1
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Kabir M, Ghosh P, Gozem S. Electronic Structure Methods for Simulating Flavin's Spectroscopy and Photophysics: Comparison of Multi-reference, TD-DFT, and Single-Reference Wave Function Methods. J Phys Chem B 2024; 128:7545-7557. [PMID: 39074870 PMCID: PMC11317985 DOI: 10.1021/acs.jpcb.4c03748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 07/31/2024]
Abstract
The use of flavins and flavoproteins in photocatalytic, sensing, and biotechnological applications has led to a growing interest in computationally modeling the excited-state electronic structure and photophysics of flavin. However, there is limited consensus regarding which computational methods are appropriate for modeling flavin's photophysics. We compare the energies of low-lying excited states of flavin computed with time-dependent density functional theory (TD-DFT), equation-of-motion coupled cluster (EOM-EE-CCSD), scaled opposite-spin configuration interaction [SOS-CIS(D)], multiconfiguration pair-density functional theory (MC-PDFT), and several multireference perturbation theory (MR-PT2) methods. In the first part, we focus on excitation energies of the first singlet excited state (S1) of five different redox and protonation states of flavin, with the goal of finding a suitable active space for MR-PT2 calculations. In the second part, we construct two sets of one-dimensional potential energy surfaces connecting the S0 and S1 equilibrium geometries (S0-S1 path) and the S1 (π,π*) and S2 (n,π*) equilibrium geometries (S1-S2 path). The first path therefore follows a Franck-Condon active mode of flavin while the second path maps crossings points between low-lying singlet and triplet states in flavin. We discuss the similarities and differences in the TD-DFT, EOM-EE-CCSD, SOS-CIS(D), MC-PDFT and MR-PT2 energy profiles along these paths. We find that (TD-)DFT methods are suitable for applications such as simulating the spectra of flavins but are inconsistent with several other methods when used for some geometry optimizations and when describing the energetics of dark (n,π*) states. MR-PT2 methods show promise for the simulation of flavin's low-lying excited states, but the selection of orbitals for the active space and the number of roots used for state averaging must be done carefully to avoid artifacts. Some properties, such as the intersystem crossing geometry and energy between the S1 (π,π*) and T2 (n,π*) states, may require additional benchmarking before they can be determined quantitatively.
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Affiliation(s)
- Mohammad
Pabel Kabir
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Paulami Ghosh
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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2
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Wijayaratna D, Sacchetta F, Pedraza-González L, Fanelli F, Sugihara T, Koyanagi M, Piyawardana S, Ghotra K, Thotamune W, Terakita A, Olivucci M, Karunarathne A. In-silico predicted mouse melanopsins with blue spectral shifts deliver efficient subcellular signaling. Cell Commun Signal 2024; 22:394. [PMID: 39118111 PMCID: PMC11312219 DOI: 10.1186/s12964-024-01753-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Melanopsin is a photopigment belonging to the G Protein-Coupled Receptor (GPCR) family expressed in a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) and responsible for a variety of processes. The bistability and, thus, the possibility to function under low retinal availability would make melanopsin a powerful optogenetic tool. Here, we aim to utilize mouse melanopsin to trigger macrophage migration by its subcellular optical activation with localized blue light, while simultaneously imaging the migration with red light. To reduce melanopsin's red light sensitivity, we employ a combination of in silico structure prediction and automated quantum mechanics/molecular mechanics modeling to predict minimally invasive mutations to shift its absorption spectrum towards the shorter wavelength region of the visible spectrum without compromising the signaling efficiency. The results demonstrate that it is possible to achieve melanopsin mutants that resist red light-induced activation but are activated by blue light and display properties indicating preserved bistability. Using the A333T mutant, we show that the blue light-induced subcellular melanopsin activation triggers localized PIP3 generation and macrophage migration, which we imaged using red light, demonstrating the optogenetic utility of minimally engineered melanopsins.
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Affiliation(s)
| | - Filippo Sacchetta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | - Francesca Fanelli
- Department of Life Sciences, Dulbecco Telethon Institute, University of Modena and Reggio Emilia, Modena, I-41125, Italy
| | - Tomohiro Sugihara
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Mitsumasa Koyanagi
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
- The OMU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Senuri Piyawardana
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Kiran Ghotra
- Department of Biology, Siena Heights University, Adrian, MI, 49221, USA
| | - Waruna Thotamune
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Akihisa Terakita
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
- The OMU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Ajith Karunarathne
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA.
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3
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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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4
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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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5
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Palombo R, Barneschi L, Pedraza-González L, Yang X, Olivucci M. Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin. Phys Chem Chem Phys 2024; 26:10343-10356. [PMID: 38501246 DOI: 10.1039/d4cp00193a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily of rhodopsins called heliorhodopsins was discovered using functional metagenomics. Heliorhodopsins, with their markedly different structural features with respect to the animal and microbial superfamilies, offer an opportunity to study how evolution has manipulated the chromophore photoisomerization to achieve adaptation. One question is related to the mechanism of such a reaction and how it differs from that of animal and microbial rhodopsins. To address this question, we use hundreds of quantum-classical trajectories to simulate the spectroscopically documented picosecond light-induced dynamics of a heliorhodopsin from the archaea thermoplasmatales archaeon (TaHeR). We show that, consistently with the observations, the trajectories reveal two excited state decay channels. However, inconsistently with previous hypotheses, only one channel is associated with the -C13C14- rotation of microbial rhodopsins while the second channel is characterized by the -C11C12- rotation typical of animal rhodopsins. The fact that such -C11C12- rotation is aborted upon decay and ground state relaxation, explains why illumination of TaHeR only produces the 13-cis isomer with a low quantum efficiency. We argue that the documented lack of regioselectivity in double-bond excited state twisting motion is the result of an "adaptation" that could be completely lost via specific residue substitutions modulating the steric hindrance experienced along the isomerization motion.
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Affiliation(s)
- Riccardo Palombo
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
| | - Laura Pedraza-González
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, I-56124 Pisa, Italy
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
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6
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Taylor JT, Tozer DJ, Curchod BFE. On the description of conical intersections between excited electronic states with LR-TDDFT and ADC(2). J Chem Phys 2023; 159:214115. [PMID: 38059547 DOI: 10.1063/5.0176140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Conical intersections constitute the conceptual bedrock of our working understanding of ultrafast, nonadiabatic processes within photochemistry (and photophysics). Accurate calculation of potential energy surfaces within the vicinity of conical intersections, however, still poses a serious challenge to many popular electronic structure methods. Multiple works have reported on the deficiency of methods like linear-response time-dependent density functional theory within the adiabatic approximation (AA LR-TDDFT) or algebraic diagrammatic construction to second-order [ADC(2)]-approaches often used in excited-state molecular dynamics simulations-to describe conical intersections between the ground and excited electronic states. In the present study, we focus our attention on conical intersections between excited electronic states and probe the ability of AA LR-TDDFT and ADC(2) to describe their topology and topography, using protonated formaldimine and pyrazine as two exemplar molecules. We also take the opportunity to revisit the performance of these methods in describing conical intersections involving the ground electronic state in protonated formaldimine-highlighting in particular how the intersection ring exhibited by AA LR-TDDFT can be perceived either as a (near-to-linear) seam of intersection or two interpenetrating cones, depending on the magnitude of molecular distortions within the branching space.
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Affiliation(s)
- Jack T Taylor
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David J Tozer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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7
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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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8
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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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9
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Arribas EV, Ibele LM, Lauvergnat D, Maitra NT, Agostini F. Significance of Energy Conservation in Coupled-Trajectory Approaches to Nonadiabatic Dynamics. J Chem Theory Comput 2023; 19:7787-7800. [PMID: 37853509 DOI: 10.1021/acs.jctc.3c00845] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Through approximating electron-nuclear correlation terms in the exact factorization approach, trajectory-based methods have been derived and successfully applied to the dynamics of a variety of light-induced molecular processes, capturing quantum (de)coherence effects rigorously. These terms account for the coupling among the trajectories, recovering the nonlocal nature of quantum nuclear dynamics that is completely overlooked in traditional independent-trajectory algorithms. Nevertheless, some of the approximations introduced in the derivation of some of these methods do not conserve the total energy. We analyze energy conservation in the coupled-trajectory mixed quantum-classical (CTMQC) algorithm and explore the performance of a modified algorithm, CTMQC-E, where some of the terms are redefined to restore energy conservation. A set of molecular models is used as a test, namely, 2-cis-penta-2,4-dienimium cation, bis(methylene) adamantyl radical cation, butatriene cation, uracil radical cation, and neutral pyrazine.
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Affiliation(s)
| | - Lea M Ibele
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
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10
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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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11
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Grigorenko B, Domratcheva T, Nemukhin A. QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules 2023; 28:molecules28052405. [PMID: 36903648 PMCID: PMC10005588 DOI: 10.3390/molecules28052405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction pathways initiated by various triplet state complexes of the molecular oxygen with the reduced flavin mononucleotide (FMN) formed in the protein cavities. According to the calculation results, these triplet-state flavin-oxygen complexes can be located at both re-side and si-side of the isoalloxazine ring of flavin. In both cases, the dioxygen moiety is activated by electron transfer from FMN, stimulating the attack of the arising reactive oxygen species at the C4a, N5, C6, and C8 positions in the isoalloxazine ring after the switch to the singlet state potential energy surface. The reaction pathways lead to the C(4a)-peroxide, N(5)-oxide, or C(6)-hydroperoxide covalent adducts or directly to the oxidized flavin, depending on the initial position of the oxygen molecule in the protein cavities.
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Affiliation(s)
- Bella Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Tatiana Domratcheva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Correspondence:
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12
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Chakraborty P, Liu Y, McClung S, Weinacht T, Matsika S. Nonadiabatic Excited State Dynamics of Organic Chromophores: Take-Home Messages. J Phys Chem A 2022; 126:6021-6031. [PMID: 36069531 DOI: 10.1021/acs.jpca.2c04671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonadiabatic excited state dynamics are important in a variety of processes. Theoretical and experimental developments have allowed for a great progress in this area, while combining the two is often necessary and the best approach to obtain insight into the photophysical behavior of molecules. In this Feature Article we use examples of our recent work combining time-resolved photoelectron spectroscopy with theoretical nonadiabatic dynamics to highlight important lessons we learned. We compare the nonadiabatic excited state dynamics of three different organic molecules with the aim of elucidating connections between structure and dynamics. Calculations and measurements are compared for uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene. The comparison highlights the role of rigidity in influencing the dynamics and the difficulty of capturing the dynamics accurately with calculations.
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Affiliation(s)
- Pratip Chakraborty
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States.,Division of Theoretical Chemistry and Biology, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Yusong Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States.,Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Samuel McClung
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Thomas Weinacht
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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13
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Ammar A, Giner E, Scemama A. Optimization of Large Determinant Expansions in Quantum Monte Carlo. J Chem Theory Comput 2022; 18:5325-5336. [PMID: 35997484 DOI: 10.1021/acs.jctc.2c00556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a new method for the optimization of large configuration interaction (CI) expansions in the quantum Monte Carlo (QMC) framework. The central idea here is to replace the nonorthogonal variational optimization of CI coefficients performed in usual QMC calculations by an orthogonal non-Hermitian optimization thanks to the so-called transcorrelated (TC) framework, the two methods yielding the same results in the limit of a complete basis set. By rewriting the TC equations as an effective self-consistent Hermitian problem, our approach requires the sampling of a single quantity per Slater determinant, leading to minimal memory requirements in the QMC code. Using analytical quantities obtained from both the TC framework and the usual CI-type calculations, we also propose improved estimators which reduce the statistical fluctuations of the sampled quantities by more than an order of magnitude. We demonstrate the efficiency of this method on wave functions containing 105-106 Slater determinants, using effective core potentials or all-electron calculations. In all the cases, a sub-milli-Hartree convergence is reached within only two or three iterations of optimization.
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Affiliation(s)
- Abdallah Ammar
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse - CNRS, 118 route de Narbonne, 31062 Toulouse cedex 09, France
| | - Emmanuel Giner
- Laboratoire de Chimie Théorique (UMR 7616), Université Paris Sorbonne - CNRS, 4 place Jussieu, 75052 Paris cedex, France
| | - Anthony Scemama
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse - CNRS, 118 route de Narbonne, 31062 Toulouse cedex 09, France
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14
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David G, Ben Amor N, Zeng T, Suaud N, Trinquier G, Malrieu JP. Difficulty of the evaluation of the barrier height of an open-shell transition state between closed shell minima: The case of small C 4n rings. J Chem Phys 2022; 156:224104. [PMID: 35705394 DOI: 10.1063/5.0090129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
C4n cyclacenes exhibit strong bond-alternation in their equilibrium geometry. In the two equivalent geometries, the system keeps an essentially closed-shell character. The two energy minima are separated by a transition state suppressing the bond-alternation, where the wave function is strongly diradical. This paper discusses the physical factors involved in this energy difference and possible evaluations of the barrier height. The barrier given as the energy difference between the restricted density functional theory (DFT)/B3LYP for the equilibrium and the broken symmetry DFT/B3LYP of the transition state is either negative or small, in contradiction with the most reliable Wave Function Theory calculations. The minimal (two electrons in two molecular orbitals) Complete Active Space self-consistent field (CASSCF) overestimates the barrier, and the subsequent second-order perturbation cancels it. Due to the collective character of the spin-polarization effect, it is necessary to perform a full π CASSCF + second-order perturbation to reach a reasonable value of the barrier, but this type of treatment cannot be applied to large molecules. DFT procedures treating on an equal foot the closed-shell and open-shell geometries have been explored, such as Mixed-Reference Spin-Flip Time-dependent-DFT and a new spin-decontamination proposal, namely, DFT-dressed configuration interaction, but the results still depend on the density functional. M06-2X without or with spin-decontamination gives the best agreement with the accurate wave function results.
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Affiliation(s)
- Grégoire David
- University Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France
| | - Nadia Ben Amor
- Laboratoire de Chimie et Physique Quantiques, IRSAMC-CNRS-UMR5626, Université Paul-Sabatier (Toulouse III), 31062 Toulouse Cedex 4, France
| | - Tao Zeng
- Department of Chemistry, York University, Toronto, Ontario M3J1P3, Canada
| | - Nicolas Suaud
- Laboratoire de Chimie et Physique Quantiques, IRSAMC-CNRS-UMR5626, Université Paul-Sabatier (Toulouse III), 31062 Toulouse Cedex 4, France
| | - Georges Trinquier
- Laboratoire de Chimie et Physique Quantiques, IRSAMC-CNRS-UMR5626, Université Paul-Sabatier (Toulouse III), 31062 Toulouse Cedex 4, France
| | - Jean-Paul Malrieu
- Laboratoire de Chimie et Physique Quantiques, IRSAMC-CNRS-UMR5626, Université Paul-Sabatier (Toulouse III), 31062 Toulouse Cedex 4, France
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15
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Sarkar R, Loos PF, Boggio-Pasqua M, Jacquemin D. Assessing the Performances of CASPT2 and NEVPT2 for Vertical Excitation Energies. J Chem Theory Comput 2022; 18:2418-2436. [PMID: 35333060 DOI: 10.1021/acs.jctc.1c01197] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Methods able to simultaneously account for both static and dynamic electron correlations have often been employed, not only to model photochemical events but also to provide reference values for vertical transition energies, hence allowing benchmarking of lower-order models. In this category, both the complete-active-space second-order perturbation theory (CASPT2) and the N-electron valence state second-order perturbation theory (NEVPT2) are certainly popular, the latter presenting the advantage of not requiring the application of the empirical ionization-potential-electron-affinity (IPEA) and level shifts. However, the actual accuracy of these multiconfigurational approaches is not settled yet. In this context, to assess the performances of these approaches, the present work relies on highly accurate (±0.03 eV) aug-cc-pVTZ vertical transition energies for 284 excited states of diverse character (174 singlet, 110 triplet, 206 valence, 78 Rydberg, 78 n → π*, 119 π → π*, and 9 double excitations) determined in 35 small- to medium-sized organic molecules containing from three to six non-hydrogen atoms. The CASPT2 calculations are performed with and without IPEA shift and compared to the partially contracted (PC) and strongly contracted (SC) variants of NEVPT2. We find that both CASPT2 with IPEA shift and PC-NEVPT2 provide fairly reliable vertical transition energy estimates, with slight overestimations and mean absolute errors of 0.11 and 0.13 eV, respectively. These values are found to be rather uniform for the various subgroups of transitions. The present work completes our previous benchmarks focused on single-reference wave function methods ( J. Chem. Theory Comput. 2018, 14, 4360; J. Chem. Theory Comput. 2020, 16, 1711), hence allowing for a fair comparison between various families of electronic structure methods. In particular, we show that ADC(2), CCSD, and CASPT2 deliver similar accuracies for excited states with a dominant single-excitation character.
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Affiliation(s)
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, CNRS, UPS, Université de Toulouse, Toulouse 31062, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques, CNRS, UPS, Université de Toulouse, Toulouse 31062, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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16
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Park JW. Analytical Gradient Theory for Spin-Free State-Averaged Second-Order Driven Similarity Renormalization Group Perturbation Theory (SA-DSRG-MRPT2) and Its Applications for Conical Intersection Optimizations. J Chem Theory Comput 2022; 18:2233-2245. [PMID: 35229599 DOI: 10.1021/acs.jctc.1c01150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Second-order multireference-driven similarity renormalization group perturbation theory (DSRG-MRPT2) provides an efficient means of correcting the dynamical correlation with the multiconfiguration reference function. The state-averaged DSRG-MRPT2 (SA-DSRG-MRPT2) method is the simplest means of treating the excited states with DSRG-MRPT2. In this method, the Hamiltonian dressed with dynamical correlation is diagonalized in the CASCI state subspace (SA-DSRG-MRPT2c) or the configuration subspace (SA-DSRG-MRPT2). This work develops analytical gradient theory for spin-free SA-DSRG-MRPT2(c) with the density-fitting approximation. We check the accuracy of the analytical gradients against the numerical gradients. We present applications for optimizing minimum energy conical intersections (MECI) of ethylene and retinal model chromophores (PSB3 and RPSB6). We investigate the dependence of the optimized geometries and energies on the flow parameters and reference relaxations. The smoothness of the SA-DSRG-MRPT2(c) potential energy surfaces near the reference (complete active space self-consistent field) MECI is comparable to the XMCQDPT2 one. These results render SA-DSRG-MRPT2(c) theory a promising approach for studies of conical intersections.
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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17
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Liu MK, Li J, Li QS, Li ZS. Theoretical insights into photo-induced isomerization mechanisms of phenylsulfinyl radical PhSO˙. Phys Chem Chem Phys 2022; 24:6266-6273. [PMID: 35229842 DOI: 10.1039/d1cp05331k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sulfinyl radicals (R-SO˙) play important roles in lots of reactions, while the isomer oxathiyl radicals (R-OS˙) and the isomerization between them are rarely observed due to the poor stability of R-OS˙. In this work, the complete active space self-consistent field (CASSCF) and its multi-state second order perturbation (MS-CASPT2) methods were employed to study the photo-induced reaction mechanisms of phenylsulfinyl radical PhSO˙ 1 and its isomer phenoxathiyl radical PhOS˙ 2. Our results show that 1 and 2 have similar singly occupied molecular orbitals in the ground state but different properties in the excited state, which determine their diverse behaviors after irradiation. Radical 1 can generate 2 by light irradiation, but 2 produces isomerization product 3 (2-hydroxyphenylthiyl radical) and ring-opening product 4 (acyclic thioketoketene radical) in two paths via S atom migration intermediate Int1 (2-carbonylcyclohexadienthiyl radical). The former path involves consequent hydrogen shift reactions with a strongly exothermic process while the latter path involves both ring-expansion and ring-opening processes with a high barrier, resulting in a structural and energetic preference for the former path. Moreover, we revealed several conical intersections that participate in the reactions and facilitate the photochemical processes. Our calculations not only remain consistent with and clarify the experimental observations (X. Zeng, et al., J. Am. Chem. Soc., 2018, 140(31), 9972-9978) but also enrich the knowledge of sulfinyl radicals and isomer oxathiyl radicals.
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Affiliation(s)
- Meng-Kai Liu
- 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.
| | - Jian 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.
| | - 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.
| | - Ze-Sheng 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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18
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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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19
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Grigorenko BL, Domratcheva T, Polyakov IV, Nemukhin AV. Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2. J Phys Chem Lett 2021; 12:8263-8271. [PMID: 34424693 DOI: 10.1021/acs.jpclett.1c02415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The role of protonation states of the chromophore and its neighboring amino acid side chains of the reversibly switching fluorescent protein rsEGFP2 upon photoswitching is characterized by molecular modeling methods. Numerous conformations of the chromophore-binding site in computationally derived model systems are obtained using the quantum chemistry and QM/MM approaches. Excitation energies are computed using the extended multiconfigurational quasidegenerate perturbation theory (XMCQDPT2). The obtained structures and absorption spectra allow us to provide an interpretation of the observed structural and spectral properties of rsEGFP2 in the active ON and inactive OFF states. The results demonstrate that in addition to the dominating anionic and neutral forms of the chromophore, the cationic and zwitterionic forms may participate in the photoswitching of rsEGFP2. Conformations and protonation forms of the Glu223 and His149 side chains in the chromophore-binding site play an essential role in stabilizing specific protonation forms of the chromophore.
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Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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20
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Matsika S. Electronic Structure Methods for the Description of Nonadiabatic Effects and Conical Intersections. Chem Rev 2021; 121:9407-9449. [PMID: 34156838 DOI: 10.1021/acs.chemrev.1c00074] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonadiabatic effects are ubiquitous in photophysics and photochemistry, and therefore, many theoretical developments have been made to properly describe them. Conical intersections are central in nonadiabatic processes, as they promote efficient and ultrafast nonadiabatic transitions between electronic states. A proper theoretical description requires developments in electronic structure and specifically in methods that describe conical intersections between states and nonadiabatic coupling terms. This review focuses on the electronic structure aspects of nonadiabatic processes. We discuss the requirements of electronic structure methods to describe conical intersections and nonadiabatic couplings, how the most common excited state methods perform in describing these effects, and what the recent developments are in expanding the methodology and implementing nonadiabatic couplings.
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Affiliation(s)
- Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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21
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Hutcheson A, Paul AC, Myhre RH, Koch H, Høyvik IM. Describing ground and excited state potential energy surfaces for molecular photoswitches using coupled cluster models. J Comput Chem 2021; 42:1419-1429. [PMID: 33973669 DOI: 10.1002/jcc.26553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/19/2021] [Accepted: 04/20/2021] [Indexed: 11/08/2022]
Abstract
In this article, we use two extensively studied systems, a retinal model system and azobenzene, to explore the use of coupled cluster models for describing ground and singlet excited state potential energy surfaces of photoswitchable systems. While not being suitable for describing nuclear dynamics of photoisomerization, coupled cluster models have useful attributes, such as the inclusion of dynamical correlation, their black box nature, and the systematic improvement offered by truncation level. Results for the studied systems show that when triple excitations (here through the CC3 model) are included, ground and excited state potential energy surfaces for isomerization paths may reliably be generated, also for states of doubly excited character. For ground state equilibrium cis- and trans-azobenzene, the molecular geometry and basis set is seen to significantly impact the vertical excitation energies for the two lowest excited states. Efficient implementations of coupled cluster models can therefore constitute valuable tools for investigating photoswitchable systems and can be used for preliminary black box studies to gather information before more complicated excited state dynamics approaches are pursued.
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Affiliation(s)
- Anders Hutcheson
- Department of Chemistry, The Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Rolf H Myhre
- Department of Chemistry, The Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Ida-Marie Høyvik
- Department of Chemistry, The Norwegian University of Science and Technology, Trondheim, Norway
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22
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Liu F, Filatov M, Martínez TJ. Analytical derivatives of the individual state energies in ensemble density functional theory. II. Implementation on graphical processing units (GPUs). J Chem Phys 2021; 154:104108. [DOI: 10.1063/5.0041389] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Fang Liu
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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23
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Giuliani G, Melaccio F, Gozem S, Cappelli A, Olivucci M. QM/MM Investigation of the Spectroscopic Properties of the Fluorophore of Bacterial Luciferase. J Chem Theory Comput 2021; 17:605-613. [PMID: 33449693 PMCID: PMC9220819 DOI: 10.1021/acs.jctc.0c01078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We employ replica-exchange molecular dynamics (REMD) and a hybrid ab initio multiconfigurational quantum mechanics/molecular mechanics (QM/MM) approach to model the absorption and fluorescence properties of bacterial luciferin-luciferase. Specifically, we employ complete active space perturbation theory (CASPT2) and study the effect of active space, basis set, and IPEA shift on the computed energies. We discuss the effect of the protein environment on the fluorophore's excited-state potential energy surface and the role that the protein plays in enhancing the fluorescence quantum yield in bacterial bioluminescence.
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Affiliation(s)
- Germano Giuliani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Federico Melaccio
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Andrea Cappelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowing Green, Ohio 43403, United States
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24
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Abstract
Herewith, we propose two new exponents for the recently introduced XDW-CASPT2 method [S. Battaglia and R. Lindh, J. Chem. Theory Comput. 16, 1555-1567 (2020)], which fix one of the largest issues hindering this approach. By using the first-order effective Hamiltonian coupling elements, the weighting scheme implicitly takes into account the symmetry of the states, thereby averaging Fock operators only if the zeroth-order wave functions interact with each other. The use of Hamiltonian couplings also provides a physically sounder approach to quantitate the relative weights; however, it introduces new difficulties when these rapidly die off to zero. The improved XDW-CASPT2 method is critically tested on several systems of photochemical relevance, and it is shown that it succeeds in its original intent of maintaining MS-CASPT2 accuracy for the evaluation of transition energies and at the same time providing smooth potential energy surfaces around near-degenerate points akin to XMS-CASPT2.
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Affiliation(s)
- Stefano Battaglia
- Department of Chemistry-BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Roland Lindh
- Department of Chemistry-BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
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25
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Kretz B, Egger DA. Accurate Molecular Geometries in Complex Excited-State Potential Energy Surfaces from Time-Dependent Density Functional Theory. J Chem Theory Comput 2021; 17:357-366. [PMID: 33284603 DOI: 10.1021/acs.jctc.0c00858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The interplay of electronic excitations and structural changes in molecules impacts nonradiative decay and charge transfer in the excited state, thus influencing excited-state lifetimes and photocatalytic reaction rates in optoelectronic and energy devices. To capture such effects requires computational methods providing an accurate description of excited-state potential energy surfaces and geometries. We suggest time-dependent density functional theory using optimally tuned range-separated hybrid (OT-RSH) functionals as an accurate approach to obtain excited-state molecular geometries. We show that OT-RSH provides accurate molecular geometries in excited-state potential energy surfaces that are complex and involve an interplay of local and charge-transfer excitations, for which conventional semilocal and hybrid functionals fail. At the same time, the nonempirical OT-RSH approach maintains the high accuracy of parametrized functionals (e.g., B3LYP) for predicting excited-state geometries of small organic molecules showing valence excited states.
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Affiliation(s)
- Bernhard Kretz
- Department of Physics, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - David A Egger
- Department of Physics, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
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26
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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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27
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Marsili E, Olivucci M, Lauvergnat D, Agostini F. Quantum and Quantum-Classical Studies of the Photoisomerization of a Retinal Chromophore Model. J Chem Theory Comput 2020; 16:6032-6048. [PMID: 32931266 DOI: 10.1021/acs.jctc.0c00679] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report an in-depth analysis of the photo-induced isomerization of the 2-cis-penta-2,4-dieniminium cation: a minimal model of the 11-cis retinal protonated Schiff base chromophore of the dim-light photoreceptor rhodopsin. Based on recently developed three-dimensional potentials parametrized on ab initio multi-state multi-configurational second-order perturbation theory data, we perform quantum-dynamical studies. In addition, simulations based on various quantum-classical methods, among which Tully surface hopping and the coupled-trajectory approach derived from the exact factorization, allow us to validate their performance against vibronic wavepacket propagation and, therefore, a purely quantum treatment. Quantum-dynamics results uncover qualitative differences with respect to the two-dimensional Hahn-Stock potentials, widely used as model potentials for the isomerization of the same chromophore, due to the increased dimensionality and three-mode correlation. Quantum-classical simulations show, instead, that three-dimensional model potentials are capable of capturing a number of features revealed by atomistic simulations and experimental observations. In particular, a recently reported vibrational phase relationship between double-bond torsion and hydrogen-out-of-plane modes critical for rhodopsin isomerization efficiency is correctly reproduced.
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Affiliation(s)
- Emanuele Marsili
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France.,Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
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28
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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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29
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Park JW, Al-Saadon R, MacLeod MK, Shiozaki T, Vlaisavljevich B. Multireference Electron Correlation Methods: Journeys along Potential Energy Surfaces. Chem Rev 2020; 120:5878-5909. [PMID: 32239929 DOI: 10.1021/acs.chemrev.9b00496] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Multireference electron correlation methods describe static and dynamical electron correlation in a balanced way and, therefore, can yield accurate and predictive results even when single-reference methods or multiconfigurational self-consistent field theory fails. One of their most prominent applications in quantum chemistry is the exploration of potential energy surfaces. This includes the optimization of molecular geometries, such as equilibrium geometries and conical intersections and on-the-fly photodynamics simulations, both of which depend heavily on the ability of the method to properly explore the potential energy surface. Because such applications require nuclear gradients and derivative couplings, the availability of analytical nuclear gradients greatly enhances the scope of quantum chemical methods. This review focuses on the developments and advances made in the past two decades. A detailed account of the analytical nuclear gradient and derivative coupling theories is presented. Emphasis is given to the software infrastructure that allows one to make use of these methods. Notable applications of multireference electron correlation methods to chemistry, including geometry optimizations and on-the-fly dynamics, are summarized at the end followed by a discussion of future prospects.
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Korea
| | - Rachael Al-Saadon
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Matthew K MacLeod
- Workday, 4900 Pearl Circle East, Suite 100, Boulder, Colorado 80301, United States
| | - Toru Shiozaki
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.,Quantum Simulation Technologies, Inc., 625 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bess Vlaisavljevich
- Department of Chemistry, University of South Dakota, 414 East Clark Street, Vermillion, South Dakota 57069, United States
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30
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Zilberg S. Design of Light‐Induced Molecular Switcher for the Driver of the Quantum Cellular Automata (QCA) Based on the Transition through the Intramolecular Charge Transfer (ICT) Structure. Isr J Chem 2020. [DOI: 10.1002/ijch.201900148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Shmuel Zilberg
- Department of Chemical SciencesAriel University 40700 Ariel Israel
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31
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Park JW. Analytical Gradient Theory for Quasidegenerate N-Electron Valence State Perturbation Theory (QD-NEVPT2). J Chem Theory Comput 2019; 16:326-339. [DOI: 10.1021/acs.jctc.9b00919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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32
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Kahremany S, Sander CL, Tochtrop GP, Kubas A, Palczewski K. Z-isomerization of retinoids through combination of monochromatic photoisomerization and metal catalysis. Org Biomol Chem 2019; 17:8125-8139. [PMID: 31455964 DOI: 10.1039/c9ob01645g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Catalytic Z-isomerization of retinoids to their thermodynamically less stable Z-isomer remains a challenge. In this report, we present a photochemical approach for the catalytic Z-isomerization of retinoids using monochromatic wavelength UV irradiation treatment. We have developed a straightforward approach for the synthesis of Z-retinoids in high yield, overcoming common obstacles normally associated with their synthesis. Calculations based on density functional theory (DFT) have allowed us to correlate the experimentally observed Z-isomer distribution of retinoids with the energies of chemically important intermediates, which include ground- and excited-state potential energy surfaces. We also demonstrate the application of the current method by synthesizing gram-scale quantities of 9-cis-retinyl acetate 9Z-a. Operational simplicity and gram-scale ability make this chemistry a very practical solution to the problem of Z-isomer retinoid synthesis.
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Affiliation(s)
- Shirin Kahremany
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697, USA.
| | - Christopher Lane Sander
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697, USA. and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Gregory P Tochtrop
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697, USA.
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33
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Burton HGA, Thom AJW. General Approach for Multireference Ground and Excited States Using Nonorthogonal Configuration Interaction. J Chem Theory Comput 2019; 15:4851-4861. [DOI: 10.1021/acs.jctc.9b00441] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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34
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Park JW. Single-State Single-Reference and Multistate Multireference Zeroth-Order Hamiltonians in MS-CASPT2 and Conical Intersections. J Chem Theory Comput 2019; 15:3960-3973. [DOI: 10.1021/acs.jctc.9b00067] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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35
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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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36
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Mai S, Atkins AJ, Plasser F, González L. The Influence of the Electronic Structure Method on Intersystem Crossing Dynamics. The Case of Thioformaldehyde. J Chem Theory Comput 2019; 15:3470-3480. [DOI: 10.1021/acs.jctc.9b00282] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straß 17, 1090 Vienna, Austria
| | - Andrew J. Atkins
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straß 17, 1090 Vienna, Austria
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straß 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straß 17, 1090 Vienna, Austria
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37
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Lee IS, Filatov M, Min SK. Formulation and Implementation of the Spin-Restricted Ensemble-Referenced Kohn–Sham Method in the Context of the Density Functional Tight Binding Approach. J Chem Theory Comput 2019; 15:3021-3032. [DOI: 10.1021/acs.jctc.9b00132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- In Seong Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Seung Kyu Min
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
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38
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Gonon B, Lasorne B, Karras G, Joubert-Doriol L, Lauvergnat D, Billard F, Lavorel B, Faucher O, Guérin S, Hertz E, Gatti F. A generalized vibronic-coupling Hamiltonian for molecules without symmetry: Application to the photoisomerization of benzopyran. J Chem Phys 2019; 150:124109. [PMID: 30927888 DOI: 10.1063/1.5085059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a model for the lowest two potential energy surfaces (PESs) that describe the photoinduced ring-opening reaction of benzopyran taken as a model compound to study the photochromic ring-opening reaction of indolinobenzospiropyran and its evolution toward its open-chain analog. The PESs are expressed in terms of three effective rectilinear coordinates. One corresponds to the direction between the equilibrium geometry in the electronic ground state, referred to as the Franck-Condon geometry, and the minimum of conical intersection (CI), while the other two span the two-dimensional branching space at the CI. The model correctly reproduces the topography of the PESs. The ab initio calculations are performed with the extended multiconfiguration quasidegenerate perturbation theory at second order method. We demonstrate that accounting for electron dynamic correlation drastically changes the global energy landscape since some zwitterionic states become strongly stabilized. Quantum dynamics calculations using this PES model produce an absorption spectrum that matches the experimental one to a good accuracy.
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Affiliation(s)
- Benjamin Gonon
- CTMM, Institut Charles Gerhardt UMR CNRS 5253-Université Montpellier, F-34095 Montpellier, France
| | - Benjamin Lasorne
- CTMM, Institut Charles Gerhardt UMR CNRS 5253-Université Montpellier, F-34095 Montpellier, France
| | - Gabriel Karras
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303-Université Bourgogne Franche-Comté, F-21078 Dijon Cedex, France
| | - Loïc Joubert-Doriol
- CTMM, Institut Charles Gerhardt UMR CNRS 5253-Université Montpellier, F-34095 Montpellier, France
| | - David Lauvergnat
- Laboratoire de Chimie Physique UMR CNRS 8000-Université Paris-Sud, F-91405 Orsay, France
| | - Franck Billard
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303-Université Bourgogne Franche-Comté, F-21078 Dijon Cedex, France
| | - Bruno Lavorel
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303-Université Bourgogne Franche-Comté, F-21078 Dijon Cedex, France
| | - Olivier Faucher
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303-Université Bourgogne Franche-Comté, F-21078 Dijon Cedex, France
| | - Stéphane Guérin
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303-Université Bourgogne Franche-Comté, F-21078 Dijon Cedex, France
| | - Edouard Hertz
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303-Université Bourgogne Franche-Comté, F-21078 Dijon Cedex, France
| | - Fabien Gatti
- CTMM, Institut Charles Gerhardt UMR CNRS 5253-Université Montpellier, F-34095 Montpellier, France
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39
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Marín MDC, De Vico L, Dong SS, Gagliardi L, Truhlar DG, Olivucci M. Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins. J Chem Theory Comput 2019; 15:1915-1923. [PMID: 30721054 PMCID: PMC7096677 DOI: 10.1021/acs.jctc.8b01069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-binding rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multiconfiguration second-order perturbation theory (in particular, CASPT2) calculation of external correlation energies. Although it was shown that ARM is capable of successfully reproducing and predicting spectroscopic property trends in chromophore-embedding protein sets, practical applications of such technology are limited by the high computational costs of the multiconfiguration perturbation theory calculations. In the present work we benchmark the more affordable multiconfiguration pair-density functional theory (MC-PDFT) method whose accuracy has been recently validated for retinal chromophores in the gas phase, indicating that MC-PDFT could potentially be used to analyze large (e.g., few hundreds) sets of rhodopsin proteins. Here, we test this theory for a set of rhodopsin QM/MM models whose experimental absorption maxima (λ a max) have been measured. The results indicate that MC-PDFT may be employed to calculate λ a max values for this important class of photoresponsive proteins.
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Affiliation(s)
- María Del Carmen Marín
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , 43403 Ohio , United States
| | - Luca De Vico
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
| | - Sijia S Dong
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Massimo Olivucci
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , 43403 Ohio , United States
- USIAS Institut d'Études Avanceés , Université de Strasbourg , 67083 Strasbourg , France
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40
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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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41
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Loos PF, Boggio-Pasqua M, Scemama A, Caffarel M, Jacquemin D. Reference Energies for Double Excitations. J Chem Theory Comput 2019; 15:1939-1956. [DOI: 10.1021/acs.jctc.8b01205] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Anthony Scemama
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Michel Caffarel
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Denis Jacquemin
- Laboratoire CEISAM (UMR 6230), CNRS, Université de Nantes, 44399 Cedex 3 Nantes, France
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42
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Zhou P, Zhao L. How Does the O6-Methylation Regulate the Excited-State Decay of Guanine Monomers. J Phys Chem B 2018; 123:201-206. [DOI: 10.1021/acs.jpcb.8b08606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, Liaoning, China
| | - Li Zhao
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China
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43
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Musbat L, Assis S, Dilger JM, El-Baba TJ, Fuller DR, Knudsen JL, Kiefer HV, Hirshfeld A, Friedman N, Andersen LH, Sheves M, Clemmer DE, Toker Y. Action and Ion Mobility Spectroscopy of a Shortened Retinal Derivative. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2152-2159. [PMID: 30062478 DOI: 10.1007/s13361-018-2033-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
The development of tandem ion mobility spectroscopy (IMS) known as IMS-IMS has led to extensive research into isomerizations of isolated molecules. Many recent works have focused on the retinal chromophore which is the optical switch used in animal vision. Here, we study a shortened derivative of the chromophore, which exhibits a rich IM spectrum allowing for a detailed analysis of its isomerization pathways, and show that the longer the chromophore is, the lower the barrier energies for isomerization are. Graphical Abstract.
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Affiliation(s)
- Lihi Musbat
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Shirrel Assis
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Jonathan M Dilger
- Spectrum Warfare Systems Department, NSWC Crane Division, Crane, IN, 47522, USA
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | - Daniel R Fuller
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | | | - Hjalte V Kiefer
- Department of Physics and Astronomy, Aarhus University, 8000, Aarhus C, Denmark
| | - Amiram Hirshfeld
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Noga Friedman
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, 8000, Aarhus C, Denmark
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - David E Clemmer
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | - Yoni Toker
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel.
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44
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Ai Y, Zhao C, Xing J, Liu Y, Wang Z, Jin J, Xia S, Cui G, Wang X. Excited-State Decay Pathways of Flavin Molecules in Five Redox Forms: The Role of Conical Intersections. J Phys Chem A 2018; 122:7954-7961. [DOI: 10.1021/acs.jpca.8b07582] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuejie Ai
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P.R. China
| | - Chaofeng Zhao
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P.R. China
| | - Jinlu Xing
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P.R. China
| | - Yang Liu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P.R. China
| | - Zhangxia Wang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P.R. China
| | - Jiaren Jin
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P.R. China
| | - Shuhua Xia
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, P.R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P.R. China
| | - Xiangke Wang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P.R. China
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45
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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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46
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Grabarek D, Andruniów T. Initial excited-state relaxation of locked retinal protonated schiff base chromophore. An insight from coupled cluster and multireference perturbation theory calculations. J Comput Chem 2018; 39:1720-1727. [PMID: 29727036 DOI: 10.1002/jcc.25346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/06/2018] [Accepted: 04/12/2018] [Indexed: 11/07/2022]
Abstract
The initial S1 excited-state relaxation of retinal protonated Schiff base (RPSB) analog with central C11C12 double bond locked by eight-membered ring (locked-11.8) was investigated by means of multireference perturbation theory methods (XMCQDPT2, XMS-CASPT2, MS-CASPT2) as well as single-reference coupled-cluster CC2 method. The analysis of XMCQDPT2-based geometries reveals rather weak coupling between in-plane and out-of-plane structural evolution and minor energetical relaxation of three locked-11.8 conformers. Therefore, a strong coupling between bonds length inversion and backbone out-of-plane deformation resulting in a very steep S1 energy profile predicted by CASSCF/CASPT2 calculations is in clear contradiction with the reference XMCQDPT2 results. Even though CC2 method predicts good quality ground-state structures, the excited-state structures display more advanced torsional deformation leading to ca. 0.2 eV exaggerated energy relaxation and significantly red shifted (0.4-0.7 eV) emission maxima. According to our findings, the initial photoisomerization process in locked-11.8, and possibly in other RPSB analogs, studied fully (both geometries and energies) by multireference perturbation theory may be somewhat slower than predicted by CASSCF/CASPT2 or CC2 methods. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- 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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47
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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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48
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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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49
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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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50
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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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