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      Interaction of Cysteine with Li + and LiF in the Presence of (H 2O) n ( n = 0–6) Clusters

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      ACS Omega
      American Chemical Society

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          Abstract

          The interaction between cysteine with Li + and LiF in the microcosmic water environment was investigated to elucidate how ions interact with amino acids and the cation–anion correlation effect involved. The structures of Cys·Li +(H 2O) n and Cys·LiF(H 2O) n ( n = 0–6) were characterized using ab initio calculations. Our studies show that the water preferentially interacts with Li +/LiF. In Cys·Li +(H 2O) 0–6, Li + interacts with amino nitrogen, carbonyl oxygen, and hydrophobic sulfur of Cys to form a tridentate mode, whereas in Cys·LiF(H 2O) n , Li + and F work in cooperation and interact with carbonyl oxygen and hydroxyl hydrogen of Cys to form a bidentate type. The neutral and zwitterionic forms are essentially isoenergetic when the water number reaches three in the presence of Li +, whereas this occurs at four water molecules in the presence of LiF. Further research revealed that the interaction between Li +/LiF and Cys was mainly electrostatic, followed by dispersion, and the weakest interaction occurs at the transition from the neutral form to zwitterionic form. Natural population analysis charge analyses show that for Cys·Li +(H 2O) n , the positive charge is mostly concentrated on Li + except for the system containing three water molecules. For Cys·LiF(H 2O) n , the positive charge is centered on the LiF unit in the range n = 0–6, and at n = 5, electron transfer from Cys to water occurs. Our study shows that the contribution of anions in zwitterionic state stabilization should be addressed more generally along with cations.

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          A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.

          The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
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            Multiwfn: a multifunctional wavefunction analyzer.

            Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com. Copyright © 2011 Wiley Periodicals, Inc.
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              Revealing noncovalent interactions.

              Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
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                Author and article information

                Journal
                ACS Omega
                ACS Omega
                ao
                acsodf
                ACS Omega
                American Chemical Society
                2470-1343
                27 May 2022
                07 June 2022
                : 7
                : 22
                : 18646-18659
                Affiliations
                School of Environmental and Chemical Engineering, Xi’an Polytechnic University , Xi’an 710048, PR China
                Author notes
                Author information
                https://orcid.org/0000-0003-0462-6919
                Article
                10.1021/acsomega.2c01315
                9178773
                7f97e307-68a9-4e44-86fe-2cefa8570351
                © 2022 The Authors. Published by American Chemical Society

                Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works ( https://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 04 March 2022
                : 19 May 2022
                Funding
                Funded by: Natural Science Foundation of Shaanxi Province, doi 10.13039/501100007128;
                Award ID: 2019JM-292
                Categories
                Article
                Custom metadata
                ao2c01315
                ao2c01315

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