1
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Navarrete-Miguel M, Giussani A, Rubio M, Boggio-Pasqua M, Borin AC, Roca-Sanjuán D. Quantum-Chemistry Study of the Photophysical Properties of 4-Thiouracil and Comparisons with 2-Thiouracil. J Phys Chem A 2024; 128:2273-2285. [PMID: 38504122 PMCID: PMC10982997 DOI: 10.1021/acs.jpca.3c06310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/16/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
DNA in living beings is constantly damaged by exogenous and endogenous agents. However, in some cases, DNA photodamage can have interesting applications, as it happens in photodynamic therapy. In this work, the current knowledge on the photophysics of 4-thiouracil has been extended by further quantum-chemistry studies to improve the agreement between theory and experiments, to better understand the differences with 2-thiouracil, and, last but not least, to verify its usefulness as a photosensitizer for photodynamic therapy. This study has been carried out by determining the most favorable deactivation paths of UV-vis photoexcited 4-thiouracil by means of the photochemical reaction path approach and an efficient combination of the complete-active-space second-order perturbation theory//complete-active-space self-consistent field (CASPT2//CASSCF), (CASPT2//CASPT2), time-dependent density functional theory (TDDFT), and spin-flip TDDFT (SF-TDDFT) methodologies. By comparing the data computed herein for both 4-thiouracil and 2-thiouracil, a rationale is provided on the relatively higher yields of intersystem crossing, triplet lifetime and singlet oxygen production of 4-thiouracil, and the relatively higher yield of phosphorescence of 2-thiouracil.
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Affiliation(s)
- Miriam Navarrete-Miguel
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Angelo Giussani
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Mercedes Rubio
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
| | - Martial Boggio-Pasqua
- Laboratoire
de Chimie et Physique Quantiques, IRSAMC,
CNRS et Université Toulouse 3, 118 route de Narbonne, 31062 Toulouse, France
| | - Antonio Carlos Borin
- Department
of Fundamental Chemistry, Institute of Chemistry,
University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo CEP 05508-000, Brazil
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
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2
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Safari AA, Anderson RJ, Manni GL. Toward a Stochastic Complete Active Space Second-Order Perturbation Theory. J Phys Chem A 2024; 128:281-291. [PMID: 38154124 PMCID: PMC10788896 DOI: 10.1021/acs.jpca.3c05109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023]
Abstract
In this work, an internally contracted stochastic complete active space second-order perturbation theory, stochastic-CASPT2, is reported. The method relies on stochastically sampled reduced density matrices (RDMs) up to rank four and contractions thereof with the generalized Fock matrix. A new protocol for calculating higher-order RDMs in full configuration interaction quantum Monte Carlo (FCIQMC) has been designed based on (1) restricting sampling of the corresponding excitations to a deterministic subspace, (2) averaging the RDMs from independent dynamics and (3) projecting them onto the closest positive semi-definite matrix. Our protocol avoids previously encountered numerical conditioning problems in the orthogonalization of the perturber overlap matrix stemming from numerical noise. The chromium dimer CASSCF(12,12)/CASPT2 binding curve is computed as a proof of concept.
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Affiliation(s)
- Arta A. Safari
- Max-Planck-Institute for Solid State
Research, 70569 Stuttgart, Germany
| | | | - Giovanni Li Manni
- Max-Planck-Institute for Solid State
Research, 70569 Stuttgart, Germany
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3
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Teles-Ferreira DC, Manzoni C, Martínez-Fernández L, Cerullo G, de Paula AM, Borrego-Varillas R. Ultrafast Excited-State Decay Mechanisms of 6-Thioguanine Followed by Sub-20 fs UV Transient Absorption Spectroscopy. Molecules 2022; 27:molecules27041200. [PMID: 35208987 PMCID: PMC8878119 DOI: 10.3390/molecules27041200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/23/2022] Open
Abstract
Understanding the primary steps following UV photoexcitation in sulphur-substituted DNA bases (thiobases) is fundamental for developing new phototherapeutic drugs. However, the investigation of the excited-state dynamics in sub-100 fs time scales has been elusive until now due to technical challenges. Here, we track the ultrafast decay mechanisms that lead to the electron trapping in the triplet manifold for 6-thioguanine in an aqueous solution, using broadband transient absorption spectroscopy with a sub-20 fs temporal resolution. We obtain experimental evidence of the fast internal conversion from the S2(ππ*) to the S1(nπ*) states, which takes place in about 80 fs and demonstrates that the S1(nπ*) state acts as a doorway to the triplet population in 522 fs. Our results are supported by MS-CASPT2 calculations, predicting a planar S2(ππ*) pseudo-minimum in agreement with the stimulated emission signal observed in the experiment.
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Affiliation(s)
| | - Cristian Manzoni
- Istituto di Fotonica e Nanotecnologie-Consiglio Nazionale delle Ricerche (IFN-CNR), Piazza Leonardo da Vinci 32, I-20133 Milano, Italy; (C.M.); (G.C.)
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain;
| | - Giulio Cerullo
- Istituto di Fotonica e Nanotecnologie-Consiglio Nazionale delle Ricerche (IFN-CNR), Piazza Leonardo da Vinci 32, I-20133 Milano, Italy; (C.M.); (G.C.)
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Rocío Borrego-Varillas
- Istituto di Fotonica e Nanotecnologie-Consiglio Nazionale delle Ricerche (IFN-CNR), Piazza Leonardo da Vinci 32, I-20133 Milano, Italy; (C.M.); (G.C.)
- Correspondence:
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4
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Teles-Ferreira DC, van Stokkum IH, Conti I, Ganzer L, Manzoni C, Garavelli M, Cerullo G, Nenov A, Borrego Varillas R, de Paula AM. Coherent vibrational modes promote the ultrafast internal conversion and intersystem crossing in thiobases. Phys Chem Chem Phys 2022; 24:21750-21758. [DOI: 10.1039/d2cp02073d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thionated nucleobases are obtained by replacing oxygen with sulphur atoms in the canonical nucleobases. They absorb light efficiently in the near-ultraviolet, populating singlet states which undergo intersystem crossing to the...
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5
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Nam Y, Keefer D, Nenov A, Conti I, Aleotti F, Segatta F, Lee JY, Garavelli M, Mukamel S. Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy. J Phys Chem Lett 2021; 12:12300-12309. [PMID: 34931839 DOI: 10.1021/acs.jpclett.1c03814] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Conical intersections (CoIns) play an important role in ultrafast relaxation channels. Their monitoring remains a formidable experimental challenge. We theoretically compare the probing of the S2 → S1 CoIn passage in 4-thiouracil by monitoring its vibronic coherences, using off-resonant X-ray-stimulated Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). The quantum nuclear wavepacket (WP) dynamics provides an accurate picture of the photoinduced dynamics. Upon photoexcitation, the WP oscillates among the Franck-Condon point, the S2 minimum, and the CoIn with a 70 fs period. A vibronic coherence first emerges at 20 fs and can be observed until the S2 state is fully depopulated. The distribution of the vibronic frequencies involved in the coherence is recorded by the TRUECARS spectrogram. The TRXD signal provides spatial images of electron densities associated with the CoIn. In combination, the two signals provide a complementary picture of the nonadiabatic passage, which helps in the study of the underlying photophysics in thiobases.
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Affiliation(s)
- Yeonsig Nam
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
- Convergence Research Center for Energy and Environmental Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Daniel Keefer
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Jin Yong Lee
- Convergence Research Center for Energy and Environmental Sciences, Sungkyunkwan University, Suwon 16419, Korea
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari," Universita' degli Studi di Bologna, I-40136 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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6
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Aleotti F, Nenov A, Salvigni L, Bonfanti M, El-Tahawy MM, Giunchi A, Gentile M, Spallacci C, Ventimiglia A, Cirillo G, Montali L, Scurti S, Garavelli M, Conti I. Spectral Tuning and Photoisomerization Efficiency in Push-Pull Azobenzenes: Designing Principles. J Phys Chem A 2020; 124:9513-9523. [PMID: 33170012 PMCID: PMC8015210 DOI: 10.1021/acs.jpca.0c08672] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
This
work demonstrates how push–pull substitution can induce spectral tuning toward the
visible range and improve the photoisomerization efficiency of azobenzene-based
photoswitches, making them good candidates for technological and biological
applications. The red-shifted bright ππ* state (S2) behaves like the lower and more productive dark nπ*
(S1) state because less potential energy along the planar
bending mode is available to reach higher energy unproductive nπ*/S0 crossing regions, which are responsible for the lower quantum
yield of the parent compound. The stabilization of the bright ππ*
state and the consequent increase in isomerization efficiency may
be regulated via the strength of push–pull substituents. Finally, the torsional
mechanism is recognized here as the unique productive route because
structures with bending values attributable to the inversion mechanism
were never detected, out of the 280 ππ* time-dependent
density functional theory (RASPT2-validated) dynamics simulations.
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Affiliation(s)
- Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Luca Salvigni
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Matteo Bonfanti
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Mohsen M El-Tahawy
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy.,Chemistry Department, Faculty of Science, Damanhour University, 22511 Damanhour, Egypt
| | - Andrea Giunchi
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Marziogiuseppe Gentile
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Claudia Spallacci
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Alessia Ventimiglia
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Giuseppe Cirillo
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Lorenzo Montali
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Stefano Scurti
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
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7
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Conti I, Cerullo G, Nenov A, Garavelli M. Ultrafast Spectroscopy of Photoactive Molecular Systems from First Principles: Where We Stand Today and Where We Are Going. J Am Chem Soc 2020; 142:16117-16139. [PMID: 32841559 PMCID: PMC7901644 DOI: 10.1021/jacs.0c04952] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Computational spectroscopy is becoming a mandatory tool for the interpretation of the
complex, and often congested, spectral maps delivered by modern non-linear multi-pulse
techniques. The fields of Electronic Structure Methods,
Non-Adiabatic Molecular Dynamics, and Theoretical
Spectroscopy represent the three pillars of the virtual ultrafast
optical spectrometer, able to deliver transient spectra in
silico from first principles. A successful simulation strategy requires a
synergistic approach that balances between the three fields, each one having its very
own challenges and bottlenecks. The aim of this Perspective is to demonstrate that,
despite these challenges, an impressive agreement between theory and experiment is
achievable now regarding the modeling of ultrafast photoinduced processes in complex
molecular architectures. Beyond that, some key recent developments in the three fields
are presented that we believe will have major impacts on spectroscopic simulations in
the very near future. Potential directions of development, pending challenges, and
rising opportunities are illustrated.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
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8
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Mohamadzade A, Ullrich S. Internal conversion and intersystem crossing dynamics of uracil upon double thionation: a time-resolved photoelectron spectroscopy study in the gas phase. Phys Chem Chem Phys 2020; 22:15608-15615. [PMID: 32613978 DOI: 10.1039/d0cp02145h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photophysical properties of 2,4-dithiouracil (2,4-DTU) in the gas phase are studied by time-resolved photoelectron spectroscopy (TRPES) with three different excitation wavelengths in direct extension of previous work on uracil (U), 2-thiouracil (2-TU) and 4-thiouracil (4-TU). Non-radiative deactivation in the canonical nucleobases like uracil mainly occurs via internal conversion (IC) along singlet excited states, although intersystem crossing (ISC) to a long-lived triplet state was confirmed to play a minor role. In thionated uracils, ISC to the triplet state becomes ultrafast and highly efficient with a quantum yield near unity; however, the lifetime of the triplet state is strongly dependent on the position of the sulfur atom. In 2-TU, ISC back to the ground state occurs within a few hundred picoseconds, whereas the population remains trapped in the lowest triplet state in the case of 4-TU. Upon doubling the degree of thionation, ISC remains highly efficient and dominates the photophysics of 2,4-DTU. However, several low-lying excited states contribute to competing IC and ISC pathways and a complex deactivation mechanism, which is evaluated here based on TRPES measurements and discussed in the context of the singly thionated uracils.
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Affiliation(s)
- Abed Mohamadzade
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
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9
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Conti I, Buma WJ, Garavelli M, Amirjalayer S. Photoinduced Forward and Backward Pedalo-Type Motion of a Molecular Switch. J Phys Chem Lett 2020; 11:4741-4746. [PMID: 32412764 DOI: 10.1021/acs.jpclett.0c01094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Photoresponsive molecular switches enable spatial and temporal control of molecular processes and are therefore crucial for the development of smart functional materials. Because the light-induced dynamics of these switching units are at the core of the resulting functionality, a detailed insight into their structural time evolution is fundamental for molecular embedding. Here, we performed a hybrid quantum mechanics (CASPT2 and TDDFT)/molecular mechanics (QM/MM) study to elucidate the photodynamics of an azodicarboxamide-based molecular switch, which is a promising candidate for implementation in highly dense environments such as polymers. In particular, we report a detailed picture of the molecular motion at the atomic level based on a relevant number of excited-state trajectories. We show that the azodicarboxamide-based molecular switch undergoes both a forward and backward pedalo-type motion upon excitation. Trans-cis photoisomerization on the other hand, which is well-known to occur for other azo-based chromophores, is shown to be a negligible pathway. By validating the volume-conserving pedalo-type motion, we provide a rational basis for the design of novel types of photoresponsive functional materials in which the active component must operate in a confined space.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Wybren Jan Buma
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Saeed Amirjalayer
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Str.10, 48149 Münster, Germany
- Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
- Center for Multiscale Theory and Computation, Wilhelm-Klemm-Str.10, 48149 Münster, Germany
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10
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Aquilante F, Autschbach J, Baiardi A, Battaglia S, Borin VA, Chibotaru LF, Conti I, De Vico L, Delcey M, Fdez Galván I, Ferré N, Freitag L, Garavelli M, Gong X, Knecht S, Larsson ED, Lindh R, Lundberg M, Malmqvist PÅ, Nenov A, Norell J, Odelius M, Olivucci M, Pedersen TB, Pedraza-González L, Phung QM, Pierloot K, Reiher M, Schapiro I, Segarra-Martí J, Segatta F, Seijo L, Sen S, Sergentu DC, Stein CJ, Ungur L, Vacher M, Valentini A, Veryazov V. Modern quantum chemistry with [Open]Molcas. J Chem Phys 2020; 152:214117. [PMID: 32505150 DOI: 10.1063/5.0004835] [Citation(s) in RCA: 220] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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Affiliation(s)
- Francesco Aquilante
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, USA
| | - Alberto Baiardi
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stefano Battaglia
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Liviu F Chibotaru
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Mickaël Delcey
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Ignacio Fdez Galván
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Nicolas Ferré
- Aix-Marseille University, CNRS, Institut Chimie Radicalaire, Marseille, France
| | - Leon Freitag
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Xuejun Gong
- Department of Chemistry, University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Stefan Knecht
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Ernst D Larsson
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Roland Lindh
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Marcus Lundberg
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Per Åke Malmqvist
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Jesper Norell
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Odelius
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Thomas B Pedersen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Quan M Phung
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Kristine Pierloot
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Javier Segarra-Martí
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, United Kingdom
| | - Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Luis Seijo
- Departamento de Química, Instituto Universitario de Ciencia de Materiales Nicolás Cabrera, and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Saumik Sen
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Christopher J Stein
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Liviu Ungur
- Department of Chemistry, University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Morgane Vacher
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 44300 Nantes, France
| | - Alessio Valentini
- Theoretical Physical Chemistry, Research Unit MolSys, Université de Liège, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Valera Veryazov
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
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11
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Segarra-Martí J, Segatta F, Mackenzie TA, Nenov A, Rivalta I, Bearpark MJ, Garavelli M. Modeling multidimensional spectral lineshapes from first principles: application to water-solvated adenine. Faraday Discuss 2020; 221:219-244. [DOI: 10.1039/c9fd00072k] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We theoretically describe spectral lineshape from first principles, providing insight into solvent–solute interactions in terms of static and dynamic disorder and how these shape experimental signals in linear and non-linear optical spectroscopies.
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Affiliation(s)
- Javier Segarra-Martí
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Tristan A. Mackenzie
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Ivan Rivalta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
- Univ Lyon
| | - Michael J. Bearpark
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
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12
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Teles‐Ferreira DC, Conti I, Borrego‐Varillas R, Nenov A, Van Stokkum IHM, Ganzer L, Manzoni C, Paula AM, Cerullo G, Garavelli M. A Unified Experimental/Theoretical Description of the Ultrafast Photophysics of Single and Double Thionated Uracils. Chemistry 2019; 26:336-343. [DOI: 10.1002/chem.201904541] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Danielle Cristina Teles‐Ferreira
- Departamento de Física Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil
- Electrical Engineering Department Federal Institute of Minas Gerais Formiga MG Brazil
| | - Irene Conti
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
| | - Rocío Borrego‐Varillas
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
| | - Ivo H. M. Van Stokkum
- Department of Physics and Astronomy Faculty of Sciences Vrije Universiteit Amsterdam De Boelelaan 1081 1081HV Amsterdam The Netherlands
| | - Lucia Ganzer
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Cristian Manzoni
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Ana Maria Paula
- Departamento de Física Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil
| | - Giulio Cerullo
- IFN-CNR Department of Physics Politecnico di Milano P.za L. da Vinci 32 20133 Milano Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale Università degli Studi di Bologna Viale del Risorgimento 4 40136 Bologna Italy
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13
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Moron V, Marazzi M, Wanko M. Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore? J Chem Theory Comput 2019; 15:4228-4240. [PMID: 31146524 DOI: 10.1021/acs.jctc.9b00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.
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Affiliation(s)
- Victor Moron
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
| | - Marco Marazzi
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry, KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering , Universidad de Alcalá, Ctra , Madrid-Barcelona Km. 33,600 , E-28805 Alcalá de Henares, Madrid , Spain
- "Andrés M. del Rı́o" (IQAR) , Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid , Spain
| | - Marius Wanko
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
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14
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Valentini A, Nucci M, Frutos LM, Marazzi M. Photosensitized Retinal Isomerization in Rhodopsin Mediated by a Triplet State. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alessio Valentini
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Department of Biotechnology, Chemistry and PharmacyUniversity of Siena via A. Moro 2 53100 Siena Italy
- Theoretical Physical Chemistry, Research Unit MolSysUniversité de Liège Allée du 6 Aôut, 11 4000 Liège Belgium
| | - Martina Nucci
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
| | - Luis Manuel Frutos
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
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15
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Borrego-Varillas R, Teles-Ferreira DC, Nenov A, Conti I, Ganzer L, Manzoni C, Garavelli M, Maria de Paula A, Cerullo G. Observation of the Sub-100 Femtosecond Population of a Dark State in a Thiobase Mediating Intersystem Crossing. J Am Chem Soc 2018; 140:16087-16093. [DOI: 10.1021/jacs.8b07057] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rocío Borrego-Varillas
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | | | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Lucia Ganzer
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Cristian Manzoni
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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