351
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Krasnoshchekov SV, Schutski RS, Craig NC, Sibaev M, Crittenden DL. Comparing the accuracy of perturbative and variational calculations for predicting fundamental vibrational frequencies of dihalomethanes. J Chem Phys 2018; 148:084102. [DOI: 10.1063/1.5020295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sergey V. Krasnoshchekov
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow 119991, Russian Federation
| | | | - Norman C. Craig
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, USA
| | - Marat Sibaev
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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352
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Mankodi TK, Bhandarkar UV, Puranik BP. Global potential energy surface of ground state singlet spin O 4. J Chem Phys 2018; 148:074305. [PMID: 29471635 DOI: 10.1063/1.5008973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new global potential energy for the singlet spin state O4 system is reported using CASPT2/aug-cc-pVTZ ab initio calculations. The geometries for the six-dimensional surface are constructed using a novel point generation scheme that employs randomly generated configurations based on the beta distribution. The advantage of this scheme is apparent in the reduction of the number of required geometries for a reasonably accurate potential energy surface (PES) and the consequent decrease in the overall computational effort. The reported surface matches well with the recently published singlet surface by Paukku et al. [J. Chem. Phys. 147, 034301 (2017)]. In addition to the O4 PES, the ground state N4 PES is also constructed using the point generation scheme and compared with the existing PES [Y. Paukku et al., J. Chem. Phys. 139, 044309 (2013)]. The singlet surface is constructed with the aim of studying high energy O2-O2 collisions and predicting collision induced dissociation cross section to be used in simulating non-equilibrium aerothermodynamic flows.
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Affiliation(s)
- Tapan K Mankodi
- Department of Mechanical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Upendra V Bhandarkar
- Department of Mechanical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Bhalchandra P Puranik
- Department of Mechanical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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353
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Zanchet A, Del Mazo P, Aguado A, Roncero O, Jiménez E, Canosa A, Agúndez M, Cernicharo J. Full dimensional potential energy surface and low temperature dynamics of the H 2CO + OH → HCO + H 2O reaction. Phys Chem Chem Phys 2018; 20:5415-5426. [PMID: 28959812 PMCID: PMC6031300 DOI: 10.1039/c7cp05307j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new method is proposed to analytically represent the potential energy surface of reactions involving polyatomic molecules capable of accurately describing long-range interactions and saddle points, needed to describe low-temperature collisions. It is based on two terms, a reactive force field term and a many-body term. The reactive force field term accurately describes the fragments, long-range interactions among them and the saddle points for reactions. The many-body term increases the desired accuracy everywhere else. This method has been applied to the OH + H2CO → H2O + HCO reaction, giving a barrier of 27.4 meV. The simulated classical rate constants with this potential are in good agreement with recent experimental results [Ocaña et al., Astrophys. J., 2017, submitted], showing an important increase at temperatures below 100 K. The reaction mechanism is analyzed in detail here, and explains the observed behavior at low energy by the formation of long-lived collision complexes, with roaming trajectories, with a capture observed for very long impact parameters, >100 a.u., determined by the long-range dipole-dipole interaction.
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Affiliation(s)
- Alexandre Zanchet
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, c/Serrano 123, 28006 Madrid, Spain.
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354
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Klinting EL, Thomsen B, Godtliebsen IH, Christiansen O. Employing general fit-bases for construction of potential energy surfaces with an adaptive density-guided approach. J Chem Phys 2018; 148:064113. [DOI: 10.1063/1.5016259] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Bo Thomsen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Ove Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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355
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Jasper AW, Gruey ZB, Harding LB, Georgievskii Y, Klippenstein SJ, Wagner AF. Anharmonic Rovibrational Partition Functions for Fluxional Species at High Temperatures via Monte Carlo Phase Space Integrals. J Phys Chem A 2018; 122:1727-1740. [DOI: 10.1021/acs.jpca.7b11722] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ahren W. Jasper
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Zackery B. Gruey
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Lawrence B. Harding
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Yuri Georgievskii
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Stephen J. Klippenstein
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Albert F. Wagner
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
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356
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Yang B, Zhang P, Qu C, Wang XH, Stancil PC, Bowman JM, Balakrishnan N, McLaughlin BM, Forrey RC. Full-Dimensional Quantum Dynamics of SiO in Collision with H2. J Phys Chem A 2018; 122:1511-1520. [PMID: 29365271 DOI: 10.1021/acs.jpca.7b09762] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benhui Yang
- Department
of Physics and Astronomy and Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, United States
| | - P. Zhang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Chen Qu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - X. H. Wang
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - P. C. Stancil
- Department
of Physics and Astronomy and Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, United States
| | - J. M. Bowman
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - N. Balakrishnan
- Department
of Chemistry, University of Nevada, Las Vegas, Nevada 89154, United States
| | - B. M. McLaughlin
- Centre
for Theoretical Atomic, Molecular and Optical Physics (CTAMOP), School
of Mathematics and Physics, Queen’s University Belfast, The
David Bates Building, 7 College Park, Belfast BT7 1NN, United Kingdom
| | - R. C. Forrey
- Department
of Physics, Penn State University, Berks Campus, Reading, Pennsylvania 19610, United States
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357
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Liu Y, Huang Y, Ma J, Li J. Classical Trajectory Study of Collision Energy Transfer between Ne and C2H2 on a Full Dimensional Accurate Potential Energy Surface. J Phys Chem A 2018; 122:1521-1530. [DOI: 10.1021/acs.jpca.7b11483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yang Liu
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| | - Yin Huang
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| | - Jianyi Ma
- Institute
of Atomic and Molecular Physics, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jun Li
- School
of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
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358
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Han YC, Tsai PY, Bowman JM, Lin KC. Photodissociation of CH 3CHO at 248 nm: identification of the channels of roaming, triple fragmentation and the transition state. Phys Chem Chem Phys 2018; 19:18628-18634. [PMID: 28692092 DOI: 10.1039/c7cp02952g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quasi-classical trajectory (QCT) calculations are performed on the molecular products CO + CH4via the tight transition state (TS) and global minimum configurations. With the aid of this theoretical evidence, we have re-examined the experimental results published previously to clarify the controversial issue of photodissociation dynamics of CH3CHO at 248 nm. For the CO (v = 0 and 1) bimodal rotational distributions obtained previously [K.-C. Hung, P.-Y. Tsai, H.-K. Li, and K.-C. Lin, J. Chem. Phys., 2014, 140, 064313], the low-rotational (J) component is re-assigned to the contribution of triple fragmentation (H + CO + CH3), whereas the high-J component is ascribed to the CH3-roaming pathway. The H-roaming pathway is not found in the calculations. Further, the QCT results have confirmed that the CO vibrational population especially at higher states and the low-energy component of CH4 vibrational bimodality obtained experimentally are mainly produced following the TS pathway, which has never been identified before. While taking into account both the theoretical and experimental results, the ratio of the molecular products (CO(v = 1) + CH4) obtained by the triple fragmentation/roaming/TS processes is evaluated to be 0.23 : 1 : 0.29.
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Affiliation(s)
- Yong-Chang Han
- Department of Physics, Dalian University of Technology, Dalian, P. R. China.
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359
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Bhandari HN, Ma X, Paul AK, Smith P, Hase WL. PSO Method for Fitting Analytic Potential Energy Functions. Application to I–(H2O). J Chem Theory Comput 2018; 14:1321-1332. [DOI: 10.1021/acs.jctc.7b01122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - A. K. Paul
- Department of Chemistry National Institute of Technology, Meghalaya, Shillong 793003 Meghalaya, India
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360
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Qu C, Bowman J. Quantum and classical IR spectra of (HCOOH)2, (DCOOH)2 and (DCOOD)2 using ab initio potential energy and dipole moment surfaces. Faraday Discuss 2018; 212:33-49. [DOI: 10.1039/c8fd00077h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Full-dimensional (24 modes) quantum calculation of the IR spectrum of (DCOOD)2, and comparison with classical MD one.
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Affiliation(s)
- Chen Qu
- Department of Chemistry
- Cherry L. Emerson Center for Scientific Computations
- Emory University
- Atlanta
- USA
| | - Joel M. Bowman
- Department of Chemistry
- Cherry L. Emerson Center for Scientific Computations
- Emory University
- Atlanta
- USA
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361
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Villar JJS, Valdez ARL, Setiadi DH, Csizmadia IG, Viskolcz B, Rágyanszki A. An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and inter-molecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ mol−1, which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations.
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Affiliation(s)
- John Justine S. Villar
- Scientific Computing Laboratory, Department of Computer Science, University of the Philippines, Diliman, 1101 Quezon City, Philippines
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
| | - Adrian Roy L. Valdez
- Scientific Computing Laboratory, Department of Computer Science, University of the Philippines, Diliman, 1101 Quezon City, Philippines
| | - David H. Setiadi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Imre G. Csizmadia
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Béla Viskolcz
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
| | - Anita Rágyanszki
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
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362
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Lu X, Shao K, Fu B, Wang X, Zhang DH. An accurate full-dimensional potential energy surface and quasiclassical trajectory dynamics of the H + H2O2 two-channel reaction. Phys Chem Chem Phys 2018; 20:23095-23105. [DOI: 10.1039/c8cp04045a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quasiclassical trajectory calculations reveal interesting dynamics features based on an accurate FI-NN PES for the H + H2O2 two-channel reaction.
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Affiliation(s)
- Xiaoxiao Lu
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026
- China
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry
| | - Kejie Shao
- 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
- People's Republic of China
| | - 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
- People's Republic of China
| | - Xingan Wang
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026
- China
| | - 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
- People's Republic of China
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363
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Ping L, Zhu Y, Li A, Song H, Li Y, Yang M. Dynamics and kinetics of the reaction OH + H2S → H2O + SH on an accurate potential energy surface. Phys Chem Chem Phys 2018; 20:26315-26324. [DOI: 10.1039/c8cp05276j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mode specificity and product energy disposal are unveiled in the reaction OH + H2S → H2O + SH.
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Affiliation(s)
- Leilei Ping
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics
- Wuhan Institute of Physics and Mathematics
- Chinese Academy of Sciences
- Wuhan 430071
- China
| | - Yongfa Zhu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics
- Wuhan Institute of Physics and Mathematics
- Chinese Academy of Sciences
- Wuhan 430071
- China
| | - Anyang Li
- College of Chemistry and Materials Science
- Northwest University
- Xi’an
- China
| | - Hongwei Song
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics
- Wuhan Institute of Physics and Mathematics
- Chinese Academy of Sciences
- Wuhan 430071
- China
| | - Yong Li
- College of Physical Science and Technology
- Huazhong Normal University
- Wuhan 430079
- China
| | - Minghui Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics
- Wuhan Institute of Physics and Mathematics
- Chinese Academy of Sciences
- Wuhan 430071
- China
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364
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Laude G, Calderini D, Tew DP, Richardson JO. Ab initio instanton rate theory made efficient using Gaussian process regression. Faraday Discuss 2018; 212:237-258. [PMID: 30230495 DOI: 10.1039/c8fd00085a] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio instanton rate theory is a computational method for rigorously including tunnelling effects into the calculations of chemical reaction rates based on a potential-energy surface computed on the fly from electronic-structure theory. This approach is necessary to extend conventional transition-state theory into the deep-tunnelling regime, but it is also more computationally expensive as it requires many more ab initio calculations. We propose an approach which uses Gaussian process regression to fit the potential-energy surface locally around the dominant tunnelling pathway. The method can be converged to give the same result as from an on-the-fly ab initio instanton calculation but it requires far fewer electronic-structure calculations. This makes it a practical approach for obtaining accurate rate constants based on high-level electronic-structure methods. We show fast convergence to reproduce benchmark H + CH4 results and evaluate new low-temperature rates of H + C2H6 in full dimensionality at a UCCSD(T)-F12b/cc-pVTZ-F12 level.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland. and On exchange from School of Chemistry, University of Edinburgh, UK
| | | | - David P Tew
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
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365
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Yuan J, He D, Wang S, Chen M, Han K. Diabatic potential energy surfaces of MgH2+ and dynamic studies for the Mg+(3p) + H2 → MgH+ + H reaction. Phys Chem Chem Phys 2018; 20:6638-6647. [DOI: 10.1039/c7cp08679b] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The global diabatic potential energy surfaces for the Mg+(3p) + H2 → MgH+ + H reaction are structured for the first time.
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Affiliation(s)
- Jiuchuang Yuan
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- Dalian 116023
- P. R. China
| | - Di He
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Shufen Wang
- Key Laboratory of Materials Modification by Laser
- Electron, and Ion Beams (Ministry of Education)
- School of Physics
- Dalian University of Technology
- Dalian 116024
| | - Maodu Chen
- Key Laboratory of Materials Modification by Laser
- Electron, and Ion Beams (Ministry of Education)
- School of Physics
- Dalian University of Technology
- Dalian 116024
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- Dalian 116023
- P. R. China
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366
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DeGregorio N, Iyengar SS. Efficient and Adaptive Methods for Computing Accurate Potential Surfaces for Quantum Nuclear Effects: Applications to Hydrogen-Transfer Reactions. J Chem Theory Comput 2017; 14:30-47. [DOI: 10.1021/acs.jctc.7b00927] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicole DeGregorio
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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367
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Sode O, Cherry JN. Development of a Flexible-Monomer Two-Body Carbon Dioxide Potential and Its Application to Clusters up to (CO 2 ) 13. J Comput Chem 2017; 38:2763-2774. [PMID: 29067701 DOI: 10.1002/jcc.25053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 07/28/2017] [Accepted: 08/03/2017] [Indexed: 12/20/2022]
Abstract
A flexible-monomer two-body potential energy function was developed that approaches the high level CCSD(T)/CBS potential energy surface (PES) of carbon dioxide (CO2 ) systems. This function was generated by fitting the electronic energies of unique CO2 monomers and dimers to permutationally invariant polynomials. More than 200,000 CO2 configurations were used to train the potential function. Comparisons of the PESs of six orientations of flexible CO2 dimers were evaluated to demonstrate the accuracy of the potential. Furthermore, the potential function was used to determine the minimum energy structures of CO2 clusters containing as many as 13 molecules. For isomers of (CO2 )3 , the potential demonstrated energetic agreement with the M06-2X functional and structural agreement of the B2PLYP-D functional at substantially reduced computational costs. A separate function, fit to MP2/aug-cc-pVDZ reference energies, was developed to directly compare the two-body potential to the ab initio MP2 level of theory. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Olaseni Sode
- Department of Chemistry, Biochemistry and Physics, The University of Tampa, Tampa, Florida, 33606
| | - Jasmine N Cherry
- Department of Chemistry, Biochemistry and Physics, The University of Tampa, Tampa, Florida, 33606
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368
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Krotos L, Czakó G. Does the Cl + CH4 → H + CH3Cl Reaction Proceed via Walden Inversion? J Phys Chem A 2017; 121:9415-9420. [DOI: 10.1021/acs.jpca.7b10226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- László Krotos
- Department of Physical Chemistry
and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- Department of Physical Chemistry
and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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369
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Guan Y, Yang S, Zhang DH. Construction of reactive potential energy surfaces with Gaussian process regression: active data selection. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1407460] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Yafu Guan
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shuo Yang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Dong H. Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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370
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Lindsey RK, Fried LE, Goldman N. ChIMES: A Force Matched Potential with Explicit Three-Body Interactions for Molten Carbon. J Chem Theory Comput 2017; 13:6222-6229. [DOI: 10.1021/acs.jctc.7b00867] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rebecca K. Lindsey
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Nir Goldman
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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371
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Wang Q(K, Bowman JM. Two-component, ab initio potential energy surface for CO2—H2O, extension to the hydrate clathrate, CO2@(H2O)20, and VSCF/VCI vibrational analyses of both. J Chem Phys 2017; 147:161714. [DOI: 10.1063/1.4994543] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Qingfeng (Kee) Wang
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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372
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Riera M, Mardirossian N, Bajaj P, Götz AW, Paesani F. Toward chemical accuracy in the description of ion–water interactions through many-body representations. Alkali-water dimer potential energy surfaces. J Chem Phys 2017; 147:161715. [DOI: 10.1063/1.4993213] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Narbe Mardirossian
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Pushp Bajaj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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373
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Szabó I, Czakó G. Dynamics and Novel Mechanisms of S N2 Reactions on ab Initio Analytical Potential Energy Surfaces. J Phys Chem A 2017; 121:9005-9019. [PMID: 28985079 DOI: 10.1021/acs.jpca.7b08140] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a novel theoretical approach to the bimolecular nucleophilic substitution (SN2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for SN2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F- + CH3Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion SN2 mechanism, (b) frontside complex formation,
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Affiliation(s)
- István Szabó
- Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged , Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged , Rerrich Béla tér 1, Szeged H-6720, Hungary
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374
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Varga Z, Paukku Y, Truhlar DG. Potential energy surfaces for O + O2 collisions. J Chem Phys 2017; 147:154312. [PMID: 29055336 DOI: 10.1063/1.4997169] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zoltan Varga
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Yuliya Paukku
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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375
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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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376
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Fábri C, Quack M, Császár AG. On the use of nonrigid-molecular symmetry in nuclear motion computations employing a discrete variable representation: A case study of the bending energy levels of C H 5 +. J Chem Phys 2017; 147:134101. [DOI: 10.1063/1.4990297] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Csaba Fábri
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry, Eötvös University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Martin Quack
- Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Attila G. Császár
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry, Eötvös University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- MTA-ELTE Complex Chemical Systems Research Group, P.O. Box 32, H-1518 Budapest 112, Hungary
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377
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Lenzen T, Manthe U. Neural network based coupled diabatic potential energy surfaces for reactive scattering. J Chem Phys 2017; 147:084105. [DOI: 10.1063/1.4997995] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tim Lenzen
- Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Uwe Manthe
- Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
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378
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Behler J. First Principles Neural Network Potentials for Reactive Simulations of Large Molecular and Condensed Systems. Angew Chem Int Ed Engl 2017; 56:12828-12840. [PMID: 28520235 DOI: 10.1002/anie.201703114] [Citation(s) in RCA: 329] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Indexed: 11/06/2022]
Abstract
Modern simulation techniques have reached a level of maturity which allows a wide range of problems in chemistry and materials science to be addressed. Unfortunately, the application of first principles methods with predictive power is still limited to rather small systems, and despite the rapid evolution of computer hardware no fundamental change in this situation can be expected. Consequently, the development of more efficient but equally reliable atomistic potentials to reach an atomic level understanding of complex systems has received considerable attention in recent years. A promising new development has been the introduction of machine learning (ML) methods to describe the atomic interactions. Once trained with electronic structure data, ML potentials can accelerate computer simulations by several orders of magnitude, while preserving quantum mechanical accuracy. This Review considers the methodology of an important class of ML potentials that employs artificial neural networks.
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Affiliation(s)
- Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstrasse 6, 37077, Göttingen, Germany
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379
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Behler J. Hochdimensionale neuronale Netze für Potentialhyperflächen großer molekularer und kondensierter Systeme. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jörg Behler
- Universität Göttingen; Institut für Physikalische Chemie, Theoretische Chemie; Tammannstraße 6 37077 Göttingen Deutschland
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380
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Brown A, Pradhan E. Fitting potential energy surfaces to sum-of-products form with neural networks using exponential neurons. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617300014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, the use of the neural network (NN) method with exponential neurons for directly fitting ab initio data to generate potential energy surfaces (PESs) in sum-of-product form will be discussed. The utility of the approach will be highlighted using fits of CS2, HFCO, and HONO ground state PESs based upon high-level ab initio data. Using a generic interface between the neural network PES fitting, which is performed in MATLAB, and the Heidelberg multi-configuration time-dependent Hartree (MCTDH) software package, the PESs have been tested via comparison of vibrational energies to experimental measurements. The review demonstrates the potential of the PES fitting method, combined with MCTDH, to tackle high-dimensional quantum dynamics problems.
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Affiliation(s)
- Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - E. Pradhan
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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381
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Wang S, Yuan J, Li H, Chen M. A neural network potential energy surface for the NaH 2 system and dynamics studies on the H( 2S) + NaH(X 1Σ +) → Na( 2S) + H 2(X 1Σ g+) reaction. Phys Chem Chem Phys 2017; 19:19873-19880. [PMID: 28597884 DOI: 10.1039/c7cp02153d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In order to study the dynamics of the reaction H(2S) + NaH(X1Σ+) → Na(2S) + H2(X1Σg+), a new potential energy surface (PES) for the ground state of the NaH2 system is constructed based on 35 730 ab initio energy points. Using basis sets of quadruple zeta quality, multireference configuration interaction calculations with Davidson correction were carried out to obtain the ab initio energy points. The neural network method is used to fit the PES, and the root mean square error is very small (0.00639 eV). The bond lengths, dissociation energies, zero-point energies and spectroscopic constants of H2(X1Σg+) and NaH(X1Σ+) obtained on the new NaH2 PES are in good agreement with the experiment data. On the new PES, the reactant coordinate-based time-dependent wave packet method is applied to study the reaction dynamics of H(2S) + NaH(X1Σ+) → Na(2S) + H2(X1Σg+), and the reaction probabilities, integral cross-sections (ICSs) and differential cross-sections (DCSs) are obtained. There is no threshold in the reaction due to the absence of an energy barrier on the minimum energy path. When the collision energy increases, the ICSs decrease from a high value at low collision energy. The DCS results show that the angular distribution of the product molecules tends to the forward direction. Compared with the LiH2 system, the NaH2 system has a larger mass and the PES has a larger well at the H-NaH configuration, which leads to a higher ICS value in the H(2S) + NaH(X1Σ+) → Na(2S) + H2(X1Σg+) reaction. Because the H(2S) + NaH(X1Σ+) → Na(2S) + H2(X1Σg+) reaction releases more energy, the product molecules can be excited to a higher vibrational state.
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Affiliation(s)
- Shufen Wang
- Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams (Ministry of Education), School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian, 116024, P. R. China.
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382
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Schmitz G, Christiansen O. Accuracy of Frequencies Obtained with the Aid of Explicitly Correlated Wave Function Based Methods. J Chem Theory Comput 2017; 13:3602-3613. [PMID: 28686442 DOI: 10.1021/acs.jctc.7b00476] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We asses the basis set convergence of harmonic frequencies using different explicitly correlated wave function based methods. All commonly available CCSD(T) variants as well as MP2-F12 and MP4(F12*) are considered, and a hierarchy of the different approaches is established. As for reaction and atomization energies, CCSD(F12*)(T*) is a close approximation to CCSD(F12)(T*) and clearly superior to the other tested approximations. The used scaling for the triples correction enhances the accuracy relative to CCSD(F12*)(T) especially for small basis sets and is very attractive since no additional computational costs are added. However, this scaling slightly breaks size consistency, and therefore we additionally study the accuracy of CCSD(F12*)(T*) and CCSD(F12*)(T) in the context of calculating anharmonic frequencies to check if this causes problems in the generation of the potential energy surface (PES). We find a fast basis set convergence for harmonic and anharmonic frequencies. Already in the cc-pVDZ-F12 basis, the RMSD to the CBS limit is only around 4-5 cm-1.
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Affiliation(s)
- Gunnar Schmitz
- Department of Chemistry, Aarhus University , Aarhus, Denmark
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383
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Unke OT, Meuwly M. Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces. J Chem Inf Model 2017; 57:1923-1931. [PMID: 28666387 DOI: 10.1021/acs.jcim.7b00090] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the early days of computation, slow processor speeds limited the amount of data that could be generated and used for scientific purposes. In the age of big data, the limiting factor usually is the method with which large amounts of data are analyzed and useful information is extracted. A typical example from chemistry are high-level ab initio calculations for small systems, which have nowadays become feasible even if energies at many different geometries are required. Molecular dynamics simulations often require several thousand distinct trajectories to be run. Under such circumstances suitable analytical representations of potential energy surfaces (PESs) based on ab initio calculations are required to propagate the dynamics at an acceptable cost. In this work we introduce a toolkit which allows the automatic construction of multidimensional PESs from gridded ab initio data based on reproducing kernel Hilbert space (RKHS) theory. The resulting representations require no tuning of parameters and allow energy and force evaluations at ab initio quality at the same cost as empirical force fields. Although the toolkit is primarily intended for constructing multidimensional potential energy surfaces for molecular systems, it can also be used for general machine learning purposes. The software is published under the MIT license and can be downloaded, modified, and used in other projects for free.
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Affiliation(s)
- Oliver T Unke
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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384
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Houston PL, Wang X, Ghosh A, Bowman JM, Quinn MS, Kable SH. Formaldehyde roaming dynamics: Comparison of quasi-classical trajectory calculations and experiments. J Chem Phys 2017; 147:013936. [DOI: 10.1063/1.4982823] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paul L. Houston
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14852, USA
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Xiaohong Wang
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Aryya Ghosh
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Mitchell S. Quinn
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Scott H. Kable
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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385
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Ceotto M, Di Liberto G, Conte R. Semiclassical "Divide-and-Conquer" Method for Spectroscopic Calculations of High Dimensional Molecular Systems. PHYSICAL REVIEW LETTERS 2017; 119:010401. [PMID: 28731742 DOI: 10.1103/physrevlett.119.010401] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 05/11/2023]
Abstract
A new semiclassical "divide-and-conquer" method is presented with the aim of demonstrating that quantum dynamics simulations of high dimensional molecular systems are doable. The method is first tested by calculating the quantum vibrational power spectra of water, methane, and benzene-three molecules of increasing dimensionality for which benchmark quantum results are available-and then applied to C_{60}, a system characterized by 174 vibrational degrees of freedom. Results show that the approach can accurately account for quantum anharmonicities, purely quantum features like overtones, and the removal of degeneracy when the molecular symmetry is broken.
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Affiliation(s)
- Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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386
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Yu HG, Song H, Yang M. A rigorous full-dimensional quantum dynamics study of tunneling splitting of rovibrational states of vinyl radical C2H3. J Chem Phys 2017; 146:224307. [DOI: 10.1063/1.4985183] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hua-Gen Yu
- Division of Chemistry, Department of Energy and Photon Sciences, Brookhaven National Laboratory, Upton, New York 11793-5000, USA
| | - Hongwei Song
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
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387
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Gabas F, Conte R, Ceotto M. On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum. J Chem Theory Comput 2017; 13:2378-2388. [PMID: 28489368 PMCID: PMC5472367 DOI: 10.1021/acs.jctc.6b01018] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We
present an on-the-fly ab initio semiclassical study of vibrational
energy levels of glycine, calculated by Fourier transform of the wavepacket
correlation function. It is based on a multiple coherent states approach
integrated with monodromy matrix regularization for chaotic dynamics.
All four lowest-energy glycine conformers are investigated by means
of single-trajectory semiclassical spectra obtained upon classical
evolution of on-the-fly trajectories with harmonic zero-point energy.
For the most stable conformer I, direct dynamics trajectories are
also run for each vibrational mode with energy equal to the first
harmonic excitation. An analysis of trajectories evolved up to 50 000
atomic time units demonstrates that, in this time span, conformers
II and III can be considered as isolated species, while conformers
I and IV show a pretty facile interconversion. Therefore, previous
perturbative studies based on the assumption of isolated conformers
are often reliable but might be not completely appropriate in the
case of conformer IV and conformer I for which interconversion occurs
promptly.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano , via Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano , via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano , via Golgi 19, 20133 Milano, Italy
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388
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Harding LB, Georgievskii Y, Klippenstein SJ. Accurate Anharmonic Zero-Point Energies for Some Combustion-Related Species from Diffusion Monte Carlo. J Phys Chem A 2017; 121:4334-4340. [DOI: 10.1021/acs.jpca.7b03082] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lawrence B. Harding
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Yuri Georgievskii
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Stephen J. Klippenstein
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
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389
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Osborn DL. Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry. Annu Rev Phys Chem 2017; 68:233-260. [DOI: 10.1146/annurev-physchem-040215-112151] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David L. Osborn
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550
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390
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Wang X, Houston PL, Bowman JM. A new (multi-reference configuration interaction) potential energy surface for H 2CO and preliminary studies of roaming. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20160194. [PMID: 28320899 PMCID: PMC5360895 DOI: 10.1098/rsta.2016.0194] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
We report a new global potential energy surface (PES) for H2CO, based on precise fitting of roughly 67 000 MRCI/cc-pVTZ energies. This PES describes the global minimum, the cis- and trans-HCOH isomers, and barriers relevant to isomerization, formation of the molecular (H2+CO) and radical (H+HCO) products, and the loose so-called roaming transition-state saddle point. The key features of the PES are reviewed and compared with a previous PES, denoted by PES04, based on five local fits that are 'stitched' together by switching functions (Zhang et al. 2004 J. Phys. Chem. A108, 8980-8986 (doi:10.1021/jp048339l)). Preliminary quasi-classical trajectory calculations are performed at the total energy of 36 233 cm-1 (103 kcal mol-1), relative to the H2CO global minimum, using the new PES, with a particular focus on roaming dynamics. When compared with the results from PES04, the new PES findings show similar rotational distributions, somewhat more roaming and substantially higher H2 vibrational excitation.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Xiaohong Wang
- Department of Chemistry, and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
| | - Paul L Houston
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14852, USA
| | - Joel M Bowman
- Department of Chemistry, and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
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391
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Essafi S, Tew DP, Harvey JN. The Dynamics of the Reaction of FeO+
and H2
: A Model for Inorganic Oxidation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Stéphanie Essafi
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
| | - David P. Tew
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
| | - Jeremy N. Harvey
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
- Department of Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
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392
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Essafi S, Tew DP, Harvey JN. The Dynamics of the Reaction of FeO+
and H2
: A Model for Inorganic Oxidation. Angew Chem Int Ed Engl 2017; 56:5790-5794. [DOI: 10.1002/anie.201702009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Stéphanie Essafi
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
| | - David P. Tew
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
| | - Jeremy N. Harvey
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
- Department of Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
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393
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Wittenbrink N, Eisfeld W. An improved spin-orbit coupling model for use within the effective relativistic coupling by asymptotic representation (ERCAR) method. J Chem Phys 2017; 146:144110. [PMID: 28411618 DOI: 10.1063/1.4979949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An improved atomic spin-orbit model is presented, which is designed to be used within the framework of the effective relativistic coupling by asymptotic representation method. This method is used for the generation of highly accurate coupled potential energy surfaces (PESs) to represent the fine structure energies of appropriate systems. The approach is demonstrated using CH3I and its photodissociation as a typical example. The method is based on a specific diabatization of electronic spin-space ("spin-free") states with respect to the asymptote at which a single relativistic atom is separated from a molecular non-relativistic fragment. Thus, the relativistic coupling effects can be treated entirely within the atomic framework. So far, an effective spin-orbit coupling operator which only accounts for intra-state coupling within each atomic spin-space state was used. In the present work, this approach is extended to account for inter-state couplings among different atomic spin-space states as well. It is shown that this extended approach improves the accuracy of the PESs significantly for higher excited states and also enhances the accuracy of low energy states. In particular, it improves the representation of the spin-orbit induced conical intersection among the 3Q0 and 1Q1 states of CH3I, which is of high relevance for the nonadiabatic quantum dynamics of the photodissociation.
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Affiliation(s)
- Nils Wittenbrink
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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394
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Carrington T. Perspective: Computing (ro-)vibrational spectra of molecules with more than four atoms. J Chem Phys 2017; 146:120902. [DOI: 10.1063/1.4979117] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario
K7L 3N6, Canada
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395
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Kolb B, Marshall P, Zhao B, Jiang B, Guo H. Representing Global Reactive Potential Energy Surfaces Using Gaussian Processes. J Phys Chem A 2017; 121:2552-2557. [DOI: 10.1021/acs.jpca.7b01182] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian Kolb
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Department
of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Paul Marshall
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Bin Zhao
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Bin Jiang
- Department
of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hua Guo
- Department
of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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396
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Rai P, Sargsyan K, Najm H, Hermes MR, Hirata S. Low-rank canonical-tensor decomposition of potential energy surfaces: application to grid-based diagrammatic vibrational Green's function theory. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1288937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Prashant Rai
- Sandia National Laboratories, Livermore, CA, USA
| | | | - Habib Najm
- Sandia National Laboratories, Livermore, CA, USA
| | - Matthew R. Hermes
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - So Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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397
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Zhao Z, Zhang Z, Liu S, Zhang DH. Dynamical barrier and isotope effects in the simplest substitution reaction via Walden inversion mechanism. Nat Commun 2017; 8:14506. [PMID: 28224993 PMCID: PMC5336572 DOI: 10.1038/ncomms14506] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/06/2017] [Indexed: 11/09/2022] Open
Abstract
Reactions occurring at a carbon atom through the Walden inversion mechanism are one of the most important and useful classes of reactions in chemistry. Here we report an accurate theoretical study of the simplest reaction of that type: the H+CH4 substitution reaction and its isotope analogues. It is found that the reaction threshold versus collision energy is considerably higher than the barrier height. The reaction exhibits a strong normal secondary isotope effect on the cross-sections measured above the reaction threshold, and a small but reverse secondary kinetic isotope effect at room temperature. Detailed analysis reveals that the reaction proceeds along a path with a higher barrier height instead of the minimum-energy path because the umbrella angle of the non-reacting methyl group cannot change synchronously with the other reaction coordinates during the reaction due to insufficient energy transfer from the translational motion to the umbrella mode.
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Affiliation(s)
- Zhiqiang Zhao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaojun Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Shu Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
- Center for Advanced Chemical Physics and 2011 Frontier Center for Quantum Science and Technology, University of Science and Technology of China, Hefei 230026, China
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398
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Olasz B, Szabó I, Czakó G. High-level ab initio potential energy surface and dynamics of the F - + CH 3I S N2 and proton-transfer reactions. Chem Sci 2017; 8:3164-3170. [PMID: 28507692 PMCID: PMC5413972 DOI: 10.1039/c7sc00033b] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/15/2017] [Indexed: 11/21/2022] Open
Abstract
Bimolecular nucleophilic substitution (SN2) and proton transfer are fundamental processes in chemistry and F- + CH3I is an important prototype of these reactions. Here we develop the first full-dimensional ab initio analytical potential energy surface (PES) for the F- + CH3I system using a permutationally invariant fit of high-level composite energies obtained with the combination of the explicitly-correlated CCSD(T)-F12b method, the aug-cc-pVTZ basis, core electron correlation effects, and a relativistic effective core potential for iodine. The PES accurately describes the SN2 channel producing I- + CH3F via Walden-inversion, front-side attack, and double-inversion pathways as well as the proton-transfer channel leading to HF + CH2I-. The relative energies of the stationary points on the PES agree well with the new explicitly-correlated all-electron CCSD(T)-F12b/QZ-quality benchmark values. Quasiclassical trajectory computations on the PES show that the proton transfer becomes significant at high collision energies and double-inversion as well as front-side attack trajectories can occur. The computed broad angular distributions and hot internal energy distributions indicate the dominance of indirect mechanisms at lower collision energies, which is confirmed by analyzing the integration time and leaving group velocity distributions. Comparison with available crossed-beam experiments shows usually good agreement.
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Affiliation(s)
- Balázs Olasz
- Department of Physical Chemistry and Materials Science , Institute of Chemistry , University of Szeged , Rerrich Béla tér 1 , Szeged H-6720 , Hungary .
| | - István Szabó
- Department of Physical Chemistry and Materials Science , Institute of Chemistry , University of Szeged , Rerrich Béla tér 1 , Szeged H-6720 , Hungary .
| | - Gábor Czakó
- Department of Physical Chemistry and Materials Science , Institute of Chemistry , University of Szeged , Rerrich Béla tér 1 , Szeged H-6720 , Hungary .
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399
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Behler J. Perspective: Machine learning potentials for atomistic simulations. J Chem Phys 2017; 145:170901. [PMID: 27825224 DOI: 10.1063/1.4966192] [Citation(s) in RCA: 534] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nowadays, computer simulations have become a standard tool in essentially all fields of chemistry, condensed matter physics, and materials science. In order to keep up with state-of-the-art experiments and the ever growing complexity of the investigated problems, there is a constantly increasing need for simulations of more realistic, i.e., larger, model systems with improved accuracy. In many cases, the availability of sufficiently efficient interatomic potentials providing reliable energies and forces has become a serious bottleneck for performing these simulations. To address this problem, currently a paradigm change is taking place in the development of interatomic potentials. Since the early days of computer simulations simplified potentials have been derived using physical approximations whenever the direct application of electronic structure methods has been too demanding. Recent advances in machine learning (ML) now offer an alternative approach for the representation of potential-energy surfaces by fitting large data sets from electronic structure calculations. In this perspective, the central ideas underlying these ML potentials, solved problems and remaining challenges are reviewed along with a discussion of their current applicability and limitations.
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Affiliation(s)
- Jörg Behler
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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400
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Pratihar S, Ma X, Homayoon Z, Barnes GL, Hase WL. Direct Chemical Dynamics Simulations. J Am Chem Soc 2017; 139:3570-3590. [DOI: 10.1021/jacs.6b12017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Xinyou Ma
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Zahra Homayoon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - George L. Barnes
- Department
of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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