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Sifuna D, Omwoma S, Lagat S, Okello F, Nelson FA, Pembere A. Theory guided engineering of zeolite adsorbents for acaricide residue adsorption from the environment. J Mol Model 2024; 30:208. [PMID: 38877313 DOI: 10.1007/s00894-024-06004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024]
Abstract
CONTEXT Zeolites have attracted attention for their potential in adsorbing environmental contaminants. However, contaminants, such as acaricides used extensively in livestock production to control ticks and mites, have received limited exploration regarding their adsorption onto zeolite surfaces. This study aimed to identify the most appropriate zeolite frameworks for the adsorption of acaricide residues, deduce the mechanism underlying the adsorption process, and evaluate the impact of surface modification on the adsorption capabilities of zeolites. METHODS Grand Canonical Monte Carlo (GCMC) was used to screen the entire zeolite database to analyze their adsorption properties, where the cloverite zeolite framework (CLO) exhibits the highest adsorption capacity (percentage weight, 54%). Machine learning was employed to rank structural feature importance on adsorption. Density and helium void fraction appeared to be the most important structural features. Thus, engineering these features is of utmost significance in harvesting the desired acaricides. The second step involved engineering the structural and electronic properties of the shortlisted zeolite frameworks via cation substitution with suitable atoms. DFT calculations involving natural bond orbital (NBO) analysis and quantum theory of atoms in molecules (QTAIM) have been done to understand the influence of cation substitution on the electronic structure.
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Affiliation(s)
- Douglas Sifuna
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo (Main) Campus, P.O. Box 210-40601, Bondo, Kenya
| | - Solomon Omwoma
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo (Main) Campus, P.O. Box 210-40601, Bondo, Kenya
| | - Silas Lagat
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo (Main) Campus, P.O. Box 210-40601, Bondo, Kenya
| | - Felix Okello
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo (Main) Campus, P.O. Box 210-40601, Bondo, Kenya
| | - Favour A Nelson
- Department of Pure and Applied Chemistry, University of Calabar, Calabar, Nigeria
| | - Anthony Pembere
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo (Main) Campus, P.O. Box 210-40601, Bondo, Kenya.
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2
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Cellupica E, Gaiassi A, Rocchio I, Rovelli G, Pomarico R, Sandrone G, Caprini G, Cordella P, Cukier C, Fossati G, Marchini M, Bebel A, Airoldi C, Palmioli A, Stevenazzi A, Steinkühler C, Vergani B. Mechanistic and Structural Insights on Difluoromethyl-1,3,4-oxadiazole Inhibitors of HDAC6. Int J Mol Sci 2024; 25:5885. [PMID: 38892072 PMCID: PMC11172862 DOI: 10.3390/ijms25115885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Histone deacetylase 6 (HDAC6) is increasingly recognized for its potential in targeted disease therapy. This study delves into the mechanistic and structural nuances of HDAC6 inhibition by difluoromethyl-1,3,4-oxadiazole (DFMO) derivatives, a class of non-hydroxamic inhibitors with remarkable selectivity and potency. Employing a combination of nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) kinetic experiments, comprehensive enzymatic characterizations, and X-ray crystallography, we dissect the intricate details of the DFMO-HDAC6 interaction dynamics. More specifically, we find that the chemical structure of a DMFO and the binding mode of its difluoroacetylhydrazide derivative are crucial in determining the predominant hydrolysis mechanism. Our findings provide additional insights into two different mechanisms of DFMO hydrolysis, thus contributing to a better understanding of the HDAC6 inhibition by oxadiazoles in disease modulation and therapeutic intervention.
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Affiliation(s)
- Edoardo Cellupica
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Aureliano Gaiassi
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Ilaria Rocchio
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Grazia Rovelli
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Roberta Pomarico
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Giovanni Sandrone
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Gianluca Caprini
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Paola Cordella
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Cyprian Cukier
- Department of Biochemistry, Selvita S.A., 30-394 Kraków, Poland; (C.C.); (A.B.)
| | - Gianluca Fossati
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Mattia Marchini
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Aleksandra Bebel
- Department of Biochemistry, Selvita S.A., 30-394 Kraków, Poland; (C.C.); (A.B.)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (C.A.); (A.P.)
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (C.A.); (A.P.)
| | - Andrea Stevenazzi
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Christian Steinkühler
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Barbara Vergani
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
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3
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Bregado JL, Secchi AR, Tavares FW. A density functional theory study on interactions in water-bridged dimeric complexes of lignin. Phys Chem Chem Phys 2024; 26:9234-9252. [PMID: 38444363 DOI: 10.1039/d4cp00312h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Lignin is the main plant cell wall component responsible for recalcitrance in the process of lignocellulosic biomass conversion into biofuels. The recalcitrance and insolubility of lignin in different reaction media are due in part to the hydrogen bonds and π interactions that hold syringyl (S) and guaiacyl (G) units together and promote the formation of stable water-bridged dimeric complexes (WBDCs): S⋯G and S⋯S, in native lignin. The current understanding of how each type of interaction influences the stability of these complexes within lignin native cell walls is still limited. Here, we found by DFT calculations that hydrogen bonding is more dominant than π-stacking interaction between aromatic rings of WBDCs. Although there is a stronger interaction of hydrogen bonds between subunits and water and higher π-stacking interaction in the S⋯S complex compared to the S⋯G complex, the former complex is less thermodynamically stable than the latter due to the entropic contribution coming from the methoxy substituents in the S-unit. Our results demonstrate that the methoxylation degree of lignin units does not significantly influence the structural geometries of WBDCs; if anything, an enhanced dispersion interaction between ring aromatics results in quasi-sandwich geometries as found in "coiled" lignin structures in the xylem tissue of wood. In the same way as that with ionic liquids, polar solvents can dissolve S-lignin by favorable interactions with the aliphatic hydroxyl group in the α-position as the key site or the aromatic hydroxyl group as the secondary site.
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Affiliation(s)
- Jurgen Lange Bregado
- Chemical Engineering Program, COPPE, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-914, Brazil.
| | - Argimiro R Secchi
- Chemical Engineering Program, COPPE, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-914, Brazil.
- Chemical and Biochemical Process Engineering Program, Escola de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-909, Brazil
| | - Frederico W Tavares
- Chemical Engineering Program, COPPE, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-914, Brazil.
- Chemical and Biochemical Process Engineering Program, Escola de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-909, Brazil
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4
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Azougagh O, Jilal I, Jabir L, El-Hammi H, Essayeh S, Mohammed N, Achalhi N, El Yousfi R, El Idrissi A, El Ouardi Y, Laatikainen K, Abou-Salama M, El Barkany S. Dissolution mechanism of cellulose in a benzyltriethylammonium/urea deep eutectic solvent (DES): DFT-quantum modeling, molecular dynamics and experimental investigation. Phys Chem Chem Phys 2023; 25:22870-22888. [PMID: 37587837 DOI: 10.1039/d3cp02335d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
In this paper, a benzyltriethylammonium/urea DES was investigated as a new green and eco-friendly medium for the progress of organic chemical reactions, particularly the dissolution and the functionalization of cellulose. In this regard, the viscosity-average molecular weight of cellulose (M̄w) during the dissolution/regeneration process was investigated, showing no significant degradation of the polymer chains. Moreover, X-ray diffraction patterns indicated that the cellulose dissolution process in the BTEAB/urea DES decreased the crystallinity index from 87% to 75%, and there was no effect on type I cellulose polymorphism. However, a drastic impact of the cosolvents (water and DMSO) on the melting point of the DES was observed. Besides, to understand the evolution of cellulose-DES interactions, the formation mechanism of the system was studied in terms of H-bond density and radial distribution function (RDF) using molecular dynamics modeling. Furthermore, density functional theory (DFT) was used to evaluate the topological characteristics of the polymeric system such as potential energy density (PED), laplacian electron density (LED), energy density, and kinetic energy density (KED) at bond critical points (BCPs) between the cellulose and the DES. The quantum theory of atoms in molecules (AIM), Bader's quantum theory (BQT), and reduced density gradient (RDG) scatter plots have been exploited to estimate and locate non-covalent interactions (NCIs). The results revealed that the dissolution process is attributed to the physical interactions, mainly the strong H-bond interactions.
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Affiliation(s)
- Omar Azougagh
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Issam Jilal
- LIMOME Laboratory, Dhar El Mehraz Faculty of Sciences, Sidi Mohamed Ben Abdellah University, B.P. 1796 Atlas, Fes 30000, Morocco
| | - Loubna Jabir
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Hayat El-Hammi
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Soumya Essayeh
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Nor Mohammed
- Applied Chemistry Unit, Sciences and Technologies Faculty, Abdelmalek Essaadi University, 32 003 Al Hoceima, Morocco
| | - Nafea Achalhi
- Laboratory Applied Chemistry and Environmental (LCAE-URAC18), Faculty of Sciences of Oujda, Mohammed 1st University, 60000 Oujda, Morocco
| | - Ridouan El Yousfi
- Laboratory Applied Chemistry and Environmental (LCAE-URAC18), Faculty of Sciences of Oujda, Mohammed 1st University, 60000 Oujda, Morocco
| | - Abderrahmane El Idrissi
- Laboratory Applied Chemistry and Environmental (LCAE-URAC18), Faculty of Sciences of Oujda, Mohammed 1st University, 60000 Oujda, Morocco
| | - Youssef El Ouardi
- LIMOME Laboratory, Dhar El Mehraz Faculty of Sciences, Sidi Mohamed Ben Abdellah University, B.P. 1796 Atlas, Fes 30000, Morocco
- Laboratory of Separation Technology, Lappeenranta University of Technology, P.O. Box 20, FI-53851 Lappeenranta, Finland
| | - Katri Laatikainen
- Laboratory of Separation Technology, Lappeenranta University of Technology, P.O. Box 20, FI-53851 Lappeenranta, Finland
| | - Mohamed Abou-Salama
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Soufian El Barkany
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
- Applied Chemistry Unit, Sciences and Technologies Faculty, Abdelmalek Essaadi University, 32 003 Al Hoceima, Morocco
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. Methylammonium Tetrel Halide Perovskite Ion Pairs and Their Dimers: The Interplay between the Hydrogen-, Pnictogen- and Tetrel-Bonding Interactions. Int J Mol Sci 2023; 24:10554. [PMID: 37445738 DOI: 10.3390/ijms241310554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The structural stability of the extensively studied organic-inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX3 (MA = CH3NH3+; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an organic cation (CH3NH3+) and an inorganic anion (TtX3-). However, the basic understanding of the underlying chemical bonding interactions in these systems that link the ionic moieties together in complex configurations is still limited. In this study, ion pair models constituting the organic and inorganic ions were regarded as the repeating units of periodic crystal systems and density functional theory simulations were performed to elucidate the nature of the non-covalent interactions between them. It is demonstrated that not only the charge-assisted N-H···X and C-H···X hydrogen bonds but also the C-N···X pnictogen bonds interact to stabilize the ion pairs and to define their geometries in the gas phase. Similar interactions are also responsible for the formation of crystalline MATtX3 in the low-temperature phase, some of which have been delineated in previous studies. In contrast, the Tt···X tetrel bonding interactions, which are hidden as coordinate bonds in the crystals, play a vital role in holding the inorganic anionic moieties (TtX3-) together. We have demonstrated that each Tt in each [CH3NH3+•TtX3-] ion pair has the capacity to donate three tetrel (σ-hole) bonds to the halides of three nearest neighbor TtX3- units, thus causing the emergence of an infinite array of 3D TtX64- octahedra in the crystalline phase. The TtX44- octahedra are corner-shared to form cage-like inorganic frameworks that host the organic cation, leading to the formation of functional tetrel halide perovskite materials that have outstanding optoelectronic properties in the solid state. We harnessed the results using the quantum theory of atoms in molecules, natural bond orbital, molecular electrostatic surface potential and independent gradient models to validate these conclusions.
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Affiliation(s)
- Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- School of Chemistry, Molecular Sciences Institute, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
| | - Helder M Marques
- School of Chemistry, Molecular Sciences Institute, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
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Chérif I, Raissi H, Abiedh K, Gassoumi B, Caccamo MT, Magazu S, Said AH, Hassen F, Boubaker T, Ayachi S. Exploration of intramolecular charge transfer in para-substituted nitrobenzofurazan: Experimental and theoretical analyses. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 301:122939. [PMID: 37285745 DOI: 10.1016/j.saa.2023.122939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/09/2023]
Abstract
The present work aims at exploring the high electrophilic character of 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) toward the morpholine group by an SNAr reaction in acetonitrile or water (thereafter referred to as NBD-Morph). The electron-donating ability of the morpholine causes intra-molecular charge transfer (ICT). In this report, we present a comprehensive study on the optical characteristics using UV-Vis, photoluminescence (cw-PL) and its time-resolved (TR-PL) to determine the properties of the emissive intramolecular charge transfer (ICT) in the NBD-Morph donor-acceptor system. An exhaustive theoretical investigation utilizing the density functional theory (DFT) and its extension TD-DFT methods is an essential complement of experiments to rationalize and understand the molecular structure and related properties. The findings from QTAIM, ELF, and RDG analyses establish that the bonding between morpholine and NBD moieties is of the electrostatic or hydrogen bond type. In addition, the Hirshfeld surfaces have been established to explore the types of interactions. Further, the non-linear optical (NLO) responses of the compound have been examined. The structure-property relationships obtained through the combined experimental and theoretical offer valuable insights for designing efficient NLO material.
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Affiliation(s)
- Imen Chérif
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the environment, 5019 Monastir, Tunisia
| | - Hanen Raissi
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11ES39), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Khouloud Abiedh
- Laboratoire de Micro-Optoélectronique et Nanostructures (LR99/ES29), Faculté des Sciences, Université de Monastir, Monastir, Tunisia
| | - Bouzid Gassoumi
- Laboratoire Interfaces et Matériaux Avancés (LIMA), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Maria Teresa Caccamo
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra Università di Messina Viale Ferdinando Stagno D', Alcontres n°31, S. Agata, 98166 Messina Italy
| | - Salvatore Magazu
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra Università di Messina Viale Ferdinando Stagno D', Alcontres n°31, S. Agata, 98166 Messina Italy
| | - Ayoub Haj Said
- Laboratoire Interfaces et Matériaux Avancés (LIMA), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia; Centre de Recherche en Microélectronique et Nanotechnologie, Technopôle de Sousse, BP 334, Sahloul, 4054 Sousse, Tunisia
| | - Fredj Hassen
- Laboratoire de Micro-Optoélectronique et Nanostructures (LR99/ES29), Faculté des Sciences, Université de Monastir, Monastir, Tunisia
| | - Taoufik Boubaker
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11ES39), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Sahbi Ayachi
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the environment, 5019 Monastir, Tunisia.
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7
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Investigation of optical, TD-DFT calculation and electrical conductivity in semiconducting [(CH3)NH3]2ZnBr4. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Pyrch MF, Bjorklund JL, Williams JM, Kasperski M, Mason SE, Forbes TZ. Investigations of the Cobalt Hexamine Uranyl Carbonate System: Understanding the Influence of Charge and Hydrogen Bonding on the Modification of Vibrational Modes in Uranyl Compounds. Inorg Chem 2022; 61:15023-15036. [PMID: 36099332 PMCID: PMC9516682 DOI: 10.1021/acs.inorgchem.2c01982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Hydrogen bonding networks within hexavalent uranium materials are complex and may influence the overall physical and chemical properties of the system. This is particularly true if hydrogen bonding takes places between the donor and the oxo group associated with the uranyl cation (UO22+). In the current study, we evaluate the impact of charge-assisted hydrogen bonding on the vibrational modes of the uranyl cation using uranyl tricarbonate [UO2(CO3)3]4- interactions with [Co(NH3)6]3+ as the model system. Herein, we report the synthesis and structural characterization of five novel compounds, [Co(NH3)6]Cl(CO3) (Co_Cl_CO3), [Co(NH3)6]4[UO2(CO3)3]3(H2O)11.67 (Co4U3), [Co(NH3)6]3[UO2(CO3)3]2Cl (H2O)7.5 (Co3U2_Cl), [Co(NH3)6]2[UO2(CO3)3]Cl2 (Co2U_Cl), and [Co(NH3)6]2[UO2(CO3)3]CO3 (Co2U_CO3), which contain differences in the crystalline packing and extended hydrogen bonding networks. We show that these slight changes in the supramolecular assembly and hydrogen bonding networks result in the modification of modes as observed by infrared and Raman spectroscopy. We use density functional theory calculations to assign the vibrational modes and provide an understanding about how uranyl bond perturbation and changes in hydrogen bonding interactions can impact the resulting spectroscopic signals.
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Ramarajan D, Đorović Jovanović J, Marković Z, Dimić D, Sudha S. Spectroscopic, molecular docking, and ecotoxicology analyses of the monomer and dimers of 3-aminocyclohexa-2,6-diene-1-sulfonic acid – a theoretical approach. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Harry SA, Vemulapalli S, Dudding T, Lectka T. Rational Computational Design of Systems Exhibiting Strong Halogen Bonding Involving Fluorine in Bicyclic Diamine Derivatives. J Org Chem 2022; 87:8413-8419. [PMID: 35658438 DOI: 10.1021/acs.joc.2c00497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Perhaps the most controversial and rare aspect of the halogen bonding interaction is the potential of fluorine in compounds to serve as a halogen bond donor. In this note, we provide clear and convincing examples of hypothetical molecules in which fluorine is strongly halogen bonding in a metastable state. Of particular note is a polycyclic system inspired by Selectfluor, which has been controversially proposed to engage in halogen bonding.
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Affiliation(s)
- Stefan Andrew Harry
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Srini Vemulapalli
- Department of Chemistry, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Travis Dudding
- Department of Chemistry, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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11
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Spiegel M. Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity. J Chem Inf Model 2022; 62:2639-2658. [PMID: 35436117 PMCID: PMC9198981 DOI: 10.1021/acs.jcim.2c00104] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The antioxidative
nature of chemicals is now routinely studied
using computational quantum chemistry. Scientists are constantly proposing
new approaches to investigate those methods, and the subject is evolving
at a rapid pace. The goal of this review is to collect, consolidate,
and present current trends in a clear, methodical, and reference-rich
manner. This paper is divided into several sections, each of which
corresponds to a different stage of elaborations: preliminary concerns,
electronic structure analysis, and general reactivity (thermochemistry
and kinetics). The sections are further subdivided based on methodologies
used. Concluding remarks and future perspectives are presented based
on the remaining elements.
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Affiliation(s)
- Maciej Spiegel
- Department of Pharmacognosy and Herbal Medicines, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
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12
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Saidj M, Djafri A, Rahmani R, Belkafouf NEH, Boukabcha N, Djafri A, Chouaih A. Molecular Structure, Experimental and Theoretical Vibrational Spectroscopy, (HOMO-LUMO, NBO) Investigation, (RDG, AIM) Analysis, (MEP, NLO) Study and Molecular Docking of Ethyl-2-{[4-Ethyl-5-(Quinolin-8-yloxyMethyl)-4H-1,2,4-Triazol-3-yl] Sulfanyl} Acetate. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2039238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Merzouk Saidj
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
| | - Ahmed Djafri
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
- Organic Synthesis Division, Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques (CRAPC), Tipaza, Algérie
| | - Rachida Rahmani
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
- Department of Process Engineering, Faculty of Sciences and Technology, Ahmed Zabana University of Relizane, Relizane, Algeria
| | - Nour El Houda Belkafouf
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
| | - Nourdine Boukabcha
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
- Chemistry Department, Faculty of Exact Sciences and Informatic, Hassiba Benbouali University, Chlef, Algeria
| | - Ayada Djafri
- Laboratoire de Synthèse Organique Appliquées (LSOA), Faculté Des Sciences Exactes et Appliquées, Département de Chimie, Université Oran-1, Algérie
| | - Abdelkader Chouaih
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
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13
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Coba‐Jiménez L, Maza J, Guerra M, Deluque‐Gómez J, Cubillán N. Interaction of Ciprofloxacin with Arabinose, Glucosamine, Glucuronic Acid and Rhamnose: Insights from Genetic Algorithm and Quantum Chemistry. ChemistrySelect 2022. [DOI: 10.1002/slct.202103836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ludis Coba‐Jiménez
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
| | - Julio Maza
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
| | - Mayamarú Guerra
- Laboratorio de Óptica y Procesamiento de Imágenes Facultad de Ciencias Básicas Universidad Tecnológica de Bolívar Turbaco Colombia
| | - Julio Deluque‐Gómez
- Programa de Ingeniería Industrial Facultad de Ingenierías Universidad de la Guajira Riohacha Colombia
| | - Néstor Cubillán
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
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14
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First synthesis of furostans bearing a 1, 3-dioxane ring at C-26. XRD, Hirshfeld surfaces analysis, DFT studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Fan C, Wen L, Shan Y, Shan Y, Cao X. Why do ammonium salt/phenol-based deep eutectic solvents show low viscosity? ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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16
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Understanding the fundamental interaction mechanism of hazardous gases and imidazolium based ionic liquids for efficient gas adsorption. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.117031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Medimagh M, Issaoui N, Gatfaoui S, Antonia Brandán S, Al-Dossary O, Marouani H, J. Wojcik M. Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and molecular docking study. Heliyon 2021; 7:e08204. [PMID: 34754970 PMCID: PMC8556648 DOI: 10.1016/j.heliyon.2021.e08204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/09/2021] [Accepted: 10/14/2021] [Indexed: 01/18/2023] Open
Abstract
In this research, the impact of non-covalent interactions on the FT-IR spectrum and structural, electronic, topological and vibrational properties of hybrid 4-methylbenzylammonium nitrate (4MBN) have been studied combining B3LYP/CC-PVTZ calculations with molecular docking. 4MBN was synthesized and characterized by using the FT-IR spectrum while the optimized structures in gas phase and in ethanol and aqueous solutions have evidenced monodentate coordination between the nitrate and methylbenzylammonium groups, in agreement with that experimental determined for this species by X-ray diffraction. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, VDW and steric effect in 4MBN were visualized and quantified by the independent gradient density (IGM) based on the promolecular density. The hyper-conjugative and the delocalization of charge in 4MBN have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MESP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The complete vibrational assignments of 69 vibration modes expected for 4MBN are reported together with the scaled force constants while the electronic transitions were evaluated by TD-DFT calculations in ethanol solution. Thermal analysis (DTA and DSC) was also determined. Molecular docking calculations have suggested that 4MBN presents biological activity and could act as a good inhibitor against schizophrenia disease.
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Affiliation(s)
- Mouna Medimagh
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir, 5079, Tunisia
| | - Noureddine Issaoui
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir, 5079, Tunisia
| | - Sofian Gatfaoui
- University of Carthage, Laboratory of Chemistry of Materials (LR13ES08), Faculty of Sciences of Bizerte, 7021, Tunisia
| | - Silvia Antonia Brandán
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, 4000, San Miguel de Tucumán, Tucumán, Argentina
| | - Omar Al-Dossary
- Department of Physics and Astronomy, College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Houda Marouani
- University of Carthage, Laboratory of Chemistry of Materials (LR13ES08), Faculty of Sciences of Bizerte, 7021, Tunisia
| | - Marek J. Wojcik
- Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Gronostajowa 2, Poland
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18
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Zarycz MNC, Schiel MA, Angelina E, Enriz RD. Covalence and π-electron delocalization influence on hydrogen bonds in proton transfer process of o-hydroxy aryl Schiff bases: A combined NMR and QTAIM analysis. J Chem Phys 2021; 155:054307. [PMID: 34364326 DOI: 10.1063/5.0058422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Within the framework of the density functional theory approach, we studied the relationship between the chemical nature of intramolecular hydrogen bonds (HBs) and nuclear magnetic resonance (NMR) parameters, J-couplings and 1H-chemical shifts [δ(1H)], of the atoms involved in such bonds in o-hydroxyaryl Schiff bases during the proton transfer process. For the first time, the shape of the dependence of the degree of covalence in HBs on 1J(N-H), 1J(O-H), 2hJ(O-N), and δ(1H) during the proton transfer process in o-hydroxyaryl Schiff bases was analyzed. Parameters obtained from Bader's theory of atoms in molecules were used to assess the dependence of covalent character in HBs with both the NMR properties. The influence of π-electronic delocalization on 2hJ(N-O) under the proton transfer process was investigated. 2hJ(O-N) in a Mannich base was also studied in order to compare the results with an unsaturated system. In addition, substituent effects on the phenolic ring were investigated. Our results indicate that the covalent character of HBs on both sides of the transition state undergoes a smooth exponential increase as the δ(1H) moves downfield. The degree of covalence of the N⋯H (O⋯H) bond increases linearly as 1J(N-H) (1J(O-H)) becomes more negative, even after reaching the transition state. Non-vanishing values of spin dipolar (SD) and paramagnetic spin orbital terms of 2hJ(O-N) show that π-electronic delocalization has a non-negligible effect on tautomeric equilibrium and gives evidence of the presence of the resonance assisted HB.Variation of the SD term of 2hJ(O-N) follows a similar pattern as the change in the para-delocalization aromaticity index of the chelate ring.
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Affiliation(s)
- M Natalia C Zarycz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - M Ayelén Schiel
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste; Instituto de Química Básica y Aplicada (IQUIBA-NEA). CONICET, Avda. Libertad 5460, 3400 Corrientes, Argentina
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
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19
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Shukla AK, Chaudhary AP, Pandey J. Synthesis, spectral analysis, molecular docking and DFT studies of 3-(2, 6-dichlorophenyl)-acrylamide and its dimer through QTAIM approach. Heliyon 2020; 6:e05016. [PMID: 33033758 PMCID: PMC7533364 DOI: 10.1016/j.heliyon.2020.e05016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
In this paper, an experimental study of (E)-3-(2,6-dichlorophenyl)-acrylamide and its associated dimer were analysed with molecular docking, DFT and QTAIM approach. To spot, describe, and measure the non-covalent interactions (NCIs) of the atoms in the molecules of the monomer and its dimer, some important topological parameters of the charge densities, ρ(r) acquired from the Bader's QTAIM tool are determined, quantitatively. The bond paths are shown to persist for a range of five types of NCIs such as weak conventional (C-H···Cl) and nonconventional (C-O···C and N-O···Cl), medium (N-H···Cl) and strong O-H···O NCIs revealed by the existence of BCPs (ranging from 1.921 - 3.259 Å). A comprehensive explanation of the spectroscopic data like vibrational, electronic, and NMR spectra is reported along with the NLO, reactivity. Hydroxamic acid exhibited an excellent nonlinear optical activity (β0 = 14.8098 × 10−30). To predict the various reactive sites in the molecule, molecular electrostatic potential diagrams were displayed.
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Affiliation(s)
- Akhilesh Kumar Shukla
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226025, Uttar Pradesh, India
| | - Aniruddh Prasad Chaudhary
- Department of Chemistry, Udai Pratap College (An Autonomous Institution) Varanasi, Uttar Pradesh, India 221002
| | - Jyoti Pandey
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226025, Uttar Pradesh, India
- Corresponding author.
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20
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Solvation of lithium ion in helium clusters: Structural properties and relative stabilities. J Mol Graph Model 2020; 98:107582. [PMID: 32200277 DOI: 10.1016/j.jmgm.2020.107582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 01/18/2023]
Abstract
Structural study and relative stabilities of Li+-doped helium clusters Li+Hen (n = 1-18) has been reported in this work using two theoretical protocols. The first one is based on the basin-hopping optimization technique, where the total energy of each cluster is described by an additive model describing Li+-He and He-He interactions. The second one is the DFT calculations, in which the initial structures are generated by ABCluster algorithm and CALYPSO software. The CSA shape was found where the first solvation shell is completed at n = 10. The relative stabilities of Li+Hen (n = 1-18) clusters have been discussed based on the variation of the binding energy, second-order difference in energy, fragmentation energy and HOMO-LUMO energy gap as a function of the cluster size. The results showed that Li+He10 is the most stable cluster. The dipole moment is calculated and showed the polar character of the Li+Hen clusters. Finally, the interatomic interactions have been examined topologically by the means of AIM and non-covalent reduced density gradient (NC-RDG) analyses.
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21
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Theoretical and experimental investigation of the spectroscopic features of and interionic interactions in 1-hexyl-3-methylimidazolium chloride, 1-hexyl-3-methylimidazolium tetrafluoroborate and 1-hexyl-3-methylimidazolium hexafluorophosphate ionic liquids. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112468] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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22
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Sethi A, Singh RP, Pathak R, Shukla D, Amandeep, Yadav P. One pot synthesis of novel pregnane-sulphur prodrugs, spectroscopic investigation, conformational analysis, chemical reactivity, Fukui function and their mathematical model. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Sanchora P, Pandey DK, Kagdada HL, Materny A, Singh DK. Impact of alkyl chain length and water on the structure and properties of 1-alkyl-3-methylimidazolium chloride ionic liquids. Phys Chem Chem Phys 2020; 22:17687-17704. [DOI: 10.1039/d0cp01686a] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformational isomerism in Cnmim Cl (n = 2, 4, 6, 8, and 10) is identified by marker IR bands for the first time.
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Affiliation(s)
- Paridhi Sanchora
- Department of Physics
- Institute of Infrastructure Technology Research and Management
- Ahmedabad
- India
| | - Deepak K. Pandey
- Department of Physics
- Institute of Infrastructure Technology Research and Management
- Ahmedabad
- India
| | - Hardik L. Kagdada
- Department of Physics
- Institute of Infrastructure Technology Research and Management
- Ahmedabad
- India
| | - Arnulf Materny
- Department of Physics and Earth Sciences
- Jacobs University Bremen
- Bremen
- Germany
| | - Dheeraj K. Singh
- Department of Physics
- Institute of Infrastructure Technology Research and Management
- Ahmedabad
- India
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24
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Sarkar S, Sruthi PK, Ramanathan N, Sundararajan K. Strong proton-shared hydrogen bonding in a methyl imidazole⋯HCl complex: evidence from matrix isolation infrared spectroscopy and ab initio computations. NEW J CHEM 2020. [DOI: 10.1039/d0nj00029a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Evidence for proton-shared hydrogen bonding is provided in a methyl imidazole⋯HCl complex using matrix isolation infrared spectroscopy and ab initio computations.
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Affiliation(s)
- Shubhra Sarkar
- Materials Chemistry & Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Center for Atomic Research
- Kalpakkam.603102
- India
| | - P. K. Sruthi
- Materials Chemistry & Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Center for Atomic Research
- Kalpakkam.603102
- India
| | - N. Ramanathan
- Materials Chemistry & Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Center for Atomic Research
- Kalpakkam.603102
- India
| | - K. Sundararajan
- Materials Chemistry & Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Center for Atomic Research
- Kalpakkam.603102
- India
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25
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Seyede Samira Hosseini, Nowroozi A, Nakhaei E, Magham AHJ. A Comprehensive Theoretical Study of Amide Resonance, Intramolecular Hydrogen Bonding, and π-Electron Delocalization in Diformyl and Dithioformyl Amine. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2019. [DOI: 10.1134/s0036024419100091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Sojka M, Tousek J, Badri Z, Foroutan-Nejad C, Necas M. Bifurcated hydrogen bonds in platinum(II) complexes with phosphinoamine ligands. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Ben Hadj Ayed M, Osmani T, Issaoui N, Berisha A, Oujia B, Ghalla H. Structures and relative stabilities of Na+Nen (n = 1–16) clusters via pairwise and DFT calculations. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2476-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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28
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Sheng X, Wang B, Song X, Ngwenya CA, Wang Y, Zhao H. Atmospheric Initial Nucleation Containing Carboxylic Acids. J Phys Chem A 2019; 123:3876-3886. [PMID: 30974943 DOI: 10.1021/acs.jpca.9b01104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xia Sheng
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Benjin Wang
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Xue Song
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Cleopatra Ashley Ngwenya
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Yuyu Wang
- College of Mathematical Science, Tianjin Normal University, Binshui West Road 393, 300387 Tianjin, China
| | - Hailiang Zhao
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
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29
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Sabzehzari M, Ajamgard M, Shamlouei HR. Influence of non-metallic atoms on the absorption of amphetamines on B12N12 nano-cages. Struct Chem 2019. [DOI: 10.1007/s11224-019-01316-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Ma X, Sun Y, Huang Z, Zhang Q, Wang W. A density functional theory study of the molecular interactions between a series of amides and sulfuric acid. CHEMOSPHERE 2019; 214:781-790. [PMID: 30296766 DOI: 10.1016/j.chemosphere.2018.08.152] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Amides, a class of nitrogen-containing organic pollutants in the atmosphere, may affect the formation of atmospheric aerosols by the interactions with sulfuric acid. Here, the molecular interactions of sulfuric acid with formamide, methylformamide, dimethylformamide, acetamide, methylacetamide and dimethylacetamide was investigated by density functional theory. Geometry optimization and Gibbs free energy calculation were carried out at M06-2X/6-311++G(3df,3pd) level. The results indicate that the addition of amides to H2SO4 might have a promoting effect on atmospheric new particle formation at 298.15 K and 1 atm. In the initial stage of new particle formation, the binding capacity of amides and sulfuric acid is stronger than ammonia, but weaker than methylamine. It is worth noting that the trans-methylacetamide could have similar capabilities of stabilizing sulfuric acid as dimethylamine. In the presence of water, amides are found to only have a weak enhancement capability on new particle formation. In addition, we can infer from evaporation rate that the small molecule clusters of formamide and sulfuric acid may be more energetically favorable than macromolecule clusters.
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Affiliation(s)
- Xiaohui Ma
- Environment Research Institute, Shandong University, Jinan 250100, PR China
| | - Yanhui Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Zixiao Huang
- Environment Research Institute, Shandong University, Jinan 250100, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Jinan 250100, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Jinan 250100, PR China
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31
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Lin X, Jiang X, Wu W, Mo Y. Induction, Resonance, and Secondary Electrostatic Interaction on Hydrogen Bonding in the Association of Amides and Imides. J Org Chem 2018; 83:13446-13453. [DOI: 10.1021/acs.joc.8b02247] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuhui Lin
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiaoyu Jiang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350108, China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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32
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Sheng X, Jiang X, Zhao H, Wan D, Liu Y, Ngwenya CA, Du L. FTIR study of hydrogen bonding interaction between fluorinated alcohol and unsaturated esters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 198:239-247. [PMID: 29549865 DOI: 10.1016/j.saa.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/25/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
The 1:1 complexes of two unsaturated esters with 2,2,2-trifluoroethanol (TFE) were investigated experimentally and computationally. The experimental observations of the spectral shifts of the OH-stretching vibrational transitions were obtained at 113cm-1 for TFE-methyl acrylate (MA) and 92cm-1 for TFE-vinyl acetate (VA). There are three docking sites in the two unsaturated esters for the incoming TFE. The predicted red shifts of the OH-stretching vibrational transitions were found to be larger for the OH⋯OC hydrogen bonded conformer than those for the OH⋯π and OH⋯O ones. The binding energies further prove that the OH⋯OC hydrogen bonded conformers are the most stable ones. On the basis of the DFT calculations as well as previous works, the carbonyl group is the best docking site for TFE. Furthermore, the thermodynamic equilibrium constants of TFE-MA and TFE-VA were obtained at 0.28 and 0.15 by combining the experimental spectra data and the DFT calculations. Consequently, the Gibbs free energies of formation were determined to be 3.2 and 4.8kJmol-1 for TFE-MA and TFE-VA, respectively. The quantum theory of atoms in molecules (AIM) and generalized Kohn-Sham energy decomposition analysis (GKS-EDA) were carried out for further characterization of the hydrogen bonding interactions. GKS-EDA shows an "electrostatic" dominated hydrogen bonding character for the OH⋯OC hydrogen bonds.
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Affiliation(s)
- Xia Sheng
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Xiaotong Jiang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China
| | - Hailiang Zhao
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China; Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China
| | - Dongjin Wan
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Yongde Liu
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Cleopatra Ashley Ngwenya
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China.
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33
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Intermolecular interactions and molecular docking investigations on 4-methoxybenzaldehyde. COMPUTATIONAL MATERIALS SCIENCE 2018. [DOI: 10.1016/j.commatsci.2018.03.042] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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34
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Hirvonen V, Myllys N, Kurtén T, Elm J. Closed-Shell Organic Compounds Might Form Dimers at the Surface of Molecular Clusters. J Phys Chem A 2018; 122:1771-1780. [PMID: 29364673 DOI: 10.1021/acs.jpca.7b11970] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of covalently bound dimer formation is studied using high-level quantum chemical methods. Reaction free energy profiles for dimer formation between common oxygen-containing functional groups are calculated, and based on the Gibbs free energy differences between transition states and reactants, we show that none of the studied two-component gas-phase reactions are kinetically feasible at 298.15 K and 1 atm. Therefore, the catalyzing effect of water, base, or acid molecules is calculated, and sulfuric acid is identified to lower the activation free energies significantly. We find that the reactions yielding hemiacetal, peroxyhemiacetal, α-hydroxyester, and geminal diol products occur with activation free energies of less than 10 kcal/mol with sulfuric acid as a catalyst, indicating that these reactions could potentially take place on the surface of sulfuric acid clusters. Additionally, the formed dimer products bind stronger onto the pre-existing cluster than the corresponding reagent monomers do. This implies that covalent dimerization reactions stabilize the existing cluster thermodynamically and make it less likely to evaporate. However, the studied small organic compounds, which contain only one functional group, are not able to form dimer products that are stable against evaporation at atmospheric conditions. Calculations of dimer formation onto a cluster surface and the clustering ability of dimer products should be extended to large terpene oxidation products in order to estimate the real atmospheric significance.
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Affiliation(s)
- Viivi Hirvonen
- Department of Physics, University of Helsinki , 00100 Helsinki, Finland
| | - Nanna Myllys
- Department of Physics, University of Helsinki , 00100 Helsinki, Finland
| | - Theo Kurtén
- Department of Chemistry, University of Helsinki , 00100 Helsinki, Finland
| | - Jonas Elm
- Department of Chemistry, Aarhus University , 8000 Aarhus C, Denmark
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Kavimani M, Balachandran V, Narayana B, Vanasundari K, Revathi B. Topological analysis (BCP) of vibrational spectroscopic studies, docking, RDG, DSSC, Fukui functions and chemical reactivity of 2-methylphenylacetic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 190:47-60. [PMID: 28898821 DOI: 10.1016/j.saa.2017.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/02/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
Experimental FT-IR and FT-Raman spectra of 2-methylphenylacetic acid (MPA) were recorded and theoretical values are also analyzed. The non-linear optical (NLO) properties were evaluated by determination of first (5.5053×10-30 e.s.u.) and second hyper-polarizabilities (7.6833×10-36 e.s.u.) of the title compound. The Multiwfn package is used to find the weak non-covalent interaction (Van der Wall interaction) and strong repulsion (steric effect) of the molecule and examined by reduced density gradient. The molecular electrostatic potential (MEP) analysis used to find the most reactive sites for the electrophilic and nucleophilic attack. The chemical activity (electronegativity, hardness, chemical softness and chemical potential) of the title compound was predicted with the help of HOMO-LUMO energy values. The natural bond orbital (NBO) has been analyzed the stability of the molecule arising from the hyper-conjugative interaction. DSSCs were discussed in structural modifications that improve the electron injection efficiency of the title compound (MPA). The Fukui functions are calculated in order to get information associated with the local reactivity properties of the title compound. The binding sites of the two receptors were reported by molecular docking field and active site bond distance is same 1.9Å. The inhibitor of the title compound forms a stable complex with 1QYV and 2H1K proteins at the binding energies are -5.38 and -5.85 (∆G in kcal/mol).
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Affiliation(s)
- M Kavimani
- Centre for Research, Department of Physics, Arignar Anna Govt. Arts College, Musiri, Tiruchirappalli 621 211, India
| | - V Balachandran
- Centre for Research, Department of Physics, Arignar Anna Govt. Arts College, Musiri, Tiruchirappalli 621 211, India.
| | - B Narayana
- Department of Studies in Chemistry, Mangalore University, Mangalagangotri, 574 199, India
| | - K Vanasundari
- Centre for Research, Department of Physics, Arignar Anna Govt. Arts College, Musiri, Tiruchirappalli 621 211, India
| | - B Revathi
- Centre for Research, Department of Physics, Arignar Anna Govt. Arts College, Musiri, Tiruchirappalli 621 211, India
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36
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Feyer V, Prince KC, Coreno M, Melandri S, Maris A, Evangelisti L, Caminati W, Giuliano BM, Kjaergaard HG, Carravetta V. Quantum Effects for a Proton in a Low-Barrier, Double-Well Potential: Core Level Photoemission Spectroscopy of Acetylacetone. J Phys Chem Lett 2018; 9:521-526. [PMID: 29314844 DOI: 10.1021/acs.jpclett.7b03175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We have performed core level photoemission spectroscopy of gaseous acetylacetone, its fully deuterated form, and two derivatives, benzoylacetone and dibenzoylmethane. These molecules show intramolecular hydrogen bonds, with a proton located in a double-well potential, whose barrier height is different for the three compounds. This has allowed us to examine the effect of the double-well potential on photoemission spectra. Two distinct O 1s core hole peaks are observed, previously assigned to two chemical states of oxygen. We provide an alternative assignment of the double-peak structure of O 1s spectra by taking full account of the extended nature of the wave function associated with the nuclear motion of the proton, the shape of the ground and final state potentials in which the proton is located, and the nonzero temperature of the samples. The peaks are explained in terms of an unusual Franck-Condon factor distribution.
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Affiliation(s)
- Vitaliy Feyer
- Elettra-Sincrotrone Trieste , in Area Science Park, I-34149 Trieste, Italy
| | - Kevin C Prince
- Elettra-Sincrotrone Trieste , in Area Science Park, I-34149 Trieste, Italy
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, Swinburne University of Technology , 3122 Melbourne, Australia
| | - Marcello Coreno
- ISM-CNR - Istituto di Struttura della Materia , LD2 unit, I-34149 Trieste, Italy
| | - Sonia Melandri
- Dipartimento di Chimica, "G. Ciamician" dell'Università , I-40126 Bologna, Italy
| | - Assimo Maris
- Dipartimento di Chimica, "G. Ciamician" dell'Università , I-40126 Bologna, Italy
| | - Luca Evangelisti
- Dipartimento di Chimica, "G. Ciamician" dell'Università , I-40126 Bologna, Italy
| | - Walther Caminati
- Dipartimento di Chimica, "G. Ciamician" dell'Università , I-40126 Bologna, Italy
| | - Barbara M Giuliano
- Departamento de Química, Universidade de Coimbra , 3004-535 Coimbra, Portugal
| | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen , 2100 Copenhagen, Denmark
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37
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Ring-Size Effects on the Stability and Spectral Shifts of Hydrogen Bonded Cyclic Ethers Complexes. Sci Rep 2018; 8:1553. [PMID: 29367625 PMCID: PMC5784011 DOI: 10.1038/s41598-017-18191-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/07/2017] [Indexed: 11/08/2022] Open
Abstract
In order to investigate ring-size effects on the stability and spectral shifts of hydrogen bonded cyclic ethers complexes, the strength of hydrogen bonds in gas phase complexes formed between 2,2,2-trifluoroethanol (TFE) and selected cyclic ethers were examined using FTIR spectroscopy. TFE was chosen as hydrogen bond donor in these complexes, while trimethylene oxide (TMO), tetrahydrofuran (THF) and tetrahydropyran (THP) were selected as hydrogen bond acceptors. Comparable OH-stretching red shifts were observed in the three kinds of complexes. The difference of red shifts is so small (<7 cm−1) for TFE−TMO/THF/THP complexes that one can conclude that their stabilities and the strength of the hydrogen bonds are nearly similar and do not show any marked dependence with the ring size of the hydrogen bond acceptor. The equilibrium constants for the complexation were determined, and atoms-in-molecules (AIM) and natural bond orbital (NBO) analyses were performed to further investigate the intermolecular interactions. Regardless of the ring size, hydrogen bonds in the complexes showed similar strength, in agreement with the observed OH-stretching red shifts.
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38
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Darugar V, Vakili M, Nekoei A, Tayyari S, Afzali R. Tautomerism, molecular structure, intramolecular hydrogen bond, and enol-enol equilibrium of para halo substituted 4,4,4-trifluoro-1-phenyl-1,3-butanedione; Experimental and theoretical studies. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Jiang X, Zhang H, Wu W, Mo Y. A Critical Check for the Role of Resonance in Intramolecular Hydrogen Bonding. Chemistry 2017; 23:16885-16891. [PMID: 29106781 DOI: 10.1002/chem.201703952] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Indexed: 11/10/2022]
Abstract
Although resonance-assisted H-bonds (RAHBs) are well recognized, the role of π resonance in RAHBs is controversial, as the seemingly enhanced H-bonds in unsaturated compounds may result from the constraints imposed by the σ skeleton. Herein the block-localized wave function (BLW) method, which can derive optimal yet resonance-quenched structures with related physiochemical properties, was employed to examine the correlation between π resonance and the strength of intramolecular RAHBs. Examination of a series of paradigmatic molecules with RAHBs and their saturated analogues showed that it is inappropriate to compare a conjugated system with its saturated counterpart, as they may have quite different σ frameworks. Nevertheless, comparison between a conjugated system and its resonance-quenched (i.e., electron-localized) state, which have identical σ skeletons, shows that in all studied cases, π resonance unanimously reduces the bonding distance by 0.111-0.477 Å, strengthens the bonding by 40-56 %, and redshifts the D-H vibrational frequency by 104-628 cm-1 . Furthermore, there is an excellent correlation between hydrogen-bonding strength and the classical Coulomb attraction between the hydrogen-bond donor and the acceptor, which suggests that the dominant role of the electrostatic interaction in H-bonds and RAHBs originates from the charge flow from H-bond donors to acceptors through π conjugation.
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Affiliation(s)
- Xiaoyu Jiang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, 350108, P. R. China
| | - Huaiyu Zhang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, P. R. China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, P. R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008, USA
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40
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Liu X, Tong Y, Wang A, Xuan X. Synthesis, structural characterization, thermal stability, vibrational spectra and density functional theoretical studies of 1,3-bis(carboxymethyl)imidazolium nitrate ionic liquid. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.09.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Ebrahimi S, Dabbagh HA, Eskandari K. Arrangement and nature of intermolecular hydrogen bonding in complex biomolecular systems: modeling the vitamin C---L-alanine interaction. Struct Chem 2017. [DOI: 10.1007/s11224-017-1046-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Ganguly A, Paul BK, Guchhait N. Arguing on the roles of various non-covalent interactions in governing the global stabilization/destabilization of 3-hydroxy-2-pyridin-2-yl-propenal: An AIM-based approach. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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43
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Lin C, Kumar M, Finney BA, Francisco JS. Intramolecular hydrogen bonding in malonaldehyde and its radical analogues. J Chem Phys 2017; 147:124309. [PMID: 28964036 DOI: 10.1063/1.4996563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MARS, and cis-MARA, both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MARA, in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MARS, in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ* orbital of acceptor O-H bond (n → σ*OH). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MARS.
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Affiliation(s)
- Chen Lin
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
| | - Manoj Kumar
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0321, USA
| | - Brian A Finney
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
| | - Joseph S Francisco
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
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44
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Nowroozi A, Ebrahimi A, Rezvani Rad O. Mutual effects of the cation-π, anion-π and intramolecular hydrogen bond in the various complexes of 1,3,5-triamino-2,4,6-trinitrobenzene with some cations (Li+, Na+, K+, Mg2+, Ca2+) and anions (F˗, Cl˗, Br˗). Struct Chem 2017. [DOI: 10.1007/s11224-017-1010-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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45
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Zhao H, Tang S, Du L. Hydrogen bond docking site competition in methyl esters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:122-130. [PMID: 28351818 DOI: 10.1016/j.saa.2017.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/07/2017] [Accepted: 03/17/2017] [Indexed: 06/06/2023]
Abstract
The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm-1)>TFE-MF (93cm-1)>TFE-MTFA (44cm-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.
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Affiliation(s)
- Hailiang Zhao
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Shanshan Tang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China.
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46
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Structural characterization, surface characteristics and non covalent interactions of a heterocyclic Schiff base: Evaluation of antioxidant potential by UV–visible spectroscopy and DFT. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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47
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Rusinska-Roszak D. Energy of Intramolecular Hydrogen Bonding in ortho-Hydroxybenzaldehydes, Phenones and Quinones. Transfer of Aromaticity from ipso-Benzene Ring to the Enol System(s). Molecules 2017; 22:E481. [PMID: 28335484 PMCID: PMC6155192 DOI: 10.3390/molecules22030481] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 01/10/2023] Open
Abstract
Intramolecular hydrogen bonding (HB) is one of the most studied noncovalent interactions of molecules. Many physical, spectral, and topological properties of compounds are under the influence of HB, and there are many parameters used to notice and to describe these changes. Hitherto, no general method of measurement of the energy of intramolecular hydrogen bond (EHB) has been put into effect. We propose the molecular tailoring approach (MTA) for EHB calculation, modified to apply it to Ar-O-H∙∙∙O=C systems. The method, based on quantum calculations, was checked earlier for hydroxycarbonyl-saturated compounds, and for structures with resonance-assisted hydrogen bonding (RAHB). For phenolic compounds, the accuracy, repeatability, and applicability of the method is now confirmed for nearly 140 structures. For each structure its aromaticity HOMA indices were calculated for the central (ipso) ring and for the quasiaromatic rings given by intramolecular HB. The comparison of calculated HB energies and values of estimated aromaticity indices allowed us to observe, in some substituted phenols and quinones, the phenomenon of transfer of aromaticity from the ipso-ring to the H-bonded ring via the effect of electron delocalization.
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Affiliation(s)
- Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, ul. Berdychowo 4, 60-965 Poznan, Poland.
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48
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Gandhimathi S, Balakrishnan C, Theetharappan M, Neelakantan MA, Venkataraman R. Noncovalent interactions from electron density topology and solvent effects on spectral properties of Schiff bases. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 175:134-144. [PMID: 28024247 DOI: 10.1016/j.saa.2016.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 12/01/2016] [Accepted: 12/11/2016] [Indexed: 06/06/2023]
Abstract
Two Schiff bases were prepared by the condensation of o-allyl substituted 2,4-dihydroxy acetophenone with 1,2-diaminopropane (L1) and ethanediamine (L2) and characterized by elemental analysis, and ESI-MS, IR, UV-Vis, 1H and 13C NMR spectral techniques. The effect of solvents with respect to different polarities on UV-Vis and emission spectra of L1 and L2 was investigated at room temperature show that the compounds exist in keto and enol forms in solution and may be attributed to the intramolecular proton transfer in the ground state. The solute-solvent interactions, change in dipole moment and solvatochromic properties of the compounds were studied based on the solvent polarity parameters. For L1 and L2, the ground and excited state electronic structure calculations were carried out by DFT and TD-DFT at B3LYP/6-311G (d,p) level, respectively. The IR, NMR and electronic absorption spectra computed were compared with the experimental observations. The intramolecular charge transfer within the molecule is evidenced from the HOMO and LUMO energy levels and surface analysis. The noncovalent interactions like hydrogen bonding and van der Waals interactions were identified from the molecular geometry and electron localization function. These interactions in molecules have been studied by using reduced density gradient and graphed by Multiwfn.
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Affiliation(s)
- S Gandhimathi
- Chemistry Research Centre, National Engineering College, K.R. Nagar, Kovilpatti, 628503 Thoothukudi District, Tamil Nadu, India; Department of Chemistry, Sri Paramakalyani College, Alwarkurichi, 627412 Tirunelveli District, Tamil Nadu, India
| | - C Balakrishnan
- Chemistry Research Centre, National Engineering College, K.R. Nagar, Kovilpatti, 628503 Thoothukudi District, Tamil Nadu, India
| | - M Theetharappan
- Chemistry Research Centre, National Engineering College, K.R. Nagar, Kovilpatti, 628503 Thoothukudi District, Tamil Nadu, India
| | - M A Neelakantan
- Chemistry Research Centre, National Engineering College, K.R. Nagar, Kovilpatti, 628503 Thoothukudi District, Tamil Nadu, India.
| | - R Venkataraman
- Department of Chemistry, Sri Paramakalyani College, Alwarkurichi, 627412 Tirunelveli District, Tamil Nadu, India
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49
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A comprehensive theoretical study of mutual interactions between the intramolecular hydrogen bond and π-electron delocalization of RAHB units with the benzene rings in salicylaldehyde and ortho-aminobenzaldehyde with their thio and seleno analogues. Struct Chem 2017. [DOI: 10.1007/s11224-017-0921-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Sethi A, Singh RP, Prakash R, Amandeep. Facile synthesis of corticosteroids prodrugs from isolated hydrocortisone acetate and their quantum chemical calculations. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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