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Louis H, Charlie DE, Amodu IO, Benjamin I, Gber TE, Agwamba EC, Adeyinka AS. Probing the Reactions of Thiourea (CH 4N 2S) with Metals (X = Au, Hf, Hg, Ir, Os, W, Pt, and Re) Anchored on Fullerene Surfaces (C 59X). ACS OMEGA 2022; 7:35118-35135. [PMID: 36211036 PMCID: PMC9535727 DOI: 10.1021/acsomega.2c04044] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/08/2022] [Indexed: 05/21/2023]
Abstract
Upon various investigations conducted in search for a nanosensor material with the best sensing performance, the need to explore these materials cannot be overemphasized as materials associated with best sensing attributes are of vast interest to researchers. Hence, there is a need to investigate the adsorption performances of various metal-doped fullerene surfaces: C59Au, C59Hf, C59Hg, C59Ir, C59Os, C59Pt, C59Re, and C59W on thiourea [SC(NH2)2] molecule using first-principles density functional theory computation. Comparative adsorption study has been carried out on various adsorption models of four functionals, M06-2X, M062X-D3, PBE0-D3, and ωB97XD, and two double-hybrid (DH) functionals, DSDPBEP86 and PBE0DH, as reference at Gen/def2svp/LanL2DZ. The visual study of weak interactions such as quantum theory of atoms in molecule analysis and noncovalent interaction analysis has been invoked to ascertain these results, and hence we arrived at a conclusive scientific report. In all cases, the weak adsorption observed is best described as physisorption phenomena, and CH4N2S@C59Pt complex exhibits better sensing attributes than its studied counterparts in the interactions between thiourea molecule and transition metal-doped fullerene surfaces. Also, in the comparative adsorption study, DH density functionals show better performance in estimating the adsorption energies due to their reduced mean absolute deviation (MAD) and root-mean-square deviation (RMSD) values of (MAD = 1.0305, RMSD = 1.6277) and (MAD = 0.9965, RMSD = 1.6101) in DSDPBEP86 and PBE0DH, respectively.
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Affiliation(s)
- Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Destiny E. Charlie
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Ismail O. Amodu
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Mathematics, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Innocent Benjamin
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Terkumbur E. Gber
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Ernest C. Agwamba
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Adedapo S. Adeyinka
- Department
of Chemical Sciences, University of Johannesburg, Johannesburg 2006, South Africa
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2
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Gu Y, Xu X. Extended Koopmans’ theorem in the adiabatic connection formalism: Applied to doubly hybrid density functionals. J Chem Phys 2020; 153:044109. [DOI: 10.1063/5.0010743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yonghao Gu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
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3
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Bourass M, El Alamy A, Bouachrine M. Structural and photophysical studies of triphenylamine-based nonlinear optical dyes: effects of π-linker moieties on the D-π-A structure. CR CHIM 2019. [DOI: 10.1016/j.crci.2019.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Su NQ, Zhu Z, Xu X. Doubly hybrid density functionals that correctly describe both density and energy for atoms. Proc Natl Acad Sci U S A 2018; 115:2287-2292. [PMID: 29444857 PMCID: PMC5878006 DOI: 10.1073/pnas.1713047115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, it was argued [Medvedev MG, et al. (2017) Science 355:49-52] that the development of density functional approximations (DFAs) is "straying from the path toward the exact functional." The exact functional should yield both exact energy and density for a system of interest; nevertheless, they found that many heavily fitted functionals for molecular energies actually lead to poor electron densities of atoms. They also observed a trend that, for the nonempirical and few-parameter functionals, densities can be improved as one climbs up the first four rungs of the Jacob's ladder of DFAs. The XYG3 type of doubly hybrid functionals (xDHs) represents a less-empirical and fewer-parameter functional on the top fifth rung, in which both the Hartree-Fock-like exchange and the second-order perturbative (MP2-like) correlation are hybridized with the low rung functionals. Here, we show that xDHs can well describe both density and energy for the same atomic set of Medvedev et al., showing that the latter trend can well be extended to the top fifth rung.
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Affiliation(s)
- Neil Qiang Su
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zhenyu Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
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5
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Chen J, Su NQ, Xu X, Zhang DH. Accurate potential energy surfaces for hydrogen abstraction reactions: A benchmark study on the XYG3 doubly hybrid density functional. J Comput Chem 2017; 38:2326-2334. [PMID: 28786211 DOI: 10.1002/jcc.24886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 11/06/2022]
Abstract
The potential energy surface (PES) for the H + CH4 system has been constructed with the recently developed XYG3 doubly hybrid functional, while those with the standard B3LYP hybrid functional, and the Møller-Plesset perturbation theory up to the second order (MP2) are also presented for comparison. Quantum dynamics studies demonstrated that satisfactory results on the reaction probabilities and the rate coefficients can be obtained on top of the XYG3-PES, as compared to the results based on the highly accurate, yet expensive, CCSD(T)-PES (Li et al., J. Chem. Phys. 2015, 142, 204302). Further investigation suggested that the XYG3 functional is useful in providing accurate rate coefficients for some larger systems involving H atom abstractions. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Jun Chen
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Neil Qiang Su
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics & Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Su NQ, Pernot P, Xu X, Savin A. When does a functional correctly describe both the structure and the energy of the transition state? J Mol Model 2017; 23:65. [PMID: 28185112 DOI: 10.1007/s00894-017-3229-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/12/2017] [Indexed: 11/30/2022]
Abstract
Requiring that several properties are well reproduced is a severe test on density functional approximations. This can be assessed through the estimation of joint and conditional success probabilities. An example is provided for a small set of molecules, for properties characterizing the transition states (geometries and energies).
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Affiliation(s)
- Neil Qiang Su
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Pascal Pernot
- CNRS, UMR8000, Laboratoire de Chimie Physique, F-91405, Orsay, France.,Univ. Paris-Sud, UMR8000, Laboratoire de Chimie Physique, F-91405, Orsay, France
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Andreas Savin
- CNRS, UMR7616, Laboratoire de Chimie Théorique, F-75005, Paris, France. .,UPMC Univ Paris 06, UMR7616, Laboratoire de Chimie Théorique, F-75005, Paris, France.
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7
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Mussard B, Toulouse J. Fractional-charge and fractional-spin errors in range-separated density-functional theory. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1213910] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Bastien Mussard
- Institut des sciences du calcul et des données, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
- Laboratoire de Chimie Théorique, Université Pierre et Marie Curie, Sorbonne Universités, CNRS, Paris, France
| | - Julien Toulouse
- Laboratoire de Chimie Théorique, Université Pierre et Marie Curie, Sorbonne Universités, CNRS, Paris, France
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8
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Su NQ, Xu X. The XYG3 type of doubly hybrid density functionals. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1274] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Neil Qiang Su
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry; Fudan University; Shanghai 200433 China
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Sancho-García JC, Pérez-Jiménez AJ, Savarese M, Brémond E, Adamo C. Importance of Orbital Optimization for Double-Hybrid Density Functionals: Application of the OO-PBE-QIDH Model for Closed- and Open-Shell Systems. J Phys Chem A 2016; 120:1756-62. [DOI: 10.1021/acs.jpca.6b00994] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. C. Sancho-García
- Departamento
de Química Física, Universidad de Alicante, 03080 Alicante, Spain
| | - A. J. Pérez-Jiménez
- Departamento
de Química Física, Universidad de Alicante, 03080 Alicante, Spain
| | - M. Savarese
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, I-16163 Genoa, Italy
| | - E. Brémond
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, I-16163 Genoa, Italy
| | - C. Adamo
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, I-16163 Genoa, Italy
- Institut de Recherche
de Chimie Paris, IRCP CNRS UMR-8247, Chimie ParisTech, École Nationale Superieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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10
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Su NQ, Xu X. Beyond energies: geometry predictions with the XYG3 type of doubly hybrid density functionals. Chem Commun (Camb) 2016; 52:13840-13860. [DOI: 10.1039/c6cc04886b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scaled mean absolute deviations (s-MADs) of the optimized geometric parameters for covalent bondings (the CCse set), nonbonded interactions (the S22G30 set) and the transition state structures (the TSG36 set), with Tot referring to the averaged s-MAD for general performances.
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Affiliation(s)
- Neil Qiang Su
- Collaborative Innovation Center of Chemistry for Energy Materials
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- MOE Laboratory for Computational Physical Science
- Department of Chemistry
- Fudan University
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- MOE Laboratory for Computational Physical Science
- Department of Chemistry
- Fudan University
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