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Shan X, Lee L, Clewes RJ, Howle CR, Sambrook MR, Clary DC. Computational analyses of the vibrational spectra of fentanyl, carfentanil and remifentanil. Spectrochim Acta A Mol Biomol Spectrosc 2022; 270:120763. [PMID: 35007908 DOI: 10.1016/j.saa.2021.120763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/30/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
The infrared (IR) spectra of fentanyl, carfentanil and remifentanil, and protonated salts, are computed using quantum chemistry methods. New experimental FTIR spectra are also reported and compared to the calculations. The accuracy of two density functional theory methods, B3LYP and M06-2X, are tested against higher level theories (MP2) and the experimental data. Gas phase IR spectra are calculated for both the neutral and protonated molecules in order to compare with the experimental data measured for various salts of fentanyl and its analogues. Key vibrational modes are selected and studied in detail using a vibrational mode locality calculation. The main contributing atomic movements in these vibrational modes are identified.
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Affiliation(s)
- Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Linda Lee
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Rhea J Clewes
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Christopher R Howle
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Mark R Sambrook
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - David C Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
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Burke MP, Casavecchia P, Cavallotti C, Clary DC, Doner A, Green WH, Grinberg Dana A, Guo H, Heathcote D, Hochlaf M, Klippenstein SJ, Kuwata KT, Lawrence JE, Lourderaj U, Mebel AM, Milesevic D, Mullin AS, Nguyen TL, Olzmann M, Orr-Ewing AJ, Osborn DL, Pazdera TM, Robertson PA, Robinson MS, Rotavera B, Seakins PW, Shannon RJ, Shiels OJ, Suits AG, Trevitt AJ, Troe J, Vallance C, Welz O, Zhang F, Zádor J. The reaction step: general discussion. Faraday Discuss 2022; 238:320-354. [DOI: 10.1039/d2fd90049a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Clary DC. Obituary for David Buckingham (1930–2021). Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Barone V, Alessandrini S, Biczysko M, Cheeseman JR, Clary DC, McCoy AB, DiRisio RJ, Neese F, Melosso M, Puzzarini C. Computational molecular spectroscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00034-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Affiliation(s)
- Timothy A. H. Burd
- Physical and Theoretical Chemical Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemical Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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7
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Abstract
It is very difficult to perform experiments on the physical parameters for the thermal decomposition of chemical nerve agents such as VX and computations, therefore, are useful. The reaction dynamics of the gas-phase pericyclic hydrogen transfer of the nerve agent VX is studied computationally. The geometries of the stationary structures are calculated at M06-2X/jul-cc-pVTZ level of theory. Single point energy calculations are carried out at the CBS/QB3 level to correct the energy barriers. Canonical reaction rate constants are calculated as a function of temperature. The one-dimensional semiclassical transition state theory is used to analyse the quantum tunneling effects. A reduced-dimensional hindered rotor model is proposed, tested, and applied to calculate the vibrational partition functions. It is found that the ester (O-side) and thioester (S-side) side chains of VX undergo pericyclic H-transfer reactions that result in decomposition of the molecule. The S-side reaction is favoured both kinetically and thermodynamically and dominates the pyrolysis over the temperature range from 600 K to 1000 K. It is predicted that VX completely decomposes in 2 s at temperatures above 750 K.
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Affiliation(s)
- Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
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8
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Abstract
A tunnelling controlled reaction is studied with semiclassical transition state theory, rationalising the results of experiment.
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Affiliation(s)
- Timothy A. H. Burd
- Physical and Theoretical Chemical Laboratory
- University of Oxford
- Oxford
- UK
| | - Xiao Shan
- Physical and Theoretical Chemical Laboratory
- University of Oxford
- Oxford
- UK
| | - David C. Clary
- Physical and Theoretical Chemical Laboratory
- University of Oxford
- Oxford
- UK
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9
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Affiliation(s)
- Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Timothy A. H. Burd
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Abstract
In order to further understand and support approaches for the degradation and destruction of toxic chemicals, the thermal decomposition of the nerve agent VX through possible pericyclic hydrogen transfer reactions is investigated using simulant molecules. A total of four simulant molecules are studied. Three of them have only one possible H-transfer site, while the other has two. They are chosen to bring physical insights into individual steps of the pericyclic reaction mechanism as well as the possible existence of competing mechanisms. The unimolecular reaction rate constants at the high-pressure limit are calculated. Geometries of stationary structures on the potential energy surfaces are calculated with the MP2 method as well as the B3LYP and M06-2X functionals and 6-311++G(d,p), jul-cc-pVTZ, and aug-cc-pVTZ basis sets. The barrier heights are corrected using energy values obtained at the CBS/QB3 level of theory. The contribution of the quantum tunneling effect to the reaction rate constants is included using one-dimensional semiclassical transition state theory. Adiabatic barrier heights, reaction rate constants, and branching ratio of the competing mechanisms are reported.
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Affiliation(s)
- Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
| | - Mark R Sambrook
- CBR Division, Defence Science and Technology Laboratory (Dstl) , Porton Down , Salisbury SP4 OJQ , United Kingdom
| | - David C Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
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Stace AJ, Clary DC. Modern theoretical chemistry: the legacy of Prof. John N. Murrell. Philos Trans A Math Phys Eng Sci 2018; 376:rsta.2017.0460. [PMID: 29431685 PMCID: PMC5805920 DOI: 10.1098/rsta.2017.0460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/13/2017] [Indexed: 06/08/2023]
Affiliation(s)
- Anthony J Stace
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - David C Clary
- Department of Physical and Theoretical Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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Shan X, Clary DC. Application of one-dimensional semiclassical transition state theory to the CH 3OH + H ⇌ CH 2OH/CH 3O + H 2 reactions. Philos Trans A Math Phys Eng Sci 2018; 376:rsta.2017.0147. [PMID: 29431675 PMCID: PMC5805916 DOI: 10.1098/rsta.2017.0147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 05/12/2023]
Abstract
The rate constants of the two branches of H-abstractions from CH3OH by the H-atom and the corresponding reactions in the reverse direction are calculated using the one-dimensional semiclassical transition state theory (1D SCTST). In this method, only the reaction mode vibration of the transition state (TS) is treated anharmonically, while the remaining internal degrees of freedom are treated as they would have been in a standard TS theory calculation. A total of eight ab initio single-point energy calculations are performed in addition to the computational cost of a standard TS theory calculation. This allows a second-order Richardson extrapolation method to be employed to improve the numerical estimation of the third- and fourth-order derivatives, which in turn are used in the calculation of the anharmonic constant. Hindered-rotor (HR) vibrations are identified in the equilibrium states of CH3OH and CH2OH, and the TSs of the reactions. The partition function of the HRs are calculated using both a simple harmonic oscillator model and a more sophisticated one-dimensional torsional eigenvalue summation (1D TES) method. The 1D TES method can be easily adapted in 1D SCTST computation. The resulting 1D SCTST with 1D TES rate constants show good agreement to previous theoretical and experimental works. The effects of the HR on rate constants for different reactions are also investigated.This article is part of the theme issue 'Modern theoretical chemistry'.
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Affiliation(s)
- Xiao Shan
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - David C Clary
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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Burd TA, Shan X, Clary DC. Tunnelling and the kinetic isotope effect in CH3+CH4→CH4+CH3: An application of semiclassical transition state theory. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
This Spiers Memorial Lecture discusses quantum effects that can be calculated and observed in the chemical reactions of small molecules.
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Affiliation(s)
- David C. Clary
- Physical and Theoretical Chemistry Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
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Abstract
Semi-classical Transition State theory can be applied to catalysed atmospheric reactions, but reaction mode anharmonicity must be treated carefully.
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Affiliation(s)
- Timothy A. H. Burd
- Physical and Theoretical Chemical Laboratory
- University of Oxford
- Oxford
- UK
| | - Xiao Shan
- Physical and Theoretical Chemical Laboratory
- University of Oxford
- Oxford
- UK
| | - David C. Clary
- Physical and Theoretical Chemical Laboratory
- University of Oxford
- Oxford
- UK
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Shan X, Vincent JC, Kirkpatrick S, Walker MD, Sambrook MR, Clary DC. A Combined Theoretical and Experimental Study of Sarin (GB) Decomposition at High Temperatures. J Phys Chem A 2017; 121:6200-6210. [PMID: 28704051 DOI: 10.1021/acs.jpca.7b04282] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Theoretical and experimental results are presented for the pyrolytic decomposition of the nerve agent sarin (GB) in the gas phase. High-level quantum chemistry calculations are performed together with a semiclassical transition-state theory for describing quantum mechanical tunneling. The experimental and theoretical results for the temperature dependence of the survival times show very good agreement, as does the calculated and measured activation energy for thermal decomposition. The combined results suggest that the thermal decomposition of GB, for temperature ranging from 350 to 500 °C, goes through a pericyclic reaction mechanism with a transition state consisting of a six-membered ring structure.
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Affiliation(s)
- Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Jack C Vincent
- CBR Division, DSTL Porton Down , Salisbury SP4 0JQ, United Kingdom
| | - Sue Kirkpatrick
- CBR Division, DSTL Porton Down , Salisbury SP4 0JQ, United Kingdom
| | - Maurice D Walker
- CBR Division, DSTL Porton Down , Salisbury SP4 0JQ, United Kingdom
| | - Mark R Sambrook
- CBR Division, DSTL Porton Down , Salisbury SP4 0JQ, United Kingdom
| | - David C Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
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Abstract
Guest editors Xueming Yang, David Clary and Daniel Neumark introduce the chemical reaction dynamics themed issue of Chemical Society Reviews.
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Affiliation(s)
- Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - David C. Clary
- Department of Physical and Theoretical Chemistry
- University of Oxford
- Oxford OX1 3QZ
- UK
| | - Daniel M. Neumark
- Department of Chemistry
- University of California
- Berkeley
- USA
- Chemical Science Division
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Abstract
This review surveys quantum scattering calculations on chemical reactions of polyatomic molecules in the gas phase published in the last ten years.
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Affiliation(s)
- Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Xiao Shan
- Physical and Theoretical Chemistry Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
| | - Dong H. Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - David C. Clary
- Physical and Theoretical Chemistry Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
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Greene SM, Shan X, Clary DC. Rate constants of chemical reactions from semiclassical transition state theory in full and one dimension. J Chem Phys 2016; 144:244116. [DOI: 10.1063/1.4954840] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Samuel M. Greene
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Affiliation(s)
- David C Clary
- Department of Physical and Theoretical Chemistry, University of Oxford, Oxford OX1 3QZ, UK.
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Greene SM, Shan X, Clary DC. An investigation of one- versus two-dimensional semiclassical transition state theory for H atom abstraction and exchange reactions. J Chem Phys 2016; 144:084113. [DOI: 10.1063/1.4942161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Samuel M. Greene
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Althorpe SC, Beniwal V, Bolhuis PG, Brandão J, Clary DC, Ellis J, Fang W, Glowacki DR, Hele TJH, Jónsson H, Kästner J, Makri N, Manolopoulos DE, McKemmish LK, Menzl G, Miller III TF, Miller WH, Pollak E, Rampino S, Richardson JO, Richter M, Roy Chowdhury P, Shalashilin D, Tennyson J, Welsch R. Fundamentals: general discussion. Faraday Discuss 2016; 195:139-169. [DOI: 10.1039/c6fd90077a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Greene SM, Shan X, Clary DC. Reduced-Dimensionality Semiclassical Transition State Theory: Application to Hydrogen Atom Abstraction and Exchange Reactions of Hydrocarbons. J Phys Chem A 2015; 119:12015-27. [DOI: 10.1021/acs.jpca.5b04379] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel M. Greene
- Physical and Theoretical Chemistry
Laboratory, Department of Chemistry, University of Oxford, South Parks
Road, Oxford, OX1 3QZ, United Kingdom
| | - Xiao Shan
- Physical and Theoretical Chemistry
Laboratory, Department of Chemistry, University of Oxford, South Parks
Road, Oxford, OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemistry
Laboratory, Department of Chemistry, University of Oxford, South Parks
Road, Oxford, OX1 3QZ, United Kingdom
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Affiliation(s)
- Xiao Shan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - David C. Clary
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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Clary DC. Historical perspective on: “Semiclassical trajectory approach to photoisomerisation” by A Warshel and M. Karplus [Chem. Phys. Lett. 32 (1) (1975) 11–17]. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Shan X, Remmert SM, Clary DC, Zhang B, Liu K. Crossed-beam and reduced dimensionality studies of the state-to-state integral cross sections of the Cl+HCD3(v)→HCl(v′)+CD3 reaction. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
One hundred years ago, Niels Bohr's pioneering paper on the electronic structure of the hydrogen atom revolutionized atomic theory.
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Affiliation(s)
- David C. Clary
- Department of Physical and Theoretical Chemistry, University of Oxford, Oxford OX1 3QZ, UK
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Shan X, Clary DC. Quantum effects in the abstraction reaction by H atoms of primary and secondary hydrogens in n-C4H10: a test of a new potential energy surface construction method. Phys Chem Chem Phys 2013; 15:1222-31. [PMID: 23223355 DOI: 10.1039/c2cp42911j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recently, von Horsten et al. suggested an efficient method to construct two dimensional potential energy surfaces (PESs) for use in quantum scattering simulations, in which they utilised the minimum energy path (MEP) and assumed harmonic behaviour of the PES near the MEP. In the same paper, the authors applied this method to various H-abstraction reactions from C1-C3 alkane molecules. In this work we demonstrate an alternative PES construction method, and apply it to the more challenging H-abstraction from n-C(4)H(10) reactions. The geometry optimizations and frequency calculations are done at the MP2/cc-pVTZ level of theory, while the energies are calculated with the CCSD(T) method with the same basis set. The calculations give adiabatic energy barrier heights of 45.9 kJ mol(-1) and 34.4 kJ mol(-1) for the primary and secondary hydrogens in n-C(4)H(10). When compared to purely classical transition state theory, quantum scattering calculations show that quantum tunnelling and zero-point effects have large contributions at low temperatures, typically below 500 K. The branching ratio study suggests that the abstraction of secondary hydrogen in n-C(4)H(10) dominates the overall reaction rate at low temperatures. The rate constants for the two abstraction channels become more comparable as the temperature increases.
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Affiliation(s)
- Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, UK.
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Ljubić I, Clary DC. Quasiclassical trajectory calculations of hydrogen absorption in the (NaAlH4)2Ti system on a model analytical potential energy surface. Phys Chem Chem Phys 2012; 14:3915-21. [DOI: 10.1039/c2cp23689c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lester MI, Green WH, Chakravarty C, Clary DC. STIMULATED EMISSION PUMPING AS A PROBE OF THE OH (X2Π) + Ar INTERMOLECULAR POTENTIAL ENERGY SURFACE. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/9789812831880_0018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Affiliation(s)
- Marsha I. Lester
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - William H. Green
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Charusita Chakravarty
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David C. Clary
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Remmert SM, Banks ST, Harvey JN, Orr-Ewing AJ, Clary DC. Reduced dimensionality spin-orbit dynamics of CH3 + HCl ⇌ CH4 + Cl on ab initio surfaces. J Chem Phys 2011; 134:204311. [DOI: 10.1063/1.3592732] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Affiliation(s)
- Boutheina Kerkeni
- a Physical and Theoretical Chemistry Laboratory , University of Oxford , Oxford , OX1 3QZ , UK
| | - David C. Clary
- a Physical and Theoretical Chemistry Laboratory , University of Oxford , Oxford , OX1 3QZ , UK
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Ljubić I, Clary DC. Towards understanding a mechanism for reversible hydrogen storage: theoretical study of transition metal catalysed dehydrogenation of sodium alanate. Phys Chem Chem Phys 2010; 12:4012-23. [DOI: 10.1039/b922617f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ivan Ljubić
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Rd., Oxford, UK OX1 3QZ.
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Banks ST, Tautermann CS, Remmert SM, Clary DC. An improved treatment of spectator mode vibrations in reduced dimensional quantum dynamics: Application to the hydrogen abstraction reactions μ+CH4, H+CH4, D+CH4, and CH3+CH4. J Chem Phys 2009; 131:044111. [DOI: 10.1063/1.3177380] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Remmert SM, Banks ST, Clary DC. Reduced Dimensionality Quantum Dynamics of CH3 + CH4 → CH4 + CH3: Symmetric Hydrogen Exchange on an Ab Initio Potential. J Phys Chem A 2009; 113:4255-64. [DOI: 10.1021/jp810803k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah M. Remmert
- Department of Chemistry, University of Oxford, PTCL, South Parks Road, Oxford, OX13QZ, United Kingdom
| | - Simon T. Banks
- Department of Chemistry, University of Oxford, PTCL, South Parks Road, Oxford, OX13QZ, United Kingdom
| | - David C. Clary
- Department of Chemistry, University of Oxford, PTCL, South Parks Road, Oxford, OX13QZ, United Kingdom
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Banks ST, Clary DC. Chemical reaction surface vibrational frequencies evaluated in curvilinear internal coordinates: Application to H+CH4⇌H2+CH3. J Chem Phys 2009; 130:024106. [DOI: 10.1063/1.3052076] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
This perspective discusses progress in the theory of bimolecular reaction dynamics in the gas phase. The examples selected show that definitive quantum dynamical computations are providing insights into the detailed mechanisms of chemical reactions.
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Affiliation(s)
- David C Clary
- Department of Physical and Theoretical Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
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40
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Affiliation(s)
- David C. Clary
- Department of Physical and Theoretical Chemistry, University of Oxford, Oxford OX1 3QZ, UK
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42
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Abstract
A reduced dimensionality (RD) approximation is developed for the title reaction which treats the angle of approach of the hydroxyl radical to the nitrogen dioxide molecule and the radial distance between the two species explicitly. All other degrees of freedom are treated adiabatically. Electronic structure calculations at the complete active space self-consistent field level are used to fit a potential energy surface (PES) in these two coordinates. Within this RD model the adiabatic capture centrifugal sudden approximation is used to calculate the high pressure limit rate constant. A correction for reflection from the PES due to rotationally nonadiabatic transitions is applied using the wave packet capture approximation. The branching ratio for the title reaction is calculated for the atmospherically significant temperature range of 200-400 K at 20 Torr without distinguishing between the conformers of HOONO. The result is k(HOONO)k(HNO(3) )=0.051 at 20 Torr and 300 K, which is in good agreement with the measured branching ratio between cis-cis-HOONO and nitric acid. This suggests that most of the different conformers of HOONO were converted to the most stable cis-cis conformer on the time scale of the measurements made.
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Affiliation(s)
- Christopher F Williams
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
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44
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Abstract
We present a new application for the Torsional Path Integral Monte Carlo (TPIMC) method in which the TPI partition functions are introduced into the calculation of Transition State Theory (TST) rate constants. In this way, an explicit treatment of torsional anharmonicity is included in the TST calculations and the magnitude of these effects can be assessed. The new method is tested on the C(2)H(6) + H hydrogen abstraction reaction and concerted hydrogen transfer in the carbonic acid dimer, for which we have developed torsional potential energy surfaces. For the C(2)H(6) + H reaction the rate constants are halved at room temperature on including a treatment of torsional anharmonicity, while the effects are found to be much smaller for the hydrogen transfer reaction in the carbonic acid dimer.
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Affiliation(s)
- Yvette K Sturdy
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, England.
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45
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Abstract
We study the reaction Cl + CH(4)--> HCl + CH(3) using a 2-D potential energy surface obtained by fitting a double Morse analytical function to high level (CCSD(T)/cc-pVTZ//MP2/cc-pVTZ)ab initio data. Dynamics simulations are performed in hyperspherical coordinates with the close-coupled equations being solved using R-matrix propagation. Quantum contributions from spectator modes are included via a harmonic zero-point correction to the ab initio data prior to fitting the potential. This is the first time this method has been applied to a heavy-light-heavy reaction and the first time it has been used to study differential cross sections. We find thermal rate constants and state-to-state differential cross sections which are in good agreement with experimental data. We discuss the applicability of our method to the study of kinetic isotope effects (KIEs), which we derive for the CH(4)/CD(4) substitution. The calculated KIE compares favourably with experiment. Finally, we discuss the sensitivity of the results of dynamics simulations on the accuracy of the fitted potential.
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Affiliation(s)
- Simon T Banks
- Physical and Theoretical Chemistry Department, University of Oxford, South Parks Road, Oxford, UK.
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46
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Abstract
In this paper we calculate the relative conformer populations of the tryptamine molecule. Our approach combines high level electronic structure conformer energies with harmonic frequencies and an anharmonic treatment of the torsional motions using the torsional path integral Monte Carlo method. We have developed a 3-D potential energy surface as a function of the torsional coordinates at the B3LYP/6-31+G(d) level using 2535 grid points. Eight conformers of tryptamine were found to be significantly populated at 430 K as opposed to the experimental observation of seven. This, along with further comparisons with various experimental data, leads us to suppose that conformer interconversion occurs during the cooling phases of many of the experiments. The ordering of the calculated populations fits well with available experimental data. Torsional anharmonicity is found to affect conformer populations more significantly at 430 K than at 100 K (although overall the effects are small), while quantum mechanical effects are not important at either temperature.
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Affiliation(s)
- Yvette K Sturdy
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK.
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47
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48
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Affiliation(s)
- David C Clary
- Department of Physical and Theoretical Chemistry, University of Oxford, Oxford OX1 3QZ, UK.
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49
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Hellman A, Baerends EJ, Biczysko M, Bligaard T, Christensen CH, Clary DC, Dahl S, van Harrevelt R, Honkala K, Jonsson H, Kroes GJ, Luppi M, Manthe U, Nørskov JK, Olsen RA, Rossmeisl J, Skúlason E, Tautermann CS, Varandas AJC, Vincent JK. Predicting Catalysis: Understanding Ammonia Synthesis from First-Principles Calculations. J Phys Chem B 2006; 110:17719-35. [PMID: 16956255 DOI: 10.1021/jp056982h] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we give a full account of a large collaborative effort toward an atomic-scale understanding of modern industrial ammonia production over ruthenium catalysts. We show that overall rates of ammonia production can be determined by applying various levels of theory (including transition state theory with or without tunneling corrections, and quantum dynamics) to a range of relevant elementary reaction steps, such as N(2) dissociation, H(2) dissociation, and hydrogenation of the intermediate reactants. A complete kinetic model based on the most relevant elementary steps can be established for any given point along an industrial reactor, and the kinetic results can be integrated over the catalyst bed to determine the industrial reactor yield. We find that, given the present uncertainties, the rate of ammonia production is well-determined directly from our atomic-scale calculations. Furthermore, our studies provide new insight into several related fields, for instance, gas-phase and electrochemical ammonia synthesis. The success of predicting the outcome of a catalytic reaction from first-principles calculations supports our point of view that, in the future, theory will be a fully integrated tool in the search for the next generation of catalysts.
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Affiliation(s)
- A Hellman
- Haldor Topsøe A/S, Nymøllevej 55, DK-2800 Lyngby, Denmark.
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Charlo D, Clary DC. Quantum-mechanical calculations on pressure and temperature dependence of three-body recombination reactions: application to ozone formation rates. J Chem Phys 2006; 120:2700-7. [PMID: 15268414 DOI: 10.1063/1.1635361] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A quantum-mechanical model is designed for the calculation of termolecular association reaction rate coefficients in the low-pressure fall-off regime. The dynamics is set up within the energy transfer mechanism and the kinetic scheme is the steady-state approximation. We applied this model to the formation of ozone O + O2 + M --> O3 + M for M = Ar, making use of semiquantitative potential energy surfaces. The stabilization process is treated by means of the vibrational close-coupling infinite order sudden scattering theory. Major approximations include the neglect of the O3 vibrational bending mode and rovibrational couplings. We calculated individual isotope-specific rate constants and rate constant ratios over the temperature range 10-1000 K and the pressure fall-off region 10(-7)-10(2) bar. The present results show a qualitative and semiquantitative agreement with available experiments, particularly in the temperature region of atmospheric interest.
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Affiliation(s)
- David Charlo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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