1
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Agarwal A, Boruah PJ, Sarkar B, Paul AK. Post-Transition-State Direct Dynamics Simulations on the Ozonolysis of Catechol. J Phys Chem A 2022; 126:5314-5327. [PMID: 35943451 DOI: 10.1021/acs.jpca.2c04028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
On-the-fly dynamics simulations are performed for the reaction of catechol + O3. The post transition state (TS) dynamics is studied at temperatures of 400 and 500 K. The PM7 semiempirical method is employed for calculating the potential energy gradient needed for integrating Hamilton's equations of motion. This semiempirical method provides excellent agreement in terms of energy and geometry of the TSs as well as minimum energy states of the system with respect to B3LYP/6-311+G (2df, 2p) calculated results. In the dynamics, first, a peroxyacid is formed, which further dissociates to different fragments. Four major channels forming CO, CO2, H2O, and small carboxylic acid (SCA) fragments are seen in this reaction. Rates of each of the channels and the overall unimolecular reaction are calculated at both temperatures. Branching ratios of all these product channels are calculated and compared with experiment. The minimum energy profile of CO2, CO, and H2O channels are calculated. A qualitative estimate of activation energies for all the channels are obtained and compared with the explicit TS energies of three product channels, which ultimately correlate with the reaction probabilities.
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Affiliation(s)
- Ankita Agarwal
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
| | - Palash Jyoti Boruah
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
| | - Biplab Sarkar
- Department of Chemistry, North Eastern Hill University, Shillong 793003, Meghalaya, India
| | - Amit K Paul
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
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2
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Lin S, Peng D, Yang W, Gu FL, Lan Z. Theoretical studies on triplet-state driven dissociation of formaldehyde by quasi-classical molecular dynamics simulation on machine-learning potential energy surface. J Chem Phys 2021; 155:214105. [PMID: 34879677 PMCID: PMC8654486 DOI: 10.1063/5.0067176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/09/2021] [Indexed: 11/15/2022] Open
Abstract
The H-atom dissociation of formaldehyde on the lowest triplet state (T1) is studied by quasi-classical molecular dynamic simulations on the high-dimensional machine-learning potential energy surface (PES) model. An atomic-energy based deep-learning neural network (NN) is used to represent the PES function, and the weighted atom-centered symmetry functions are employed as inputs of the NN model to satisfy the translational, rotational, and permutational symmetries, and to capture the geometry features of each atom and its individual chemical environment. Several standard technical tricks are used in the construction of NN-PES, which includes the application of clustering algorithm in the formation of the training dataset, the examination of the reliability of the NN-PES model by different fitted NN models, and the detection of the out-of-confidence region by the confidence interval of the training dataset. The accuracy of the full-dimensional NN-PES model is examined by two benchmark calculations with respect to ab initio data. Both the NN and electronic-structure calculations give a similar H-atom dissociation reaction pathway on the T1 state in the intrinsic reaction coordinate analysis. The small-scaled trial dynamics simulations based on NN-PES and ab initio PES give highly consistent results. After confirming the accuracy of the NN-PES, a large number of trajectories are calculated in the quasi-classical dynamics, which allows us to get a better understanding of the T1-driven H-atom dissociation dynamics efficiently. Particularly, the dynamics simulations from different initial conditions can be easily simulated with a rather low computational cost. The influence of the mode-specific vibrational excitations on the H-atom dissociation dynamics driven by the T1 state is explored. The results show that the vibrational excitations on symmetric C-H stretching, asymmetric C-H stretching, and C=O stretching motions always enhance the H-atom dissociation probability obviously.
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Affiliation(s)
| | | | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Feng Long Gu
- Authors to whom correspondence should be addressed: and
| | - Zhenggang Lan
- Authors to whom correspondence should be addressed: and
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3
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Zhang K, Wang Y, Zhu H, Peng Q. Advances on Quasi-classical Molecular Dynamics of Organic Reaction Mechanisms. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202102036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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4
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Lee JU, Kim Y, Kim WY, Oh HB. Graph theory-based reaction pathway searches and DFT calculations for the mechanism studies of free radical-initiated peptide sequencing mass spectrometry (FRIPS MS): a model gas-phase reaction of GGR tri-peptide. Phys Chem Chem Phys 2020; 22:5057-5069. [PMID: 32073000 DOI: 10.1039/c9cp05433b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Graph theory-based reaction pathway searches (ACE-Reaction program) and density functional theory calculations were performed to shed light on the mechanisms for the production of [an + H]+, xn+, yn+, zn+, and [yn + 2H]+ fragments formed in free radical-initiated peptide sequencing (FRIPS) mass spectrometry measurements of a small model system of glycine-glycine-arginine (GGR). In particular, the graph theory-based searches, which are rarely applied to gas-phase reaction studies, allowed us to investigate reaction mechanisms in an exhaustive manner without resorting to chemical intuition. As expected, radical-driven reaction pathways were favorable over charge-driven reaction pathways in terms of kinetics and thermodynamics. Charge- and radical-driven pathways for the formation of [yn + 2H]+ fragments were carefully compared, and it was revealed that the [yn + 2H]+ fragments observed in our FRIPS MS spectra originated from the radical-driven pathway, which is in contrast to the general expectation. The acquired understanding of the FRIPS fragmentation mechanism is expected to aid in the interpretation of FRIPS MS spectra. It should be emphasized that graph theory-based searches are powerful and effective methods for studying reaction mechanisms, including gas-phase reactions in mass spectrometry.
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Affiliation(s)
- Jae-Ung Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea.
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5
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Pratihar S, Ma X, Xie J, Scott R, Gao E, Ruscic B, Aquino AJA, Setser DW, Hase WL. Post-transition state dynamics and product energy partitioning following thermal excitation of the F⋯HCH2CN transition state: Disagreement with experiment. J Chem Phys 2017; 147:144301. [DOI: 10.1063/1.4985894] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Subha Pratihar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
| | - Xinyou Ma
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
| | - Jing Xie
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Rebecca Scott
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
| | - Eric Gao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
| | - Branko Ruscic
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA and Computation Institute, University of Chicago, Chicago, Illinois 60637, USA
| | - Adelia J. A. Aquino
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Institute for Soil Research University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Donald W. Setser
- Institute for Soil Research University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
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6
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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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7
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Maeda S, Taketsugu T, Ohno K, Morokuma K. From Roaming Atoms to Hopping Surfaces: Mapping Out Global Reaction Routes in Photochemistry. J Am Chem Soc 2015; 137:3433-45. [DOI: 10.1021/ja512394y] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Satoshi Maeda
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koichi Ohno
- Graduate
School of Science, Tohoku University, Sendai 980-8578, Japan
- Institute for Quantum Chemical Exploration, Tokyo 108-0022, Japan
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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8
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Affiliation(s)
- Joel M. Bowman
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA, USA
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9
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Li J, Guo H. Mode specificity and product energy disposal in unimolecular reactions: insights from the sudden vector projection model. J Phys Chem A 2014; 118:2419-25. [PMID: 24617859 DOI: 10.1021/jp501255t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple model is proposed to predict mode specificity and product energy disposal in unimolecular dissociation reactions. This so-called Sudden Vector Projection (SVP) model quantifies the coupling of a reactant or product mode with the reaction coordinate at the transition state by projecting the corresponding normal mode vector onto the imaginary frequency mode at the saddle point. Due to the sudden assumption, SVP predictions for mode specificity are expected to be valid only when the reactant molecule has weak intermodal coupling. On the other hand, the sudden limit is generally satisfied for its predictions of product energy disposal in unimolecular reactions with a tight barrier. The SVP model is applied to several prototypical systems and the agreement with available experimental and theoretical results is satisfactory.
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Affiliation(s)
- Jun Li
- Department of Chemistry and Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
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10
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Liang S, Roitberg AE. AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in Complex Environments: Development and Testing. J Chem Theory Comput 2013; 9:4470-80. [DOI: 10.1021/ct400471m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuai Liang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Adrian E. Roitberg
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
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11
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Exploring Multiple Potential Energy Surfaces: Photochemistry of Small Carbonyl Compounds. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/268124] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In theoretical studies of chemical reactions involving multiple potential energy surfaces (PESs) such as photochemical reactions, seams of intersection among the PESs often complicate the analysis. In this paper, we review our recipe for exploring multiple PESs by using an automated reaction path search method which has previously been applied to single PESs. Although any such methods for single PESs can be employed in the recipe, the global reaction route mapping (GRRM) method was employed in this study. By combining GRRM with the proposed recipe, all critical regions, that is, transition states, conical intersections, intersection seams, and local minima, associated with multiple PESs, can be explored automatically. As illustrative examples, applications to photochemistry of formaldehyde and acetone are described. In these examples as well as in recent applications to other systems, the present approach led to discovery of many unexpected nonadiabatic pathways, by which some complicated experimental data have been explained very clearly.
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12
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Affiliation(s)
- Lai Xu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Charles E. Doubleday
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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13
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Yang Z, Chai K, Ji H. Selective inclusion and separation of cinnamaldehyde and benzaldehyde by insoluble β-cyclodextrin polymer. Sep Purif Technol 2011. [DOI: 10.1016/j.seppur.2011.04.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Wong SYY, Benoit DM, Lewerenz M, Brown A, Roy PN. Determination of molecular vibrational state energies using the ab initio semiclassical initial value representation: application to formaldehyde. J Chem Phys 2011; 134:094110. [PMID: 21384953 DOI: 10.1063/1.3553179] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have demonstrated the use of ab initio molecular dynamics (AIMD) trajectories to compute the vibrational energy levels of molecular systems in the context of the semiclassical initial value representation (SC-IVR). A relatively low level of electronic structure theory (HF/3-21G) was used in this proof-of-principle study. Formaldehyde was used as a test case for the determination of accurate excited vibrational states. The AIMD-SC-IVR vibrational energies have been compared to those from curvilinear and rectilinear vibrational self-consistent field/vibrational configuration interaction with perturbation selected interactions-second-order perturbation theory (VSCF/VCIPSI-PT2) and correlation-corrected vibrational self-consistent field (cc-VSCF) methods. The survival amplitudes were obtained from selecting different reference wavefunctions using only a single set of molecular dynamics trajectories. We conclude that our approach is a further step in making the SC-IVR method a practical tool for first-principles quantum dynamics simulations.
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Affiliation(s)
- Stephanie Y Y Wong
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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15
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Affiliation(s)
| | - Benjamin C. Shepler
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322;
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16
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Fu B, Shepler BC, Bowman JM. Three-State Trajectory Surface Hopping Studies of the Photodissociation Dynamics of Formaldehyde on ab Initio Potential Energy Surfaces. J Am Chem Soc 2011; 133:7957-68. [DOI: 10.1021/ja201559r] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bina Fu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Benjamin C. Shepler
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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17
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Nádasdi R, Zügner GL, Farkas M, Dóbé S, Maeda S, Morokuma K. Photochemistry of Methyl Ethyl Ketone: Quantum Yields and S
1
/S
0
‐Diradical Mechanism of Photodissociation. Chemphyschem 2010; 11:3883-95. [DOI: 10.1002/cphc.201000522] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rebeka Nádasdi
- Institute of Materials and Environmental Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59‐67, 1025 Budapest (Hungary), Fax: +36‐1‐438‐1147
| | - Gábor L. Zügner
- Institute of Materials and Environmental Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59‐67, 1025 Budapest (Hungary), Fax: +36‐1‐438‐1147
| | - Mária Farkas
- Institute of Materials and Environmental Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59‐67, 1025 Budapest (Hungary), Fax: +36‐1‐438‐1147
| | - Sándor Dóbé
- Institute of Materials and Environmental Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59‐67, 1025 Budapest (Hungary), Fax: +36‐1‐438‐1147
| | - Satoshi Maeda
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606‐8501 (Japan), Fax: +81‐75‐781‐4757
- The Hakubi Center, Kyoto University, Kyoto 606‐8501 (Japan)
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606‐8501 (Japan), Fax: +81‐75‐781‐4757
- Department of Chemistry and Cherry L. Emerson Centre for Scientific Computation, Emory University, Atlanta, GA 30322 (USA)
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18
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Koyano Y, Takenaka N, Nakagawa Y, Nagaoka M. An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework. J Comput Chem 2010; 31:2628-41. [DOI: 10.1002/jcc.21558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Bolton K, Hase WL, Doubleday C. Isomerisation of deuterated cyclopropanes - The possibility for stereochemical control. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19971010314] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Layfield JP, Troya D. Theoretical study of the dynamics of F+alkanethiol self-assembled monolayer hydrogen-abstraction reactions. J Chem Phys 2010; 132:134307. [DOI: 10.1063/1.3364858] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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21
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Rauhut G, Hartke B. Modeling of high-order many-mode terms in the expansion of multidimensional potential energy surfaces: Application to vibrational spectra. J Chem Phys 2009; 131:014108. [DOI: 10.1063/1.3160668] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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22
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Zhang P, Maeda S, Morokuma K, Braams BJ. Photochemical reactions of the low-lying excited states of formaldehyde: T1/S0 intersystem crossings, characteristics of the S1 and T1 potential energy surfaces, and a global T1 potential energy surface. J Chem Phys 2009; 130:114304. [DOI: 10.1063/1.3085952] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Layfield JP, Sweeney AF, Troya D. Direct-Dynamics Study of the F + CH4, C2H6, C3H8, and i-C4H10 Reactions. J Phys Chem A 2009; 113:4294-304. [DOI: 10.1021/jp810929e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joshua P. Layfield
- Department of Chemistry, Virginia Tech, 107 Davidson Hall, Blacksburg, Virginia 24061-0212
| | - Andrew F. Sweeney
- Department of Chemistry, Virginia Tech, 107 Davidson Hall, Blacksburg, Virginia 24061-0212
| | - Diego Troya
- Department of Chemistry, Virginia Tech, 107 Davidson Hall, Blacksburg, Virginia 24061-0212
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24
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Tishchenko O, Truhlar DG. Efficient global representations of potential energy functions: Trajectory calculations of bimolecular gas-phase reactions by multiconfiguration molecular mechanics. J Chem Phys 2009; 130:024105. [DOI: 10.1063/1.3042145] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Takenaka N, Koyano Y, Nakagawa Y, Nagaoka M. An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution. J Comput Chem 2009; 31:1287-96. [DOI: 10.1002/jcc.21416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Chang DT, Schenter GK, Garrett BC. Self-consistent polarization neglect of diatomic differential overlap: application to water clusters. J Chem Phys 2008; 128:164111. [PMID: 18447425 DOI: 10.1063/1.2905230] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Semiempirical self-consistent field (SCF) methods based on the neglect of diatomic differential overlap (NDDO) formalism have the ability to treat the formation and breaking of chemical bonds but have been found to poorly describe hydrogen bonding and weak electrostatic complexes. In contrast, most empirical potentials are not able to describe bond breaking and formation but have the ability to add missing elements of hydrogen bonding by using classical electrostatic interactions. We present a new method which combines aspects of both NDDO-based SCF techniques and classical descriptions of polarization to describe the diffuse nature of the electronic wavefunction in a self-consistent manner. We develop the "self-consistent polarization neglect of diatomic differential overlap" (SCP-NDDO) theory with the additional description of molecular dispersion developed as a second-order perturbation theory expression. The current study seeks to model water-water interactions as a test case. To this end, we have parametrized the method to accurate ab initio complete basis set limit estimates of small water cluster binding energies of Xantheas and co-workers [J. Chem. Phys. 116, 1493 (2002); 120, 823 (2004)]. Overall agreement with the ab initio binding energies (n=2-6, and 8) is achieved with a rms error of 0.19 kcal/mol. We achieve noticeable improvements in the structure, vibrational frequencies, and energetic predictions of water clusters (n< or =21) relative to standard NDDO-based methods.
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Affiliation(s)
- Daniel T Chang
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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27
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Shepler BC, Braams BJ, Bowman JM. “Roaming” Dynamics in CH3CHO Photodissociation Revealed on a Global Potential Energy Surface. J Phys Chem A 2008; 112:9344-51. [DOI: 10.1021/jp802331t] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin C. Shepler
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322
| | - Bastiaan J. Braams
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322
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28
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Lourderaj U, Park K, Hase WL. Classical trajectory simulations of post-transition state dynamics. INT REV PHYS CHEM 2008. [DOI: 10.1080/01442350802045446] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Farnum JD, Bowman JM. Phase Space Analysis of Formaldehyde Dissociation Branching and Comparison with Quasiclassical Trajectory Calculations†. J Phys Chem A 2007; 111:10376-80. [PMID: 17629255 DOI: 10.1021/jp072617+] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the dependence of the branching ratio of formaldehyde dissociation to molecular and radical products on the total energy and angular momentum and the HCO rotational state distributions by using a combination of transition state/Rice-Ramsperger-Kassel-Marcus theory and phase space theory. Comparisons are made with recent quasiclassical trajectory (QCT) calculations [Farnum, J. D.; Zhang, X.; Bowman, J. M. J. Chem. Phys. 2007, 126, 134305]. The combined phase-space analysis is in semiquantitative agreement with the QCT results for the rotational distributions of HCO but is only in qualitative agreement for the branching ratio. Nevertheless, that level of agreement serves to provide insight into the QCT results, which showed suppression of the radical channel with increasing total angular momentum for a fixed total energy.
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Affiliation(s)
- John D Farnum
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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30
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Farnum JD, Zhang X, Bowman JM. Formaldehyde photodissociation: Dependence on total angular momentum and rotational alignment of the CO product. J Chem Phys 2007; 126:134305. [PMID: 17430030 DOI: 10.1063/1.2715586] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quasiclassical trajectory calculations are reported to investigate the effects of rotational excitation of formaldehyde on the branching ratios of the fragmentation products, H2+CO and H+HCO. The results of tens of thousands of trajectories show that increased rotational excitation causes suppression of the radical channel and enhancement of the molecular channel. Decomposing the molecular channel into "direct" and "roaming" channels shows that increased rotation switches from suppressing to enhancing the roaming products across our chosen energy range. However, decomposition into these pathways is difficult because the difference between them does not appear to have a distinct boundary. A vector correlation investigation of the CO rotation shows different characteristics in the roaming versus direct channels and this difference is a potentially useful signature of the roaming mechanism, as first speculated by Kable and Houston in their experimental study of photodissociation of acetaldehyde [P. L. Houston and S. H. Kable, Proc. Nat. Acad. Sci. 103, 16079 (2006)].
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Affiliation(s)
- John D Farnum
- Department of Chemistry, and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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Lourderaj U, Song K, Windus TL, Zhuang Y, Hase WL. Direct dynamics simulations using Hessian-based predictor-corrector integration algorithms. J Chem Phys 2007; 126:044105. [PMID: 17286460 DOI: 10.1063/1.2437214] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In previous research [J. Chem. Phys. 111, 3800 (1999)] a Hessian-based integration algorithm was derived for performing direct dynamics simulations. In the work presented here, improvements to this algorithm are described. The algorithm has a predictor step based on a local second-order Taylor expansion of the potential in Cartesian coordinates, within a trust radius, and a fifth-order correction to this predicted trajectory. The current algorithm determines the predicted trajectory in Cartesian coordinates, instead of the instantaneous normal mode coordinates used previously, to ensure angular momentum conservation. For the previous algorithm the corrected step was evaluated in rotated Cartesian coordinates. Since the local potential expanded in Cartesian coordinates is not invariant to rotation, the constants of motion are not necessarily conserved during the corrector step. An approximate correction to this shortcoming was made by projecting translation and rotation out of the rotated coordinates. For the current algorithm unrotated Cartesian coordinates are used for the corrected step to assure the constants of motion are conserved. An algorithm is proposed for updating the trust radius to enhance the accuracy and efficiency of the numerical integration. This modified Hessian-based integration algorithm, with its new components, has been implemented into the VENUS/NWChem software package and compared with the velocity-Verlet algorithm for the H(2)CO-->H(2)+CO, O(3)+C(3)H(6), and F(-)+CH(3)OOH chemical reactions.
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Affiliation(s)
- Upakarasamy Lourderaj
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
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32
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Yonehara T, Kato S. Quantum dynamics study on multichannel dissociation and isomerization reactions of formaldehyde. J Chem Phys 2006; 125:084307. [PMID: 16965012 DOI: 10.1063/1.2338041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study quantum dynamics of the multichannel reactions of H(2)CO including the molecular and radical dissociation channels as well as the isomerization ones, H(2)CO-->trans-HCOH and trans-HCOH-->cis-HCOH. For this purpose, the previously developed potential energy function [T. Yonehara and S. Kato, J. Chem. Phys. 117, 11131 (2002)] is refined to give accurate transition state energies and to describe the radical dissociation channel. The cumulative reaction probabilities for the molecular dissociation and two isomerization channels are calculated by using the full Watson Hamiltonian. We also carry out wave packet dynamics calculations starting from the transition state region for the molecular dissociation. A contracted basis set for the angular coordinates is constructed to reduce the size of dynamics calculations. The intramolecular vibrational relaxation dynamics is found to be fast and almost complete within 300 fs. Using the energy filtered wave functions, the time propagation of HCOH population is obtained in the energy range from 81 to 94 kcal/mol. The branching ratio of the radical product is estimated by calculating the time dependent reactive fluxes to the molecular and radical dissociation products.
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Affiliation(s)
- Takehiro Yonehara
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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Bowman JM, Zhang X. New insights on reaction dynamics from formaldehyde photodissociation. Phys Chem Chem Phys 2006; 8:321-32. [PMID: 16482274 DOI: 10.1039/b512847c] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the photodissociation dynamics of formaldehyde with an emphasis on recent calculations that make use of a global ab initio-based potential energy surface for the S(0) state. These calculations together with recent experiments reveal striking departures from conventional transition state theory for the formation of the molecular products H(2) + CO. The evidence for this departure is reviewed in detail by examining properties of the new potential surface and results of quasiclassical trajectory dynamics calculations using this surface. We also review very recent work on the dynamics governing the formation of radical products, H + HCO. These products can be formed on the T(1) surface as well as the S(0) one, and we present some results contrasting the dynamics on these two surfaces. This work makes use of a new semi-global ab initio-based T(1) potential energy surface.
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Affiliation(s)
- Joel M Bowman
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, GA 30322, USA.
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Salazar MR. Molecular Dynamics of Complex Gas-Phase Reactive Systems by Time-Dependent Groups. J Phys Chem A 2005; 109:11515-20. [PMID: 16354042 DOI: 10.1021/jp053551q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel way of assembling the total potential for performing molecular dynamical studies of complex gas-phase reactive chemical systems is introduced. The method breaks the calculation of the total potential and gradients of the potential into time-dependent groups that are governed by spatial cutoffs. These groups evolve during the course of the simulation and their number may increase or diminish as the dynamics of the system determine. In an effort to extend the simulation time of these complex reactive processes and to use high levels of theory when necessary, multiple levels of theory may be used over the groups for the calculation of both the intragroup and intergroup interactions. Representative simulations are performed to illustrate the method and a computationally facile method of obtaining the groups of a simulation are also discussed.
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Affiliation(s)
- Michael R Salazar
- Department of Chemistry, Union University, 1050 Union University Dr., Jackson, Tennessee 38305, USA.
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Rheinecker J, Zhang X, Bowman * J. Quasiclassical trajectory studies of the dynamics of H2CO on a globalab initio-based potential energy surface. Mol Phys 2005. [DOI: 10.1080/00268970412331333483] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhang X, Rheinecker JL, Bowman JM. Quasiclassical trajectory study of formaldehyde unimolecular dissociation: H2CO→H2+CO, H+HCO. J Chem Phys 2005; 122:114313. [PMID: 15836221 DOI: 10.1063/1.1872838] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report quasiclassical trajectory calculations of the dynamics of the two reaction channels of formaldehyde dissociation on a global ab initio potential energy surface: the molecular channel H(2)CO-->H(2) + CO and the radical H(2)CO-->H + HCO. For the molecular channel, it is confirmed that above the threshold of the radical channel a second, intramolecular hydrogen abstraction pathway is opened to produce CO with low rotation and vibrationally hot H(2). The low-j(CO) and high-nu(H(2) ) products from the second pathway increase with the total energy. The competition between the molecular and radical pathways is also studied. It shows that the branching ratio of the molecular products decreases with increasing energy, while the branching ratio of the radical products increases. The results agree well with very recent velocity-map imaging experiments of Suits and co-workers and solves a mystery first posed by Moore and co-workers. For the radical channel, we present the translational energy distributions and HCO rotation distributions at various energies. There is mixed agreement with the experiments of Wittig and co-workers, and this provides an indirect confirmation of their speculation that the triplet surface plays a role in the formation of the radical products.
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Affiliation(s)
- Xiubin Zhang
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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González-Vázquez J, Martínez-Núñez E, Vázquez S, Santamaría J, Bañares L. RRKM and direct MP2/6-31G(d,p) quasiclassical trajectory study of the H2 elimination in the photodissociation of vinyl chloride at 193 nm. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.08.031] [Citation(s) in RCA: 7] [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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Further investigation of the HCl elimination in the photodissociation of vinyl chloride at 193 nm: a direct MP2/6-31G(d,p) trajectory study. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.01.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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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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Yonehara T, Kato S. Role of isomerization channel in unimolecular dissociation reaction H2CO→H2+CO: Ab initio global potential energy surface and classical trajectory analysis. J Chem Phys 2002. [DOI: 10.1063/1.1523058] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [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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Schlegel HB, Iyengar SS, Li X, Millam JM, Voth GA, Scuseria GE, Frisch MJ. Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals. III. Comparison with Born–Oppenheimer dynamics. J Chem Phys 2002. [DOI: 10.1063/1.1514582] [Citation(s) in RCA: 365] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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42
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Kurosaki Y, Yokoyama K. Photodissociation of Acetaldehyde, CH3CHO → CH4 + CO: Direct ab Initio Dynamics Study. J Phys Chem A 2002. [DOI: 10.1021/jp020998f] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yuzuru Kurosaki
- Advanced Photon Research Center, Japan Atomic Energy Research Institute, Umemidai, Kizu-cho, Soraku-gun, Kyoto 619-0215, Japan
| | - Keiichi Yokoyama
- Advanced Photon Research Center, Japan Atomic Energy Research Institute, Umemidai, Kizu-cho, Soraku-gun, Kyoto 619-0215, Japan
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Anand S, Schlegel HB. Unimolecular Dissociation of Formyl Halides HXCO → CO + HX (X= F, Cl): An Ab Initio Direct Classical Trajectory Study. J Phys Chem A 2002. [DOI: 10.1021/jp021495c] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Smriti Anand
- Department of Chemistry and Institute of Scientific Computing, Wayne State University, Detroit, Michigan 48202
| | - H. Bernhard Schlegel
- Department of Chemistry and Institute of Scientific Computing, Wayne State University, Detroit, Michigan 48202
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Vach H, Chaâbane N, Peslherbe GH. Direct versus complex-mediated processes for Si+(2P)+H2 reactive scattering. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(01)01438-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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45
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Martínez-Núñez E, Marques JMC, Vázquez SA. A direct dynamics study of the H2 elimination from 2,5-dihydrofuran. J Chem Phys 2001. [DOI: 10.1063/1.1409359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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46
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Koch DM, Khieu NH, Peslherbe GH. Ab Initio Studies of the Glyoxal Unimolecular Dissociation Pathways. J Phys Chem A 2001. [DOI: 10.1021/jp0039013] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Denise M. Koch
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada H3G 1M8
| | - Nam Huan Khieu
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada H3G 1M8
| | - Gilles H. Peslherbe
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada H3G 1M8
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Li X, Millam JM, Schlegel HB. Ab initio molecular dynamics studies of the photodissociation of formaldehyde, H2CO→H2+CO: Direct classical trajectory calculations by MP2 and density functional theory. J Chem Phys 2000. [DOI: 10.1063/1.1323503] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Martı́nez-Núñez E, Vázquez SA. Three-center vs. four-center HF elimination from vinyl fluoride: a direct dynamics study. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)01198-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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