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Liu Z, He J, Li Y, Bai Y, Lin Q, Guo Y, Zhang F, Wu H, Jia J. Dative versus electron-sharing bonding in the isoelectronic argon compounds ArR + (R = CH 3, NH 2, OH, and F). NEW J CHEM 2021. [DOI: 10.1039/d0nj05326k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the series of isoelectronic ArR+ (R = CH3, NH2, OH, and F) complexes, the nature of the bonding between Ar and R shifts from an Ar → R+ dative σ bond in ArCH3+ and ArNH2+ to an Ar+–R electron-sharing σ bond in ArOH+ and ArF+.
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Affiliation(s)
- Zhiling Liu
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Jing He
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Ya Li
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Yan Bai
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Qingyang Lin
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Yurong Guo
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Fuqiang Zhang
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Haishun Wu
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Jianfeng Jia
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
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2
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Jin J, Li W, Liu Y, Wang G, Zhou M. Preparation and characterization of chemically bonded argon-boroxol ring cation complexes. Chem Sci 2017; 8:6594-6600. [PMID: 28989687 PMCID: PMC5627188 DOI: 10.1039/c7sc02472j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/17/2017] [Indexed: 11/21/2022] Open
Abstract
The cation complexes [ArB3O4]+, [ArB3O5]+, [ArB4O6]+ and [ArB5O7]+ were prepared via a laser vaporization supersonic ion source in the gas phase. Their vibrational spectra were measured via mass-selected infrared photodissociation spectroscopy. Spectroscopy combined with quantum chemical calculations revealed that the [ArB3O5]+, [ArB4O6]+ and [ArB5O7]+ cation complexes have planar structures each involving an aromatic boroxol ring and an argon-boron covalent bond. In contrast, the [ArB3O4]+ cation is characterized to be a weakly bound complex with a B3O4+ chain structure.
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Affiliation(s)
- Jiaye Jin
- Department of Chemistry , Collaborative Innovation Center of Chemistry for Energy Materials , Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai 200433 , China .
| | - Wei Li
- Department of Chemistry , Collaborative Innovation Center of Chemistry for Energy Materials , Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai 200433 , China .
| | - Yuhong Liu
- Department of Chemistry , Collaborative Innovation Center of Chemistry for Energy Materials , Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai 200433 , China .
| | - Guanjun Wang
- Department of Chemistry , Collaborative Innovation Center of Chemistry for Energy Materials , Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai 200433 , China .
| | - Mingfei Zhou
- Department of Chemistry , Collaborative Innovation Center of Chemistry for Energy Materials , Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai 200433 , China .
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Leonis G, Czyżnikowska Ż, Megariotis G, Reis H, Papadopoulos MG. Computational studies of darunavir into HIV-1 protease and DMPC bilayer: necessary conditions for effective binding and the role of the flaps. J Chem Inf Model 2012; 52:1542-58. [PMID: 22587384 DOI: 10.1021/ci300014z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the main targets toward AIDS therapy. We have selected the potent drug darunavir and a weak inhibitor (fullerene analog) as HIV-1 PR substrates to compare protease's conformational features upon binding. Molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and quantum-mechanical (QM) calculations indicated the importance of the stability of HIV-1 PR flaps toward effective binding: a weak inhibitor may induce flexibility to the flaps, which convert between closed and semiopen states. A water molecule in the darunavir-HIV-1 PR complex bridged the two flap tips of the protease through hydrogen bonding (HB) interactions in a stable structure, a feature that was not observed for the fullerene-HIV-1 PR complex. Additionally, despite that van der Waals interactions and nonpolar contribution to solvation favored permanent fullerene entrapment into the cavity, these interactions alone were not sufficient for effective binding; enhanced electrostatic interactions as observed in the darunavir-complex were the crucial component of the binding energy. An alternative pathway to the usual way of a ligand to access the cavity was also observed for both compounds. Each ligand entered the binding cavity through an opening between the one flap of the protease and a neighboring loop. This suggested that access to the cavity is not necessarily regulated by flap opening. Darunavir exerts its biological action inside the cell, after crossing the membrane barrier. Thus, we also initiated a study on the interactions between darunavir and the DMPC bilayer to reveal that the drug was accommodated inside the bilayer in conformations that resembled its structure into HIV-1 PR, being stabilized via HBs with the lipids and water molecules.
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Affiliation(s)
- Georgios Leonis
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece.
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Dopfer O. IR Spectroscopy of Microsolvated Aromatic Cluster Ions: Ionization-Induced Switch in Aromatic Molecule–Solvent Recognition. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zpch.219.2.125.57302] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
IR spectroscopy, mass spectrometry, and quantum chemical calculations are employed to characterize the intermolecular interaction of a variety of aromatic cations (A+) with several types of solvents. For this purpose, isolated ionic complexes of the type A+–L
n
, in which A+ is microsolvated by a controlled number (n) of ligands (L), are prepared in a supersonic plasma expansion, and their spectra are obtained by IR photodissociation (IRPD) spectroscopy in a tandem mass spectrometer. Two prototypes of aromatic ion–solvent recognition are considered: (i) microsolvation of acidic aromatic cations in a nonpolar hydrophobic solvent and (ii) microsolvation of bare aromatic hydrocarbon cations in a polar hydrophilic solvent. The analysis of the IRPD spectra of A+–L dimers provides detailed information about the intermolecular interaction between the aromatic ion and the neutral solvent, such as ion–ligand binding energies, the competition between different intermolecular binding motifs (H-bonds, π-bonds, charge–dipole bonds), and its dependence on chemical properties of both the A+ cation and the solvent type L. IRPD spectra of larger A+–L
n
clusters yield detailed insight into the cluster growth process, including the formation of structural isomers, the competition between ion–solvent and solvent–solvent interactions, and the degree of (non)cooperativity of the intermolecular interactions as a function of solvent type and degree of solvation. The systematic A+–L
n
cluster studies are shown to reveal valuable new information about fundamental chemical properties of the bare A+ cation, such as proton affinity, acidity, and reactivity. Because of the additional attraction arising from the excess charge, the interaction in the A+–L
n
cation clusters differs largely from that in the corresponding neutral A–L
n
clusters with respect to both the interaction strength and the most stable structure, implying in most cases an ionization-induced switch in the preferred aromatic molecule–solvent recognition motif. This process causes severe limitations for the spectroscopic characterization of ion–ligand complexes using popular photoionization techniques, due to the restrictions imposed by the Franck–Condon principle. The present study circumvents these limitations by employing an electron impact cluster ion source for A+–L
n
generation, which generates predominantly the most stable isomer of a given cluster ion independent of its geometry.
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Alekseyev AB, Liebermann HP, Buenker RJ. On the ultraviolet photofragmentation of CH3Xe+. J Chem Phys 2009; 130:024309. [DOI: 10.1063/1.3055909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pierrefixe S, Poater J, Im C, Bickelhaupt F. Hypervalent versus Nonhypervalent Carbon in Noble-Gas Complexes. Chemistry 2008; 14:6901-11. [DOI: 10.1002/chem.200800013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Andrei HS, Nizkorodov S, Dopfer O. IR Spectra of Protonated Carbonic Acid and Its Isomeric H3O+⋅CO2 Complex. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700750] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Andrei HS, Nizkorodov SA, Dopfer O. IR Spectra of Protonated Carbonic Acid and Its Isomeric H3O+⋅CO2 Complex. Angew Chem Int Ed Engl 2007; 46:4754-6. [PMID: 17487916 DOI: 10.1002/anie.200700750] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Horia-Sorin Andrei
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
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9
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Isayev O, Gorb L, Leszczynski J. Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately? J Comput Chem 2007; 28:1598-1609. [PMID: 17340602 DOI: 10.1002/jcc.20696] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and density functional (BLYP, B3LYP) theories augmented by Dunnings correlation-consistent basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed, and the results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anharmonicity to the zero point energy and TDeltaSint values is fairly small. The new, economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. In addition, interaction energy (De) and free energy change (DeltaA) for considered species have been evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and static BLYP-plane wave calculations. The free energy change along the reaction paths were determined by the thermodynamic integration/"Blue Moon Ensemble" technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. We found that the accuracy of CPMD simulations is affected by several factors, including statistical uncertainty and convergence of constrained forces (TD integration), and the nature of DFT (density functional theory) functional. The results show that CPMD technique is capable of reproducing interaction and free energy with an accuracy of 1 kcal/mol and 2-3 kcal/mol respectively.
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Affiliation(s)
- Olexandr Isayev
- Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217
| | - Leonid Gorb
- Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217
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Szymczak JJ, Urban J, Roszak S, Leszczynski J. The Nature of Variations of Ammonia Proton Affinity in an Argon Environment. J Phys Chem A 2006; 110:13099-105. [PMID: 17134171 DOI: 10.1021/jp057166c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The presence of solvent molecules, even inert, may significantly influence processes taking place in the gas phase. The reason for the solvent activity may be found in studies of complexes originating from microsolvation. The structure, thermodynamics, and vibrational properties of NH(4)(+)Ar(n) (n = 0-5) and NH(3)Ar(n) (n = 0-4) complexes are presented in this work with the aim to elucidate the effect of microsolvation on protonation/deprotonation processes. The relation between the nature of interactions in cationic and neutral clusters and the proton affinity is studied as a function of the number of ligands in complexes.
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Affiliation(s)
- Jaroslaw J Szymczak
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, Jackson, Mississippi 39217, USA
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Cunje A, Hopkinson AC, Yamabe S, Hiraoka K, Nakagawa F, Ishida M, Fujita K, Takao K, Wada A, Hiizumi K. Methyl and Ethyl Cation Affinities of Rare Gas Atoms and N2. J Phys Chem A 2004. [DOI: 10.1021/jp040133x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - S. Yamabe
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan
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Affiliation(s)
- Szczepan Roszak
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910 J. R. Lynch Street, 39217 Jackson, Mississippi, and Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jerzy Leszczynski
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910 J. R. Lynch Street, 39217 Jackson, Mississippi, and Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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13
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Sheng Y, Gora RW, Roszak S, Kaczorowska M, Leszczynski J. The Molecular Structures, Energetics, and Nature of Interactions in Arn-N2H+ (n = 1−12) Complexes. J Phys Chem A 2002. [DOI: 10.1021/jp0207984] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yinghong Sheng
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, J.R. Lynch Street, Jackson, Mississippi 39217, and Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Robert W. Gora
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, J.R. Lynch Street, Jackson, Mississippi 39217, and Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Szczepan Roszak
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, J.R. Lynch Street, Jackson, Mississippi 39217, and Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Malgorzata Kaczorowska
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, J.R. Lynch Street, Jackson, Mississippi 39217, and Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jerzy Leszczynski
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, J.R. Lynch Street, Jackson, Mississippi 39217, and Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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Dopfer O, Solcà N, Olkhov RV, Maier JP. Microsolvation of the ammonia cation in argon: II. IR photodissociation spectra of NH3+–Arn (n=1–6). Chem Phys 2002. [DOI: 10.1016/s0301-0104(02)00497-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Dopfer O. Microsolvation of the ammonia cation in argon: I. Ab initio and density functional calculations of NH3+–Arn (n=0–5). Chem Phys 2002. [DOI: 10.1016/s0301-0104(02)00639-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Dopfer O, Luckhaus D. Rovibrational calculations for CH3+–Rg (Rg=He,Ne): The prototype disk-and-ball dimer. J Chem Phys 2002. [DOI: 10.1063/1.1421614] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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