1
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Stolar T, Pearce BK, Etter M, Truong KN, Ostojić T, Krajnc A, Mali G, Rossi B, Molčanov K, Lončarić I, Meštrović E, Užarević K, Grisanti L. Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity. iScience 2024; 27:109894. [PMID: 38783999 PMCID: PMC11112615 DOI: 10.1016/j.isci.2024.109894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/18/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Ben K.D. Pearce
- Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263 Neu-Isenburg, Germany
| | - Tea Ostojić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Andraž Krajnc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Mali
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | | | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Ernest Meštrović
- Faculty of Chemical Engineering and Technology, University of Zagreb, Trg Marka Marulića 19, 10000 Zagreb, Croatia
| | | | - Luca Grisanti
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- National Research Council - Materials Foundry Institute (CNR-IOM) c/o SISSA (International School for Advanced Studies), Via Bonomea 265, 34136 Trieste, Italy
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2
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Chang XP, Wang JL, Peng LY, Cen XJ, Yin BW, Xie BB. Mechanistic photophysics of tellurium-substituted cytosine: Electronic structure calculations and nonadiabatic dynamics simulations. Photochem Photobiol 2024; 100:339-354. [PMID: 37435854 DOI: 10.1111/php.13835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
Previously, the MS-CASPT2 method was performed to study the static and qualitative photophysics of tellurium-substituted cytosine (TeC). To get quantitative information, we used our recently developed QTMF-FSSH dynamics method to simulate the excited-state decay of TeC. The CASSCF method was adopted to reduce the calculation costs, which was confirmed to provide reliable structures and energies as those of MS-CASPT2. A detailed structural analysis showed that only 5% trajectories will hop to the lower triplet or singlet state via the twisted (S2 /S1 /T2 )T intersection, while 67% trajectories will choose the planar intersections of (S2 /S1 /T3 /T2 /T1 )P and (S2 /S1 /T2 /T1 )P but subsequently become twisted in other electronic states. By contrast, ~28% trajectories will maintain in a plane throughout dynamics. Electronic population revealed that the S2 population will ultrafast transfer to the lower triplet or singlet state. Later, the TeC system will populate in the spin-mixed electronic states composed of S1 , T1 and T2 . At the end of 300 fs, most trajectories (~74%) will decay to the ground state and only 17.4% will survive in the triplet states. Our dynamics simulation verified that tellurium substitution will enhance the intersystem crossings, but the very short triplet lifetime (ca. 125 fs) will make TeC a less effective photosensitizer.
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Affiliation(s)
- Xue-Ping Chang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou, China
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang, China
| | - Jie-Lei Wang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou, China
| | - Ling-Ya Peng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Xu-Jiang Cen
- Ningbo Zhongtian Engineering Co., Ltd., Ningbo, China
| | - Bo-Wen Yin
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou, China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou, China
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3
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Bezabih MS, Kaliakin DS, Blanco-González A, Barneschi L, Tarnovsky AN, Olivucci M. Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories. J Phys Chem B 2023; 127:10871-10879. [PMID: 38055701 DOI: 10.1021/acs.jpcb.3c06433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.
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Affiliation(s)
- Meseret Simachew Bezabih
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Danil S Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Leonardo Barneschi
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Alexander N Tarnovsky
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
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4
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Karak P, Moitra T, Ruud K, Chakrabarti S. Photophysics of uracil: an explicit time-dependent generating function-based method combining both nonadiabatic and spin-orbit coupling effects. Phys Chem Chem Phys 2023; 25:8209-8219. [PMID: 36881024 DOI: 10.1039/d2cp05955j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
We present a composite framework for calculating the rates of non-radiative deactivation processes, namely internal conversion (IC) and intersystem crossing (ISC), on an equal footing by explicitly computing the non-adiabatic coupling (NAC) and spin-orbit coupling (SOC) constants, respectively. The stationary-state approach uses a time-dependent generating function based on Fermi's golden rule. We validate the applicability of the framework by computing the rate of IC for azulene, obtaining comparable rates to experimental and previous theoretical results. Next, we investigate the photophysics associated with the complex photodynamics of the uracil molecule. Interestingly, our simulated rates corroborate experimental observations. Detailed analyses using Duschinsky rotation matrices, displacement vectors and NAC matrix elements are presented to interpret the findings alongside testing the suitability of the approach for such molecular systems. The suitability of the Fermi's golden rule based method is explained qualitatively in terms of single-mode potential energy surfaces.
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Affiliation(s)
- Pijush Karak
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
| | - Torsha Moitra
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway. .,Norwegian Defence Research Establishment, P.O.Box 25, 2027 Kjeller, Norway
| | - Swapan Chakrabarti
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
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Otis L, Neuscamman E. A promising intersection of excited‐state‐specific methods from quantum chemistry and quantum Monte Carlo. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Leon Otis
- Department of Physics University of California Berkeley Berkeley California USA
| | - Eric Neuscamman
- Department of Chemistry University of California Berkeley Berkeley California USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley California USA
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6
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Wang M, Fang WH, Li C. Assessment of State-Averaged Driven Similarity Renormalization Group on Vertical Excitation Energies: Optimal Flow Parameters and Applications to Nucleobases. J Chem Theory Comput 2023; 19:122-136. [PMID: 36534617 DOI: 10.1021/acs.jctc.2c00966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present a comprehensive excited-state benchmark for the state-averaged (SA) driven similarity renormalization group (DSRG) [Li, C.; Evangelista, F. A. J. Chem. Phys. 2018, 148, 124106]. Following the QUEST database [Véril, M.; Scemama, A.; Caffarel, M.; Lipparini, F.; Boggio-Pasqua, M.; Jacquemin, D.; Loos, P.-F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2021, 11, e1517], 280 vertical transition energies of 35 medium-sized molecules are computed using the SA-DSRG derived second- and third-order perturbation theories (PT2/PT3) along with a nonperturbative approach [sq-LDSRG(2)]. Comparing to the theoretical best estimates, the optimal flow parameter is found to be 0.35 and 2.0 Eh-2 for SA-DSRG-PT2 and SA-DSRG-PT3, respectively. For SA-sq-LDSRG(2), a flow parameter of 1.5 Eh-2 provides converged equations without compromising the accuracy. We then assess the accuracy of the SA-DSRG hierarchy using these parameters. The SA-DSRG-PT2 scheme outperforms the level-shifted CASPT2 by 0.10 eV in mean absolute error (MAE), yet this accuracy is slightly inferior than that of CASPT2 with the ionization-potential-electron-affinity shift. Both SA-DSRG-PT3 and SA-sq-LDSRG(2) yield a MAE of 0.10 eV, which is comparable to that of CASPT3 (0.09 eV). Finally, we compute vertical excitation energies of several low-lying singlet states of nucleobases. The SA-sq-LDSRG(2) approach provides highly accurate results for π → π* excitations, while n → π* transitions are better described by SA-DSRG-PT3.
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Affiliation(s)
- Meng Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Chenyang Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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7
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Fedotov DA, Paul AC, Koch H, Santoro F, Coriani S, Improta R. Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study. Phys Chem Chem Phys 2022; 24:4987-5000. [PMID: 35142309 DOI: 10.1039/d1cp04340d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, namely, equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the ππ* states (one for pyrimidine, two for purines) associated with the lowest-energy absorption band, and for the close-lying nπ* state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effects by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the nπ* state. Finally, ESA spectra have been computed from the minima of the lowest energy ππ* state, and found in line with the available experimental transient absorption spectra of the nucleosides in solution, providing further validation of our computational approach.
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Affiliation(s)
- Daniil A Fedotov
- DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Alexander C Paul
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavalieri, 7, I-56126, Pisa, Italy.
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, I-56124 Pisa, Italy.
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark. .,Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, I-80134 Napoli, Italy.
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8
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Zhu YH, Tang XF, Chang XP, Zhang TS, Xie BB, Cui G. Mechanistic Photophysics of Tellurium-Substituted Uracils: Insights from Multistate Complete-Active-Space Second-Order Perturbation Calculations. J Phys Chem A 2021; 125:8816-8826. [PMID: 34606278 DOI: 10.1021/acs.jpca.1c06169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The photophysical mechanisms of tellurium-substituted uracils were studied at the multistate complete-active-space second-order perturbation level with a particular focus on how the position and number of tellurium substitutions affect their nonadiabatic relaxation processes. Electronic structure analysis reveals that the lowest several excited states are closely concerned with the n and π orbitals at the Te7-C2 [Te8-C4] moiety of 2-tellurouracil (2TeU) [4TeU and 24TeU]. Both planar and twisted minima were optimized for 2TeU, whereas only planar ones were obtained for 4TeU and 24TeU, except for a twisted T1 minimum of 4TeU. Based on intersection structures and linearly interpolated internal coordinate paths, we proposed several feasible excited-state deactivation paths. It is found that the relaxation channels for 2TeU are more complicated than those of 4TeU and 24TeU. The electronic population transfer to the T1 state for 2TeU is easier than that for 4TeU and 24TeU in consideration of the barrier heights from the S2 Franck-Condon point to the S2/S1 or S2/T2 intersections. In addition, the recovery of the ground state from the T1 state for 2TeU will be more efficient than that for the other two systems as well.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiu-Fang Tang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Xue-Ping Chang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, P. R. China
| | - Teng-Shuo Zhang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, P R. China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, 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
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9
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Kochman MA, Durbeej B, Kubas A. Simulation and Analysis of the Transient Absorption Spectrum of 4-( N, N-Dimethylamino)benzonitrile (DMABN) in Acetonitrile. J Phys Chem A 2021; 125:8635-8648. [PMID: 34550700 PMCID: PMC8503879 DOI: 10.1021/acs.jpca.1c06166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/03/2021] [Indexed: 12/17/2022]
Abstract
4-(N,N-Dimethylamino)benzonitrile (DMABN) is a well-known model compound for dual fluorescence-in sufficiently polar solvents, it exhibits two distinct fluorescence emission bands. The interpretation of its transient absorption (TA) spectrum in the visible range is the subject of a long-standing controversy. In the present study, we resolve this issue by calculating the TA spectrum on the basis of nonadiabatic molecular dynamics simulations. An unambiguous assignment of spectral signals to specific excited-state structures is achieved by breaking down the calculated spectrum into contributions from twisted and nontwisted molecular geometries. In particular, the much-discussed excited-state absorption band near 1.7 eV (ca. 700 nm) is attributed to the near-planar locally excited (LE) minimum on the S1 state. On the technical side, our study demonstrates that the second-order approximate coupled cluster singles and doubles (CC2) method can be used successfully to calculate the TA spectra of moderately large organic molecules, provided that the system in question does not approach a crossing between the lowest excited state and the singlet ground state within the time frame of the simulation.
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Affiliation(s)
- Michał Andrzej Kochman
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Ul. Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Bo Durbeej
- Division
of Theoretical Chemistry, Department of Physics, Chemistry and Biology
(IFM), Linköping University, 581 83 Linköping, Sweden
| | - Adam Kubas
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Ul. Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
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Green JA, Jouybari MY, Aranda D, Improta R, Santoro F. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules 2021; 26:1743. [PMID: 33804640 PMCID: PMC8003674 DOI: 10.3390/molecules26061743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.
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Affiliation(s)
- James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Martha Yaghoubi Jouybari
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Daniel Aranda
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Fabrizio Santoro
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
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11
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Tsuru S, Vidal ML, Pápai M, Krylov AI, Møller KB, Coriani S. An assessment of different electronic structure approaches for modeling time-resolved x-ray absorption spectroscopy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:024101. [PMID: 33786337 PMCID: PMC7986275 DOI: 10.1063/4.0000070] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/11/2021] [Indexed: 05/06/2023]
Abstract
We assess the performance of different protocols for simulating excited-state x-ray absorption spectra. We consider three different protocols based on equation-of-motion coupled-cluster singles and doubles, two of them combined with the maximum overlap method. The three protocols differ in the choice of a reference configuration used to compute target states. Maximum-overlap-method time-dependent density functional theory is also considered. The performance of the different approaches is illustrated using uracil, thymine, and acetylacetone as benchmark systems. The results provide guidance for selecting an electronic structure method for modeling time-resolved x-ray absorption spectroscopy.
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Affiliation(s)
- Shota Tsuru
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Marta L. Vidal
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Mátyás Pápai
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Klaus B. Møller
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
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