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Jacobson GM, Cheng L, Bhethanabotla VC, Sun J, McCoy AB. Machine Learning Approaches for Developing Potential Surfaces: Applications to OH -(H 2O) n ( n = 1-3) Complexes. J Phys Chem A 2025; 129:2958-2972. [PMID: 40105223 DOI: 10.1021/acs.jpca.4c08826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
Abstract
An approach for obtaining high-level ab initio potential surfaces is described. The approach takes advantage of machine learning strategies in a two-step process. In the first, the molecular-orbital based machine learning (MOB-ML) model uses Gaussian process regression to learn the correlation energy at the CCSD(T) level using the molecular orbitals obtained from Hartree-Fock calculations. In this work, the MOB-ML approach is expanded to use orbitals obtained using a smaller basis set, aug-cc-pVDZ, as features for learning the correlation energies at the complete basis set (CBS) limit. This approach is combined with the development of a neural-network potential, where the sampled geometries and energies that provide the training data for the potential are obtained using a diffusion Monte Carlo (DMC) calculation, which was run using the MOB-ML model. Protocols are developed to make full use of the structures that are obtained from the DMC calculation in the training process. These approaches are used to develop potentials for OH-(H2O) and H3O+(H2O), which are used for subsequent DMC calculations. The results of these calculations are compared to those performed using previously reported potentials. Overall, the results of the two sets of DMC calculations are in good agreement for these very floppy molecules. Potentials are also developed for OH-(H2O)2 and OH-(H2O)3, for which there are not available potential surfaces. The results of DMC calculations for these ions are compared to those for the corresponding H3O+(H2O)2 and H3O+(H2O)3 ions. It is found that the level of delocalization of the shared proton is similar for a hydroxide or hydronium ion bound to the same number of water molecules. This finding is consistent with the experimental observation that these sets of ions have similar spectra.
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Affiliation(s)
- Greta M Jacobson
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lixue Cheng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Microsoft Research AI for Science, Berlin 10178, Germany
| | - Vignesh C Bhethanabotla
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jiace Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Moonkaen P, McCoy AB. Evaluation of Infrared Intensities Using Diffusion Monte Carlo. J Phys Chem A 2025; 129:2705-2717. [PMID: 40053322 DOI: 10.1021/acs.jpca.4c08576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2025]
Abstract
Approaches for evaluating excited state wave functions and energies using diffusion Monte Carlo (DMC) with guiding functions (guided DMC) are discussed. For this work, the guiding functions are functions of a subset of the 3N - 6 coordinates that are needed to describe the structure of the molecule of interest. The DMC wave functions are used to evaluate intensities using two approaches. In the trial wave function approach, the product of the molecular wave function for one of the states involved in the transition and the guiding function for the second state is used to evaluate the matrix elements of the dipole moment. In the descendant weighting approach, descendant weights are used to evaluate the value of the wave function for one of the states involved in the transition at the geometries sampled by the DMC wave function for the second state. The descendant weighting approximation is shown to be more accurate as well as computationally more expensive compared to approximations that are based on various forms of the trial wave function approach. Strategies are explored, which combine results of different forms of the trial wave function approximation to minimize the errors in this approach. The trial wave function and descendant weighting approaches are applied to a study of a harmonic oscillator, where the sensitivity of the calculated energies and intensities to the quality of the trial wave function is explored. The two approaches are also applied to calculations of frequencies and intensities of transitions in water, H3O2-, a four-dimensional (4D) model based on H3O2- and H5O2+. We also show how comparisons of the results obtained using several forms of the trial wave function approach allow us to explore how couplings among vibrational motions are reflected in the intensities.
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Affiliation(s)
- Pattarapon Moonkaen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Finney JM, McCoy AB. Correlations between the Structures and Spectra of Protonated Water Clusters. J Phys Chem A 2024; 128:868-879. [PMID: 38265889 DOI: 10.1021/acs.jpca.3c07338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Badger's rule-like correlations between OH stretching frequencies and intensities and the OH bond length are used to develop a spectral mapping procedure for studies of pure and protonated water clusters. This approach utilizes the vibrationally averaged OH bond lengths, which were obtained from diffusion Monte Carlo simulations that were performed using the general potential developed by Yu and Bowman. Good agreement is achieved between the spectra obtained using this approach and previously reported spectra for H+(H2O)n clusters, with n = 3, 4, and 5, as well as their perdeuterated analogues. The analysis of the spectra obtained by this spectral mapping approach supports previous work that assigned the spectrum of H+(H2O)6 to a mixture of Eigen and Zundel-like structures. Analysis of the calculated spectra also suggests a reassignment of the frequency of one of the transitions that involves the OH stretching vibration of the OH bonds in the hydronium core in the Eigen-like structure of H+(H2O)6 from 1917 cm-1 to roughly 2100 cm-1. For D+(D2O)6, comparison of the measured spectrum to those obtained by using the spectral mapping approach suggests that the carrier of the measured spectrum is one or more of the isomers of D+(D2O)6 that contain a four-membered ring and two flanking water molecules. While there are several candidate structures, the two flanking water molecules most likely form a chain that is bound to the hydronium core.
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Affiliation(s)
- Jacob M Finney
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Schiltz C, Rappoport D, Mandelshtam VA. Implementation of the self-consistent phonons method with ab initio potentials (AI-SCP). J Chem Phys 2023; 158:2890485. [PMID: 37184023 DOI: 10.1063/5.0146682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives. These averages are computed efficiently by the quasi-Monte Carlo method utilizing low-discrepancy sequences leading to a fast convergence with respect to the number, S, of the AI energy evaluations. Moreover, a further substantial (an-order-of-magnitude) improvement in efficiency is achieved once a numerically cheap approximation of the AI potential is available. This is based on using a perturbation theory-like (the two-grid) approach in which it is the average of the difference between the AI and the approximate potential that is computed. The corresponding codes and scripts are provided.
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Affiliation(s)
- Colin Schiltz
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - Dmitrij Rappoport
- Department of Chemistry, University of California, Irvine, California 92697, USA
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Finney JM, Choi TH, Huchmala RM, Heindel JP, Xantheas SS, Jordan KD, McCoy AB. Isotope Effects in the Zundel-Eigen Isomerization of H +(H 2O) 6. J Phys Chem Lett 2023; 14:4666-4672. [PMID: 37167485 DOI: 10.1021/acs.jpclett.3c00952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The isomerization pathway between the energetically low-lying Zundel and Eigen isomers of the protonated water hexamer was investigated using high-level ab initio calculations including a treatment of zero-point corrections. On the basis of these calculations, the Zundel-Eigen isomerization was found to proceed through a stable intermediate isomer, which consists of a four-membered ring with two single acceptor water molecules. The inclusion of vibrational zero-point energy is shown to be important for accurately establishing the relative energies of the three relevant isomers involved in the Zundel-Eigen isomerization. Diffusion Monte Carlo calculations including anharmonic vibrational effects show that all three isomers of H+(H2O)6 and D+(D2O)6 have well-defined structures. The energetic ordering of the three isomers changes upon deuteration. The implications of these results for the vibrational spectra of H+(H2O)6 and D+(D2O)6 are also discussed.
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Affiliation(s)
- Jacob M Finney
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Tae Hoon Choi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rachel M Huchmala
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS J7-10, Richland, Washington 99352, United States
| | - Kenneth D Jordan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Mendive-Tapia D, Meyer HD, Vendrell O. Optimal Mode Combination in the Multiconfiguration Time-Dependent Hartree Method through Multivariate Statistics: Factor Analysis and Hierarchical Clustering. J Chem Theory Comput 2023; 19:1144-1156. [PMID: 36716214 DOI: 10.1021/acs.jctc.2c01089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The multiconfiguration time-dependent Hartree (MCTDH) method and its multilayer extension (ML-MCTDH) are powerful algorithms for the efficient computation of nuclear quantum dynamics in high-dimensional systems. By providing time-dependent variational orbitals and an optimal choice of layered effective degrees of freedom, one is able to reduce the computational cost to an amenable number of configurations. However, choices related to selecting properly the mode grouping and tensor tree are strongly system dependent and, thus far, subjectively based on intuition and/or experience. Therefore, herein we detail a new protocol based on multivariate statistics─more specifically, factor analysis and hierarchical clustering─for a reliable and convenient guiding in the optimal design of such complex "system-of-systems" tensor-network decompositions. The advantages of employing the new algorithm and its applicability are tested on water and two floppy protonated water clusters with large amplitude motions.
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Affiliation(s)
- David Mendive-Tapia
- Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120Heidelberg, Germany
| | - Hans-Dieter Meyer
- Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120Heidelberg, Germany
| | - Oriol Vendrell
- Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120Heidelberg, Germany
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Moonkaen P, Finney JM, McCoy AB. Isotope Effects on Ground and Excited States of Ethyl Cation, H +(C 2H 4). J Phys Chem A 2023; 127:1196-1205. [PMID: 36705480 DOI: 10.1021/acs.jpca.2c07334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The structure and spectra of ethyl cation, H+(C2H4), and its deuterated analogues are investigated using diffusion Monte Carlo (DMC). These calculations all show that the ground state wave function for H+(C2H4) is localized near the minimum energy configuration in which the excess proton is in a bridging configuration, although the amplitude of the vibrational motions of the bridging proton is large. Deuteration of the bridging proton reduces the amplitude of this motion, while deuteration of only the ethylenic hydrogen atoms in H+(C2D4) has little effect on the amplitude of the motion of the bridging proton. Excited states that are accessed by spectroscopically observed transitions in H+(C2H4) are calculated using fixed-node DMC. The calculated and measured frequencies for the states with one quantum of excitation in the ethylenic CH stretching vibrations show good agreement. We also explore the excited state with one quantum of excitation in the proton transfer vibration of the bridging proton and obtain a frequency of 616 cm-1 for H+(C2H4). This frequency increases to 629 cm-1 in H+(C2D4). Deuteration decreases this frequency to 491 and 495 cm-1 in D+(C2H4) and D+(C2D4), respectively. The effects of partial deuteration on the frequencies of the CH stretching vibrations, and the corresponding probability amplitudes are also explored. Finally, we report the vibrationally averaged rotational constants for the four isotopologues of ethyl cation considered in this study.
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Affiliation(s)
- Pattarapon Moonkaen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jacob M Finney
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Lu F, Cheng L, DiRisio RJ, Finney JM, Boyer MA, Moonkaen P, Sun J, Lee SJR, Deustua JE, Miller TF, McCoy AB. Fast Near Ab Initio Potential Energy Surfaces Using Machine Learning. J Phys Chem A 2022; 126:4013-4024. [PMID: 35715227 DOI: 10.1021/acs.jpca.2c02243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A machine-learning based approach for evaluating potential energies for quantum mechanical studies of properties of the ground and excited vibrational states of small molecules is developed. This approach uses the molecular-orbital-based machine learning (MOB-ML) method to generate electronic energies with the accuracy of CCSD(T) calculations at the same cost as a Hartree-Fock calculation. To further reduce the computational cost of the potential energy evaluations without sacrificing the CCSD(T) level accuracy, GPU-accelerated Neural Network Potential Energy Surfaces (NN-PES) are trained to geometries and energies that are collected from small-scale Diffusion Monte Carlo (DMC) simulations, which are run using energies evaluated using the MOB-ML model. The combined NN+(MOB-ML) approach is used in variational calculations of the ground and low-lying vibrational excited states of water and in DMC calculations of the ground states of water, CH5+, and its deuterated analogues. For both of these molecules, comparisons are made to the results obtained using potentials that were fit to much larger sets of electronic energies than were required to train the MOB-ML models. The NN+(MOB-ML) approach is also used to obtain a potential surface for C2H5+, which is a carbocation with a nonclassical equilibrium structure for which there is currently no available potential surface. This potential is used to explore the CH stretching vibrations, focusing on those of the bridging hydrogen atom. For both CH5+ and C2H5+ the MOB-ML model is trained using geometries that were sampled from an AIMD trajectory, which was run at 350 K. By comparison, the structures sampled in the ground state calculations can have energies that are as much as ten times larger than those used to train the MOB-ML model. For water a higher temperature AIMD trajectory is needed to obtain accurate results due to the smaller thermal energy. A second MOB-ML model for C2H5+ was developed with additional higher energy structures in the training set. The two models are found to provide nearly identical descriptions of the ground state of C2H5+.
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Affiliation(s)
- Fenris Lu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lixue Cheng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Ryan J DiRisio
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jacob M Finney
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark A Boyer
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Pattarapon Moonkaen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jiace Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Sebastian J R Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - J Emiliano Deustua
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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