1
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Tsutsumi T, Ono Y, Taketsugu T. Multi-state Energy Landscape for Photoreaction of Stilbene and Dimethyl-stilbene. J Chem Theory Comput 2022; 18:7483-7495. [PMID: 36351076 DOI: 10.1021/acs.jctc.2c00560] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have recently developed the reaction space projector (ReSPer) method, which constructs a reduced-dimensionality reaction space uniquely determined from reference reaction paths for a polyatomic molecular system and projects classical trajectories into the same reaction space. In this paper, we extend ReSPer to the analysis of photoreaction dynamics and relaxation processes of stilbene and present the concept of a "multi-state energy landscape," incorporating the ground- and excited-state reaction subspaces. The multi-state energy landscape successfully explains the previously established photoreaction processes of cis-stilbene, such as the cis-trans photoisomerization and photocyclization. In addition, we discuss the difference in the excited-state reaction dynamics between stilbene and 1,1'-dimethyl stilbene based on a common reaction subspace determined from the framework part of reference structures with different number of atoms. This approach allows us to target any molecule with a common framework, greatly expanding the applicability of the ReSPer analysis. The multi-state energy landscape provides fruitful insight into photochemical reactions, exploring the excited- and ground-state potential energy surfaces, as well as comprehensive reaction processes with nonradiative transitions between adiabatic states, within the stage of a reduced-dimensionality reaction space.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo060-0810, Japan.,L-Station, Creative Research Institution (CRI), Hokkaido University, Sapporo060-0812, Japan
| | - Yuriko Ono
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo001-0021, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo001-0021, Japan
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2
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Tsutsumi T, Ono Y, Taketsugu T. Reaction Space Projector (ReSPer) for Visualizing Dynamic Reaction Routes Based on Reduced-Dimension Space. Top Curr Chem (Cham) 2022; 380:19. [PMID: 35266073 DOI: 10.1007/s41061-022-00377-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/21/2022] [Indexed: 11/26/2022]
Abstract
To analyze chemical reaction dynamics based on a reaction path network, we have developed the "Reaction Space Projector" (ReSPer) method with the aid of the dimensionality reduction method. This program has two functions: the construction of a reduced-dimensionality reaction space from a molecular structure dataset, and the projection of dynamic trajectories into the low-dimensional reaction space. In this paper, we apply ReSPer to isomerization and bifurcation reactions of the Au5 cluster and succeed in analyzing dynamic reaction routes involved in multiple elementary reaction processes, constructing complicated networks (called "closed islands") of nuclear permutation-inversion (NPI) isomerization reactions, and elucidating dynamic behaviors in bifurcation reactions with reference to bundles of trajectories. Interestingly, in the second application, we find a correspondence between the contribution ratios in the ability to visualize and the symmetry of the morphology of closed islands. In addition, the third application suggests the existence of boundaries that determine the selectivity in bifurcation reactions, which was discussed in the phase space. The ReSPer program is a versatile and robust tool to clarify dynamic reaction mechanisms based on the reduced-dimensionality reaction space without prior knowledge of target reactions.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuriko Ono
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.
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3
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Sharipov AS, Loukhovitski BI. Energy disposal into the vibrational degrees of freedom of bimolecular reaction products: Key factors and simple model. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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4
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Gelin MF, Huang X, Xie W, Chen L, Došlić NA, Domcke W. Ab Initio Surface-Hopping Simulation of Femtosecond Transient-Absorption Pump-Probe Signals of Nonadiabatic Excited-State Dynamics Using the Doorway-Window Representation. J Chem Theory Comput 2021; 17:2394-2408. [PMID: 33755464 DOI: 10.1021/acs.jctc.1c00109] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
An ab initio theoretical framework for the simulation of femtosecond time-resolved transient absorption (TA) pump-probe (PP) spectra with quasi-classical trajectories is presented. The simulations are based on the classical approximation to the doorway-window (DW) representation of third-order four-wave-mixing signals. The DW formula accounts for the finite duration and spectral shape of the pump and probe pulses. In the classical DW formalism, classical trajectories are stochastically sampled from a positive definite doorway distribution, and the signals are evaluated by averaging over a positive definite window distribution. Nonadiabatic excited-state dynamics is described by a stochastic surface-hopping algorithm. The method has been implemented for the pyrazine molecule with the second-order algebraic-diagrammatic construction (ADC(2)) ab initio electronic-structure method. The methodology is illustrated by ab initio simulations of the ground-state bleach, stimulated emission, and excited-state absorption contributions to the TA PP spectrum of gas-phase pyrazine.
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Affiliation(s)
- Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Xiang Huang
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Weiwei Xie
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Lipeng Chen
- Max Planck Institute for the Physics of Complex Systems, D-01187 Dresden, Germany
| | - Nad A Došlić
- Department of Physical Chemistry, Ruder Boscovic Institute, HR-10000 Zagreb, Croatia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
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5
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Ootani Y, Satoh A, Harabuchi Y, Taketsugu T. Trajectory on-the-fly molecular dynamics approach to tunneling splitting in the electronic excited state: A case of tropolone. J Comput Chem 2020; 41:1549-1556. [PMID: 32239685 DOI: 10.1002/jcc.26199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 11/10/2022]
Abstract
The semiclassical tunneling method is applied to evaluate the tunneling splitting of tropolone due to the intramolecular proton transfer in the electronic excited state, first time, in a framework of the trajectory on-the-fly molecular dynamics (TOF-MD) approach. To prevent unphysical zero-point vibrational energy transfer among the normal modes of vibration, quantum zero-point vibrational energies are assigned only to the vibrational modes related to intramolecular proton transfer, whereas the remaining modes are treated as bath modes. Practical ways to determine the tunnel-initiating points and tunneling path are introduced. It is shown that the tunneling splitting decreases as the bath-mode energy increases. The experimental tunneling splitting value is well reproduced by the present TOF-MD approach based on the Wentzel-Kramers-Brillouin (WKB) approximation.
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Affiliation(s)
- Yusuke Ootani
- Institute for Materials Research, Tohoku University, Sendai, Japan
| | - Aya Satoh
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
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6
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Kamiya M, Taketsugu T. Ab initio surface hopping excited-state molecular dynamics approach on the basis of spin-orbit coupled states: An application to the A-band photodissociation of CH 3 I. J Comput Chem 2018; 40:456-463. [PMID: 30451310 DOI: 10.1002/jcc.25727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/06/2022]
Abstract
Ab initio molecular dynamics approach has been extended to multi-state dynamics on the basis of the spin-orbit coupled electronic states that are obtained through diagonalization of the spin-orbit coupling matrix with the multi-state second-order multireference perturbation theory energies in diagonal elements and the spin-orbit coupling terms at the state-averaged complete active space self-consistent field level in off-diagonal elements. Nonadiabatic transitions over the spin-orbit coupled states were taken into account explicitly by a surface hopping scheme with utilizing the nonadiabatic coupling terms calculated by numerical differentiation of the spin-orbit coupled wavefunctions and analytical nonadiabatic coupling terms. The present method was applied to the A-band photodissociation of methyl iodide, CH3 I + hv → CH3 + I (2 P3/2 )/I* (2 P1/2 ), for which a pioneering theoretical work was reported by Amatatsu, Yabushita, and Morokuma. The present results reproduced well the experimental branching ratio and energy distributions in the dissociative products. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Muneaki Kamiya
- Faculty of Regional Studies, Gifu University, Gifu, 501-1132, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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7
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Tsutsumi T, Harabuchi Y, Ono Y, Maeda S, Taketsugu T. Analyses of trajectory on-the-fly based on the global reaction route map. Phys Chem Chem Phys 2018; 20:1364-1372. [PMID: 29260170 DOI: 10.1039/c7cp06528k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A methodology to analyze a trajectory on-the-fly (TOF) based on a global reaction route map consisting of intrinsic reaction coordinate (IRC) pathways is proposed. By using the distance functions in the configurational space, the location of each point on the trajectories is detected, providing a dynamical picture that the molecular system goes over several minima and transition states in the reaction path network. In its application to structural transformations of an Au5 cluster, a variety of reaction routes are obtained, and the hopping from one IRC to another IRC (IRC-jump) is analyzed. The branching of trajectories over many minima on the potential energy surface via valley-ridge transition points is also discussed.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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8
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Bera A, Ghosh J, Bhattacharya A. Ab initio multiple spawning dynamics study of dimethylnitramine and dimethylnitramine-Fe complex to model their ultrafast nonadiabatic chemistry. J Chem Phys 2017; 147:044308. [DOI: 10.1063/1.4993947] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Anupam Bera
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Jayanta Ghosh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Atanu Bhattacharya
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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9
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Kudo T, Taketsugu T, Gordon MS. Ab initio Molecular Dynamics Study of H 2Formation inside POSS Compounds. 2. The Effect of an Encapsulated Hydrogen Molecule. J Phys Chem A 2016; 120:8699-8715. [DOI: 10.1021/acs.jpca.6b07907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takako Kudo
- Division of Pure and Applied Science, Graduate School of Science and Technology, Gunma University, Kiryu 376-8515, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-2030, United States
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10
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Tsai PY, Li HK, Kasai T, Lin KC. Roaming as the dominant mechanism for molecular products in the photodissociation of large aliphatic aldehydes. Phys Chem Chem Phys 2015; 17:23112-20. [DOI: 10.1039/c5cp03408f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photodissociation of isobutyraldehyde (C3H7CHO) at 248 nm is investigated using time-resolved Fourier-transform infrared emission spectroscopy to demonstrate the growing importance of the roaming pathway with increasing molecular size of aliphatic aldehydes.
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Affiliation(s)
- Po-Yu Tsai
- Department of Chemistry
- National Chung Hsing University
- Taichung 402
- Taiwan
| | - Hou-Kuan Li
- Department of Chemistry
- National Taiwan University
- and Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
| | - Toshio Kasai
- Department of Chemistry
- National Taiwan University
- and Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
| | - King-Chuen Lin
- Department of Chemistry
- National Taiwan University
- and Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
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11
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Gaenko A, DeFusco A, Varganov SA, Martínez TJ, Gordon MS. Interfacing the Ab Initio Multiple Spawning Method with Electronic Structure Methods in GAMESS: Photodecay of trans-Azomethane. J Phys Chem A 2014; 118:10902-8. [DOI: 10.1021/jp508242j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Albert DeFusco
- Center
for Simulation and Modeling, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sergey A. Varganov
- Department
of Chemistry, University of Nevada, Reno, Reno Nevada 89557-0216, United States
| | - Todd J. Martínez
- Department
of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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12
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Harabuchi Y, Keipert K, Zahariev F, Taketsugu T, Gordon MS. Dynamics Simulations with Spin-Flip Time-Dependent Density Functional Theory: Photoisomerization and Photocyclization Mechanisms of cis-Stilbene in ππ* States. J Phys Chem A 2014; 118:11987-98. [DOI: 10.1021/jp5072428] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Harabuchi
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kristopher Keipert
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Federico Zahariev
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Tetsuya Taketsugu
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Mark S. Gordon
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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13
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Gerber RB, Shemesh D, Varner ME, Kalinowski J, Hirshberg B. Ab initio and semi-empirical Molecular Dynamics simulations of chemical reactions in isolated molecules and in clusters. Phys Chem Chem Phys 2014; 16:9760-75. [DOI: 10.1039/c3cp55239j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent progress in “on-the-fly” trajectory simulations of molecular reactions, using different electronic structure methods is discussed, with analysis of the insights that such calculations can provide and of the strengths and limitations of the algorithms available.
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Affiliation(s)
- R. B. Gerber
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
- Department of Chemistry
- University of California
| | - D. Shemesh
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
| | - M. E. Varner
- Department of Chemistry
- University of California
- Irvine 92697, USA
| | - J. Kalinowski
- Department of Chemistry
- University of Helsinki
- , Finland
| | - B. Hirshberg
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
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14
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Yu F. Ab initio direct classical trajectory investigation on the SN2 reaction of F- with NH2F: nonstatistical central barrier recrossing dynamics. J Comput Chem 2011; 33:401-5. [PMID: 22121003 DOI: 10.1002/jcc.21979] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/02/2011] [Accepted: 10/03/2011] [Indexed: 01/07/2023]
Abstract
The bimolecular nucleophilic substitution (S(N)2) reaction of F(a)(-) with NH(2)F(b) has been investigated with the ab initio direct classical trajectory method. According to our trajectory calculations, a dynamic behavior of nonstatistical central barrier recrossing is revealed. Among the 64 trajectories calculated in this work, 45 trajectories follow the dynamic reaction pathways as assumed by statistical theory and other 19 trajectories with central barrier recrossings are nonstatistical. For the nonstatistical trajectories, the central barrier recrossings may originate from the inefficient kinetic energy transfer from the intramolecular modes of the NH(2)F(a) moiety in the dynamic F(b)(-)…H-NH-F(a) complex to the intermolecular modes of the dynamic F(b)(-)…H-NH-F(a) complex on the exit-channel potential energy surface. With respect to the dynamic behavior of the nonstatistical central barrier recrossing, the statistical theories such as the Rice-Ramsperger-Kassel-Marcus and transition state theories without further corrections cannot be used to model the reaction kinetics for this S(N)2 reaction.
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Affiliation(s)
- Feng Yu
- Department of Physics, School of Science, Xi'an Technological University, No. 4 Jinhua North Road, Xi'an, Shaanxi 710032, China.
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15
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PARK SEUNGC, BRAAMS BASTIAANJ, BOWMAN JOELM. CONSTRUCTION OF A GLOBAL POTENTIAL ENERGY SURFACE FROM NOVEL AB INITIO MOLECULAR DYNAMICS FOR THE O(3P) + C3H3 REACTION. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633605001350] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We present a global potential energy surface (PES) for the 2 A state of the O (3 P ) + C 3 H 3 radical reaction. The global PES is constructed mainly using direct ab initio molecular dynamics and further sampling is done using the Diffusion Monte Carlo method. The potential is fully invariant with respect to permutational symmetry of like atoms. Special techniques, based on invariant theory of finite groups, have been used to develop basis functions for fitting that display this symmetry. The resultant potential energy surface shows multiple reaction paths with six different product channels. The products of the reactions are CO + C 2 H 3 radicals H + C 3 H 2 O radicals (with two isomers, propynal and propa-1,2-dien-1-one) and OH + C 3 H 2 radicals (with three isomers, vinylidenecarbene, propargylene and cyclopropenylidene). Energies of the PES are in excellent agreement with ab initio energies for each stationary point, the reactants and the products. Most stationary points are fitted at the sub Kcal/mol level. The global potential surface represents all the stationary points and six different product channels correctly. Preliminary dynamics calculations show abstraction and insertion mechanisms for the OH + vinylidenecarbene channel and the H + propynal channel, respectively.
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Affiliation(s)
- SEUNG C. PARK
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746 KOREA and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
| | - BASTIAAN J. BRAAMS
- Department of Mathematics and Computer Science and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, 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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16
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Fontanesi C, Bortolotti CA, Vanossi D, Marcaccio M. Dissociation Dynamics of Asymmetric Alkynyl(Aryl)Iodonium Radicals: An ab Initio DRC Approach to Predict the Surface Functionalization Selectivity. J Phys Chem A 2011; 115:11715-22. [DOI: 10.1021/jp2032115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Claudio Fontanesi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - Carlo Augusto Bortolotti
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - Davide Vanossi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - Massimo Marcaccio
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
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17
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Ootani Y, Taketsugu T. Ab initio molecular dynamics approach to tunneling splitting in polyatomic molecules. J Comput Chem 2011; 33:60-5. [DOI: 10.1002/jcc.21943] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 08/15/2011] [Accepted: 08/17/2011] [Indexed: 11/08/2022]
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18
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Shmilovits-Ofir M, Gerber RB. Proton Transfer and Dissociation of GlyLysH+ following O–H and N–H Stretching Mode Excitations: Dynamics Simulations. J Am Chem Soc 2011; 133:16510-7. [DOI: 10.1021/ja205634b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michaela Shmilovits-Ofir
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - R. Benny Gerber
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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19
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Shmilovits-Ofir M, Miller Y, Gerber RB. Conformational transitions of glycine induced by vibrational excitation of the O-H stretch. Phys Chem Chem Phys 2011; 13:8715-22. [PMID: 20922237 DOI: 10.1039/c0cp01385d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ν=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (ν=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.
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Affiliation(s)
- Michaela Shmilovits-Ofir
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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20
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Kudo T, Taketsugu T, Gordon MS. Ab Initio Molecular Dynamics Study of H2 Formation Inside POSS Compounds. J Phys Chem A 2011; 115:2679-91. [DOI: 10.1021/jp1105778] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Takako Kudo
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University, Kiryu 376-8515, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-2030, United States
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21
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Njegic B, Raff JD, Finlayson-Pitts BJ, Gordon MS, Gerber RB. Catalytic Role for Water in the Atmospheric Production of ClNO. J Phys Chem A 2010; 114:4609-18. [DOI: 10.1021/jp912155a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bosiljka Njegic
- Department of Chemistry, University of California, Irvine, California 92697-2025, Department of Chemistry, Iowa State University, Ames, Iowa 50011, and The Institute of Chemistry, The Hebrew University, Jerusalem, 91904, Israel
| | - Jonathan D. Raff
- Department of Chemistry, University of California, Irvine, California 92697-2025, Department of Chemistry, Iowa State University, Ames, Iowa 50011, and The Institute of Chemistry, The Hebrew University, Jerusalem, 91904, Israel
| | - Barbara J. Finlayson-Pitts
- Department of Chemistry, University of California, Irvine, California 92697-2025, Department of Chemistry, Iowa State University, Ames, Iowa 50011, and The Institute of Chemistry, The Hebrew University, Jerusalem, 91904, Israel
| | - Mark S. Gordon
- Department of Chemistry, University of California, Irvine, California 92697-2025, Department of Chemistry, Iowa State University, Ames, Iowa 50011, and The Institute of Chemistry, The Hebrew University, Jerusalem, 91904, Israel
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697-2025, Department of Chemistry, Iowa State University, Ames, Iowa 50011, and The Institute of Chemistry, The Hebrew University, Jerusalem, 91904, Israel
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Mullin JM, Roskop LB, Pruitt SR, Collins MA, Gordon MS. Systematic fragmentation method and the effective fragment potential: an efficient method for capturing molecular energies. J Phys Chem A 2010; 113:10040-9. [PMID: 19739681 DOI: 10.1021/jp9036183] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The systematic fragmentation method fragments a large molecular system into smaller pieces, in such a way as to greatly reduce the computational cost while retaining nearly the accuracy of the parent ab initio electronic structure method. In order to attain the desired (sub-kcal/mol) accuracy, one must properly account for the nonbonded interactions between the separated fragments. Since, for a large molecular species, there can be a great many fragments and therefore a great many nonbonded interactions, computations of the nonbonded interactions can be very time-consuming. The present work explores the efficacy of employing the effective fragment potential (EFP) method to obtain the nonbonded interactions since the EFP method has been shown previously to capture nonbonded interactions with an accuracy that is often comparable to that of second-order perturbation theory. It is demonstrated that for nonbonded interactions that are not high on the repulsive wall (generally >2.7 A), the EFP method appears to be a viable approach for evaluating the nonbonded interactions. The efficacy of the EFP method for this purpose is illustrated by comparing the method to ab initio methods for small water clusters, the ZOVGAS molecule, retinal, and the alpha-helix. Using SFM with EFP for nonbonded interactions yields an error of 0.2 kcal/mol for the retinal cis-trans isomerization and a mean error of 1.0 kcal/mol for the isomerization energies of five small (120-170 atoms) alpha-helices.
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23
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Chlorine activation indoors and outdoors via surface-mediated reactions of nitrogen oxides with hydrogen chloride. Proc Natl Acad Sci U S A 2009; 106:13647-54. [PMID: 19620710 DOI: 10.1073/pnas.0904195106] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gaseous HCl generated from a variety of sources is ubiquitous in both outdoor and indoor air. Oxides of nitrogen (NO(y)) are also globally distributed, because NO formed in combustion processes is oxidized to NO(2), HNO(3), N(2)O(5) and a variety of other nitrogen oxides during transport. Deposition of HCl and NO(y) onto surfaces is commonly regarded as providing permanent removal mechanisms. However, we show here a new surface-mediated coupling of nitrogen oxide and halogen activation cycles in which uptake of gaseous NO(2) or N(2)O(5) on solid substrates generates adsorbed intermediates that react with HCl to generate gaseous nitrosyl chloride (ClNO) and nitryl chloride (ClNO(2)), respectively. These are potentially harmful gases that photolyze to form highly reactive chlorine atoms. The reactions are shown both experimentally and theoretically to be enhanced by water, a surprising result given the availability of competing hydrolysis reaction pathways. Airshed modeling incorporating HCl generated from sea salt shows that in coastal urban regions, this heterogeneous chemistry increases surface-level ozone, a criteria air pollutant, greenhouse gas and source of atmospheric oxidants. In addition, it may contribute to recently measured high levels of ClNO(2) in the polluted coastal marine boundary layer. This work also suggests the potential for chlorine atom chemistry to occur indoors where significant concentrations of oxides of nitrogen and HCl coexist.
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Ootani Y, Satoh K, Nakayama A, Noro T, Taketsugu T. Ab initio molecular dynamics simulation of photoisomerization in azobenzene in the nπ[sup ∗] state. J Chem Phys 2009; 131:194306. [DOI: 10.1063/1.3263918] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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25
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Kina D, Nakayama A, Noro T, Taketsugu T, Gordon MS. Ab Initio QM/MM Molecular Dynamics Study on the Excited-State Hydrogen Transfer of 7-Azaindole in Water Solution. J Phys Chem A 2008; 112:9675-83. [DOI: 10.1021/jp804368p] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daisuke Kina
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Nakayama
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takeshi Noro
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
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26
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Tao HR, Fang DC. Thermal [1,3] sigmatropic rearrangements of bicyclic and tricyclic vinylcyclobutanes: a gray zone between the concerted and stepwise extremes. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0453-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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An ab initio molecular dynamics study on the dissociative recombination reaction of HD2O+ + e−. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0314-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Shemesh D, Gerber RB. Classical Trajectory Simulations of Photoionization Dynamics of Tryptophan: Intramolecular Energy Flow, Hydrogen-Transfer Processes and Conformational Transitions. J Phys Chem A 2006; 110:8401-8. [PMID: 16821822 DOI: 10.1021/jp0570869] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
One-photon and two-photon ionization dynamics of tryptophan is studied by classical trajectory simulations using the semiempirical parametric method number 3 (PM3) potential surface in "on the fly" calculations. The tryptophan conformer is assumed to be in the vibrational ground state prior to ionization. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for that state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. For the two-photon ionization process the ionization is assumed to go resonantively through the first excited state. Most trajectories are computed, and the analysis is carried out for the first 10 ps. A range of interesting effects are observed. The main findings are as follows: (1) Multiple conformational transitions are observed in most of the trajectories within the ultrafast duration of 10 ps. (2) Hydrogen transfer from the carboxyl group to the amino group and back has been observed. A zwitterion is formed as a transient state. (3) Two new isomers are formed during the dynamics, which have apparently not been previously observed. (4) Fast energy flow between the ring modes and the amino acid backbone is observed for both one- and two-photon ionization. However, the effective vibrational temperatures only approach the same value after 90 ps. The conformation transition dynamics, the proton-transfer processes and the vibrational energy flow are discussed and analyzed.
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Affiliation(s)
- Dorit Shemesh
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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29
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Kayanuma M, Taketsugu T, Ishii K. Ab initio surface hopping simulation on dissociative recombination of H3O+. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2005.11.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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The molecular and electronic structures of the halogen pseudohalides, a comparison of ab initio and DFT calculated structural and vibrational results with spectroscopic data. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert ATB, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA, Lochan RC, Wang T, Beran GJO, Besley NA, Herbert JM, Lin CY, Van Voorhis T, Chien SH, Sodt A, Steele RP, Rassolov VA, Maslen PE, Korambath PP, Adamson RD, Austin B, Baker J, Byrd EFC, Dachsel H, Doerksen RJ, Dreuw A, Dunietz BD, Dutoi AD, Furlani TR, Gwaltney SR, Heyden A, Hirata S, Hsu CP, Kedziora G, Khalliulin RZ, Klunzinger P, Lee AM, Lee MS, Liang W, Lotan I, Nair N, Peters B, Proynov EI, Pieniazek PA, Rhee YM, Ritchie J, Rosta E, Sherrill CD, Simmonett AC, Subotnik JE, Woodcock HL, Zhang W, Bell AT, Chakraborty AK, Chipman DM, Keil FJ, Warshel A, Hehre WJ, Schaefer HF, Kong J, Krylov AI, Gill PMW, Head-Gordon M. Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys 2006; 8:3172-91. [PMID: 16902710 DOI: 10.1039/b517914a] [Citation(s) in RCA: 2122] [Impact Index Per Article: 117.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
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Affiliation(s)
- Yihan Shao
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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32
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Ziegler T, Autschbach J. Theoretical methods of potential use for studies of inorganic reaction mechanisms. Chem Rev 2005; 105:2695-722. [PMID: 15941226 DOI: 10.1021/cr0307188] [Citation(s) in RCA: 367] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tom Ziegler
- Department of Chemistry, University of Calgary, Canada.
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33
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Shemesh D, Gerber RB. Different chemical dynamics for different conformers of biological molecules: Photoionization of glycine. J Chem Phys 2005; 122:241104. [PMID: 16035739 DOI: 10.1063/1.1937407] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.
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Affiliation(s)
- D Shemesh
- Department of Physical Chemistry, The Hebrew University, Jerusalem, Israel
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34
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Shemesh D, Baer R, Seideman T, Gerber RB. Photoionization dynamics of glycine adsorbed on a silicon cluster: “On-the-fly” simulations. J Chem Phys 2005; 122:184704. [PMID: 15918744 DOI: 10.1063/1.1894052] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.
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Affiliation(s)
- Dorit Shemesh
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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35
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Yagi K, Hirao K, Taketsugu T, Schmidt MW, Gordon MS. Ab initiovibrational state calculations with a quartic force field: Applications to H2CO, C2H4, CH3OH, CH3CCH, and C6H6. J Chem Phys 2004; 121:1383-9. [PMID: 15260682 DOI: 10.1063/1.1764501] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
For polyatomic molecules, n-mode coupling representations of the quartic force field (nMR-QFF) are presented, which include terms up to n normal coordinate couplings in a fourth-order polynomial potential energy function. The computational scheme to evaluate third-and fourth-order derivatives by finite differentiations of the energy is fully described. The code to generate the nMR-QFF has been implemented into GAMESS program package and interfaced with the vibrational self-consistent field (VSCF) and correlation corrected VSCF (cc-VSCF) methods. As a demonstration, fundamental frequencies have been calculated by the cc-VSCF method based on 2MR-QFF for formaldehyde, ethylene, methanol, propyne, and benzene. The applications show that 2MR-QFF is a highly accurate potential energy function, with errors of 1.0-1.9% relative to the experimental value in fundamental frequencies. This approach will help quantitative evaluations of vibrational energies of a general molecule with a reasonable computational cost.
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Affiliation(s)
- Kiyoshi Yagi
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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36
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Lin H, Pu J, Albu TV, Truhlar DG. Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics Using Partial Electronic Structure Hessians. J Phys Chem A 2004. [DOI: 10.1021/jp049972+] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Rudić S, Murray C, Harvey JN, Orr-Ewing AJ. On-the-flyab initiotrajectory calculations of the dynamics of Cl atom reactions with methane, ethane and methanol. J Chem Phys 2004; 120:186-98. [PMID: 15267276 DOI: 10.1063/1.1629670] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dynamics of Cl atom reactions with methane, ethane, and methanol have been studied by calculation of quasi-classical trajectories, with computation of potential energies and gradients only at the geometries through which the trajectories pass. Trajectories were started from the transition state, with 2 kcal mol(-1) of energy given to the mode with an imaginary frequency (representing the reaction coordinate at the transition state) and inclusion of zero-point energy in some or all of the remaining vibrational modes. The trajectories were propagated as far as separated products, with the majority of potential energy calculations performed at the HF/6-31G level of theory. The rotational quantum state population distributions of the HCl products from the reactions of Cl atoms with methane, ethane and methanol peaked at J'=1, 2, and 6, respectively. The calculations thereby exhibit somewhat greater rotational excitation than is found experimentally, but correctly describe the trend of increasing HCl product rotation for the three respective reactions. In agreement with previous observations, only 4% of the energy available to the products of the reaction of Cl atoms with methane was channeled into CH3 radical internal energy, and 1% into HCl rotation, with 92% ending up as translational energy. For the reaction of Cl atoms with ethane and with methanol, the corresponding values for radical internal energy, HCl rotation and product translation are 21, 3, and 78%, and 46, 13, and 42%, respectively. For the latter two reactions, the radical internal energy is mostly accounted for by rotational motion. The clear increase in rotational excitation of the HCl products from the Cl atom reaction with methanol is explained in terms of a dipole-dipole interaction between the departing polar fragments. A smaller set of more computationally expensive trajectory calculations using potentials and gradients from the MP2/6-311G(d,p) level of theory were performed for reactions of Cl atoms with methanol, and give results in better agreement with experimentally measured HCl rotational excitation, consistent with the model of dipole-induced product rotation because the MP2/6-311G(d,p) calculations give smaller dipole moments for both products than the HF/6-31G calculations. The calculated angles between the rotational angular momentum vectors and recoil velocities of the radical peak sharply at 90 degrees for the reactions of Cl atoms with ethane and methanol, but exhibit a much broader distribution for reaction with methane.
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Affiliation(s)
- Svemir Rudić
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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38
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Schlegel HB. Exploring potential energy surfaces for chemical reactions: an overview of some practical methods. J Comput Chem 2003; 24:1514-27. [PMID: 12868114 DOI: 10.1002/jcc.10231] [Citation(s) in RCA: 280] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described.
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Affiliation(s)
- H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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39
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Netzloff HM, Gordon MS, Christe K, Wilson WW, Vij A, Vij V, Boatz JA. On the Existence of FN5, a Theoretical and Experimental Study. J Phys Chem A 2003. [DOI: 10.1021/jp030157o] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Yagi K, Oyanagi C, Taketsugu T, Hirao K. Ab initio potential energy surface for vibrational state calculations of H2CO. J Chem Phys 2003. [DOI: 10.1063/1.1531105] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Webb SP, Iordanov T, Hammes-Schiffer S. Multiconfigurational nuclear-electronic orbital approach: Incorporation of nuclear quantum effects in electronic structure calculations. J Chem Phys 2002. [DOI: 10.1063/1.1494980] [Citation(s) in RCA: 215] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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42
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Yagi K, Taketsugu T, Hirao K. A new analytic form ofab initiopotential energy function: An application to H2O. J Chem Phys 2002. [DOI: 10.1063/1.1448828] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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43
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On the dissociation dynamics of the benzyl chloride radical anion. An ab initio dynamic reaction coordinate analysis study. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(00)00863-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Taketsugu T, Kumeda Y. An ab initio direct-trajectory study of the kinetic isotope effect on the bifurcating reaction. J Chem Phys 2001. [DOI: 10.1063/1.1358864] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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45
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Bakken V, Danovich D, Shaik S, Schlegel HB. A single transition state serves two mechanisms: an ab initio classical trajectory study of the electron transfer and substitution mechanisms in reactions of ketyl radical anions with alkyl halides. J Am Chem Soc 2001; 123:130-4. [PMID: 11273609 DOI: 10.1021/ja002799k] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Molecular dynamics has been used to investigate the reaction of a series of ketyl anion radicals and alkyl halides, CH2O(*)(-) + CH3X (X = F, Cl, Br) and NCCHO(*)(-) + CH3Cl. In addition to a floppy outer-sphere transition state which leads directly to ET products, there is a strongly bound transition state that yields both electron transfer (ET) and C-alkylated (SUB(C)) products. This common transition state has significant C-- C bonding and gives ET and SUB(C) products via a bifurcation on a single potential energy surface. Branching ratios have been estimated from ab initio classical trajectory calculations. The SUB(C) products are favored for transition states with short C--C bonds and ET for long C--C bonds. ET reactivity can be observed even at short distances of r(C)(-)(C) = ca. 2.4 A as in the transition state for the reaction NCCHO(*)(-) + CH3Cl. Therefore, the ET/SUB(C) reactivity is entangled over a significant range of the C--C distance. The mechanistic significance of the molecular dynamics study is discussed.
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Affiliation(s)
- V Bakken
- Contributions from the Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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46
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Yagi K, Taketsugu T, Hirao K, Gordon MS. Direct vibrational self-consistent field method: Applications to H2O and H2CO. J Chem Phys 2000. [DOI: 10.1063/1.481881] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Ben-Nun M, Quenneville J, Martínez TJ. Ab Initio Multiple Spawning: Photochemistry from First Principles Quantum Molecular Dynamics. J Phys Chem A 2000. [DOI: 10.1021/jp994174i] [Citation(s) in RCA: 644] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Ben-Nun
- Department of Chemistry and The Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Jason Quenneville
- Department of Chemistry and The Beckman Institute, University of Illinois, Urbana, Illinois 61801
| | - Todd J. Martínez
- Department of Chemistry and The Beckman Institute, University of Illinois, Urbana, Illinois 61801
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48
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Knospe O, Jungwirth P. Electron photodetachment in C60−: Quantum molecular dynamics with a non-empirical, `on-the-fly' calculated potential. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(99)01401-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Taketsugu T, Watanabe N, Hirao K. Multidimensional tunneling dynamics on HSiOH cis-trans isomerization with interpolated potential energy surface. J Chem Phys 1999. [DOI: 10.1063/1.479625] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Yarkony DR. Determining the molecular Aharonov–Bohm phase angle: A rigorous approach employing a molecular properties based adiabatic to diabatic states transformation. J Chem Phys 1999. [DOI: 10.1063/1.477917] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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