Molecular fragment electric moments derived from the fit of the experimental electrostatic potential. Application to the water molecule

Bouhmaida, Nouzha; Ghermani, Nour‐Eddine; Lecomte, Claude; Thalal, Abdelmalek

doi:10.1107/s0108767399000689

Cited by 21 publications

(23 citation statements)

References 21 publications

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“…Evidently, we can neglect these points comparing the relatively low electron densities at the CP position. The H … CP and O … CP distances are either close or slightly larger than those systematically observed for a large series of small peptides 11, i.e., from 0.28–0.71 Å for H … CP and from 1.02–1.35 Å for O … CP. From Table V, note that the parameters of the waterwater and zeolitewater HBs are close in all aspects, with the exception of the bond ellipticity, before and after optimization of the LiABW zeolite.…”

Section: Resultsmentioning

confidence: 44%

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Influence of hydrogen bonding on the properties of water molecules adsorbed in zeolite frameworks

Larin

Trubnikov

Vercauteren

2003

Int J of Quantum Chemistry

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Three hydrated aluminosilicate frameworks-LiABW, NaNAT, and BaEDI-are partly optimized with the periodic Hartree-Fock CRYSTAL95 code. In particular, we optimized the positions of the adsorbed water molecules including the positions of the framework cations (ABW, NAT) or part of the framework atomic positions (ABW). This allowed us to compare cation-water clusters in the gas and adsorbed states and discuss the influence of hydrogen bonding to the framework oxygen atoms or to the neighbor water molecules on the atomic properties (quadrupole coupling constant, anisotropy of electric field gradient) of the adsorbed water molecules. The LiBIK structure obtained from X-ray diffraction is also considered to illustrate the hydrogen bonds occurring between adsorbed water molecules.

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Section: Resultsmentioning

confidence: 44%

“…Surely, MMs can be interesting properties. MMs of H 2 O linked to small peptides or adsorbed in NaNAT zeolite have, for example, already been carefully analyzed 11. Such study revealed the variation of the H 2 O dipole as compared to the gas state with a nonzero dipole component in the direction perpendicular to the HOH plane.…”

Section: Introductionmentioning

confidence: 99%

Influence of hydrogen bonding on the properties of water molecules adsorbed in zeolite frameworks

Larin

Trubnikov

Vercauteren

2003

Int J of Quantum Chemistry

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“…The experimental electrostatic potentials were computed from the electron density at the refined geometry with ELECTROS (27) in two ways: first [electrostatic potential obtained directly from multipolar data base (TRF) (7)], using directly the charge density parameters transferred from the multipolar atoms database (7,28); and, second (MUL), using the parameters obtained from the preliminary multipole refinement of the protein main-chain atoms. The experimental potential of NADP ϩ was derived from the NAD ϩ charge density analysis reported previously (11).…”

Section: Methodsmentioning

confidence: 99%

Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations

Muzet

Guillot

Jelsch

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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106

109

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The electron density and electrostatic potential in an aldose reductase holoenzyme complex have been studied by density functional theory (DFT) and diffraction methods. Aldose reductase is involved in the reduction of glucose in the polyol pathway by using NADPH as a cofactor. The ultra-high resolution of the diffraction data and the low thermal-displacement parameters of the structure allow accurate atomic positions and an experimental charge density analysis. Based on the x-ray structural data, order-N DFT calculations have been performed on subsets of up to 711 atoms in the active site of the molecule. The charge density refinement of the protein was performed with the program MOPRO by using the transferability principle and our database of charge density parameters built from crystallographic analyses of peptides and amino acids. Electrostatic potentials calculated from the charge density database, the preliminary experimental electron density analysis, DFT computations, and atomic charges taken from the AMBER software dictionary are compared. The electrostatic complementarity between the cofactor NADP ؉ and the active site shows up clearly. The anchoring of the inhibitor is due mainly to hydrophobic forces and to only two polar interaction sites within the enzyme cavity. The potentials calculated by x-ray and DFT techniques agree reasonably well. At the present stage of the refinement, the potentials obtained directly from the database are in excellent agreement with the experimental ones. In addition, these results demonstrate the significant contribution of electron lone pairs and of atomic polarization effects to the host and guest mechanism.

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“…Since MESP is electron density derived quantity, its experimental determination is possible using X-ray crystallography. Lecomte et al have reported experimental techniques of determining MESP in molecular crystals [79][80][81][82]. The features of topography of three dimensional scalar field such as MED, MESP etc.…”

Section: Use Of Molecular Electrostatic Potential For Probing Lone Pamentioning

confidence: 98%

Understanding Lone Pair-π Interactions from Electrostatic Viewpoint

Gadre

Kumar

2015

Challenges and Advances in Computational Chemistry and Physics

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Over the last two decades, studies on lone pair-π interaction have attracted lot of attention of experimental as well as theoretical chemists due to its intriguing nature and its suspected presence in biological systems. The present Chapter begins with a brief overview of the earlier theoretical and experimental work done in this area. This is followed by exploration of the nuances of bonding in lone pair-π interaction, employing the tool of molecular electrostatic potential (MESP) since such weak interactions are mainly dominated by electrostatic features of host and guest molecules. The critical points associated with the scalar field of MESP are exploited for scrutinizing the directionality and bonding sites involved in the lone pair-π complexes. Furthermore, the electrostatic potential for intermolecular complexation (EPIC) model developed by Gadre et al., has been employed for finding out the electrostatically optimized structures and interaction energies of these complexes. The outcomes of EPIC model are compared with the results obtained from quantum chemical calculations of the complexes employing M06L/6-311++G(d,p) level of theory. The present study details out four different cases of lone pair-π complexes, which are currently in vogue. Hexafluorobenzene, one of the most explored π -deficient host in the present context, is initially taken up to demonstrate various facets of MESP for gaining insights into this interaction. This is followed by the scrutiny of special classes of recently synthesized highly π -deficient molecules, viz. tetraoxacalix [2]arene[2]triazine and naphthalenediimide, which are known to have specificity and large affinity, respectively, towards the electron rich species. The chapter ends with the description of lone pair-π interaction in the case of urate oxidase, an enzyme present in biological systems.

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Molecular fragment electric moments derived from the fit of the experimental electrostatic potential. Application to the water molecule

Cited by 21 publications

References 21 publications

Influence of hydrogen bonding on the properties of water molecules adsorbed in zeolite frameworks

Influence of hydrogen bonding on the properties of water molecules adsorbed in zeolite frameworks

Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations

Understanding Lone Pair-π Interactions from Electrostatic Viewpoint

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