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Souza Mattos R, Mukherjee S, Barbatti M. Legion: A Platform for Gaussian Wavepacket Nonadiabatic Dynamics. J Chem Theory Comput 2025; 21:2189-2205. [PMID: 40025765 PMCID: PMC11948330 DOI: 10.1021/acs.jctc.4c01697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 02/18/2025] [Accepted: 02/19/2025] [Indexed: 03/04/2025]
Abstract
Nonadiabatic molecular dynamics is crucial in investigating the time evolution of excited states in molecular systems. Among the various methods for performing such dynamics, those employing frozen Gaussian wavepacket propagation, particularly the multiple spawning approach, offer a favorable balance between computational cost and reliability. It propagates on-the-fly trajectories used to build and propagate the nuclear wavepacket. Despite its potential, efficient, flexible, and easily accessible software for Gaussian wavepacket propagation is less common compared to other methods, such as surface hopping. To address this, we present Legion, a software that facilitates the development and application of classical-trajectory-guided quantum wavepacket methods. The version presented here already contains a highly flexible and fully functional ab initio multiple spawning implementation, with different strategies to improve efficiency. Legion is written in Python for data management and NumPy/Fortran for numerical operations. It is created under the umbrella of the Newton-X platform and inherits all of its electronic structure interfaces beyond other direct interfaces. It also contains new approximations that allow it to circumvent the computation of the nonadiabatic coupling, extending the electronic structure methods that can be used for multiple spawning dynamics. We test, validate, and demonstrate Legion's functionalities through multiple spawning dynamics of fulvene (CASSCF and CASPT2) and DMABN (TDDFT).
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Affiliation(s)
| | - Saikat Mukherjee
- Aix
Marseille University, CNRS, ICR, Marseille 13397, France
- Faculty
of Chemistry, Nicolaus Copernicus University
in Torun, Torun 87100, Poland
| | - Mario Barbatti
- Aix
Marseille University, CNRS, ICR, Marseille 13397, France
- Institut
Universitaire de France, Paris 75231, France
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2
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Lassmann Y, Curchod BFE. Probing the sensitivity of ab initio multiple spawning to its parameters. Theor Chem Acc 2023; 142:66. [PMID: 37520272 PMCID: PMC10382418 DOI: 10.1007/s00214-023-03004-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023]
Abstract
Full multiple spawning (FMS) offers a strategy to simulate the nonadiabatic dynamics of molecular systems by describing their nuclear wavefunctions by a linear combination of coupled trajectory basis functions (TBFs). Applying a series of controlled approximations to the full multiple spawning (FMS) equations leads to the ab initio multiple spawning (AIMS), which is compatible with an on-the-fly propagation of the TBFs and an accurate description of nonadiabatic processes. The AIMS strategy and its numerical implementations, however, rely on a series of user-defined parameters. Herein, we investigate the influence of these parameters on the electronic-state population of two molecular systems- trans-azomethane and a two-dimensional model of the butatriene cation. This work highlights the stability of AIMS with respect to most of its parameters, underlines the specific parameters that require particular attention from the user of the method, and offers prescriptions for an informed selection of their value. Supplementary Information The online version contains supplementary material available at 10.1007/s00214-023-03004-w.
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Affiliation(s)
- Yorick Lassmann
- Centre for Computational Chemistry, School of Chemistry, Cantock’s Close, University of Bristol, Bristol, BS8 1TS UK
| | - Basile F. E. Curchod
- Centre for Computational Chemistry, School of Chemistry, Cantock’s Close, University of Bristol, Bristol, BS8 1TS UK
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Lassmann Y, Hollas D, Curchod BFE. Extending the Applicability of the Multiple-Spawning Framework for Nonadiabatic Molecular Dynamics. J Phys Chem Lett 2022; 13:12011-12018. [PMID: 36541684 PMCID: PMC9806853 DOI: 10.1021/acs.jpclett.2c03295] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Ab initio multiple-spawning (AIMS) describes the nonadiabatic dynamics of molecules by expanding nuclear wave functions in a basis of traveling multidimensional Gaussians called trajectory basis functions (TBFs). New TBFs can be spawned whenever nuclear amplitude is transferred between electronic states due to nonadiabatic transitions. While the adaptive size of the TBF basis grants AIMS its characteristic accuracy in describing nonadiabatic processes, it also leads to a fast and uncontrolled growth of the number of TBFs, penalizing computational efficiency. A different flavor of AIMS, called AIMS with informed stochastic selections (AIMSWISS), has recently been proposed to reduce the number of TBFs dramatically. Herein, we test the performance of AIMSWISS for a series of challenging nonadiabatic processes─photodynamics of two-dimensional model systems, 1,2-dithiane and chromium (0) hexacarbonyl─and show that this method is robust and extends the range of molecular systems that can be simulated within the multiple-spawning framework.
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Marsili E, Prlj A, Curchod BFE. A Theoretical Perspective on the Actinic Photochemistry of 2-Hydroperoxypropanal. J Phys Chem A 2022; 126:5420-5433. [PMID: 35900368 PMCID: PMC9393889 DOI: 10.1021/acs.jpca.2c03783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The photochemical reactions triggered by the sunlight
absorption
of transient volatile organic compounds in the troposphere are notoriously
difficult to characterize experimentally due to the unstable and short-lived
nature of these organic molecules. Some members of this family of
compounds are likely to exhibit a rich photochemistry given the diversity
of functional groups they can bear. Even more interesting is the photochemical
fate of volatile organic compounds bearing more than one functional
group that can absorb light—this is the case, for example,
of α-hydroperoxycarbonyls, which are formed during the oxidation
of isoprene. Experimental observables characterizing the photochemistry
of these molecules like photoabsorption cross-sections or photolysis
quantum yields are currently missing, and we propose here to leverage
a recently developed computational protocol to predict in silico the
photochemical fate of 2-hydroperoxypropanal (2-HPP) in the actinic
region. We combine different levels of electronic structure methods—SCS-ADC(2)
and XMS-CASPT2—with the nuclear ensemble approach and trajectory
surface hopping to understand the mechanistic details of the possible
nonradiative processes of 2-HPP. In particular, we predict the photoabsorption
cross-section and the wavelength-dependent quantum yields for the
observed photolytic pathways and combine them to determine in silico
photolysis rate constants. The limitations of our protocol and possible
future improvements are discussed.
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Affiliation(s)
- Emanuele Marsili
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Antonio Prlj
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
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Maskri R, Joubert-Doriol L. The moving crude adiabatic alternative to the adiabatic representation in excited state dynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200379. [PMID: 35341311 DOI: 10.1098/rsta.2020.0379] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The choice of the electronic representation in on-the-fly quantum dynamics is crucial. The adiabatic representation is appealing since adiabatic states are readily available from quantum chemistry packages. The nuclear wavepackets are then expanded in a basis of Gaussian functions, which follow trajectories to explore the potential energy surfaces and approximate the potential using a local expansion of the adiabatic quantities. Nevertheless, the adiabatic representation is plagued with severe limitations when conical intersections are involved: the diagonal Born-Oppenheimer corrections (DBOCs) are non-integrable, and the geometric phase effect on the nuclear wavepackets cannot be accounted for unless a model is available. To circumvent these difficulties, the moving crude adiabatic (MCA) representation was proposed and successfully tested in low energy dynamics where the wavepacket skirts the conical intersection. We assess the MCA representation in the case of non-adiabatic transitions through conical intersections. First, we show that using a Gaussian basis in the adiabatic representation indeed exhibits the aforementioned difficulties with a special emphasis on the possibility to regularize the DBOC terms. Then, we show that MCA is indeed able to properly model non-adiabatic transitions. Tests are done on linear vibronic coupling models for the bis(methylene) adamantyl cation and the butatriene cation. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.
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Affiliation(s)
- Rosa Maskri
- Univ Gustave Eiffel, Univ Paris Est Creteil, CNRS, UMR 8208, MSME, F-77454 Marne-la-Vallée, France
| | - Loïc Joubert-Doriol
- Univ Gustave Eiffel, Univ Paris Est Creteil, CNRS, UMR 8208, MSME, F-77454 Marne-la-Vallée, France
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Westermayr J, Marquetand P. Machine Learning for Electronically Excited States of Molecules. Chem Rev 2021; 121:9873-9926. [PMID: 33211478 PMCID: PMC8391943 DOI: 10.1021/acs.chemrev.0c00749] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.
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Affiliation(s)
- Julia Westermayr
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Data
Science @ Uni Vienna, University of Vienna, Währinger Strasse 29, 1090 Vienna, Austria
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Abstract
Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.
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Affiliation(s)
- Julia Westermayr
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Data Science @ Uni Vienna, University of Vienna, Währinger Strasse 29, 1090 Vienna, Austria
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Abstract
In this article, we review nonadiabatic molecular dynamics (NAMD) methods for modeling spin-crossover transitions. First, we discuss different representations of electronic states employed in the grid-based and direct NAMD simulations. The nature of interstate couplings in different representations is highlighted, with the main focus on nonadiabatic and spin-orbit couplings. Second, we describe three NAMD methods that have been used to simulate spin-crossover dynamics, including trajectory surface hopping, ab initio multiple spawning, and multiconfiguration time-dependent Hartree. Some aspects of employing different electronic structure methods to obtain information about potential energy surfaces and interstate couplings for NAMD simulations are also discussed. Third, representative applications of NAMD to spin crossovers in molecular systems of different sizes and complexities are highlighted. Finally, we pose several fundamental questions related to spin-dependent processes. These questions should be possible to address with future methodological developments in NAMD.
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Affiliation(s)
- Saikat Mukherjee
- Institut de Chimie Radicalaire, CNRS 7273, Aix-Marseille University, 13013 Marseille, France;
| | - Dmitry A Fedorov
- Oak Ridge Associated Universities, Oak Ridge, Tennessee 37830, USA;
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, USA;
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Ibele LM, Lassmann Y, Martínez TJ, Curchod BFE. Comparing (stochastic-selection) ab initio multiple spawning with trajectory surface hopping for the photodynamics of cyclopropanone, fulvene, and dithiane. J Chem Phys 2021; 154:104110. [DOI: 10.1063/5.0045572] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Lea M. Ibele
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Yorick Lassmann
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Todd J. Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, USA and PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Basile F. E. Curchod
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
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Westermayr J, Marquetand P. Machine learning and excited-state molecular dynamics. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/ab9c3e] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Westermayr J, Gastegger M, Marquetand P. Combining SchNet and SHARC: The SchNarc Machine Learning Approach for Excited-State Dynamics. J Phys Chem Lett 2020; 11:3828-3834. [PMID: 32311258 PMCID: PMC7246974 DOI: 10.1021/acs.jpclett.0c00527] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/20/2020] [Indexed: 05/26/2023]
Abstract
In recent years, deep learning has become a part of our everyday life and is revolutionizing quantum chemistry as well. In this work, we show how deep learning can be used to advance the research field of photochemistry by learning all important properties-multiple energies, forces, and different couplings-for photodynamics simulations. We simplify such simulations substantially by (i) a phase-free training skipping costly preprocessing of raw quantum chemistry data; (ii) rotationally covariant nonadiabatic couplings, which can either be trained or (iii) alternatively be approximated from only ML potentials, their gradients, and Hessians; and (iv) incorporating spin-orbit couplings. As the deep-learning method, we employ SchNet with its automatically determined representation of molecular structures and extend it for multiple electronic states. In combination with the molecular dynamics program SHARC, our approach termed SchNarc is tested on two polyatomic molecules and paves the way toward efficient photodynamics simulations of complex systems.
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Affiliation(s)
- Julia Westermayr
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Michael Gastegger
- Machine
Learning Group, Technical University of
Berlin, 10587 Berlin, Germany
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
- Data
Science @ Uni Vienna, University of Vienna, Währinger Str. 29, 1090 Vienna, Austria
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12
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Ludeña EV, Torres FJ, Becerra M, Rincón L, Liu S. Shannon Entropy and Fisher Information from a Non-Born-Oppenheimer Perspective. J Phys Chem A 2020; 124:386-394. [PMID: 31846329 DOI: 10.1021/acs.jpca.9b10503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We study the Shannon entropy and the Fisher information in a non-Born-Oppenheimer (nBO) regime, where these quantities are constructed from one-particle densities obtained from an exact nBO analytic wave function for a Coulomb-Hooke model of a four-particle system. This model consists of two electrons and two protons with Coulombic interactions between like particles and Hookean interactions otherwise [ Becerra , M. et al. Int. J. Quantum Chem 2013 , 113 ( 10 ), 1584 - 1590 ]. In the nBO case, there arise densities for both the nuclei and electrons. Furthermore, these densities vary with respect to a particular point of reference from which they are calculated. We consider, in the present work, electron and nuclear densities calculated from the following reference points: a global center of mass, the geometric center between the electrons, and the geometric center between the protons. A comparison of the nBO Shannon entropy and Fisher information, with respect to their counterparts computed from Born-Oppenheimer densities, suggests that the former quantities provide more insights into the chemical reactivity because of the nonuniqueness nature of the nBO electron density as well as the availability and access to the nBO nuclear density. Finally, some comments are made concerning the nBO vs the BO regimes in relation to this particular chemical reactivity indicator.
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Affiliation(s)
- Eduardo V Ludeña
- Grupo de Química Computacional y Teórica (QCT-USFQ) , Universidad San Francisco de Quito, USFQ , Diego de Robles s/n y Vía Interoceánica , Quito , Ecuador 170901
| | - F Javier Torres
- Grupo de Química Computacional y Teórica (QCT-USFQ) , Universidad San Francisco de Quito, USFQ , Diego de Robles s/n y Vía Interoceánica , Quito , Ecuador 170901.,Instituto de Simulación Computacional (ISC-USFQ) , Universidad San Francisco de Quito, USFQ , Diego de Robles s/n y Vía Interoceánica , Quito , Ecuador 170901
| | - Marcos Becerra
- Grupo de Química Computacional y Teórica (QCT-USFQ) , Universidad San Francisco de Quito, USFQ , Diego de Robles s/n y Vía Interoceánica , Quito , Ecuador 170901
| | - Luis Rincón
- Grupo de Química Computacional y Teórica (QCT-USFQ) , Universidad San Francisco de Quito, USFQ , Diego de Robles s/n y Vía Interoceánica , Quito , Ecuador 170901.,Instituto de Simulación Computacional (ISC-USFQ) , Universidad San Francisco de Quito, USFQ , Diego de Robles s/n y Vía Interoceánica , Quito , Ecuador 170901
| | - Shubin Liu
- Research Computing Center , University of North Carolina , Chapel Hill , North Carolina 27599-3420 , United States
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Ibele LM, Curchod BFE. A molecular perspective on Tully models for nonadiabatic dynamics. Phys Chem Chem Phys 2020; 22:15183-15196. [DOI: 10.1039/d0cp01353f] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We present a series of standardized molecular tests for nonadiabatic dynamics, reminiscent of the one-dimensional Tully models proposed in 1990.
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Affiliation(s)
- Lea M. Ibele
- Department of Chemistry
- Durham University
- Durham DH1 3LE
- UK
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