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Yao Y, Kanai Y. Nuclear Quantum Effect and Its Temperature Dependence in Liquid Water from Random Phase Approximation via Artificial Neural Network. J Phys Chem Lett 2021; 12:6354-6362. [PMID: 34231366 DOI: 10.1021/acs.jpclett.1c01566] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report structural and dynamical properties of liquid water described by the random phase approximation (RPA) correlation together with the exact exchange energy (EXX) within density functional theory. By utilizing thermostated ring polymer molecular dynamics, we examine the nuclear quantum effects and their temperature dependence. We circumvent the computational limitation of performing direct first-principles molecular dynamics simulation at this high level of electronic structure theory by adapting an artificial neural network model. We show that the EXX+RPA level of theory accurately describes liquid water in terms of both dynamical and structural properties.
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Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
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2
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Martins ACV, de-Lima-Neto P, Caetano EWS, Freire VN. An improved quantum biochemistry description of the glutamate–GluA2 receptor binding within an inhomogeneous dielectric function framework. NEW J CHEM 2017. [DOI: 10.1039/c6nj03939a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new methodology to define the inhomogeneous dielectric constant of protein residues, to apply to the calculation of protein–ligand properties such as the electrostatic interaction.
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Affiliation(s)
- A. C. V. Martins
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - P. de-Lima-Neto
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - E. W. S. Caetano
- Federal Institute of Education
- Science and Technology of Ceara
- 60040-531 Fortaleza
- Brazil
| | - V. N. Freire
- Department of Physics
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
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3
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Biswas S, Melgar D, Srimany A, Rodríguez-Fortea A, Pradeep T, Bo C, Poblet JM, Roy S. Direct Observation of the Formation Pathway of [Mo132] Keplerates. Inorg Chem 2016; 55:8285-91. [DOI: 10.1021/acs.inorgchem.5b02570] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Subharanjan Biswas
- Eco-Friendly Applied Materials Laboratory (EFAML), Materials
Science Centre, Department of Chemical Sciences, Indian Institute of Science Education and Research-Kolkata (IISER-Kolkata), Mohanpur Campus, Mohanpur 741246, India
| | - Dolores Melgar
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain
- Departament d’Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Av. dels Països Catalans, 26, 43007 Tarragona, Spain
| | - Amitava Srimany
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Antonio Rodríguez-Fortea
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Thalappil Pradeep
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Josep M. Poblet
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Soumyajit Roy
- Eco-Friendly Applied Materials Laboratory (EFAML), Materials
Science Centre, Department of Chemical Sciences, Indian Institute of Science Education and Research-Kolkata (IISER-Kolkata), Mohanpur Campus, Mohanpur 741246, India
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Martins AC, Ribeiro FW, Zanatta G, Freire VN, Morais S, de Lima-Neto P, Correia AN. Modeling of laccase inhibition by formetanate pesticide using theoretical approaches. Bioelectrochemistry 2016; 108:46-53. [DOI: 10.1016/j.bioelechem.2015.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/12/2015] [Accepted: 12/17/2015] [Indexed: 02/07/2023]
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Sousa BL, Barroso-Neto IL, Oliveira EF, Fonseca E, Lima-Neto P, Ladeira LO, Freire VN. Explaining RANKL inhibition by OPG through quantum biochemistry computations and insights into peptide-design for the treatment of osteoporosis. RSC Adv 2016. [DOI: 10.1039/c6ra16712h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Quantum biochemistry computations are applied to precisely describe important protein–protein interactions, providing a basis for the design of inhibitory peptides against osteoporosis.
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Affiliation(s)
- Bruno L. Sousa
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Ito L. Barroso-Neto
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | | | - Emerson Fonseca
- Departamento de Física
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Pedro Lima-Neto
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Luiz O. Ladeira
- Departamento de Física
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
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Girleanu M, Alphazan T, Boudene Z, Bonduelle-Skrzypczak A, Legens C, Gay AS, Copéret C, Ersen O, Raybaud P. Magnifying the Morphology Change Induced by a Nickel Promoter in Tungsten(IV) Sulfide Industrial Hydrocracking Catalyst: A HAADF-STEM and DFT Study. ChemCatChem 2014. [DOI: 10.1002/cctc.201402115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Corral Valero M, Raybaud P. Cobalt Catalyzed Fischer–Tropsch Synthesis: Perspectives Opened by First Principles Calculations. Catal Letters 2012. [DOI: 10.1007/s10562-012-0930-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Piękoś Ł, Mitoraj MP. Theoretical description of dihydrogen/hydride and trihydride molybdocene complexes: An insight from static and molecular dynamics simulations. J Comput Chem 2012; 34:294-304. [DOI: 10.1002/jcc.23129] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 12/22/2022]
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Barroso-Neto IL, Marques JPC, da Costa RF, Caetano EWS, Cavada BS, Gottfried C, Freire VN. Inactivation of Ovine Cyclooxygenase-1 by Bromoaspirin and Aspirin: A Quantum Chemistry Description. J Phys Chem B 2012; 116:3270-9. [DOI: 10.1021/jp206397z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ito L. Barroso-Neto
- Department of Biochemistry, Universidade Federal do Ceará, Fortaleza 60455-760, Ceará, Brazil
| | - João Paulo C. Marques
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
| | - Roner F. da Costa
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
| | - Ewerton W. S. Caetano
- Instituto
Federal de Educação, Ciência e Tecnologia do Ceará, Fortaleza 60040-531, Ceará,
Brazil
| | - Benildo S. Cavada
- Department of Biochemistry, Universidade Federal do Ceará, Fortaleza 60455-760, Ceará, Brazil
| | - Carmem Gottfried
- Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre
90035-003, Rio Grande do Sul, Brazil
| | - Valder N. Freire
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
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Chotard JN, Tang WS, Raybaud P, Janot R. Potassium Silanide (KSiH3): A Reversible Hydrogen Storage Material. Chemistry 2011; 17:12302-9. [PMID: 21953694 DOI: 10.1002/chem.201101865] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Indexed: 11/12/2022]
Affiliation(s)
- Jean-Noël Chotard
- Laboratoire de Réactivité et Chimie des Solides, UMR 6007 CNRS Université de Picardie Jules Verne, 33 rue St Leu, 80039 Amiens, France
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