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Moscato D, Mandelli G, Bondanza M, Lipparini F, Conte R, Mennucci B, Ceotto M. Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine. J Am Chem Soc 2024; 146:8179-8188. [PMID: 38470354 DOI: 10.1021/jacs.3c12700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
We introduce a quantum mechanics/molecular mechanics semiclassical method for studying the solvation process of molecules in water at the nuclear quantum mechanical level with atomistic detail. We employ it in vibrational spectroscopy calculations because this is a tool that is very sensitive to the molecular environment. Specifically, we look at the vibrational spectroscopy of thymidine in liquid water. We find that the C═O frequency red shift and the C═C frequency blue shift, experienced by thymidyne upon solvation, are mainly due to reciprocal polarization effects, that the molecule and the water solvent exert on each other, and nuclear zero-point energy effects. In general, this work provides an accurate and practical tool to study quantum vibrational spectroscopy in solution and condensed phase, incorporating high-level and computationally affordable descriptions of both electronic and nuclear problems.
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Affiliation(s)
- Davide Moscato
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Giacomo Mandelli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
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Bonnet L. Semiclassical initial value representation: From Møller to Miller. II. J Chem Phys 2023; 158:114112. [PMID: 36948824 DOI: 10.1063/5.0137725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
As shown by W. H. Miller in a seminal article [J. Chem. Phys. 53, 3578 (1970)], the most convenient and accurate semiclassical (SC) theory of molecular scattering in action-angle coordinates is based on the initial value representation (IVR) and the use of shifted angles, which are different from the natural angles usually used in the quantum and classical treatments. Here, we show for an inelastic molecular collision that the initial and final shifted angles define three-segment classical paths that are exactly those involved in the classical-limit of Tannor-Weeks quantum scattering theory [J. Chem. Phys. 98, 3884 (1993)], provided that the translational wave packets |g+⟩ and |g-⟩ into play in this theory are both taken at |0⟩. Assuming this to be the case, using van Vleck propagators, and applying the stationary phase approximation, Miller's SCIVR expression of S-matrix elements is found, with an additional cut-off factor canceling the energetically forbidden transition probabilities. This factor, however, is close to unity in most practical cases. Furthermore, these developments show that the Møller operators underlie Miller's formulation, thus confirming, for molecular collisions, the results recently established in the simpler case of light-induced rotational transitions [L. Bonnet, J. Chem. Phys. 153, 174102 (2020)]. Last but not least, we show, based on the previous results, that for processes involving long-range anisotropic forces, implementing the Skinner-Miller method [Chem. Phys. Lett. 300, 20 (1999)] in shifted coordinates makes its predictions both easier and more accurate than in natural coordinates.
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Affiliation(s)
- Laurent Bonnet
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France
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Bonnet L, Crespos C, Monnerville M. Chemical reaction thresholds according to classical-limit quantum dynamics. J Chem Phys 2022; 157:094114. [PMID: 36075739 DOI: 10.1063/5.0101311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Classical-limit quantum dynamics is used to explain the origin of the quantum thresholds of chemical reactions from their classical dynamics when these are vibrationally nonadiabatic across the interaction region. This study is performed within the framework of an elementary model of chemical reaction that mimics the passage from the free rotation of the reagents to the bending vibration at the transition state to the free rotation of the products.
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Affiliation(s)
- L Bonnet
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France
| | - C Crespos
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France
| | - M Monnerville
- Univ. Lille, CNRS, PhLAM, UMR 8523, 59655 Villeneuve d'Ascq, France
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Bonnet L. Semiclassical descriptions of rotational transitions in natural and shifted angles: Analysis of unexpected results. J Chem Phys 2021; 155:174103. [PMID: 34742210 DOI: 10.1063/5.0071227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the semiclassical theory of rotational transitions, S-matrix elements are expressed as integrals over initial and final angles of probability amplitudes calculated along the classical paths joining these angles, before final passage to an initial value representation [W. H. Miller, J. Phys. Chem. A 105, 2942 (2001)]. These angles can be either natural angles fixing the orientation of the rotor or angles shifted with respect to the previous ones so as to vary only within the interaction region causing the transitions. The two approaches, however, were recently shown to lead to different predictions. While the theory in natural angles lacks precision and exhibits unphysical behavior, the theory in shifted angles is much more accurate and physically well behaved [L. Bonnet, J. Chem. Phys. 153, 174102 (2020)]. The present work is devoted to the analysis of this unexpected finding.
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Affiliation(s)
- Laurent Bonnet
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France
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Mandal B, Semenov A, Babikov D. Adiabatic Trajectory Approximation within the Framework of Mixed Quantum/Classical Theory. J Phys Chem A 2020; 124:9877-9888. [DOI: 10.1021/acs.jpca.0c07547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bikramaditya Mandal
- Chemistry Department, Wehr Chemistry Building, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Alexander Semenov
- Chemistry Department, Wehr Chemistry Building, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Dmitri Babikov
- Chemistry Department, Wehr Chemistry Building, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
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Bonnet L. Semiclassical initial value representation: From Møller to Miller. J Chem Phys 2020; 153:174102. [PMID: 33167624 DOI: 10.1063/5.0023137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The initial value representation (IVR) was proposed five decades ago by Miller [J. Chem. Phys. 53, 3578 (1970)] in order to improve the feasibility and accuracy of semiclassical (SC) scattering calculations. Møller operators, which play a fundamental role in quantum scattering theory, do not appear in his formulation based on action-angle coordinates. These operators were introduced much later by Garashchuk and Light [J. Chem. Phys. 114, 1060 (2001)] in SC-IVR calculations performed in Cartesian coordinates within the Tannor and Weeks [J. Chem. Phys. 98, 3884 (1993)] formulation of quantum scattering theory. Remarkably, Møller operators were found to boost the numerical efficiency of SC-IVR calculations. The purpose of this work is to show within a simple model of light-induced rotational transitions that, in fact, Møller operators were already underlying Miller's pioneering formulation. In line with the results of Garashchuk and Light [J. Chem. Phys. 114, 1060 (2001)], removing the action of these operators in Miller's theory strongly decreases its numerical efficiency.
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Rodríguez-Fernández A, Bonnet L, Crespos C, Larrégaray P, Díez Muiño R. When classical trajectories get to quantum accuracy: II. The scattering of rotationally excited H2 on Pd(111). Phys Chem Chem Phys 2020; 22:22805-22814. [DOI: 10.1039/d0cp02655g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The classical trajectory method in a quantum spirit assigns statistical weights to classical paths on the basis of two semiclassical corrections: Gaussian binning and the adiabaticity correction.
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Affiliation(s)
| | | | | | | | - Ricardo Díez Muiño
- Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU)
- 20018 Donostia-SanSebastián
- Spain
- Donostia International Physics Center (DIPC)
- 20018 Donostia-SanSebastián
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Bonnet L, Larrégaray P, Lara M, Launay JM. Theoretical Study of Barrierless Chemical Reactions Involving Nearly Elastic Rebound: The Case of S( 1D) + X 2, X = H, D. J Phys Chem A 2019; 123:6439-6454. [PMID: 31329443 DOI: 10.1021/acs.jpca.9b04938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For some values of the total angular momentum consistent with reaction, the title processes involve nonreactive trajectories proceeding through a single rebound mechanism during which the internal motion of the reagent diatom is nearly unperturbed. When such paths are in a significant amount, the classical reaction probability is found to be markedly lower than the quantum mechanical one. This finding was recently attributed to an unusual quantum effect called diffraction-mediated trapping, and a semiclassical correction was proposed in order to take into account this effect in the classical trajectory method. In the present work, we apply the resulting approach to the calculation of opacity functions as well as total and state-resolved integral cross sections (ICSs) and compare the values obtained with exact quantum ones, most of which are new. As the title reactions proceed through a deep insertion well, mean potential statistical calculations are also presented. Seven values of the collision energy, ranging from 30 to 1127 K, are considered. Two remarkable facts stand out: (i) The corrected classical treatment strongly improves the accuracy of the opacity function as compared to the usual classical treatment. When the entrance transition state is tight, however, those trajectories crossing it with a bending vibrational energy below the zero point energy must be discarded. (ii) The quantum opacity function, particularly its cutoff, is finely reproduced by the statistical approach. Consequently, the total ICS is also very well described by the two previous approximate methods. These, however, do not predict state-resolved ICSs with the same accuracy, proving thereby that (i) one or several genuine quantum effects involved in the dynamics are missed by the corrected classical treatment and (ii) the dynamics are not fully statistical.
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Affiliation(s)
- L Bonnet
- Université de Bordeaux, ISM , UMR 5255, F-33400 Talence , France.,CNRS , ISM , UMR 5255, F-33400 Talence , France
| | - P Larrégaray
- Université de Bordeaux, ISM , UMR 5255, F-33400 Talence , France.,CNRS , ISM , UMR 5255, F-33400 Talence , France
| | - M Lara
- Departamento de Química Física Aplicada, Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain
| | - J-M Launay
- Institut de Physique de Rennes, UMR CNRS 6251 , Université de Rennes I , F-35042 Rennes , France
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