Literature DB >> 19621871

Polar coordinate representation of Hb(rc) versus (h2/8m)nabla2rhob(rc) at BCP in AIM analysis: classification and evaluation of weak to strong interactions.

Waro Nakanishi1, Satoko Hayashi, Kenji Narahara.   

Abstract

Polar coordinate (R, theta) representation is proposed for the plot of Hb(rc) versus (h2/8m)nabla2rhob(rc) in AIM analysis to classify, evaluate, and understand weak to strong interactions in a unified way and in more detail; Hb(rc) and nabla2rhob(rc) are total electron energy densities and the Laplacian of rhob(rc) at bond critical points (BCPs: rc), respectively, where rhob(rc) are electron densities at rc. Both the x- and y-axes of the plot are expressed in the common unit of energy since Hb(rc) = Gb(rc) + Vb(rc) and (h2/8m)nabla2rhob(rc) = Hb(rc) - Vb(rc)/2 (= Gb(rc) + Vb(rc)/2), where Gb(rc) and Vb(rc) are kinetic energy densities and potential energy densities, respectively. Data employed for the plot are calculated at BCPs for full-optimized structures and optimized structures with the fixed distances (r) of r = r(o) + wa(o), where r(o) are the full-optimized distances, a(o) is the Bohr radius, and w = +/-0.1 and +/-0.2. The plot draws a helical stream starting from near origin (Hb(rc) = (h2/8m)nabla2rhob(rc) = 0) for very weak interactions and turns to the right as interactions become stronger. The helical stream is well described by the polar coordinate representation with (R, theta); R is given in the energy unit, and theta in degrees is measured from the y-axis. The ratio of Vb(rc)/Gb(rc) (= k) controls theta, of which an acceptable range in the plot is 45.0 < theta < 206.6 degrees. Each plot for an interaction gives a curve, which supplies important information. It is expressed by theta(p) and kappa(p); theta(p) corresponds to the tangent line measured from the y-direction, and kappa(p) is the curvature of the plot at w = 0. The polar coordinate (R, theta) representation with (theta(p), kappa(p)) helps us to classify, evaluate, and understand the nature of weak to strong interactions in a unified way.

Entities:  

Year:  2009        PMID: 19621871     DOI: 10.1021/jp903622a

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  15 in total

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Authors:  Daniel Hernández-Valdés; Zalua Rodríguez-Riera; Alicia Díaz-García; Eric Benoist; Ulises Jáuregui-Haza
Journal:  J Mol Model       Date:  2016-07-12       Impact factor: 1.810

2.  A computational study of the inclusion of β-cyclodextrin and nicotinic acid: DFT, DFT-D, NPA, NBO, QTAIM, and NCI-RDG studies.

Authors:  Houdhaifa R Belhouchet; Tahar Abbaz; Amel Bendjedou; Abdelkrim Gouasmia; Didier Villemin
Journal:  J Mol Model       Date:  2022-10-08       Impact factor: 2.172

3.  Structures and stabilities of naturally occurring cyclodextrins: a theoretical study of symmetrical conformers.

Authors:  Juan José Gamboa-Carballo; Vijay Kumar Rana; Joëlle Levalois-Grützmacher; Sarra Gaspard; Ulises Jáuregui-Haza
Journal:  J Mol Model       Date:  2017-10-20       Impact factor: 1.810

4.  Bonding, structural and thermodynamic analysis of dissociative adsorption of H3O+ ion onto calcite (101⁻4) surface: CPMD and DFT calculations.

Authors:  Mohammad Hadi Ghatee; Mohammad Mehdi Koleini
Journal:  J Mol Model       Date:  2017-11-06       Impact factor: 1.810

5.  Intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs and its behavior, elucidated with QTAIM dual functional analysis and QC calculations.

Authors:  Waro Nakanishi; Satoko Hayashi; Taro Nishide
Journal:  RSC Adv       Date:  2020-07-01       Impact factor: 3.361

6.  Intrinsic Dynamic Nature of Neutral Hydrogen Bonds Elucidated with QTAIM Dual Functional Analysis: Role of the Compliance Force Constants and QTAIM-DFA Parameters in Stability.

Authors:  Taro Nishide; Satoko Hayashi; Waro Nakanishi
Journal:  ChemistryOpen       Date:  2018-06-06       Impact factor: 2.911

7.  Behavior of the E-E' Bonds (E, E' = S and Se) in Glutathione Disulfide and Derivatives Elucidated by Quantum Chemical Calculations with the Quantum Theory of Atoms-in-Molecules Approach.

Authors:  Satoko Hayashi; Yutaka Tsubomoto; Waro Nakanishi
Journal:  Molecules       Date:  2018-02-17       Impact factor: 4.411

8.  Linear Multiselenium Interactions in Dicationic Oligomers of 1,5-(Diselena)canes: Behavior of Semc σ(mc c-ne e) (6≤mc ≤16) Elucidated with QTAIM Dual Functional Analysis.

Authors:  Satoko Hayashi; Taro Nishide; Kengo Nagata; Waro Nakanishi
Journal:  ChemistryOpen       Date:  2021-05-02       Impact factor: 2.630

9.  Intrinsic Dynamic and Static Nature of π···π Interactions in Fused Benzene-Type Helicenes and Dimers, Elucidated with QTAIM Dual Functional Analysis.

Authors:  Taro Nishide; Satoko Hayashi
Journal:  Nanomaterials (Basel)       Date:  2022-01-19       Impact factor: 5.076

10.  Intrinsic Dynamic and Static Nature of Halogen Bonding in Neutral Polybromine Clusters, with the Structural Feature Elucidated by QTAIM Dual-Functional Analysis and MO Calculations.

Authors:  Satoko Hayashi; Taro Nishide; Eiichiro Tanaka; Waro Nakanishi
Journal:  Molecules       Date:  2021-05-14       Impact factor: 4.411

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