1
|
Aarabi M, Aranda D, Gholami S, Meena SK, Lerouge F, Bretonniere Y, Gürol I, Baldeck P, Parola S, Dumoulin F, Cerezo J, Garavelli M, Santoro F, Rivalta I. Quantum-Classical Protocol for Efficient Characterization of Absorption Lineshape and Fluorescence Quenching upon Aggregation: The Case of Zinc Phthalocyanine Dyes. J Chem Theory Comput 2023; 19:5938-5957. [PMID: 37641958 PMCID: PMC10500990 DOI: 10.1021/acs.jctc.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Indexed: 08/31/2023]
Abstract
A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.
Collapse
Affiliation(s)
- Mohammad Aarabi
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Daniel Aranda
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
- Instituto
de Ciencia Molecular (ICMol), Universidad
de Valencia, Catedrático
J. Beltrán 2, 46980 Paterna, Valencia, Spain
| | - Samira Gholami
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Santosh Kumar Meena
- Department
of Chemical Engineering, Indian Institute
of Technology Ropar, Rupnagar, 140001 Punjab, India
| | - Frederic Lerouge
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Yann Bretonniere
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Ilke Gürol
- TÜBITAK
Marmara Research Center, Materials Technologies, Gebze, 41470 Kocaeli, Türkiye
| | - Patrice Baldeck
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Stephane Parola
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Fabienne Dumoulin
- Department
of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Türkiye
| | - Javier Cerezo
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
- Departamento
de Química and Institute for Advanced Research in Chemical
Sciences (IAdChem), Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Fabrizio Santoro
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| |
Collapse
|
2
|
Segalina A, Aranda D, Green JA, Cristino V, Caramori S, Prampolini G, Pastore M, Santoro F. How the Interplay among Conformational Disorder, Solvation, Local, and Charge-Transfer Excitations Affects the Absorption Spectrum and Photoinduced Dynamics of Perylene Diimide Dimers: A Molecular Dynamics/Quantum Vibronic Approach. J Chem Theory Comput 2022; 18:3718-3736. [PMID: 35377648 PMCID: PMC9202308 DOI: 10.1021/acs.jctc.2c00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
In this contribution
we present a mixed quantum-classical dynamical
approach for the computation of vibronic absorption spectra of molecular
aggregates and their nonadiabatic dynamics, taking into account the
coupling between local excitations (LE) and charge-transfer (CT) states.
The approach is based on an adiabatic (Ad) separation between the
soft degrees of freedom (DoFs) of the system and the stiff vibrations,
which are described by the quantum dynamics (QD) of wave packets (WPs)
moving on the coupled potential energy surfaces (PESs) of the LE and
CT states. These PESs are described with a linear vibronic coupling
(LVC) Hamiltonian, parameterized by an overlap-based diabatization
on the grounds of time-dependent density functional theory computations.
The WPs time evolution is computed with the multiconfiguration time-dependent
Hartree method, using effective modes defined through a hierarchical
representation of the LVC Hamiltonian. The soft DoFs are sampled with
classical molecular dynamics (MD), and the coupling between the slow
and fast DoFs is included by recomputing the key parameters of the
LVC Hamiltonians, specifically for each MD configuration. This method,
named Ad-MD|gLVC, is applied to a perylene diimide (PDI) dimer in
acetonitrile and water solutions, and it is shown to accurately reproduce
the change in the vibronic features of the absorption spectrum upon
aggregation. Moreover, the microscopic insight offered by the MD trajectories
allows for a detailed understanding of the role played by the fluctuation
of the aggregate structure on the shape of the vibronic spectrum and
on the population of LE and CT states. The nonadiabatic QD predicts
an extremely fast (∼50 fs) energy transfer between the two
LEs. CT states have only a moderate effect on the absorption spectrum,
despite the fact that after photoexcitation they are shown to acquire
a fast and non-negligible population, highlighting their relevance
in dictating the charge separation and transport in PDI-based optical
devices.
Collapse
Affiliation(s)
- Alekos Segalina
- Université de Lorraine and CNRS, LPCT, UMR 7019, F-54000 Nancy, France
| | - Daniel Aranda
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia, Catedrático J. Beltrán 2, 46980 Paterna, Valencia, Spain
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Vito Cristino
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Stefano Caramori
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche, (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | | | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche, (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| |
Collapse
|
3
|
Nematiaram T, Padula D, Troisi A. Bright Frenkel Excitons in Molecular Crystals: A Survey. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2021; 33:3368-3378. [PMID: 34526736 PMCID: PMC8432684 DOI: 10.1021/acs.chemmater.1c00645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/14/2021] [Indexed: 05/12/2023]
Abstract
We computed the optical properties of a large set of molecular crystals (∼2200 structures) composed of molecules whose lowest excited states are strongly coupled and generate wide excitonic bands. Such bands are classified in terms of their dimensionality (1-, 2-, and 3-dimensional), the position of the optically allowed state in relation with the excitonic density of states, and the presence of Davydov splitting. The survey confirms that one-dimensional aggregates are rare in molecular crystals highlighting the need to go beyond the simple low-dimensional models. Furthermore, this large set of data is used to search for technologically interesting and less common properties. For instance, we considered the largest excitonic bandwidth that is achievable within known molecular crystals and identified materials with strong super-radiant states. Finally, we explored the possibility that strong excitonic coupling can be used to generate emissive states in the near-infrared region in materials formed by molecules with bright visible absorption and we could identify the maximum allowable red shift in this material class. These insights with the associated searchable database provide practical guidelines for designing materials with interesting optical properties.
Collapse
Affiliation(s)
- Tahereh Nematiaram
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Daniele Padula
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, via A. Moro 2, Siena 53100, Italy
| | - Alessandro Troisi
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 7ZD, U.K.
| |
Collapse
|
4
|
Ozcelik A, Aranda D, Gil‐Guerrero S, Pola‐Otero XA, Talavera M, Wang L, Behera SK, Gierschner J, Peña‐Gallego Á, Santoro F, Pereira‐Cameselle R, Alonso‐Gómez JL. Distinct Helical Molecular Orbitals through Conformational Lock**. Chemistry 2020; 26:17342-17349. [DOI: 10.1002/chem.202002561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ani Ozcelik
- Departamento de Química Orgánica Universidad de Vigo Campus Universitario 36310 Vigo Spain
| | - Daniel Aranda
- Istituto di Chimica dei Composti Organometallici Consiglio Nazionale delle Ricerche Pisa Italy
- Departamento de Química Física Universidad de Málaga Bulevar Louis Pasteur 31 Málaga 29010 Spain
| | - Sara Gil‐Guerrero
- Departamento de Química Física Universidad de Vigo Campus Universitario 36310 Vigo Spain
| | - Xaquín A. Pola‐Otero
- Departamento de Química Orgánica Universidad de Vigo Campus Universitario 36310 Vigo Spain
| | - Maria Talavera
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Liangxuan Wang
- Madrid Institute for Advanced Studies IMDEA Nanoscience C/ Faraday 9, Ciudad Universitaria de Cantoblanco 28049 Madrid Spain
| | - Santosh Kumar Behera
- Madrid Institute for Advanced Studies IMDEA Nanoscience C/ Faraday 9, Ciudad Universitaria de Cantoblanco 28049 Madrid Spain
| | - Johannes Gierschner
- Madrid Institute for Advanced Studies IMDEA Nanoscience C/ Faraday 9, Ciudad Universitaria de Cantoblanco 28049 Madrid Spain
| | - Ángeles Peña‐Gallego
- Departamento de Química Física Universidad de Vigo Campus Universitario 36310 Vigo Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici Consiglio Nazionale delle Ricerche Pisa Italy
| | | | | |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- Daniel Aranda
- Department of Physical Chemistry, Faculty of Science, University of Málaga, E-29071-Málaga, Spain
| | | | | | | | | | | |
Collapse
|
6
|
Hestand NJ, Spano FC. Expanded Theory of H- and J-Molecular Aggregates: The Effects of Vibronic Coupling and Intermolecular Charge Transfer. Chem Rev 2018; 118:7069-7163. [PMID: 29664617 DOI: 10.1021/acs.chemrev.7b00581] [Citation(s) in RCA: 694] [Impact Index Per Article: 115.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The electronic excited states of molecular aggregates and their photophysical signatures have long fascinated spectroscopists and theoreticians alike since the advent of Frenkel exciton theory almost 90 years ago. The influence of molecular packing on basic optical probes like absorption and photoluminescence was originally worked out by Kasha for aggregates dominated by Coulombic intermolecular interactions, eventually leading to the classification of J- and H-aggregates. This review outlines advances made in understanding the relationship between aggregate structure and photophysics when vibronic coupling and intermolecular charge transfer are incorporated. An assortment of packing geometries is considered from the humble molecular dimer to more exotic structures including linear and bent aggregates, two-dimensional herringbone and "HJ" aggregates, and chiral aggregates. The interplay between long-range Coulomb coupling and short-range charge-transfer-mediated coupling strongly depends on the aggregate architecture leading to a wide array of photophysical behaviors.
Collapse
Affiliation(s)
- Nicholas J Hestand
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Frank C Spano
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| |
Collapse
|
7
|
Tanaka H, Inoue Y, Mori T. Circularly Polarized Luminescence and Circular Dichroisms in Small Organic Molecules: Correlation between Excitation and Emission Dissymmetry Factors. CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201800015] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hiroki Tanaka
- Department of Applied Chemistry, Graduate School of Engineering; Osaka University; 2-1 Yamada-oka Suita 565-0871 Japan
| | - Yoshihisa Inoue
- Department of Applied Chemistry, Graduate School of Engineering; Osaka University; 2-1 Yamada-oka Suita 565-0871 Japan
| | - Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering; Osaka University; 2-1 Yamada-oka Suita 565-0871 Japan
| |
Collapse
|
8
|
Kaminský J, Chalupský J, Štěpánek P, Kříž J, Bouř P. Vibrational Structure in Magnetic Circular Dichroism Spectra of Polycyclic Aromatic Hydrocarbons. J Phys Chem A 2017; 121:9064-9073. [PMID: 29112435 DOI: 10.1021/acs.jpca.7b10120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Absorption and magnetic circular dichroism (MCD) spectroscopies are powerful and simple methods to discriminate among various compounds. Polycyclic aromatic hydrocarbons provide particularly strong signal, which, for example, facilitates their detection in the environment. However, interpretation of the spectra is often based on quantum-chemical simulations, providing a limited precision only. In the present work, we use time-dependent density functional theory and complete active space second-order perturbation theories to understand spectral features observed in a series of naphthalene, anthracene, phenanthrene, and three larger compounds. The electronic computations provided reasonable agreement with the experiment for the smaller molecules, while a large error persisted for the bigger ones. However, many discrepancies could be explained by vibrational splitting of the electronic transitions across the entire spectral range. Compared to plain absorption, MCD spectral bands and their vibrational splitting were more specific for each aromatic molecule. The computational tools allowing simulations of detailed vibrational features in the electronic spectra thus promise to open a qualitatively new chapter in the spectroscopy of aromatic compounds.
Collapse
Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Petr Štěpánek
- NMR Research Unit, Faculty of Science, University of Oulu , P.O. Box 3000, 90014 Oulu, Finland
| | - Jan Kříž
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| |
Collapse
|
9
|
Padula D, Cerezo J, Pescitelli G, Santoro F. The shape of the electronic circular dichroism spectrum of (2,6-dimethylphenyl)(phenyl)methanol: interplay between conformational equilibria and vibronic effects. Phys Chem Chem Phys 2017; 19:32349-32360. [DOI: 10.1039/c7cp06369e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Analysis of the interplay between conformational equilibria, solvent effects and vibronic contributions in the ECD spectra.
Collapse
Affiliation(s)
- Daniele Padula
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Javier Cerezo
- Departamento de Química Física
- Universidad de Murcia
- 30100 Murcia
- Spain
| | - Gennaro Pescitelli
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche – CNR
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- Pisa
- Italy
| |
Collapse
|
10
|
Zinna F, Bruhn T, Guido CA, Ahrens J, Bröring M, Di Bari L, Pescitelli G. Circularly Polarized Luminescence from Axially Chiral BODIPY DYEmers: An Experimental and Computational Study. Chemistry 2016; 22:16089-16098. [PMID: 27658919 DOI: 10.1002/chem.201602684] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Indexed: 11/10/2022]
Abstract
With our new home-built circularly polarized luminescence (CPL) instrument, we measured fluorescence and CPL spectra of the enantiomeric pairs of two quasi-isomeric BODIPY DYEmers 1 and 2, endowed with axial chirality. The electronic circular dichroism (ECD) and CPL spectra of these atropisomeric dimers are dominated by the exciton coupling between the main π-π* transitions (550-560 nm) of the two BODIPY rings. Compound 1 has strong ECD and CPL spectra (glum =4×10-3 ) well reproduced by TD-DFT and SCS-CC2 (spin-component scaled second-order approximate coupled-cluster) calculations using DFT-optimized ground- and excited-state structures. Compound 2 has weaker ECD and CPL spectra (glum =4×10-4 ), partly due to the mutual cancellation of electric-electric and electric-magnetic exciton couplings, and partly to its conformational freedom. This compound is computationally very challenging. Starting from the optimized excited-state geometries, we predicted the wrong sign for the CPL band of 2 using TD-DFT with the most recommended hybrid and range-separated functionals, whereas SCS-CC2 or a DFT functional with full exact exchange provided the correct sign.
Collapse
Affiliation(s)
- Francesco Zinna
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy
| | - Torsten Bruhn
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ciro A Guido
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy
| | - Johannes Ahrens
- Institut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany.,Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Martin Bröring
- Institut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy.
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy.
| |
Collapse
|
11
|
Štěpánek P, Cowie TY, Šafařík M, Šebestík J, Pohl R, Bouř P. Resolving Electronic Transitions in Synthetic Fluorescent Protein Chromophores by Magnetic Circular Dichroism. Chemphyschem 2016; 17:2348-54. [PMID: 27124359 DOI: 10.1002/cphc.201600313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Indexed: 11/08/2022]
Abstract
The detailed electronic structures of fluorescent chromophores are important for their use in imaging of living cells. A series of green fluorescent protein chromophore derivatives is examined by magnetic circular dichroism (MCD) spectroscopy, which allows the resolution of more bands than plain absorption and fluorescence. Observed spectral patterns are rationalized with the aid of time-dependent density functional theory (TDDFT) computations and the sum-over-state (SOS) formalism, which also reveals a significant dependence of MCD intensities on chromophore conformation. The combination of organic and theoretical chemistry with spectroscopic techniques also appears useful in the rational design of fluorescence labels and understanding of the chromophore's properties. For example, the absorption threshold can be heavily affected by substitution on the phenyl ring but not much on the five-member ring, and methoxy groups can be used to further tune the electronic levels.
Collapse
Affiliation(s)
- Petr Štěpánek
- NMR Research Group, Faculty of Science, University of Oulu, PO Box 3000, 90014, Oulu, Finland
| | - Thomas Y Cowie
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic.
| |
Collapse
|
12
|
Bruhn T, Pescitelli G, Witterauf F, Ahrens J, Funk M, Wolfram B, Schneider H, Radius U, Bröring M. Cryptochirality in 2,2′-Coupled BODIPY DYEmers. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600585] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Torsten Bruhn
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; Via Moruzzi 13 56124 Pisa Italy
| | - Franziska Witterauf
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Johannes Ahrens
- Institut für Anorganische und Analytische Chemie (IAAC); Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Markus Funk
- Institut für Anorganische und Analytische Chemie (IAAC); Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Benedikt Wolfram
- Institut für Anorganische und Analytische Chemie (IAAC); Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Heidi Schneider
- Institut für Anorganische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Udo Radius
- Institut für Anorganische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Martin Bröring
- Institut für Anorganische und Analytische Chemie (IAAC); Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| |
Collapse
|
13
|
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
| |
Collapse
|
14
|
Štěpánek P, Straka M, Šebestík J, Bouř P. Magnetic circular dichroism of chlorofullerenes: Experimental and computational study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.01.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Padula D, Santoro F, Pescitelli G. A simple dimeric model accounts for the vibronic ECD spectra of chiral polythiophenes in their aggregated states. RSC Adv 2016. [DOI: 10.1039/c6ra05500a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aggregates of chiral polythiophenes (PTs) show exciton-coupled electronic circular dichroism (ECD) spectra with a unique vibronic structure, which can be reproduced by quantum dynamical simulations on the coupled states of small dimeric models.
Collapse
Affiliation(s)
- Daniele Padula
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale Via G. Moruzzi 13
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche – CNR
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- UOS di Pisa
- I-56124 Pisa
- Italy
| | - Gennaro Pescitelli
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale Via G. Moruzzi 13
- I-56124 Pisa
- Italy
| |
Collapse
|
16
|
Hall J, Renger T, Picorel R, Krausz E. Circularly polarized luminescence spectroscopy reveals low-energy excited states and dynamic localization of vibronic transitions in CP43. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:115-128. [PMID: 26449206 DOI: 10.1016/j.bbabio.2015.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/23/2015] [Accepted: 09/29/2015] [Indexed: 11/26/2022]
Abstract
Circularly polarized luminescence (CPL) spectroscopy is an established but relatively little-used technique that monitors the chirality of an emission. When applied to photosynthetic pigment assemblies, we find that CPL provides sensitive and detailed information on low-energy exciton states, reflecting the interactions, site energies and geometries of interacting pigments. CPL is the emission analog of circular dichroism (CD) and thus spectra explore the optical activity only of fluorescent states of the pigment-protein complex and consequently the nature of the lowest-energy excited states (trap states), whose study is a critical area of photosynthesis research. In this work, we develop the new approach of temperature-dependent CPL spectroscopy, over the 2-120 K temperature range, and apply it to the CP43 proximal antenna protein of photosystem II. Our results confirm strong excitonic interactions for at least one of the two well-established emitting states of CP43 named "A" and "B". Previous structure-based models of CP43 spectra are evaluated in the light of the new CPL data. Our analysis supports the assignments of Shibata et al. [Shibata et al. J. Am. Chem. Soc. 135 (2013) 6903-6914], particularly for the highly-delocalized B-state. This state dominates CPL spectra and is attributed predominantly to chlorophyll a's labeled Chl 634 and Chl 636 (alternatively labeled Chl 43 and 45 by Shibata et al.). The absence of any CPL intensity in intramolecular vibrational sidebands associated with the delocalized "B" excited state is attributed to the dynamic localization of intramolecular vibronic transitions.
Collapse
Affiliation(s)
- Jeremy Hall
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität, Linz, Austria
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC), Avda. Montañana, Zaragoza, Spain
| | - Elmars Krausz
- Research School of Chemistry, Australian National University, Canberra, Australia.
| |
Collapse
|
17
|
Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal VK, Altavilla SF, Mukamel S, Garavelli M. Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations. Faraday Discuss 2015; 177:345-62. [PMID: 25607949 DOI: 10.1039/c4fd00175c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The SOS//QM/MM [Rivalta et al., Int. J. Quant. Chem., 2014, 114, 85] method consists of an arsenal of computational tools allowing accurate simulation of one-dimensional (1D) and bi-dimensional (2D) electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy. Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as charge-transfer states arise naturally through the fully quantum-mechanical description of the aggregates. In this contribution the SOS//QM/MM approach is extended to simulate time-resolved 2D spectra that can be used to characterize ultrafast excited state relaxation dynamics with atomistic details. We demonstrate how critical structures on the excited state potential energy surface, obtained through state-of-the-art quantum chemical computations, can be used as snapshots of the excited state relaxation dynamics to generate spectral fingerprints for different de-excitation channels. The approach is based on high-level multi-configurational wavefunction methods combined with non-linear response theory and incorporates the effects of the solvent/environment through hybrid quantum mechanics/molecular mechanics (QM/MM) techniques. Specifically, the protocol makes use of the second-order Perturbation Theory (CASPT2) on top of Complete Active Space Self Consistent Field (CASSCF) strategy to compute the high-lying excited states that can be accessed in different 2D experimental setups. As an example, the photophysics of the stacked adenine-adenine dimer in a double-stranded DNA is modeled through 2D near-ultraviolet (NUV) spectroscopy.
Collapse
Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Andrushchenko V, Padula D, Zhivotova E, Yamamoto S, Bouř P. Magnetic Circular Dichroism of Porphyrin Lanthanide M3+Complexes. Chirality 2014; 26:655-62. [DOI: 10.1002/chir.22365] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 07/15/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences; Prague Czech Republic
| | - Daniele Padula
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences; Prague Czech Republic
| | - Elena Zhivotova
- Department of Physics; National University of Pharmacy; Ukraine
| | - Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science; Osaka University; Osaka Japan
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences; Prague Czech Republic
| |
Collapse
|
19
|
Podlech J, Fleck SC, Metzler M, Bürck J, Ulrich AS. Determination of the absolute configuration of perylene quinone-derived mycotoxins by measurement and calculation of electronic circular dichroism spectra and specific rotations. Chemistry 2014; 20:11463-70. [PMID: 25056998 DOI: 10.1002/chem.201402567] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Indexed: 01/14/2023]
Abstract
Altertoxins I-III, alterlosins I and II, alteichin (alterperylenol), stemphyltoxins I-IV, stemphyperylenol, stemphytriol, 7-epi-8-hydroxyaltertoxin I, and 6-epi-stemphytriol are mycotoxins derived from perylene quinone, for which the absolute configuration was not known. Electronic circular dichroism (ECD) spectra were calculated for these compounds and compared with measured spectra of altertoxins I-III, alteichin, and stemphyltoxin III and with reported Cotton effects. Specific rotations were calculated and compared with reported specific rotations. The absolute configuration of all the toxins, except for stemphyltoxin IV, could thus be determined. The validity of the assignment was high whenever reported ECD data were available for comparison, and the validity was lower when the assignment was based only on the comparison of calculated and reported specific rotations. ECD spectra are intrinsically different for toxins with a biphenyl substructure and for toxins derived from dihydroanthracene.
Collapse
Affiliation(s)
- Joachim Podlech
- Institute for Organic Chemistry, Karlsruhe Institute for Technology (KIT), Campus South, Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany), Fax: (+49) 721-608-47652.
| | | | | | | | | |
Collapse
|
20
|
Liu Y, Lin N, Fan W, Zhao X. First principles studies on one-, two-, and three-photon absorption properties of a symmetric carbazole derivative both in gas phase and solution. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2013.10.024] [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]
|
21
|
Lin N, Barone V, Cappelli C, Zhao X, Ruud K, Santoro F. Effective time-independent studies on resonance Raman spectroscopy of trans-stilbene including the Duschinsky effect. Mol Phys 2013. [DOI: 10.1080/00268976.2013.809490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Na Lin
- a State Key Laboratory of Crystal Materials , Shandong University , Shandong , China
- b Centre for Theoretical and Computational Chemistry, Department of Chemistry , University of Tromsø , Tromsø , Norway
| | - Vincenzo Barone
- c Scuola Normale Superiore, Piazza dei Cavalieri 7 , Pisa , Italy
| | - Chiara Cappelli
- c Scuola Normale Superiore, Piazza dei Cavalieri 7 , Pisa , Italy
- d Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Pisa , Italy
| | - Xian Zhao
- a State Key Laboratory of Crystal Materials , Shandong University , Shandong , China
| | - Kenneth Ruud
- b Centre for Theoretical and Computational Chemistry, Department of Chemistry , University of Tromsø , Tromsø , Norway
| | - Fabrizio Santoro
- e Consiglio Nazionale delle Ricerche – CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , Pisa , Italy
| |
Collapse
|