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Ali MA, Sheikh H, Yaseen M, Faruqe MO, Ullah I, Kumar N, Bhat MA, Mollah MNH. Exploring the Therapeutic Potential of Petiveria alliacea L. Phytochemicals: A Computational Study on Inhibiting SARS-CoV-2's Main Protease (Mpro). Molecules 2024; 29:2524. [PMID: 38893400 PMCID: PMC11173994 DOI: 10.3390/molecules29112524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/21/2024] Open
Abstract
The outbreak of SARS-CoV-2, also known as the COVID-19 pandemic, is still a critical risk factor for both human life and the global economy. Although, several promising therapies have been introduced in the literature to inhibit SARS-CoV-2, most of them are synthetic drugs that may have some adverse effects on the human body. Therefore, the main objective of this study was to carry out an in-silico investigation into the medicinal properties of Petiveria alliacea L. (P. alliacea L.)-mediated phytocompounds for the treatment of SARS-CoV-2 infections since phytochemicals have fewer adverse effects compared to synthetic drugs. To explore potential phytocompounds from P. alliacea L. as candidate drug molecules, we selected the infection-causing main protease (Mpro) of SARS-CoV-2 as the receptor protein. The molecular docking analysis of these receptor proteins with the different phytocompounds of P. alliacea L. was performed using AutoDock Vina. Then, we selected the three top-ranked phytocompounds (myricitrin, engeletin, and astilbin) as the candidate drug molecules based on their highest binding affinity scores of -8.9, -8.7 and -8.3 (Kcal/mol), respectively. Then, a 100 ns molecular dynamics (MD) simulation study was performed for their complexes with Mpro using YASARA software, computed RMSD, RMSF, PCA, DCCM, MM/PBSA, and free energy landscape (FEL), and found their almost stable binding performance. In addition, biological activity, ADME/T, DFT, and drug-likeness analyses exhibited the suitable pharmacokinetics properties of the selected phytocompounds. Therefore, the results of this study might be a useful resource for formulating a safe treatment plan for SARS-CoV-2 infections after experimental validation in wet-lab and clinical trials.
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Affiliation(s)
- Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
- Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Humaira Sheikh
- Department of Chemistry, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj 8100, Bangladesh;
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, Faculty of Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ihsan Ullah
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur 313001, Rajasthan, India;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
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2
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Determan JJ, Wilson AK. Correlation consistent basis sets designed for density functional theory: Third-row atoms (Ga-Br). J Chem Phys 2024; 160:084105. [PMID: 38385513 DOI: 10.1063/5.0176964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/02/2024] [Indexed: 02/23/2024] Open
Abstract
The correlation consistent basis sets (cc-pVnZ with n = D, T, Q, 5) for the Ga-Br elements have been redesigned, tuning the sets for use for density functional approximations. Steps to redesign these basis sets for an improved correlation energy recovery and efficiency include truncation of higher angular momentum functions, recontraction of basis set coefficients, and reoptimization of basis set exponents. These redesigned basis sets are compared with conventional cc-pVnZ basis sets and other basis sets, which are, in principle, designed to achieve systematic improvement with respect to increasing basis set size. The convergence of atomic energies, bond lengths, bond dissociation energies, and enthalpies of formation to the Kohn-Sham limit is improved relative to other basis sets where convergence to the Kohn-Sham limit is typically not observed.
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Affiliation(s)
- John J Determan
- Department of Chemistry, Western Illinois University, Macomb, Illinois 61455, USA
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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Lobato JCM, Arouche TDS, Nero JD, Filho T, Borges RDS, Neto AMDJC. Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics. J Mol Struct 2023; 1286:135604. [PMID: 37089815 PMCID: PMC10111146 DOI: 10.1016/j.molstruc.2023.135604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/01/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
Molecular modeling techniques are used to describe the process of interaction between nanotubes and the main structures of the Covid-19 virus: the envelope protein, the main protease, and the Spike glycoprotein. Molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics simulations provide information on the mean squared deviation of atomic positions between 0.5 and 3.0 Å. The Gibbs free energy model and solvent accessible surface area approaches are used. Through the results obtained through molecular dynamics simulations, it is noted that the zig-zag nanotube prefers to interact with E-pro, M-pro, and S-gly, respectively. Molecular couplings and free energy showed that the S-gly active site residues strongly interact with zigzag, chiral, and armchair nanotubes, in this order. The interactions demonstrated in this manuscript may predict some promising candidates for virus antagonists, which may be confirmed through experimental approaches.
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Affiliation(s)
- Júlio Cesar Mendes Lobato
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
- Proderna, Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
| | - Tiago da Silva Arouche
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
| | - Jordan Del Nero
- Physics Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, 66075-110, Belém, PA, Brazil
| | - TarcisoAndrade Filho
- Federal University of the South and Southeast of Pará. 68507-590, Marabá - PA, Brazil
| | - Rosivaldo Dos Santos Borges
- Pharmacy Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
| | - Antonio Maia de Jesus Chaves Neto
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
- Physics Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, 66075-110, Belém, PA, Brazil
- Chemistry and Biochemistry, The University of Texas at Arlington, Box 19065, 700 Planetarium Place, Room 130, Arlington, TX 76019-0065
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4
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Bartashevich EV, Mukhitdinova SE, Klyuev IV, Tsirelson VG. Can We Merge the Weak and Strong Tetrel Bonds? Electronic Features of Tetrahedral Molecules Interacted with Halide Anions. Molecules 2022; 27:molecules27175411. [PMID: 36080180 PMCID: PMC9458139 DOI: 10.3390/molecules27175411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Using the orbital-free quantum crystallography approach, we have disclosed the quantitative trends in electronic features for bonds of different strengths formed by tetrel (Tt) atoms in stable molecular complexes consisting of electrically neutral tetrahedral molecules and halide anions. We have revealed the role of the electrostatic and exchange-correlation components of the total one-electron static potential that are determined by the equilibrium atomic structure and by kinetic Pauli potential, which reflects the spin-dependent electron motion features of the weak and strong bonds. The gap between the extreme positions in the electrostatic and total static potentials along the line linking the Tt atom and halide anion is wide for weak bonds and narrow for strong ones. It is in very good agreement with the number of minima in the Pauli potential between the bounded atoms. This gap exponentially correlates with the exchange-correlation potential in various series with a fixed nucleophilic fragment. A criterion for categorizing the noncovalent tetrel bonds (TtB) based on the potential features is suggested.
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Affiliation(s)
- Ekaterina V Bartashevich
- Chemistry Department, South Ural State University (National Research University), 76, Lenin Av., 454080 Chelyabinsk, Russia
| | - Svetlana E Mukhitdinova
- Chemistry Department, South Ural State University (National Research University), 76, Lenin Av., 454080 Chelyabinsk, Russia
| | - Iliya V Klyuev
- Chemistry Department, South Ural State University (National Research University), 76, Lenin Av., 454080 Chelyabinsk, Russia
| | - Vladimir G Tsirelson
- Chemistry Department, South Ural State University (National Research University), 76, Lenin Av., 454080 Chelyabinsk, Russia
- Quantum Chemistry Department, D.I. Mendeleev University of Chemical Technology, 125047 Moscow, Russia
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The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength. Molecules 2022; 27:molecules27154848. [PMID: 35956799 PMCID: PMC9369751 DOI: 10.3390/molecules27154848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 12/12/2022] Open
Abstract
In this study, we present results of a detailed topological analysis of electron density (ED) of 145 halogen-bonded complexes formed by various fluorine-, chlorine-, bromine-, and iodine-containing compounds with trimethylphosphine oxide, Me3PO. To characterize the halogen bond (XB) strength, we used the complexation enthalpy, the interatomic distance between oxygen and halogen, as well as the typical set of electron density properties at the bond critical points calculated at B3LYP/jorge-ATZP level of theory. We show for the first time that it is possible to predict the XB strength based on the distance between the minima of ED and molecular electrostatic potential (ESP) along the XB path. The gap between ED and ESP minima exponentially depends on local electronic kinetic energy density at the bond critical point and tends to be a common limiting value for the strongest halogen bond.
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Alencar WLM, da Silva Arouche T, Neto AFG, de Castro Ramalho T, de Carvalho Júnior RN, de Jesus Chaves Neto AM. Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics. Sci Rep 2022; 12:3316. [PMID: 35228662 PMCID: PMC8885651 DOI: 10.1038/s41598-022-07396-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values of - 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and - 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.
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Affiliation(s)
- Wilson Luna Machado Alencar
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil
- Federal Institute of Pará (IFPA), C. P. BR 316, Km 61, Castanhal, PA, 68740-970, Brazil
| | - Tiago da Silva Arouche
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil
| | | | | | - Raul Nunes de Carvalho Júnior
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil
- Pos-Graduation Program in Chemical Engineering, ITEC, Federal University of Pará, C. P. 479, Belém, PA, 66075-900, Brazil
| | - Antonio Maia de Jesus Chaves Neto
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil.
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil.
- Pos-Graduation Program in Chemical Engineering, ITEC, Federal University of Pará, C. P. 479, Belém, PA, 66075-900, Brazil.
- National Professional Master's in Physics Teaching, Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil.
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7
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Canal Neto A, Ferreira I, Jorge F, de Oliveira A. All-electron triple zeta basis sets for ZORA calculations: Application in studies of atoms and molecules. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138548] [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]
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8
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Babashpour S, Atabaki H. Unravelling the Origin of the Linear Structures Distortions of the Acetylene Isoelectronic Compounds (Disilyne, Digermyne, and Distannyne). RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2021. [DOI: 10.1134/s0036024421030055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Frati F, de Groot F, Cerezo J, Santoro F, Cheng L, Faber R, Coriani S. Coupled cluster study of the x-ray absorption spectra of formaldehyde derivatives at the oxygen, carbon, and fluorine K-edges. J Chem Phys 2019. [DOI: 10.1063/1.5097650] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Federica Frati
- Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 GC Utrecht, The Netherlands
| | - Frank de Groot
- Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 GC Utrecht, The Netherlands
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM–CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Lan Cheng
- Department of Chemistry, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rasmus Faber
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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10
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Mamun AA, Toda MJ, Kozlowski PM. Can photolysis of the Co C bond in coenzyme B12-dependent enzymes be used to mimic the native reaction? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 191:175-184. [DOI: 10.1016/j.jphotobiol.2018.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022]
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11
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Segmented all-electron basis sets of triple zeta quality for the lanthanides: application to structure calculations of lanthanide monoxides. J Mol Model 2019; 25:38. [DOI: 10.1007/s00894-019-3924-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/03/2019] [Indexed: 10/27/2022]
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12
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Xu L, Li QS, King RB. Coupling of fluoroborylene ligands in manganese carbonyl chemistry to give a difluorodiborene ligand. NEW J CHEM 2019. [DOI: 10.1039/c9nj01209e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bridging difluorodiborene μ-B2F2 ligand has been observed in two of the three lowest energy Mn2(BF)2(CO)7 structures as well as in the lowest energy Mn2(BF)2(CO)6 structure.
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Affiliation(s)
- Liancai Xu
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 450002
- P. R. China
| | - Qian-shu Li
- Center for Computational Quantum Chemistry
- South China Normal University
- Guangzhou 510631
- P. R. China
- Institute of Chemical Physics
| | - R. Bruce King
- Center for Computational Quantum Chemistry
- South China Normal University
- Guangzhou 510631
- P. R. China
- Department of Chemistry and Center for Computational Chemistry
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14
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Zaragoza IP, Soriano-Agueda LA, Hernández-Esparza R, Vargas R, Garza J. Analyzing ZnO clusters through the density-functional theory. J Mol Model 2018; 24:164. [PMID: 29909582 DOI: 10.1007/s00894-018-3691-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/22/2018] [Indexed: 11/27/2022]
Abstract
The potential energy surface of Zn n O n clusters (n = 2, 4, 6, 8) has been explored by using a simulated annealing method. For n = 2, 4, and 6, the CCSD(T)/TZP method was used as the reference, and from here it is shown that the M06-2X/TZP method gives the lowest deviations over PBE, PBE0, B3LYP, M06, and MP2 methods. Thus, with the M06-2X method we predict isomers of Zn n O n clusters, which coincide with some isomers reported previously. By using the atoms in molecules analysis, possible contacts between Zn and O atoms were found for all structures studied in this article. The bond paths involved in several clusters suggest that Zn n O n clusters can be obtained from the zincite (ZnO crystal), such an observation was confirmed for clusters with n = 2 - 9,18 and 20. The structure with n = 23 was obtained by the procedure presented here, from crystal information, which could be important to confirm experimental data delivered for n = 18 and 23.
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Affiliation(s)
- Irineo-Pedro Zaragoza
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México Campus Instituto Tecnológico de Tlalnepantla, Av. Mario Colín S/N, La Comunidad, Tlalnepantla de Baz, C.P. 54070, Estado de México, México
| | - Luis-Antonio Soriano-Agueda
- 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
| | - Raymundo Hernández-Esparza
- 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
| | - 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.
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15
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Montgomery JM, Mazziotti DA. Strong Electron Correlation in Nitrogenase Cofactor, FeMoco. J Phys Chem A 2018; 122:4988-4996. [DOI: 10.1021/acs.jpca.8b00941] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jason M. Montgomery
- Department of Chemistry, Biochemistry, and Physics, Florida Southern College, Lakeland, Florida 33801, United States
| | - David A. Mazziotti
- Department of Chemistry and The James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
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16
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Segmented all-electron Gaussian basis sets of double and triple zeta qualities for Fr, Ra, and Ac. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Gresh N, Naseem-Khan S, Lagardère L, Piquemal JP, Sponer JE, Sponer J. Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li +, Na +, K +, and Rb + Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential. J Phys Chem B 2017; 121:3997-4014. [PMID: 28363025 DOI: 10.1021/acs.jpcb.7b01836] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stacking of guanine quartets (GQs) can trigger the formation of DNA or RNA quadruple helices, which play numerous biochemical roles. The GQs are stabilized by alkali cations, mainly K+ and Na+, which can reside in, or channel through, the central axis of the GQ stems. Further, ion conduction through GQ wires can be leveraged for nanochemistry applications. G-quadruplex systems have been extensively studied by classical molecular dynamics (MD) simulations using pair-additive force fields or by quantum-chemical (QC) calculations. However, the non-polarizable force fields are very approximate, while QC calculations lack the necessary sampling. Thus, ultimate description of GQ systems would require long-enough simulations using advanced polarizable molecular mechanics (MM). However, to perform such calculations, it is first mandatory to evaluate the method's accuracy using benchmark QC. We report such an evaluation for SIBFA polarizable MM, bearing on the channeling (movement) of an alkali cation (Li+, Na+, K+, or Rb+) along the axis of two stacked G quartets interacting with either one or two ions. The QC energy profiles display markedly different features depending upon the cation but can be retrieved in the majority of cases by the SIBFA profiles. An appropriate balance of first-order (electrostatic and short-range repulsion) and second-order (polarization, charge-transfer, and dispersion) contributions within ΔE is mandatory. With two cations in the channel, the relative weights of the second-order contributions increase steadily upon increasing the ion size. In the G8 complexes with two K+ or two Rb+ cations, the sum of polarization and charge-transfer exceeds the first order terms for all ion positions.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Sehr Naseem-Khan
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France.,Institut Universitaire de France, Paris Cedex 05, 75231, France.,Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas, 78712, United States
| | - Judit E Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovpolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovpolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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18
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Affiliation(s)
- Balazs Nagy
- Department of Chemistry; Aarhus University; Aarhus Denmark
| | - Frank Jensen
- Department of Chemistry; Aarhus University; Aarhus Denmark
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19
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Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths. J Mol Model 2017; 23:50. [DOI: 10.1007/s00894-017-3212-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/09/2017] [Indexed: 01/14/2023]
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Jian T, Li WL, Popov IA, Lopez GV, Chen X, Boldyrev AI, Li J, Wang LS. Manganese-centered tubular boron cluster - MnB16 (-): A new class of transition-metal molecules. J Chem Phys 2017; 144:154310. [PMID: 27389223 DOI: 10.1063/1.4946796] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report the observation of a manganese-centered tubular boron cluster (MnB16 (-)), which is characterized by photoelectron spectroscopy and ab initio calculations. The relatively simple pattern of the photoelectron spectrum indicates the cluster to be highly symmetric. Ab initio calculations show that MnB16 (-) has a Mn-centered tubular structure with C4v symmetry due to first-order Jahn-Teller effect, while neutral MnB16 reduces to C2v symmetry due to second-order Jahn-Teller effect. In MnB16 (-), two unpaired electrons are observed, one on the Mn 3dz(2) orbital and another on the B16 tube, making it an unusual biradical. Strong covalent bonding is found between the Mn 3d orbitals and the B16 tube, which helps to stabilize the tubular structure. The current result suggests that there may exist a whole class of metal-stabilized tubular boron clusters. These metal-doped boron clusters provide a new bonding modality for transition metals, as well as a new avenue to design boron-based nanomaterials.
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Affiliation(s)
- Tian Jian
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Wan-Lu Li
- Department of Chemistry & Key Laboratory of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Ivan A Popov
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, USA
| | - Gary V Lopez
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Xin Chen
- Department of Chemistry & Key Laboratory of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Alexander I Boldyrev
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, USA
| | - Jun Li
- Department of Chemistry & Key Laboratory of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Lai-Sheng Wang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
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Characterization of B-H agostic compounds involved in the dehydrogenation of amine-boranes by group 4 metallocenes. J Mol Model 2016; 22:294. [PMID: 27888405 DOI: 10.1007/s00894-016-3165-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/08/2016] [Indexed: 10/20/2022]
Abstract
For over a decade, amine-borane has been considered as a potential chemical hydrogen vector in the context of a search for cleaner energy sources. When catalyzed by organometallic complexes, the reaction mechanisms currently considered involve the formation of β-BH agostic intermediates. A thorough understanding of these intermediates may constitute a crucial step toward the identification of ideal catalysts. Topological approaches such as QTAIM and ELF revealed to be particularly suitable for the description of β-agostic interactions. When studying model catalysts, accurate theoretical calculations may be carried out. However, for a comparison with experimental data, calculations should also be carried out on large organo-metallic species, often including transition metals belonging to the second or the third row. In such a case, DFT methods are particularly attractive. Unfortunately, triple-ζ all electrons basis sets are not easily available for heavy transition metal elements. Thus, a subtle balance should be reached between the affordable level of calculations and the required accuracy of the electronic description of the systems. Herein we propose the use of B3LYP functional in combination with the LanL2DZ pseudopotential for the metal atom and 6-311++G(2d,2p) basis set for the other atoms, followed by a single point using the DKH2 relativistic Hamiltonian in combination with the B3LYP/DZP-DKH level, as a "minimum level of theory" leading to a consistent topological description of the interaction within the ELF and QTAIM framework, in the context of isolated (gas-phase) group 4 metallocene catalysts.
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22
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Ab initio calculations of NMR shielding of Sc3+, Y3+ and La3+ ions in the water solution and 45Sc, 89Y, 138La and 139La nuclear magnetic dipole moments. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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Kobera L, Southern SA, Rao GK, Richeson DS, Bryce DL. New Experimental Insight into the Nature of Metal−Metal Bonds in Digallium Compounds:JCoupling between Quadrupolar Nuclei. Chemistry 2016; 22:9565-73. [DOI: 10.1002/chem.201600999] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Libor Kobera
- Department of Chemistry and Biomolecular Sciences and Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie Curie Pvt. D'Iorio Hall Ottawa Ontario K1N 6N5 Canada
| | - Scott A. Southern
- Department of Chemistry and Biomolecular Sciences and Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie Curie Pvt. D'Iorio Hall Ottawa Ontario K1N 6N5 Canada
| | - Gyandshwar Kumar Rao
- Department of Chemistry and Biomolecular Sciences and Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie Curie Pvt. D'Iorio Hall Ottawa Ontario K1N 6N5 Canada
| | - Darrin S. Richeson
- Department of Chemistry and Biomolecular Sciences and Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie Curie Pvt. D'Iorio Hall Ottawa Ontario K1N 6N5 Canada
| | - David L. Bryce
- Department of Chemistry and Biomolecular Sciences and Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie Curie Pvt. D'Iorio Hall Ottawa Ontario K1N 6N5 Canada
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Makarewicz E, Lundell J, Gordon AJ, Berski S. The nature of inter- and intramolecular interactions in F2OXe(…)HX (X= F, Cl, Br, I) complexes. J Mol Model 2016; 22:119. [PMID: 27146283 PMCID: PMC4856722 DOI: 10.1007/s00894-016-2970-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/24/2016] [Indexed: 12/01/2022]
Abstract
Electronic structure of the XeOF2 molecule and its two complexes with HX (X= F, Cl, Br, I) molecules have been studied in the gas phase using quantum chemical topology methods: topological analysis of electron localization function (ELF), electron density, ρ(r), reduced gradient of electron density |RDG(r)| in real space, and symmetry adapted perturbation theory (SAPT) in the Hilbert space. The wave function has been approximated by the MP2 and DFT methods, using APF-D, B3LYP, M062X, and B2PLYP functionals, with the dispersion correction as proposed by Grimme (GD3). For the Xe-F and Xe=O bonds in the isolated XeOF2 molecule, the bonding ELF-localization basins have not been observed. According to the ELF results, these interactions are not of covalent nature with shared electron density. There are two stable F2OXe…HF complexes. The first one is stabilized by the F-H…F and Xe…F interactions (type I) and the second by the F-H…O hydrogen bond (type II). The SAPT analysis confirms the electrostatic term, Eelst(1) and the induction energy, Eind(2) to be the major contributors to stabilizing both types of complexes.
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Affiliation(s)
- Emilia Makarewicz
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 15, 50-383, Wroclaw, Poland
| | - Jan Lundell
- Department of Chemistry, University of Jyväskylä, PO Box 35, 40014, Jyväskylä, Finland
| | - Agnieszka J Gordon
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 15, 50-383, Wroclaw, Poland
| | - Slawomir Berski
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 15, 50-383, Wroclaw, Poland.
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25
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Ferromagnetic ground state for a hypothetical iron-based extended metal atom chain. J Mol Model 2016; 22:63. [DOI: 10.1007/s00894-016-2928-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/04/2016] [Indexed: 10/22/2022]
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26
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Jensen F. Unifying General and Segmented Contracted Basis Sets. Segmented Polarization Consistent Basis Sets. J Chem Theory Comput 2015; 10:1074-85. [PMID: 26580184 DOI: 10.1021/ct401026a] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We propose a method, denoted P-orthogonalization, for converting a general contracted basis set to a computationally more efficient segmented contracted basis set, while inheriting the full accuracy of the general contracted basis set. The procedure can be used for any general contracted basis set to remove the redundancies between general contracted functions in terms of primitive functions. The P-orthogonalization procedure is used to construct a segmented contracted version of the polarization consistent basis sets, which are optimized for density functional theory calculations. Benchmark calculations show that the new pcs-n basis sets provide uniform error control of the basis set incompleteness for molecular systems composed of atoms from the first three rows in the periodic table (H-Kr) and for different exchange-correlation functionals. The basis set errors at a given zeta quality level are lower than other existing basis sets, and the pcs-n basis sets are furthermore shown to be among the computationally most efficient. The pcs-n basis sets are available in qualities ranging from (unpolarized) double-zeta to pentuple zeta quality and should therefore be well suited for both routine and benchmark calculations using density functional theory methods in general.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
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27
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Martins L, Jorge F, Machado S. All-electron segmented contraction basis sets of triple zeta valence quality for the fifth-row elements. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1040095] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Jensen F. Segmented Contracted Basis Sets Optimized for Nuclear Magnetic Shielding. J Chem Theory Comput 2014; 11:132-8. [DOI: 10.1021/ct5009526] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Frank Jensen
- Department
of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
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Wrackmeyer B, Klimkina EV, Milius W. Reactions of 1,3,2‐Diselenaphospholanes with Lewis Acids: Borane and (Pentamethylcyclopentadienyl)rhodium and ‐iridium Dichloride. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402486] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Bernd Wrackmeyer
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany, http://www.ac2.uni‐bayreuth.de
| | - Elena V. Klimkina
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany, http://www.ac2.uni‐bayreuth.de
| | - Wolfgang Milius
- Anorganische Chemie I, Universität Bayreuth, 95440 Bayreuth, Germany
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Oxidation of 1,3,2-diselenaphospholanes with an annelated dicarba-closo-dodecaborane(12) unit by addition of sulfur and selenium. Molecular structure of a novel 1,2,4,5-tetraselena-3-phospha heterocycle. J Organomet Chem 2013. [DOI: 10.1016/j.jorganchem.2013.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Augmented Gaussian basis sets for the elements K, Sc–Kr, Rb, and Y–Xe: Application in HF, MP2, and DFT calculations of molecular electric properties. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.03.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Gaussian basis sets of quadruple zeta quality for potassium through xenon: application in CCSD(T) atomic and molecular property calculations. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1339-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Jensen F. Polarization consistent basis sets. VIII. The transition metals Sc-Zn. J Chem Phys 2013; 138:014107. [DOI: 10.1063/1.4773017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Jensen F. Atomic orbital basis sets. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1123] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Campos C, Jorge F. Triple zeta quality basis sets for atoms Rb through Xe: application in CCSD(T) atomic and molecular property calculations. Mol Phys 2012. [DOI: 10.1080/00268976.2012.709282] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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Wrackmeyer B, Klimkina EV, Milius W. Selective Consecutive Insertion of Alkynes into the B-Se Bonds of 1,3,2-Diselenaborolane Derivatives: Synthesis and Molecular Structures of Nine-Membered Rings. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200471] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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37
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Wrackmeyer B, Klimkina EV, Milius W. 2‐Halogeno‐1,3,2‐diselenaphospholanes with an Annelated Dicarba‐
closo
‐dodecaborane(12) Unit: Synthesis, Molecular Structure and Reactivity. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200163] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bernd Wrackmeyer
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany, Fax: +49‐921‐552157
| | - Elena V. Klimkina
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany, Fax: +49‐921‐552157
| | - Wolfgang Milius
- Anorganische Chemie I, Universität Bayreuth, 95440 Bayreuth, Germany
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38
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Jensen F. Polarization consistent basis sets. VII. The elements K, Ca, Ga, Ge, As, Se, Br, and Kr. J Chem Phys 2012; 136:114107. [DOI: 10.1063/1.3690460] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
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39
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Wrackmeyer B, Klimkina EV, Milius W. Molecular Structures, Reactivity, and NMR Spectroscopic Studies of Cyclic and Non-cyclic Silyl-substituted 1, 2-Dicarba-closo-dodecaborane(12) Derivatives. Z Anorg Allg Chem 2012. [DOI: 10.1002/zaac.201200027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Wrackmeyer B, Klimkina EV, Milius W, Bauer T, Kempe R. Synthesis and reactivity of 4,5-[1,2-dicarba-closo-dodecaborano(12)]-1,3-diselenacyclopentane: opening of the icosahedron to give a zwitterionic intermediate and conversion into 7,8-dicarba-nido-undecaborate(1-). Chemistry 2011; 17:3238-51. [PMID: 21308806 DOI: 10.1002/chem.201002277] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Indexed: 12/21/2022]
Abstract
The reaction of the 1,2-diselenolato-1,2-dicarba-closo-dodecaborane(12) dianion [1,2-(1,2-C(2)B(10)H(10))Se(2)](2-) with dichloromethane (CH(2)Cl(2) or CD(2)Cl(2)) in the presence of donor solvents gave 4,5-[1,2-dicarba-closo-dodecaborano(12)]-1,3-diselenacyclopentane, the title compound, which was characterized by X-ray structural analysis and NMR spectroscopy ((1)H, (11)B, (13)C, and (77)Se). In the presence of pyridine, opening of the icosahedron took place, and a zwitterionic intermediate was isolated and fully characterized in the solid state by X-ray diffraction and in solution by multinuclear magnetic resonance techniques. Although such types of intermediates, prior to deboronation of the ortho-carborane cage, have been proposed several times, this is first example for which the structure has been confirmed unambiguously. This intermediate possesses a nido structure and contains a 7,8-dicarba-nido-undecaborate(1-) anion and a boronium cation, the latter with two pyridine rings linked to the boron atom, which has been extruded from the cage. It was shown that this process is reversible as long as the deboronation is not complete. The formation of the intermediate is accompanied by deboronation, which leads to the 7,8-dicarba-nido-undecaborate(1-) anion. The latter was prepared independently by conventional routes from the title compound, isolated as crystalline material as the tetrabutyl ammonium salt, and characterized by X-ray structural analysis and multinuclear magnetic resonance spectroscopy ((1)H, (11)B, (13)C, and (77)Se).
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Affiliation(s)
- Bernd Wrackmeyer
- Anorganische Chemie II, Universität Bayreuth, Universitätsstrasse 30, NW I, 95440 Bayreuth, Germany.
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Barros C, de Oliveira P, Jorge F, Canal Neto A, Campos M. Gaussian basis set of double zeta quality for atoms Rb through Xe: application in non-relativistic and relativistic calculations of atomic and molecular properties. Mol Phys 2010. [DOI: 10.1080/00268976.2010.499377] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Camiletti G, Canal Neto A, Jorge F, Machado S. Augmented Gaussian basis sets of double and triple zeta valence qualities for the atoms K and Sc–Kr: Applications in HF, MP2, and DFT calculations of molecular electric properties. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.06.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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