1
|
El-Khoury R, Cabrero C, Movilla S, Kaur H, Friedland D, Domínguez A, Thorpe JD, Roman M, Orozco M, González C, Damha MJ. Formation of left-handed helices by C2'-fluorinated nucleic acids under physiological salt conditions. Nucleic Acids Res 2024:gkae508. [PMID: 38874502 DOI: 10.1093/nar/gkae508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 05/06/2024] [Accepted: 06/12/2024] [Indexed: 06/15/2024] Open
Abstract
Recent findings in cell biology have rekindled interest in Z-DNA, the left-handed helical form of DNA. We report here that two minimally modified nucleosides, 2'F-araC and 2'F-riboG, induce the formation of the Z-form under low ionic strength. We show that oligomers entirely made of these two nucleosides exclusively produce left-handed duplexes that bind to the Zα domain of ADAR1. The effect of the two nucleotides is so dramatic that Z-form duplexes are the only species observed in 10 mM sodium phosphate buffer and neutral pH, and no B-form is observed at any temperature. Hence, in contrast to other studies reporting formation of Z/B-form equilibria by a preference for purine glycosidic angles in syn, our NMR and computational work revealed that sequential 2'F…H2N and intramolecular 3'H…N3' interactions stabilize the left-handed helix. The equilibrium between B- and Z- forms is slow in the 19F NMR time scale (≥ms), and each conformation exhibited unprecedented chemical shift differences in the 19F signals. This observation led to a reliable estimation of the relative population of B and Z species and enabled us to monitor B-Z transitions under different conditions. The unique features of 2'F-modified DNA should thus be a valuable addition to existing techniques for specific detection of new Z-binding proteins and ligands.
Collapse
Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Cristina Cabrero
- Instituto de Química Física Blas Cabrera, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Santiago Movilla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Harneesh Kaur
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - David Friedland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Arnau Domínguez
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
- IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - James D Thorpe
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Morgane Roman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Carlos González
- Instituto de Química Física Blas Cabrera, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| |
Collapse
|
2
|
Deepakvijay K, Prakasam A. Exploring the effects of mono-bromination on hole-electron transport and distribution in dibenzofuran and dibenzothiophene isomers: a first-principles study. J Mol Model 2024; 30:171. [PMID: 38761303 DOI: 10.1007/s00894-024-05966-5] [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: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024]
Abstract
CONTEXT This study delves into hole-electron transport and distribution properties inherent in mono-brominated dibenzofuran (DBF) and dibenzothiophene (DBT) isomers. As determined by frontier molecular orbitals, all brominated structures have narrower bandgaps than their primary structures. The TD-DFT calculation showed that 2BDBT had the highest absorption wavelength of all molecules at 315.35 nm. Notably, the study unveils remarkably low electron and hole reorganization energies due to bromine substitution in DBF and DBT molecules. Specifically, the 4BDBF has the lowest hole reorganization energy of all DBF configurations, 0.229 eV. In addition, 3BDBF has 0.226 eV less electron reorganization energy than all other molecules. Compared to DBT, 3BDBT has the lowest electron reorganization energy of 0.254 eV. Overall, this research sheds significant light on the fundamental electronic and hole transport characteristics of bromine-substituted DBF and DBT isomers, highlighting their promising role in polymer design as donors/acceptors for advanced organic electronic applications. METHODS Molecular structures were optimized using Density Functional Theory (DFT) B3LYP/6-311 + + G (d, p) level of theory, and the study further elucidates these molecules' energy levels and absorption spectra through Time-Dependent Density Functional Theory TD-DFT; these calculations were performed using Gaussian 09W software package. The key parameters such as reorganization energies, Electron Localization Function map, Laplacian Bond Order, and NCI-RDG were meticulously examined for the molecules with the results of DFT calculations were analyzed and displayed by utilizing the software packages VMD 1.9.4 and Multiwfn 3.8, aiming to comprehend their charge transport and distribution properties.
Collapse
Affiliation(s)
- K Deepakvijay
- Computational & Theoretical Physics Laboratory, PG & Research Department of Physics, Thiruvalluvar Govt. Arts College, Rasipuram, 637408, Tamil Nadu, India.
| | - A Prakasam
- Computational & Theoretical Physics Laboratory, PG & Research Department of Physics, Thiruvalluvar Govt. Arts College, Rasipuram, 637408, Tamil Nadu, India.
| |
Collapse
|
3
|
Asif M, Kosar N, Sajid H, Qureshi S, Gilani MA, Ayub K, Arshad M, Imran M, Hamid MHS, Bayach I, Sheikh NS, Mahmood T. Exploring the Sensing Potential of g-C 3N 4 versus Li/g-C 3N 4 Nanoflakes toward Hazardous Organic Volatiles: A DFT Simulation Study. ACS OMEGA 2024; 9:3541-3553. [PMID: 38284053 PMCID: PMC10810007 DOI: 10.1021/acsomega.3c07350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024]
Abstract
Ab initio calculations were performed to determine the sensing behavior of g-C3N4 and Li metal-doped g-C3N4 (Li/g-C3N4) quantum dots toward toxic compounds acetamide (AA), benzamide (BA), and their thio-analogues, namely, thioacetamide (TAA) and thiobenzamide (TAA). For optimization and interaction energies, the ωB97XD/6-31G(d,p) level of theory was used. Interaction energies (Eint) illustrate the high thermodynamic stabilities of the designed complexes due to the presence of the noncovalent interactions. The presence of electrostatic forces in some complexes is also observed. The observed trend of Eint in g-C3N4 complexes was BA > TAA > AA > TBA, while in Li/g-C3N4, the trend was BA > AA > TBA > TAA. The electronic properties were studied by frontier molecular orbital (FMO) and natural bond orbital analyses. According to FMO, lithium metal doping greatly enhanced the conductivity of the complexes by generating new HOMOs near the Fermi level. A significant amount of charge transfer was also observed in complexes, reflecting the increase in charge conductivity. NCI and QTAIM analyses evidenced the presence of significant noncovalent dispersion and electrostatic forces in Li/g-C3N4 and respective complexes. Charge decomposition analysis gave an idea of the transfer of charge density between quantum dots and analytes. Finally, TD-DFT explained the optical behavior of the reported complexes. The findings of this study suggested that both bare g-C3N4 and Li/g-C3N4 can effectively be used as atmospheric sensors having excellent adsorbing properties toward toxic analytes.
Collapse
Affiliation(s)
- Misbah Asif
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Naveen Kosar
- Department
of Chemistry, University of Management and
Technology (UMT), C-11, Johar Town, Lahore 54782, Pakistan
| | - Hasnain Sajid
- School
of Science and Technology, Nottingham Trent
University, Clifton Lane, Nottingham NG11 8NS, U.K.
| | - Sana Qureshi
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Mazhar Amjad Gilani
- Department
of Chemistry, COMSATS University Islamabad,
Lahore Campus, Lahore 54000, Pakistan
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Muhammad Arshad
- Institute
of Chemistry, The Islamia University of
Bahawalpur, Baghdad-ul-Jadeed Campus, Bahawalpur 63100, Pakistan
| | - Muhammad Imran
- Department
of Chemistry, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Malai Haniti S.
A. Hamid
- Chemical
Sciences, Faculty of Science, Universiti
Brunei Darussalam, Jalan Tungku
Link, Gadong BE1410, Brunei Darussalam
| | - Imene Bayach
- Department
of Chemistry, College of Science, King Faisal
University, Al-Ahsa 31982, Saudi Arabia
| | - Nadeem S. Sheikh
- Chemical
Sciences, Faculty of Science, Universiti
Brunei Darussalam, Jalan Tungku
Link, Gadong BE1410, Brunei Darussalam
| | - Tariq Mahmood
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
- Department
of Chemistry, College of Science, University
of Bahrain, P.O. Box 32038, Sakhir 1054, Bahrain
| |
Collapse
|
4
|
Gutiérrez-Flores J, H Huerta E, Cuevas G, Garza J, Vargas R. Revealing the Role of Noncovalent Interactions on the Conformation of the Methyl Group in Tricyclic Orthoamide. J Org Chem 2024; 89:257-268. [PMID: 38100710 PMCID: PMC10921461 DOI: 10.1021/acs.joc.3c02016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
Tricyclic orthoamides are valuable molecules with wide-ranging applications, including organic synthesis and molecular recognition. Their structural properties make them intriguing, particularly the eclipsed all-trans conformer, which is typically less stable than the alternated conformation and is a rare phenomenon in organic chemistry. However, it gains stability in crystalline and hydrated settings, challenging the existing theoretical explanations. This study investigates which factors make eclipsed conformers more stable using experimentally reported anhydrous (ATO) and hydrated (HTO) crystal structures. Employing the quantum theory of atoms in molecules, noncovalent interaction index, and pairwise energy decomposition analysis, we delve into the noncovalent interaction environment surrounding the molecule of interest. In ATO, dispersive interactions dominate, whereas in HTO, both dispersive and electrostatic contributions are observed due to the presence of water molecules. Anchored to the lone pairs of the nitrogen atom in the orthoamide tricycle, water molecules prompt the methyl group's eclipsing through intermolecular and intramolecular interactions. This work resolves the long-standing conflict behind why tricyclic orthoamide has an eclipsed conformation by establishing the stabilization factors. These insights have implications for crystal engineering and design, enhancing our understanding of structural behavior in both crystalline and hydrated environments.
Collapse
Affiliation(s)
- Jorge Gutiérrez-Flores
- Departamento
de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C.P. 09340 Ciudad
de México, México
| | - Eduardo H Huerta
- Insituto
de Química, Universidad Nacional
Autónoma de México, Circuito Exterior, Ciudad Universitaria, Alcaldía Coyoacán C.P. 04510 Ciudad
de México, México
| | - Gabriel Cuevas
- Insituto
de Química, Universidad Nacional
Autónoma de México, Circuito Exterior, Ciudad Universitaria, Alcaldía Coyoacán C.P. 04510 Ciudad
de México, México
| | - Jorge Garza
- Departamento
de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C.P. 09340 Ciudad
de México, México
| | - Rubicelia Vargas
- Departamento
de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C.P. 09340 Ciudad
de México, México
| |
Collapse
|
5
|
Aarabi M, Gholami S, Grabowski SJ. Double Centrosymmetric Si···π Tetrel Bonds as New Synthons─Evidence from Crystal Structures and DFT Calculations. J Phys Chem A 2023; 127:9995-10007. [PMID: 37975750 DOI: 10.1021/acs.jpca.3c06514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The crystal structure of bis((μ2-ethynylsilyloxo)-dichloro-aluminum), BEDCA, and a few related structures are characterized by the occurrence of tetrel bonds that link molecules. Particularly, centosymmetric dimers in such structures occur that are connected by two equivalent Si···π tetrel bonds. The dimer of BEDCA and dimers of other model species that similarly are linked by two equivalent Si···π tetrel bonds are analyzed theoretically. Some of the complexes calculated here are also characterized by the occurrence of triel bonds. Thus, ωB97XD/aug-cc-pVTZ calculations are performed and these DFT results are further supported by calculations with the use of other theoretical approaches: the quantum theory of atoms in molecules, QTAIM; the natural bond orbital, NBO; the energy decomposition analysis, EDA; and the noncovalent interactions method, NCI. The results show that the tetrel bonds analyzed here are rather weak, and they are not detected by the QTAIM approach; however, they are detected by other approaches, like NBO, for example. On the other hand, the triel bonds that occur in a few complexes discussed here are very strong and possess characteristics of covalent bonds.
Collapse
Affiliation(s)
- Mohammad Aarabi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Samira Gholami
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Sławomir J Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
| |
Collapse
|
6
|
Maalaoui A, Agwamba EC, Louis H, Mathias GE, Rzaigui M, Akriche S. Combined Experimental and Computational Study of V-Substituted Lindqvist Polyoxotungstate: Screening by Docking for Potential Antidiabetic Activity. Inorg Chem 2023; 62:14279-14290. [PMID: 37616561 PMCID: PMC10481374 DOI: 10.1021/acs.inorgchem.3c01651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 08/26/2023]
Abstract
In the current work, a novel vanadotungstate compound, (C6H9N2)4[V2W4O19]·2H2O (1), is isolated by a simple stepwise synthesis method and characterized by a combined experimental and computational study. Molecular docking is conducted for the first time for this kind of substituted Lindqvist polyoxometalates to elucidate for potential antidiabetic activity. Hence, the modeling results revealed a significant docking score of the reported compound to bind to the active sites of α-glucosidase with the lowest binding energy of -5.7 kcal/mol, where the standard drug acarbose (ACB) had -4.6 kcal/mol binding energy. The stability of binding was enhanced by strong H-bonding, van der Waals, and electrostatic interactions occurring in the three-dimensional (3D) supramolecular network of polyanionic vanadotungstate subunits templated with organic moieties as shown by X-ray diffraction and Hirshfeld analyses. Furthermore, density functional theory (DFT) calculations supported with photophysical measurements are also discussed to predict the most chemical and biological reactivity. In this view, the complete description of electronic and biological features of (1) is enhanced by determination of the highest occupied molecular orbital (HOMO)/least unoccupied molecular orbital (LUMO) energy, electronic density, ionization potential, electron affinity, etc. These chemical descriptors, intermolecular interactions, docking score, and binding free energy estimation are essential in understanding the reactivity of this bioactive compound offering potential inhibition of the α-glucosidase enzyme.
Collapse
Affiliation(s)
- Ahlem Maalaoui
- Laboratory
of Materials Chemistry, Faculty of Sciences
of Bizerte, 7021 Zarzouna, Bizerte, Tunisia
| | - Ernest C. Agwamba
- Department
of Chemistry, Covenant University, Idiroko Road, P.M.B, Ota 1023, Ogun
State, Nigeria
- Computational
and Bio-Simulation Research Group, University
of Calabar, P.M.B. 1115, Calabar 540221, Nigeria
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, P.M.B. 1115, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, University
of Calabar, P.M.B. 1115, Calabar 540221, Nigeria
| | - Gideon E. Mathias
- Computational
and Bio-Simulation Research Group, University
of Calabar, P.M.B. 1115, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, University
of Calabar, P.M.B. 1115, Calabar 540221, Nigeria
| | - Mohamed Rzaigui
- Laboratory
of Materials Chemistry, Faculty of Sciences
of Bizerte, 7021 Zarzouna, Bizerte, Tunisia
| | - Samah Akriche
- Laboratory
of Materials Chemistry, Faculty of Sciences
of Bizerte, 7021 Zarzouna, Bizerte, Tunisia
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Novoa T, Laplaza R, Peccati F, Fuster F, Contreras-García J. The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems. J Chem Inf Model 2023; 63:4483-4489. [PMID: 37537899 DOI: 10.1021/acs.jcim.3c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.
Collapse
Affiliation(s)
- Trinidad Novoa
- Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F-75005 Paris, France
- Laboratoire Jacques-Louis Lions, LJLL, Sorbonne Université, CNRS, F-75005 Paris, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F-75005 Paris, France
| | - Francesca Peccati
- Basque Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Franck Fuster
- Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F-75005 Paris, France
| | | |
Collapse
|
9
|
Azzouzi M, Ouafi ZE, Azougagh O, Daoudi W, Ghazal H, Barkany SE, Abderrazak R, Mazières S, Aatiaoui AE, Oussaid A. Design, synthesis, and computational studies of novel imidazo[1,2- a]pyrimidine derivatives as potential dual inhibitors of hACE2 and spike protein for blocking SARS-CoV-2 cell entry. J Mol Struct 2023; 1285:135525. [PMID: 37057139 PMCID: PMC10080474 DOI: 10.1016/j.molstruc.2023.135525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
In the present work, a new series of imidazo[1,2-a]pyrimidine Schiff base derivatives have been obtained using an easy and conventional synthetic route. The synthesized compounds were spectroscopically characterized using 1H, 13C NMR, LC-MS(ESI), and FT-IR techniques. Green metric calculations indicate adherence to several green chemistry principles. The energy of Frontier Molecular Orbitals (FMO), Molecular Electrostatic Potential (MEP), Quantum Theory of Atoms in Molecules (QTAIM), and Reduced Density Gradient (RDG) were determined by the Density Functional Theory (DFT) method at B3LYP/6-31 G (d, p) as the basis set. Moreover, molecular docking studies targeting the human ACE2 and the spike, key entrance proteins of the severe acute respiratory syndrome coronavirus-2 were carried out along with hACE2 natural ligand Angiotensin II, the MLN-4760 inhibitor as well as the Cannabidiolic Acid CBDA which has been demonstrated to bind to the spike protein and block cell entry. The molecular modeling results showed auspicious results in terms of binding affinity as the top-scoring compound exhibited a remarkable affinity (-9.1 and -7.3 kcal/mol) to the ACE2 and spike protein respectively compared to CBDA (-5.7 kcal/mol), the MLN-4760 inhibitor (-7.3 kcal/mol), and angiotensin II (-9.2 kcal/mol). These findings suggest that the synthesized compounds may potentially act as effective entrance inhibitors, preventing the SARS-CoV-2 infection of human cells. Furthermore, in silico, ADMET, and drug-likeness prediction expressed promising drug-like characteristics.
Collapse
Affiliation(s)
- Mohamed Azzouzi
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Zainab El Ouafi
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences Casablanca, Casablanca, Morocco
| | - Omar Azougagh
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Walid Daoudi
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Hassan Ghazal
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences Casablanca, Casablanca, Morocco
- Electronic Systems, Sensors and Nanobiotechnologies (E2SN), École Nationale Supérieure des Arts et Métiers (ENSAM), Mohammed V University, Rabat, Morocco
| | - Soufian El Barkany
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Rfaki Abderrazak
- National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Stéphane Mazières
- Laboratory of IMRCP, University Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse 31062, France
| | - Abdelmalik El Aatiaoui
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Adyl Oussaid
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| |
Collapse
|
10
|
Nwankwo U, Wang YD, Lam CH, Onofrio N. Charge equilibration model with shielded long-range Coulomb for reactive molecular dynamics simulations. J Chem Phys 2023; 159:044104. [PMID: 37486045 DOI: 10.1063/5.0150280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Atomic description of electrochemical systems requires reactive interaction potential to explicitly describe the chemistry between atoms and molecules and the evolving charge distribution and polarization effects. Calculating Coulomb electrostatic interactions and polarization effects requires a better estimate of the partial charge distribution in molecular systems. However, models such as reactive force fields and charge equilibration (QEq) include Coulomb interactions up to a short-distance cutoff for better computational speeds. Ignoring long-distance electrostatic interaction affects the ability to describe electrochemistry in large systems. We studied the long-range Coulomb effects among charged particles and extended the QEq method to include long-range effects. By this extension, we anticipate a proper account of Coulomb interactions in reactive molecular dynamics simulations. We validate the approach by computing charges on a series of metal-organic frameworks and some simple systems. Results are compared to regular QEq and quantum mechanics calculations. The study shows slightly overestimated charge values in the regular QEq approach. Moreover, our method was combined with Ewald summation to compute forces and evaluate the long-range effects of simple capacitor configurations. There were noticeable differences between the calculated charges with/without long-range Coulomb interactions. The difference, which may have originated from the long-range influence on the capacitor ions, makes the Ewald method a better descriptor of Coulomb electrostatics for charged electrodes. The approach explored in this study enabled the atomic description of electrochemical systems with realistic electrolyte thickness while accounting for the electrostatic effects of charged electrodes throughout the dielectric layer in devices like batteries and emerging solid-state memory.
Collapse
Affiliation(s)
- Udoka Nwankwo
- Department of Applied Physics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yi-Di Wang
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Chi-Hang Lam
- Department of Applied Physics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Nicolas Onofrio
- Department of Applied Physics, The Hong Kong Polytechnic University, Hong Kong, China
| |
Collapse
|
11
|
Nguyen TH, Nguyen TH, Le TTT, Vu Dang H, Nguyen HMT. Interactions between Paracetamol and Formaldehyde: Theoretical Investigation and Topological Analysis. ACS OMEGA 2023; 8:11725-11735. [PMID: 37033805 PMCID: PMC10077466 DOI: 10.1021/acsomega.2c05023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/02/2022] [Indexed: 06/19/2023]
Abstract
In this work, noncovalent interactions including hydrogen bonds, C···C, N···O, and van der Waals forces between paracetamol and formaldehyde were investigated using the second-order perturbation theory MP2 in conjunction with the correlation consistent basis sets (aug-cc-pVDZ and aug-cc-pVTZ). Two molecular conformations of paracetamol were considered. Seven equilibrium geometries of dimers were found from the result of the interactions with formaldehyde for each conformation of paracetamol. Interaction energies of complexes with both ZPE and BSSE corrections range from -7.0 to -21.7 kJ mol-1. Topological parameters (such as electron density, its Laplacian, and local electron energy density at the bond critical points) of the bonds from atoms in molecules theory were analyzed in detail. The natural bond orbital analysis showed that the stability of complexes was controlled by noncovalent interactions including O-H···O, N-H···O, C-H···O, C-H···N, C-H···H-C, C···C, and N···O. The red- and blue-shifted hydrogen bonds could both be observed in these complexes. The properties of these interactions were also further examined in water using a polarized continuum model. In water, the stability of the complex was slightly reduced as compared to that in the gas phase.
Collapse
Affiliation(s)
- Tho Huu Nguyen
- Faculty
of Natural Sciences Pedagogy, Saigon University, 273 An Duong Vuong, Ward 3, District
5, Ho Chi Minh City 700000, Vietnam
| | - Tri Huu Nguyen
- Faculty
of Natural Sciences Pedagogy, Saigon University, 273 An Duong Vuong, Ward 3, District
5, Ho Chi Minh City 700000, Vietnam
| | - Thi Thanh Thuy Le
- Faculty
of Natural Sciences Pedagogy, Saigon University, 273 An Duong Vuong, Ward 3, District
5, Ho Chi Minh City 700000, Vietnam
| | - Hoang Vu Dang
- Department
of Analytical Chemistry and Toxicology, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 100000, Vietnam
| | - Hue Minh Thi Nguyen
- Faculty
of Chemistry and Center for Computational Science, Hanoi National University of Education, 136 Xuan Thuy Street, Cau Giay, Hanoi 100000, Vietnam
| |
Collapse
|
12
|
Seijas LE, Zambrano CH, Almeida R, Alí-Torres J, Rincón L, Torres FJ. Exploring the Non-Covalent Bonding in Water Clusters. Int J Mol Sci 2023; 24:ijms24065271. [PMID: 36982342 PMCID: PMC10049637 DOI: 10.3390/ijms24065271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
QTAIM and source function analysis were used to explore the non-covalent bonding in twelve different water clusters (H2O)n obtained by considering n = 2–7 and various geometrical arrangements. A total of seventy-seven O−H⋯O hydrogen bonds (HBs) were identified in the systems under consideration, and the examination of the electron density at the bond critical point (BCP) of these HBs revealed the existence of a great diversity of O−H⋯O interactions. Furthermore, the analysis of quantities, such as |V(r)|/G(r) and H(r), allowed a further description of the nature of analogous O−H⋯O interactions within each cluster. In the case of 2-D cyclic clusters, the HBs are nearly equivalent between them. However, significant differences among the O−H⋯O interactions were observed in 3-D clusters. The assessment of the source function (SF) confirmed these findings. Finally, the ability of SF to decompose the electron density (ρ) into atomic contributions allowed the evaluation of the localized or delocalized character of these contributions to ρ at the BCP associated to the different HBs, revealing that weak O−H⋯O interactions have a significant spread of the atomic contributions, whereas strong interactions have more localized atomic contributions. These observations suggest that the nature of the O−H⋯O hydrogen bond in water clusters is determined by the inductive effects originated by the different spatial arrangements of the water molecules in the studied clusters.
Collapse
Affiliation(s)
- Luis E. Seijas
- Grupo de Química Computacional y Teórica (QCT-UR), Escuela de Ingeniería Ciencia y Tecnología (EICT), Universidad del Rosario, Bogotá 111221, Colombia
| | - Cesar H. Zambrano
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Rafael Almeida
- Laboratorio de Procesos Dinámicos en Química, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Jorge Alí-Torres
- Departamento de Química, Universidad Nacional de Colombia, Av. Cra. 30 #45-03, Bogotá 111321, Colombia
| | - Luis Rincón
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Fernando Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Escuela de Ingeniería Ciencia y Tecnología (EICT), Universidad del Rosario, Bogotá 111221, Colombia
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Correspondence:
| |
Collapse
|
13
|
Mhadhbi N, Dgachi S, Ben Ahmed A, Issaoui N, Nasr S, Badraoui R, Badraoui B, Naïli H. Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsonate Salt of 4-Aminopyridine. CHEMISTRY AFRICA 2023. [PMCID: PMC9926452 DOI: 10.1007/s42250-023-00620-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
In this work, a structural and electronic properties of a novel organic arsenate template by 4-aminopyridine, with the general formula (C5H7N2)(C5H8N2)[AsO4]·H2O ((4-APH)(4-APH2)[AsO4]·H2O) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The examination of the vibrational spectrum was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. Besides, the thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO–LUMO energy gap, NLO characteristic and Hirshfeld surface analysis were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Molecular docking studies were also conducted as part of this study. The theoretical results showed an excellent agreement with the experimental values.
Collapse
Affiliation(s)
- Noureddine Mhadhbi
- grid.412124.00000 0001 2323 5644Laboratory of Solid State, Department of Chemistry, Faculty of Sciences of Sfax, University of Sfax, B.P. N°1171, 3000 Sfax, Tunisia
| | - Souad Dgachi
- grid.412124.00000 0001 2323 5644Laboratory of Solid State, Department of Chemistry, Faculty of Sciences of Sfax, University of Sfax, B.P. N°1171, 3000 Sfax, Tunisia
| | - Ali Ben Ahmed
- grid.412124.00000 0001 2323 5644Laboratory of Applied Physics, Department of Physics, Faculty of Sciences of Sfax, University of Sfax, B.P. N°802, 3018 Sfax, Tunisia
| | - Noureddine Issaoui
- grid.411838.70000 0004 0593 5040Laboratory of Quantum and Statistical Physics, Department of Physics, Faculty of Sciences of Monastir, University of Monastir, 5079 Monastir, Tunisia
| | - Samia Nasr
- grid.442525.00000 0000 9284 9597Preparatory Institute for Engineering Studies Kairouan, Electrochemistry, Materials and Environment, University of Kairouan, Kairouan, Tunisia
| | - Riadh Badraoui
- grid.12574.350000000122959819Section of Histology-Cytology, Medicine Faculty of Tunis, University of Tunis El Manar, La Rabta, 1007 Tunis, Tunisia
| | - Bechir Badraoui
- grid.411838.70000 0004 0593 5040Research Unity of Materials and Et Organic Synthesis, Preparatory Institute for Engineering Studies of Monastir, University of Monastir, 5019 Monastir, Tunisia
| | - Houcine Naïli
- grid.412124.00000 0001 2323 5644Laboratory of Solid State, Department of Chemistry, Faculty of Sciences of Sfax, University of Sfax, B.P. N°1171, 3000 Sfax, Tunisia
| |
Collapse
|
14
|
Wieduwilt EK, Boto RA, Macetti G, Laplaza R, Contreras-García J, Genoni A. Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses. J Chem Theory Comput 2023; 19:1063-1079. [PMID: 36656682 DOI: 10.1021/acs.jctc.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.
Collapse
Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Roberto A Boto
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| |
Collapse
|
15
|
Louis H, Akem MU, Benjamin I, Chukwu UG, Asogwa FC, Adeyinka AS. Modelling of Tungsten (C
59
W), Osmium (C
59
O
s
), and Platinum (C
59
Pt) Doped Fullerenes for Drug Delivery of Biguanides (BNG) and Metformin (MET): DFT Perspective. ChemistrySelect 2023. [DOI: 10.1002/slct.202203298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hitler Louis
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Martilda U. Akem
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Innocent Benjamin
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Microbiology Faculty of Biological Sciences University of Calabar Calabar Nigeria
| | - Udochukwu G. Chukwu
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Fredrick C. Asogwa
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Adedapo S. Adeyinka
- Department of Chemical Sciences University of Johannesburg 2006 Johannesburg South-Africa
| |
Collapse
|
16
|
Quantum chemical studies on hydrogen bonds in helical secondary structures. Biophys Rev 2023; 14:1369-1378. [PMID: 36659988 PMCID: PMC9842822 DOI: 10.1007/s12551-022-01034-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/30/2022] [Indexed: 01/07/2023] Open
Abstract
We present a brief review of our recent computational studies of hydrogen bonds (H-bonds) in helical secondary structures of proteins, α-helix and 310-helix, using a Negative Fragmentation Approach with density functional theory. We found that the depolarized electronic structures of the carbonyl oxygen of the ith residue and the amide hydrogen of the (i + 4)th residue cause weaker H-bond in an α-helix than in an isolated H-bond. Our calculations showed that the H-bond energies in the 310-helix were also weaker than those of the isolated H-bonds. In the 310-helices, the adjacent N-H group at the (i + 1)th residue was closer to the C=O group of the H-bond pair than the adjacent C=O group in the 310-helices, whereas the adjacent C=O group at the (i + 1)th residue was close to the H-bond acceptor in α-helices. Therefore, the destabilization of the H-bond is attributed to the depolarization caused by the adjacent residue of the helical backbone connecting the H-bond donor and acceptor. The differences in the change in electron density revealed that such depolarizations were caused by the local electronic interactions in their neighborhood inside the helical structure and redistributed the electron density. We also present the improvements in the force field of classical molecular simulation, based on our findings. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-022-01034-5.
Collapse
|
17
|
Nature of the Dative Nitrogen-Coinage Metal Bond in Molecular Motors. Evaluation of NHC-M Pyrazine Bond (M=Cu, Ag, Au) from Relativistic DFT. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
18
|
Al-Otaibi JS, Sheena Mary Y, Fazil S, Mary YS, Sarala S. Modeling the structure and reactivity landscapes of a pyrazole-ammonium ionic derivative using wavefunction-dependent characteristics and screening for potential anti-inflammatory activity. J Biomol Struct Dyn 2022; 40:11190-11202. [PMID: 34328395 DOI: 10.1080/07391102.2021.1957020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Spectroscopic investigations of 1-phenyl -2,3-dimethyl-5-oxo-1,2-dihydro-1H-pyrazol-4-ammonium 2[(2-carboxyphenyl) disulfanyl]benzoate (PACB) reported experimentally and theoretically. NH-O interaction is observed and there is a very large downshift for NH-O stretching frequency. Reactive sites are identified from the chemical and electronic properties. For PACB the maximum repulsion was around H33, H55 and H57 atom. LOL shows red regions between C-C and blue around C atoms are surrounded by a delocalized electron cloud. The red ring is a hallmark of electron density depletion from the NCI plot due to electrostatic repulsion and its existences suggests that coordination sphere for PACB is minimally strained around the central ion. Atomic contact energy values and high score of the docking results obtained propose that, PACB may have inhibitory properties and have a significant function in pharmacological chemistry. Molecular dynamics simulation was performed to validate the stability of the title compound with the Bovine thrombin-activatable fibrinolysis inhibitor protein.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Shiji Fazil
- Department of Chemistry, Mannaniya College of Arts and Science, Pangode, Kerala, India
| | | | - S Sarala
- Department of Physics, Kanchi Shri Krishna College of Arts and Science, Kanchipuram, Tamil Nadu, India
| |
Collapse
|
19
|
Buvaylo EA, Nesterova OV, Goreshnik EA, Vyshniakova HV, Petrusenko SR, Nesterov DS. Supramolecular Diversity, Theoretical Investigation and Antibacterial Activity of Cu, Co and Cd Complexes Based on the Tridentate N,N,O-Schiff Base Ligand Formed In Situ. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238233. [PMID: 36500325 PMCID: PMC9740120 DOI: 10.3390/molecules27238233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
The four new complexes, [Cu(HL1)(L2)Cl] (1), [Cu(HL1)(L1)]∙Cl∙2H2O (2), [Co(L1)2]∙Cl (3) and [Cd(HL1)I2]∙dmso (4), have been prepared by one-pot reactions of the respective chloride or iodide metal salt with a non-aqueous solution of the polydentate Schiff base, HL1, resulted from in situ condensation of benzhydrazide and 2-pyridinecarboxaldehyde, while a ligand HL2, in case of 1, has been formed due to the oxidation of 2-pyridinecarboxaldehyde under reaction conditions. The crystallographic analysis revealed that the molecular building units in 1-4 are linked together into complex structures by hydrogen bonding, resulting in 1D, 2D and 3D supramolecular architectures for 1, 2 and 4, respectively, and the supramolecular trimer for 3. The electronic structures of 1-4 were investigated by the DFT theoretical calculations. The non-covalent interactions in the crystal structures of 1-4 were studied by means of the Hirshfeld surface analysis and the QTAIM theory with a special focus on the C-H⋯Cl bonding. From the DFT/DLPNO-CCSD(T) calculations, using a series of charged model {R3C-H}0⋯Cl- assemblies, we propose linear regressions for assessment of the interaction enthalpy (ΔH, kcal mol-1) and the binding energy (BE, kcal mol-1) between {R3C-H}0 and Cl- sites starting from the electron density at the bond critical point (ρ(rBCP), a.u.): ΔH = -678 × ρ(r) + 3 and BE = -726 × ρ(r) + 4. It was also has been found that compounds 1, 3 and 4 during in vitro screening showed an antibacterial activity toward the nine bacteria species, comprising both Gram-positive and Gram-negative, with MIC values ranging from 156.2 to 625 mg/L. The best results have been obtained against Acinetobacter baumannii MβL.
Collapse
Affiliation(s)
- Elena A. Buvaylo
- Department of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska 64/13, 01601 Kyiv, Ukraine
| | - Oksana V. Nesterova
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Evgeny A. Goreshnik
- Department of Inorganic Chemistry and Technology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Hanna V. Vyshniakova
- L.V. Gromashevsky Institute of Epidemiology and Infectious Diseases NAMS of Ukraine, M. Amosova 5, 03038 Kyiv, Ukraine
| | - Svitlana R. Petrusenko
- Department of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska 64/13, 01601 Kyiv, Ukraine
| | - Dmytro S. Nesterov
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Correspondence:
| |
Collapse
|
20
|
Yakiyama Y. Molecular-Shape-Organized Stimuli-Responsive Functional Crystalline Systems. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.1036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yumi Yakiyama
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University
| |
Collapse
|
21
|
Formation of C60-SnI4 Adducts. Insights of the role of σ-hole and Tetrel-bonding in the Strength and Interaction Nature from DFT calculations. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
22
|
Depolarizing Effects in Hydrogen Bond Energy in 3 10-Helices Revealed by Quantum Chemical Analysis. Int J Mol Sci 2022; 23:ijms23169032. [PMID: 36012292 PMCID: PMC9409261 DOI: 10.3390/ijms23169032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/18/2022] Open
Abstract
Hydrogen-bond (H-bond) energies in 310-helices of short alanine peptides were systematically examined by precise DFT calculations with the negative fragmentation approach (NFA), a modified method based on the molecular tailoring approach. The contribution of each H-bond was evaluated in detail from the 310-helical conformation of total energies (whole helical model, WH3-10 model), and the results were compared with the property of H-bond in α-helix from our previous study. The H-bond energies of the WH3-10 model exhibited tendencies different from those exhibited by the α-helix in that they depended on the helical position of the relevant H-bond pair. H-bond pairs adjacent to the terminal H-bond pairs were observed to be strongly destabilized. The analysis of electronic structures indicated that structural characteristics cause the destabilization of the H-bond in 310-helices. We also found that the longer the helix length, the more stable the H-bond in the terminal pairs of the WH3-10 model, suggesting the action of H-bond cooperativity.
Collapse
|
23
|
A combined experimental and theoretical studies of two new decavanadatet: (C6N2H9)4[H2V10O28]·4H2O and (C7H9NF)4[H2V10O28]·2H2O. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
24
|
N LT, K HM, S KC, S S, L M, P M, R JR, A SM, Karnan M, K LN. N-[2-(5-bromo-2-chloro-pyrimidin-4-yl)thio)-4-methoxy-phenyl]-4-chlorobenzenesulfonamide: The existence of H-bond and halogen bond interactions assisted supramolecular architecture – A quantum chemical investigation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
25
|
Deb Roy JS, Chowdhury D, Sanfui MH, Hassan N, Mahapatra M, Ghosh NN, Majumdar S, Chattopadhyay PK, Roy S, Singha NR. Ratiometric pH Sensing, Photophysics, and Cell Imaging of Nonaromatic Light-Emitting Polymers. ACS APPLIED BIO MATERIALS 2022; 5:2990-3005. [PMID: 35579235 DOI: 10.1021/acsabm.2c00297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Here, four nontraditional fluorescent polymers (NTFPs) of varying N,N-dimethyl-2-propenamide (DMPA) and butyl prop-2-enoate (BPE) mole ratios, i.e., 2:1 (NTFP1), 4:1 (NTFP2), 8:1 (NTFP3), and 16:1 (NTFP4), are prepared via random polymerization in water. The maximum fluorescence enhancement of NTFP3 makes it suitable for ratiometric pH sensing, Cu(II) sensing, and pH-dependent cell imaging of Madin-Darby canine kidney (MDCK) cells. The oxygen donor functionalities of NTFP3 involved in binding and sensing with Cu(II) ions are studied by absorption, emission, electron paramagnetic resonance, Fourier transform infrared (FTIR), and O1s/Cu2p X-ray photoelectron spectroscopies (XPS). The spectral responses of the ratiometric pH sensor within 1.5-11.5 confirm 22 and 44 nm red shifts in absorption and ratiometric emission, respectively. The striking color changes from blue (436 nm) to green (480 nm) via an increase in pH are thought to be the stabilization of the charged canonical form of tertiary amide, i.e., -C(O-)═N+(CH3)2, realized from the changes in the absorption/fluorescence spectra and XPS/FTIR analyses. The through-space n-π* interactions in the NTFP3 aggregate, N-branching-associated rigidity, and nonconventional intramolecular hydrogen bondings of adjacent NTFP3 moieties in the NTFP3 aggregate contribute to aggregation-enhanced emissions (AEEs). Here, structures of NTFP3, NTFP3 aggregate, and Cu(II)-NTFP3; absorption; n-π* interactions; hydrogen bondings; AEEs; and binding with Cu(II) are ascertained by density functional theory, time-dependent density functional theory, and reduced density gradient calculations. The excellent limits of detection and Stern-Volmer constants of NTFP3 are 2.24 nM/0.14234 ppb and 4.26 × 103 M-1 at pH = 6.5 and 0.95 nM/0.06037 ppb and 4.90 × 103 M-1 at pH = 8.0, respectively. Additionally, the Stokes shift and binding energy of NTFP3 are 13,636 cm-1/1.69 eV and -4.64 eV, respectively. The pH-dependent MDCK cell imaging ability of noncytotoxic NTFP3 is supported via fluorescence imaging and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay.
Collapse
Affiliation(s)
- Joy Sankar Deb Roy
- Advanced Polymer Laboratory, Department of Polymer Science and Technology, Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata, West Bengal 700106, India
| | - Deepak Chowdhury
- Advanced Polymer Laboratory, Department of Polymer Science and Technology, Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata, West Bengal 700106, India
| | - Md Hussain Sanfui
- Advanced Polymer Laboratory, Department of Polymer Science and Technology, Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata, West Bengal 700106, India
| | - Nadira Hassan
- Advanced Polymer Laboratory, Department of Polymer Science and Technology, Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata, West Bengal 700106, India
| | - Manas Mahapatra
- Advanced Polymer Laboratory, Department of Polymer Science and Technology, Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata, West Bengal 700106, India
| | - Narendra Nath Ghosh
- Department of Chemistry, University of Gour Banga, Mokdumpur, Malda, West Bengal 732103, India
| | - Swapan Majumdar
- Department of Chemistry, Tripura University, Suryamaninagar, Agartala 799022, India
| | - Pijush Kanti Chattopadhyay
- Department of Leather Technology, Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata, West Bengal 700106, India
| | - Subhasis Roy
- Department of Chemical Engineering, University of Calcutta, 92, A.P.C. Road, Kolkata, West Bengal 700009, India
| | - Nayan Ranjan Singha
- Advanced Polymer Laboratory, Department of Polymer Science and Technology, Government College of Engineering and Leather Technology (Post Graduate), Maulana Abul Kalam Azad University of Technology, Salt Lake City, Kolkata, West Bengal 700106, India
| |
Collapse
|
26
|
Keil H, Herbst-Irmer R, Rathjen S, Girschik C, Müller T, Stalke D. Si-H···Se Chalcogen-Hydride Bond Quantified by Diffraction and Topological Analyses. Inorg Chem 2022; 61:6319-6325. [PMID: 35420429 DOI: 10.1021/acs.inorgchem.2c00629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Si-H···Se contact in 1-mesitylselanyl-8-(dimethylsilyl)naphthalene (1), which exhibits the spatial arrangement of a δ-agostic interaction from geometric considerations, was investigated. Is this just enforced by close 1,8-proximity or is this a favorable interaction? Charge density studies are best suited to investigate the exact origin of the interaction and to quantify the properties. Hence, they are most elucidating. High-resolution X-ray diffraction data of 1 were collected, and a multipole refinement followed by a topological analysis using Bader's quantum theory of atoms in molecules was employed. The resulting bond properties were set in relation to high-level computational parameters. The comparison to Si-H···[M] agostics, hydride bonding, chalcogen bonds, and charge-inverted hydrogen bonds qualified the Si-H···Se noncovalent interaction to be best classified as a chalcogen-hydride bond.
Collapse
Affiliation(s)
- Helena Keil
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Regine Herbst-Irmer
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Saskia Rathjen
- Institut für Chemie, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Corinna Girschik
- Institut für Chemie, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Thomas Müller
- Institut für Chemie, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Dietmar Stalke
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| |
Collapse
|
27
|
Ding K, Yin S, Li Z, Jiang S, Yang Y, Zhou W, Zhang Y, Huang B. Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein–Ligand Interaction Research. J Chem Inf Model 2022; 62:1734-1743. [DOI: 10.1021/acs.jcim.1c01406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kang Ding
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Shiqiu Yin
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Zhongwei Li
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Shiju Jiang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Yang Yang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Wenbiao Zhou
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Yingsheng Zhang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Bo Huang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| |
Collapse
|
28
|
Nguyen HT, Bui TQ, Nhat PV, Lan DTP, Nhung NTA. A DFT study of the molecular and electronic structures of cis-dioxidomolybdenum (VI) complex of 8-hydroxyquinoline and 4-benzoyl-3-methyl-1-phenyl-2-pyrazolin-5-one with water. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02868-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
29
|
Chalcogen Bonding in the Molecular Dimers of WCh 2 (Ch = S, Se, Te): On the Basic Understanding of the Local Interfacial and Interlayer Bonding Environment in 2D Layered Tungsten Dichalcogenides. Int J Mol Sci 2022; 23:ijms23031263. [PMID: 35163185 PMCID: PMC8835845 DOI: 10.3390/ijms23031263] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 01/28/2023] Open
Abstract
Layered two-dimensional transition metal dichalcogenides and their heterostructures are of current interest, owing to the diversity of their applications in many areas of materials nanoscience and technologies. With this in mind, we have examined the three molecular dimers of the tungsten dichalcogenide series, (WCh2)2 (Ch = S, Se, Te), using density functional theory to provide insight into which interactions, and their specific characteristics, are responsible for the interfacial/interlayer region in the room temperature 2H phase of WCh2 crystals. Our calculations at various levels of theory suggested that the Te···Te chalcogen bonding in (WTe2)2 is weak, whereas the Se···Se and S···S bonding interactions in (WSe2)2 and (WS2)2, respectively, are of the van der Waals type. The presence and character of Ch···Ch chalcogen bonding interactions in the dimers of (WCh2)2 are examined with a number of theoretical approaches and discussed, including charge-density-based approaches, such as the quantum theory of atoms in molecules, interaction region indicator, independent gradient model, and reduced density gradient non-covalent index approaches. The charge-density-based topological features are shown to be concordant with the results that originate from the extrema of potential on the electrostatic surfaces of WCh2 monomers. A natural bond orbital analysis has enabled us to suggest a number of weak hyperconjugative charge transfer interactions between the interacting monomers that are responsible for the geometry of the (WCh2)2 dimers at equilibrium. In addition to other features, we demonstrate that there is no so-called van der Waals gap between the monolayers in two-dimensional layered transition metal tungsten dichalcogenides, which are gapless, and that the (WCh2)2 dimers may be prototypes for a basic understanding of the physical chemistry of the chemical bonding environments associated with the local interfacial/interlayer regions in layered 2H-WCh2 nanoscale systems.
Collapse
|
30
|
Molecular structure, spectroscopy, quantum chemical and antibacterial activity investigations of 2-methylbenzylammonium perchlorate. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
31
|
Al-Otaibi JS, Mary YS, Mary YS, Yadav R. Structural and reactivity studies of pravadoline –An ionic liquid, with reference to its wavefunction-relative properties using DFT and MD simulation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
32
|
Hajji M, Abad N, Habib MA, Elmgirhi SMH, Guerfel T. Computational chemistry methods for modelling non-covalent interactions and chemical reactivity— An overview. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
33
|
Intermolecular hydrogen bonds interactions in water clusters of ammonium sulfamate: FTIR, X-ray diffraction, AIM, DFT, RDG, ELF, NBO analysis. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117475] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
34
|
Yakiyama Y, Fujinaka T, Nishimura M, Seki R, Sakurai H. Pyridine Ring Modification of Indane‐1,3‐dione Dimers for Control of their Crystal Structure. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yumi Yakiyama
- Division of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita, Osaka 565-0871 Japan
- Innovative Catalysis Science Division Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI) Osaka University 2-1 Yamadaoka Suita, Osaka 565-0871 Japan
| | - Takahisa Fujinaka
- Division of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita, Osaka 565-0871 Japan
| | - Mio Nishimura
- Division of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita, Osaka 565-0871 Japan
| | - Ryotaro Seki
- Division of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita, Osaka 565-0871 Japan
| | - Hidehiro Sakurai
- Division of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita, Osaka 565-0871 Japan
- Innovative Catalysis Science Division Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI) Osaka University 2-1 Yamadaoka Suita, Osaka 565-0871 Japan
| |
Collapse
|
35
|
Bellia SA, Teodoro LI, Traver J, Guillet GL, Zeller M, Hillesheim PC. Structural, surface, and computational analysis of two vitamin-B1 crystals with sulfonimide-based anions. Z KRIST-CRYST MATER 2021. [DOI: 10.1515/zkri-2021-2040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Two crystals incorporating the thiamine·HCl cation and the fluorinated anion 1,3-disulfonylhexafluoropropyleneimide have been characterized via single-crystal X-ray diffraction. The host-guest interactions of thiamine with the anions are analyzed and characterized using Hirshfeld surface analysis. The cations in both structures form a dimer in the solid-state via reciprocal hydrogen bonding through the amine and hydroxyl moieties. Additional investigation into the interactions responsible for dimer formation found that the sulfur atom in the thiazolium ring interacting with several hydrogen atoms to form stabilizing interactions. These interactions in the dimer are further analyzed using reduced density gradient analysis and the results are correlated to the fingerprint plots derived from the Hirshfeld surfaces. Moreover, specific interactions are observed from the cyclical anions, with both the fluorine and sulfonyl oxygen atoms participating in bridging interactions, displaying the diverse host-guest properties of thiamine.
Collapse
Affiliation(s)
- Sophia A. Bellia
- Department of Chemistry and Physics , Ave Maria University , Ave Maria , FL 34142 , USA
| | - Lara I. Teodoro
- Department of Chemistry and Physics , Ave Maria University , Ave Maria , FL 34142 , USA
| | - Joseph Traver
- Department of Chemistry and Physics , Ave Maria University , Ave Maria , FL 34142 , USA
| | - Gary L. Guillet
- Department of Chemistry and Biochemistry , Georgia Southern University , Savannah , GA 31419 , USA
| | - Matthias Zeller
- Department of Chemistry , Purdue University , West Lafayette , IN 47907 , USA
| | - Patrick C. Hillesheim
- Department of Chemistry and Physics , Ave Maria University , Ave Maria , FL 34142 , USA
- Department of Chemistry and Physics , Florida Gulf Coast University , Fort Myers , FL 33965 , USA
| |
Collapse
|
36
|
Hiremath SM. Vibrational, electronic and reactivity insight on (5-chloro-benzofuran-3-yl)-acetic acid hydrazide: A Spectroscopic and DFT approach. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
37
|
Thatipamula KC, Bhargavi G, Rajasekharan MV. Structural Trends in 3 d–4 f Systems. Part II:
Ln
(NO
3
)
3
‐Cu(NO
3
)
2
‐2,2‐biyridine/5,5‐dimethyl‐2,2‐bipyridine (
Ln
=La‐Nd, Sm‐Lu). ChemistrySelect 2021. [DOI: 10.1002/slct.202101566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
38
|
Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions. Chemistry 2021; 27:7789-7809. [PMID: 33769620 DOI: 10.1002/chem.202005497] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/16/2023]
Abstract
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
Collapse
Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| |
Collapse
|
39
|
Heidarpoor Saremi L, Dadashi Noshahr K, Ebrahimi A, Khalegian A, Abdi K, Lagzian M. Multi-stage screening to predict the specific anticancer activity of Ni(II) mixed-ligand complex on gastric cancer cells; biological activity, FTIR spectrum, DNA binding behavior and simulation studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119377. [PMID: 33440284 DOI: 10.1016/j.saa.2020.119377] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/08/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
The anticancer activity of a transition metal complex with [Ni(L1)2L2]H2O (where L1 and L2 were acetylacetonato (acac) and 2-aminopyridine (2-ampy), respectively) was evaluated in MKN45 cell line. Methyl thiazolyl tetrazolium (MTT) assay was performed to assess the antitumor capacity of the Ni(II) complex against gastric cancer cell line MKN45. The complexexhibited high in vitro antitumor activity against MKN45 cells with IC50values of 1.99 μM in 48 hrs. The alterations in the structure of cellular biomolecules (proteins, lipids, carbohydrates, and especially DNA) by the Ni(II) complex were confirmed by bio spectroscopic studies. Fourier Transformed Infrared (FTIR) spectroscopy analysis revealed significant differences between untreated and treated MKN45 cell line in the region of glycogen, nucleic acid, amide I and amide II bands (1000, 1100, ~1650, and ~1577 cm-1). The absorption bands 1150 cm-1 and 1020-1025 cm-1 can be assigned to the CO bond of glycogen and other carbohydrates and are significantly overlapped by DNA. The interaction of calf thymus (CT) DNA with Ni(II) complex was explored using absorption spectral method. The UV-visible studies demonstrated that this complex was able to bind with DNA via groove, non-covalent, and electrostatic interactions, and binding constant (Kb) was found to be 3 * 104. Docking simulation and Non Covalent Interaction (NCI) topological analysis were conducted to provide insights into the nature of DNA/complex interactions. The binding affinity and binding stability of complex was validated by 400-ns MD simulations.
Collapse
Affiliation(s)
- Leily Heidarpoor Saremi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan, Iran
| | - Karim Dadashi Noshahr
- Semnan University of Medical Science, Faculty of Medicine, Medical Biotechnology Department, Semnan, Iran
| | - Ali Ebrahimi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan, Iran.
| | - Ali Khalegian
- Semnan University of Medical Science, Faculty of Medicine, Biochemistry Department, Semnan, Iran.
| | - Khatereh Abdi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Milad Lagzian
- Department of Biology, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
| |
Collapse
|
40
|
Kuznetsov ML. Strength of the [Z-I···Hal] - and [Z-Hal···I] - Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy. Molecules 2021; 26:2083. [PMID: 33916483 PMCID: PMC8038634 DOI: 10.3390/molecules26072083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 11/29/2022] Open
Abstract
Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, Eint, using relationships between Eint and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between Eint and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z-I···Hal]- and [Z-Hal···I]- types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06-4.76 kcal/mol.
Collapse
Affiliation(s)
- Maxim L. Kuznetsov
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal; ; Tel.: +351-218-419-236
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia
| |
Collapse
|
41
|
Muñoz-Castro A, Wang G, Ponduru TT, Dias HVR. Synthesis and characterization of N-heterocyclic carbene-MOEt 2 complexes (M = Cu, Ag, Au). Analysis of solvated auxiliary-ligand free [(NHC)M] + species. Phys Chem Chem Phys 2021; 23:1577-1583. [PMID: 33406199 DOI: 10.1039/d0cp05222a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis, characterization and computational analysis of coinage metal-ether complexes supported by N-heterocyclic carbenes (NHC), SIPr and Et2CAAC. The related water adducts are also included. The [(NHC)M]+(M = Cu, Ag, Au) species show the noteworthy ability to bind Et2O and H2O. This interaction towards Et2O and H2O is partly ascribed to a σ-hole bonding with an almost linear disposition, taking advantage of the enhanced σ-hole potential evaluated for such [(NHC)M]+ species. This enhanced ability is larger than those found for non-covalent interactions involving main group species.
Collapse
Affiliation(s)
- Alvaro Muñoz-Castro
- Grupo de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería, Universidad Autonoma de Chile, El Llano Subercaseaux 2801, Santiago, Chile.
| | - Guocang Wang
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA.
| | - Tharun Teja Ponduru
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA.
| | - H V Rasika Dias
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA.
| |
Collapse
|
42
|
A triorganotin(IV) cocrystal with pyridinic phosphoramide: crystal structure and DFT calculations. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-020-01461-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
43
|
Wieduwilt EK, Boisson JC, Terraneo G, Hénon E, Genoni A. A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. J Chem Inf Model 2021; 61:795-809. [PMID: 33444021 DOI: 10.1021/acs.jcim.0c01188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.
Collapse
Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Jean-Charles Boisson
- CReSTIC EA 3804, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milan I-20131, Italy
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| |
Collapse
|
44
|
Multiresolution non-covalent interaction analysis for ligand–protein promolecular electron density distributions. Theor Chem Acc 2021. [DOI: 10.1007/s00214-020-02705-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
45
|
Rojas-Poblete M, Rodríguez-Kessler PL, Guajardo Maturana R, Muñoz-Castro A. Coinage-metal pillarplexes hosts. Insights into host-guest interaction nature and luminescence quenching effects. Phys Chem Chem Phys 2021; 23:15917-15924. [PMID: 34086020 DOI: 10.1039/d1cp00849h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Host-guest chemistry is a relevant issue in materials science, which encourages further development of versatile host structures. Here the particular features of coinage-metal pillarplexes are evaluated towards formation of host-guest aggregates by the inclusion of 1,8-diaminooctane, as characterized for [M8(LMe)2]4+ (M = Ag, and, Au). The obtained results denotes the main contribution from van der Waals type interaction (50%), followed by a contribution from orbital polarization and electrostatic nature (20% and 30%), involving both orbitalary and electrostatic terms. Throughout the different coinage-metal based hosts (M = Cu, Ag, and Au), a similar interaction energy is found given by the large contribution of the π-surface from the organic ligand backbone to both van de Waals and electrostatic interactions. This suggests that a similar host structure can be obtained for the lighter copper counterpart, retaining similar how-guest features. Moreoves, the [Au8(LMe)2]4+ host exhibits inherent luminescent properties, involving the shortening of Au(i)-Au(i) contacts at the excited state, which is partially avoided when the guest is incorporated, accounting for the observed quenching from titration experiments. This results encourages further exploration of coinage metal hosts in the formation of inclusion complexes.
Collapse
Affiliation(s)
- Macarena Rojas-Poblete
- Instituto de Ciencias Químicas Aplicadas, Laboratorio de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería, Universidad Autonoma de Chile, El Llano Subercaseaux 2801, Santiago, Chile.
| | | | | | | |
Collapse
|
46
|
Laplaza R, Peccati F, A. Boto R, Quan C, Carbone A, Piquemal J, Maday Y, Contreras‐García J. NCIPLOT
and the analysis of noncovalent interactions using the reduced density gradient. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1497] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rubén Laplaza
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Departamento de Química Física Universidad de Zaragoza Zaragoza Spain
| | - Francesca Peccati
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université Paris France
| | - Roberto A. Boto
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Centro de Física de Materiales CFM‐MPC (CSIC‐UPV/EHU) Donostia Spain
| | - Chaoyu Quan
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université Paris France
- SUSTech International Center for Mathematics, and Department of Mathematics Southern University of Science and Technology Shenzhen China
| | - Alessandra Carbone
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB) Sorbonne Université Paris France
- Institut Universitaire de France Paris France
| | - Jean‐Philip Piquemal
- CNRS, Laboratoire de Chimie Théorique, LCT Sorbonne Université Paris France
- Institut Universitaire de France Paris France
| | - Yvon Maday
- SUSTech International Center for Mathematics, and Department of Mathematics Southern University of Science and Technology Shenzhen China
- Institut Universitaire de France Paris France
| | | |
Collapse
|
47
|
Jomaa I, Noureddine O, Gatfaoui S, Issaoui N, Roisnel T, Marouani H. Experimental, computational, and in silico analysis of (C8H14N2)2[CdCl6] compound. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128186] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
48
|
Ernst M, Genoni A, Macchi P. Analysis of crystal field effects and interactions using X-ray restrained ELMOs. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127975] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
49
|
Tikhomirova KA, Tantardini C, Sukhanova EV, Popov ZI, Evlashin SA, Tarkhov MA, Zhdanov VL, Dudin AA, Oganov AR, Kvashnin DG, Kvashnin AG. Exotic Two-Dimensional Structure: The First Case of Hexagonal NaCl. J Phys Chem Lett 2020; 11:3821-3827. [PMID: 32330050 DOI: 10.1021/acs.jpclett.0c00874] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
NaCl is one of the simplest compounds and was thought to be well-understood, and yet, unexpected complexities related to it were uncovered at high pressure and in low-dimensional states. Here, exotic hexagonal NaCl thin films on the (110) diamond surface were crystallized in the experiment following a theoretical prediction based on ab initio evolutionary algorithm USPEX. State-of-the-art calculations and experiments showed the existence of a hexagonal NaCl thin film, which is due to the strong chemical interaction of the NaCl film with the diamond substrate.
Collapse
Affiliation(s)
- Kseniya A Tikhomirova
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
| | - Christian Tantardini
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
| | - Ekaterina V Sukhanova
- Emanuel Institute of Biochemical Physics RAS, 4 Kosigina Street, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Pereulok, Dolgoprudny 141700, Russia
| | - Zakhar I Popov
- Emanuel Institute of Biochemical Physics RAS, 4 Kosigina Street, Moscow 119334, Russia
| | - Stanislav A Evlashin
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
| | - Mikhail A Tarkhov
- Institute of Nanotechnologies of Microelectronics of the Russian Academy of Sciences, 32 A Leninsky Prospekt, Moscow 119991, Russia
| | | | - Alexander A Dudin
- Institute of Nanotechnologies of Microelectronics of the Russian Academy of Sciences, 32 A Leninsky Prospekt, Moscow 119991, Russia
| | - Artem R Oganov
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Pereulok, Dolgoprudny 141700, Russia
- International Center for Materials Discovery, Northwestern Polytechnical University, Xi'an 710072, China
| | - Dmitry G Kvashnin
- Emanuel Institute of Biochemical Physics RAS, 4 Kosigina Street, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Pereulok, Dolgoprudny 141700, Russia
| | - Alexander G Kvashnin
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
| |
Collapse
|
50
|
The Volumetric Source Function: Looking Inside van der Waals Interactions. Sci Rep 2020; 10:7816. [PMID: 32385337 PMCID: PMC7210285 DOI: 10.1038/s41598-020-64261-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/14/2020] [Indexed: 01/23/2023] Open
Abstract
The study of van der Waals interactions plays a central role in the understanding of bonding across a range of biological, chemical and physical phenomena. The presence of van der Waals interactions can be identified through analysis of the reduced density gradient, a fundamental parameter at the core of Density Functional Theory. An extension of Bader’s Quantum Theory of Atoms in Molecules is developed here through combination with the analysis of the reduced density gradient. Through this development, a new quantum chemical topological tool is presented: the volumetric source function. This technique allows insight into the atomic composition of van der Waals interactions, offering the first route towards applying the highly successful source function to these disperse interactions. A new algorithm has been implemented in the open-source code, CRITIC2, and tested on acetone, adipic and maleic acids molecular crystals, each stabilized by van der Waals interactions. This novel technique for studying van der Waals interactions at an atomic level offers unprecedented opportunities in the fundamental study of intermolecular interactions and molecular design for crystal engineering, drug design and bio-macromolecular processes.
Collapse
|