1
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Fang W, Zhu YC, Cheng Y, Hao YP, Richardson JO. Robust Gaussian Process Regression Method for Efficient Tunneling Pathway Optimization: Application to Surface Processes. J Chem Theory Comput 2024; 20:3766-3778. [PMID: 38708859 PMCID: PMC11099967 DOI: 10.1021/acs.jctc.4c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024]
Abstract
Simulation of surface processes is a key part of computational chemistry that offers atomic-scale insights into mechanisms of heterogeneous catalysis, diffusion dynamics, and quantum tunneling phenomena. The most common theoretical approaches involve optimization of reaction pathways, including semiclassical tunneling pathways (called instantons). The computational effort can be demanding, especially for instanton optimizations with an ab initio electronic structure. Recently, machine learning has been applied to accelerate reaction-pathway optimization, showing great potential for a wide range of applications. However, previous methods still suffer from numerical and efficiency issues and were not designed for condensed-phase reactions. We propose an improved framework based on Gaussian process regression for general transformed coordinates, which has improved efficiency and numerical stability, and we propose a descriptor that combines internal and Cartesian coordinates suitable for modeling surface processes. We demonstrate with 11 instanton optimizations in three representative systems that the improved approach makes ab initio instanton optimization significantly cheaper, such that it becomes not much more expensive than a classical transition-state theory rate calculation.
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Affiliation(s)
- Wei Fang
- Department
of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative
Materials, Fudan University, Shanghai 200438, P. R. China
- Laboratory
of Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
- State
Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical
Computational Chemistry, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yu-Cheng Zhu
- State
Key Laboratory for Artificial Microstructure and Mesoscopic Physics,
Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, China
| | - Yihan Cheng
- State
Key Laboratory for Artificial Microstructure and Mesoscopic Physics,
Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, China
| | - Yi-Ping Hao
- State
Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical
Computational Chemistry, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Jeremy O. Richardson
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Zürich 8093, Switzerland
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2
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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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3
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Nejad A, Li X, Zhu T, Liu Y, Duan C. Mid-infrared Laser Spectroscopy of Jet-Cooled Formic Acid Trimer: Mode-Dependent Line Broadening in the C-O Stretching Region. J Phys Chem Lett 2023; 14:7795-7801. [PMID: 37616473 PMCID: PMC10786437 DOI: 10.1021/acs.jpclett.3c01860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Building on recent progress in the vibrational spectroscopy of the formic acid trimer, we present the first high-resolution measurements of the jet-cooled laser absorption spectrum of (HCOOH)3. The spectra of the lowest- and highest-frequency C-O stretching fundamentals are analyzed whereas the third band is not observed, complicated by monomer and dimer absorptions at 1219 cm-1 (8.2 μm). Vibration-rotation parameters are obtained for the band at 1172.31512(68) cm-1 whereas the C-O stretch at 1246.33(5) cm-1 exhibits a significantly larger breadth, allowing only resolution of the coarse PQR structure. Vibrational predissociation can be ruled out, and intramolecular vibrational redistribution mechanisms are discussed, particularly coupling to the concerted proton exchange within the cyclic dimer subunit. Ultimately, the question remains open. The prospects of high-resolution measurements of other trimer bands or isotope substitution experiments, which might assist in revealing the mode-specificity of the underlying broadening mechanisms, are discussed.
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Affiliation(s)
- Arman Nejad
- Institute
of Physical Chemistry, Georg-August University
of Göttingen, Tammannstraße 6, Göttingen 37077, Germany
| | - Xiang Li
- College
of Physical Science and Technology, Central
China Normal University, Wuhan 430079, China
| | - Tianxin Zhu
- College
of Physical Science and Technology, Central
China Normal University, Wuhan 430079, China
| | - Yun Liu
- College
of Physical Science and Technology, Central
China Normal University, Wuhan 430079, China
| | - Chuanxi Duan
- College
of Physical Science and Technology, Central
China Normal University, Wuhan 430079, China
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4
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Trenins G, Meuser L, Bertschi H, Vavourakis O, Flütsch R, Richardson JO. Exact tunneling splittings from symmetrized path integrals. J Chem Phys 2023; 159:034108. [PMID: 37466233 DOI: 10.1063/5.0158879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
We develop a new simulation technique based on path-integral molecular dynamics for calculating ground-state tunneling splitting patterns from ratios of symmetrized partition functions. In particular, molecular systems are rigorously projected onto their J = 0 rotational state by an "Eckart spring" that connects two adjacent beads in a ring polymer. Using this procedure, the tunneling splitting can be obtained from thermodynamic integration at just one (sufficiently low) temperature. Converged results are formally identical to the values that would have been obtained by solving the full rovibrational Schrödinger equation on a given Born-Oppenheimer potential energy surface. The new approach is showcased with simulations of hydronium and methanol, which are in good agreement with wavefunction-based calculations and experimental measurements. The method will be of particular use for the study of low-barrier methyl rotations and other floppy modes, where instanton theory is not valid.
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Affiliation(s)
- George Trenins
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Lars Meuser
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Hannah Bertschi
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Odysseas Vavourakis
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Reto Flütsch
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jeremy O Richardson
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
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5
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Videla PE, Foguel L, Vaccaro PH, Batista VS. Proton-Tunneling Dynamics along Low-Barrier Hydrogen Bonds: A Full-Dimensional Instanton Study of 6-Hydroxy-2-formylfulvene. J Phys Chem Lett 2023:6368-6375. [PMID: 37418693 DOI: 10.1021/acs.jpclett.3c01337] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Understanding the dynamics of proton transfer along low-barrier hydrogen bonds remains an outstanding challenge of great fundamental and practical interest, reflecting the central role of quantum effects in reactions of chemical and biological importance. Here, we combine ab initio calculations with the semiclassical ring-polymer instanton method to investigate tunneling processes on the ground electronic state of 6-hydroxy-2-formylfulvene (HFF), a prototypical neutral molecule supporting low-barrier hydrogen-bonding. The results emerging from a full-dimensional ab initio instanton analysis reveal that the tunneling path does not pass through the instantaneous transition-state geometry. Instead, the tunneling process involves a multidimensional reaction coordinate with concerted reorganization of the heavy-atom skeletal framework to substantially reduce the donor-acceptor distance and drive the ensuing intramolecular proton-transfer event. The predicted tunneling-induced splittings for HFF isotopologues are in good agreement with experimental findings, leading to percentage deviations of only 20-40%. Our full-dimensional results allow us to characterize vibrational contributions along the tunneling path, highlighting the intrinsically multidimensional nature of the attendant hydron-migration dynamics.
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Affiliation(s)
- Pablo E Videla
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Lidor Foguel
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Patrick H Vaccaro
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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6
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Dickinson JA, Yu Q, Hammes-Schiffer S. Generalized Nuclear-Electronic Orbital Multistate Density Functional Theory for Multiple Proton Transfer Processes. J Phys Chem Lett 2023:6170-6178. [PMID: 37379485 DOI: 10.1021/acs.jpclett.3c01422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Proton transfer and hydrogen tunneling play pivotal roles in many chemical and biological processes. The nuclear-electronic orbital multistate density functional theory (NEO-MSDFT) approach was developed to describe hydrogen tunneling systems within the multicomponent NEO framework, where the transferring proton is quantized and treated with molecular orbital techniques on the same level as the electrons. Herein, the NEO-MSDFT framework is generalized to an arbitrary number of quantum protons to allow applications to systems involving the transfer and tunneling of multiple protons. The generalized NEO-MSDFT approach is shown to produce delocalized, bilobal proton densities and accurate tunneling splittings for fixed geometries of the formic acid dimer and asymmetric substituted variants, as well as the porphycene molecule. Investigation of a protonated water chain highlights the applicability of this approach to proton relay systems. This work provides the foundation for nuclear-electronic quantum dynamics simulations of a wide range of multiple proton transfer processes.
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Affiliation(s)
- Joseph A Dickinson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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7
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Li F, Yang X, Liu X, Cao J, Bian W. An Ab Initio Neural Network Potential Energy Surface for the Dimer of Formic Acid and Further Quantum Tunneling Dynamics. ACS OMEGA 2023; 8:17296-17303. [PMID: 37214673 PMCID: PMC10193396 DOI: 10.1021/acsomega.3c02169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
We construct a full-dimensional ab initio neural network potential energy surface (PES) for the isomerization system of the formic acid dimer (FAD). This is based upon ab initio calculations using the DLPNO-CCSD(T) approach with the aug-cc-pVTZ basis set, performed at over 14000 symmetry-unique geometries. An accurate fit to the obtained energies is generated using a general neural network fitting procedure combined with the fundamental invariant method, and the overall energy-weighted root-mean-square fitting error is about 6.4 cm-1. Using this PES, we present a multidimensional quantum dynamics study on tunneling splittings with an efficient theoretical scheme developed by our group. The ground-state tunneling splitting of FAD calculated with a four-mode coupled method is in good agreement with the most recent experimental measurements. The PES can be applied for further dynamics studies. The effectiveness of the present scheme for constructing a high-dimensional PES is demonstrated, and this scheme is expected to be feasible for larger molecular systems.
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Affiliation(s)
- Fengyi Li
- Beijing
National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100049, People’s
Republic of China
| | - Xingyu Yang
- Beijing
National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100049, People’s
Republic of China
| | - Xiaoxi Liu
- Beijing
National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100049, People’s
Republic of China
| | - Jianwei Cao
- Beijing
National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Wensheng Bian
- Beijing
National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100049, People’s
Republic of China
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8
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Käser S, Richardson JO, Meuwly M. Transfer Learning for Affordable and High-Quality Tunneling Splittings from Instanton Calculations. J Chem Theory Comput 2022; 18:6840-6850. [DOI: 10.1021/acs.jctc.2c00790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | | | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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9
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Töpfer K, Käser S, Meuwly M. Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity. Phys Chem Chem Phys 2022; 24:13869-13882. [PMID: 35620978 PMCID: PMC9176184 DOI: 10.1039/d2cp01583h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The double proton transfer (DPT) reaction in the hydrated formic acid dimer (FAD) is investigated at molecular-level detail. For this, a global and reactive machine learned (ML) potential energy surface (PES) is developed to run extensive (more than 100 ns) mixed ML/MM molecular dynamics (MD) simulations in explicit molecular mechanics (MM) solvent at MP2-quality for the solute. Simulations with fixed – as in a conventional empirical force field – and conformationally fluctuating – as available from the ML-based PES – charge models for FAD show a significant impact on the competition between DPT and dissociation of FAD into two formic acid monomers. With increasing temperature the barrier height for DPT in solution changes by about 10% (∼1 kcal mol−1) between 300 K and 600 K. The rate for DPT is largest, ∼1 ns−1, at 350 K and decreases for higher temperatures due to destabilisation and increased probability for dissociation of FAD. The water solvent is found to promote the first proton transfer by exerting a favourable solvent-induced Coulomb force along the O–H⋯O hydrogen bond whereas the second proton transfer is significantly controlled by the O–O separation and other conformational degrees of freedom. Double proton transfer in hydrated FAD is found to involve a subtle interplay and balance between structural and electrostatic factors. Simulation of double proton transfer in formic acid dimer by reactive ML potential in explicit molecular mechanics water solvent.![]()
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Affiliation(s)
- Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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10
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Ansari IM, Heller ER, Trenins G, Richardson JO. Instanton theory for Fermi's golden rule and beyond. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200378. [PMID: 35341312 PMCID: PMC8958279 DOI: 10.1098/rsta.2020.0378] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/22/2021] [Indexed: 05/29/2023]
Abstract
Instanton theory provides a semiclassical approximation for computing quantum tunnelling effects in complex molecular systems. It is typically applied to proton-transfer reactions for which the Born-Oppenheimer approximation is valid. However, many processes in physics, chemistry and biology, such as electron transfers, are non-adiabatic and are correctly described instead using Fermi's golden rule. In this work, we discuss how instanton theory can be generalized to treat these reactions in the golden-rule limit. We then extend the theory to treat fourth-order processes such as bridge-mediated electron transfer and apply the method to simulate an electron moving through a model system of three coupled quantum dots. By comparison with benchmark quantum calculations, we demonstrate that the instanton results are much more reliable than alternative approximations based on superexchange-mediated effective coupling or a classical sequential mechanism. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.
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Affiliation(s)
| | - Eric R. Heller
- Laboratory of Physical Chemistry, ETH, Zürich, Switzerland
| | - George Trenins
- Laboratory of Physical Chemistry, ETH, Zürich, Switzerland
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11
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Nejad A, Meyer KAE, Kollipost F, Xue Z, Suhm MA. Slow monomer vibrations in formic acid dimer: Stepping up the ladder with FTIR and Raman jet spectroscopy. J Chem Phys 2021; 155:224301. [PMID: 34911308 DOI: 10.1063/5.0075272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In an effort to extend the cold gas phase spectroscopic database of the cyclic formic acid dimer (FAD), we present and analyze the jet-cooled vibrational infrared and Raman spectrum of (HCOOH)2 in the monomer fingerprint region between 600 and 1500 cm-1. The present study bridges the gap between the intermolecular dimerization-induced and the carbonyl stretching fundamentals that have already been reexamined using jet-cooled or high-resolution spectroscopy. This completes the characterization of the jet-cooled vibrational (HCOOH)2 spectrum below the complex OH (CH) stretching fundamentals, and we report resonance-induced FAD combination/overtone transitions that will serve as a valuable reference for a theoretical modeling of its vibrational dynamics. As a by-product, several new formic acid trimer fundamentals are identified in the jet spectra and assigned with the help of second-order vibrational perturbation theory (VPT2). The polar formic acid dimer still eludes detection in a supersonic jet, but we are able to estimate an experimental upper-bound of the polar dimer-to-trimer-to-cyclic dimer intensity ratio to about 1:10:100 under typical expansion conditions. Using VPT2 with resonance treatment (VPT2+K), we reinvestigate the notorious ν22 resonance triad. Generally, we find that VPT2, which is, of course, inadequate for modeling the resonance-rich OH stretching spectrum of FAD, is performing very satisfactorily in predicting fundamental and two-quantum state term values for the slower modes below 1500 cm-1. As these modes are the building blocks for the ultrafast energy dissipation in the OH stretching region, the present work opens the door for its quantitative understanding.
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Affiliation(s)
- Arman Nejad
- Institute of Physical Chemistry, Georg August University of Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Katharina A E Meyer
- Institute of Physical Chemistry, Georg August University of Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Franz Kollipost
- Institute of Physical Chemistry, Georg August University of Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Zhifeng Xue
- Institute of Physical Chemistry, Georg August University of Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Martin A Suhm
- Institute of Physical Chemistry, Georg August University of Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
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12
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Käser S, Meuwly M. Transfer learned potential energy surfaces: accurate anharmonic vibrational dynamics and dissociation energies for the formic acid monomer and dimer. Phys Chem Chem Phys 2021; 24:5269-5281. [PMID: 34792523 PMCID: PMC8890265 DOI: 10.1039/d1cp04393e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational dynamics of the formic acid monomer (FAM) and dimer (FAD) is investigated from machine-learned potential energy surfaces at the MP2 (PESMP2) and transfer-learned (PESTL) to the CCSD(T) levels of theory. The normal mode (MAEs of 17.6 and 25.1 cm−1) and second order vibrational perturbation theory (VPT2, MAEs of 6.7 and 17.1 cm−1) frequencies from PESTL for all modes below 2000 cm−1 for FAM and FAD agree favourably with experiment. For the OH stretch mode the experimental frequencies are overestimated by more than 150 cm−1 for both FAM and FAD from normal mode calculations. Conversely, VPT2 calculations on PESTL for FAM reproduce the experimental OH frequency to within 22 cm−1. For FAD the VPT2 calculations find the high-frequency OH stretch at 3011 cm−1, compared with an experimentally reported, broad (∼100 cm−1) absorption band with center frequency estimated at ∼3050 cm−1. In agreement with earlier reports, MD simulations at higher temperature shift the position of the OH-stretch in FAM to the red, consistent with improved sampling of the anharmonic regions of the PES. However, for FAD the OH-stretch shifts to the blue and for temperatures higher than 1000 K the dimer partly or fully dissociates using PESTL. Including zero-point energy corrections from diffusion Monte Carlo simulations for FAM and FAD and corrections due to basis set superposition and completeness errors yields a dissociation energy of D0 = −14.23 ± 0.08 kcal mol−1 compared with an experimentally determined value of −14.22 ± 0.12 kcal mol−1. Neural network based PESs are constructed for formic acid monomer and dimer at the MP2 and transfer learned to the CCSD(T) level of theory. The PESs are used to study the vibrational dynamics and dissociation energy of the molecules.![]()
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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13
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Tikhonov DS. A simplistic computational procedure for tunneling splittings caused by proton transfer. Struct Chem 2021. [DOI: 10.1007/s11224-021-01845-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractIn this manuscript, we present an approach for computing tunneling splittings for large amplitude motions. The core of the approach is a solution of an effective one-dimensional Schrödinger equation with an effective mass and an effective potential energy surface composed of electronic and harmonic zero-point vibrational energies of small amplitude motions in the molecule. The method has been shown to work in cases of three model motions: nitrogen inversion in ammonia, single proton transfer in malonaldehyde, and double proton transfer in the formic acid dimer. In the current work, we also investigate the performance of different DFT and post-Hartree–Fock methods for prediction of the proton transfer tunneling splittings, quality of the effective Schrödinger equation parameters upon the isotopic substitution, and possibility of a complete basis set (CBS) extrapolation for the resulting tunneling splittings.
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14
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Sahu N, Richardson JO, Berger R. Instanton calculations of tunneling splittings in chiral molecules. J Comput Chem 2021; 42:210-221. [PMID: 33259074 DOI: 10.1002/jcc.26447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 11/11/2022]
Abstract
We report the ground state tunneling splittings (ΔE± ) of a number of axially chiral molecules using the ring-polymer instanton (RPI) method (J. Chem. Phys., 2011, 134, 054109). The list includes isotopomers of hydrogen dichalcogenides H2 X2 (X = O, S, Se, Te, and Po), hydrogen thioperoxide HSOH and dichlorodisulfane S2 Cl2 . Ab initio electronic-structure calculations have been performed on the level of second-order Møller-Plesset perturbation (MP2) theory either with split-valance basis sets or augmented correlation-consistent basis sets on H, O, S, and Cl atoms. Energy-consistent pseudopotential and corresponding triple zeta basis sets of the Stuttgart group are used on Se, Te, and Po atoms. The results are further improved using single point calculations performed at the coupled cluster level with iterative singles and doubles and perturbative triples amplitudes. When available for comparison, our computed values of ΔE± are found to lie within the same order of magnitude as values reported in the literature, although RPI also provides predictions for H2 Po2 and S2 Cl2 , which have not previously been directly calculated. Since RPI is a single-shot method which does not require detailed prior knowledge of the optimal tunneling path, it offers an effective way for estimating the tunneling dynamics of more complex chiral molecules, and especially those with small tunneling splittings.
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Affiliation(s)
- Nityananda Sahu
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
| | | | - Robert Berger
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
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15
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Litman Y, Rossi M. Multidimensional Hydrogen Tunneling in Supported Molecular Switches: The Role of Surface Interactions. PHYSICAL REVIEW LETTERS 2020; 125:216001. [PMID: 33275002 DOI: 10.1103/physrevlett.125.216001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/08/2020] [Indexed: 06/12/2023]
Abstract
The nuclear tunneling crossover temperature (T_{c}) of hydrogen transfer reactions in supported molecular-switch architectures can lie close to room temperature. This calls for the inclusion of nuclear quantum effects (NQEs) in the calculation of reaction rates even at high temperatures. However, computations of NQEs relying on standard parametrized dimensionality-reduced models quickly become inadequate in these environments. In this Letter, we study the paradigmatic molecular switch based on porphycene molecules adsorbed on metallic surfaces with full-dimensional calculations that combine density-functional theory for the electrons with the semiclassical ring-polymer instanton approximation for the nuclei. We show that the double intramolecular hydrogen transfer (DHT) rate can be enhanced by orders of magnitude due to surface fluctuations in the deep-tunneling regime. We also explain the origin of an Arrhenius temperature dependence of the rate below T_{c} and why this dependence differs at different surfaces. We propose a simple model to rationalize the temperature dependence of DHT rates spanning diverse fcc [110] surfaces.
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Affiliation(s)
- Yair Litman
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany and Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Mariana Rossi
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany and MPI for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
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Liu H, Cao J, Bian W. Efficient Quantum Mechanical Calculations of Mode-Specific Tunneling Splittings upon Fundamental Excitation in the Dimer of Formic Acid. J Phys Chem A 2020; 124:6536-6543. [PMID: 32662997 DOI: 10.1021/acs.jpca.0c05471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formic acid dimer (FAD) is an important benchmark system for understanding the double hydrogen transfer process. Most recently, Zhang et al. measured a few tunneling splittings upon fundamental excitation of FAD precisely (Zhang, Y. et al. J. Chem. Phys. 2017, 146, 244306); however, relevant theoretical studies are very limited. Here, we present a multidimensional quantum dynamics study on mode-specific tunneling splittings upon fundamental excitation in FAD with an efficient theoretical scheme developed by our group in which the process-oriented basis function customization strategy is combined with the preconditioned inexact spectral transform method. Various mode-specific tunneling splittings upon fundamental excitation are systematically calculated, and interesting mode-specific excitation effects on tunneling rate are identified. In particular, the calculated tunneling splittings for the ν22 and ν21 states are in good agreement with experiment, and the remarkable mode-specific suppression effects upon excitation should result from that the antisymmetric vibrational modes hinder the concerted double H-transfer. The present work is helpful to acquire a better understanding of the mode-specific excitation effects on tunneling processes.
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Affiliation(s)
- Hao Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190 Beijing, China.,School of Chemical Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jianwei Cao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190 Beijing, China
| | - Wensheng Bian
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 100190 Beijing, China.,School of Chemical Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
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Laude G, Calderini D, Welsch R, Richardson JO. Calculations of quantum tunnelling rates for muonium reactions with methane, ethane and propane. Phys Chem Chem Phys 2020; 22:16843-16854. [PMID: 32666960 DOI: 10.1039/d0cp01346c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermal rate constants for Mu + CH4, Mu + C2H6 and Mu + C3H8 and their equivalent reactions with H were evaluated with ab initio instanton rate theory. The potential-energy surfaces are fitted using Gaussian process regression to high-level electronic-structure calculations evaluated around the tunnelling pathway. This method was able to successfully reproduce various experimental measurements for the rate constant of these reactions. However, it was not able to reproduce the faster-than-expected rate of Mu + C3H8 at 300 K reported by Fleming et al. [Phys. Chem. Chem. Phys., 2015, 17, 19901 and Phys. Chem. Chem. Phys., 2020, 22, 6326]. Analysis of our results indicates that the kinetic isotope effect at this temperature is not significantly influenced by quantum tunnelling. We consider many possible factors for the discrepancy between theory and experiment but conclude that in each case, the instanton approximation is unlikely to be the cause of the error. This is in part based on the good agreement we find between the instanton predictions and new multiconfigurational time-dependent Hartree (MCTDH) calculations for Mu + CH4 using the same potential-energy surface. Further experiments will therefore be needed to resolve this issue.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zürich, Switzerland.
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18
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Houston P, Conte R, Qu C, Bowman JM. Permutationally invariant polynomial potential energy surfaces for tropolone and H and D atom tunneling dynamics. J Chem Phys 2020; 153:024107. [DOI: 10.1063/5.0011973] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Paul 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
| | - Chen Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, 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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19
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Burd TAH, Clary DC. Analytic Route to Tunneling Splittings Using Semiclassical Perturbation Theory. J Chem Theory Comput 2020; 16:3486-3493. [DOI: 10.1021/acs.jctc.0c00207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy A. H. Burd
- Physical and Theoretical Chemical Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemical Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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20
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Cvitaš MT, Richardson JO. Quantum tunnelling pathways of the water pentamer. Phys Chem Chem Phys 2020; 22:1035-1044. [DOI: 10.1039/c9cp05561d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Five tunnelling rearrangement pathways in water pentamer are responsible for the ground-state tunnelling splitting pattern of 320 states.
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Affiliation(s)
- Marko T. Cvitaš
- Department of Physical Chemistry
- Ruđer Bošković Institute
- Croatia
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21
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Abstract
AbstractFormic acid dimer as the prototypical doubly hydrogen-bonded gas-phase species is discussed from the perspective of the three translational and the three rotational degrees of freedom which are lost when two formic acid molecules form a stable complex. The experimental characterisation of these strongly hindered translations and rotations is reviewed, as are attempts to describe the associated fundamental vibrations, their combinations, and their thermal shifts by different electronic structure calculations and vibrational models. A remarkable match is confirmed for the combination of a CCSD(T)-level harmonic treatment and an MP2-level anharmonic VPT2 correction. Qualitatively correct thermal shifts of the vibrational spectra can be obtained from classical molecular dynamics in CCSD(T)-quality force fields. A detailed analysis suggests that this agreement between experiment and composite theoretical treatment is not strongly affected by fortuitous error cancellation but fully converged variational treatments of the six pair or intermolecular modes and their overtones and combinations in this model system would be welcome.
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22
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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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Abstract
Abstract
Anthracene can be used as a scaffold for intramolecular SN2 degenerate reactions of the “bell clapper” type, where a central boron atom or its isoelectronic carbocation bonds alternatively towards one or the other lateral Lewis bases at the first and eight anthracene positions. This ping-pong bond-switching reaction possesses a symmetrical double-well potential with low activation barrier and relatively narrow barrier width. Herein we show by computational means the active role played by heavy atom quantum tunneling in this degenerate rearrangement reaction at cryogenic temperatures. At these conditions the thermal “over the barrier” reaction is forbidden, whereas the tunneling effect enhances the rate of reaction up to an experimentally measurable half-life. Kinetic isotope effects and cryogenic NMR spectroscopy can, in principle, experimentally demonstrate the tunneling mechanism.
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Winter P, Richardson JO. Divide-and-Conquer Method for Instanton Rate Theory. J Chem Theory Comput 2019; 15:2816-2825. [DOI: 10.1021/acs.jctc.8b01267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pierre Winter
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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25
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Thapa MJ, Fang W, Richardson JO. Nonadiabatic quantum transition-state theory in the golden-rule limit. I. Theory and application to model systems. J Chem Phys 2019; 150:104107. [DOI: 10.1063/1.5081108] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Manish J. Thapa
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Wei Fang
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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Meisner J, Hallmen PP, Kästner J, Rauhut G. Vibrational analysis of methyl cation—Rare gas atom complexes: CH3+—Rg (Rg = He, Ne, Ar, Kr). J Chem Phys 2019; 150:084306. [DOI: 10.1063/1.5084100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jan Meisner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Philipp P. Hallmen
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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Li W, Evangelisti L, Gou Q, Caminati W, Meyer R. The Barrier to Proton Transfer in the Dimer of Formic Acid: A Pure Rotational Study. Angew Chem Int Ed Engl 2019; 58:859-865. [DOI: 10.1002/anie.201812754] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Weixing Li
- Dipartimento di Chimica “G. Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “G. Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Qian Gou
- School of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Rolf Meyer
- Sonnenbergstrasse 18 5621 Zufikon Switzerland
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28
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Qu C, Bowman JM. Quantum approaches to vibrational dynamics and spectroscopy: is ease of interpretation sacrificed as rigor increases? Phys Chem Chem Phys 2019; 21:3397-3413. [DOI: 10.1039/c8cp04990d] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The subject of this Perspective is quantum approaches, beyond the harmonic approximation, to vibrational dynamics and IR spectroscopy.
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Affiliation(s)
- Chen Qu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University
- Atlanta
- USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University
- Atlanta
- USA
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29
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Li W, Evangelisti L, Gou Q, Caminati W, Meyer R. Barrier to Proton Transfer in the Dimer of Formic Acid: A Pure Rotational Study. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Weixing Li
- Dipartimento di Chimica “G. Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “G. Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Qian Gou
- School of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Rolf Meyer
- Sonnenbergstrasse 18 5621 Zufikon Switzerland
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30
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Qu C, Bowman JM. High-dimensional fitting of sparse datasets of CCSD(T) electronic energies and MP2 dipole moments, illustrated for the formic acid dimer and its complex IR spectrum. J Chem Phys 2018; 148:241713. [DOI: 10.1063/1.5017495] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chen Qu
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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33
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Qu C, Bowman JM. IR Spectra of (HCOOH) 2 and (DCOOH) 2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces. J Phys Chem Lett 2018; 9:2604-2610. [PMID: 29709189 DOI: 10.1021/acs.jpclett.8b00447] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH)2 and (DCOOH)2, using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm-1. Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm-1. In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.
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Affiliation(s)
- Chen Qu
- 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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34
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Affiliation(s)
- 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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35
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Mattiat J, Richardson JO. Effects of tunnelling and asymmetry for system-bath models of electron transfer. J Chem Phys 2018; 148:102311. [PMID: 29544261 DOI: 10.1063/1.5001116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We apply the newly derived nonadiabatic golden-rule instanton theory to asymmetric models describing electron-transfer in solution. The models go beyond the usual spin-boson description and have anharmonic free-energy surfaces with different values for the reactant and product reorganization energies. The instanton method gives an excellent description of the behaviour of the rate constant with respect to asymmetry for the whole range studied. We derive a general formula for an asymmetric version of the Marcus theory based on the classical limit of the instanton and find that this gives significant corrections to the standard Marcus theory. A scheme is given to compute this rate based only on equilibrium simulations. We also compare the rate constants obtained by the instanton method with its classical limit to study the effect of tunnelling and other quantum nuclear effects. These quantum effects can increase the rate constant by orders of magnitude.
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Affiliation(s)
- Johann Mattiat
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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36
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Oswald S, Meyer E, Suhm MA. Dinitrogen as a Sensor for Metastable Carboxylic Acid Dimers and a Weak Hydrogen Bond Benchmarking Tool. J Phys Chem A 2018. [DOI: 10.1021/acs.jpca.8b00334] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sönke Oswald
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Enno Meyer
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
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37
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Qu C, Bowman J. Quantum and classical IR spectra of (HCOOH)2, (DCOOH)2 and (DCOOD)2 using ab initio potential energy and dipole moment surfaces. Faraday Discuss 2018; 212:33-49. [DOI: 10.1039/c8fd00077h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Full-dimensional (24 modes) quantum calculation of the IR spectrum of (DCOOD)2, and comparison with classical MD one.
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Affiliation(s)
- Chen Qu
- Department of Chemistry
- Cherry L. Emerson Center for Scientific Computations
- Emory University
- Atlanta
- USA
| | - Joel M. Bowman
- Department of Chemistry
- Cherry L. Emerson Center for Scientific Computations
- Emory University
- Atlanta
- USA
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38
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Laude G, Calderini D, Tew DP, Richardson JO. Ab initio instanton rate theory made efficient using Gaussian process regression. Faraday Discuss 2018; 212:237-258. [PMID: 30230495 DOI: 10.1039/c8fd00085a] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio instanton rate theory is a computational method for rigorously including tunnelling effects into the calculations of chemical reaction rates based on a potential-energy surface computed on the fly from electronic-structure theory. This approach is necessary to extend conventional transition-state theory into the deep-tunnelling regime, but it is also more computationally expensive as it requires many more ab initio calculations. We propose an approach which uses Gaussian process regression to fit the potential-energy surface locally around the dominant tunnelling pathway. The method can be converged to give the same result as from an on-the-fly ab initio instanton calculation but it requires far fewer electronic-structure calculations. This makes it a practical approach for obtaining accurate rate constants based on high-level electronic-structure methods. We show fast convergence to reproduce benchmark H + CH4 results and evaluate new low-temperature rates of H + C2H6 in full dimensionality at a UCCSD(T)-F12b/cc-pVTZ-F12 level.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland. and On exchange from School of Chemistry, University of Edinburgh, UK
| | | | - David P Tew
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
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39
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Karandashev K, Xu ZH, Meuwly M, Vaníček J, Richardson JO. Kinetic isotope effects and how to describe them. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061501. [PMID: 29282447 PMCID: PMC5729036 DOI: 10.1063/1.4996339] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 08/23/2017] [Indexed: 06/01/2023]
Abstract
We review several methods for computing kinetic isotope effects in chemical reactions including semiclassical and quantum instanton theory. These methods describe both the quantization of vibrational modes as well as tunneling and are applied to the ⋅H + H2 and ⋅H + CH4 reactions. The absolute rate constants computed with the semiclassical instanton method both using on-the-fly electronic structure calculations and fitted potential-energy surfaces are also compared directly with exact quantum dynamics results. The error inherent in the instanton approximation is found to be relatively small and similar in magnitude to that introduced by using fitted surfaces. The kinetic isotope effect computed by the quantum instanton is even more accurate, and although it is computationally more expensive, the efficiency can be improved by path-integral acceleration techniques. We also test a simple approach for designing potential-energy surfaces for the example of proton transfer in malonaldehyde. The tunneling splittings are computed, and although they are found to deviate from experimental results, the ratio of the splitting to that of an isotopically substituted form is in much better agreement. We discuss the strengths and limitations of the potential-energy surface and based on our findings suggest ways in which it can be improved.
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Affiliation(s)
- Konstantin Karandashev
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jeremy O Richardson
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich (ETHZ), CH-8093 Zürich, Switzerland
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40
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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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41
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Wu F, Ren Y. Primary and secondary isotope effect on tunnelling in malonaldehyde using a quantum mechanical scheme. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1317371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Feng Wu
- Department of Physics, Yancheng Institute of Technology, Yancheng, China
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Yinghui Ren
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
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Brovarets' OO, Voiteshenko IS, Pérez-Sánchez H, Hovorun DM. A QM/QTAIM research under the magnifying glass of the DPT tautomerisation of the wobble mispairs involving 2-aminopurine. NEW J CHEM 2017. [DOI: 10.1039/c7nj00717e] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, a comprehensive survey of the changes of the physico-chemical parameters at each point of the IRC for the biologically important T·2AP*(w) ↔ T*·2AP(w) and G·2AP*(w) ↔ G*·2AP(w) DPT tautomerisation reactions involved in the point mutations (transitions and transversions) induced by 2-aminopurine (2AP) in DNA is provided.
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Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
| | - Ivan S. Voiteshenko
- Department of Molecular Biotechnology and Bioinformatics
- Institute of High Technologies
- Taras Shevchenko National University of Kyiv
- 03022 Kyiv
- Ukraine
| | - Horacio Pérez-Sánchez
- Computer Science Department
- Bioinformatics and High Performance Computing (BIO-HPC) Research Group
- Universidad Católica San Antonio de Murcia (UCAM)
- 30107 Guadalupe (Murcia)
- Spain
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
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