1
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Ghysbrecht S, Keller BG. Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics. J Comput Chem 2024; 45:1390-1403. [PMID: 38414274 DOI: 10.1002/jcc.27332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations. This is a formidable challenge since the accessible simulation timescales are many orders of magnitude smaller than typical timescales of chemical reactions. To overcome these limitations, rare event methods involving enhanced molecular dynamics sampling are employed. In this work, thermal isomerization of retinal is studied using tight-binding density functional theory. Results from transition state theory are compared to those obtained from enhanced sampling. Rates obtained from dynamical reweighting using infrequent metadynamics simulations were in close agreement with those from transition state theory. Meanwhile, rates obtained from application of Kramers' rate equation to a sampled free energy profile along a torsional dihedral reaction coordinate were found to be up to three orders of magnitude higher. This discrepancy raises concerns about applying rate methods to one-dimensional reaction coordinates in chemical reactions.
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Affiliation(s)
- Simon Ghysbrecht
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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2
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Nakano K, Sorella S, Alfè D, Zen A. Beyond Single-Reference Fixed-Node Approximation in Ab Initio Diffusion Monte Carlo Using Antisymmetrized Geminal Power Applied to Systems with Hundreds of Electrons. J Chem Theory Comput 2024; 20:4591-4604. [PMID: 38788330 PMCID: PMC11171267 DOI: 10.1021/acs.jctc.4c00139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Diffusion Monte Carlo (DMC) is an exact technique to project out the ground state (GS) of a Hamiltonian. Since the GS is always bosonic, in Fermionic systems, the projection needs to be carried out while imposing antisymmetric constraints, which is a nondeterministic polynomial hard problem. In practice, therefore, the application of DMC on electronic structure problems is made by employing the fixed-node (FN) approximation, consisting of performing DMC with the constraint of having a fixed, predefined nodal surface. How do we get the nodal surface? The typical approach, applied in systems having up to hundreds or even thousands of electrons, is to obtain the nodal surface from a preliminary mean-field approach (typically, a density functional theory calculation) used to obtain a single Slater determinant. This is known as single reference. In this paper, we propose a new approach, applicable to systems as large as the C60 fullerene, which improves the nodes by going beyond the single reference. In practice, we employ an implicitly multireference ansatz (antisymmetrized geminal power wave function constraint with molecular orbitals), initialized on the preliminary mean-field approach, which is relaxed by optimizing a few parameters of the wave function determining the nodal surface by minimizing the FN-DMC energy. We highlight the improvements of the proposed approach over the standard single-reference method on several examples and, where feasible, the computational gain over the standard multireference ansatz, which makes the methods applicable to large systems. We also show that physical properties relying on relative energies, such as binding energies, are affordable and reliable within the proposed scheme.
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Affiliation(s)
- Kousuke Nakano
- Center
for Basic Research on Materials, National
Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0047, Japan
- International
School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Sandro Sorella
- International
School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Dario Alfè
- Dipartimento
di Fisica Ettore Pancini, Università
di Napoli Federico II, Monte S. Angelo, 80126 Napoli, Italy
- Department
of Earth Sciences, University College London, Gower Street, London WC1E 6BT, U.K.
- Thomas
Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, U.K.
| | - Andrea Zen
- Dipartimento
di Fisica Ettore Pancini, Università
di Napoli Federico II, Monte S. Angelo, 80126 Napoli, Italy
- Department
of Earth Sciences, University College London, Gower Street, London WC1E 6BT, U.K.
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3
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Barneschi L, Kaliakin D, Huix-Rotllant M, Ferré N, Filatov Gulak M, Olivucci M. Assessment of the Electron Correlation Treatment on the Quantum-Classical Dynamics of Retinal Protonated Schiff Base Models: XMS-CASPT2, RMS-CASPT2, and REKS Methods. J Chem Theory Comput 2023; 19:8189-8200. [PMID: 37937990 DOI: 10.1021/acs.jctc.3c00879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
We compare the performance of three different multiconfigurational wave function-based electronic structure methods and two implementations of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method. The study is characterized by three features: (i) it uses a small set of quantum-classical trajectories rather than potential energy surface mapping, (ii) it focuses, exclusively, on the photoisomerization of retinal protonated Schiff base models, and (iii) it probes the effect of both methyl substitution and the increase in length of the conjugate π-system. For each tested method, the corresponding analytical gradients are used to drive the quantum-classical (Tully's FSSH method) trajectory propagation, including the recent multistate XMS-CASPT2 and RMS-CASPT2 gradients. It is shown that while CASSCF, XMS-CASPT2, and RMS-CASPT2 yield consistent photoisomerization dynamics descriptions, REKS produces, in some of these systems, qualitatively different behavior that is attributed to a flatter and topographically different excited state potential energy surface. The origin of this behavior can be traced back to the effect of the employed density functional approximation. The above studies are further expanded by benchmarking, at the CASSCF and REKS levels, the electronic structure methods using a QM/MM model of the visual pigment rhodopsin.
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Affiliation(s)
- Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Danil Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Miquel Huix-Rotllant
- Aix-Marseille Université, CNRS, Institut Chimie Radicalaire, 13013 Marseille, France
| | - Nicolas Ferré
- Aix-Marseille Université, CNRS, Institut Chimie Radicalaire, 13013 Marseille, France
| | - Michael Filatov Gulak
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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4
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Komarov K, Park W, Lee S, Huix-Rotllant M, Choi CH. Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory. J Chem Theory Comput 2023; 19:7671-7684. [PMID: 37844129 DOI: 10.1021/acs.jctc.3c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.
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Affiliation(s)
- Konstantin Komarov
- Center for Quantum Dynamics, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul, 151-747, South Korea
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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5
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Mu D, Li QS. A theoretical study on the photochemical generation of phenylborylene from phenyldiazidoborane. Phys Chem Chem Phys 2023; 25:8074-8081. [PMID: 36876656 DOI: 10.1039/d2cp05349g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Organic borylenes are a kind of highly reactive species, which play important roles in a lot of reactions as vigorous intermediates. In this work, we investigated the photochemical generation mechanisms of phenylborylene (PhB) together with the side product N-phenylnitrenoiminoborane (PhNBN) from phenyldiazidoborane (PhBN6) by extrusion of dinitrogen in the two lowest electronic singlet states (S0 and S1) based on the complete active space self-consistent field (CASSCF) and its second-order perturbation (CASPT2) methods combined with time-dependent density functional theory (TD-DFT) calculations. Our results show that the reaction PhBN6 → PhB + 3N2 involves stepwise N2 extrusion three times and the azido region rearrangement. Moreover, we found that the studied photo-induced processes are kinetically feasible because the highest energy barrier is only 0.36 eV and excitation with light of wavelength 254 nm can provide enough excess energy to overcome these energy barriers. Importantly, we revealed that several conical intersections between S1 and S0 states participate and facilitate the studied photochemical processes. Our results not only clarify the experimental observations, (H. F. Bettinger, J. Am. Chem. Soc. 2006, 128, 2534), but also provide valuable insights into borylene chemistry.
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Affiliation(s)
- Di Mu
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Quan-Song Li
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
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6
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Lee S, Park W, Nakata H, Filatov M, Choi CH. Recent advances in ensemble density functional theory and linear response theory for strong correlation. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Seunghoon Lee
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena California USA
| | - Woojin Park
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Hiroya Nakata
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Michael Filatov
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Cheol Ho Choi
- Department of Chemistry Kyungpook National University Daegu South Korea
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7
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Ha JK, Kim K, Min SK. Machine Learning-Assisted Excited State Molecular Dynamics with the State-Interaction State-Averaged Spin-Restricted Ensemble-Referenced Kohn-Sham Approach. J Chem Theory Comput 2021; 17:694-702. [PMID: 33470100 DOI: 10.1021/acs.jctc.0c01261] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We present a machine learning-assisted excited state molecular dynamics (ML-ESMD) based on the ensemble density functional theory framework. Since we represent a diabatic Hamiltonian in terms of generalized valence bond ansatz within the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS) method, we can avoid singularities near conical intersections, which are crucial in excited state molecular dynamics simulations. We train the diabatic Hamiltonian elements and their analytical gradients with the SchNet architecture to construct machine learning models, while the phase freedom of off-diagonal elements of the Hamiltonian is cured by introducing the phase-less loss function. Our machine learning models show reasonable accuracy with mean absolute errors of ∼0.1 kcal/mol and ∼0.5 kcal/mol/Å for the diabatic Hamiltonian elements and their gradients, respectively, for penta-2,4-dieniminium cation. Moreover, by exploiting the diabatic representation, our models can predict correct conical intersection structures and their topologies. In addition, our ML-ESMD simulations give almost identical result with a direct dynamics at the same level of theory.
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Affiliation(s)
- Jong-Kwon Ha
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, South Korea
| | - Kicheol Kim
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, South Korea
| | - Seung Kyu Min
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, South Korea
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8
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Li J, Liu MK, Li QS, Li ZS. Theoretical study on the photochemistry of furoylazides: Curtius rearrangement and subsequent reactions. Phys Chem Chem Phys 2020; 22:28317-28324. [PMID: 33300534 DOI: 10.1039/d0cp05539e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Organic azides are an efficient source of nitrenes, which serve as vigorous intermediates in many useful organic reactions. In this work, the complete active space self-consistent field (CASSCF) and its second-order perturbation (CASPT2) methods were employed to study the photochemistry of 2-furoylazide 1 and 3-furoylazide 5, including the Curtius rearrangement to two furylisocyanates (3 and 7) and subsequent reactions to the final product cyanoacrolein 9. Our calculations show that the photoinduced Curtius rearrangement of the two furoylazides takes place through similar stepwise mechanisms via two bistable furoylnitrenes 2 and 6. However, the decarbonylation and ring-opening process of 7 to 9 prefers a stepwise mechanism involving the 3-furoylnitrene intermediate 8, while 3 to 9 goes in a concerted asynchronous way without the corresponding 2-furoylnitrene intermediate 4. Importantly, we revealed that several conical intersections play key roles in the photochemistry of furoylazides. Our results are not only consistent and also make clear the experimental observations (X. Zeng, et al., J. Am. Chem. Soc., 2018, 140, 10-13), but additionally provide important information on the chemistry of furoylazides and nitrenes.
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Affiliation(s)
- Jian Li
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China.
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9
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Mai S, González L. Molecular Photochemistry: Recent Developments in Theory. Angew Chem Int Ed Engl 2020; 59:16832-16846. [PMID: 32052547 PMCID: PMC7540682 DOI: 10.1002/anie.201916381] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/12/2020] [Indexed: 12/16/2022]
Abstract
Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light-induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non-adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.
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Affiliation(s)
- Sebastian Mai
- Photonics InstituteVienna University of TechnologyGusshausstrasse 27–291040ViennaAustria
| | - Leticia González
- Institute of Theoretical ChemistryFaculty of ChemistryUniversity of ViennaWähringer Strasse 171090ViennaAustria
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10
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Mai S, González L. Molekulare Photochemie: Moderne Entwicklungen in der theoretischen Chemie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sebastian Mai
- Institut für Photonik Technische Universität Wien Gußhausstraße 27–29 1040 Wien Österreich
| | - Leticia González
- Institut für theoretische Chemie Fakultät für Chemie Universität Wien Währinger Straße 17 1090 Wien Österreich
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11
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Filatov M, Lee S, Choi CH. Computation of Molecular Ionization Energies Using an Ensemble Density Functional Theory Method. J Chem Theory Comput 2020; 16:4489-4504. [PMID: 32421323 DOI: 10.1021/acs.jctc.0c00218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Computation of the ionization energies and of the respective Dyson orbitals based on the use of the extended Koopmans theorem (EKT) is implemented in connection with an ensemble density functional theory (eDFT) method, the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method. The new methodology enables fast computation of the ionization energies and evaluation of the respective Dyson orbitals, the square norms of which are related with the ionization probabilities, in the ground and excited electronic states of molecules. As the application of EKT recycles the intermediate quantities from the SSR analytical energy gradient, evaluation of the ionization energies and probabilities can be carried out on-the-fly during the nonadiabatic molecular dynamics simulations. This opens up a perspective for fast theoretical simulation of the time-resolved photoelectron spectroscopy observations. In the present work, the new methodology is tested in the computation of the ionization energies and Dyson orbitals of several molecules in the ground and excited electronic states, including strongly correlated species, such as the ozone molecule, dissociating chemical bonds, and conical intersections.
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Affiliation(s)
- Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
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12
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Nakano K, Attaccalite C, Barborini M, Capriotti L, Casula M, Coccia E, Dagrada M, Genovese C, Luo Y, Mazzola G, Zen A, Sorella S. TurboRVB: A many-body toolkit for ab initio electronic simulations by quantum Monte Carlo. J Chem Phys 2020; 152:204121. [DOI: 10.1063/5.0005037] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Kousuke Nakano
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
- Japan Advanced Institute of Science and Technology (JAIST), Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Claudio Attaccalite
- Aix-Marseille Université, CNRS, CINaM UMR 7325, Campus de Luminy, 13288 Marseille, France
| | | | - Luca Capriotti
- New York University, Tandon School of Engineering, 6 MetroTech Center, Brooklyn, New York 11201, USA
- Department of Mathematics, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Michele Casula
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, CNRS UMR 7590, IRD UMR 206, MNHN, 4 Place Jussieu, 75252 Paris, France
| | - Emanuele Coccia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Mario Dagrada
- Forescout Technologies, John F. Kennedylaan 2, 5612AB Eindhoven, The Netherlands
| | - Claudio Genovese
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Ye Luo
- Computational Science Division, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, Illinois 60439, USA
- Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, Illinois 60439, USA
| | | | - Andrea Zen
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Sandro Sorella
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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13
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Agathangelou D, Orozco-Gonzalez Y, Del Carmen Marín M, Roy PP, Brazard J, Kandori H, Jung KH, Léonard J, Buckup T, Ferré N, Olivucci M, Haacke S. Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin. Faraday Discuss 2019; 207:55-75. [PMID: 29388996 DOI: 10.1039/c7fd00200a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time. A detailed analysis of the vibrational spectra of AT and 13C, and their photo-products in wild-type ASR obtained through femtosecond (pump-) four-wave-mixing is reported for the first time, and compared to bacterio- and channelrhodopsin. As part of an extensive study of ASR mutants with blue-shifted absorption spectra, we present here a detailed computational analysis of the origin of the mutation-induced blue-shift of the absorption spectra, and identify electrostatic interactions as dominating steric effects that would entail a red-shift. The excited state lifetimes and isomerization reaction times (IRT) for the three mutants V112N, W76F, and L83Q are studied experimentally by femtosecond broadband transient absorption spectroscopy. Interestingly, in all three mutants, isomerization is accelerated for AT with respect to wild-type ASR, and this the more, the shorter the wavelength of maximum absorption. On the contrary, the 13C photo-reaction is slightly slowed down, leading to an inversion of the ESLs of AT and 13C, with respect to wt-ASR, in the blue-most absorbing mutant L83Q. Possible mechanisms for these mutation effects, and their steric and electrostatic origins are discussed.
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Affiliation(s)
- D Agathangelou
- University of Strasbourg, CNRS, Inst. de Physique et Chimie des Matériaux de Strasbourg, 67034 Strasbourg, France.
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14
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Lee S, Kim EE, Nakata H, Lee S, Choi CH. Efficient implementations of analytic energy gradient for mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT). J Chem Phys 2019; 150:184111. [DOI: 10.1063/1.5086895] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Emma Eunji Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Hiroya Nakata
- R & D Center Kagoshima, Kyocera, 1-4 Kokubu Yamashita-cho, Kirishima-shi, Kagoshima 899-4312, Japan
| | - Sangyoub Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
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15
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Marsili E, Farag MH, Yang X, De Vico L, Olivucci M. Two-State, Three-Mode Parametrization of the Force Field of a Retinal Chromophore Model. J Phys Chem A 2019; 123:1710-1719. [PMID: 30753077 DOI: 10.1021/acs.jpca.8b10010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, the potential energy surfaces of the penta-2,4-dieniminium cation have been investigated using several electronic structure methods. The resulting pool of geometrical, electronic, and energy data provides a suitable basis for the construction of a topographically correct analytical model of the molecule force field and, therefore, for a better understanding of this class of molecules, which includes the chromophore of visual pigments. In the present contribution, we report the construction of such a model for regions of the force field that drive the photochemical and thermal isomerization of the central double bound of the cation. While previous models included only two modes, it is here shown that the proposed three-mode model and corresponding set of parameters are able to reproduce the complex topographical and electronic structure features seen in electronically correlated data obtained at the XMCQDPT2//CASSCF/6-31G* level of theory.
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Affiliation(s)
- Emanuele Marsili
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy
| | - Marwa H Farag
- Department of Chemistry , University of Southern California , Los Angeles , California 90089-0482 , United States
| | - Xuchun Yang
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States and
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States and.,Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 , Université de Strasbourg-CNRS , F-67034 Strasbourg , France
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16
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Barborini M, Sorella S, Rontani M, Corni S. Angle-resolved photoemission spectroscopy from first-principles quantum Monte Carlo. J Chem Phys 2018; 149:154102. [DOI: 10.1063/1.5038864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | - Sandro Sorella
- Scuola Internazionale Superiore di Studi Avanzati (SISSA) and CNR-IOM Democritos National Simulation Center, Via Bonomea 265, 34136 Trieste, Italy
| | | | - Stefano Corni
- CNR-NANO, Via Campi 213/a, 41125 Modena, Italy
- Dipartimento di Scienze Chimiche—Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
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17
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Lee S, Filatov M, Lee S, Choi CH. Eliminating spin-contamination of spin-flip time dependent density functional theory within linear response formalism by the use of zeroth-order mixed-reference (MR) reduced density matrix. J Chem Phys 2018; 149:104101. [DOI: 10.1063/1.5044202] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Michael Filatov
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Sangyoub Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
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18
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Sen S, Schapiro I. A comprehensive benchmark of the XMS-CASPT2 method for the photochemistry of a retinal chromophore model. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1501112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Saumik Sen
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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19
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Wolański Ł, Grabarek D, Andruniów T. Is the choice of a standard zeroth-order hamiltonian in CASPT2 ansatz optimal in calculations of excitation energies in protonated and unprotonated schiff bases of retinal? J Comput Chem 2018; 39:1470-1480. [PMID: 29635695 DOI: 10.1002/jcc.25217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 11/07/2022]
Abstract
To account for systematic error of CASPT2 method empirical modification of the zeroth-order Hamiltonian with Ionization Potential-Electron Affinity (IPEA) shift was introduced. The optimized IPEA value (0.25 a.u.), called standard IPEA (S-IPEA), was recommended but due to its unsatisfactory performance in multiple metallic and organic compounds it has been questioned lately as a general parameter working properly for all molecules under CASPT2 study. As we are interested in Schiff bases of retinal, an important question emerging from this conflict of choice, to use or not to use S-IPEA, is whether the introduction of the modified zeroth-order Hamiltonian into CASPT2 ansatz does really improve their energetics. To achieve this goal, we assessed an impact of the IPEA shift value, in a range of 0-0.35 a.u., on vertical excitation energies to low-lying singlet states of two protonated (RPSBs) and two unprotonated (RSBs) Schiff bases of retinal for which experimental data in gas phase are available. In addition, an effect of geometry, basis set, and active space on computed VEEs is also reported. We find, that for these systems, the choice of S-IPEA significantly overestimates both S0 →S1 and S0 →S2 energies and the best theoretical estimate, in reference to the experimental data, is provided with either unmodified zeroth-order Hamiltonian or small value of the IPEA shift in a range of 0.05-0.15 a.u., depending on active space and basis set size, equilibrium geometry, and character of the excited state. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Łukasz Wolański
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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20
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Filatov M, Min SK, Kim KS. Direct Nonadiabatic Dynamics by Mixed Quantum-Classical Formalism Connected with Ensemble Density Functional Theory Method: Application to trans-Penta-2,4-dieniminium Cation. J Chem Theory Comput 2018; 14:4499-4512. [DOI: 10.1021/acs.jctc.8b00217] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Michael Filatov
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Seung Kyu Min
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Kwang S. Kim
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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21
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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22
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Filatov M, Liu F, Martínez TJ. Analytical derivatives of the individual state energies in ensemble density functional theory method. I. General formalism. J Chem Phys 2018; 147:034113. [PMID: 28734302 DOI: 10.1063/1.4994542] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The state-averaged (SA) spin restricted ensemble referenced Kohn-Sham (REKS) method and its state interaction (SI) extension, SI-SA-REKS, enable one to describe correctly the shape of the ground and excited potential energy surfaces of molecules undergoing bond breaking/bond formation reactions including features such as conical intersections crucial for theoretical modeling of non-adiabatic reactions. Until recently, application of the SA-REKS and SI-SA-REKS methods to modeling the dynamics of such reactions was obstructed due to the lack of the analytical energy derivatives. In this work, the analytical derivatives of the individual SA-REKS and SI-SA-REKS energies are derived. The final analytic gradient expressions are formulated entirely in terms of traces of matrix products and are presented in the form convenient for implementation in the traditional quantum chemical codes employing basis set expansions of the molecular orbitals. The implementation and benchmarking of the derived formalism will be described in a subsequent article of this series.
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Affiliation(s)
- Michael Filatov
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, South Korea
| | - Fang Liu
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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23
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Mussard B, Coccia E, Assaraf R, Otten M, Umrigar CJ, Toulouse J. Time-Dependent Linear-Response Variational Monte Carlo. ADVANCES IN QUANTUM CHEMISTRY 2018. [DOI: 10.1016/bs.aiq.2017.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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24
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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25
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Isomerization of the RPSB chromophore in the gas phase along the torsional pathways using QTAIM. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.07.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Coccia E, Varsano D, Guidoni L. Theoretical S1 ← S0 Absorption Energies of the Anionic Forms of Oxyluciferin by Variational Monte Carlo and Many-Body Green’s Function Theory. J Chem Theory Comput 2017; 13:4357-4367. [DOI: 10.1021/acs.jctc.7b00505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Emanuele Coccia
- S3
Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | - Daniele Varsano
- S3
Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | - Leonardo Guidoni
- Dipartimento
di Scienze Fisiche e Chimiche, Universitá degli Studi dell’Aquila, via Vetoio, 67100, L’Aquila, Italy
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27
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Al-Hamdani YS, Rossi M, Alfè D, Tsatsoulis T, Ramberger B, Brandenburg JG, Zen A, Kresse G, Grüneis A, Tkatchenko A, Michaelides A. Properties of the water to boron nitride interaction: From zero to two dimensions with benchmark accuracy. J Chem Phys 2017; 147:044710. [DOI: 10.1063/1.4985878] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yasmine S. Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Mariana Rossi
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Theodoros Tsatsoulis
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Benjamin Ramberger
- University of Vienna, Faculty of Physics and Center for Computational Materials Sciences, Sensengasse 8/12, 1090 Wien, Austria
| | - Jan Gerit Brandenburg
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AH, United Kingdom
| | - Andrea Zen
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Georg Kresse
- University of Vienna, Faculty of Physics and Center for Computational Materials Sciences, Sensengasse 8/12, 1090 Wien, Austria
| | - Andreas Grüneis
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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28
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Szefczyk B, Grabarek D, Walczak E, Andruniów T. Excited-state minima and emission energies of retinal chromophore analogues: Performance of CASSCF and CC2 methods as compared with CASPT2. J Comput Chem 2017; 38:1799-1810. [PMID: 28512740 DOI: 10.1002/jcc.24821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 11/08/2022]
Abstract
This study provides gas-phase S1 excited-state geometries along with emission and adiabatic energies for methylated/demethylated and ring-locked analogues of protonated Schiff base retinal models comprising system of five conjugated double bonds (PSB5), using second order multiconfiguration perturbation theory (CASPT2). CASPT2 results serve as reference data to assess the performance of CC2 (second-order approximate coupled cluster singles and doubles) and a commonly used CASSCF/CASPT2 protocol, that is, complete active space self-consistent field (CASSCF) geometry optimization followed by CASPT2 energy calculation. We find that the CASSCF methodology fails to locate planar S1 minimum energy structures for four out of five investigated planar models in contrast to CC2 and CASPT2 methods. However, for those which were found: one planar and two twisted minima, there is an excellent agreement between CASSCF and CASPT2 results in terms of geometrical parameters, one-electron properties, as well as emission and adiabatic energies. CC2 performs well for in-plane S1 minima and their spectroscopic and electronic properties. However, this picture deteriorates for twisted minima. As expected, the CC2 description of the S2 electronic state, with strong multireference and significant double excitation character, is very poor, exhibiting errors in transition energies exceeding 1 eV. They may be substantially diminished by recalculating transition energies with CASPT2 method. Our work shows that CASSCF/CASPT2 and CC2 shortcomings may influence gas-phase retinal analogues' excited state description in a dramatic way. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Borys Szefczyk
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Elżbieta Walczak
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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29
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Guo Y, Hendrickson HP, Videla PE, Chen YN, Ho J, Sekharan S, Batista VS, Tully JC, Yan ECY. Probing the remarkable thermal kinetics of visual rhodopsin with E181Q and S186A mutants. J Chem Phys 2017; 146:215104. [DOI: 10.1063/1.4984818] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ying Guo
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Heidi P. Hendrickson
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Pablo E. Videla
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Ya-Na Chen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Junming Ho
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Sivakumar Sekharan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - John C. Tully
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
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30
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Dubecký M. Bias cancellation in one-determinant fixed-node diffusion Monte Carlo: Insights from fermionic occupation numbers. Phys Rev E 2017; 95:033308. [PMID: 28415179 DOI: 10.1103/physreve.95.033308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 06/07/2023]
Abstract
The accuracy of the fixed-node diffusion Monte Carlo (FNDMC) depends on the node location of the supplied trial state Ψ_{T}. The practical FNDMC approaches available for large systems rely on compact yet effective Ψ_{T}, most often containing an explicitly correlated single Slater determinant (SD). However, SD nodes may be better suited to one system than to another, which may possibly lead to inaccurate FNDMC energy differences. It remains a challenge how to estimate nonequivalence or appropriateness of SDs. Here we use the differences of a measure based on the Euclidean distance between the natural orbital occupation number (NOON) vector of the SD and the exact solution in the NOON vector space, which can be viewed as a measure of SD nonequivalence and as a qualitative measure of the expected degree of nondynamic-correlation-related bias in FNDMC energy differences. This is explored on a set of small noncovalent complexes and covalent bond breaking of Si_{2} vs N_{2}. It turns out that NOON-based measures well reflect the magnitude and sign of the bias present in the data available, thus providing insights into the nature of bias cancellation in SD FNDMC energy differences.
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Affiliation(s)
- Matúš Dubecký
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic and ATRI, Faculty of Materials Science and Technology, Slovak University of Technology, Paulínska 16, 917 24 Trnava, Slovakia
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31
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Varsano D, Caprasecca S, Coccia E. Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.
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Affiliation(s)
- Daniele Varsano
- S3 Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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32
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Chu S, Coccia E, Barborini M, Guidoni L. Role of Electron Correlation along the Water Splitting Reaction. J Chem Theory Comput 2016; 12:5803-5810. [DOI: 10.1021/acs.jctc.6b00632] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shibing Chu
- Dipartimento
di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio (Coppito), 67100 L’Aquila, Italy
| | - Emanuele Coccia
- Dipartimento
di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio (Coppito), 67100 L’Aquila, Italy
- Sorbonne Universités,
UPMC Univ Paris 06, CNRS, Laboratoire de Chimie Théorique, CC 137-4 place Jussieu, F. 75252 Paris Cedex 05, France
| | | | - Leonardo Guidoni
- Dipartimento
di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio (Coppito), 67100 L’Aquila, Italy
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33
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Barborini M, Sorella S, Rontani M, Corni S. Correlation Effects in Scanning Tunneling Microscopy Images of Molecules Revealed by Quantum Monte Carlo. J Chem Theory Comput 2016; 12:5339-5349. [PMID: 27709944 DOI: 10.1021/acs.jctc.6b00710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scanning tunneling microscopy (STM) and spectroscopy probe the local density of states of single molecules electrically insulated from the substrate. The experimental images, although usually interpreted in terms of single-particle molecular orbitals, are associated with quasiparticle wave functions dressed by the whole electron-electron interaction. Here we propose an ab initio approach based on quantum Monte Carlo to calculate the quasiparticle wave functions of molecules. Through the comparison between Monte Carlo wave functions and their uncorrelated Hartree-Fock counterparts we visualize the electronic correlation embedded in the simulated STM images, highlighting the many-body features that might be observed.
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Affiliation(s)
| | - Sandro Sorella
- Scuola Internazionale Superiore di Studi Avanzati (SISSA) and CNR-IOM Democritos National Simulation Center, via Bonomea 265, 34136 Trieste, Italy
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34
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Barborini M, Guidoni L. Geometries of low spin states of multi-centre transition metal complexes through extended broken symmetry variational Monte Carlo. J Chem Phys 2016; 145:124107. [DOI: 10.1063/1.4963015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matteo Barborini
- Dipartimento di Ingegneria, Scienze dell’Informazione e Matematica, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
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35
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Tuna D, Lefrancois D, Wolański Ł, Gozem S, Schapiro I, Andruniów T, Dreuw A, Olivucci M. Assessment of Approximate Coupled-Cluster and Algebraic-Diagrammatic-Construction Methods for Ground- and Excited-State Reaction Paths and the Conical-Intersection Seam of a Retinal-Chromophore Model. J Chem Theory Comput 2015; 11:5758-81. [PMID: 26642989 DOI: 10.1021/acs.jctc.5b00022] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As a minimal model of the chromophore of rhodopsin proteins, the penta-2,4-dieniminium cation (PSB3) poses a challenging test system for the assessment of electronic-structure methods for the exploration of ground- and excited-state potential-energy surfaces, the topography of conical intersections, and the dimensionality (topology) of the branching space. Herein, we report on the performance of the approximate linear-response coupled-cluster method of second order (CC2) and the algebraic-diagrammatic-construction scheme of the polarization propagator of second and third orders (ADC(2) and ADC(3)). For the ADC(2) method, we considered both the strict and extended variants (ADC(2)-s and ADC(2)-x). For both CC2 and ADC methods, we also tested the spin-component-scaled (SCS) and spin-opposite-scaled (SOS) variants. We have explored several ground- and excited-state reaction paths, a circular path centered around the S1/S0 surface crossing, and a 2D scan of the potential-energy surfaces along the branching space. We find that the CC2 and ADC methods yield a different dimensionality of the intersection space. While the ADC methods yield a linear intersection topology, we find a conical intersection topology for the CC2 method. We present computational evidence showing that the linear-response CC2 method yields a surface crossing between the reference state and the first response state featuring characteristics that are expected for a true conical intersection. Finally, we test the performance of these methods for the approximate geometry optimization of the S1/S0 minimum-energy conical intersection and compare the geometries with available data from multireference methods. The present study provides new insight into the performance of linear-response CC2 and polarization-propagator ADC methods for molecular electronic spectroscopy and applications in computational photochemistry.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, University of Heidelberg , 69120 Heidelberg, Germany
| | - Łukasz Wolański
- Department of Chemistry, Wrocław University of Technology , 50370 Wrocław, Poland
| | - Samer Gozem
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Igor Schapiro
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504 , Strasbourg 67034, France
| | - Tadeusz Andruniów
- Department of Chemistry, Wrocław University of Technology , 50370 Wrocław, Poland
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, University of Heidelberg , 69120 Heidelberg, Germany
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Universitá de Siena , 53100 Siena, Italy
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Barborini M, Coccia E. Investigating Disjoint Non-Kekulé Diradicals with Quantum Monte Carlo: The Tetramethyleneethane Molecule through the Jastrow Antisymmetrized Geminal Power Wave Function. J Chem Theory Comput 2015; 11:5696-704. [DOI: 10.1021/acs.jctc.5b00819] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matteo Barborini
- S3
Research Center, CNR-NANO, Via Campi 213/a, 41125 Modena, Modena, Italy
| | - Emanuele Coccia
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Univ Paris 06 & CNRS, UMR 7616, F-75005 Paris, France
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Barborini M, Guidoni L. Ground State Geometries of Polyacetylene Chains from Many-Particle Quantum Mechanics. J Chem Theory Comput 2015; 11:4109-18. [PMID: 26405437 PMCID: PMC4570661 DOI: 10.1021/acs.jctc.5b00427] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Indexed: 11/28/2022]
Abstract
Due to the crucial role played by electron correlation, the accurate determination of ground state geometries of π-conjugated molecules is still a challenge for many quantum chemistry methods. Because of the high parallelism of the algorithms and their explicit treatment of electron correlation effects, Quantum Monte Carlo calculations can offer an accurate and reliable description of the electronic states and of the geometries of such systems, competing with traditional quantum chemistry approaches. Here, we report the structural properties of polyacetylene chains H-(C₂H₂)(N)-H up to N = 12 acetylene units, by means of Variational Monte Carlo (VMC) calculations based on the multi-determinant Jastrow Antisymmetrized Geminal Power (JAGP) wave function. This compact ansatz can provide for such systems an accurate description of the dynamical electronic correlation as recently detailed for the 1,3-butadiene molecule [J. Chem. Theory Comput. 2015 11 (2), 508-517]. The calculated Bond Length Alternation (BLA), namely the difference between the single and double carbon bonds, extrapolates, for N → ∞, to a value of 0.0910(7) Å, compatible with the experimental data. An accurate analysis was able to distinguish between the influence of the multi-determinantal AGP expansion and of the Jastrow factor on the geometrical properties of the fragments. Our size-extensive and self-interaction-free results provide new and accurate ab initio references for the structures of the ground state of polyenes.
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Affiliation(s)
- Matteo Barborini
- Dipartimento
di Ingegneria e Scienze dell’Informazione e Matematica, Università degli studi dell’Aquila, Via Vetoio (Coppito), 67100 L’Aquila, Italy
- Dipartimento
di Scienze Fisiche e Chimiche, Università
degli studi dell’Aquila, Via Vetoio (Coppito), 67100 L’Aquila, Italy
| | - Leonardo Guidoni
- Dipartimento
di Scienze Fisiche e Chimiche, Università
degli studi dell’Aquila, Via Vetoio (Coppito), 67100 L’Aquila, Italy
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38
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Zen A, Luo Y, Mazzola G, Guidoni L, Sorella S. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo. J Chem Phys 2015; 142:144111. [PMID: 25877566 DOI: 10.1063/1.4917171] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
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Affiliation(s)
- Andrea Zen
- Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome, Italy
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United Kingdom
| | - Ye Luo
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
| | - Guglielmo Mazzola
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
| | - Leonardo Guidoni
- Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila, Italy
| | - Sandro Sorella
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
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