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Weir H, Williams M, Parrish RM, Hohenstein EG, Martínez TJ. Nonadiabatic Dynamics of Photoexcited cis-Stilbene Using Ab Initio Multiple Spawning. J Phys Chem B 2020; 124:5476-5487. [DOI: 10.1021/acs.jpcb.0c03344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Hayley Weir
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Monika Williams
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Robert M. Parrish
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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Morrow Z, Liu C, Kelley CT, Jakubikova E. Approximating Periodic Potential Energy Surfaces with Sparse Trigonometric Interpolation. J Phys Chem B 2019; 123:9677-9684. [PMID: 31631663 DOI: 10.1021/acs.jpcb.9b08210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in computational chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as local minima, maxima, and transition states. Construction of full-dimensional PESs for molecules with more than 10 atoms is computationally expensive and often not feasible. Previous work in our group used sparse interpolation with polynomial basis functions to construct a surrogate reduced-dimensional PESs along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. However, polynomial interpolation does not preserve the periodicity of the PES gradient with respect to angular components of geometry, such as torsion angles, which can lead to nonphysical phenomena. In this work, we construct a surrogate PES using trigonometric basis functions, for a system where the selected reaction coordinates all correspond to the torsion angles, resulting in a periodically repeating PES. We find that a trigonometric interpolation basis not only guarantees periodicity of the gradient but also results in slightly lower approximation error than polynomial interpolation.
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Affiliation(s)
- Zachary Morrow
- Department of Mathematics , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Chang Liu
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - C T Kelley
- Department of Mathematics , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Elena Jakubikova
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695 , United States
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3
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Liu C, Kelley CT, Jakubikova E. Molecular Dynamics Simulations on Relaxed Reduced-Dimensional Potential Energy Surfaces. J Phys Chem A 2019; 123:4543-4554. [PMID: 31038956 DOI: 10.1021/acs.jpca.9b02298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations with full-dimensional potential energy surfaces (PESs) obtained from high-level ab initio calculations are frequently used to model reaction dynamics of small molecules (i.e., molecules with up to 10 atoms). Construction of full-dimensional PESs for larger molecules is, however, not feasible since the number of ab initio calculations required grows rapidly with the increase of dimension. Only a small number of coordinates are often essential for describing the reactivity of even very large systems, and reduced-dimensional PESs with these coordinates can be built for reaction dynamics studies. While analytical methods based on transition-state theory framework are well established for analyzing the reduced-dimensional PESs, MD simulation algorithms capable of generating trajectories on such surfaces are more rare. In this work, we present a new MD implementation that utilizes the relaxed reduced-dimensional PES for standard microcanonical (NVE) and canonical (NVT) MD simulations. The method is applied to the pyramidal inversion of a NH3 molecule. The results from the MD simulations on a reduced, three-dimensional PES are validated against the ab initio MD simulations, as well as MD simulations on full-dimensional PES and experimental data.
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Fletcher K, Krämer M, Bunz UH, Dreuw A. The π-conjugation length determines the fluorescence quenching mechanism of aromatic aldehydes in water. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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5
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Photoisomerization induced scission of rod-like micelles unravelled with multiscale modeling. J Colloid Interface Sci 2018; 510:357-367. [DOI: 10.1016/j.jcis.2017.09.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 11/21/2022]
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6
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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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7
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Lei Y, Yu L, Zhou B, Zhu C, Wen Z, Lin SH. Landscapes of four-enantiomer conical intersections for photoisomerization of stilbene: CASSCF calculation. J Phys Chem A 2014; 118:9021-31. [PMID: 24977930 DOI: 10.1021/jp5020109] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photoisomerization of cis- and trans-stilbene through conical intersections (CI) is mainly governed by four dihedral angles around central C═C double bonds. The two of them are C-C═C-C and H-C═C-H dihedral angles that are found to form a mirror rotation coordinate, and the mirror plane appears at the two dihedral angles equal to zeros with which the middle state is defined through partial optimization. There exist the first-type of hula-twist-CI enantiomers, the second-type of hula-twist-CI enantiomers, the first-type of one-bond-flip-CI enantiomers, and the second type of one-bond-flip-CI enantiomers as well as cis-enantiomers and trans-enantiomers with respect to this mirror plane. The complete active space self-consistent field method is employed to calculate minimum potential energy profile along the mirror rotation coordinate for each enantiomers, and it is found that the left-hand manifold and the right-hand manifold of potential energy surfaces can be energetically transferred via photoisomerization. Furthermore, two-dimensional potential energy surfaces in terms of the branching plane g-h coordinates are constructed at vicinity of each conical intersection, and the landscapes of conical intersections show distinct feature, and in excited-state four potential wells separated in different section of g-h plane related to different conical intersections which indicate different photoisomerization pathways.
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Affiliation(s)
- Yibo Lei
- Department of Applied Chemistry, Institute of Molecular Science and Center for Interdisciplinary Molecular Science, National Chiao-Tung University , Hsinchu 300, Taiwan
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Ioffe IN, Granovsky AA. Photoisomerization of Stilbene: The Detailed XMCQDPT2 Treatment. J Chem Theory Comput 2013; 9:4973-90. [PMID: 26583415 DOI: 10.1021/ct400647w] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the detailed XMCQDPT2/cc-pVTZ study of trans-cis photoisomerization in one of the core systems of both experimental and computational photochemistry-the stilbene molecule. For the first time, the potential energy surface (PES) of the S1 state has been directly optimized and scanned using a multistate multiconfiguration second-order perturbation theory. We characterize the trans-stilbene, pyramidalized (phantom), and DHP-cis-stilbene geometric domains of the S1 state and describe their stationary points including the transition states between them, as well as S1/S0 intersections. Also reported are the minima and the activation barriers in the ground state. Our calculations correctly predict the kinetic isotope effect due to H/D exchange at ethylenic hydrogens, the dynamic behavior of excited cis-stilbene, and trans-cis branching ratio after relaxation to S0 through a rather unsymmetric conical intersection. In general, the XMCQDPT2 results confirm the qualitative adequacy of the TDDFT (especially SF-TDDFT) picture of the excited stilbene but also reveal quantitative discrepancies that deserve further exploration.
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Affiliation(s)
- I N Ioffe
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
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9
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Minezawa N, Gordon MS. Photoisomerization of stilbene: a spin-flip density functional theory approach. J Phys Chem A 2011; 115:7901-11. [PMID: 21639100 DOI: 10.1021/jp203803a] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photoisomerization process of 1,2-diphenylethylene (stilbene) is investigated using the spin-flip density functional theory (SFDFT), which has recently been shown to be a promising approach for locating conical intersection (CI) points (Minezawa, N.; Gordon, M. S. J. Phys. Chem. A2009, 113, 12749). The SFDFT method gives valuable insight into twisted stilbene to which the linear response time-dependent DFT approach cannot be applied. In contrast to the previous SFDFT study of ethylene, a distinct twisted minimum is found for stilbene. The optimized structure has a sizable pyramidalization angle and strong ionic character, indicating that a purely twisted geometry is not a true minimum. In addition, the SFDFT approach can successfully locate two CI points: the twisted-pyramidalized CI that is similar to the ethylene counterpart and another CI that possibly lies on the cyclization pathway of cis-stilbene. The mechanisms of the cis--trans isomerization reaction are discussed on the basis of the two-dimensional potential energy surface along the twisting and pyramidalization angles.
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Affiliation(s)
- Noriyuki Minezawa
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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Jiang CW, Xie RH, Li FL, Allen RE. Photocyclization of trans-stilbene induced by an ultrafast laser pulse. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.01.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Molecular dynamics simulations and mechanism of organic reactions: non-TST behaviors. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0065-3160(08)44004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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12
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Jiang C, Xie R, Li F, Allen RE. Trans-to-cis isomerization of stilbene following an ultrafast laser pulse. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.04.079] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Karamertzanis† PG, Pantelides CC. Ab initiocrystal structure prediction. II. Flexible molecules. Mol Phys 2007. [DOI: 10.1080/00268970601143317] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Stefanović J, Pantelides CC. Molecular Dynamics as a Mathematical Mapping. III. Efficient Evaluation of the Differentiable Force Functions and Their Derivatives. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020108023017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Nguyen PH, Gorbunov RD, Stock G. Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study. Biophys J 2006; 91:1224-34. [PMID: 16731560 PMCID: PMC1518633 DOI: 10.1529/biophysj.106.084996] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates reveals that the conformational rearrangement of the peptide is rather complex and occurs on at least four timescales: 1) After photoexcitation, the azobenzene unit of the molecule undergoes nonadiabatic photoisomerization within 0.2 ps. 2) On the picosecond timescale, the cooling (13 ps) and the stretching (14 ps) of the photoexcited peptide is observed. 3) Most reaction coordinates exhibit a 50-100 ps component reflecting a fast conformational rearrangement. 4) The 500-1000 ps component observed in the simulation accounts for the slow diffusion-controlled conformational equilibration of the system. The simulation of the photoinduced molecular processes is in remarkable agreement with time-resolved optical and infrared experiments, although the calculated cooling as well as the initial conformational rearrangements of the peptide appear to be somewhat too slow. Based on an ab initio parameterized vibrational Hamiltonian, the time-dependent amide I frequency shift is calculated. Both intramolecular and solvent-induced contributions to the frequency shift were found to change by < or = 2 cm(-1), in reasonable agreement with experiment. The potential of transient infrared spectra to characterize the conformational dynamics of peptides is discussed in some detail.
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Affiliation(s)
- Phuong H Nguyen
- Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Frankfurt, Germany
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17
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Witkoskie JB, Doren DJ. Neural Network Models of Potential Energy Surfaces: Prototypical Examples. J Chem Theory Comput 2004; 1:14-23. [DOI: 10.1021/ct049976i] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James B. Witkoskie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Douglas J. Doren
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
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18
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Dou Y, Allen RE. Detailed dynamics of a complex photochemical reaction: Cis–trans photoisomerization of stilbene. J Chem Phys 2003. [DOI: 10.1063/1.1621621] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Quenneville J, Martínez TJ. Ab Initio Study of Cis−Trans Photoisomerization in Stilbene and Ethylene. J Phys Chem A 2003. [DOI: 10.1021/jp021210w] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- 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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Quenneville J, Ben-Nun M, Martı́nez TJ. Photochemistry from first principles — advances and future prospects. J Photochem Photobiol A Chem 2001. [DOI: 10.1016/s1010-6030(01)00452-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Hahn S, Stock G. Theoretical Description of Secondary Emission Reflecting Ultrafast Nonadiabatic Isomerization. J Phys Chem A 2001. [DOI: 10.1021/jp003788g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susanne Hahn
- Theoretical Quantum Dynamics, Faculty of Physics, University Freiburg, D-79104 Freiburg, Germany
| | - Gerhard Stock
- Theoretical Quantum Dynamics, Faculty of Physics, University Freiburg, D-79104 Freiburg, Germany
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25
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Hahn S, Stock G. Quantum-Mechanical Modeling of the Femtosecond Isomerization in Rhodopsin. J Phys Chem B 2000. [DOI: 10.1021/jp992939g] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susanne Hahn
- Faculty of Physics, University of Freiburg, D-79104 Freiburg, Germany
| | - Gerhard Stock
- Faculty of Physics, University of Freiburg, D-79104 Freiburg, Germany
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26
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Amatatsu Y. Ab initio study on the electronic structures of stilbene at the conical intersection. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)01042-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Berweger CD, van Gunsteren WF, Müller-Plathe F. Viscosity dependence and solvent effects in the photoisomerization of cis-stilbene: Insight from a molecular dynamics study with an ab initio potential-energy function. J Chem Phys 1999. [DOI: 10.1063/1.480242] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Berweger CD, van Gunsteren WF, Müller-Plathe F. Die Photoisomerisierung voncis-Stilben folgt nicht dem Weg minimaler Energie. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990903)111:17<2771::aid-ange2771>3.0.co;2-g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Eckert F, Werner HJ. Local interpolation of ab initio potential energy surfaces for direct dynamics studies of chemical reactions. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)00132-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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