1
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Käser S, Meuwly M. Numerical Accuracy Matters: Applications of Machine Learned Potential Energy Surfaces. J Phys Chem Lett 2024:3419-3424. [PMID: 38506827 DOI: 10.1021/acs.jpclett.3c03405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The role of numerical accuracy in training and evaluating neural network-based potential energy surfaces is examined for different experimental observables. For observables that require third- and fourth-order derivatives of the potential energy with respect to Cartesian coordinates single-precision arithmetics as is typically used in ML-based approaches is insufficient and leads to roughness of the underlying PES as is explicitly demonstrated. Increasing the numerical accuracy to double-precision gives a smooth PES with higher-order derivatives that are numerically stable and yield meaningful anharmonic frequencies and tunneling splitting as is demonstrated for H2CO and malonaldehyde. For molecular dynamics simulations, which only require first-order derivatives, single-precision arithmetics appears to be sufficient, though.
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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2
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Suzuki H, Wang L, Bertinshaw J, Strand HUR, Käser S, Krautloher M, Yang Z, Wentzell N, Parcollet O, Jerzembeck F, Kikugawa N, Mackenzie AP, Georges A, Hansmann P, Gretarsson H, Keimer B. Distinct spin and orbital dynamics in Sr 2RuO 4. Nat Commun 2023; 14:7042. [PMID: 37923750 PMCID: PMC10624926 DOI: 10.1038/s41467-023-42804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
The unconventional superconductor Sr2RuO4 has long served as a benchmark for theories of correlated-electron materials. The determination of the superconducting pairing mechanism requires detailed experimental information on collective bosonic excitations as potential mediators of Cooper pairing. We have used Ru L3-edge resonant inelastic x-ray scattering to obtain comprehensive maps of the electronic excitations of Sr2RuO4 over the entire Brillouin zone. We observe multiple branches of dispersive spin and orbital excitations associated with distinctly different energy scales. The spin and orbital dynamical response functions calculated within the dynamical mean-field theory are in excellent agreement with the experimental data. Our results highlight the Hund metal nature of Sr2RuO4 and provide key information for the understanding of its unconventional superconductivity.
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Affiliation(s)
- H Suzuki
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany.
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, 980-8578, Japan.
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai, 980-8578, Japan.
| | - L Wang
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany
| | - J Bertinshaw
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany
| | - H U R Strand
- School of Science and Technology, Örebro University, Fakultetsgatan 1, SE-701 82, Örebro, Sweden
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, the Netherlands
| | - S Käser
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany
- Department of Physics, Friedrich-Alexander-University (FAU) of Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - M Krautloher
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany
| | - Z Yang
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany
| | - N Wentzell
- Center for Computational Quantum Physics, Flatiron Institute, Simons Foundation, 162 5th Avenue, New York, 10010, USA
| | - O Parcollet
- Center for Computational Quantum Physics, Flatiron Institute, Simons Foundation, 162 5th Avenue, New York, 10010, USA
- Université Paris-Saclay, CNRS, CEA, Institut de physique théorique, 91191, Gif-sur-Yvette, France
| | - F Jerzembeck
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187, Dresden, Germany
| | - N Kikugawa
- National Institute for Materials Science, Tsukuba, Ibaraki, 305-0003, Japan
| | - A P Mackenzie
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187, Dresden, Germany
| | - A Georges
- Center for Computational Quantum Physics, Flatiron Institute, Simons Foundation, 162 5th Avenue, New York, 10010, USA
- Collége de France, 11 place Marcelin Berthelot, 75005, Paris, France
- Centre de Physique Théorique (CPHT), CNRS, Ecole Polytechnique, IP Paris, 91128, Palaiseau, France
- Department of Quantum Matter Physics, University of Geneva, 24 Quai Ernest-Ansermet, 1211, Geneva 4, Switzerland
| | - P Hansmann
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany
- Department of Physics, Friedrich-Alexander-University (FAU) of Erlangen-Nürnberg, 91058, Erlangen, Germany
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187, Dresden, Germany
| | - H Gretarsson
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany.
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607, Hamburg, Germany.
| | - B Keimer
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, D-70569, Stuttgart, Germany.
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Fischer TL, Bödecker M, Schweer SM, Dupont J, Lepère V, Zehnacker-Rentien A, Suhm MA, Schröder B, Henkes T, Andrada DM, Balabin RM, Singh HK, Bhattacharyya HP, Sarma M, Käser S, Töpfer K, Vazquez-Salazar LI, Boittier ED, Meuwly M, Mandelli G, Lanzi C, Conte R, Ceotto M, Dietrich F, Cisternas V, Gnanasekaran R, Hippler M, Jarraya M, Hochlaf M, Viswanathan N, Nevolianis T, Rath G, Kopp WA, Leonhard K, Mata RA. The first HyDRA challenge for computational vibrational spectroscopy. Phys Chem Chem Phys 2023; 25:22089-22102. [PMID: 37610422 DOI: 10.1039/d3cp01216f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the vacuum-isolated monohydrates of formaldehyde, tetrahydrofuran, pyridine, tetrahydrothiophene, trifluoroethanol, methyl lactate, dimethylimidazolidinone, cyclooctanone, trifluoroacetophenone and 1-phenylcyclohexane-cis-1,2-diol are provided. The results of the challenge show promising predictive properties in both purely quantum mechanical approaches as well as regression and other machine learning strategies.
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Affiliation(s)
- Taija L Fischer
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstraße 6, Göttingen, Germany.
| | - Margarethe Bödecker
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstraße 6, Göttingen, Germany.
| | - Sophie M Schweer
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstraße 6, Göttingen, Germany.
| | - Jennifer Dupont
- Institut des Sciences Moléculaires dOrsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Valéria Lepère
- Institut des Sciences Moléculaires dOrsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Anne Zehnacker-Rentien
- Institut des Sciences Moléculaires dOrsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Martin A Suhm
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstraße 6, Göttingen, Germany.
| | - Benjamin Schröder
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstraße 6, Göttingen, Germany.
| | - Tobias Henkes
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Diego M Andrada
- Institute for Inorganic Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Roman M Balabin
- Bond Street Holdings, Long Point Road, KN-1002 Henville Building 9, Charlestown, KN10 Nevis, St. Kitts and Nevis
| | - Haobam Kisan Singh
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam-781039, India
| | | | - Manabendra Sarma
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam-781039, India
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Luis I Vazquez-Salazar
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Giacomo Mandelli
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Cecilia Lanzi
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Fabian Dietrich
- Department of Physics Science, Universidad de La Frontera, Francisco Salazar 01145, Temuco, Chile
| | - Vicente Cisternas
- Department of Physics Science, Universidad de La Frontera, Francisco Salazar 01145, Temuco, Chile
| | - Ramachandran Gnanasekaran
- Vellore Institute of Technology, School of Advanced Sciences (SAS), ChemistryDivision, Chennai 600 027, India
| | - Michael Hippler
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| | - Mahmoud Jarraya
- U. Gustave Eiffel, COSYS/IMSE, 5 BD Descartes 77454, Champs-sur-Marne, France
| | - Majdi Hochlaf
- U. Gustave Eiffel, COSYS/IMSE, 5 BD Descartes 77454, Champs-sur-Marne, France
| | - Narasimhan Viswanathan
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstraße 8, D-52072 Aachen, Germany
| | - Thomas Nevolianis
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstraße 8, D-52072 Aachen, Germany
| | - Gabriel Rath
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstraße 8, D-52072 Aachen, Germany
| | - Wassja A Kopp
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstraße 8, D-52072 Aachen, Germany
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstraße 8, D-52072 Aachen, Germany
| | - Ricardo A Mata
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstraße 6, Göttingen, Germany.
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4
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Song K, Käser S, Töpfer K, Vazquez-Salazar LI, Meuwly M. PhysNet meets CHARMM: A framework for routine machine learning/molecular mechanics simulations. J Chem Phys 2023; 159:024125. [PMID: 37435940 DOI: 10.1063/5.0155992] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/19/2023] [Indexed: 07/13/2023] Open
Abstract
Full-dimensional potential energy surfaces (PESs) based on machine learning (ML) techniques provide a means for accurate and efficient molecular simulations in the gas and condensed phase for various experimental observables ranging from spectroscopy to reaction dynamics. Here, the MLpot extension with PhysNet as the ML-based model for a PES is introduced into the newly developed pyCHARMM application programming interface. To illustrate the conception, validation, refining, and use of a typical workflow, para-chloro-phenol is considered as an example. The main focus is on how to approach a concrete problem from a practical perspective and applications to spectroscopic observables and the free energy for the -OH torsion in solution are discussed in detail. For the computed IR spectra in the fingerprint region, the computations for para-chloro-phenol in water are in good qualitative agreement with experiment carried out in CCl4. Moreover, relative intensities are largely consistent with experimental findings. The barrier for rotation of the -OH group increases from ∼3.5 kcal/mol in the gas phase to ∼4.1 kcal/mol from simulations in water due to favorable H-bonding interactions of the -OH group with surrounding water molecules.
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Affiliation(s)
- Kaisheng Song
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | | | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
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5
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Käser S, Meuwly M. Transfer-learned potential energy surfaces: Toward microsecond-scale molecular dynamics simulations in the gas phase at CCSD(T) quality. J Chem Phys 2023; 158:2893719. [PMID: 37260004 DOI: 10.1063/5.0151266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/30/2023] [Indexed: 06/02/2023] Open
Abstract
The rise of machine learning has greatly influenced the field of computational chemistry and atomistic molecular dynamics simulations in particular. One of its most exciting prospects is the development of accurate, full-dimensional potential energy surfaces (PESs) for molecules and clusters, which, however, often require thousands to tens of thousands of ab initio data points restricting the community to medium sized molecules and/or lower levels of theory (e.g., density functional theory). Transfer learning, which improves a global PES from a lower to a higher level of theory, offers a data efficient alternative requiring only a fraction of the high-level data (on the order of 100 are found to be sufficient for malonaldehyde). This work demonstrates that even with Hartree-Fock theory and a double-zeta basis set as the lower level model, transfer learning yields coupled-cluster single double triple [CCSD(T)]-level quality for H-transfer barrier energies, harmonic frequencies, and H-transfer tunneling splittings. Most importantly, finite-temperature molecular dynamics simulations on the sub-μs time scale in the gas phase are possible and the infrared spectra determined from the transfer-learned PESs are in good agreement with the experiment. It is concluded that routine, long-time atomistic simulations on PESs fulfilling CCSD(T)-standards become possible.
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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6
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Kilaj A, Käser S, Wang J, Straňák P, Schwilk M, Xu L, von Lilienfeld OA, Küpper J, Meuwly M, Willitsch S. Conformational and state-specific effects in reactions of 2,3-dibromobutadiene with Coulomb-crystallized calcium ions. Phys Chem Chem Phys 2023; 25:13933-13945. [PMID: 37190820 DOI: 10.1039/d3cp01416a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Recent advances in experimental methodology enabled studies of the quantum-state- and conformational dependence of chemical reactions under precisely controlled conditions in the gas phase. Here, we generated samples of selected gauche and s-trans 2,3-dibromobutadiene (DBB) by electrostatic deflection in a molecular beam and studied their reaction with Coulomb crystals of laser-cooled Ca+ ions in an ion trap. The rate coefficients for the total reaction were found to strongly depend on both the conformation of DBB and the electronic state of Ca+. In the (4p)2P1/2 and (3d)2D3/2 excited states of Ca+, the reaction is capture-limited and faster for the gauche conformer due to long-range ion-dipole interactions. In the (4s)2S1/2 ground state of Ca+, the reaction rate for s-trans DBB still conforms with the capture limit, while that for gauche DBB is strongly suppressed. The experimental observations were analysed with the help of adiabatic capture theory, ab initio calculations and reactive molecular dynamics simulations on a machine-learned full-dimensional potential energy surface of the system. The theory yields near-quantitative agreement for s-trans-DBB, but overestimates the reactivity of the gauche-conformer compared to the experiment. The present study points to the important role of molecular geometry even in strongly reactive exothermic systems and illustrates striking differences in the reactivity of individual conformers in gas-phase ion-molecule reactions.
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Affiliation(s)
- Ardita Kilaj
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
| | - Jia Wang
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Patrik Straňák
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
| | - Max Schwilk
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
| | - Lei Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
| | - O Anatole von Lilienfeld
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
- Vector Institute for Artificial Intelligence, Toronto, ON, M5S 1M1, Canada
- Departments of Chemistry, Materials Science and Engineering, and Physics, University of Toronto, St. George Campus, Toronto, ON M5S 3H6, Canada
- Machine Learning Group, Technische Universität Berlin, 10587 Berlin, Germany
- Berlin Institute for the Foundations of Learning and Data - BIFOLD, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
- Department of Chemistry, Brown University, Providence, RI 02912, USA
| | - Stefan Willitsch
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
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Käser S, Vazquez-Salazar LI, Meuwly M, Töpfer K. Neural network potentials for chemistry: concepts, applications and prospects. Digit Discov 2023; 2:28-58. [PMID: 36798879 PMCID: PMC9923808 DOI: 10.1039/d2dd00102k] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Artificial Neural Networks (NN) are already heavily involved in methods and applications for frequent tasks in the field of computational chemistry such as representation of potential energy surfaces (PES) and spectroscopic predictions. This perspective provides an overview of the foundations of neural network-based full-dimensional potential energy surfaces, their architectures, underlying concepts, their representation and applications to chemical systems. Methods for data generation and training procedures for PES construction are discussed and means for error assessment and refinement through transfer learning are presented. A selection of recent results illustrates the latest improvements regarding accuracy of PES representations and system size limitations in dynamics simulations, but also NN application enabling direct prediction of physical results without dynamics simulations. The aim is to provide an overview for the current state-of-the-art NN approaches in computational chemistry and also to point out the current challenges in enhancing reliability and applicability of NN methods on a larger scale.
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel Klingelbergstrasse 80 CH-4056 Basel Switzerland
| | | | - Markus Meuwly
- Department of Chemistry, University of Basel Klingelbergstrasse 80 CH-4056 Basel Switzerland
| | - Kai Töpfer
- Department of Chemistry, University of Basel Klingelbergstrasse 80 CH-4056 Basel Switzerland
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8
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Käser S, Richardson JO, Meuwly M. Transfer Learning for Affordable and High-Quality Tunneling Splittings from Instanton Calculations. J Chem Theory Comput 2022; 18:6840-6850. [DOI: 10.1021/acs.jctc.2c00790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | | | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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9
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Käser S, Meuwly M. Correction: Transfer learned potential energy surfaces: accurate anharmonic vibrational dynamics and dissociation energies for the formic acid monomer and dimer. Phys Chem Chem Phys 2022; 24:17899. [PMID: 35852230 PMCID: PMC9328181 DOI: 10.1039/d2cp90126a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for ‘Transfer learned potential energy surfaces: accurate anharmonic vibrational dynamics and dissociation energies for the formic acid monomer and dimer’ by Silvan Käser et al., Phys. Chem. Chem. Phys., 2022, 24, 5269–5281, https://doi.org/10.1039/D1CP04393E.
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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10
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Töpfer K, Käser S, Meuwly M. Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity. Phys Chem Chem Phys 2022; 24:13869-13882. [PMID: 35620978 PMCID: PMC9176184 DOI: 10.1039/d2cp01583h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The double proton transfer (DPT) reaction in the hydrated formic acid dimer (FAD) is investigated at molecular-level detail. For this, a global and reactive machine learned (ML) potential energy surface (PES) is developed to run extensive (more than 100 ns) mixed ML/MM molecular dynamics (MD) simulations in explicit molecular mechanics (MM) solvent at MP2-quality for the solute. Simulations with fixed – as in a conventional empirical force field – and conformationally fluctuating – as available from the ML-based PES – charge models for FAD show a significant impact on the competition between DPT and dissociation of FAD into two formic acid monomers. With increasing temperature the barrier height for DPT in solution changes by about 10% (∼1 kcal mol−1) between 300 K and 600 K. The rate for DPT is largest, ∼1 ns−1, at 350 K and decreases for higher temperatures due to destabilisation and increased probability for dissociation of FAD. The water solvent is found to promote the first proton transfer by exerting a favourable solvent-induced Coulomb force along the O–H⋯O hydrogen bond whereas the second proton transfer is significantly controlled by the O–O separation and other conformational degrees of freedom. Double proton transfer in hydrated FAD is found to involve a subtle interplay and balance between structural and electrostatic factors. Simulation of double proton transfer in formic acid dimer by reactive ML potential in explicit molecular mechanics water solvent.![]()
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Affiliation(s)
- Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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11
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Salehi SM, Käser S, Töpfer K, Diamantis P, Pfister R, Hamm P, Rothlisberger U, Meuwly M. Hydration dynamics and IR spectroscopy of 4-fluorophenol. Phys Chem Chem Phys 2022; 24:26046-26060. [PMID: 36268728 PMCID: PMC9627945 DOI: 10.1039/d2cp02857c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of para-fluorophenol (F-PhOH) and phenol (PhOH) is investigated in the gas phase and in water using a combination of experiment and molecular dynamics (MD) simulations. The gas phase and solvent dynamics around F-PhOH and PhOH is characterized from atomistic simulations using empirical energy functions with point charges or multipoles for the electrostatics, Machine Learning (ML) based parametrizations and with full ab initio (QM) and mixed Quantum Mechanical/Molecular Mechanics (QM/MM) simulations with a particular focus on the CF- and OH-stretch region. The CF-stretch band is heavily mixed with other modes whereas the OH-stretch in solution displays a characteristic high-frequency peak around 3600 cm−1 most likely associated with the –OH group of PhOH and F-PhOH together with a characteristic progression below 3000 cm−1 due to coupling with water modes which is also reproduced by several of the simulations. Solvent and radial distribution functions indicate that the CF-site is largely hydrophobic except for simulations using point charges which renders them unsuited for correctly describing hydration and dynamics around fluorinated sites. The hydrophobic character of the CF-group is particularly relevant for applications in pharmaceutical chemistry with a focus on local hydration and interaction with the surrounding protein. Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy.![]()
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Polydefkis Diamantis
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Rolf Pfister
- Department of Chemistry, University of Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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Käser S, Meuwly M. Transfer learned potential energy surfaces: accurate anharmonic vibrational dynamics and dissociation energies for the formic acid monomer and dimer. Phys Chem Chem Phys 2021; 24:5269-5281. [PMID: 34792523 PMCID: PMC8890265 DOI: 10.1039/d1cp04393e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational dynamics of the formic acid monomer (FAM) and dimer (FAD) is investigated from machine-learned potential energy surfaces at the MP2 (PESMP2) and transfer-learned (PESTL) to the CCSD(T) levels of theory. The normal mode (MAEs of 17.6 and 25.1 cm−1) and second order vibrational perturbation theory (VPT2, MAEs of 6.7 and 17.1 cm−1) frequencies from PESTL for all modes below 2000 cm−1 for FAM and FAD agree favourably with experiment. For the OH stretch mode the experimental frequencies are overestimated by more than 150 cm−1 for both FAM and FAD from normal mode calculations. Conversely, VPT2 calculations on PESTL for FAM reproduce the experimental OH frequency to within 22 cm−1. For FAD the VPT2 calculations find the high-frequency OH stretch at 3011 cm−1, compared with an experimentally reported, broad (∼100 cm−1) absorption band with center frequency estimated at ∼3050 cm−1. In agreement with earlier reports, MD simulations at higher temperature shift the position of the OH-stretch in FAM to the red, consistent with improved sampling of the anharmonic regions of the PES. However, for FAD the OH-stretch shifts to the blue and for temperatures higher than 1000 K the dimer partly or fully dissociates using PESTL. Including zero-point energy corrections from diffusion Monte Carlo simulations for FAM and FAD and corrections due to basis set superposition and completeness errors yields a dissociation energy of D0 = −14.23 ± 0.08 kcal mol−1 compared with an experimentally determined value of −14.22 ± 0.12 kcal mol−1. Neural network based PESs are constructed for formic acid monomer and dimer at the MP2 and transfer learned to the CCSD(T) level of theory. The PESs are used to study the vibrational dynamics and dissociation energy of the molecules.![]()
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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Käser S, Boittier ED, Upadhyay M, Meuwly M. Transfer Learning to CCSD(T): Accurate Anharmonic Frequencies from Machine Learning Models. J Chem Theory Comput 2021; 17:3687-3699. [PMID: 33960787 DOI: 10.1021/acs.jctc.1c00249] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The calculation of the anharmonic modes of small- to medium-sized molecules for assigning experimentally measured frequencies to the corresponding type of molecular motions is computationally challenging at sufficiently high levels of quantum chemical theory. Here, a practical and affordable way to calculate coupled-cluster quality anharmonic frequencies using second-order vibrational perturbation theory (VPT2) from machine-learned models is presented. The approach, referenced as "NN + VPT2", uses a high-dimensional neural network (PhysNet) to learn potential energy surfaces (PESs) at different levels of theory from which harmonic and VPT2 frequencies can be efficiently determined. The NN + VPT2 approach is applied to eight small- to medium-sized molecules (H2CO, trans-HONO, HCOOH, CH3OH, CH3CHO, CH3NO2, CH3COOH, and CH3CONH2) and frequencies are reported from NN-learned models at the MP2/aug-cc-pVTZ, CCSD(T)/aug-cc-pVTZ, and CCSD(T)-F12/aug-cc-pVTZ-F12 levels of theory. For the largest molecules and at the highest levels of theory, transfer learning (TL) is used to determine the necessary full-dimensional, near-equilibrium PESs. Overall, NN + VPT2 yields anharmonic frequencies to within 20 cm-1 of experimentally determined frequencies for close to 90% of the modes for the highest quality PES available and to within 10 cm-1 for more than 60% of the modes. For the MP2 PESs only ∼60% of the NN + VPT2 frequencies were within 20 cm-1 of the experiment, with outliers up to ∼150 cm-1, compared to the experiment. It is also demonstrated that the approach allows to provide correct assignments for strongly interacting modes such as the OH bending and the OH torsional modes in formic acid monomer and the CO-stretch and OH-bend mode in acetic acid.
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Meenu Upadhyay
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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Käser S, Koner D, Christensen AS, von Lilienfeld OA, Meuwly M. Machine Learning Models of Vibrating H2CO: Comparing Reproducing Kernels, FCHL, and PhysNet. J Phys Chem A 2020; 124:8853-8865. [DOI: 10.1021/acs.jpca.0c05979] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Debasish Koner
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Anders S. Christensen
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - O. Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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Arnold J, Koner D, Käser S, Singh N, Bemish RJ, Meuwly M. Machine Learning for Observables: Reactant to Product State Distributions for Atom–Diatom Collisions. J Phys Chem A 2020; 124:7177-7190. [DOI: 10.1021/acs.jpca.0c05173] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julian Arnold
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Debasish Koner
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Narendra Singh
- Department of Mechanical Engineering, Stanford University Stanford, California 94305, United States
| | - Raymond J. Bemish
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland AFB, New Mexico 87117, United States
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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Käser S, Unke OT, Meuwly M. Isomerization and decomposition reactions of acetaldehyde relevant to atmospheric processes from dynamics simulations on neural network-based potential energy surfaces. J Chem Phys 2020; 152:214304. [DOI: 10.1063/5.0008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Oliver T. Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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Unke OT, Koner D, Patra S, Käser S, Meuwly M. High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning. Mach Learn : Sci Technol 2020. [DOI: 10.1088/2632-2153/ab5922] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Käser S, von Braunmühl T, Ruzicka T, Ruini C. Thumb necrotic ulcers caused by weeverfish: case report and review of the literature. J Eur Acad Dermatol Venereol 2018; 32:e333-e334. [PMID: 29485225 DOI: 10.1111/jdv.14893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S Käser
- Department of Dermatology and Allergology, University Hospital of the Ludwig Maximilian University, Frauenlobstr. 9-11, 80337, Munich, Germany.,Department of Dermatology, Municipal Hospital of Munich, Thalkirchnerstrasse 48, 80337, Munich, Germany
| | - T von Braunmühl
- Department of Dermatology and Allergology, University Hospital of the Ludwig Maximilian University, Frauenlobstr. 9-11, 80337, Munich, Germany
| | - T Ruzicka
- Department of Dermatology and Allergology, University Hospital of the Ludwig Maximilian University, Frauenlobstr. 9-11, 80337, Munich, Germany.,Department of Dermatology, Municipal Hospital of Munich, Thalkirchnerstrasse 48, 80337, Munich, Germany
| | - C Ruini
- Department of Dermatology and Allergology, University Hospital of the Ludwig Maximilian University, Frauenlobstr. 9-11, 80337, Munich, Germany.,Department of Dermatology, Municipal Hospital of Munich, Thalkirchnerstrasse 48, 80337, Munich, Germany
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Käser S, Ruini C, Ezmerli M, von Braunmühl T, Hartmann D, Ruzicka T, Reinholz M. EGFRI-induced papulopustular rosacea-like rash successfully treated with topical ivermectin. J Eur Acad Dermatol Venereol 2017; 31:e302-e304. [DOI: 10.1111/jdv.14089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Käser
- Department of Dermatology and Allergology; Ludwig Maximilian University; Munich Germany
| | - C. Ruini
- Department of Dermatology and Allergology; Ludwig Maximilian University; Munich Germany
| | - M. Ezmerli
- Department of Dermatology and Allergology; Ludwig Maximilian University; Munich Germany
| | - T. von Braunmühl
- Department of Dermatology and Allergology; Ludwig Maximilian University; Munich Germany
| | - D. Hartmann
- Department of Dermatology and Allergology; Ludwig Maximilian University; Munich Germany
| | - T. Ruzicka
- Department of Dermatology and Allergology; Ludwig Maximilian University; Munich Germany
| | - M. Reinholz
- Department of Dermatology and Allergology; Ludwig Maximilian University; Munich Germany
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Käser S, Ruchti C, Fankhauser G. Uterusartiger Knoten im großen Netz. Geburtshilfe Frauenheilkd 2008. [DOI: 10.1055/s-2007-989434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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