101
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Zhang H, Jiang Y, Yan H, Cui Z, Yin C. Comparative Assessment of Computational Methods for Free Energy Calculations of Ionic Hydration. J Chem Inf Model 2017; 57:2763-2775. [DOI: 10.1021/acs.jcim.7b00485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Hai Yan
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Ziheng Cui
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Chunhua Yin
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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102
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Zou C, Huang W, Zhao G, Wan X, Hu X, Jin Y, Li J, Liu J. Determination of the Bridging Ligand in the Active Site of Tyrosinase. Molecules 2017; 22:molecules22111836. [PMID: 29143758 PMCID: PMC6150207 DOI: 10.3390/molecules22111836] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 01/06/2023] Open
Abstract
Tyrosinase is a type-3 copper enzyme that is widely distributed in plants, fungi, insects, and mammals. Developing high potent inhibitors against tyrosinase is of great interest in diverse fields including tobacco curing, food processing, bio-insecticides development, cosmetic development, and human healthcare-related research. In the crystal structure of Agaricus bisporus mushroom tyrosinase, there is an oxygen atom bridging the two copper ions in the active site. It is unclear whether the identity of this bridging oxygen is a water molecule or a hydroxide anion. In the present study, we theoretically determine the identity of this critical bridging oxygen by performing first-principles hybrid quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area (QM/MM-PBSA) calculations along with a thermodynamic cycle that aim to improve the accuracy. Our results show that the binding with water molecule is energy favored and the QM/MM-optimized structure is very close to the crystal structure, whereas the binding with hydroxide anions causes the increase of energy and significant structural changes of the active site, indicating that the identity of the bridging oxygen must be a water molecule rather than a hydroxide anion. The different binding behavior between water and hydroxide anions may explain why molecules with a carboxyl group or too many negative charges have lower inhibitory activity. In light of this, the design of high potent active inhibitors against tyrosinase should satisfy both the affinity to the copper ions and the charge neutrality of the entire molecule.
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Affiliation(s)
- Congming Zou
- Yunnan Academy of Tobacco Agricultural Sciences, 33 Yuantong Street, Kunming 650021, China.
| | - Wei Huang
- Yunnan Academy of Tobacco Agricultural Sciences, 33 Yuantong Street, Kunming 650021, China.
| | - Gaokun Zhao
- Yunnan Academy of Tobacco Agricultural Sciences, 33 Yuantong Street, Kunming 650021, China.
| | - Xiao Wan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China.
| | - Xiaodong Hu
- Yunnan Academy of Tobacco Agricultural Sciences, 33 Yuantong Street, Kunming 650021, China.
| | - Yan Jin
- Yunnan Academy of Tobacco Agricultural Sciences, 33 Yuantong Street, Kunming 650021, China.
| | - Junying Li
- Yunnan Academy of Tobacco Agricultural Sciences, 33 Yuantong Street, Kunming 650021, China.
| | - Junjun Liu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China.
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103
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Šebesta F, Brela MZ, Diaz S, Miranda S, Murray JS, Gutiérrez-Oliva S, Toro-Labbé A, Michalak A, Burda JV. The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study. J Comput Chem 2017; 38:2680-2692. [PMID: 28925001 DOI: 10.1002/jcc.24911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/09/2017] [Accepted: 07/18/2017] [Indexed: 11/11/2022]
Abstract
This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+ , Zn2+ , and Hg2+ . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
| | - Mateusz Z Brela
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Silvia Diaz
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Sebastian Miranda
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, 70148
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Artur Michalak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
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104
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Fisicaro G, Genovese L, Andreussi O, Mandal S, Nair NN, Marzari N, Goedecker S. Soft-Sphere Continuum Solvation in Electronic-Structure Calculations. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00375] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Giuseppe Fisicaro
- Department
of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Luigi Genovese
- Laboratoire
de simulation atomistique (L_Sim), SP2M, INAC, CEA-UJF, F-38054 Grenoble, France
| | - Oliviero Andreussi
- Institute
of Computational Science, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6904 Lugano, Switzerland
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - Sagarmoy Mandal
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nicola Marzari
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - Stefan Goedecker
- Department
of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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105
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Zhang H, Jiang Y, Yan H, Yin C, Tan T, van der Spoel D. Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton. J Phys Chem Lett 2017; 8:2705-2712. [PMID: 28561580 DOI: 10.1021/acs.jpclett.7b01125] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Computational free-energy correction strategies and the choice of experimental proton hydration free energy, ΔGs*(H+), are analyzed to investigate the apparent controversy in experimental thermodynamics of ionic hydration. Without corrections, the hydration free-energy (ΔGhyd) calculations match experiments with ΔGs*(H+) = -1064 kJ/mol as reference. Using the Galvani surface potential the resulting (real) ΔGhyd are consistent with ΔGs*(H+) = -1098 kJ/mol. When applying, in an ad hoc manner, the discrete solvent correction, ΔGhyd matching the "consensus" ΔGs*(H+) of -1112 kJ/mol are obtained. This analysis rationalizes reports on ΔGhyd calculations for ions using different experimental references. For neutral amino acid side chains ΔGhyd are independent of the water model, whereas there are large differences in ΔGhyd due to the water model for charged species, suggesting that long-range ordering of water around ions yields an important contribution to the ΔGhyd. These differences are reduced significantly when applying consistent corrections, but to obtain the most accurate results it is recommended to use the water model belonging to the force field.
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Affiliation(s)
- Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing , 100083 Beijing, China
| | - Yang Jiang
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Box 53, 100029 Beijing, China
| | - Hai Yan
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing , 100083 Beijing, China
| | - Chunhua Yin
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing , 100083 Beijing, China
| | - Tianwei Tan
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Box 53, 100029 Beijing, China
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
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106
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Wang Z, Zhou Y, Lam WH, Lin Z. DFT Studies of Ru-Catalyzed C–O versus C–H Bond Functionalization of Aryl Ethers with Organoboronates. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Zheng Wang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
| | - Yu Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
| | - Wai Han Lam
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
| | - Zhenyang Lin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
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107
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Riniker S. Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. J Chem Inf Model 2017; 57:726-741. [DOI: 10.1021/acs.jcim.6b00778] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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108
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Ringe S, Oberhofer H, Reuter K. Transferable ionic parameters for first-principles Poisson-Boltzmann solvation calculations: Neutral solutes in aqueous monovalent salt solutions. J Chem Phys 2017; 146:134103. [DOI: 10.1063/1.4978850] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Stefan Ringe
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
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109
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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110
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Phifer JR, Cox CE, da Silva LF, Nogueira GG, Barbosa AKP, Ley RT, Bozada SM, O’Loughlin EJ, Paluch AS. Predicting the equilibrium solubility of solid polycyclic aromatic hydrocarbons and dibenzothiophene using a combination of MOSCED plus molecular simulation or electronic structure calculations. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1284356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jeremy R. Phifer
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Courtney E. Cox
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Larissa Ferreira da Silva
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
- Departamento de Engenharia Química, Universidade Federal de São João del-Rei, Ouro Branco, Brazil
| | - Gabriel Gonçalves Nogueira
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
- Departamento de Engenharia Química, Universidade Federal de São João del-Rei, Ouro Branco, Brazil
| | - Ana Karolyne Pereira Barbosa
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
- Instituto de Ciência e Tecnologia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brazil
| | - Ryan T. Ley
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Samantha M. Bozada
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | | | - Andrew S. Paluch
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
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111
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Caudle MR, Cox CE, Ley RT, Paluch AS. A molecular study of the wastewater contaminants atenolol and atrazine in 1-n-butyl-3-methylimidazolium based ionic liquids for potential treatment applications. Mol Phys 2017. [DOI: 10.1080/00268976.2016.1278478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Miranda R. Caudle
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Courtney E. Cox
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Ran T. Ley
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Andrew S. Paluch
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
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112
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Sidorkin VF, Belogolova EF, Wang Y, Jouikov V, Doronina EP. Electrochemical Oxidation and Radical Cations of Structurally Non-rigid Hypervalent Silatranes: Theoretical and Experimental Studies. Chemistry 2017; 23:1910-1919. [PMID: 27906483 DOI: 10.1002/chem.201604663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Indexed: 11/06/2022]
Abstract
Using 18 silatranes XSi(OCH2 CH2 )3 N (1) as examples, the potentials of electrochemical oxidation E0 of the hypervalent compounds of Si were calculated for the first time at the ab initio and DFT levels. The experimental peak potentials Ep (acetonitrile) show an excellent agreement (MAE=0.03) with the MP2//B3PW91 calculated E0 (C-PCM). Radical cations of 1 reveal a stretch isomerism of the N→Si dative bond. Localization of the spin density (SD) on the substituent X and the short (s) coordination contact Si⋅⋅⋅N (dSiN <2.13 Å) along with the high five-coordinate character of Si are typical for the first isomer 1+.(s) , whereas the second one, 1+.(l) , has a longer (l) Si⋅⋅⋅N distance (dSiN >3.0 Å), the four-coordinate Si and the SD localized on the silatrane nitrogen atom Ns . The vertical model of adiabatic ionization (1→1+.(s) or 1→1+.(l) ) was developed. It allows, in accordance with an original experimental test (electrooxidation of 1 in the presence of ferrocene), a reliable prediction of the most probable pathways of the silatrane oxidation. The reliable relationships of E0 (1) with the strength characteristics of the dative contact N→Si were revealed.
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Affiliation(s)
- Valery F Sidorkin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky, 1, Irkutsk, 664033, Russian Federation
| | - Elena F Belogolova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky, 1, Irkutsk, 664033, Russian Federation
| | - Yu Wang
- University of Rennes I, Molecular Chemistry and Photonics, UMR 6226 ISCR, 35042, Rennes, France
| | - Viatcheslav Jouikov
- University of Rennes I, Molecular Chemistry and Photonics, UMR 6226 ISCR, 35042, Rennes, France
| | - Evgeniya P Doronina
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky, 1, Irkutsk, 664033, Russian Federation
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113
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Soleymani E, Alinezhad H, Darvish Ganji M, Tajbakhsh M. Enantioseparation performance of CNTs as chiral selectors for the separation of ibuprofen isomers: a dispersion corrected DFT study. J Mater Chem B 2017; 5:6920-6929. [PMID: 32264341 DOI: 10.1039/c7tb00755h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The enantioseparation of chiral drugs has been of great interest in the modern pharmaceutical industry since the majority of bioorganic compounds are chiral.
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Affiliation(s)
- Elham Soleymani
- Department of Organic Chemistry
- Faculty of Chemistry
- University of Mazandran
- Babolsar
- Iran
| | | | - Masoud Darvish Ganji
- Department of Nanochemistry
- Faculty of Pharmaceutical Chemistry
- Islamic Azad University
- Pharmaceutical Sciences Branch (IAUPS)
- Tehran
| | - Mahmood Tajbakhsh
- Department of Organic Chemistry
- Faculty of Chemistry
- University of Mazandran
- Babolsar
- Iran
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114
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Housecroft CE, Brooke Jenkins HD. Absolute ion hydration enthalpies and the role of volume within hydration thermodynamics. RSC Adv 2017. [DOI: 10.1039/c6ra25804b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This paper reports that various thermodynamic properties in aqueous media for certain individual ions and for compounds are linear functions of the inverse cube root of the solid respective ionic and compound solid state volumes, Vm−1/3.
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115
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Joung JF, Kim S, Park S. Ionic effects on the proton transfer mechanism in aqueous solutions. Phys Chem Chem Phys 2017; 19:25509-25517. [DOI: 10.1039/c7cp04392a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proton dissociation (PD) reactions of weak acids and proton transfer (PT) processes in aqueous solutions are strongly influenced by ions.
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Affiliation(s)
| | - Sangin Kim
- Department of Chemistry
- Korea University
- Seoul
- Korea
| | - Sungnam Park
- Department of Chemistry
- Korea University
- Seoul
- Korea
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116
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Mazmanian K, Sargsyan K, Grauffel C, Dudev T, Lim C. Preferred Hydrogen-Bonding Partners of Cysteine: Implications for Regulating Cys Functions. J Phys Chem B 2016; 120:10288-10296. [PMID: 27635780 DOI: 10.1021/acs.jpcb.6b08109] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrogen-bonding interactions of cysteine, which can serve as a hydrogen-bond donor and/or acceptor, play a central role in cysteine's diverse functional roles in proteins. They affect the balance between the neutral thiol (SH) or thiolate (S-) and the charge distribution in the rate-limiting transition state of a reaction. Despite their importance, no study has determined the preferred hydrogen-bonding partners of cysteine serving as a hydrogen-bond donor or acceptor. By computing the free energy for displacing a peptide backbone hydrogen-bonded to cysteine with amino acid side chains in various protein environments, we have evaluated how the strength of the hydrogen bond to the cysteine thiol/thiolate depends on its hydrogen-bonding partner and its local environment. The predicted hydrogen-bonding partners preferred by cysteine are consistent with the hydrogen-bonding interactions made by cysteines in 9138 nonredundant X-ray structures. Our results suggest a mechanism to regulate the reactivity of cysteines and a strategy to design drugs based on the hydrogen-bonding preference of cysteine.
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Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 10617, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University , Sofia 1164, Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 300, Taiwan
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117
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Dudev T, Grauffel C, Lim C. Influence of the Selectivity Filter Properties on Proton Selectivity in the Influenza A M2 Channel. J Am Chem Soc 2016; 138:13038-13047. [DOI: 10.1021/jacs.6b08041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Todor Dudev
- Faculty
of Chemistry and Pharmacy, Sofia University, Sofia 1164, Bulgaria
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Cédric Grauffel
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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118
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Grigoriev FV, Sulimov VB. Simple combined explicit/implicit water model. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1218488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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119
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Jones MR, Brooks BR, Wilson AK. Partition coefficients for the SAMPL5 challenge using transfer free energies. J Comput Aided Mol Des 2016; 30:1129-1138. [PMID: 27646287 DOI: 10.1007/s10822-016-9964-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/02/2016] [Indexed: 10/21/2022]
Abstract
SAMPL challenges (Mobley et al. in J Comput Aided Mol Des 28:135-150, 2014; Skillman in J Comput Aided Mol Des 26:473-474, 2012; Geballe in J Comput Aided Mol Des 24:259-279, 2010; Guthrie in J Phys Chem B 113:4501-4507, 2009) provide excellent opportunities to assess theoretical approaches on new data sets with a goal of gaining greater insight towards protein and ligand modeling. In the SAMPL5 experiment, cyclohexane-water partition coefficients were determined using a vertical solvation scheme in conjunction with the SMD continuum solvent model. Several DFT functionals partnered with correlation consistent basis sets were evaluated for the prediction of the partition coefficients. The approach chosen for the competition, a B3PW91 vertical solvation scheme, yields a mean absolute deviation of 1.9 logP units and performs well at estimating the correct hydrophilicity and hydrophobicity for the full SAMPL5 molecule set.
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Affiliation(s)
- Michael R Jones
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln, East Lansing, MI, 48824, USA.,Laboratory of Computational Biology, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln, East Lansing, MI, 48824, USA.
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120
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Rayne S, Forest K. Air-water partition coefficients for a suite of polycyclic aromatic and other C10 through C20 unsaturated hydrocarbons. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2016; 51:938-953. [PMID: 27336293 DOI: 10.1080/10934529.2016.1191812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The air-water partition coefficients (Kaw) for 86 large polycyclic aromatic hydrocarbons and their unsaturated relatives were estimated using high-level G4(MP2) gas and aqueous phase calculations with the SMD, IEFPCM-UFF, and CPCM solvation models. An extensive method validation effort was undertaken which involved confirming that, via comparisons to experimental enthalpies of formation, gas-phase energies at the G4(MP2) level for the compounds of interest were at or near thermochemical accuracy. Investigations of the three solvation models using a range of neutral and ionic compounds suggested that while no clear preferential solvation model could be chosen in advance for accurate Kaw estimates of the target compounds, the employment of increasingly higher levels of theory would result in lower Kaw errors. Subsequent calculations on the polycyclic aromatic and unsaturated hydrocarbons at the G4(MP2) level revealed excellent agreement for the IEFPCM-UFF and CPCM models against limited available experimental data. The IEFPCM-UFF-G4(MP2) and CPCM-G4(MP2) solvation energy calculation approaches are anticipated to give Kaw estimates within typical experimental ranges, each having general Kaw errors of less than 0.5 log10 units. When applied to other large organic compounds, the method should allow development of a broad and reliable Kaw database for multimedia environmental modeling efforts on various contaminants.
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Affiliation(s)
- Sierra Rayne
- a Chemologica Research , Moose Jaw , Saskatchewan , Canada
| | - Kaya Forest
- b Department of Environmental Engineering Technology , Saskatchewan Polytechnic , Moose Jaw , Saskatchewan , Canada
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121
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Tielker N, Tomazic D, Heil J, Kloss T, Ehrhart S, Güssregen S, Schmidt KF, Kast SM. The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane-water log D. J Comput Aided Mol Des 2016; 30:1035-1044. [PMID: 27554666 DOI: 10.1007/s10822-016-9939-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/17/2016] [Indexed: 12/01/2022]
Abstract
We predict cyclohexane-water distribution coefficients (log D 7.4) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the "embedded cluster reference interaction site model" (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (pK a) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the "Minnesota Solvation Database" (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol-1 for water and 0.8-0.9 kcal mol-1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical pK a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2-3 for each solvent and two for the pK a) for training solvation and acidity models. Applying the final models to the log D 7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0-2.1 for the RMSE with the first and 2.2-2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.
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Affiliation(s)
- Nicolas Tielker
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Daniel Tomazic
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Thomas Kloss
- IPhT, L'Orme des Merisiers, CEA-Saclay, 91191, Gif-sur-Yvette, France
| | | | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - K Friedemann Schmidt
- Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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122
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Göttle AJ, Koper MTM. Proton-coupled electron transfer in the electrocatalysis of CO 2 reduction: prediction of sequential vs. concerted pathways using DFT. Chem Sci 2016; 8:458-465. [PMID: 28451193 PMCID: PMC5298188 DOI: 10.1039/c6sc02984a] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/20/2016] [Indexed: 12/23/2022] Open
Abstract
Herein we investigate computationally in detail the mechanism of the formation of the carboxylate adduct during the electroreduction of CO2 in water catalysed by cobalt porphyrin complexes. Specifically, we address qualitatively the competition between the concerted and sequential pathways for the proton-coupled electron transfer. We use a simple methodology for accurate computation of the pKa of the neutral and anionic carboxylate intermediates, [CoP-COOH] and [CoP-COOH]- (where CoP is a cobalt porphine complex), based on the isodesmic proton-exchange reaction scheme. The predicted values are used as in input for a theoretical model that describes the transition between the sequential and concerted pathways. The activation of the sequential pathway (ET-PT) that leads to the formation of the neutral [CoP-COOH] intermediate at pH ≈ 3.5 (pKa[CoP-COOH] = 3.5 ± 0.4), as predicted by the calculations, is in good agreement with the drastic increase in the faradaic efficiency of the CO2 reduction reaction towards CO at pH = 3 compared to pH = 1, as experimentally observed. This confirms the existence of the CO2 anionic adduct [CoP-CO2]- as a viable intermediate at pH = 3 and its crucial role for the pH dependence of the faradaic efficiency for the CO2 reduction. The analysis also shows that when the pH is significantly higher than the pKa of the neutral carboxylate adduct, the CO2 reduction has to go through an alternative pathway with the formation of the anionic carboxylate intermediate [CoP-COOH]-. It is formed through a concerted proton-electron transfer step from the anionic CO2 adduct [CoP-CO2]- when the pH is below ∼8.6 (pKa[CoP-COOH]- = 8.6 ± 0.4). At pH ≈ 8.6 and above, another decoupled ET-PT is predicted to take place, leading to the formation of a dianionic CO2 adduct [CoP-CO2]2-.
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Affiliation(s)
- Adrien J Göttle
- Leiden Institute of Chemistry , Leiden University , PO Box 9502 , 2300 RA Leiden , The Netherlands .
| | - Marc T M Koper
- Leiden Institute of Chemistry , Leiden University , PO Box 9502 , 2300 RA Leiden , The Netherlands .
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123
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Rizvi MA, Mane M, Khuroo MA, Peerzada GM. Computational survey of ligand properties on iron(III)–iron(II) redox potential: exploring natural attenuation of nitroaromatic compounds. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-016-1813-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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124
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Bradshaw RT, Essex JW. Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field. J Chem Theory Comput 2016; 12:3871-83. [PMID: 27341007 DOI: 10.1021/acs.jctc.6b00276] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed-point-charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard but showed substantially worse results than those using the fixed-point-charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 data set, we evaluate the cumulative effects of a series of incremental improvements in parametrization protocol, including both solute and solvent model changes. Ultimately, the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein-ligand binding studies.
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Affiliation(s)
- Richard T Bradshaw
- School of Chemistry, University of Southampton, Highfield Campus , Southampton SO17 1BJ, U.K
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield Campus , Southampton SO17 1BJ, U.K
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125
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Ringe S, Oberhofer H, Hille C, Matera S, Reuter K. Function-Space-Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT. J Chem Theory Comput 2016; 12:4052-66. [PMID: 27323006 DOI: 10.1021/acs.jctc.6b00435] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol.
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Affiliation(s)
- Stefan Ringe
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Christoph Hille
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sebastian Matera
- Fachbereich f. Mathematik u. Informatik, Freie Universität Berlin , Otto-von-Simson-Str. 19, D-14195 Berlin, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstr. 4, D-85747 Garching, Germany
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126
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Peeples CA, Schreckenbach G. Implementation of the SM12 Solvation Model into ADF and Comparison with COSMO. J Chem Theory Comput 2016; 12:4033-41. [PMID: 27322858 DOI: 10.1021/acs.jctc.6b00410] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this article, an implementation of the newest iteration of the Minnesota solvation model, SM12, into the Amsterdam density functional (ADF) computational package is presented. ADF makes exclusive use of Slater-type orbitals (STO), which correctly represent the true atomic orbitals for atoms, whereas SM12 and the underlying charge model 5 (CM5) have previously only been tested on Gaussian-type orbitals (GTO). This new implementation is used to prove the basis set independence of both CM5 and SM12. A detailed comparison of the SM12 and COSMO solvation models, as implemented in ADF, is also presented. We show that this new implementation of SM12 has a mean unsigned error (MUE) of 0.68 kcal/mol for 272 molecules in water solvent, 4.10 kcal/mol MUE for 112 charged ions in water, and 0.92 kcal/mol MUE for 197 solvent calculations of various molecules. SM12 outperforms COSMO for all neutral molecules and performs as well as COSMO for cationic molecules, only falling short when anionic molecules are taken into consideration, likely due to CM5's use of Hirshfeld charges and their poor description of anionic molecules, though CM5 seems to improve upon this discrepancy.
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Affiliation(s)
- Craig A Peeples
- Department of Chemistry, University of Manitoba Winnipeg , Winnipeg, MB R3T 2N2, Canada
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba Winnipeg , Winnipeg, MB R3T 2N2, Canada
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127
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Zheng Z, Wang T, Li P, Merz KM. KECSA-Movable Type Implicit Solvation Model (KMTISM). J Chem Theory Comput 2016; 11:667-82. [PMID: 25691832 PMCID: PMC4325602 DOI: 10.1021/ct5007828] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Indexed: 11/30/2022]
Abstract
![]()
Computation
of the solvation free energy for chemical and biological
processes has long been of significant interest. The key challenges
to effective solvation modeling center on the choice of potential
function and configurational sampling. Herein, an energy sampling
approach termed the “Movable Type” (MT) method, and
a statistical energy function for solvation modeling, “Knowledge-based
and Empirical Combined Scoring Algorithm” (KECSA) are developed
and utilized to create an implicit solvation model: KECSA-Movable
Type Implicit Solvation Model (KMTISM) suitable for the study of chemical
and biological systems. KMTISM is an implicit solvation model, but
the MT method performs energy sampling at the atom pairwise level.
For a specific molecular system, the MT method collects energies from
prebuilt databases for the requisite atom pairs at all relevant distance
ranges, which by its very construction encodes all possible molecular
configurations simultaneously. Unlike traditional statistical energy
functions, KECSA converts structural statistical information into
categorized atom pairwise interaction energies as a function of the
radial distance instead of a mean force energy function. Within the
implicit solvent model approximation, aqueous solvation free energies
are then obtained from the NVT ensemble partition function generated
by the MT method. Validation is performed against several subsets
selected from the Minnesota Solvation Database v2012. Results are
compared with several solvation free energy calculation methods, including
a one-to-one comparison against two commonly used classical implicit
solvation models: MM-GBSA and MM-PBSA. Comparison against a quantum
mechanics based polarizable continuum model is also discussed (Cramer
and Truhlar’s Solvation Model 12).
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Affiliation(s)
- Zheng Zheng
- Institute for Cyber Enabled Research, Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
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128
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Kuechler ER, Giese TJ, York DM. VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions. J Chem Phys 2016; 144:164115. [PMID: 27131539 PMCID: PMC4851621 DOI: 10.1063/1.4946779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/01/2016] [Indexed: 12/23/2022] Open
Abstract
To better represent the solvation effects observed along reaction pathways, and of ionic species in general, a charge-dependent variable-radii smooth conductor-like screening model (VR-SCOSMO) is developed. This model is implemented and parameterized with a third order density-functional tight binding quantum model, DFTB3/3OB-OPhyd, a quantum method which was developed for organic and biological compounds, utilizing a specific parameterization for phosphate hydrolysis reactions. Unlike most other applications with the DFTB3/3OB model, an auxiliary set of atomic multipoles is constructed from the underlying DFTB3 density matrix which is used to interact the solute with the solvent response surface. The resulting method is variational, produces smooth energies, and has analytic gradients. As a baseline, a conventional SCOSMO model with fixed radii is also parameterized. The SCOSMO and VR-SCOSMO models shown have comparable accuracy in reproducing neutral-molecule absolute solvation free energies; however, the VR-SCOSMO model is shown to reduce the mean unsigned errors (MUEs) of ionic compounds by half (about 2-3 kcal/mol). The VR-SCOSMO model presents similar accuracy as a charge-dependent Poisson-Boltzmann model introduced by Hou et al. [J. Chem. Theory Comput. 6, 2303 (2010)]. VR-SCOSMO is then used to examine the hydrolysis of trimethylphosphate and seven other phosphoryl transesterification reactions with different leaving groups. Two-dimensional energy landscapes are constructed for these reactions and calculated barriers are compared to those obtained from ab initio polarizable continuum calculations and experiment. Results of the VR-SCOSMO model are in good agreement in both cases, capturing the rate-limiting reaction barrier and the nature of the transition state.
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Affiliation(s)
- Erich R Kuechler
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
| | - Timothy J Giese
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
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129
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Martínez JP, Garcia-Borràs M, Osuna S, Poater J, Bickelhaupt FM, Solà M. Reaction Mechanism and Regioselectivity of the Bingel-Hirsch Addition of Dimethyl Bromomalonate to La@C2v -C82. Chemistry 2016; 22:5953-62. [PMID: 26991842 DOI: 10.1002/chem.201504668] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Indexed: 11/09/2022]
Abstract
We quantum chemically explore the thermodynamics and kinetics of all 65 possible mechanistic pathways of the Bingel-Hirsch addition of dimethyl bromomalonate to the endohedral metallofullerene La@C2v -C82 that result from the combination of 24 nonequivalent carbon atoms and 35 different bonds present in La@C2v -C82 by using dispersion-corrected DFT calculations. Experimentally, this reaction leads to four singly bonded derivatives and one fulleroid adduct. Of these five products, only the singly bonded derivative on C23 could be experimentally identified unambiguously. Our calculations show that La@C2v -C82 is not particularly regioselective under Bingel-Hirsch conditions. From the obtained results, however, it is possible to make a tentative assignment of the products observed experimentally. We propose that the observed fulleroid adduct results from the attack at bond 19 and that the singly bonded derivatives correspond to the C2, C19, C21, and C23 initial attacks. However, other possibilities cannot be ruled out completely.
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Affiliation(s)
- Juan Pablo Martínez
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Catalonia, Spain
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Catalonia, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Catalonia, Spain
| | - Jordi Poater
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boeleaan 1083, 1081 HV, Amsterdam, The Netherlands.,Departament de Química Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Catalonia, Spain
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boeleaan 1083, 1081 HV, Amsterdam, The Netherlands. .,Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Catalonia, Spain.
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130
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Garcia-Ratés M, López N. Multigrid-Based Methodology for Implicit Solvation Models in Periodic DFT. J Chem Theory Comput 2016; 12:1331-41. [PMID: 26771105 DOI: 10.1021/acs.jctc.5b00949] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Continuum solvation models have become a widespread approach for the study of environmental effects in Density Functional Theory (DFT) methods. Adding solvation contributions mainly relies on the solution of the Generalized Poisson Equation (GPE) governing the behavior of the electrostatic potential of a system. Although multigrid methods are especially appropriate for the solution of partial differential equations, up to now, their use is not much extended in DFT-based codes because of their high memory requirements. In this Article, we report the implementation of an accelerated multigrid solver-based approach for the treatment of solvation effects in the Vienna ab initio Simulation Package (VASP). The stated implicit solvation model, named VASP-MGCM (VASP-Multigrid Continuum Model), uses an efficient and transferable algorithm for the product of sparse matrices that highly outperforms serial multigrid solvers. The calculated solvation free energies for a set of molecules, including neutral and ionic species, as well as adsorbed molecules on metallic surfaces, agree with experimental data and with simulation results obtained with other continuum models.
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Affiliation(s)
- Miquel Garcia-Ratés
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology , Avinguda dels Països Catalans 16, 43007 Tarragona, Spain
| | - Núria López
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology , Avinguda dels Països Catalans 16, 43007 Tarragona, Spain
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131
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Grishaeva TN, Maslii AN, Bakovets VV, Kuznetsov AM. Inclusion compounds based on nickel(II) dimethylglyoxymate and cucurbit[8]uril: A quantum chemical prediction of the structure and thermodynamic parameters of formation. J STRUCT CHEM+ 2016. [DOI: 10.1134/s0022476615080016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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132
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Skyner RE, McDonagh JL, Groom CR, van Mourik T, Mitchell JBO. A review of methods for the calculation of solution free energies and the modelling of systems in solution. Phys Chem Chem Phys 2016; 17:6174-91. [PMID: 25660403 DOI: 10.1039/c5cp00288e] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past decade, pharmaceutical companies have seen a decline in the number of drug candidates successfully passing through clinical trials, though billions are still spent on drug development. Poor aqueous solubility leads to low bio-availability, reducing pharmaceutical effectiveness. The human cost of inefficient drug candidate testing is of great medical concern, with fewer drugs making it to the production line, slowing the development of new treatments. In biochemistry and biophysics, water mediated reactions and interactions within active sites and protein pockets are an active area of research, in which methods for modelling solvated systems are continually pushed to their limits. Here, we discuss a multitude of methods aimed towards solvent modelling and solubility prediction, aiming to inform the reader of the options available, and outlining the various advantages and disadvantages of each approach.
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Affiliation(s)
- R E Skyner
- School of Chemistry, University of St Andrews, Purdie Building, North Haugh, St Andrews, Fife KY16 9ST, UK.
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133
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Dudev T, Mazmanian K, Lim C. Factors controlling the selectivity for Na+over Mg2+in sodium transporters and enzymes. Phys Chem Chem Phys 2016; 18:16986-97. [DOI: 10.1039/c6cp01937d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The paper discloses the key factors and physical bases that render a given binding site either Mg2+or Na+-selective.
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Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
| | - Karine Mazmanian
- Institute of Biomedical Sciences
- Academia Sinica
- Taipei 11529
- Taiwan
- Chemical Biology and Molecular Biophysics Program
| | - Carmay Lim
- Institute of Biomedical Sciences
- Academia Sinica
- Taipei 11529
- Taiwan
- Department of Chemistry
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134
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Marenich AV, Olson RM, Chamberlin AC, Cramer CJ, Truhlar DG. Polarization Effects in Aqueous and Nonaqueous Solutions. J Chem Theory Comput 2015; 3:2055-67. [PMID: 26636201 DOI: 10.1021/ct7001539] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Polarization effects in aqueous and nonaqueous solutions were analyzed for nine neutral and three charged organic solutes by the SM8 universal implicit solvation model and class IV partial atomic charges based on Charge Model 4M (CM4M) with the M06-2X density functional. The CM4M partial atomic charges in neutral and ionic solutes and in the corresponding clustered solutes (supersolutes), which included one solute molecule and one or two solvent molecules, were modeled in three solvents (benzene, methylene chloride, and water) and compared to those in the gas phase. The use of the supersolute approach (microsolvation) allows one to account for charge transfer from the solute to the solvent, and we find charge transfers as large as 0.06 atomic units for neutral solutes (pyridine in water) and 0.32 atomic units for ions (methoxide anion in water). Relaxation of the electronic structure of the solute in the presence of solvent increases the polarization free energy of the neutral solutes studied here, on average, by 16% in benzene, 30% in methylene chloride, and 43% in water. The increase for the ions in water averaged 43%.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Ryan M Olson
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Adam C Chamberlin
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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135
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Marenich AV, Olson RM, Kelly CP, Cramer CJ, Truhlar DG. Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges. J Chem Theory Comput 2015; 3:2011-33. [PMID: 26636198 DOI: 10.1021/ct7001418] [Citation(s) in RCA: 360] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new universal continuum solvation model (where "universal" denotes applicable to all solvents), called SM8, is presented. It is an implicit solvation model, also called a continuum solvation model, and it improves on earlier SMx universal solvation models by including free energies of solvation of ions in nonaqueous media in the parametrization. SM8 is applicable to any charged or uncharged solute composed of H, C, N, O, F, Si, P, S, Cl, and/or Br in any solvent or liquid medium for which a few key descriptors are known, in particular dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters. It does not require the user to assign molecular-mechanics types to an atom or group; all parameters are unique and continuous functions of geometry. It may be used with any level of electronic structure theory as long as accurate partial charges can be computed for that level of theory; we recommend using it with self-consistently polarized Charge Model 4 or other self-consistently polarized class IV charges, in which case analytic gradients are available. The model separates the observable solvation free energy into two components: the long-range bulk electrostatic contribution arising from a self-consistent reaction field treatment using the generalized Born approximation for electrostatics is augmented by the non-bulk-electrostatic contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. The cavities for the bulk electrostatics calculation are defined by superpositions of nuclear-centered spheres whose sizes are determined by intrinsic atomic Coulomb radii. The radii used for aqueous solution are the same as parametrized previously for the SM6 aqueous solvation model, and the radii for nonaqueous solution are parametrized by a training set of 220 bare ions and 21 clustered ions in acetonitrile, methanol, and dimethyl sulfoxide. The non-bulk-electrostatic terms are proportional to the solvent-accessible surface areas of the atoms of the solute and have been parametrized using solvation free energies for a training set of 2346 solvation free energies for 318 neutral solutes in 90 nonaqueous solvents and water and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The model is tested with three density functionals and with four basis sets: 6-31+G(d,p), 6-31+G(d), 6-31G(d), and MIDI!6D. The SM8 model achieves mean unsigned errors of 0.5-0.8 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 2.2-7.0 kcal/mol for ions. The model outperforms the earlier SM5.43R and SM7 universal solvation models as well as the default Polarizable Continuum Model (PCM) implemented in Gaussian 98/03, the Conductor-like PCM as implemented in GAMESS, Jaguar's continuum model based on numerical solution of the Poisson equation, and the GCOSMO model implemented in NWChem.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Ryan M Olson
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Casey P Kelly
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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136
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Higashi M, Truhlar DG. Combined Electrostatically Embedded Multiconfiguration Molecular Mechanics and Molecular Mechanical Method: Application to Molecular Dynamics Simulation of a Chemical Reaction in Aqueous Solution with Hybrid Density Functional Theory. J Chem Theory Comput 2015; 4:1032-9. [PMID: 26636356 DOI: 10.1021/ct8000816] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We here combine the electrostatically embedded multiconfiguration molecular mechanics (EE-MCMM) method for generating global potential energy surfaces in the presence of an electrostatic potential with molecular mechanics (MM). The resulting EE-MCMM/MM method is illustrated by applying it to carry out a molecular dynamics simulation for the symmetric bimolecular reaction Cl(-) + CH3Cl' → ClCH3 + Cl'(-) in aqueous solution with hybrid density functional theory as the quantum mechanical level. The potential of mean force is calculated, and the free energy barrier is found to be 25.3 kcal/mol, which is in good agreement with previous work. The advantage of the combined EE-MCMM and MM method is that the number of quantum mechanical calculations required for the active subsystem is very small compared to straight direct dynamics.
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Affiliation(s)
- Masahiro Higashi
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
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137
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Palazzo TA, Patra D, Yang JS, Khoury EE, Appleton MG, Haddadin MJ, Tantillo DJ, Kurth MJ. Dibenzonaphthyridinones: Heterocycle-to-Heterocycle Synthetic Strategies and Photophysical Studies. Org Lett 2015; 17:5732-5. [PMID: 26574652 PMCID: PMC4816217 DOI: 10.1021/acs.orglett.5b02680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A heterocycle-to-heterocycle strategy is presented for the preparation of highly fluorescent and solvatochromic dibenzonaphthyridinones (DBNs) via methodology that leads to the formation of a tertiary, spiro-fused carbon center. A linear correlation between the results of photophysical experiments and time dependent density functional theory calculations was observed for the λ(max) of excitation for DBNs with varying electronic character.
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Affiliation(s)
- Teresa A. Palazzo
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis CA 95616
| | - Digambara Patra
- Department of Chemistry, American University of Beirut, Beirut, Lebanon
| | - Joung S. Yang
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis CA 95616
| | - Elsy El Khoury
- Department of Chemistry, American University of Beirut, Beirut, Lebanon
| | - Mackenzie G. Appleton
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis CA 95616
| | | | - Dean J. Tantillo
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis CA 95616
| | - Mark J. Kurth
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis CA 95616
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138
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Swanson JMJ, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions. J Chem Theory Comput 2015; 3:170-83. [PMID: 26627162 DOI: 10.1021/ct600216k] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate implicit solvent models require parameters that have been optimized in a system- or atom-specific manner on the basis of experimental data or more rigorous explicit solvent simulations. Models based on the Poisson or Poisson-Boltzmann equation are particularly sensitive to the nature and location of the boundary which separates the low dielectric solute from the high dielectric solvent. Here, we present a novel method for optimizing the solute radii, which define the dielectric boundary, on the basis of forces and energies from explicit solvent simulations. We use this method to optimize radii for protein systems defined by AMBER ff99 partial charges and a spline-smoothed solute surface. The spline-smoothed surface is an atom-centered dielectric function that enables stable and efficient force calculations. We explore the relative performance of radii optimized with forces alone and those optimized with forces and energies. We show that our radii reproduce the explicit solvent forces and energies more accurately than four other parameter sets commonly used in conjunction with the AMBER force field, each of which has been appropriately scaled for spline-smoothed surfaces. Finally, we demonstrate that spline-smoothed surfaces show surprising accuracy for small, compact systems but may have limitations for highly solvated protein systems. The optimization method presented here is efficient and applicable to any system with explicit solvent parameters. It can be used to determine the optimal continuum parameters when experimental solvation energies are unavailable and the computational costs of explicit solvent charging free energies are prohibitive.
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Affiliation(s)
- Jessica M J Swanson
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - Jason A Wagoner
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - Nathan A Baker
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
| | - J A McCammon
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365
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139
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Vorobyov I, Anisimov VM, Greene S, Venable RM, Moser A, Pastor RW, MacKerell AD. Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers. J Chem Theory Comput 2015; 3:1120-33. [PMID: 26627431 DOI: 10.1021/ct600350s] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas- and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.
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Affiliation(s)
- Igor Vorobyov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Victor M Anisimov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shannon Greene
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard M Venable
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Adam Moser
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard W Pastor
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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140
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Ribeiro RF, Marenich AV, Cramer CJ, Truhlar DG. Solvent Dependence of (14)N Nuclear Magnetic Resonance Chemical Shielding Constants as a Test of the Accuracy of the Computed Polarization of Solute Electron Densities by the Solvent. J Chem Theory Comput 2015; 5:2284-300. [PMID: 26616615 DOI: 10.1021/ct900258f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although continuum solvation models have now been shown to provide good quantitative accuracy for calculating free energies of solvation, questions remain about the accuracy of the perturbed solute electron densities and properties computed from them. Here we examine those questions by applying the SM8, SM8AD, SMD, and IEF-PCM continuum solvation models in combination with the M06-L density functional to compute the (14)N magnetic resonance nuclear shieldings of CH3CN, CH3NO2, CH3NCS, and CH3ONO2 in multiple solvents, and we analyze the dependence of the chemical shifts on solvent dielectric constant. We examine the dependence of the computed chemical shifts on the definition of the molecular cavity (both united-atom models and models based on superposed individual atomic spheres) and three kinds of treatments of the electrostatics, namely the generalized Born approximation with the Coulomb field approximation, the generalized Born model with asymmetric descreening, and models based on approximate numerical solution schemes for the nonhomogeneous Poisson equation. Our most systematic analyses are based on the computation of relative (14)N chemical shifts in a series of solvents, and we compare calculated shielding constants relative to those in CCl4 for various solvation models and density functionals. While differences in the overall results are found to be reasonably small for different solvation models and functionals, the SMx models SM8, and SM8AD, using the same cavity definitions (which for these models means the same atomic radii) as those employed for the calculation of free energies of solvation, exhibit the best agreement with experiment for every functional tested. This suggests that in addition to predicting accurate free energies of solvation, the SM8 and SM8AD generalized Born models also describe the solute polarization in a manner reasonably consistent with experimental (14)N nuclear magnetic resonance spectroscopy. Models based on the nonhomogeneous Poisson equation show slightly reduced accuracy. Scaling the intrinsic Coulomb radii to larger values (as has sometimes been suggested in the past) does not uniformly improve the results for any kind of solvent model; furthermore it uniformly degrades the results for generalized Born models. Use of a basis set that increases the outlying charge diminishes the accuracy of continuum models that solve the nonhomogeneous Poisson equation, which we ascribe to the inability of the numerical schemes for approximately solving the nonhomogeneous Poisson equation to fully account for the effects of electronic charge outside the solute cavity.
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Affiliation(s)
- Raphael F Ribeiro
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Aleksandr V Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
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141
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142
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Martínez JP, Solà M, Poater A. On the Reaction Mechanism of the Rhodium-Catalyzed Arylation of Fullerene (C60) with Organoboron Compounds in the Presence of Water. ChemistryOpen 2015; 4:774-8. [PMID: 27308203 PMCID: PMC4906499 DOI: 10.1002/open.201500093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Indexed: 11/25/2022] Open
Abstract
Density functional theory (DFT) calculations were carried out to study the reaction mechanism of the Suzuki-Miyaura rhodium-catalyzed hydroarylation of fullerene (C60) by phenylboronic acid in the presence of water. As found experimentally, our results confirm that addition of the phenyl group and the hydrogen atom in C60 occurs at the [6,6] bond. The rate-determining step corresponds to the simultaneous transfer of a hydrogen atom from a water molecule to C60 and the recovery of the active species. The use of 2-phenyl-1,3,2-dioxaborinane and the 4,4,5,5-tetramethyl-2-phenyl-1,3,2,-dioxaborolane instead of phenylboronic acid as organoborate agents does not lead to great modifications of the energy profile. The possible higher steric hindrance of 4,4,5,5-tetramethyl-2-phenyl-1,3,2,-dioxaborolane should not inhibit its use in the hydroarylation of C60. Overall, we show how organoboron species arylate C60 in rhodium-based catalysis assisted by water as a source of protons.
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Affiliation(s)
- Juan Pablo Martínez
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCampus Montilivi17071GironaCataloniaSpain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCampus Montilivi17071GironaCataloniaSpain
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCampus Montilivi17071GironaCataloniaSpain
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143
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Tummanapelli AK, Vasudevan S. Ab Initio MD Simulations of the Brønsted Acidity of Glutathione in Aqueous Solutions: Predicting pKa Shifts of the Cysteine Residue. J Phys Chem B 2015; 119:15353-8. [PMID: 26550841 DOI: 10.1021/acs.jpcb.5b10093] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pKa value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared with the isolated cysteine amino acid.
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Affiliation(s)
- Anil Kumar Tummanapelli
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
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144
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Skelton JM, da Silva EL, Crespo-Otero R, Hatcher LE, Raithby PR, Parker SC, Walsh A. Electronic excitations in molecular solids: bridging theory and experiment. Faraday Discuss 2015; 177:181-202. [PMID: 25631401 DOI: 10.1039/c4fd00168k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
As the spatial and temporal resolution accessible to experiment and theory converge, computational chemistry is an increasingly powerful tool for modelling and interpreting spectroscopic data. However, the study of molecular processes, in particular those related to electronic excitations (e.g. photochemistry), frequently pushes quantum-chemical techniques to their limit. The disparity in the level of theory accessible to periodic and molecular calculations presents a significant challenge when modelling molecular crystals, since accurate calculations require a high level of theory to describe the molecular species, but must also take into account the influence of the crystalline environment on their properties. In this article, we briefly review the different classes of quantum-chemical techniques, and present an overview of methods that account for environmental influences with varying levels of approximation. Using a combination of solid-state and molecular calculations, we quantitatively evaluate the performance of implicit-solvent models for the [Ni(Et4dien)(η2-O,ON)(η1-NO2)] linkage-isomer system as a test case. We focus particularly on the accurate reproduction of the energetics of the isomerisation, and on predicting spectroscopic properties to compare with experimental results. This work illustrates how the synergy between periodic and molecular calculations can be exploited for the study of molecular crystals, and forms a basis for the investigation of more challenging phenomena, such as excited-state dynamics, and for further methodological developments.
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Affiliation(s)
- Jonathan M Skelton
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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145
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Grishaeva TN, Masliy AN, Bakovets VV, Kuznetsov AM. Inclusion compound based on Bis(ethylenediamine)copper(II) complex and cucurbit[8]uril: Quantum chemical prediction for structure and formation thermodynamic parameters. RUSS J INORG CHEM+ 2015. [DOI: 10.1134/s0036023615100071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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146
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Dodda LS, Vilseck JZ, Cutrona KJ, Jorgensen WL. Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling. J Chem Theory Comput 2015; 11:4273-82. [PMID: 26575922 PMCID: PMC4857764 DOI: 10.1021/acs.jctc.5b00414] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Partial atomic charges for neutral molecules from quantum mechanical calculations are typically scaled for use in molecular modeling of liquid-phase systems. Optimal scale factors of 1.14 for CM1A and 1.27 for CM5 charges were previously determined for minimizing errors in free energies of hydration. The adequacy of the 1.14*CM1A and 1.27*CM5 models are evaluated here in pure liquid simulations in combination with the OPLS-AA force field. For 22 organic liquids, the 1.14*CM1A and 1.27*CM5 models yield mean unsigned errors (MUEs) of ca. 1.40 kcal/mol for heats of vaporization. Not surprisingly, this reflects overpolarization with the scale factors derived for aqueous media. Prediction of pure liquid properties using CM5 charges is optimized using a scale factor of 1.14, which reduces the MUE for heats of vaporization to 0.89 kcal/mol. However, due to the impracticality of using different scale factors in different explicit-solvent condensed-phase simulations, a universal scale factor of 1.20 emerged for CM5 charges. This provides a balance between errors in computed pure liquid properties and free energies of hydration. Computation of free energies of hydration by the GB/SA method further found that 1.20 is equally suited for use in explicit or implicit treatments of aqueous solvation. With 1.20*CM5 charges, a variety of condensed-phase simulations can be pursued while maintaining average errors of 1.0 kcal/mol in key thermodynamic properties.
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Affiliation(s)
- Leela S. Dodda
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Jonah Z. Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Kara J. Cutrona
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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147
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Tummanapelli AK, Vasudevan S. Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pKa Values from Metadynamics Sampling. J Phys Chem B 2015; 119:12249-55. [PMID: 26331783 DOI: 10.1021/acs.jpcb.5b05211] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation-deprotonation reaction of the 20 canonical α amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metadynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pKa values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error, with respect to experimental results, of 0.2 pKa units.
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Affiliation(s)
- Anil Kumar Tummanapelli
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
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148
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Peixoto MM, Bauerfeldt GF, Herbst MH, Pereira MS, da Silva CO. Study of the stepwise deprotonation reactions of glyphosate and the corresponding pKa values in aqueous solution. J Phys Chem A 2015; 119:5241-9. [PMID: 25629880 DOI: 10.1021/jp5099552] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Glyphosate (N-(phosphonomethyl)glycine) (Gph) is a herbicide that is broadly used in several countries. Its application to eliminate weeds may have the undesired effect of diminishing the metallic cations found in the soil (e.g., Ni(2+) and Zn(2+)), due to a complexation reaction that depends on the soil's pH. To better understand the molecular structures of glyphosate that are involved in such a complexation reaction, we have studied all possible glyphosate conformations in aqueous solution that may be involved in deprotonation reactions in the pH range from 2 to 11 using the polarizable continuum method (PCM). We have also compared direct (or absolute) methods to calculate pKa values, the cluster-continuum model and the proton-exchange scheme, using different thermodynamic cycles. The best result was achieved when using a proton-exchange scheme, which was able to properly reproduce three glyphosate experimental pKa values predicted for the glyphosate structures and conformations previously determined.
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Affiliation(s)
- Miqueias M Peixoto
- Departamento de Química-ICE, Universidade Federal Rural do Rio de Janeiro, Rodovia BR465, km 47, Seropédica - RJ, 23897-000, Brazil
| | - Glauco F Bauerfeldt
- Departamento de Química-ICE, Universidade Federal Rural do Rio de Janeiro, Rodovia BR465, km 47, Seropédica - RJ, 23897-000, Brazil
| | - Marcelo H Herbst
- Departamento de Química-ICE, Universidade Federal Rural do Rio de Janeiro, Rodovia BR465, km 47, Seropédica - RJ, 23897-000, Brazil
| | - Marcio S Pereira
- Departamento de Química-ICE, Universidade Federal Rural do Rio de Janeiro, Rodovia BR465, km 47, Seropédica - RJ, 23897-000, Brazil
| | - Clarissa O da Silva
- Departamento de Química-ICE, Universidade Federal Rural do Rio de Janeiro, Rodovia BR465, km 47, Seropédica - RJ, 23897-000, Brazil
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149
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Melchior A, Tolazzi M, Martínez JM, Pappalardo RR, Sánchez Marcos E. Hydration of Two Cisplatin Aqua-Derivatives Studied by Quantum Mechanics and Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:1735-44. [DOI: 10.1021/ct500975a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Andrea Melchior
- Department
of Environmental and Physical Chemistry, University of Udine, 33100 Udine, Udine, Italy
| | - Marilena Tolazzi
- Department
of Environmental and Physical Chemistry, University of Udine, 33100 Udine, Udine, Italy
| | - José Manuel Martínez
- Department
of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
| | - Rafael R. Pappalardo
- Department
of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
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Skara G, Pinter B, Top J, Geerlings P, De Proft F, De Vleeschouwer F. Conceptual Quantum Chemical Analysis of Bonding and Noncovalent Interactions in the Formation of Frustrated Lewis Pairs. Chemistry 2015; 21:5510-9. [DOI: 10.1002/chem.201405891] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Indexed: 12/20/2022]
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