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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] [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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2
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Tachikawa H. Proton Transfer vs Complex Formation Channels in Ionized Formic Acid Dimer: A Direct Ab Initio Molecular Dynamics Study. J Phys Chem A 2020; 124:3048-3054. [PMID: 32250620 DOI: 10.1021/acs.jpca.0c01729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Photoirradiation to a hydrogen-bonded system plays an important role in the initial DNA and enzyme damage processes. The formic acid (FA) dimer is a model compound of double proton transfer systems, such as DNA base pairs. In the present study, the reactions of the FA dimer cation, formed upon ionization of the neutral dimer, have been investigated by the direct ab initio molecular dynamics method. Two reaction channels were identified for the FA dimer cation: complex formation and proton transfer (PT). In the complex formation channel, the carbonyl oxygen atoms of the two FA monomers were bound symmetrically, and a face-to-face complex was formed. In the PT channel, the proton of FA+ was transferred to FA, forming the H+(HCOOH)--HCO2 radical cation as product. At low temperature, the complex channel was dominant, whereas the PT channel increased with increasing temperature. The asymmetric spin distribution on the FA dimer cation exhibited a strong correlation with the PT channel.
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Affiliation(s)
- Hiroto Tachikawa
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
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3
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Liu H, Cao J, Bian W. Double Proton Transfer in the Dimer of Formic Acid: An Efficient Quantum Mechanical Scheme. Front Chem 2019; 7:676. [PMID: 31750286 PMCID: PMC6842929 DOI: 10.3389/fchem.2019.00676] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
Double proton transfer plays an important role in biology and chemistry, such as with DNA base pairs, proteins and molecular clusters, and direct information about these processes can be obtained from tunneling splittings. Carboxylic acid dimers are prototypes for multiple proton transfer, of which the formic acid dimer is the simplest one. Here, we present efficient quantum dynamics calculations of ground-state and fundamental excitation tunneling splittings in the formic acid dimer and its deuterium isotopologues. These are achieved with a multidimensional scheme developed by us, in which the saddle-point normal coordinates are chosen, the basis functions are customized for the proton transfer process, and the preconditioned inexact spectral transform method is used to solve the resultant eigenvalue problem. Our computational results are in excellent agreement with the most recent experiments (Zhang et al., 2017; Li et al., 2019).
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Affiliation(s)
- Hao Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jianwei Cao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Wensheng Bian
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
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4
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Affiliation(s)
- Susy Lopes
- CQC, Department of Chemistry, University of Coimbra Coimbra, Portugal
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra Coimbra, Portugal
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5
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Meyer KAE, Suhm MA. Vibrational exciton coupling in homo and hetero dimers of carboxylic acids studied by linear infrared and Raman jet spectroscopy. J Chem Phys 2018; 149:104307. [DOI: 10.1063/1.5043400] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Katharina A. E. Meyer
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
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6
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Schreiner PR. Tunneling Control of Chemical Reactions: The Third Reactivity Paradigm. J Am Chem Soc 2017; 139:15276-15283. [DOI: 10.1021/jacs.7b06035] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Peter R. Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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7
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Zhang Y, Li W, Luo W, Zhu Y, Duan C. High resolution jet-cooled infrared absorption spectra of (HCOOH)2, (HCOOD)2, and HCOOH—HCOOD complexes in 7.2 μm region. J Chem Phys 2017; 146:244306. [DOI: 10.1063/1.4989863] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Yuluan Zhang
- College of Physical Science and Technology, Central China Normal University, Wuhan 430079, China
| | - Wenguang Li
- College of Physical Science and Technology, Central China Normal University, Wuhan 430079, China
| | - Wei Luo
- College of Physical Science and Technology, Central China Normal University, Wuhan 430079, China
| | - Yu Zhu
- College of Physics and Telecommunicaiton Engineering, Zhoukou Normal University, Zhoukou 466001, China
| | - Chuanxi Duan
- College of Physical Science and Technology, Central China Normal University, Wuhan 430079, China
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8
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Xu J, Finlayson-Pitts BJ, Gerber RB. Proton Transfer in Mixed Clusters of Methanesulfonic Acid, Methylamine, and Oxalic Acid: Implications for Atmospheric Particle Formation. J Phys Chem A 2017; 121:2377-2385. [DOI: 10.1021/acs.jpca.7b01223] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Xu
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | | | - R. Benny Gerber
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
- Institute
of Chemistry, Fritz Haber Research Center, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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9
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Asymmetric hydrogen bonding in formic acid–nitric acid dimer observed by quantum molecular dynamics simulations. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2057-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Mardyukov A, Quanz H, Schreiner PR. Conformer-specific hydrogen atom tunnelling in trifluoromethylhydroxycarbene. Nat Chem 2016; 9:71-76. [DOI: 10.1038/nchem.2609] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/09/2016] [Indexed: 11/09/2022]
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11
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Theoretical study on ground-state proton/H-atom exchange in formic acid clusters through different H-bonded bridges. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1144-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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12
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Mackenzie RB, Dewberry CT, Leopold KR. The Trimethylamine–Formic Acid Complex: Microwave Characterization of a Prototype for Potential Precursors to Atmospheric Aerosol. J Phys Chem A 2016; 120:2268-73. [DOI: 10.1021/acs.jpca.6b01500] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Rebecca B. Mackenzie
- Department of Chemistry, University of Minnesota, 207 Pleasant
Street, SE, Minneapolis, Minnesota 55455, United States
| | - Christopher T. Dewberry
- Department of Chemistry, University of Minnesota, 207 Pleasant
Street, SE, Minneapolis, Minnesota 55455, United States
| | - Kenneth R. Leopold
- Department of Chemistry, University of Minnesota, 207 Pleasant
Street, SE, Minneapolis, Minnesota 55455, United States
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13
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Kleiner I, Hougen JT. A Hybrid Program for Fitting Rotationally Resolved Spectra of Floppy Molecules with One Large-Amplitude Rotatory Motion and One Large-Amplitude Oscillatory Motion. J Phys Chem A 2015; 119:10664-76. [PMID: 26439709 PMCID: PMC4758688 DOI: 10.1021/acs.jpca.5b08437] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new hybrid-model fitting program for methylamine-like molecules has been developed, on the basis of an effective Hamiltonian in which the ammonia-like inversion motion is treated using a tunneling formalism, whereas the internal-rotation motion is treated using an explicit kinetic energy operator and potential energy function. The Hamiltonian in the computer program is set up as a 2 × 2 partitioned matrix, where each diagonal block contains a traditional torsion-rotation Hamiltonian (as in the earlier program BELGI), and the two off-diagonal blocks contain tunneling terms. This hybrid formulation permits the use of the permutation-inversion group G6 (isomorphic to C(3v)) for terms in the two diagonal blocks but requires G12 for terms in the off-diagonal blocks. The first application of the new program is to 2-methylmalonaldehyde. Microwave data for this molecule were previously fit using an all-tunneling Hamiltonian formalism to treat both large-amplitude motions. For 2-methylmalonaldehyde, the hybrid program achieves the same quality of fit as was obtained with the all-tunneling program, but fits with the hybrid program eliminate a large discrepancy between internal rotation barriers in the OH and OD isotopologs of 2-methylmalonaldehyde that arose in fits with the all-tunneling program. This large isotopic shift in internal rotation barrier is thus almost certainly an artifact of the all-tunneling model. Other molecules for application of the hybrid program are mentioned.
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Affiliation(s)
- Isabelle Kleiner
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR 7583 CNRS/IPSL, Universités Paris Est & Paris Diderot , 61 avenue du Général de Gaulle, F-94010 Créteil cedex, France
| | - Jon T Hougen
- Sensor Science Division, NIST , Gaithersburg, Maryland 20899-8441, United States
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14
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Pejlovas AM, Lin W, Kukolich SG. Microwave spectra and structure of the cyclopropanecarboxylic acid-formic acid dimer. J Chem Phys 2015; 143:124311. [DOI: 10.1063/1.4931923] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Aaron M. Pejlovas
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Wei Lin
- Department of Chemistry, University of Texas Rio Grande Valley, Brownsville, Texas 78520, USA
| | - Stephen G. Kukolich
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
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15
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Mackenzie RB, Dewberry CT, Coulston E, Cole GC, Legon AC, Tew DP, Leopold KR. Intramolecular competition between n-pair and π-pair hydrogen bonding: Microwave spectrum and internal dynamics of the pyridine–acetylene hydrogen-bonded complex. J Chem Phys 2015; 143:104309. [DOI: 10.1063/1.4929997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Rebecca B. Mackenzie
- Department of Chemistry, University of Minnesota, 207 Pleasant St., SE, Minneapolis, Minnesota 55455, USA
| | - Christopher T. Dewberry
- Department of Chemistry, University of Minnesota, 207 Pleasant St., SE, Minneapolis, Minnesota 55455, USA
| | - Emma Coulston
- Department of Chemistry, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - George C. Cole
- Department of Chemistry, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Anthony C. Legon
- Department of Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - David P. Tew
- Department of Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Kenneth R. Leopold
- Department of Chemistry, University of Minnesota, 207 Pleasant St., SE, Minneapolis, Minnesota 55455, USA
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16
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Vigorito A, Gou Q, Calabrese C, Melandri S, Maris A, Caminati W. How CO2Interacts with Carboxylic Acids: A Rotational Study of Formic Acid-CO2. Chemphyschem 2015; 16:2961-7. [DOI: 10.1002/cphc.201500531] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 12/24/2022]
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17
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Schreiner PR, Wagner JP, Reisenauer HP, Gerbig D, Ley D, Sarka J, Császár AG, Vaughn A, Allen WD. Domino Tunneling. J Am Chem Soc 2015; 137:7828-34. [DOI: 10.1021/jacs.5b03322] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter R. Schreiner
- Institute
of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - J. Philipp Wagner
- Institute
of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Hans Peter Reisenauer
- Institute
of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Dennis Gerbig
- Institute
of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - David Ley
- Institute
of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - János Sarka
- Laboratory
of Molecular Structure and Dynamics, Institute of Chemistry, Eötvös University, PO Box 32, Budapest 112, Hungary, H-1518
- MTA-ELTE
Complex Chemical Systems Research Group, Eötvös University, Budapest, Pázmány Péter
Sétány 1/A, Hungary, H-1117
| | - Attila G. Császár
- Laboratory
of Molecular Structure and Dynamics, Institute of Chemistry, Eötvös University, PO Box 32, Budapest 112, Hungary, H-1518
- MTA-ELTE
Complex Chemical Systems Research Group, Eötvös University, Budapest, Pázmány Péter
Sétány 1/A, Hungary, H-1117
| | - Alexander Vaughn
- Center
for Computational Quantum Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Wesley D. Allen
- Center
for Computational Quantum Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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