1
|
Tóbiás R, Simkó I, Császár AG. Unusual Dynamics and Vibrational Fingerprints of van der Waals Dimers Formed by Linear Molecules and Rare-Gas Atoms. J Chem Theory Comput 2023. [PMID: 38032107 DOI: 10.1021/acs.jctc.3c00914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Detailed structural, dynamical, and vibrational analyses have been performed for systems composed of linear triatomic molecules solvated by a single rare-gas atom, He, Ne, or Ar. Among the chromophores of these van der Waals (vdW) dimers, there are four neutral molecules (CO2, CS2, N2O, and OCS) and six molecular cations (HHe2+, HNe2+, HAr2+, HHeNe+, HHeAr+, and HNeAr+), both of apolar and polar nature. Following the exploration of bonding preferences, high-level four-dimensional (4D) potential energy surfaces (PESs) have been developed for 24 vdW dimers, keeping the two intramonomer bond lengths fixed. For these 24 complexes, over 1500 bound vibrational states have been obtained via quasi-variational nuclear-motion computations, employing exact kinetic-energy operators together with the accurate 4D PESs and their 2D/3D cuts. The reduced-dimensional (2D to 4D) dimer models have been compared with full-dimensional (6D) ones in the cases of the neutral CO2·Ar and charged HHe2+·He dimers, corroborating the high accuracy of the 2D to 4D vibrational energies. The reduced-dimensional models suggest that (a) while the equilibrium structures are T-shaped and planar, the effective ground-state structures are nonplanar, (b) certain bound states belong to collinear molecular structures, even when they are not minima, (c) the vdW vibrations are heavily mixed and many states have amplitudes corresponding to both the T-shaped and collinear structures, (d) there are a few dimers, for which even some of the vdW fundamentals lie above the first dissociation limit, and (e) the vdW vibrations are almost fully decoupled from the intramonomer bending motion.
Collapse
Affiliation(s)
- Roland Tóbiás
- HUN-REN-ELTE Complex Chemical Systems Research Group, P.O. Box 32, H-1518 Budapest 112, Hungary
| | - Irén Simkó
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Attila G Császár
- HUN-REN-ELTE Complex Chemical Systems Research Group, P.O. Box 32, H-1518 Budapest 112, Hungary
- Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| |
Collapse
|
2
|
Li Y, Zhai Y, Li H. MLRNet: Combining the Physics-Motivated Potential Models with Neural Networks for Intermolecular Potential Energy Surface Construction. J Chem Theory Comput 2023; 19:1421-1431. [PMID: 36826225 DOI: 10.1021/acs.jctc.2c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
A physics-based machine learning model called MLRNet has been developed to construct the high-accuracy two-body intermolecular potential energy surface (IPES). The outputs of the neural network are integrated into the physically realistic Morse/long-range (MLR) function, which ensures that the MLRNet has meaningful extrapolation at both short and long ranges and solves the asymptotic problem in common neural network potential (NNP) models. The neural network representation of the MLR parameters is more flexible and more efficient than the polynomial expansion in the conventional mdMLR model, especially for systems containing nonrigid monomer(s). The present work illustrates the basic framework of the current MLRNet model, including (i) how to combine the physically meaningful MLR function with different possible NN structures, (ii) the preservation of permutation symmetry, and (iii) the predetermination of the long-range function uLR. We choose two realistic systems to demonstrate the performance of MLRNet: the three-dimensional IPES of CO2-He including the CO2 antisymmetric vibration Q3 and the six-dimensional IPES of the H2O-Ar system. In both cases, the fitting errors of the MLRNet are several times smaller than those of the conventional mdMLR model. Both short-range and long-range extrapolation tests were performed to illustrate the extrapolation ability of the MLRNet and its damping function version. Moreover, for the 6-D H2O-Ar system, the MLRNet only needs 1596 trainable parameters, which is almost equal to the number needed for the 5-D mdMLR model (1509) and half that needed for the PIP-NN model (3501) within similar accuracy, which illustrates the model efficiency in high-dimensional IPES fitting.
Collapse
Affiliation(s)
- You Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Yu Zhai
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Hui Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| |
Collapse
|
3
|
Dridi N, Jellali C, Hmida F, Hui L, Kwabia Tchana F, Landsheere X, Hammami K, Rotger M, Aroui H. Line intensity parameters, He-broadening and line shift coefficients in the 2v20 and 3v21 − v21 bands of OCS. Mol Phys 2021. [DOI: 10.1080/00268976.2021.2010821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- N. Dridi
- Laboratoire de Spectroscopie et Dynamique Moléculaire, Université de Tunis, Tunis, Tunisia
- Université de Reims Champagne Ardenne, Reims, France
| | - C. Jellali
- Laboratoire de Spectroscopie et Dynamique Moléculaire, Université de Tunis, Tunis, Tunisia
| | - F. Hmida
- Laboratoire de Spectroscopie et Dynamique Moléculaire, Université de Tunis, Tunis, Tunisia
- Université de Reims Champagne Ardenne, Reims, France
| | - L. Hui
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | | | - X. Landsheere
- Université de Paris and Univ Paris Est Creteil, Paris, France
| | - K. Hammami
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El Manar, Tunis, Tunisia
| | - M. Rotger
- Université de Reims Champagne Ardenne, Reims, France
| | - H. Aroui
- Laboratoire de Spectroscopie et Dynamique Moléculaire, Université de Tunis, Tunis, Tunisia
| |
Collapse
|
4
|
Davies JA, Besley NA, Yang S, Ellis AM. Infrared spectroscopy of a small ion solvated by helium: OH stretching region of HeN−HOCO+. J Chem Phys 2019; 151:194307. [DOI: 10.1063/1.5124137] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Julia A. Davies
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Shengfu Yang
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Andrew M. Ellis
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| |
Collapse
|
5
|
Kodrycka M, Patkowski K. Platinum, gold, and silver standards of intermolecular interaction energy calculations. J Chem Phys 2019; 151:070901. [DOI: 10.1063/1.5116151] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Monika Kodrycka
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
| |
Collapse
|
6
|
Liu JM, Zhang XL, Zhai Y, Li H. Theoretical Study of Infrared Spectra of OCS-( pH 2) 2, OCS-( oD 2) 2, OCS-(HD) 2, and Mixed OCS- pH 2-He Trimers. J Phys Chem A 2018; 122:2915-2926. [DOI: 10.1021/acs.jpca.7b12708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing-Min Liu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Xiao-Long Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Yu Zhai
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Hui Li
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| |
Collapse
|
7
|
Zhai Y, Li H, Le Roy RJ. Constructing high-accuracy intermolecular potential energy surface with multi-dimension Morse/Long-Range model. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1429687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Yu Zhai
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Hui Li
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Robert J. Le Roy
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| |
Collapse
|
8
|
The He2-OCS complex: Comparison between theory and experiment. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
9
|
Faulkner T, Miller I, Raston PL. Quantum cascade laser spectroscopy of OCS isotopologues in 4He nanodroplets: A test of adiabatic following for a heavy rotor. J Chem Phys 2018; 148:044308. [DOI: 10.1063/1.5009908] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ty Faulkner
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, USA
| | - Isaac Miller
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, USA
| | - Paul L. Raston
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, USA
| |
Collapse
|
10
|
Liu JM, Zhai Y, Li H. Explicit correlation treatment of the six-dimensional potential energy surface and predicted infrared spectra for OCS–H2. J Chem Phys 2017; 147:044313. [DOI: 10.1063/1.4996086] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jing-Min Liu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People’s Republic of China
| | - Yu Zhai
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People’s Republic of China
| | - Hui Li
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People’s Republic of China
| |
Collapse
|
11
|
Xue RJ, Grofe A, Yin H, Qu Z, Gao J, Li H. Perturbation Approach for Computing Infrared Spectra of the Local Mode of Probe Molecules. J Chem Theory Comput 2017; 13:191-201. [PMID: 28068771 DOI: 10.1021/acs.jctc.6b00733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Linear and two-dimensional infrared (IR) spectroscopy of site-specific probe molecules provides an opportunity to gain a molecular-level understanding of the local hydrogen-bonding network, conformational dynamics, and long-range electrostatic interactions in condensed-phase and biological systems. A challenge in computation is to determine the time-dependent vibrational frequencies that incorporate explicitly both nuclear quantum effects of vibrational motions and an electronic structural representation of the potential energy surface. In this paper, a nuclear quantum vibrational perturbation (QVP) method is described for efficiently determining the instantaneous vibrational frequency of a chromophore in molecular dynamics simulations. Computational efficiency is achieved through the use of (a) discrete variable representation of the vibrational wave functions, (b) a perturbation theory to evaluate the vibrational energy shifts due to solvent dynamic fluctuations, and (c) a combined QM/MM potential for the systems. It was found that first-order perturbation is sufficiently accurate, enabling time-dependent vibrational frequencies to be obtained on the fly in molecular dynamics. The QVP method is illustrated in the mode-specific linear and 2D-IR spectra of the H-Cl stretching frequency in the HCl-water clusters and the carbonyl stretching vibration of acetone in aqueous solution. To further reduce computational cost, a hybrid strategy was proposed, and it was found that the computed vibrational spectral peak position and line shape are in agreement with experimental results. In addition, it was found that anharmonicity is significant in the H-Cl stretching mode, and hydrogen-bonding interactions further enhance anharmonic effects. The present QVP method complements other computational approaches, including path integral-based molecular dynamics, and represents a major improvement over the electrostatics-based spectroscopic mapping procedures.
Collapse
Affiliation(s)
- Rui-Jie Xue
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Adam Grofe
- Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street, SE, Minneapolis, Minnesota 55455, United States
| | - He Yin
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Zexing Qu
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Jiali Gao
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China.,Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street, SE, Minneapolis, Minnesota 55455, United States
| | - Hui Li
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| |
Collapse
|
12
|
Hou D, Ma YT, Zhang XL, Li H. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface. J Chem Phys 2016; 144:014301. [DOI: 10.1063/1.4939089] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dan Hou
- Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People’s Republic of China
| | - Yong-Tao Ma
- Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People’s Republic of China
| | - Xiao-Long Zhang
- Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People’s Republic of China
| | - Hui Li
- Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People’s Republic of China
| |
Collapse
|
13
|
Zhang XL, Li H, Le Roy RJ, Roy PN. Microwave and infrared spectra of CO–(pH2)2, CO–(oD2)2, and mixed CO–pH2–He trimers. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1568-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
14
|
Ma YT, Zeng T, Li H. Analytical Morse/long-Range model potential and predicted infrared and microwave spectra for a symmetric top-atom dimer: A case study of CH3F–He. J Chem Phys 2014; 140:214309. [DOI: 10.1063/1.4879956] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
15
|
Zang L, Dai W, Zheng L, Duan C, Lu Y, Yang M. Theoretical prediction of the linear isomers for rare gas-carbon disulfide complexes: He-CS₂, Ne-CS₂, and Ar-CS₂. J Chem Phys 2014; 140:114310. [PMID: 24655183 DOI: 10.1063/1.4868325] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Theoretical studies of the potential energy surfaces (PESs) and bound states are performed for rare gas-carbon disulfide complexes, He-CS2, Ne-CS2, and Ar-CS2. Three two-dimensional intermolecular PESs are constructed from ab initio data points which are calculated at the CCSD(T) level with aug-cc-pVTZ basis set supplemented with bond functions. We find that the three PESs have very similar features and each PES can be characterized by a global T-shaped minimum, two equivalent local linear minima, and the saddle points between them. The T-shaped isomer is energetically more stable than the linear isomer for each complex. The linear isomers, which have not been observed in experiment so far, are predicted from our PESs and further identified by bound state calculations. Moreover, we assign several intermolecular vibrational states for both the T-shaped and linear isomers of the three complexes via the analysis of wavefunctions. The corresponding vibrational frequencies are calculated from the bound state energies for these assigned states. These frequencies could be helpful for further experimental studies, especially for the linear isomers. We also calculate the rovibrational transition frequencies for the three T-shaped isomers and the pure rotational transition frequencies for the linear isomers, respectively. The accuracy of the PESs is validated by the good agreement between theoretical and experimental results for the rovibrational transition frequencies and spectroscopic parameters.
Collapse
Affiliation(s)
- Limin Zang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Wei Dai
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Limin Zheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Chuanxi Duan
- College of Physical Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| |
Collapse
|
16
|
Li H, Zhang XL, Le Roy RJ, Roy PN. Analytic Morse/long-range potential energy surfaces and predicted infrared spectra for CO–H2 dimer and frequency shifts of CO in (para-H2)N N = 1–20 clusters. J Chem Phys 2013; 139:164315. [DOI: 10.1063/1.4826595] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|