A simple and efficient dispersion correction to the Hartree–Fock theory

Yoshida, Tatsusada; Mashima, Akira; Sasahara, Katsunori; Chuman, Hiroshi

doi:10.1016/j.bmcl.2014.01.020

Cited by 6 publications

(3 citation statements)

References 41 publications

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“…The primary focus of a study of the complexes of benzene with H 2 S and DMS was density functional and semiempirical methods incorporating corrections for the dispersion energy that can be an important component of weak intermolecular interactions. , Two configurations for the benzene/DMS complex were examined using MP2/aug-cc-pVDZ calculations. The configuration in which the DMS is above the plane of the benzene ring with the sulfur directed away from the ring face (Figure A) was about 1.8 kcal/mol more stable than the second complex structure.…”

Section: Computational Studies Of Sulfur···aromatic Model Systemsmentioning

confidence: 99%

A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design

et al. 2015

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Electron deficient, bivalent sulfur atoms have two areas of positive electrostatic potential, a consequence of the low-lying σ* orbitals of the C-S bond that are available for interaction with electron donors including oxygen and nitrogen atoms and, possibly, π-systems. Intramolecular interactions are by far the most common manifestation of this effect, which offers a means of modulating the conformational preferences of a molecule. Although a well-documented phenomenon, a priori applications in drug design are relatively sparse and this interaction, which is often isosteric with an intramolecular hydrogen-bonding interaction, appears to be underappreciated by the medicinal chemistry community. In this Perspective, we discuss the theoretical basis for sulfur σ* orbital interactions and illustrate their importance in the context of drug design and organic synthesis. The role of sulfur interactions in protein structure and function is discussed and although relatively rare, intermolecular interactions between ligand C-S σ* orbitals and proteins are illustrated.

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Section: Computational Studies Of Sulfur···aromatic Model Systemsmentioning

confidence: 99%

A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design

et al. 2015

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“…88 A detailed description of how to treat ion blocks in the FMO calculations is shown in Fig. † In order to obtain the dispersion interaction energy E disp , all the HF energies were corrected for dispersion forces using Grimme's dispersion correction scheme D3, 76,[89][90][91] which is computationally inexpensive but can reasonably account for E disp . † In order to obtain the dispersion interaction energy E disp , all the HF energies were corrected for dispersion forces using Grimme's dispersion correction scheme D3, 76,[89][90][91] which is computationally inexpensive but can reasonably account for E disp .…”

Section: Formulation Of the Lere-qsar Equationmentioning

confidence: 99%

“…S1. † In order to obtain the dispersion interaction energy E disp , all the HF energies were corrected for dispersion forces using Grimme's dispersion correction scheme D3, 76,[89][90][91] which is computationally inexpensive but can reasonably account for E disp . 92,93 The polar solvation free-energy change ΔG polar sol was calculated with the continuum solvation model based on the generalized Born (GB) approximation.…”

Section: Calculation Of Representative Energy Termsmentioning

confidence: 99%

A QSAR study on the inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs based on molecular orbital calculations

2015

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A binding mechanism between human matrix metalloproteinase-12 (MMP-12) and eight arylsulfone analogs having two types of carboxylic and hydroxamic acids as the most representative zinc binding group is investigated using a quantitative structure-activity relationship (QSAR) analysis based on a linear expression by representative energy terms (LERE). The LERE-QSAR analysis quantitatively reveals that the variation in the observed (experimental) inhibitory potency among the arylsulfone analogs is decisively governed by those in the intrinsic binding and dispersion interaction energies. The results show that the LERE-QSAR analysis not only can excellently reproduce the observed overall free-energy change but also can determine the contributions of representative free-energy changes. An inter-fragment interaction energy difference (IFIED) analysis based on the fragment molecular orbital (FMO) method (FMO-IFIED) leads to the identification of key residues governing the variation in the inhibitory potency as well as to the understanding of the difference between the interactions of the carboxylic and hydroxamic acid zinc binding groups. The current results that have led to the optimization of the inhibitory potency of arylsulfone analogs toward MMP-12 to be used in the treatment of chronic obstructive pulmonary disease may be useful for the development of a new potent MMP-12 inhibitor.

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