1
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Conte R, Aieta C, Cazzaniga M, Ceotto M. A Perspective on the Investigation of Spectroscopy and Kinetics of Complex Molecular Systems with Semiclassical Approaches. J Phys Chem Lett 2024; 15:7566-7576. [PMID: 39024505 DOI: 10.1021/acs.jpclett.4c01338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
In this Perspective we show that semiclassical methods provide a rigorous hierarchical way to study the vibrational spectroscopy and kinetics of complex molecular systems. The time averaged approach to spectroscopy and the semiclassical transition state theory for kinetics, which have been first adopted and then further developed in our group, provide accurate quantum results on rigorous physical grounds and can be applied even when dealing with a large number of degrees of freedom. In spectroscopy, the multiple coherent, divide-and-conquer, and adiabatically switched semiclassical approaches have practically permitted overcoming issues related to the convergence of results. In this Perspective we demonstrate the possibility of studying the semiclassical vibrational spectroscopy of a molecule adsorbed on an anatase (101) surface, a system made of 51 atoms. In kinetics, the semiclassical transition state theory is able to account for anharmonicity and the coupling between the reactive and bound modes. Our group has developed this technique for practical applications involving the study of phenomena like kinetic isotope effect, heavy atom tunneling, and elusive conformer lifetimes. Here, we show that our multidimensional anharmonic quantum approach is able to tackle on-the-fly the thermal kinetic rate constant of a 135 degree-of-freedom system. Overall, semiclassical methods open up the possibility to describe at the quantum mechanical level systems characterized by hundreds of degrees of freedom leading to the accurate spectroscopic and kinetic description of biomolecules and complex molecular systems.
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Affiliation(s)
- Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Chiara Aieta
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Marco Cazzaniga
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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2
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Moghaddasi Fereidani R, Vaníček JJL. High-order geometric integrators for the local cubic variational Gaussian wavepacket dynamics. J Chem Phys 2024; 160:044113. [PMID: 38284658 DOI: 10.1063/5.0180070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Gaussian wavepacket dynamics has proven to be a useful semiclassical approximation for quantum simulations of high-dimensional systems with low anharmonicity. Compared to Heller's original local harmonic method, the variational Gaussian wavepacket dynamics is more accurate, but much more difficult to apply in practice because it requires evaluating the expectation values of the potential energy, gradient, and Hessian. If the variational approach is applied to the local cubic approximation of the potential, these expectation values can be evaluated analytically, but they still require the costly third derivative of the potential. To reduce the cost of the resulting local cubic variational Gaussian wavepacket dynamics, we describe efficient high-order geometric integrators, which are symplectic, time-reversible, and norm-conserving. For small time steps, they also conserve the effective energy. We demonstrate the efficiency and geometric properties of these integrators numerically on a multidimensional, nonseparable coupled Morse potential.
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Affiliation(s)
- Roya Moghaddasi Fereidani
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří J L Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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3
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Wenzel M, Mitric R. Prediction of fluorescence quantum yields using the extended thawed Gaussian approximation. J Chem Phys 2023; 159:234113. [PMID: 38108487 DOI: 10.1063/5.0178106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/26/2023] [Indexed: 12/19/2023] Open
Abstract
Spontaneous emission and internal conversion rates are calculated within harmonic approximations and compared to the results obtained within the semi-classical extended thawed Gaussian approximation (ETGA). This is the first application of the ETGA in the calculation of internal conversion and emission rates for real molecular systems, namely, formaldehyde, fluorobenzene, azulene, and a dicyano-squaraine dye. The viability of the models as black-box tools for prediction of spontaneous emission and internal conversion rates is assessed. All calculations were done using a consistent protocol in order to investigate how different methods perform without previous experimental knowledge using density functional theory (DFT) and time-dependent DFT (TD-DFT) with B3LYP, PBE0, ωB97XD, and CAM-B3LYP functionals. Contrasting the results with experimental data shows that there are further improvements required before theoretical predictions of emission and internal conversion rates can be used as reliable indicators for the photo-luminescence properties of molecules. We find that the ETGA performs rather similar to the vertical harmonical model. Including anharmonicities in the calculation of internal conversion rates has a moderate effect on the quantitative results in the studied systems. The emission rates are fairly stable with respect to computational parameters, but the internal conversion rate reveals itself to be highly dependent on the choice of the spectral line shape function, particularly the width of the Lorentzian function, associated with homogeneous broadening.
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Affiliation(s)
- Michael Wenzel
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer Str. 42, 97074 Würzburg, Germany
| | - Roland Mitric
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer Str. 42, 97074 Würzburg, Germany
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4
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Sorour MI, Marcus AH, Matsika S. Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer. J Phys Chem A 2023; 127:9530-9540. [PMID: 37934679 PMCID: PMC10774018 DOI: 10.1021/acs.jpca.3c06090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
The indocarbocyanine Cy3 dye is widely used to probe the dynamics of proteins and DNA. Excitonically coupled Cy3 dimers exhibit very unique spectral signatures that depend on the interchromophoric geometrical orientation induced by the environment, making them powerful tools to infer the dynamics of their surroundings. Understanding the origin of the dimeric spectral signatures is a necessity for an accurate interpretation of the experimental results. In this work, we simulate the vibronic spectrum of an experimentally well-studied Cy3 dimer, and we explain the origin of the experimental signatures present in its linear absorption spectrum. The Franck-Condon harmonic approximations, among other tests, are used to probe the factors contributing to the spectrum. It is found that the first peak in the absorption spectrum originates from the lower energy excitonic state, while the next two peaks are vibrational progressions of the higher energy excitonic state. The polar solvent plays a crucial role in the appearance of the spectrum, being responsible for the localized S1 minimum, which results in an increased intensity of the first peak.
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Affiliation(s)
- Mohammed I Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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5
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Franzke Y, Holzer C, Andersen JH, Begušić T, Bruder F, Coriani S, Della Sala F, Fabiano E, Fedotov DA, Fürst S, Gillhuber S, Grotjahn R, Kaupp M, Kehry M, Krstić M, Mack F, Majumdar S, Nguyen BD, Parker SM, Pauly F, Pausch A, Perlt E, Phun GS, Rajabi A, Rappoport D, Samal B, Schrader T, Sharma M, Tapavicza E, Treß RS, Voora V, Wodyński A, Yu JM, Zerulla B, Furche F, Hättig C, Sierka M, Tew DP, Weigend F. TURBOMOLE: Today and Tomorrow. J Chem Theory Comput 2023; 19:6859-6890. [PMID: 37382508 PMCID: PMC10601488 DOI: 10.1021/acs.jctc.3c00347] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Indexed: 06/30/2023]
Abstract
TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light-matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE's functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches. Select features under development are reviewed to illustrate the continuous growth of the program suite, including nuclear electronic orbital methods, Hartree-Fock-based adiabatic connection models, simplified time-dependent density functional theory, relativistic effects and magnetic properties, and multiscale modeling of optical properties.
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Affiliation(s)
- Yannick
J. Franzke
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Christof Holzer
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Josefine H. Andersen
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Tomislav Begušić
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Florian Bruder
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Sonia Coriani
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabio Della Sala
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Eduardo Fabiano
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Daniil A. Fedotov
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Susanne Fürst
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Sebastian Gillhuber
- Institute
of Inorganic Chemistry, Karlsruhe Institute
of Technology (KIT), Engesserstr. 15, 76131 Karlsruhe, Germany
| | - Robin Grotjahn
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Martin Kaupp
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Max Kehry
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Marjan Krstić
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Fabian Mack
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Sourav Majumdar
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Brian D. Nguyen
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Shane M. Parker
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106 United States
| | - Fabian Pauly
- Institute
of Physics, University of Augsburg, Universitätsstr. 1, 86159 Augsburg, Germany
| | - Ansgar Pausch
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Eva Perlt
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Gabriel S. Phun
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Ahmadreza Rajabi
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Dmitrij Rappoport
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Bibek Samal
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Tim Schrader
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Manas Sharma
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Enrico Tapavicza
- Department
of Chemistry and Biochemistry, California
State University, Long Beach, 1250 Bellflower Boulevard, Long
Beach, California 90840-9507, United States
| | - Robert S. Treß
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vamsee Voora
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Artur Wodyński
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Jason M. Yu
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Benedikt Zerulla
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz-Platz
1, 76344 Eggenstein-Leopoldshafen Germany
| | - Filipp Furche
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Christof Hättig
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Marek Sierka
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - David P. Tew
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
| | - Florian Weigend
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
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6
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Wenzel M, Mitric R. Internal conversion rates from the extended thawed Gaussian approximation: Theory and validation. J Chem Phys 2023; 158:034105. [PMID: 36681643 DOI: 10.1063/5.0130340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The theoretical prediction of the rates of nonradiative processes in molecules is fundamental in assessing their emissive properties. In this context, global harmonic models have been widely used to simulate vibronic spectra as well as internal conversion rates and to predict photoluminescence quantum yields. However, these simplified models suffer from the limitations that are inherent to the harmonic approximation and can have a severe effect on the calculated internal conversion rates. Therefore, the development of more accurate semiclassical methods is highly desirable. Here, we introduce a procedure for the calculation of nonradiative rates in the framework of the time-dependent semi-classical Extended Thawed Gaussian Approximation (ETGA). We systematically investigate the performance of the ETGA method by comparing it to the adiabatic and vertical harmonic methods, which belong to the class of widely used global harmonic models. Its performance is tested in potentials that cannot be treated adequately by global harmonic models, beginning with Morse potentials of varying anharmonicity followed by a double well potential. The calculated radiative and nonradiative internal conversion rates are compared to reference values based on exact quantum dynamics. We find that the ETGA has the capability to predict internal conversion rates in anharmonic systems with an appreciable energy gap, whereas the global harmonic models prove to be insufficient.
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Affiliation(s)
- Michael Wenzel
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer Str. 42, 97074 Würzburg, Germany
| | - Roland Mitric
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer Str. 42, 97074 Würzburg, Germany
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7
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Sorour MI, Marcus AH, Matsika S. Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3. Molecules 2022; 27:4062. [PMID: 35807308 PMCID: PMC9268038 DOI: 10.3390/molecules27134062] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022] Open
Abstract
Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck-Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck-Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck-Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.
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Affiliation(s)
- Mohammed I. Sorour
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA;
| | - Andrew H. Marcus
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA;
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA;
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8
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Begušić T, Tapavicza E, Vaníček J. Applicability of the Thawed Gaussian Wavepacket Dynamics to the Calculation of Vibronic Spectra of Molecules with Double-Well Potential Energy Surfaces. J Chem Theory Comput 2022; 18:3065-3074. [PMID: 35420803 DOI: 10.1021/acs.jctc.2c00030] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Simulating vibrationally resolved electronic spectra of anharmonic systems, especially those involving double-well potential energy surfaces, often requires expensive quantum dynamics methods. Here, we explore the applicability and limitations of the recently proposed single-Hessian thawed Gaussian approximation for the simulation of spectra of systems with double-well potentials, including 1,2,4,5-tetrafluorobenzene, ammonia, phosphine, and arsine. This semiclassical wavepacket approach is shown to be more robust and to provide more accurate spectra than the conventional harmonic approximation. Specifically, we identify two cases in which the Gaussian wavepacket method is especially useful due to the breakdown of the harmonic approximation: (i) when the nuclear wavepacket is initially at the top of the potential barrier but delocalized over both wells, e.g., along a low-frequency mode, and (ii) when the wavepacket has enough energy to classically go over the low potential energy barrier connecting the two wells. The method is efficient and requires only a single classical ab initio molecular dynamics trajectory, in addition to the data required to compute the harmonic spectra. We also present an improved algorithm for computing the wavepacket autocorrelation function, which guarantees that the evaluated correlation function is continuous for arbitrary size of the time step.
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Affiliation(s)
- Tomislav Begušić
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Enrico Tapavicza
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, California 90840-9507, United States
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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9
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Schwabe B, Niemeyer JC. Deep Zoom-In Simulation of a Fuzzy Dark Matter Galactic Halo. PHYSICAL REVIEW LETTERS 2022; 128:181301. [PMID: 35594112 DOI: 10.1103/physrevlett.128.181301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/04/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Fuzzy dark matter (FDM) made of ultralight bosonic particles is a viable alternative to cold dark matter with clearly distinguishable small-scale features in collapsed structures. On large scales, it behaves gravitationally like cold dark matter deviating only by a cutoff in the initial power spectrum and can be studied using N-body methods. In contrast, wave interference effects near the de Broglie scale result in new phenomena unique to FDM. Interfering modes in filaments and halos yield a stochastically oscillating granular structure which condenses into solitonic cores during halo formation. Investigating these highly nonlinear wave phenomena requires the spatially resolved numerical integration of the Schrödinger equation. In previous papers we introduced a hybrid zoom-in scheme that combines N-body methods to model the large-scale gravitational potential around and the mass accretion onto pre-selected halos with simulations of the Schrödinger-Poisson equation to capture wave-like effects inside these halos. In this work, we present a new, substantially improved reconstruction method for the wave function inside of previously collapsed structures. We demonstrate its capabilities with a deep zoom-in simulation of a well-studied sub-L_{*}-sized galactic halo from cosmological initial conditions. With a particle mass of m=2.5×10^{-22} eV and halo mass M_{vir}=1.7×10^{11} M_{⊙} in a (60 h^{-1} comoving Mpc)^{3} cosmological box, it reaches an effective resolution of 20 comoving pc. This pushes the values of m and M accessible to simulations significantly closer to those relevant for studying galaxy evolution in the allowed range of FDM masses.
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Affiliation(s)
- Bodo Schwabe
- CAPA and Departamento de Física Teórica, Universidad de Zaragoza, 50009 Zaragoza, Spain and Institut für Astrophysik, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany
| | - Jens C Niemeyer
- Institut für Astrophysik, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany
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10
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Botti G, Aieta C, Conte R. The complex vibrational spectrum of proline explained through the adiabatically switched semiclassical initial value representation. J Chem Phys 2022; 156:164303. [DOI: 10.1063/5.0089720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proline, a 17-atom amino acid with a closed-ring side chain, has a complex potential energy surface characterized by several minima. Its IR experimental spectrum, reported in the literature, is of difficult and controversial assignment. In particular, the experimental signal at 3559 cm−1 associated with the OH stretch is interesting because it is inconsistent with the global minimum, trans-proline conformer. This suggests the possibility that multiple conformers may contribute to the IR spectrum. The same conclusion is obtained by investigating the splitting of the CO stretch at 1766 and 1789 cm−1 and other, more complex spectroscopic features involving CH stretches and COH/CNH bendings. In this work, we perform full-dimensional, on-the-fly adiabatically switched semiclassical initial value representation simulations employing the ab initio dft-d3-B3LYP level of theory with aug-cc-pVDZ basis set. We reconstruct the experimental spectrum of proline in its main features by studying the vibrational features of trans-proline and cis1-proline, and provide a new assignment for the OH stretch of trans-proline.
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Affiliation(s)
| | - Chiara Aieta
- Dipartimento di Chimica, Università degli Studi di Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Italy
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11
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Scheidegger A, Vaníček J, Golubev NV. Search for long-lasting electronic coherence using on-the-fly ab initio semiclassical dynamics. J Chem Phys 2022; 156:034104. [DOI: 10.1063/5.0076609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Alan Scheidegger
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nikolay V. Golubev
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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12
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Roulet J, Vaníček J. An implicit split-operator algorithm for the nonlinear time-dependent Schrödinger equation. J Chem Phys 2021; 155:204109. [PMID: 34852494 DOI: 10.1063/5.0071153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The explicit split-operator algorithm is often used for solving the linear and nonlinear time-dependent Schrödinger equations. However, when applied to certain nonlinear time-dependent Schrödinger equations, this algorithm loses time reversibility and second-order accuracy, which makes it very inefficient. Here, we propose to overcome the limitations of the explicit split-operator algorithm by abandoning its explicit nature. We describe a family of high-order implicit split-operator algorithms that are norm-conserving, time-reversible, and very efficient. The geometric properties of the integrators are proven analytically and demonstrated numerically on the local control of a two-dimensional model of retinal. Although they are only applicable to separable Hamiltonians, the implicit split-operator algorithms are, in this setting, more efficient than the recently proposed integrators based on the implicit midpoint method.
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Affiliation(s)
- Julien Roulet
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénieries Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénieries Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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13
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Gandolfi M, Ceotto M. Unsupervised Machine Learning Neural Gas Algorithm for Accurate Evaluations of the Hessian Matrix in Molecular Dynamics. J Chem Theory Comput 2021; 17:6733-6746. [PMID: 34705463 PMCID: PMC8582248 DOI: 10.1021/acs.jctc.1c00707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 11/29/2022]
Abstract
The Hessian matrix of the potential energy of molecular systems is employed not only in geometry optimizations or high-order molecular dynamics integrators but also in many other molecular procedures, such as instantaneous normal mode analysis, force field construction, instanton calculations, and semiclassical initial value representation molecular dynamics, to name a few. Here, we present an algorithm for the calculation of the approximated Hessian in molecular dynamics. The algorithm belongs to the family of unsupervised machine learning methods, and it is based on the neural gas idea, where neurons are molecular configurations whose Hessians are adopted for groups of molecular dynamics configurations with similar geometries. The method is tested on several molecular systems of different dimensionalities both in terms of accuracy and computational time versus calculating the Hessian matrix at each time-step, that is, without any approximation, and other Hessian approximation schemes. Finally, the method is applied to the on-the-fly, full-dimensional simulation of a small synthetic peptide (the 46 atom N-acetyl-l-phenylalaninyl-l-methionine amide) at the level of DFT-B3LYP-D/6-31G* theory, from which the semiclassical vibrational power spectrum is calculated.
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Affiliation(s)
- Michele Gandolfi
- Dipartimento di Chimica, Università
degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università
degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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14
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Golubev NV, Vaníček J, Kuleff AI. Core-Valence Attosecond Transient Absorption Spectroscopy of Polyatomic Molecules. PHYSICAL REVIEW LETTERS 2021; 127:123001. [PMID: 34597071 DOI: 10.1103/physrevlett.127.123001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 07/01/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Tracing ultrafast processes induced by interaction of light with matter is often very challenging. In molecular systems, the initially created electronic coherence becomes damped by the slow nuclear rearrangement on a femtosecond timescale which makes real-time observations of electron dynamics in molecules particularly difficult. In this work, we report an extension of the theory underlying the attosecond transient absorption spectroscopy (ATAS) for the case of molecules, including a full account for the coupled electron-nuclear dynamics in the initially created wave packet, and apply it to probe the oscillations of the positive charge created after outer-valence ionization of the propiolic acid molecule. By taking advantage of element-specific core-to-valence transitions induced by x-ray radiation, we show that the resolution of ATAS makes it possible to trace the dynamics of electron density with atomic spatial resolution.
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Affiliation(s)
- Nikolay V Golubev
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alexander I Kuleff
- Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany and ELI-ALPS, Wolfgang Sandner utca 3, H-6728 Szeged, Hungary
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15
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Begušić T, Vaníček J. Finite-Temperature, Anharmonicity, and Duschinsky Effects on the Two-Dimensional Electronic Spectra from Ab Initio Thermo-Field Gaussian Wavepacket Dynamics. J Phys Chem Lett 2021; 12:2997-3005. [PMID: 33733773 PMCID: PMC8006135 DOI: 10.1021/acs.jpclett.1c00123] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/08/2021] [Indexed: 05/28/2023]
Abstract
Accurate description of finite-temperature vibrational dynamics is indispensable in the computation of two-dimensional electronic spectra. Such simulations are often based on the density matrix evolution, statistical averaging of initial vibrational states, or approximate classical or semiclassical limits. While many practical approaches exist, they are often of limited accuracy and difficult to interpret. Here, we use the concept of thermo-field dynamics to derive an exact finite-temperature expression that lends itself to an intuitive wavepacket-based interpretation. Furthermore, an efficient method for computing finite-temperature two-dimensional spectra is obtained by combining the exact thermo-field dynamics approach with the thawed Gaussian approximation for the wavepacket dynamics, which is exact for any displaced, distorted, and Duschinsky-rotated harmonic potential but also accounts partially for anharmonicity effects in general potentials. Using this new method, we directly relate a symmetry breaking of the two-dimensional signal to the deviation from the conventional Brownian oscillator picture.
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16
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Rognoni A, Conte R, Ceotto M. Caldeira-Leggett model vs ab initio potential: A vibrational spectroscopy test of water solvation. J Chem Phys 2021; 154:094106. [PMID: 33685187 DOI: 10.1063/5.0040494] [Citation(s) in RCA: 8] [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 present a semiclassically approximate quantum treatment of solvation with the purpose of investigating the accuracy of the Caldeira-Leggett model. We do that by simulating the vibrational features of water solvation by means of two different approaches. One is entirely based on the adoption of an accurate ab initio potential to describe water clusters of increasing dimensionality. The other one consists of a model made of a central water molecule coupled to a high-dimensional Caldeira-Leggett harmonic bath. We demonstrate the role of quantum effects in the detection of water solvation and show that the computationally cheap approach based on the Caldeira-Leggett bath is only partially effective. The main conclusion of the study is that quantum methods associated with high-level potential energy surfaces are necessary to correctly study solvation features, while simplified models, even if attractive owing to their reduced computational cost, can provide some useful insights but are not able to come up with a comprehensive description of the solvation phenomenon.
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Affiliation(s)
- Alessandro Rognoni
- Dipartimento di Chimica, Universitá degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Universitá degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Universitá degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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17
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Werther M, Choudhury SL, Großmann F. Coherent state based solutions of the time-dependent Schrödinger equation: hierarchy of approximations to the variational principle. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1823168] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Michael Werther
- Max-Planck-Institut für Physik Komplexer Systeme, Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, Dresden, Germany
| | | | - Frank Großmann
- Institut für Theoretische Physik, Technische Universität Dresden, Dresden, Germany
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18
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Golubev NV, Begušić T, Vaníček J. On-the-Fly Ab Initio Semiclassical Evaluation of Electronic Coherences in Polyatomic Molecules Reveals a Simple Mechanism of Decoherence. PHYSICAL REVIEW LETTERS 2020; 125:083001. [PMID: 32909765 DOI: 10.1103/physrevlett.125.083001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
Irradiation of a molecular system by an intense laser field can trigger dynamics of both electronic and nuclear subsystems. The lighter electrons usually move on much faster, attosecond timescale but the slow nuclear rearrangement damps ultrafast electronic oscillations, leading to the decoherence of the electronic dynamics within a few femtoseconds. We show that a simple, single-trajectory semiclassical scheme can evaluate the electronic coherence time in polyatomic molecules accurately by demonstrating an excellent agreement with full-dimensional quantum calculations. In contrast to numerical quantum methods, the semiclassical one reveals the physical mechanism of decoherence beyond the general blame on nuclear motion. In the propiolic acid, the rate of decoherence and the large deviation from the static frequency of electronic oscillations are quantitatively described with just two semiclassical parameters-the phase space distance and signed area between the trajectories moving on two electronic surfaces. Because it evaluates the electronic structure on the fly, the semiclassical technique avoids the "curse of dimensionality" and should be useful for preselecting molecules for experimental studies.
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Affiliation(s)
- Nikolay V Golubev
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tomislav Begušić
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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19
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Begušić T, Vaníček J. On-the-fly ab initio semiclassical evaluation of vibronic spectra at finite temperature. J Chem Phys 2020; 153:024105. [PMID: 32668922 DOI: 10.1063/5.0013677] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To compute and analyze vibrationally resolved electronic spectra at zero temperature, we have recently implemented the on-the-fly ab initio extended thawed Gaussian approximation [A. Patoz et al., J. Phys. Chem. Lett. 9, 2367 (2018)], which accounts for anharmonicity, mode-mode coupling, and Herzberg-Teller effects. Here, we generalize this method in order to evaluate spectra at non-zero temperature. In line with thermo-field dynamics, we transform the von Neumann evolution of the coherence component of the density matrix to the Schrödinger evolution of a wavefunction in an augmented space with twice as many degrees of freedom. Due to the efficiency of the extended thawed Gaussian approximation, this increase in the number of coordinates results in nearly no additional computational cost. More specifically, compared to the original, zero-temperature approach, the finite-temperature method requires no additional ab initio electronic structure calculations. At the same time, the new approach allows for a clear distinction among finite-temperature, anharmonicity, and Herzberg-Teller effects on spectra. We show, on a model Morse system, the advantages of the finite-temperature thawed Gaussian approximation over the commonly used global harmonic methods and apply it to evaluate the symmetry-forbidden absorption spectrum of benzene, where all of the aforementioned effects contribute.
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Affiliation(s)
- Tomislav Begušić
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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20
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Gabas F, Conte R, Ceotto M. Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields. J Chem Theory Comput 2020; 16:3476-3485. [PMID: 32374992 PMCID: PMC7901649 DOI: 10.1021/acs.jctc.0c00127] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Semiclassical spectroscopy is a practical way to get an accurately approximate quantum
description of spectral features starting from ab initio molecular
dynamics simulations. The computational bottleneck for the method is represented by the
cost of ab initio potential, gradient, and Hessian matrix estimates.
This drawback is particularly severe for biological systems due to their unique
complexity and large dimensionality. The main goal of this manuscript is to demonstrate
that quantum dynamics and spectroscopy, at the level of semiclassical approximation, are
doable even for sizable biological systems. To this end, we investigate the possibility
of performing semiclassical spectroscopy simulations when ab initio
calculations are replaced by computationally cheaper force field evaluations. Both
polarizable (AMOEBABIO18) and nonpolarizable (AMBER14SB) force fields are tested.
Calculations of some particular vibrational frequencies of four nucleosides, i.e.,
uridine, thymidine, deoxyguanosine, and adenosine, show that ab initio
simulations are accurate and widely applicable. Conversely, simulations based on
AMBER14SB are limited to harmonic approximations, but those relying on AMOEBABIO18 yield
acceptable semiclassical values if the investigated conformation has been included in
the force field parametrization. The main conclusion is that AMOEBABIO18 may provide a
viable route to assist semiclassical spectroscopy in the study of large biological
molecules for which an ab initio approach is not computationally
affordable.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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21
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Cazzaniga M, Micciarelli M, Moriggi F, Mahmoud A, Gabas F, Ceotto M. Anharmonic calculations of vibrational spectra for molecular adsorbates: A divide-and-conquer semiclassical molecular dynamics approach. J Chem Phys 2020; 152:104104. [PMID: 32171221 DOI: 10.1063/1.5142682] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational spectroscopy of adsorbates is becoming an important investigation tool for catalysis and material science. This paper presents a semiclassical molecular dynamics method able to reproduce the vibrational energy levels of systems composed by molecules adsorbed on solid surfaces. Specifically, we extend our divide-and-conquer semiclassical method for power spectra calculations to gas-surface systems and interface it with plane-wave electronic structure codes. The Born-Oppenheimer classical dynamics underlying the semiclassical calculation is full dimensional, and our method includes not only the motion of the adsorbate but also those of the surface and the bulk. The vibrational spectroscopic peaks related to the adsorbate are accounted together with the most coupled phonon modes to obtain spectra amenable to physical interpretations. We apply the method to the adsorption of CO, NO, and H2O on the anatase-TiO2 (101) surface. We compare our semiclassical results with the single-point harmonic estimates and the classical power spectra obtained from the same trajectory employed in the semiclassical calculation. We find that CO and NO anharmonic effects of fundamental vibrations are similarly reproduced by the classical and semiclassical dynamics and that H2O adsorption is fully and properly described in its overtone and combination band relevant components only by the semiclassical approach.
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Affiliation(s)
- Marco Cazzaniga
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Marco Micciarelli
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Francesco Moriggi
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Agnes Mahmoud
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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22
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Prlj A, Begušić T, Zhang ZT, Fish GC, Wehrle M, Zimmermann T, Choi S, Roulet J, Moser JE, Vaníček J. Semiclassical Approach to Photophysics Beyond Kasha's Rule and Vibronic Spectroscopy Beyond the Condon Approximation. The Case of Azulene. J Chem Theory Comput 2020; 16:2617-2626. [PMID: 32119547 DOI: 10.1021/acs.jctc.0c00079] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Azulene is a prototypical molecule with an anomalous fluorescence from the second excited electronic state, thus violating Kasha's rule, and with an emission spectrum that cannot be understood within the Condon approximation. To better understand the photophysics and spectroscopy of azulene and other nonconventional molecules, we developed a systematic, general, and efficient computational approach combining the semiclassical dynamics of nuclei with ab initio electronic structure. First, to analyze the nonadiabatic effects, we complement the standard population dynamics by a rigorous measure of adiabaticity, estimated with the multiple-surface dephasing representation. Second, we propose a new semiclassical method for simulating non-Condon spectra, which combines the extended thawed Gaussian approximation with the efficient single-Hessian approach. S1 ← S0 and S2 ← S0 absorption and S2 → S0 emission spectra of azulene, recorded in a new set of experiments, agree very well with our calculations. We find that accuracy of the evaluated spectra requires the treatment of anharmonicity, Herzberg-Teller, and mode-mixing effects.
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Affiliation(s)
- Antonio Prlj
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tomislav Begušić
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Zhan Tong Zhang
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - George Cameron Fish
- Photochemical Dynamics Group, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Marius Wehrle
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tomáš Zimmermann
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Seonghoon Choi
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Julien Roulet
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jacques-Edouard Moser
- Photochemical Dynamics Group, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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23
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Choi S, Vaníček J. A time-reversible integrator for the time-dependent Schrödinger equation on an adaptive grid. J Chem Phys 2019; 151:234102. [PMID: 31864241 DOI: 10.1063/1.5127856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the most accurate methods for solving the time-dependent Schrödinger equation uses a combination of the dynamic Fourier method with the split-operator algorithm on a tensor-product grid. To reduce the number of required grid points, we let the grid move together with the wavepacket but find that the naïve algorithm based on an alternate evolution of the wavefunction and grid destroys the time reversibility of the exact evolution. Yet, we show that the time reversibility is recovered if the wavefunction and grid are evolved simultaneously during each kinetic or potential step; this is achieved by using the Ehrenfest theorem together with the splitting method. The proposed algorithm is conditionally stable, symmetric, and time-reversible and conserves the norm of the wavefunction. The preservation of these geometric properties is shown analytically and demonstrated numerically on a three-dimensional harmonic model and collinear model of He-H2 scattering. We also show that the proposed algorithm can be symmetrically composed to obtain time-reversible integrators of an arbitrary even order. We observed 10 000-fold speedup by using the tenth-order instead of the second-order method to obtain a solution with a time discretization error below 10-9. Moreover, using the adaptive grid instead of the fixed grid resulted in a 64-fold reduction in the required number of grid points in the harmonic system and made it possible to simulate the He-H2 scattering for six times longer while maintaining reasonable accuracy. Applicability of the algorithm to high-dimensional quantum dynamics is demonstrated using the strongly anharmonic eight-dimensional Hénon-Heiles model.
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Affiliation(s)
- Seonghoon Choi
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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24
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Conte R, Parma L, Aieta C, Rognoni A, Ceotto M. Improved semiclassical dynamics through adiabatic switching trajectory sampling. J Chem Phys 2019; 151:214107. [PMID: 31822104 DOI: 10.1063/1.5133144] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce an improved semiclassical dynamics approach to quantum vibrational spectroscopy. In this method, a harmonic-based phase space sampling is preliminarily driven toward non-harmonic quantization by slowly switching on the actual potential. The new coordinates and momenta serve as initial conditions for the semiclassical dynamics calculation, leading to a substantial decrease in the number of chaotic trajectories to deal with. Applications are presented for model and molecular systems of increasing dimensionality characterized by moderate or high chaoticity. They include a bidimensional Henon-Heiles potential, water, formaldehyde, and methane. The method improves accuracy and precision of semiclassical results and it can be easily interfaced with all pre-existing semiclassical theories.
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Affiliation(s)
- Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Lorenzo Parma
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Chiara Aieta
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Alessandro Rognoni
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
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25
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Bertaina G, Di Liberto G, Ceotto M. Reduced rovibrational coupling Cartesian dynamics for semiclassical calculations: Application to the spectrum of the Zundel cation. J Chem Phys 2019; 151:114307. [PMID: 31542046 DOI: 10.1063/1.5114616] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the vibrational spectrum of the protonated water dimer, by means of a divide-and-conquer semiclassical initial value representation of the quantum propagator, as a first step in the study of larger protonated water clusters. We use the potential energy surface from the work of Huang et al. [J. Chem. Phys. 122, 044308 (2005)]. To tackle such an anharmonic and floppy molecule, we employ fully Cartesian dynamics and carefully reduce the coupling to global rotations in the definition of normal modes. We apply the time-averaging filter and obtain clean power spectra relative to suitable reference states that highlight the spectral peaks corresponding to the fundamental excitations of the system. Our trajectory-based approach allows for the physical interpretation of the very challenging proton transfer modes. We find that it is important, for such a floppy molecule, to selectively avoid initially exciting lower energy modes, in order to obtain cleaner spectra. The estimated vibrational energies display a mean absolute error (MAE) of ∼29 cm-1 with respect to available multiconfiguration time-dependent Hartree calculations and MAE ∼ 14 cm-1 when compared to the optically active experimental excitations of the Ne-tagged Zundel cation. The reasonable scaling in the number of trajectories for Monte Carlo convergence is promising for applications to higher dimensional protonated cluster systems.
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Affiliation(s)
- G Bertaina
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - G Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - M Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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26
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Conte R, Gabas F, Botti G, Zhuang Y, Ceotto M. Semiclassical vibrational spectroscopy with Hessian databases. J Chem Phys 2019; 150:244118. [PMID: 31255076 DOI: 10.1063/1.5109086] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report on a new approach to ease the computational overhead of ab initio "on-the-fly" semiclassical dynamics simulations for vibrational spectroscopy. The well known bottleneck of such computations lies in the necessity to estimate the Hessian matrix for propagating the semiclassical pre-exponential factor at each step along the dynamics. The procedure proposed here is based on the creation of a dynamical database of Hessians and associated molecular geometries able to speed up calculations while preserving the accuracy of results at a satisfactory level. This new approach can be interfaced to both analytical potential energy surfaces and on-the-fly dynamics, allowing one to study even large systems previously not achievable. We present results obtained for semiclassical vibrational power spectra of methane, glycine, and N-acetyl-L-phenylalaninyl-L-methionine-amide, a molecule of biological interest made of 46 atoms.
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Affiliation(s)
- Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Giacomo Botti
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Yu Zhuang
- Department of Computer Science, Texas Tech University, Lubbock, Texas 79409-3104, USA
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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