1
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Pandey P, Arandhara M, Houston PL, Qu C, Conte R, Bowman JM, Ramesh SG. Assessing Permutationally Invariant Polynomial and Symmetric Gradient Domain Machine Learning Potential Energy Surfaces for H 3O 2. J Phys Chem A 2024; 128:3212-3219. [PMID: 38624168 PMCID: PMC11056970 DOI: 10.1021/acs.jpca.4c01044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
The singly hydrated hydroxide anion OH-(H2O) is of central importance to a detailed molecular understanding of water; therefore, there is strong motivation to develop a highly accurate potential to describe this anion. While this is a small molecule, it is necessary to have an extensive data set of energies and, if possible, forces to span several important stationary points. Here, we assess two machine-learned potentials, one using the symmetric gradient domain machine learning (sGDML) method and one based on permutationally invariant polynomials (PIPs). These are successors to a PIP potential energy surface (PES) reported in 2004. We describe the details of both fitting methods and then compare the two PESs with respect to precision, properties, and speed of evaluation. While the precision of the potentials is similar, the PIP PES is much faster to evaluate for energies and energies plus gradient than the sGDML one. Diffusion Monte Carlo calculations of the ground vibrational state, using both potentials, produce similar large anharmonic downshift of the zero-point energy compared to the harmonic approximation of the PIP and sGDML potentials. The computational time for these calculations using the sGDML PES is roughly 300 times greater than using the PIP one.
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Affiliation(s)
- Priyanka Pandey
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Mrinal Arandhara
- Department
of Inorganic and Physical Chemistry, Indian
Institute of Science, Bangalore 560012, India
| | - Paul L. Houston
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- Department
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Chen Qu
- Independent
Researcher, Toronto, Ontario M9B0E3, Canada
| | - Riccardo Conte
- Dipartimento
di Chimica, Università degli Studi
di Milano, Milano 20133, Italy
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Sai G. Ramesh
- Department
of Inorganic and Physical Chemistry, Indian
Institute of Science, Bangalore 560012, India
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2
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Ge F, Wang R, Qu C, Zheng P, Nandi A, Conte R, Houston PL, Bowman JM, Dral PO. Tell Machine Learning Potentials What They Are Needed For: Simulation-Oriented Training Exemplified for Glycine. J Phys Chem Lett 2024; 15:4451-4460. [PMID: 38626460 DOI: 10.1021/acs.jpclett.4c00746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Machine learning potentials (MLPs) are widely applied as an efficient alternative way to represent potential energy surfaces (PESs) in many chemical simulations. The MLPs are often evaluated with the root-mean-square errors on the test set drawn from the same distribution as the training data. Here, we systematically investigate the relationship between such test errors and the simulation accuracy with MLPs on an example of a full-dimensional, global PES for the glycine amino acid. Our results show that the errors in the test set do not unambiguously reflect the MLP performance in different simulation tasks, such as relative conformer energies, barriers, vibrational levels, and zero-point vibrational energies. We also offer an easily accessible solution for improving the MLP quality in a simulation-oriented manner, yielding the most precise relative conformer energies and barriers. This solution also passed the stringent test by diffusion Monte Carlo simulations.
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Affiliation(s)
- Fuchun Ge
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, Fujian 361005, China
| | - Ran Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, Fujian 361005, China
| | - Chen Qu
- Independent Researcher, Toronto, Ontario M9B0E3, Canada
| | - Peikun Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, Fujian 361005, China
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, Fujian 361005, China
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3
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Houston PL, Qu C, Yu Q, Pandey P, Conte R, Nandi A, Bowman JM. No Headache for PIPs: A PIP Potential for Aspirin Runs Much Faster and with Similar Precision Than Other Machine-Learned Potentials. J Chem Theory Comput 2024; 20:3008-3018. [PMID: 38593438 DOI: 10.1021/acs.jctc.4c00054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Assessments of machine-learning (ML) potentials are an important aspect of the rapid development of this field. We recently reported an assessment of the linear-regression permutationally invariant polynomial (PIP) method for ethanol, using the widely used (revised) rMD17 data set. We demonstrated that the PIP approach outperformed numerous other methods, e.g., ANI, PhysNet, sGDML, and p-KRR, with respect to precision and notably with respect to speed [Houston et al., J. Chem. Phys. 2022, 156, 044120]. Here, we extend this assessment to the 21-atom aspirin molecule, using the rMD17 data set, with a focus on the speed of evaluation. Both energies and forces are used for training, and the precision of several PIPs is examined for both. Normal mode frequencies, the methyl torsional potential, and 1d vibrational energies for an OH stretch are presented. We show that the PIP approach achieves the level of precision obtained from other ML methods, e.g., atom-centered neural network methods, linear regression ACE, and kernel methods, as reported by Kovács et al. in J. Chem. Theory Comput. 2021, 17, 7696-7711. More significantly, we show that the PIP PESs run much faster than all other ML methods, whose timings were evaluated in that paper. We also show that the PIP PES extrapolates well enough to describe several internal motions of aspirin, including an OH stretch.
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Affiliation(s)
- Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Qu
- Independent Researcher, Toronto, Ontario M9B0E3, Canada
| | - Qi Yu
- Department of Chemistry, Fudan University, Shanghai 200438, P. R. China
| | - Priyanka Pandey
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
| | - Joel M Bowman
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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Houston PL, Qu C, Yu Q, Pandey P, Conte R, Nandi A, Bowman JM, Kukolich SG. Formic Acid-Ammonia Heterodimer: A New Δ-Machine Learning CCSD(T)-Level Potential Energy Surface Allows Investigation of the Double Proton Transfer. J Chem Theory Comput 2024; 20:1821-1828. [PMID: 38382541 DOI: 10.1021/acs.jctc.3c01273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The formic acid-ammonia dimer is an important example of a hydrogen-bonded complex in which a double proton transfer can occur. Its microwave spectrum has recently been reported and rotational constants and quadrupole coupling constants were determined. Calculated estimates of the double-well barrier and the internal barriers to rotation were also reported. Here, we report a full-dimensional potential energy surface (PES) for this complex, using two closely related Δ-machine learning methods to bring it to the CCSD(T) level of accuracy. The PES dissociates smoothly and accurately. Using a 2d quantum model the ground vibrational-state tunneling splitting is estimated to be less than 10-4 cm-1. The dipole moment along the intrinsic reaction coordinate is calculated along with a Mullikan charge analysis and supports the mildly ionic character of the minimum and strongly ionic character at the double-well barrier.
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Affiliation(s)
- Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, U.S.A. and Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Qu
- Independent Researcher, Toronto, Ontario M9B0E3, Canada
| | - Qi Yu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Priyanka Pandey
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, Via Golgi 19, Milano 20133, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Stephen G Kukolich
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Avenue, Tucson, Arizona 85721, United States
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5
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Pandey P, Qu C, Nandi A, Yu Q, Houston PL, Conte R, Bowman JM. Ab Initio Potential Energy Surface for NaCl-H 2 with Correct Long-Range Behavior. J Phys Chem A 2024; 128:902-908. [PMID: 38271992 PMCID: PMC10860134 DOI: 10.1021/acs.jpca.3c07687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/26/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
We report a full dimensional ab initio potential energy surface for NaCl-H2 based on precise fitting of a large data set of CCSD(T)/aug-cc-pVTZ energies. A major goal of this fit is to describe the very long-range interaction accurately. This is done in this instance via the dipole-quadrupole interaction. The NaCl dipole and the H2 quadrupole are available through previous works over a large range of internuclear distances. We use these to obtain exact effect charges on each atom. Diffusion Monte Carlo calculations are done for the ground vibrational state using the new potential.
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Affiliation(s)
- Priyanka Pandey
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia, 30322, United States
| | - Chen Qu
- Independent
Researcher, Toronto ON M9B 0E3, Canada
| | - Apurba Nandi
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia, 30322, United States
- Department
of Physics and Materials Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
| | - Qi Yu
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia, 30322, United States
| | - Paul L. Houston
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- Department
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Riccardo Conte
- Dipartimento
di Chimica, Università Degli Studi
di Milano, Via Golgi 19, Milano 20133, Italy
| | - 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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6
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Houston PL, Qu C, Yu Q, Pandey P, Conte R, Nandi A, Bowman JM. A New A Priori Method to Avoid Calculation of Negligible Hamiltonian Matrix Elements in CI Calculation. J Phys Chem A 2024; 128:479-487. [PMID: 38180902 DOI: 10.1021/acs.jpca.3c06985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
Hamiltonian matrices typically contain many elements that are negligibly small compared to the diagonal elements, even with methods to prune the underlying basis. Because for general potentials the calculation of H-matrix elements is a major part of the computational effort to obtain eigenvalues and eigenfunctions of the Hamiltonian, there is strong motivation to investigate locating these negligible elements without calculating them or at least avoid calculating them. We recently demonstrated an effective means to "learn" negligible elements using machine learning classification (J. Chem. Phys. 2023, 159, 071101). Here we present a simple, new method to avoid calculating them by using a cut-off value for the absolute difference in the quantum numbers for the bra and ket. This method is demonstrated for many of the same case studies as were used in the paper above, namely for realistic H-matrices of H2O, the vinyl radical, C2H3, and glycine, C2H5NO2. The new method is compared to the recently reported machine learning approach. In addition, we point out an important synergy between the two methods.
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Affiliation(s)
- Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Qu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Qi Yu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Priyanka Pandey
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - 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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Yu Q, Qu C, Houston PL, Nandi A, Pandey P, Conte R, Bowman JM. A Status Report on "Gold Standard" Machine-Learned Potentials for Water. J Phys Chem Lett 2023; 14:8077-8087. [PMID: 37656898 PMCID: PMC10510435 DOI: 10.1021/acs.jpclett.3c01791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Owing to the central importance of water to life as well as its unusual properties, potentials for water have been the subject of extensive research over the past 50 years. Recently, five potentials based on different machine learning approaches have been reported that are at or near the "gold standard" CCSD(T) level of theory. The development of such high-level potentials enables efficient and accurate simulations of water systems using classical and quantum dynamical approaches. This Perspective serves as a status report of these potentials, focusing on their methodology and applications to water systems across different phases. Their performances on the energies of gas phase water clusters, as well as condensed phase structural and dynamical properties, are discussed.
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Affiliation(s)
- Qi Yu
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent
Researcher, Toronto, Ontario M9B 0E3, Canada
| | - Paul L. Houston
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- Department of Chemistry
and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Apurba Nandi
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Priyanka Pandey
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento
di Chimica, Università degli Studi
di Milano, via Golgi 19, 20133 Milano, Italy
| | - 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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8
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Qu C, Houston PL, Yu Q, Conte R, Pandey P, Nandi A, Bowman JM. Machine learning classification can significantly reduce the cost of calculating the Hamiltonian matrix in CI calculations. J Chem Phys 2023; 159:071101. [PMID: 37584439 DOI: 10.1063/5.0168590] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Hamiltonian matrices in electronic and nuclear contexts are highly computation intensive to calculate, mainly due to the cost for the potential matrix. Typically, these matrices contain many off-diagonal elements that are orders of magnitude smaller than diagonal elements. We illustrate that here for vibrational H-matrices of H2O, C2H3 (vinyl), and C2H5NO2 (glycine) using full-dimensional ab initio-based potential surfaces. We then show that many of these small elements can be replaced by zero with small errors of the resulting full set of eigenvalues, depending on the threshold value for this replacement. As a result of this empirical evidence, we investigate three machine learning approaches to predict the zero elements. This is shown to be successful for these H-matrices after training on a small set of calculated elements. For H-matrices of vinyl and glycine, of order 15 552 and 8828, respectively, training on a percent or so of elements is sufficient to obtain all eigenvalues with a mean absolute error of roughly 2 cm-1.
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Affiliation(s)
- Chen Qu
- Independent Researcher, Toronto, Ontario M9B 0E3, Canada
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA and Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Qi Yu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Priyanka Pandey
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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Qu C, Yu Q, Houston PL, Conte R, Nandi A, Bowman JM. Interfacing q-AQUA with a Polarizable Force Field: The Best of Both Worlds. J Chem Theory Comput 2023. [PMID: 37249502 DOI: 10.1021/acs.jctc.3c00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Polarizable force fields are pervasive in the fields of computational chemistry and biochemistry; however, their empirical or semiempirical nature gives them both weaknesses and strengths. Here, we have developed a hybrid water potential, named q-AQUA-pol, by combining our recent ab initio q-AQUA potential with the TTM3-F water potential. The new potential demonstrates unprecedented accuracy ranging from gas-phase clusters, e.g., the eight low-lying isomers of the water hexamer, to the condensed phase, e.g., radial distribution functions, the self-diffusion coefficient, triplet OOO distribution, and the temperature dependence of the density. This represents a significant advancement in the field of polarizable machine learning potential and computational modeling.
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Affiliation(s)
- Chen Qu
- Independent Researcher, Toronto, Ontario M9B0E3, Canada
| | - Qi Yu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- 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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Nandi A, Laude G, Khire SS, Gurav ND, Qu C, Conte R, Yu Q, Li S, Houston PL, Gadre SR, Richardson JO, Evangelista FA, Bowman JM. Ring-Polymer Instanton Tunneling Splittings of Tropolone and Isotopomers using a Δ-Machine Learned CCSD(T) Potential: Theory and Experiment Shake Hands. J Am Chem Soc 2023; 145:9655-9664. [PMID: 37078852 PMCID: PMC10161208 DOI: 10.1021/jacs.3c00769] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Tropolone, a 15-atom cyclic molecule, has received much interest both experimentally and theoretically due to its H-transfer tunneling dynamics. An accurate theoretical description is challenging owing to the need to develop a high-level potential energy surface (PES) and then to simulate quantum-mechanical tunneling on this PES in full dimensionality. Here, we tackle both aspects of this challenge and make detailed comparisons with experiments for numerous isotopomers. The PES, of near CCSD(T)-quality, is obtained using a Δ-machine learning approach starting from a pre-existing low-level DFT PES and corrected by a small number of approximate CCSD(T) energies obtained using the fragmentation-based molecular tailoring approach. The resulting PES is benchmarked against DF-FNO-CCSD(T) and CCSD(T)-F12 calculations. Ring-polymer instanton calculations of the splittings, obtained with the Δ-corrected PES are in good agreement with previously reported experiments and a significant improvement over those obtained using the low-level DFT PES. The instanton path includes heavy-atom tunneling effects and cuts the corner, thereby avoiding passing through the conventional saddle-point transition state. This is in contradistinction with typical approaches based on the minimum-energy reaction path. Finally, the subtle changes in the splittings for some of the heavy-atom isotopomers seen experimentally are reproduced and explained.
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Affiliation(s)
- Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Subodh S Khire
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Nalini D Gurav
- Organisch-Chemisches Institut, University of Münster, 48149 Münster, Germany
| | - Chen Qu
- Independent Researcher, Toronto M9B0E3, Canada
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Shuhang Li
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Shridhar R Gadre
- Department of Scientific Computing, Modelling and Simulation, Savitribai Phule Pune University, Pune 411 007, India
| | | | - Francesco A Evangelista
- 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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11
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Houston PL. Autobiography of Paul L. Houston. J Phys Chem A 2023; 127:2065-2067. [PMID: 36891675 DOI: 10.1021/acs.jpca.3c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Affiliation(s)
- Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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12
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Houston PL, Qu C, Yu Q, Conte R, Nandi A, Li JK, Bowman JM. PESPIP: Software to fit complex molecular and many-body potential energy surfaces with permutationally invariant polynomials. J Chem Phys 2023; 158:044109. [PMID: 36725524 DOI: 10.1063/5.0134442] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We wish to describe a potential energy surface by using a basis of permutationally invariant polynomials whose coefficients will be determined by numerical regression so as to smoothly fit a dataset of electronic energies as well as, perhaps, gradients. The polynomials will be powers of transformed internuclear distances, usually either Morse variables, exp(-ri,j/λ), where λ is a constant range hyperparameter, or reciprocals of the distances, 1/ri,j. The question we address is how to create the most efficient basis, including (a) which polynomials to keep or discard, (b) how many polynomials will be needed, (c) how to make sure the polynomials correctly reproduce the zero interaction at a large distance, (d) how to ensure special symmetries, and (e) how to calculate gradients efficiently. This article discusses how these questions can be answered by using a set of programs to choose and manipulate the polynomials as well as to write efficient Fortran programs for the calculation of energies and gradients. A user-friendly interface for access to monomial symmetrization approach results is also described. The software for these programs is now publicly available.
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Affiliation(s)
- Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA and Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Chen Qu
- Independent Researcher, Toronto, Ontario M9B0E3, Canada
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Jeffrey K Li
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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13
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Abstract
There has been great progress in developing machine-learned potential energy surfaces (PESs) for molecules and clusters with more than 10 atoms. Unfortunately, this number of atoms generally limits the level of electronic structure theory to less than the "gold standard" CCSD(T) level. Indeed, for the well-known MD17 dataset for molecules with 9-20 atoms, all of the energies and forces were obtained with DFT calculations (PBE). This Perspective is focused on a Δ-machine learning method that we recently proposed and applied to bring DFT-based PESs to close to CCSD(T) accuracy. This is demonstrated for hydronium, N-methylacetamide, acetyl acetone, and ethanol. For 15-atom tropolone, it appears that special approaches (e.g., molecular tailoring, local CCSD(T)) are needed to obtain the CCSD(T) energies. A new aspect of this approach is the extension of Δ-machine learning to force fields. The approach is based on many-body corrections to polarizable force field potentials. This is examined in detail using the TTM2.1 water potential. The corrections make use of our recent CCSD(T) datasets for 2-b, 3-b, and 4-b interactions for water. These datasets were used to develop a new fully ab initio potential for water, termed q-AQUA.
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Affiliation(s)
- Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent Researcher, Toronto, Canada 66777
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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14
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Conte R, Nandi A, Qu C, Yu Q, Houston PL, Bowman JM. Semiclassical and VSCF/VCI Calculations of the Vibrational Energies of trans- and gauche-Ethanol Using a CCSD(T) Potential Energy Surface. J Phys Chem A 2022; 126:7709-7718. [PMID: 36240438 DOI: 10.1021/acs.jpca.2c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recent full-dimensional Δ-Machine learning potential energy surface (PES) for ethanol is employed in semiclassical and vibrational self-consistent field (VSCF) and virtual-state configuration interaction (VCI) calculations, using MULTIMODE, to determine the anharmonic vibrational frequencies of vibration for both the trans and gauche conformers of ethanol. Both semiclassical and VSCF/VCI energies agree well with the experimental data. We find significant mixing between the VSCF basis states due to Fermi resonances between bending and stretching modes. The same effects are also accurately described by the full-dimensional semiclassical calculations. These are the first high-level anharmonic calculations using a PES, in particular a "gold-standard" CCSD(T) one.
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Affiliation(s)
- Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent Researcher, Toronto, Ontario M9B0E3, Canada
| | - Qi Yu
- Department of Chemistry Yale University, New Haven, Connecticut 06520, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, 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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15
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Houston PL, Nandi A, Bowman JM. A Machine Learning Approach for Rate Constants. III. Application to the Cl( 2P) + CH 4 → CH 3 + HCl Reaction. J Phys Chem A 2022; 126:5672-5679. [PMID: 35960874 DOI: 10.1021/acs.jpca.2c04376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The temperature dependence of the thermal rate constant for the reaction Cl(3P) + CH4 → HCl + CH3 is calculated using a Gaussian Process machine learning (ML) approach to train on and predict thermal rate constants over a large temperature range. Following procedures developed in two previous reports, we use a training data set of approximately 40 reaction/potential surface combinations, each of which is used to calculate the corresponding database of rate constant at approximately eight temperatures. For the current application, we train on the entire data set and then predict the temperature dependence of the title reaction employing a "split" data set for correction at low and high temperatures to capture both tunneling and recrossing. The results are an improvement on recent RPMD calculations compared to accurate quantum ones, using the same high-level ab initio potential energy surface. Both tunneling at low temperatures and significant recrossing at high temperatures are observed to influence the rate constants. The recrossing effects, which are not described by TST and even sophisticated tunneling corrections, do appear in experiment at temperatures above around 600 K. The ML results describe these effects and in fact merge at 600 K with RPMD results (which can describe recrossing), and both are close to experiment at the highest experimental temperatures. These results are in accord with a recent high-level experiment-theory study of this reaction.
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Affiliation(s)
- Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Apurba Nandi
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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16
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Nandi A, Conte R, Qu C, Houston PL, Yu Q, Bowman JM. Quantum Calculations on a New CCSD(T) Machine-Learned Potential Energy Surface Reveal the Leaky Nature of Gas-Phase Trans and Gauche Ethanol Conformers. J Chem Theory Comput 2022; 18:5527-5538. [PMID: 35951990 PMCID: PMC9476654 DOI: 10.1021/acs.jctc.2c00760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Ethanol is a molecule of fundamental interest in combustion,
astrochemistry,
and condensed phase as a solvent. It is characterized by two methyl
rotors and trans (anti) and gauche conformers, which are known to be very close in energy.
Here we show that based on rigorous quantum calculations of the vibrational
zero-point state, using a new ab initio potential
energy surface (PES), the ground state resembles the trans conformer, but substantial delocalization to the gauche conformer is present. This explains experimental issues about identification
and isolation of the two conformers. This “leak” effect
is partially quenched when deuterating the OH group, which further
demonstrates the need for a quantum mechanical approach. Diffusion
Monte Carlo and full-dimensional semiclassical dynamics calculations
are employed. The new PES is obtained by means of a Δ-machine
learning approach starting from a pre-existing low level density functional
theory surface. This surface is brought to the CCSD(T) level of theory
using a relatively small number of ab initio CCSD(T)
energies. Agreement between the corrected PES and direct ab
initio results for standard tests is excellent. One- and
two-dimensional discrete variable representation calculations focusing
on the trans–gauche torsional
motion are also reported, in reasonable agreement with experiment.
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Affiliation(s)
- Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Chen Qu
- Independent Researcher, Toronto 66777, Canada
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, 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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Bowman JM, Qu C, Conte R, Nandi A, Houston PL, Yu Q. The MD17 datasets from the perspective of datasets for gas-phase “small” molecule potentials. J Chem Phys 2022; 156:240901. [DOI: 10.1063/5.0089200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
There has been great progress in developing methods for machine-learned potential energy surfaces. There have also been important assessments of these methods by comparing so-called learning curves on datasets of electronic energies and forces, notably the MD17 database. The dataset for each molecule in this database generally consists of tens of thousands of energies and forces obtained from DFT direct dynamics at 500 K. We contrast the datasets from this database for three “small” molecules, ethanol, malonaldehyde, and glycine, with datasets we have generated with specific targets for the potential energy surfaces (PESs) in mind: a rigorous calculation of the zero-point energy and wavefunction, the tunneling splitting in malonaldehyde, and, in the case of glycine, a description of all eight low-lying conformers. We found that the MD17 datasets are too limited for these targets. We also examine recent datasets for several PESs that describe small-molecule but complex chemical reactions. Finally, we introduce a new database, “QM-22,” which contains datasets of molecules ranging from 4 to 15 atoms that extend to high energies and a large span of configurations.
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Affiliation(s)
- Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Chen Qu
- Independent Researcher, Toronto, Canada
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Paul L. Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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18
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Yu Q, Qu C, Houston PL, Conte R, Nandi A, Bowman JM. q-AQUA: A Many-Body CCSD(T) Water Potential, Including Four-Body Interactions, Demonstrates the Quantum Nature of Water from Clusters to the Liquid Phase. J Phys Chem Lett 2022; 13:5068-5074. [PMID: 35652912 DOI: 10.1021/acs.jpclett.2c00966] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many model potential energy surfaces (PESs) have been reported for water; however, none are strictly from "first-principles". Here we report such a potential, based on a many-body representation at the CCSD(T) level of theory up to the four-body interaction. The new PES is benchmarked for the isomers of the water hexamer for dissociation energies, harmonic frequencies, and unrestricted diffusion Monte Carlo (DMC) calculations of the zero-point energies of the Prism, Book, and Cage isomers. Dissociation energies of several isomers of the 20-mer agree well with recent benchmark energies. Exploratory DMC calculations on this cluster verify the robustness of the new PES for quantum simulations. The accuracy and speed of the new PES are demonstrated for standard condensed phase properties, i.e., the radial distribution function and the self-diffusion constant. Quantum effects are shown to be substantial for these observables and also needed to bring theory into excellent agreement with experiment.
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Affiliation(s)
- Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Chen Qu
- Independent Researcher, Toronto, Ontario, Canada
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- 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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19
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Houston PL, Qu C, Nandi A, Conte R, Yu Q, Bowman JM. Permutationally invariant polynomial regression for energies and gradients, using reverse differentiation, achieves orders of magnitude speed-up with high precision compared to other machine learning methods. J Chem Phys 2022; 156:044120. [DOI: 10.1063/5.0080506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Paul L. Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA and Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Chen Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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20
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Endo T, Neville SP, Lassonde P, Qu C, Fujise H, Fushitani M, Hishikawa A, Houston PL, Bowman JM, Légaré F, Schuurman MS, Ibrahim H. Electronic relaxation and dissociation dynamics in formaldehyde: pump wavelength dependence. Phys Chem Chem Phys 2022; 24:1779-1786. [PMID: 34985091 DOI: 10.1039/d1cp04264e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The effect of the incident UV pump wavelength on the subsequent excited state dynamics, electronic relaxation, and ultimate dissociation of formaldehyde is studied using first principles simulation and Coulomb explosion imaging (CEI) experiments. Transitions in a vibronic progression in the à ← X̃ absorption band are systematically prepared using a tunable UV source which generates pulses centered at 304, 314, 329, and 337 nm. We find, both via ab initio simulation and experimental results, that the rate of excited state decay and subsequent dissociation displays a prominent dependence on which vibronic transition in the absorption band is prepared by the pump. Our simulations predict that nonadiabatic transition rates and dissociation yields will increase by a factor of >100 as the pump wavelength is decreased from 337 to 304 nm. The experimental results and theoretical simulations are in broad agreement and both indicate that the dissociation rate plateaus rapidly after ≈2 ps following an ultrafast sub-ps rise.
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Affiliation(s)
- Tomoyuki Endo
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 Boulevard Lionel-Boulet, Varennes, QC J3X 1S2, Canada. .,Kansai Photon Science Institute, National Institutes for Quantum Science and Technology, Umemidai, Kizugawa, Kyoto 619-0215, Japan.
| | - Simon P Neville
- National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - Philippe Lassonde
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 Boulevard Lionel-Boulet, Varennes, QC J3X 1S2, Canada.
| | - Chen Qu
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Hikaru Fujise
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Mizuho Fushitani
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Akiyoshi Hishikawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.,Research Center for Materials Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14852, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - François Légaré
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 Boulevard Lionel-Boulet, Varennes, QC J3X 1S2, Canada.
| | - Michael S Schuurman
- National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, ON K1N 6N5, Canada.
| | - Heide Ibrahim
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 Boulevard Lionel-Boulet, Varennes, QC J3X 1S2, Canada.
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21
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Abstract
High-level, ab initio calculations find that the 4-body (4-b) interaction is needed to account for near-100% of the total interaction energy for water clusters as large as the 21-mer. Motivated by this, we report a permutationally invariant polynomial potential energy surface (PES) for the 4-body interaction. This machine-learned PES is a fit to 2119 symmetry-unique, CCSD(T)-F12a/haTZ 4-b interaction energies. Configurations for these come from tetramer direct-dynamics calculations, fragments from an MD water simulation at 300 K, and tetramer fragments in a variety of water clusters. The PIP basis is purified to ensure that the PES goes rigorously to zero in monomer+trimer and dimer+dimer dissociations. The 4-b energies of isomers of the hexamer calculated with the new PES are shown to be in better agreement with benchmark CCSD(T) results than those from the MB-pol potential. Tests on larger clusters further validate the high-fidelity of the PES. The PES is shown to be fast to evaluate, taking 2.4 s for 105 evaluations on a single core of 2.4 GHz Intel Xeon processor, and significantly faster using a parallel version of the PES.
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Affiliation(s)
- Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, 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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22
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Qu C, Houston PL, Conte R, Nandi A, Bowman JM. MULTIMODE Calculations of Vibrational Spectroscopy and 1d Interconformer Tunneling Dynamics in Glycine Using a Full-Dimensional Potential Energy Surface. J Phys Chem A 2021; 125:5346-5354. [PMID: 34110169 DOI: 10.1021/acs.jpca.1c03738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A full-dimensional, permutationally invariant polynomial potential energy surface for glycine recently reported (R. Conte et al., J. Chem. Phys. 2020, 153, 244301) is used with the code MULTIMODE to determine the IR absorption spectra for Conformers I and II using a new separable dipole moment function. The calculated spectra agree well with the experimental ones. The full-dimensional nature of the potential allows us also to examine dynamical results, such as tunneling rates. Remarkably, using a one-dimensional path based on the potential energy surface to estimate the tunneling rate from Conformer VI to Conformer I, good agreement is found with the recent experimental measurement. Finally a brief comparison of our potential energy surface with a recently reported sGDML one is made.
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Affiliation(s)
- Chen Qu
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- 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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23
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Qu C, Houston PL, Conte R, Nandi A, Bowman JM. Breaking the Coupled Cluster Barrier for Machine-Learned Potentials of Large Molecules: The Case of 15-Atom Acetylacetone. J Phys Chem Lett 2021; 12:4902-4909. [PMID: 34006096 PMCID: PMC8279733 DOI: 10.1021/acs.jpclett.1c01142] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Machine-learned potential energy surfaces (PESs) for molecules with more than 10 atoms are typically forced to use lower-level electronic structure methods such as density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2). While these are efficient and realistic, they fall short of the accuracy of the "gold standard" coupled-cluster method, especially with respect to reaction and isomerization barriers. We report a major step forward in applying a Δ-machine learning method to the challenging case of acetylacetone, whose MP2 barrier height for H-atom transfer is low by roughly 1.1 kcal/mol relative to the benchmark CCSD(T) barrier of 3.2 kcal/mol. From a database of 2151 local CCSD(T) energies and training with as few as 430 energies, we obtain a new PES with a barrier of 3.5 kcal/mol in agreement with the LCCSD(T) barrier of 3.5 kcal/mol and close to the benchmark value. Tunneling splittings due to H-atom transfer are calculated using this new PES, providing improved estimates over previous ones obtained using an MP2-based PES.
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Affiliation(s)
- Chen Qu
- Department
of Chemistry & Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Paul L. Houston
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
- Department
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United
States
| | - Riccardo Conte
- Dipartimento
di Chimica, Università degli Studi
di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- 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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24
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Nandi A, Qu C, Houston PL, Conte R, Bowman JM. Δ-machine learning for potential energy surfaces: A PIP approach to bring a DFT-based PES to CCSD(T) level of theory. J Chem Phys 2021; 154:051102. [DOI: 10.1063/5.0038301] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Chen Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Paul L. Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA and Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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25
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Qu C, Conte R, Houston PL, Bowman JM. Full-dimensional potential energy surface for acetylacetone and tunneling splittings. Phys Chem Chem Phys 2021; 23:7758-7767. [DOI: 10.1039/d0cp04221h] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New, full-dimensional potential energy surface for acetylacetone allows for description of H-tunneling dynamics and characterization of stationary points.
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Affiliation(s)
- Chen Qu
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
| | - Riccardo Conte
- Dipartimento di Chimica
- Università Degli Studi di Milano
- 20133 Milano
- Italy
| | - Paul L. Houston
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
- Department of Chemistry and Biochemistry
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry
- Atlanta
- USA
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26
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Conte R, Houston PL, Qu C, Li J, Bowman JM. Full-dimensional, ab initio potential energy surface for glycine with characterization of stationary points and zero-point energy calculations by means of diffusion Monte Carlo and semiclassical dynamics. J Chem Phys 2020; 153:244301. [DOI: 10.1063/5.0037175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Paul L. Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA and Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Chen Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Jeffrey Li
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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27
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Endo T, Neville SP, Wanie V, Beaulieu S, Qu C, Deschamps J, Lassonde P, Schmidt BE, Fujise H, Fushitani M, Hishikawa A, Houston PL, Bowman JM, Schuurman MS, Légaré F, Ibrahim H. Capturing roaming molecular fragments in real time. Science 2020; 370:1072-1077. [DOI: 10.1126/science.abc2960] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/16/2020] [Accepted: 10/23/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Tomoyuki Endo
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Quebec J3X 1S2, Canada
- Kansai Photon Science Institute, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| | - Simon P. Neville
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Vincent Wanie
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Quebec J3X 1S2, Canada
| | - Samuel Beaulieu
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Quebec J3X 1S2, Canada
| | - Chen Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Jude Deschamps
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Quebec J3X 1S2, Canada
| | - Philippe Lassonde
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Quebec J3X 1S2, Canada
| | | | - Hikaru Fujise
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Mizuho Fushitani
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Akiyoshi Hishikawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Paul L. Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14852, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
| | - Michael S. Schuurman
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - François Légaré
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Quebec J3X 1S2, Canada
| | - Heide Ibrahim
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Quebec J3X 1S2, Canada
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28
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Quinn MS, Nauta K, Jordan MJT, Bowman JM, Houston PL, Kable SH. Rotational resonances in the H
2
CO roaming reaction are revealed by detailed correlations. Science 2020; 369:1592-1596. [DOI: 10.1126/science.abc4088] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/19/2020] [Indexed: 11/03/2022]
Affiliation(s)
- Mitchell S. Quinn
- School of Chemistry, University of New South Wales, Kensington, NSW, 2052, Australia
| | - Klaas Nauta
- School of Chemistry, University of New South Wales, Kensington, NSW, 2052, Australia
| | | | - Joel M. Bowman
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Paul L. Houston
- Department of Chemistry and Biochemistry, Cornell University, Ithaca, NY, USA
| | - Scott H. Kable
- School of Chemistry, University of New South Wales, Kensington, NSW, 2052, Australia
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29
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Abstract
![]()
An
efficient method is described for generating a fragmented, permutationally
invariant polynomial basis to fit electronic energies and, if available,
gradients for large molecules. The method presented rests on the fragmentation
of a large molecule into any number of fragments while maintaining
the permutational invariance and uniqueness of the polynomials. The
new approach improves on a previous one reported by Qu and Bowman
by avoiding repetition of polynomials in the fitting basis set and
speeding up gradient evaluations while keeping the accuracy of the
PES. The method is demonstrated for CH3–NH–CO–CH3 (N-methylacetamide) and NH2–CH2–COOH (glycine).
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Affiliation(s)
- Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Chen Qu
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, 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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30
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Sun G, Lucas M, Song Y, Zhang J, Brazier C, Houston PL, Bowman JM. H atom Product Channels in the Ultraviolet Photodissociation of the 2-Propenyl Radical. J Phys Chem A 2019; 123:9957-9965. [DOI: 10.1021/acs.jpca.9b07797] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ge Sun
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Michael Lucas
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Yu Song
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Jingsong Zhang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Christopher Brazier
- Department of Chemistry and Biochemistry, California State University, Long Beach, Long Beach, California 90840, United States
| | - Paul L. Houston
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States and
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, 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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31
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Abstract
We report a machine learning approach to train and predict bimolecular thermal rate constants over a large temperature range. The approach uses Gaussian process (GP) regression to evaluate the difference between accurate quantum results and Eckart-corrected conventional transition state theory, mostly for collinear reactions. Training is done on a database of rate constants for 13 reaction/potential surface combinations, and testing is performed on a set of 39 reaction/potential surface combinations. Averaged over all test reactions, the GP method is within 80% of the accurate answer, whereas transition state theory (TST) is only within 330% and Eckart-corrected TST (ECK) is within 110%. In the tunneling region, GP is generally (with a few exceptions) more accurate and sometimes much more accurate. In the high-temperature recrossing region, GP is significantly more accurate than either TST or ECK, neither of which addresses the possibility of recrossing. The GP predictions for the 3D reactions O(3P) + H2, OH + H2, O(3P) + CH4, and H + CH4, for which accurate quantum results are available, provide further encouragement to the machine learning approach.
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Affiliation(s)
- Paul L Houston
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientic Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientic Computation, Emory University, Atlanta, Georgia 30322, United States
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32
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Goodson T, Houston PL, McCrary VR. A Tribute to William M. Jackson, Jr. J Phys Chem A 2019; 123:1905-1907. [DOI: 10.1021/acs.jpca.8b12308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Abstract
A new paradigm for assigning vibrational spectra is described. Instead of proceeding from potential to Hamiltonian to eigenvalues/eigenvectors/intensities to spectrum, the new method goes "backwards" directly from spectrum to eigenvectors. The eigenvectors then "assign" the spectrum, in that they identify the basis states that contribute to each eigenvalue. To start, we demonstrate an algorithm that can obtain useful estimates of the eigenvectors connecting a real, symmetric Hamiltonian to its eigenvalues even if the only available information about the Hamiltonian is its diagonal elements. When this algorithm is augmented with information about transition intensities, it can be used to assign a complex vibrational spectrum using only information about (1) eigenvalues (the peak centers of the spectrum) and (2) a harmonic basis set (taken to be the diagonal elements of the Hamiltonian). Examples will be discussed, including application to the vibrationally complex spectral region of the formic acid dimer.
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Affiliation(s)
- Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell Universtiy, Ithaca, NY 14853, USA. and School of Chemistry and Biochemistry, Georgia Inst. of Technology, Atlanta, GA 30332-0400, USA
| | - Brian L Van Hoozen
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Chen Qu
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Qi Yu
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M Bowman
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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34
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Abstract
The phenomenon of roaming in chemical reactions has now become both commonly observed in experiment and extensively supported by theory and simulations. Roaming occurs in highly-excited molecules when the trajectories of atomic motion often bypass the minimum energy pathway and produce reaction in unexpected ways from unlikely geometries. The prototypical example is the unimolecular dissociation of formaldehyde (H2CO), in which the "normal" reaction proceeds through a tight transition state to yield H2 + CO but for which a high fraction of dissociations take place via a "roaming" mechanism in which one H atom moves far from the HCO, almost to dissociation, and then returns to abstract the second H atom. We review below the theories and simulations that have recently been developed to address and understand this new reaction phenomenon.
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Affiliation(s)
- Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University Atlanta, Georgia 30322, USA.
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35
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Houston PL, Wang X, Ghosh A, Bowman JM, Quinn MS, Kable SH. Formaldehyde roaming dynamics: Comparison of quasi-classical trajectory calculations and experiments. J Chem Phys 2017; 147:013936. [DOI: 10.1063/1.4982823] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paul L. Houston
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14852, USA
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Xiaohong Wang
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Aryya Ghosh
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Mitchell S. Quinn
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Scott H. Kable
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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36
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Abstract
Since the first ion imaging experiment [D. W. Chandler and P. L. Houston, J. Chem. Phys. 87, 1445-1447 (1987)], demonstrating the capability of collecting an image of the photofragments from a unimolecular dissociation event and analyzing that image to obtain the three-dimensional velocity distribution of the fragments, the efficacy and breadth of application of the ion imaging technique have continued to improve and grow. With the addition of velocity mapping, ion/electron centroiding, and slice imaging techniques, the versatility and velocity resolution have been unmatched. Recent improvements in molecular beam, laser, sensor, and computer technology are allowing even more advanced particle imaging experiments, and eventually we can expect multi-mass imaging with co-variance and full coincidence capability on a single shot basis with repetition rates in the kilohertz range. This progress should further enable "complete" experiments-the holy grail of molecular dynamics-where all quantum numbers of reactants and products of a bimolecular scattering event are fully determined and even under our control.
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Affiliation(s)
- David W Chandler
- Sandia National Laboratories, Combustion Research Facility, Livermore, California 94550, USA
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - David H Parker
- Department of Laser and Molecular Physics, Radboud University of Nijmegen, Nijmegen, Netherlands
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37
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Wang X, Houston PL, Bowman JM. A new (multi-reference configuration interaction) potential energy surface for H 2CO and preliminary studies of roaming. Philos Trans A Math Phys Eng Sci 2017; 375:20160194. [PMID: 28320899 PMCID: PMC5360895 DOI: 10.1098/rsta.2016.0194] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
We report a new global potential energy surface (PES) for H2CO, based on precise fitting of roughly 67 000 MRCI/cc-pVTZ energies. This PES describes the global minimum, the cis- and trans-HCOH isomers, and barriers relevant to isomerization, formation of the molecular (H2+CO) and radical (H+HCO) products, and the loose so-called roaming transition-state saddle point. The key features of the PES are reviewed and compared with a previous PES, denoted by PES04, based on five local fits that are 'stitched' together by switching functions (Zhang et al. 2004 J. Phys. Chem. A108, 8980-8986 (doi:10.1021/jp048339l)). Preliminary quasi-classical trajectory calculations are performed at the total energy of 36 233 cm-1 (103 kcal mol-1), relative to the H2CO global minimum, using the new PES, with a particular focus on roaming dynamics. When compared with the results from PES04, the new PES findings show similar rotational distributions, somewhat more roaming and substantially higher H2 vibrational excitation.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Xiaohong Wang
- Department of Chemistry, and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
| | - Paul L Houston
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14852, USA
| | - Joel M Bowman
- Department of Chemistry, and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
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38
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Affiliation(s)
- Michael Lucas
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Yu Song
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Jingsong Zhang
- Department of Chemistry and Air Pollution
Research Center, University of California at Riverside, Riverside, California 92521, United States
| | - Christopher Brazier
- Department of Chemistry and Biochemistry, California State University, Long Beach Long Beach, California 90840, United States
| | - Paul L. Houston
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332
- Department of Chemical Biology, Cornell University, Ithaca, New York 14850, 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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39
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Affiliation(s)
- Paul L. Houston
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Department
of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14852, United States
| | - Riccardo Conte
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Dipartimento
di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | - 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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40
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Conte R, Houston PL, Bowman JM. Trajectory and Model Studies of Collisions of Highly Excited Methane with Water Using an ab Initio Potential. J Phys Chem A 2015; 119:12304-17. [DOI: 10.1021/acs.jpca.5b06595] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Riccardo Conte
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L. Houston
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Department
of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14852, 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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41
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Affiliation(s)
- Paul L. Houston
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Riccardo Conte
- 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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42
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Qu C, Conte R, Houston PL, Bowman JM. “Plug and play” full-dimensional ab initio potential energy and dipole moment surfaces and anharmonic vibrational analysis for CH4–H2O. Phys Chem Chem Phys 2015; 17:8172-81. [DOI: 10.1039/c4cp05913a] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The first full-dimensional potential energy surface of CH4–H2O dimer is presented, and vibrational analysis of this dimer is performed.
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Affiliation(s)
- Chen Qu
- Department of Chemistry and Cherry L. Emerson Centrer for Scientific Computations
- Emory University
- Atlanta
- USA
| | - Riccardo Conte
- Department of Chemistry and Cherry L. Emerson Centrer for Scientific Computations
- Emory University
- Atlanta
- USA
| | - Paul L. Houston
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- Department of Chemistry and Chemical Biology
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Centrer for Scientific Computations
- Emory University
- Atlanta
- USA
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43
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Affiliation(s)
- Paul L. Houston
- School of Chemistry
and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14852, United States
| | - Riccardo Conte
- 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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44
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Conte R, Houston PL, Bowman JM. Trajectory Study of Energy Transfer and Unimolecular Dissociation of Highly Excited Allyl with Argon. J Phys Chem A 2014; 118:7742-57. [DOI: 10.1021/jp5062013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Riccardo Conte
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L. Houston
- School
of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Department
of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14852, 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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45
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Conte R, Houston PL, Bowman JM. Communication: A benchmark-quality, full-dimensional ab initio potential energy surface for Ar-HOCO. J Chem Phys 2014. [DOI: 10.1063/1.4871371] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Chen J, Strangfeld BR, Houston PL. NO dissociation through ns, np, and nf Rydberg states: angular distributions. J Chem Phys 2014; 140:034315. [PMID: 25669387 DOI: 10.1063/1.4861662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Velocity-mapped imaging and theoretical calculations have been used to study the angular distribution of the products of NO predissociation following its excitation to the 11s, 10p, 11p, and 9f Rydberg levels based on the NO(+) (X (2)Σ(+)) core. The Rydberg states were reached from the NO (A (2)Σ(+), v = 0, N = 2, J = 1.5) level prepared with strong alignment by excitation with linear polarization from NO (X (2)Π, v = 0, N = 1, J = 0.5). Ion dip spectra of the Rydberg states were recorded along with velocity-mapped images at the major peaks. The results are compared to calculations based on a previous theoretical approach modified to include transitions to states of Hund's case (d) coupling. The reasonable agreement shows the predictive value of the theory. The theory has also been used to reassess and explain previous results and to understand variations in the rate of photodissociation with components of the 10p and 11p Rydberg states.
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Affiliation(s)
- J Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - B R Strangfeld
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - P L Houston
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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47
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Lee KLK, Quinn MS, Maccarone AT, Nauta K, Houston PL, Reid SA, Jordan MJT, Kable SH. Two roaming pathways in the photolysis of CH3CHO between 328 and 308 nm. Chem Sci 2014. [DOI: 10.1039/c4sc02266a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We attribute the two product-state distributions previously seen in CH3CHO photodissociation to CH3-roaming and H-roaming, unifying all previous experimental results.
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Affiliation(s)
- Kin Long K. Lee
- School of Chemistry
- University of New South Wales
- Kensington, Australia
| | - Mitchell S. Quinn
- School of Chemistry
- University of New South Wales
- Kensington, Australia
| | | | - Klaas Nauta
- School of Chemistry
- University of New South Wales
- Kensington, Australia
| | - Paul L. Houston
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
| | - Scott A. Reid
- School of Chemistry
- University of Sydney
- Sydney, Australia
| | | | - Scott H. Kable
- School of Chemistry
- University of New South Wales
- Kensington, Australia
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48
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Conte R, Houston PL, Bowman JM. Classical Trajectory Study of Energy Transfer in Collisions of Highly Excited Allyl Radical with Argon. J Phys Chem A 2013; 117:14028-41. [DOI: 10.1021/jp410315r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Riccardo Conte
- Department of Chemistry and Cherry L. Emerson
Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L. Houston
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, 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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49
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Ulrich CK, Chen J, Tokel O, Houston PL, Grebenshchikov SY. Photodissociation of ozone from 321 to 329 nm: the relative yields of O(3P2) with O2(X 3Σg(-)), O2(a 1Δg) and O2(b 1Σg(+)). J Phys Chem A 2013; 117:12011-9. [PMID: 23795961 DOI: 10.1021/jp4041088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Product imaging of O((3)P2) following dissociation of ozone has been used to determine the relative yields of the product channels O((3)P2) + O2(X (3)Σg(-)) of ozone. All three channels are prominent at all wavelengths investigated. O2 vibrational distributions for each channel and each wavelength are also estimated assuming Boltzmann rotational distributions. Averaged over wavelength in the measured range, the yields of the O((3)P2) + O2(X (3)Σg(-)), O((3)P2) + O2(a (1)Δg), and O((3)P2) + O2(b (1)Σg(+)) channels are 0.36, 0.31,and 0.34, respectively. Photofragment distributions in the spin-allowed channel O((3)P) + O2(X (3)Σg(-)) are compared with the results of quantum mechanical calculations on the vibronically coupled PESs of the singlet states B (optically bright) and R (repulsive). The experiments suggest that considerably more vibrational excitation and less rotational excitation occur than predicted by the quantum calculations. The rotational distributions, adjusted to fit the experimental images, suggest that the dissociation takes place from a more linear configuration than the Franck-Condon bending angle of 117°. The dissociation at most wavelengths results in a positive value of the anisotropy parameter, β, both in the experiment and in the calculations. Calculations indicate that both nonadiabatic transitions and intersystem crossings substantially reduce β below the nominal value of 2.
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Affiliation(s)
- C K Ulrich
- School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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Houston PL, Cosofret BR, Dixit A, Dylewski SM, Geiser JD, Mueller JA, Wilson RJ, Pisano PJ, Westley MS, Lorenz KT, Chandler DW. Product Imaging Studies of Photodissociation and Bimolecular Reaction Dynamics. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200100048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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