66x8 database using one single value for the associated interaction parameters. The values of those parameters can be considered universal and can also be used for dimers not present in the original database used for fitting. For the induction component such an approach is only viable for the dispersion-dominated dimers in the S66x8 database. For other dimers (such as hydrogen-bonded complexes), we show that our methodology remains applicable. However the interaction parameter needs to be determined on a case-specific basis.As an external validation, the force field predicts interaction energies in good agreement with CCSD(T)/CBS values for dispersion-dominated dimers extracted from an HIV-II protease crystal structure with a bound ligand (indinavir). Furthermore, experimental second virial coefficients of small alkanes and alkenes are well reproduced.

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Intermolecular interactions: Elaboration on an additive procedure including an explicit charge‐transfer contribution

Cited by 100 publications

References 26 publications

ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order

ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order

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

The Monomer Electron Density Force Field (MEDFF): A Physically Inspired Model for Noncovalent Interactions

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