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Böhmer T, Kleinschmidt M, Marian CM. Toward the improvement of vibronic spectra and non-radiative rate constants using the vertical Hessian method. J Chem Phys 2024; 161:094114. [PMID: 39234963 DOI: 10.1063/5.0220361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/15/2024] [Indexed: 09/06/2024] Open
Abstract
For the computation of vibrationally resolved electronic spectra, various approaches can be employed. Adiabatic approaches simulate vibronic transitions using harmonic potentials of the initial and final states, while vertical approaches extrapolate the final state potential from the gradients and Hessian at the Franck-Condon point, avoiding a full exploration of the potential energy surface of the final state. Our implementation of the vertical Hessian (VH) method has been validated with a benchmark set of four small molecules, each presenting unique challenges, such as complex topologies, problematic low-frequency vibrations, or significant geometrical changes upon electronic excitation. We assess the quality of both adiabatic and vertical approaches for simulating vibronic transitions. For two types of donor-acceptor compounds with promising thermally activated delayed fluorescence properties, our computations confirm that the vertical approaches outperform the adiabatic ones. The VH method significantly reduces computational costs and yields meaningful emission spectra, where adiabatic models fail. More importantly, we pioneer the use of the VH method for the computation of rate constants for non-radiative processes, such as intersystem crossing and reverse intersystem crossing along a relaxed interpolated pathway of a donor-acceptor compound. This study highlights the potential of the VH method to advance computational vibronic spectroscopy by providing meaningful simulations of intricate decay pathway mechanisms in complex molecular systems.
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Affiliation(s)
- Tobias Böhmer
- Institute for Theoretical and Computational Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Martin Kleinschmidt
- Institute for Theoretical and Computational Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Christel M Marian
- Institute for Theoretical and Computational Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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2
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do Casal MT, Veys K, Bousquet MHE, Escudero D, Jacquemin D. First-Principles Calculations of Excited-State Decay Rate Constants in Organic Fluorophores. J Phys Chem A 2023; 127:10033-10053. [PMID: 37988002 DOI: 10.1021/acs.jpca.3c06191] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
In this Perspective, we discuss recent advances made to evaluate from first-principles the excited-state decay rate constants of organic fluorophores, focusing on the so-called static strategy. In this strategy, one essentially takes advantage of Fermi's golden rule (FGR) to evaluate rate constants at key points of the potential energy surfaces, a procedure that can be refined in a variety of ways. In this way, the radiative rate constant can be straightforwardly obtained by integrating the fluorescence line shape, itself determined from vibronic calculations. Likewise, FGR allows for a consistent calculation of the internal conversion (related to the non-adiabatic couplings) in the weak-coupling regime and intersystem crossing rates, therefore giving access to estimates of the emission yields when no complex photophysical phenomenon is at play. Beyond outlining the underlying theories, we summarize here the results of benchmarks performed for various types of rates, highlighting that both the quality of the vibronic calculations and the accuracy of the relative energies are crucial to reaching semiquantitative estimates. Finally, we illustrate the successes and challenges in determining the fluorescence quantum yields using a series of organic fluorophores.
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Affiliation(s)
- Mariana T do Casal
- Department of Chemistry, Physical Chemistry and Quantum Chemistry Division, KU Leuven, 3001 Leuven, Belgium
| | - Koen Veys
- Department of Chemistry, Physical Chemistry and Quantum Chemistry Division, KU Leuven, 3001 Leuven, Belgium
| | | | - Daniel Escudero
- Department of Chemistry, Physical Chemistry and Quantum Chemistry Division, KU Leuven, 3001 Leuven, Belgium
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), FR-75005 Paris, France
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3
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Sitkiewicz SP, Matito E, Luis JM, Zaleśny R. Pitfall in simulations of vibronic TD-DFT spectra: diagnosis and assessment. Phys Chem Chem Phys 2023; 25:30193-30197. [PMID: 37905423 DOI: 10.1039/d3cp04276f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In this Communication, we study the effect of spurious oscillations in the profiles of energy derivatives with respect to nuclear coordinates calculated with density functional approximations (DFAs) for formaldehyde, pyridine, and furan in their ground and electronic excited states. These spurious oscillations, which can only be removed using extensive integration grids that increase enormously the CPU cost of DFA calculations, are significant in the case of third- and fourth-order energy derivatives of the ground and excited states computed by M06-2X and ωB97X functionals. The errors in question propagate to anharmonic vibronic spectra computed under the Franck-Condon approximation, i.e., positions and intensities of vibronic transitions are affected to a large extent (shifts as significant as hundreds of cm-1 were observed). On the other hand, the LC-BLYP and CAM-B3LYP functionals show a much less pronounced effect due to spurious oscillations. Based on the results presented herein, we recommend either LC-BLYP or CAM-B3LYP with integration grids (250, 974) (or larger) for numerically stable simulations of vibronic spectra including anharmonic effects.
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Affiliation(s)
- Sebastian P Sitkiewicz
- Wrocław Centre for Networking and Supercomputing, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, Wrocław PL-50370, Poland.
| | - Eduard Matito
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, Donostia 20018, Euskadi, Spain
- Ikerbasque Foundation for Science, Bilbao 48011, Euskadi, Spain
| | - Josep M Luis
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003, Girona, Catalonia, Spain.
| | - Robert Zaleśny
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland.
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4
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Ieritano C, Haack A, Hopkins WS. Chemical Transformations Can Occur during DMS Separations: Lessons Learned from Beer's Bittering Compounds. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37310853 DOI: 10.1021/jasms.3c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
While developing a DMS-based separation method for beer's bittering compounds, we observed that the argentinated forms of humulone tautomers (i.e., [Hum + Ag]+) were partially resolvable in a N2 environment seeded with 1.5 mol % of isopropyl alcohol (IPA). Attempting to improve the separation by introducing resolving gas unexpectedly caused the peaks for the cis-keto and trans-keto tautomers of [Hum + Ag]+ to coalesce. To understand why resolution loss occurred, we first confirmed that each of the tautomeric forms (i.e., dienol, cis-keto, and trans-keto) responsible for the three peaks in the [Hum + Ag]+ ionogram were assigned to the correct species by employing collision-induced dissociation, UV photodissociation spectroscopy, and hydrogen-deuterium exchange (HDX). The observation of HDX indicated that proton transfer was stimulated by dynamic clustering processes between IPA and [Hum + Ag]+ during DMS transit. Because IPA accretion preferentially occurs at Ag+, which can form pseudocovalent bonds with a suitable electron donor, solvent clustering also facilitated the formation of exceptionally stable microsolvated ions. The exceptional stability of these microsolvated configurations disproportionately impacted the compensation voltage (CV) required to elute each tautomer when the temperature within the DMS cell was varied. The disparity in CV response caused the peaks for the cis- and trans-keto species to merge when a temperature gradient was induced by the resolving gas. Moreover, simulations showed that microsolvation with IPA mediates dienol to trans-keto tautomerization during DMS transit, which, to the best of our knowledge, is the first observation of keto/enol tautomerization occurring within an ion-mobility device.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
| | - Alexander Haack
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
- Centre for Eye and Vision Research, 17 W Hong Kong Science Park, Shatin, New Territories 999077, Hong Kong
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5
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Mavroskoufis A, Lohani M, Weber M, Hopkinson MN, Götze JP. A (TD-)DFT study on photo-NHC catalysis: photoenolization/Diels-Alder reaction of acid fluorides catalyzed by N-heterocyclic carbenes. Chem Sci 2023; 14:4027-4037. [PMID: 37063806 PMCID: PMC10094231 DOI: 10.1039/d2sc04732b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
A comprehensive mechanistic study on the N-heterocyclic carbene (NHC) catalyzed photoenolization/Diels-Alder (PEDA) reaction of acid fluorides was performed in the framework of (time-dependent) density functional theory ((TD)-DFT). The 1,5-hydrogen atom transfer (1,5-HAT) during photoenolization of an ortho-toluoyl azolium salt was found to be feasible via, first, singlet excitation and photoenolization, and then, after crossing to the triplet manifold, populating a biradical dienol which allows for the formation of two ortho-quinodimethane (o-QDM) isomers due to a low rotational barrier. The (Z)-isomer is mostly unproductive through sigmatropic rearrangement back to the starting material while the (E)-isomer reacts in a subsequent concerted Diels-Alder reaction likely as the deprotonated dienolate. The experimentally observed diastereoselectivity is correctly predicted by theory and is determined by a more favorable endo trajectory in the cycloaddition step. These findings demonstrate that ortho-toluoyl azolium species exhibit similar photophysical properties as structurally related benzophenones, highlighting the unique ability of the NHC organocatalyst to transiently alter the excited state properties of an otherwise photoinactive carboxylic acid derivative, thereby expanding the scope of classical carbonyl photochemistry.
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Affiliation(s)
- Andreas Mavroskoufis
- Institut für Chemie und Biochemie, Freie Universität Berlin Fabeckstrasse 34-36 14195 Berlin Germany
| | - Manish Lohani
- Institut für Chemie und Biochemie, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Manuela Weber
- Institut für Chemie und Biochemie, Freie Universität Berlin Fabeckstrasse 34-36 14195 Berlin Germany
| | - Matthew N Hopkinson
- Institut für Chemie und Biochemie, Freie Universität Berlin Fabeckstrasse 34-36 14195 Berlin Germany
- School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Jan P Götze
- Institut für Chemie und Biochemie, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
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6
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Petrusevich EF, Bousquet MHE, Ośmiałowski B, Jacquemin D, Luis JM, Zaleśny R. Cost-Effective Simulations of Vibrationally-Resolved Absorption Spectra of Fluorophores with Machine-Learning-Based Inhomogeneous Broadening. J Chem Theory Comput 2023; 19:2304-2315. [PMID: 37096370 PMCID: PMC10134414 DOI: 10.1021/acs.jctc.2c01285] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
The results of electronic and vibrational structure simulations are an invaluable support for interpreting experimental absorption/emission spectra, which stimulates the development of reliable and cost-effective computational protocols. In this work, we contribute to these efforts and propose an efficient first-principle protocol for simulating vibrationally-resolved absorption spectra, including nonempirical estimations of the inhomogeneous broadening. To this end, we analyze three key aspects: (i) a metric-based selection of density functional approximation (DFA) so to benefit from the computational efficiency of time-dependent density function theory (TD-DFT) while safeguarding the accuracy of the vibrationally-resolved spectra, (ii) an assessment of two vibrational structure schemes (vertical gradient and adiabatic Hessian) to compute the Franck-Condon factors, and (iii) the use of machine learning to speed up nonempirical estimations of the inhomogeneous broadening. In more detail, we predict the absorption band shapes for a set of 20 medium-sized fluorescent dyes, focusing on the bright ππ★ S0 → S1 transition and using experimental results as references. We demonstrate that, for the studied 20-dye set which includes structures with large structural variability, the preselection of DFAs based on an easily accessible metric ensures accurate band shapes with respect to the reference approach and that range-separated functionals show the best performance when combined with the vertical gradient model. As far as band widths are concerned, we propose a new machine-learning-based approach for determining the inhomogeneous broadening induced by the solvent microenvironment. This approach is shown to be very robust offering inhomogeneous broadenings with errors as small as 2 cm-1 with respect to genuine electronic-structure calculations, with a total CPU time reduced by 98%.
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Affiliation(s)
- Elizaveta F. Petrusevich
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | | | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina Street 7, PL-87-100 Toruń, Poland
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Josep M. Luis
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Robert Zaleśny
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
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7
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Cerezo J, Santoro F. FCclasses3: Vibrationally-resolved spectra simulated at the edge of the harmonic approximation. J Comput Chem 2023; 44:626-643. [PMID: 36380723 PMCID: PMC10100349 DOI: 10.1002/jcc.27027] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/03/2022] [Accepted: 10/16/2022] [Indexed: 11/17/2022]
Abstract
We introduce FCclasses3, a code to carry out vibronic simulations of electronic spectra and nonradiative rates, based on the harmonic approximation. Key new features are: implementation of the full family of vertical and adiabatic harmonic models, vibrational analysis in curvilinear coordinates, extension to several electronic spectroscopies and implementation of time-dependent approaches. The use of curvilinear valence internal coordinates allows the adoption of quadratic model potential energy surfaces (PES) of the initial and final states expanded at arbitrary configurations. Moreover, the implementation of suitable projectors provides a robust framework for defining reduced-dimensionality models by sorting flexible coordinates out of the harmonic subset, so that they can then be treated at anharmonic level, or with mixed quantum classical approaches. A set of tools to facilitate input preparation and output analysis is also provided. We show the program at work in the simulation of different spectra (one and two-photon absorption, emission and resonance Raman) and internal conversion rate of a typical rigid molecule, anthracene. Then, we focus on absorption and emission spectra of a series of flexible polyphenyl molecules, highlighting the relevance of some of the newly implemented features. The code is freely available at http://www.iccom.cnr.it/en/fcclasses/.
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Affiliation(s)
- Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de MadridMadridSpain
- Consiglio Nazionale delle RicercheIstituto di Chimica dei Composti Organo Metallici (ICCOM‐CNR)PisaItaly
| | - Fabrizio Santoro
- Consiglio Nazionale delle RicercheIstituto di Chimica dei Composti Organo Metallici (ICCOM‐CNR)PisaItaly
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8
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Sorour MI, Marcus AH, Matsika S. Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3. Molecules 2022; 27:4062. [PMID: 35807308 PMCID: PMC9268038 DOI: 10.3390/molecules27134062] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022] Open
Abstract
Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck-Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck-Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck-Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.
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Affiliation(s)
- Mohammed I. Sorour
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA;
| | - Andrew H. Marcus
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA;
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA;
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9
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Hilal R. Photodissociation of 1,2-dioxetane: An excited state nonadiabatic dynamics study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Götze JP, Anders F, Petry S, Felix Witte J, Lokstein H. Spectral Characterization of the Main Pigments in the Plant Photosynthetic Apparatus by Theory and Experiment. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Petry S, Götze JP. Effect of protein matrix on CP29 spectra and energy transfer pathways. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148521. [PMID: 34896078 DOI: 10.1016/j.bbabio.2021.148521] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/25/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
We investigate energy transfer pathways between strongly coupled chlorophylls (Chls) in the CP29 (LHCII B4.1) antenna complex of Pisum sativum, including the possibility of higher energy states. We test for the environmental effects caused by the protein, membrane and solvent using a hybrid QM/MM approach. Classical molecular dynamics simulations of the full CP29 complex embedded in a DOPC membrane have been performed, followed by calculations of the time dependent DFT spectra of all Chls at several timesteps. The relative orientations of transition dipole moments (TDMs) were specifically analyzed, including and excluding the point charge field (PCF) of the surrounding environment. The PCF is found to drastically shift the spectra of specific Chls, while the majority of Chls is mostly unaffected. The net effect on the sum spectrum is however found to be negligible: The few strong changes in Chl spectra cancel each other due to being opposite in sign. We further find that the spectra of the Chls coordinating to water show a blue shift upon introduction of the environment. Conversely, the spectra of the Chls coordinating to glutamine show a red shift upon activation of the PCF. As the main influence of the PCF for tuning the couplings, we identify the energetic position of the individual chromophores. The fine-tuning, especially for states energetically above the Qy state, is however controlled by the changes in the TDM orientations. We also find an indication for the PCF to steer potentially harmful high energy excitations away from the PSII core complex.
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Affiliation(s)
- S Petry
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - J P Götze
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
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12
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Mashmoushi N, Juhász DR, Coughlan NJA, Schneider BB, Le Blanc JCY, Guna M, Ziegler BE, Campbell JL, Hopkins WS. UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban. J Phys Chem A 2021; 125:8187-8195. [PMID: 34432451 DOI: 10.1021/acs.jpca.1c05564] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two ion populations of protonated Rivaroxaban, [C19H18ClN3O5S + H]+, are separated under pure N2 conditions using differential mobility spectrometry prior to characterization in a hybrid triple quadrupole linear ion trap mass spectrometer. These populations are attributed to bare protonated Rivaroxaban and to a proton-bound Rivaroxaban-ammonia complex, which dissociates prior to mass-selecting the parent ion. Ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) studies indicate that both protonated Rivaroxaban ion populations are comprised of the computed global minimum prototropic isomer. Two ion populations are also observed when the collision environment is modified with 1.5% (v/v) acetonitrile. In this case, the protonated Rivaroxaban ion populations are produced by the dissociation of the ammonium complex and by the dissociation of a proton-bound Rivaroxaban-acetonitrile complex prior to mass selection. Again, both populations exhibit a similar CID behavior; however, UVPD spectra indicate that the two ion populations are associated with different prototropic isomers. The experimentally acquired spectra are compared with computed spectra and are assigned to two prototropic isomers that exhibit proton sharing between distal oxygen centers.
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Affiliation(s)
- Nour Mashmoushi
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Daniel R Juhász
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Neville J A Coughlan
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | | | | | - Mircea Guna
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Blake E Ziegler
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada.,Bedrock Scientific, Milton, Ontario L6T 6J9, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada.,Centre for Eye and Vision Research, New Territories 999077, Hong Kong
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13
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Yusuf TL, Akintemi EO, Olagboye S, Tolufashe GF. Investigating the biological actions of some Schiff bases using density functional theory study. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2019-0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Schiff base ligands have wide varieties of application in several fields. One of which is the biological actions they possess such as anti-fungal, anti-bacterial, anti-malarial, and anti-viral characteristics. In this study, some synthesized phenylimino-based Schiff bases were investigated using density functional theory (DFT) to unravel their biological descriptors. The gas-phase quantum chemical calculation was done on the Schiff base 3-((E)-(phenylimino)methyl)benzene-1,2-diol and other synthesized analogues to evaluate their reactivity and stability properties including the substituent effect on the basic molecule. The Coulomb-attenuating method (CAM-B3LYP) functional was employed for the theoretical calculations. The Nuclear Magnetic Resonance (NMR), Fourier Transform-Infrared (FT-IR), Ultraviolet/visible spectroscopies calculated agrees with the experimental values. The obtained charge transfer and electronic features provide useful information regarding the active sites for biological application in the compounds.
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Affiliation(s)
- Tunde L. Yusuf
- Department of Chemistry , Ekiti State University , Ado-Ekiti , Nigeria
- Department of Chemical Science , University of Johannesburg , Johannesburg , South Africa
| | - Eric O. Akintemi
- Department of Physical Sciences , Wesley University , P.M.B. 507 , Ondo Town , Ondo State , Nigeria
| | - Sulaimon Olagboye
- Department of Chemistry , Ekiti State University , Ado-Ekiti , Nigeria
| | - Gideon F. Tolufashe
- Department of Chemistry & Biochemistry, Faculty of Sciences , University of Porto , 4169-007 Porto , Portugal
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14
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Hilal R, Aziz SG. Solvent-assisted excited state proton transfer and photoacidity of 2-hydroxypyridine. A nonadiabatic dynamics study. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1547821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Rifaat Hilal
- Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Saadullah G. Aziz
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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15
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Aranda D, Cerezo J, Pescitelli G, Avila Ferrer FJ, Soto J, Santoro F. A computational study of the vibrationally-resolved electronic circular dichroism spectra of single-chain transoid and cisoid oligothiophenes in chiral conformations. Phys Chem Chem Phys 2018; 20:21864-21880. [PMID: 30105334 DOI: 10.1039/c8cp03482f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We simulate the vibronic profile of the electronic circular dichroism (ECD) spectra of oligothiophenes in cisoid and transoid chiral arrangements. We consider oligomers of different lengths, from two to fifteen units, and investigate extensively how the ECD spectral shapes depend on the inter-ring torsions. In general, the molecular structures we consider are not stationary points of the ground state potential energy surface. Therefore, in order to perform vibronic calculations, we present a new computational protocol able to define reduced-dimensionality models where the effect of the off-equilibrium modes is removed. This is done adopting a description of the vibrational motions in curvilinear internal coordinates, and vertical harmonic models coupled with an iterative application of projectors to define energy Hessians, and therefore effective normal modes, in the space complementary to the one of the off-equilibrium coordinates. Although we consider both Franck-Condon and Herzberg-Teller contributions, the results show that transoid twisted ribbons always give rise to monosignated ECD spectra, while bi-signated and multi-signated spectra are expected for cisoid helices. These findings are explained on the basis of the different transition strengths of the lowest electronic states imparted by the different spatial arrangement, that is almost linear for transoid structures and more globular for cisoid ones. We predicted the chiroptical response of a large number of possible molecular arrangements. These data are employed to critically discuss the experimental ECD of polythiophenes in different experimental conditions, forming either aggregates or host-guest complexes. The method here proposed to perform vibronic calculations in reduced-dimensionality models is of general applicability and its potential interest goes beyond the practical application presented here.
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Affiliation(s)
- Daniel Aranda
- Department of Physical Chemistry, Faculty of Science, University of Málaga, E-29071-Málaga, Spain
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16
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Giacomozzi L, Kjær C, Langeland Knudsen J, Andersen LH, Brøndsted Nielsen S, Stockett MH. Absorption and luminescence spectroscopy of mass-selected flavin adenine dinucleotide mono-anions. J Chem Phys 2018; 148:214309. [PMID: 29884035 DOI: 10.1063/1.5024028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We report the absorption profile of isolated Flavin Adenine Dinucleotide (FAD) mono-anions recorded using photo-induced dissociation action spectroscopy. In this charge state, one of the phosphoric acid groups is deprotonated and the chromophore itself is in its neutral oxidized state. These measurements cover the first four optical transitions of FAD with excitation energies from 2.3 to 6.0 eV (210-550 nm). The S0 → S2 transition is strongly blue shifted relative to aqueous solution, supporting the view that this transition has a significant charge-transfer character. The remaining bands are close to their solution-phase positions. This confirms that the large discrepancy between quantum chemical calculations of vertical transition energies and solution-phase band maxima cannot be explained by solvent effects. We also report the luminescence spectrum of FAD mono-anions in vacuo. The gas-phase Stokes shift for S1 is 3000 cm-1, which is considerably larger than any previously reported for other molecular ions and consistent with a significant displacement of the ground and excited state potential energy surfaces. Consideration of the vibronic structure is thus essential for simulating the absorption and luminescence spectra of flavins.
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Affiliation(s)
- L Giacomozzi
- Department of Physics, Stockholm University, Stockholm, Sweden
| | - C Kjær
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - L H Andersen
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - M H Stockett
- Department of Physics, Stockholm University, Stockholm, Sweden
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17
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Picconi D, Grebenshchikov SY. Photodissociation dynamics in the first absorption band of pyrrole. I. Molecular Hamiltonian and the Herzberg-Teller absorption spectrum for the A21(πσ*)←X̃1 A1(ππ) transition. J Chem Phys 2018; 148:104103. [DOI: 10.1063/1.5019735] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David Picconi
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Sergy Yu. Grebenshchikov
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
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18
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Jang H, Kim NJ, Heo J. Benchmarking study on time-dependent density functional theory calculations of electronic circular dichroism for gas-phase molecules. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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Lincke K, Langeland J, Madsen AØ, Kiefer HV, Skov L, Gruber E, Mikkelsen KV, Andersen LH, Nielsen MB. Elucidation of the intrinsic optical properties of hydrogen-bonded and protonated flavin chromophores by photodissociation action spectroscopy. Phys Chem Chem Phys 2018; 20:28678-28684. [DOI: 10.1039/c8cp05368e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The intrinsic optical properties of the flavin chromophore when engaged in hydrogen bonding or being protonated were elucidated by photo-induced action spectroscopy and computations.
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Affiliation(s)
- Kasper Lincke
- Department of Chemistry, University of Copenhagen
- DK-2100 Copenhagen Ø
- Denmark
| | - Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University
- DK-8000 Aarhus C
- Denmark
| | | | - Hjalte V. Kiefer
- Department of Physics and Astronomy, Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Louise Skov
- Department of Chemistry, University of Copenhagen
- DK-2100 Copenhagen Ø
- Denmark
| | - Elisabeth Gruber
- Department of Physics and Astronomy, Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen
- DK-2100 Copenhagen Ø
- Denmark
| | - Lars H. Andersen
- Department of Physics and Astronomy, Aarhus University
- DK-8000 Aarhus C
- Denmark
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20
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Bednarska J, Zaleśny R, Bartkowiak W, Ośmiałowski B, Medved’ M, Jacquemin D. Quantifying the Performances of DFT for Predicting Vibrationally Resolved Optical Spectra: Asymmetric Fluoroborate Dyes as Working Examples. J Chem Theory Comput 2017; 13:4347-4356. [DOI: 10.1021/acs.jctc.7b00469] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joanna Bednarska
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
| | - Robert Zaleśny
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
| | - Wojciech Bartkowiak
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
| | - Borys Ośmiałowski
- Faculty
of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, PL-85326 Bydgoszcz, Poland
| | - Miroslav Medved’
- Department
of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, 974 01 Banská Bystrica, Slovak Republic
| | - Denis Jacquemin
- Laboratoire
CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la
Houssinière, BP92208, 44322 Cedex 3 Nantes, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 5, France
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21
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Elroby SA, Aziz SG, Hilal RH. The electronic structure of alloxan monohydrate. Spectroscopic and density functional synergic approach. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Stauch T, Dreuw A. Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis. Chem Rev 2016; 116:14137-14180. [PMID: 27767298 DOI: 10.1021/acs.chemrev.6b00458] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.
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Affiliation(s)
- Tim Stauch
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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23
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Cerezo J, Santoro F. Revisiting Vertical Models To Simulate the Line Shape of Electronic Spectra Adopting Cartesian and Internal Coordinates. J Chem Theory Comput 2016; 12:4970-4985. [PMID: 27586086 DOI: 10.1021/acs.jctc.6b00442] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Vertical models for the simulation of spectroscopic line shapes expand the potential energy surface (PES) of the final state around the equilibrium geometry of the initial state. These models provide, in principle, a better approximation of the region of the band maximum. At variance, adiabatic models expand each PES around its own minimum. In the harmonic approximation, when the minimum energy structures of the two electronic states are connected by large structural displacements, adiabatic models can breakdown and are outperformed by vertical models. However, the practical application of vertical models faces the issues related to the necessity to perform a frequency analysis at a nonstationary point. In this contribution we revisit vertical models in harmonic approximation adopting both Cartesian (x) and valence internal curvilinear coordinates (s). We show that when x coordinates are used, the vibrational analysis at nonstationary points leads to a deficient description of low-frequency modes, for which spurious imaginary frequencies may even appear. This issue is solved when s coordinates are adopted. It is however necessary to account for the second derivative of s with respect to x, which here we compute analytically. We compare the performance of the vertical model in the s-frame with respect to adiabatic models and previously proposed vertical models in x- or Q1-frame, where Q1 are the normal coordinates of the initial state computed as combination of Cartesian coordinates. We show that for rigid molecules the vertical approach in the s-frame provides a description of the final state very close to the adiabatic picture. For sizable displacements it is a solid alternative to adiabatic models, and it is not affected by the issues of vertical models in x- and Q1-frames, which mainly arise when temperature effects are included. In principle the G matrix depends on s, and this creates nonorthogonality problems of the Duschinsky matrix connecting the normal modes of initial and final states in adiabatic approaches. We highlight that such a dependence of G on s is also an issue in vertical models, due to the necessity to approximate the kinetic term in the Hamiltonian when setting up the so-called GF problem. When large structural differences exist between the initial and the final-state minima, the changes in the G matrix can become too large to be disregarded.
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Affiliation(s)
- Javier Cerezo
- Istituto di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Richerche (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Richerche (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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24
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Cerezo J, Martínez-Fernández L, Improta R, Santoro F. Vibronic approach to the calculation of the decay rate of the photoexcited charge-transfer state of Guanine–Cytosine stacked dimer in water solution. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1955-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Baiardi A, Bloino J, Barone V. General formulation of vibronic spectroscopy in internal coordinates. J Chem Phys 2016; 144:084114. [PMID: 26931688 DOI: 10.1063/1.4942165] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Our general platform integrating time-independent and time-dependent evaluations of vibronic effects at the harmonic level for different kinds of absorption and emission one-photon, conventional and chiral spectroscopies has been extended to support various sets of internal coordinates. Thanks to the implementation of analytical first and second derivatives of different internal coordinates with respect to cartesian ones, both vertical and adiabatic models are available, with the inclusion of mode mixing and, possibly, Herzberg-Teller contributions. Furthermore, all supported non-redundant sets of coordinates are built from a fully automatized algorithm using only a primitive redundant set derived from a bond order-based molecular topology. Together with conventional stretching, bending, and torsion coordinates, the availability of additional coordinates (including linear and out-of-plane bendings) allows a proper treatment of specific systems, including, for instance, inter-molecular hydrogen bridges. A number of case studies are analysed, showing that cartesian and internal coordinates are nearly equivalent for semi-rigid systems not experiencing significant geometry distortions between initial and final electronic states. At variance, delocalized (possibly weighted) internal coordinates become much more effective than their cartesian counterparts for flexible systems and/or in the presence of significant geometry distortions accompanying electronic transitions.
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Affiliation(s)
- Alberto Baiardi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Julien Bloino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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26
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Santoro F, Jacquemin D. Going beyond the vertical approximation with time-dependent density functional theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1260] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche; Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR); Pisa Italy
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230; Université de Nantes; Nantes France
- Institut Universitaire de France; Paris France
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27
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Davari MD, Kopka B, Wingen M, Bocola M, Drepper T, Jaeger KE, Schwaneberg U, Krauss U. Photophysics of the LOV-Based Fluorescent Protein Variant iLOV-Q489K Determined by Simulation and Experiment. J Phys Chem B 2016; 120:3344-52. [DOI: 10.1021/acs.jpcb.6b01512] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mehdi D. Davari
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52056 Aachen, Germany
| | - Benita Kopka
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Marcus Wingen
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Marco Bocola
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52056 Aachen, Germany
| | - Thomas Drepper
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
- Institut
für Bio- und Geowissenschaften, IBG-1, Biotechnologie, Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52056 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
| | - Ulrich Krauss
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
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28
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Huang CH, Chou SY, Jang SB, Lin YC, Li CE, Chen CC, Chang JL. Insights into the Photoelectron Spectroscopy of Chlorofluoroethenes Studied by Density-Functional and Coupled-Cluster Theories. J Phys Chem A 2016; 120:1175-83. [PMID: 26884146 DOI: 10.1021/acs.jpca.5b11158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first two ionic states of chlorofluoroethenes were studied by using both time-independent and time-dependent density-functional theories. We calculated the equilibrium geometries and harmonic vibrational frequencies of 1,1-, cis-, and trans-C2H2FCl and their cations by using the B3LYP and B3PW91 functionals together with the cc-pVTZ and aug-cc-pVTZ basis sets. Franck-Condon factors were computed by the method developed in our group, in which the Duschinsky effect was treated explicitly. A new technique, named alignment transformation, followed by Euler transformations was developed to achieve the Eckart conditions. The adiabatic ionization energies were calculated by the CCSD(T) method extrapolated to the complete basis set limit. Insights into the simulated photoelectron spectra of C2H2FCl indicate that the resolutions of recent threshold photoelectron experiments are not high enough to detect individual transitions. The high-resolution photoelectron spectra of C2H2FCl are predicted for future reference. The computed adiabatic ionization energies of the three isomers of C2H2FCl are in accord with the experiments with the absolute deviations ranging from 0.004 to 0.021 eV. We suggest that the agreement between experimental and theoretical spectra should be a key criterion to judge whether a spectral assignment is reasonable.
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Affiliation(s)
- Cyong-Huei Huang
- Department of Science Education and Application, National Taichung University of Education , Taichung 40306, Taiwan, Republic of China
| | - Shang-Yi Chou
- Department of Science Education and Application, National Taichung University of Education , Taichung 40306, Taiwan, Republic of China
| | - Shiu-Bau Jang
- Department of Science Education and Application, National Taichung University of Education , Taichung 40306, Taiwan, Republic of China
| | - Yu-Chieh Lin
- Department of Science Education and Application, National Taichung University of Education , Taichung 40306, Taiwan, Republic of China
| | - Chien-En Li
- Department of Science Education and Application, National Taichung University of Education , Taichung 40306, Taiwan, Republic of China
| | - Chiing-Chang Chen
- Department of Science Education and Application, National Taichung University of Education , Taichung 40306, Taiwan, Republic of China
| | - Jia-Lin Chang
- Department of Science Education and Application, National Taichung University of Education , Taichung 40306, Taiwan, Republic of China
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29
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Racine J, Hagebaum-Reignier D, Carissan Y, Humbel S. Recasting wave functions into valence bond structures: A simple projection method to describe excited states. J Comput Chem 2016; 37:771-9. [DOI: 10.1002/jcc.24267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Julien Racine
- Aix Marseille Université, CNRS, Centrale Marseille; iSm2 UMR 7313 Marseille 13397 France
| | | | - Yannick Carissan
- Aix Marseille Université, CNRS, Centrale Marseille; iSm2 UMR 7313 Marseille 13397 France
| | - Stéphane Humbel
- Aix Marseille Université, CNRS, Centrale Marseille; iSm2 UMR 7313 Marseille 13397 France
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30
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Liu Y, Cerezo J, Santoro F, Rizzo A, Lin N, Zhao X. Theoretical investigation of the broad one-photon absorption line-shape of a flexible symmetric carbazole derivative. Phys Chem Chem Phys 2016; 18:22889-905. [DOI: 10.1039/c6cp04162k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The one-photon absorption spectrum of a carbazole derivative has been studied by employing density functional response theory combined with a mixed quantum/classical approach to simulate the spectral shape.
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Affiliation(s)
- Yanli Liu
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
- CNR – Consiglio Nazionale delle Ricerche
| | - Javier Cerezo
- CNR – Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- CNR – Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- I-56124 Pisa
- Italy
| | - Antonio Rizzo
- CNR – Consiglio Nazionale delle Ricerche
- Istituto per i Processi Chimico Fisici (IPCF-CNR)
- I-56124 Pisa
- Italy
| | - Na Lin
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
| | - Xian Zhao
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
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31
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Karasulu B, Götze JP, Thiel W. Assessment of Franck-Condon Methods for Computing Vibrationally Broadened UV-vis Absorption Spectra of Flavin Derivatives: Riboflavin, Roseoflavin, and 5-Thioflavin. J Chem Theory Comput 2015; 10:5549-66. [PMID: 26583238 DOI: 10.1021/ct500830a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We address the performance of the vertical and adiabatic Franck-Condon (VFC/AFC) approaches combined with time-independent or time-dependent (TI/TD) formalisms in simulating the one-photon absorption spectra of three flavin compounds with distinct structural features. Calculations were done in the gas phase and in two solvents (water, benzene) for which experimental reference measurements are available. We utilized the independent mode displaced harmonic oscillator model without or with frequency alteration (IMDHO/IMDHO-FA) and also accounted for Duschinsky mixing effects. In the initial validation on the first excited singlet state of riboflavin, the range-separated functionals, CAM-B3LYP and ωB97xD, showed the best performance, but B3LYP also gave a good compromise between peak positions and spectral topology. Large basis sets were not mandatory to obtain high-quality spectra for the selected systems. The presence of a symmetry plane facilitated the computation of vibrationally broadened spectra, since different FC variants yield similar results and the harmonic approximation holds rather well. Compared with the AFC approach, the VFC approach performed equally well or even better for all three flavins while offering several advantages, such as avoiding error-prone geometry optimization procedures on excited-state surfaces. We also explored the advantages of curvilinear displacements and of a Duschinsky treatment for the AFC spectra in cases when a rotatable group is present on the chromophore. Taken together, our findings indicate that the combination of the VFC approach with the TD formalism and the IMDHO-FA model offers the best overall performance.
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Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Jan Philipp Götze
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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32
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Banerjee S, Stüker T, Saalfrank P. Vibrationally resolved optical spectra of modified diamondoids obtained from time-dependent correlation function methods. Phys Chem Chem Phys 2015; 17:19656-69. [PMID: 26151912 DOI: 10.1039/c5cp02615f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Optical properties of modified diamondoids have been studied theoretically using vibrationally resolved electronic absorption, emission and resonance Raman spectra. A time-dependent correlation function approach has been used for electronic two-state models, comprising a ground state (g) and a bright, excited state (e), the latter determined from linear-response, time-dependent density functional theory (TD-DFT). The harmonic and Condon approximations were adopted. In most cases origin shifts, frequency alteration and Duschinsky rotation in excited states were considered. For other cases where no excited state geometry optimization and normal mode analysis were possible or desired, a short-time approximation was used. The optical properties and spectra have been computed for (i) a set of recently synthesized sp(2)/sp(3) hybrid species with C[double bond, length as m-dash]C double-bond connected saturated diamondoid subunits, (ii) functionalized (mostly by thiol or thione groups) diamondoids and (iii) urotropine and other C-substituted diamondoids. The ultimate goal is to tailor optical and electronic features of diamondoids by electronic blending, functionalization and substitution, based on a molecular-level understanding of the ongoing photophysics.
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Affiliation(s)
- Shiladitya Banerjee
- Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany.
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33
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Barton D, König C, Neugebauer J. Vibronic-structure tracking: a shortcut for vibrationally resolved UV/Vis-spectra calculations. J Chem Phys 2015; 141:164115. [PMID: 25362280 DOI: 10.1063/1.4898665] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational coarse structure and the band shapes of electronic absorption spectra are often dominated by just a few molecular vibrations. By contrast, the simulation of the vibronic structure even in the simplest theoretical models usually requires the calculation of the entire set of normal modes of vibration. Here, we exploit the idea of the mode-tracking protocol [M. Reiher and J. Neugebauer, J. Chem. Phys. 118, 1634 (2003)] in order to directly target and selectively calculate those normal modes which have the largest effect on the vibronic band shape for a certain electronic excitation. This is achieved by defining a criterion for the importance of a normal mode to the vibrational progressions in the absorption band within the so-called "independent mode, displaced harmonic oscillator" (IMDHO) model. We use this approach for a vibronic-structure investigation for several small test molecules as well as for a comparison of the vibronic absorption spectra of a truncated chlorophyll a model and the full chlorophyll a molecule. We show that the method allows to go beyond the often-used strategy to simulate absorption spectra based on broadened vertical excitation peaks with just a minimum of computational effort, which in case of chlorophyll a corresponds to about 10% of the cost for a full simulation within the IMDHO approach.
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Affiliation(s)
- Dennis Barton
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Carolin König
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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Baiardi A, Bloino J, Barone V. Accurate Simulation of Resonance-Raman Spectra of Flexible Molecules: An Internal Coordinates Approach. J Chem Theory Comput 2015; 11:3267-80. [DOI: 10.1021/acs.jctc.5b00241] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alberto Baiardi
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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Mewes JM, You ZQ, Wormit M, Kriesche T, Herbert JM, Dreuw A. Experimental Benchmark Data and Systematic Evaluation of Two a Posteriori, Polarizable-Continuum Corrections for Vertical Excitation Energies in Solution. J Phys Chem A 2015; 119:5446-64. [DOI: 10.1021/jp511163y] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jan-Michael Mewes
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
| | - Zhi-Qiang You
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael Wormit
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
| | - Thomas Kriesche
- Institute
for Physical Chemistry, Ruprechts-Karls University, 69120 Heidelberg, Germany
| | - John M. Herbert
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andreas Dreuw
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
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Karasulu B, Thiel W. Photoinduced Intramolecular Charge Transfer in an Electronically Modified Flavin Derivative: Roseoflavin. J Phys Chem B 2014; 119:928-43. [DOI: 10.1021/jp506101x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470, Mülheim, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470, Mülheim, Germany
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A theoretical study on the equilibrium structures, vibrational frequencies and photoelectron spectroscopy of thiocarbonyl fluoride by using density functional and coupled-cluster theories. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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