1
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Puglisi A, Giovannini T, Antonov L, Cappelli C. Interplay between conformational and solvent effects in UV-visible absorption spectra: curcumin tautomers as a case study. Phys Chem Chem Phys 2019; 21:15504-15514. [PMID: 31259324 DOI: 10.1039/c9cp00907h] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a combined theoretical and experimental study on the UV-vis spectra of enol-keto (EK) and keto-keto (KK) tautomeric forms of curcumin dissolved in aqueous solution. Solvent effects have been investigated by resorting to the implicit polarizable continuum model (QM/PCM) and non-polarizable and fully polarizable QM/MM approaches, the latter based on the fluctuating charges (FQ) force-field. In particular, all methods are challenged to rationalize the contribution of conformational, electrostatic and polarization effects in the calculation of the vertical excitation spectra of curcumin tautomers. The obtained results highlight that for both tautomers specific solute-solvent hydrogen-bond interactions play a minor role with respect to conformational and electrostatic effects.
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Affiliation(s)
| | | | - Liudmil Antonov
- Bulgarian Academy of Sciences, Institute of Organic Chemistry with Centre of Phytochemistry, Acad. G. Bonchev str., Bldg. 9, Sofia 1113, Bulgaria
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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2
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Abstract
The photophysical properties of a deep-red fluorescent squaraine dye can be improved by encapsulating it within a tetralactam macrocycle. Three new tetralactams are described with different substituents (methyl, methoxy, methylenedioxy) on the macrocycle aromatic sidewalls. The capability of each tetralactam to encapsulate a squaraine dye in chloroform solution was determined experimentally using absorption, fluorescence, and NMR spectroscopy. Two of the tetralactams were found to thread a squaraine dye with association constants on the order of 106 M-1, while a third macrocycle exhibited no squaraine affinity. An X-ray crystal structure of the third tetralactam showed that the substituents sterically blocked squaraine association. Of the two tetralactams that encapsulate a squaraine, one induces an increase in squaraine fluorescence quantum yield, while the other quenches the squaraine fluorescence. The results suggest that these new squaraine binding systems will be useful for biological imaging and diagnostics applications.
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Affiliation(s)
- Janel M Dempsey
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
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3
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Marazzi M, Gattuso H, Monari A, Assfeld X. Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules. Front Chem 2018; 6:86. [PMID: 29666792 PMCID: PMC5891624 DOI: 10.3389/fchem.2018.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/12/2018] [Indexed: 01/05/2023] Open
Abstract
Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.
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Affiliation(s)
- Marco Marazzi
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Logroño, Spain
| | - Hugo Gattuso
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Xavier Assfeld
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
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4
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Giovannini T, Lafiosca P, Cappelli C. A General Route to Include Pauli Repulsion and Quantum Dispersion Effects in QM/MM Approaches. J Chem Theory Comput 2017; 13:4854-4870. [PMID: 28898079 DOI: 10.1021/acs.jctc.7b00776] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A methodology to account for nonelectrostatic interactions in Quantum Mechanical (QM)/Molecular Mechanics (MM) approaches is developed. Formulations for Pauli repulsion and dispersion energy, explicitly depending on the QM density, are derived. Such expressions are based on the definition of an auxiliary density on the MM portion and the Tkatchenko-Scheffler (TS) approach, respectively. The developed method is general enough to be applied to any QM/MM method and partition, provided an accurate tuning of a small number of parameters is obtained. The coupling of the method with both nonpolarizable and fully polarizable QM/fluctuating charge (FQ) approaches is reported and applied. A suitable parametrization for the aqueous solution, so that its most representative features are well reproduced, is outlined. Then, the obtained parametrization and method are applied to calculate the nonelectrostatic (repulsion and dispersion) interaction energy of nicotine in aqueous solution.
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Affiliation(s)
| | - Piero Lafiosca
- Scuola Normale Superiore , Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore , Piazza dei Cavalieri 7, 56126 Pisa, Italy
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5
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Jarvis TS, Collins CG, Dempsey JM, Oliver AG, Smith BD. Synthesis and Structure of 3,3-Dimethylindoline Squaraine Rotaxanes. J Org Chem 2017; 82:5819-5825. [DOI: 10.1021/acs.joc.7b00655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Tia S. Jarvis
- Department of Chemistry and
Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Carleton G. Collins
- Department of Chemistry and
Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Janel M. Dempsey
- Department of Chemistry and
Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Allen G. Oliver
- Department of Chemistry and
Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Bradley D. Smith
- Department of Chemistry and
Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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6
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Molecular aspects of squaraine dyes aggregation and its influence on spectroscopic properties. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1971-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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7
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Effect of UV-irradiation on spectral properties of squaraine dye in diluted solutions. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2015.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Liu W, Peck EM, Smith BD. High Affinity Macrocycle Threading by a Near-Infrared Croconaine Dye with Flanking Polymer Chains. J Phys Chem B 2016; 120:995-1001. [PMID: 26807599 DOI: 10.1021/acs.jpcb.5b11961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Croconaine dyes have narrow and intense absorption bands at ∼800 nm, very weak fluorescence, and high photostabilities, which combine to make them very attractive chromophores for absorption-based imaging or laser heating technologies. The physical supramolecular properties of croconaine dyes have rarely been investigated, especially in water. This study focuses on a molecular threading process that encapsulates a croconaine dye inside a tetralactam macrocycle in organic or aqueous solvent. Macrocycle association and rate constant data are reported for a series of croconaine structures with different substituents attached to the ends of the dye. The association constants were highest in water (Ka ∼ 10(9) M(-1)), and the threading rate constants (kon) increased in the solvent order H2O > MeOH > CHCl3. Systematic variation of croconaine substituents located just outside the croconaine/macrocycle complexation interface hardly changed Ka but had a strong influence on kon. A croconaine dye with N-propyl groups at each end of the structure exhibited a desirable mixture of macrocycle threading properties; that is, there was rapid and quantitative croconaine/macrocycle complexation at relatively high concentrations in water, and no dissociation of the preassembled complex when it was diluted into a solution of fetal bovine serum, even after laser-induced photothermal heating of the solution. The combination of favorable near-infrared absorption properties and tunable mechanical stability makes threaded croconaine/macrocycle complexes very attractive as molecular probes or as supramolecular composites for various applications in absorption-based imaging or photothermal therapy.
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Affiliation(s)
- Wenqi Liu
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Evan M Peck
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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9
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Jacquemin D, Duchemin I, Blase X. 0-0 Energies Using Hybrid Schemes: Benchmarks of TD-DFT, CIS(D), ADC(2), CC2, and BSE/GW formalisms for 80 Real-Life Compounds. J Chem Theory Comput 2015; 11:5340-59. [PMID: 26574326 PMCID: PMC4642227 DOI: 10.1021/acs.jctc.5b00619] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 02/05/2023]
Abstract
The 0-0 energies of 80 medium and large molecules have been computed with a large panel of theoretical formalisms. We have used an approach computationally tractable for large molecules, that is, the structural and vibrational parameters are obtained with TD-DFT, the solvent effects are accounted for with the PCM model, whereas the total and transition energies have been determined with TD-DFT and with five wave function approaches accounting for contributions from double excitations, namely, CIS(D), ADC(2), CC2, SCS-CC2, and SOS-CC2, as well as Green's function based BSE/GW approach. Atomic basis sets including diffuse functions have been systematically applied, and several variations of the PCM have been evaluated. Using solvent corrections obtained with corrected linear-response approach, we found that three schemes, namely, ADC(2), CC2, and BSE/GW allow one to reach a mean absolute deviation smaller than 0.15 eV compared to the measurements, the two former yielding slightly better correlation with experiments than the latter. CIS(D), SCS-CC2, and SOS-CC2 provide significantly larger deviations, though the latter approach delivers highly consistent transition energies. In addition, we show that (i) ADC(2) and CC2 values are extremely close to each other but for systems absorbing at low energies; (ii) the linear-response PCM scheme tends to overestimate solvation effects; and that (iii) the average impact of nonequilibrium correction on 0-0 energies is negligible.
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Affiliation(s)
- Denis Jacquemin
- Laboratoire
CEISAM - UMR CNR 6230, Université
de Nantes, 2 Rue de la
Houssinière, BP 92208, 44322 Nantes Cedex 3, France
- Institut
Universitaire de France, 103 bd St. Michel, 75005 Paris Cedex 5, France
| | - Ivan Duchemin
- INAC, SP2M/L_Sim,
CEA/UJF, Cedex 09, 38054 Grenoble, France
- Institut
NEEL, Univ. Grenoble Alpes, F-38042 Grenoble, France
| | - Xavier Blase
- Institut
NEEL, Univ. Grenoble Alpes, F-38042 Grenoble, France
- Institut
NEEL, CNRS, F-38042 Grenoble, France
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10
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Laurent AD, Adamo C, Jacquemin D. Dye chemistry with time-dependent density functional theory. Phys Chem Chem Phys 2015; 16:14334-56. [PMID: 24548975 DOI: 10.1039/c3cp55336a] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.
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Affiliation(s)
- Adèle D Laurent
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS no. 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes, Cedex 3, France.
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11
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Xue M, Yang Y, Chi X, Yan X, Huang F. Development of Pseudorotaxanes and Rotaxanes: From Synthesis to Stimuli-Responsive Motions to Applications. Chem Rev 2015; 115:7398-501. [DOI: 10.1021/cr5005869] [Citation(s) in RCA: 605] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Min Xue
- State Key Laboratory of Chemical Engineering, Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Yong Yang
- Department
of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, People’s Republic of China
| | - Xiaodong Chi
- State Key Laboratory of Chemical Engineering, Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Xuzhou Yan
- State Key Laboratory of Chemical Engineering, Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Feihe Huang
- State Key Laboratory of Chemical Engineering, Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, People’s Republic of China
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12
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Rivail JL, Monari A, Assfeld X. The Non Empirical Local Self Consistent Field Method: Application to Quantum Mechanics/Molecular Mechanics (QM/MM) Modeling of Large Biomolecular Systems. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Mennucci B. QM/MM Approaches for the Modeling of Photoinduced Processes in Biological Systems. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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14
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Jacquemin D, Adamo C. Computational Molecular Electronic Spectroscopy with TD-DFT. DENSITY-FUNCTIONAL METHODS FOR EXCITED STATES 2015; 368:347-75. [DOI: 10.1007/128_2015_638] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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15
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Etienne T, Assfeld X, Monari A. QM/MM calculation of absorption spectra of complex systems: The case of human serum albumin. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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QM/MM modeling of Harmane cation fluorescence spectrum in water solution and interacting with DNA. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Chibani S, Jacquemin D, Laurent AD. Modelling solvent effects on the absorption and emission spectra of constrained cyanines with both implicit and explicit QM/EFP models. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Wang J, Bai FQ, Xia BH, Zhang HX, Cui T. Accurate simulation of geometry, singlet-singlet and triplet-singlet excitation of cyclometalated iridium(III) complex. J Mol Model 2014; 20:2108. [PMID: 24595718 DOI: 10.1007/s00894-014-2108-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Abstract
In the current contribution, we present a critical study of the theoretical protocol used for the determination of the electronic spectra properties of luminescent cyclometalated iridium(III) complex, [Ir(III)(ppy)₂H₂dcbpy]⁺ (where, ppy = 2-phenylpyridine, H₂dcbpy = 2,2'-bipyridine-4,4'-dicarboxylic acid), considered as a representative example of the various problems related to the prediction of electronic spectra of transition metal complex. The choice of the exchange-correlation functional is crucial for the validity of the conclusions that would be drawn from the numerical results. The influence of the exchange-correlation on geometry parameter and absorption/emission band, the role of solvent effects on time-dependent density function theory (TD-DFT) calculations, as well as the importance of the chosen proper procedure to optimize triplet excited geometry, have been thus examined in detail. From the obtained results, some general conclusions and guidelines are presented: i) PBE0 functional is the most accurate in prediction of ground state geometry; ii) the well-established B3LYP, B3P86, PBE0, and X3LYP have similar accuracy in calculation of absorption spectrum; and iii) the hybrid approach TD-DFT//CIS gives out excellent agreement in the evaluation of triplet excitation energy.
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Affiliation(s)
- Jian Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, China
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19
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UV–vis absorption spectrum of a novel Ru(II) complex intercalated in DNA: [Ru(2,2′-bipy)(dppz)(2,2′-ArPy)]+. J Mol Model 2014; 20:2082. [DOI: 10.1007/s00894-014-2082-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 10/09/2013] [Indexed: 12/26/2022]
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20
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Chantzis A, Very T, Daniel C, Monari A, Assfeld X. Theoretical evidence of photo-induced charge transfer from DNA to intercalated ruthenium (II) organometallic complexes. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.068] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Adamo C, Jacquemin D. The calculations of excited-state properties with Time-Dependent Density Functional Theory. Chem Soc Rev 2013; 42:845-56. [PMID: 23117144 DOI: 10.1039/c2cs35394f] [Citation(s) in RCA: 1095] [Impact Index Per Article: 99.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this tutorial review, we show how Time-Dependent Density Functional Theory (TD-DFT) has become a popular tool for computing the signatures of electronically excited states, and more specifically, the properties directly related to the optical (absorption and emission) spectra of molecules. We discuss the properties that can be obtained with widely available programs as well as how to account for the environmental effects (solvent and surfaces) and present recent applications in these fields. We next expose the transformation of the TD-DFT results into chemically intuitive parameters (colours as well as charge-transfer distances). Eventually, the non-specialised reader will find a series of advices and warnings necessary to perform her/his first TD-DFT calculations.
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Affiliation(s)
- Carlo Adamo
- Laboratoire LECIME, CNRS UMR-7575, Chimie-ParisTech, 11 rue P. et M. Curie, F-75231 Paris Cedex 05, France
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22
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Etienne T, Very T, Perpète EA, Monari A, Assfeld X. A QM/MM Study of the Absorption Spectrum of Harmane in Water Solution and Interacting with DNA: The Crucial Role of Dynamic Effects. J Phys Chem B 2013; 117:4973-80. [DOI: 10.1021/jp4017882] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Thibaud Etienne
- Université de Lorraine - Nancy, Théorie-Modélisation-Simulation,
SRSMC, Boulevard des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy
- CNRS, Théorie-Modélisation-Simulation, SRSMC, Boulevard
des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy
- Unité de Chimie Théorique
et Structurale, Université de Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Thibaut Very
- Université de Lorraine - Nancy, Théorie-Modélisation-Simulation,
SRSMC, Boulevard des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy
- CNRS, Théorie-Modélisation-Simulation, SRSMC, Boulevard
des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy
| | - Eric A. Perpète
- Unité de Chimie Théorique
et Structurale, Université de Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Antonio Monari
- Université de Lorraine - Nancy, Théorie-Modélisation-Simulation,
SRSMC, Boulevard des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy
- CNRS, Théorie-Modélisation-Simulation, SRSMC, Boulevard
des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy
| | - Xavier Assfeld
- Université de Lorraine - Nancy, Théorie-Modélisation-Simulation,
SRSMC, Boulevard des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy
- CNRS, Théorie-Modélisation-Simulation, SRSMC, Boulevard
des Aiguillettes, BP 70239, 54506, Vandoeuvre-lès-Nancy
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23
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Monari A, Rivail JL, Assfeld X. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations. Acc Chem Res 2013; 46:596-603. [PMID: 23249409 DOI: 10.1021/ar300278j] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of the atom: for an sp(3) carbon atom, we consider the two core 1s electrons and treat that carbon as an atom with three electrons. This results in an LSCF+3 model. Similarly, a nitrogen atom with a lone pair of electrons available for conjugation is treated as an atom with five electrons (LSCF+5). This approach is particularly well suited to splitting peptide bonds and other bonds that include carbon or nitrogen atoms. To embed the induced polarization within the calculation, researchers must use a polarizable force field. However, because the parameters of the usual force fields include an average of the induction effects, researchers typically can obtain satisfactory results without explicitly introducing the polarization. When considering electronic transitions, researchers must take into account the changes in the electronic polarization. One approach is to simulate the electronic cloud of the surroundings by a continuum whose dielectric constant is equal to the square of the refractive index. This Electronic Response of the Surroundings (ERS) methodology allows researchers to model the changes in induced polarization easily. We illustrate this approach by modeling the electronic absorption of tryptophan in human serum albumin (HSA).
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Affiliation(s)
- Antonio Monari
- Théorie Modélisation Simulation, Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
- Théorie Modélisation Simulation, CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
| | - Jean-Louis Rivail
- Théorie Modélisation Simulation, Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
- Théorie Modélisation Simulation, CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
| | - Xavier Assfeld
- Théorie Modélisation Simulation, Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
- Théorie Modélisation Simulation, CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
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Collins CG, Peck EM, Kramer PJ, Smith BD. Squaraine rotaxane shuttle as a ratiometric deep-red optical chloride sensor. Chem Sci 2013. [DOI: 10.1039/c3sc50535a] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Wang X, Xu J, Li M, Fang D, Chen B, Wang L, Xu W. Highly efficient unsymmetrical squaraines for panchromatic dye-sensitized solar cells: A computational study. RSC Adv 2013. [DOI: 10.1039/c3ra40193f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Labat F, Le Bahers T, Ciofini I, Adamo C. First-principles modeling of dye-sensitized solar cells: challenges and perspectives. Acc Chem Res 2012; 45:1268-77. [PMID: 22497694 DOI: 10.1021/ar200327w] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Since dye-sensitized solar cells (DSSCs) appeared as a promising inexpensive alternative to the traditional silicon-based solar cells, DSSCs have attracted a considerable amount of experimental and theoretical interest. In contrast with silicon-based solar cells, DSSCs use different components for the light-harvesting and transport functions, which allow researchers to fine-tune each material and, under ideal conditions, to optimize their overall performance in assembled devices. Because of the variety of elementary components present in these cells and their multiple possible combinations, this task presents experimental challenges. The photoconversion efficiencies obtained up to this point are still low, despite the significant experimental efforts spent in their optimization. The development of a low-cost and efficient computational protocol that could qualitatively (or even quantitatively) identify the promising semiconductors, dyes, and electrolytes, as well as their assembly, could save substantial experimental time and resources. In this Account, we describe our computational approach that allows us to understand and predict the different elementary mechanisms involved in DSSC working principles. We use this computational framework to propose an in silico route for the ab initio design of these materials. Our approach relies on a unique density functional theory (DFT) based model, which allows for an accurate and balanced treatment of electronic and spectroscopic properties in different phases (such as gas, solution, or interfaces) and avoids or minimizes spurious computational effects. Using this tool, we reproduced and predicted the properties of the isolated components of the DSSC assemblies. We accessed the microscopic measurable characteristics of the cells such as the short circuit current (J(sc)) or the open circuit voltage (V(oc)), which define the overall photoconversion efficiency of the cell. The absence of empirical or material-related parameters in our approach should allow for its wide application to the optimization of existing devices or the design of new ones.
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Affiliation(s)
- Frédéric Labat
- LECIME, Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, UMR 7575 CNRS, Ecole Nationale Supérieure de Chimie de Paris − Chimie ParisTech, 11 rue P. et M. Curie, 75231 Paris Cedex 05, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
| | - Tangui Le Bahers
- LECIME, Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, UMR 7575 CNRS, Ecole Nationale Supérieure de Chimie de Paris − Chimie ParisTech, 11 rue P. et M. Curie, 75231 Paris Cedex 05, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
| | - Ilaria Ciofini
- LECIME, Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, UMR 7575 CNRS, Ecole Nationale Supérieure de Chimie de Paris − Chimie ParisTech, 11 rue P. et M. Curie, 75231 Paris Cedex 05, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
| | - Carlo Adamo
- LECIME, Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, UMR 7575 CNRS, Ecole Nationale Supérieure de Chimie de Paris − Chimie ParisTech, 11 rue P. et M. Curie, 75231 Paris Cedex 05, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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Puyad AL, Chaitanya GK, Prabhakar C, Bhanuprakash K. A comparative study of semi-squaraine and squaraine dyes using computational techniques: tuning the charge transfer/biradicaloid character by substitution. J Mol Model 2012; 19:275-87. [DOI: 10.1007/s00894-012-1543-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/23/2012] [Indexed: 12/20/2022]
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28
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Monari A, Very T, Rivail JL, Assfeld X. A QM/MM study on the spinach plastocyanin: Redox properties and absorption spectra. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.11.026] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Monari A, Very T, Rivail JL, Assfeld X. Effects of mutations on the absorption spectra of copper proteins: a QM/MM study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1221-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Chantzis A, Very T, Monari A, Assfeld X. Improved Treatment of Surrounding Effects: UV/vis Absorption Properties of a Solvated Ru(II) Complex. J Chem Theory Comput 2012; 8:1536-41. [DOI: 10.1021/ct300129c] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Agisilaos Chantzis
- Equipe
de Chimie et Biochimie Théoriques, SRSMC
UMR 7565, Université de Lorraine—Nancy and CNRS, Boulevard des Aiguilletes BP
70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Thibaut Very
- Equipe
de Chimie et Biochimie Théoriques, SRSMC
UMR 7565, Université de Lorraine—Nancy and CNRS, Boulevard des Aiguilletes BP
70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Equipe
de Chimie et Biochimie Théoriques, SRSMC
UMR 7565, Université de Lorraine—Nancy and CNRS, Boulevard des Aiguilletes BP
70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Xavier Assfeld
- Equipe
de Chimie et Biochimie Théoriques, SRSMC
UMR 7565, Université de Lorraine—Nancy and CNRS, Boulevard des Aiguilletes BP
70239, 54506 Vandoeuvre-lès-Nancy, France
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31
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Very T, Despax S, Hébraud P, Monari A, Assfeld X. Spectral properties of polypyridyl ruthenium complexes intercalated in DNA: theoretical insights into the surrounding effects of [Ru(dppz)(bpy)2]2+. Phys Chem Chem Phys 2012; 14:12496-504. [DOI: 10.1039/c2cp40935f] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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32
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Murugan NA, Kongsted J, Rinkevicius Z, Ågren H. Color modeling of protein optical probes. Phys Chem Chem Phys 2012; 14:1107-12. [DOI: 10.1039/c1cp23060c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Jacquemin D, Mennucci B, Adamo C. Excited-state calculations with TD-DFT: from benchmarks to simulations in complex environments. Phys Chem Chem Phys 2011; 13:16987-98. [PMID: 21881657 DOI: 10.1039/c1cp22144b] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this perspective, we present an overview of recent progress on Time-Dependent Density Functional Theory (TD-DFT) with a specific focus on its accuracy and on models able to take into account environmental effects, including complex media. To this end, we first summarise recent benchmarks and define an average TD-DFT accuracy in reproducing excitation energies when a conventional approach is used. Next, coupling of TD-DFT with models able to account for different kinds of interactions between a central chromophore and nearby chemical objects (solvent, organic cage, metal as well as semi-conducting surface) is investigated. Examples of application to excitation properties are presented, allowing to briefly describe several recent computational strategies. In addition, an extension of TD-DFT to describe a phenomenon involving interacting chromophores, e.g. the electronic energy transfer (EET), is presented to illustrate that this methodology can be applied to processes beyond the vertical excitation. This perspective therefore aims to provide to non-specialists a flavour of recent trends in the field of simulations of excited states in "realistic" situations.
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Affiliation(s)
- Denis Jacquemin
- Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS no. 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes Cedex 3, France.
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34
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Pedone A, Prampolini G, Monti S, Barone V. Absorption and emission spectra of fluorescent silica nanoparticles from TD-DFT/MM/PCM calculations. Phys Chem Chem Phys 2011; 13:16689-97. [PMID: 21858292 DOI: 10.1039/c1cp21475f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A multi-scale computational protocol, which combines Quantum Mechanics and Molecular Mechanics (QM/MM) calculations with the polarisable continuum model (PCM), has been used to study the tetramethylrhodamine isothiocyanate (TRITC) fluorophore, embedded in three different environments, namely in water, on an amorphous silica surface and covalently encapsulated in a silica nanoparticle (C dot). Absorption and emission spectra have been simulated by using TD-B3LYP/PCM calculations, performed on the TRITC ground and excited state geometries, optimized at the QM/MM level. The results are in good agreement with experimental data confirming the caging effect played by the silica shell on the mobility of the TRITC molecule when covalently encapsulated in silica nanoparticles. This could result in a decrease of the nonradiative decay rate and thus an increase of the quantum yield of the molecule.
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Affiliation(s)
- Alfonso Pedone
- Dipartimento di Chimica, Università di Modena e Reggio Emilia, Modena, Italy.
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35
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Monari A, Assfeld X, Beley M, Gros PC. Theoretical study of new ruthenium-based dyes for dye-sensitized solar cells. J Phys Chem A 2011; 115:3596-603. [PMID: 21428400 DOI: 10.1021/jp201058v] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Two relevant, recently reported, ruthenium-based complexes to be used as sensitizers in Grätzel photovoltaic cells are theoretically studied. The UV/vis absorption spectra have been computed within the time-dependent density functional theory formalism. The obtained excitation energies are compared with the experimental results, and the nature of the transition is analyzed in terms of the electronic density. A preliminary study on the performance of different functionals against the equation of motion coupled cluster is performed on a smaller model system.
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Affiliation(s)
- Antonio Monari
- Equipe de Chimie et Biochimie Théoriques, Institut Jean Barriol, Nancy Université, Vandoeuvre-lès-Nancy, France.
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36
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Rocha-Rinza T, Sneskov K, Christiansen O, Ryde U, Kongsted J. Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein. Phys Chem Chem Phys 2011; 13:1585-9. [DOI: 10.1039/c0cp01075h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Lee JJ, Baumes JM, Connell RD, Oliver AG, Smith BD. Squaraine [2]catenanes: synthesis, structure and molecular dynamics. Chem Commun (Camb) 2011; 47:7188-90. [DOI: 10.1039/c1cc10946d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Acridine orange in a pumpkin-shaped macrocycle: Beyond solvent effects in the UV–visible spectra simulation of dyes. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.01.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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39
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Jacquemin D, Perpète EA, Ciofini I, Adamo C, Valero R, Zhao Y, Truhlar DG. On the Performances of the M06 Family of Density Functionals for Electronic Excitation Energies. J Chem Theory Comput 2010; 6:2071-85. [DOI: 10.1021/ct100119e] [Citation(s) in RCA: 339] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Denis Jacquemin
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Eric A. Perpète
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Ilaria Ciofini
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Carlo Adamo
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Rosendo Valero
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Yan Zhao
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Donald G. Truhlar
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
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Effect of the Enhanced Cyan Fluorescent Protein framework on the UV/visible absorption spectra of some chromophores. Interdiscip Sci 2010; 2:38-47. [DOI: 10.1007/s12539-010-0084-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 11/09/2009] [Accepted: 11/10/2009] [Indexed: 10/19/2022]
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41
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Fu N, Gassensmith JJ, Smith BD. New Class of Hydroxy-Substituted Squaraine Rotaxane. Aust J Chem 2010; 63:792-796. [PMID: 20634969 PMCID: PMC2903750 DOI: 10.1071/ch09671] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A templated macrocyclization reaction was used to permanently encapsulate a highly fluorescent hydroxy-substituted squaraine dye inside a tetralactam macrocycle. The free squaraine dye is quite rigid due to internal hydrogen bonding and its photophysical properties hardly change upon encapsulation. A combination of X-ray and NMR data show that the surrounding tetralactam macrocycle adopts an unusually rigid chair conformation and does not undergo rapid pirouetting. Because of its large size and conformational rigidity, the macrocycle creates anisotropic NMR shielding zones that extend over the N,N-dibutylamino groups at each end of the squaraine thread. This shielding anisotropy allows hindered aryl-N rotation to be observed by NMR and provides direct experimental evidence that quinoid-like resonance structures are major contributors to the bis(N,N-dialkylaminophenyl)squaraine resonance hybrid.
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Affiliation(s)
- Na Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46545, USA
| | - Jeremiah J. Gassensmith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46545, USA
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46545, USA
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Patsenker LD, Tatarets AL, Klochko OP, Terpetschnig EA. Conjugates, Complexes, and Interlocked Systems Based on Squaraines and Cyanines. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY II 2010. [DOI: 10.1007/978-3-642-04701-5_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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43
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Rodríguez-Ropero F, Zanuy D, Alemán C. Electronic characterization of all-thiophene conducting dendrimers: Molecules and assemblies. POLYMER 2010. [DOI: 10.1016/j.polymer.2009.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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44
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Rodríguez-Ropero F, Zanuy D, Assfeld X, Alemán C. Modeling an electronic conductor based on natural peptide sequences. Biomacromolecules 2009; 10:2338-43. [PMID: 19603792 DOI: 10.1021/bm900524v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we used quantum mechanical calculations, molecular dynamics simulations, and QM/MM methods to examine the formation of a pi-stacking ladder and the existence of charge transfer processes in a tubular nanostructure constructed using protein building blocks. Initially, the conformational properties of beta-3-thienylalanine, a synthetic amino acid with an aromatic side group, were studied using quantum mechanical calculations. Next, this amino acid was used to substitute the natural residues at selected positions of the nanotube. Molecular dynamics simulations showed that a rational design of the targeted replacements enhances the stability of the tubular nanostructure and forms a pi-stacking ladder in the inner core of the tube. Finally, QM/MM calculations on the oxidized nanotube evidenced the delocalization of the pi-electron deficiency between the thienyl side groups of the different synthetic residues. The overall results reflected that the system under study is a potential candidate to be used as a nanowire.
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Affiliation(s)
- Francisco Rodríguez-Ropero
- Departament d'Enginyeria Quimica, ETS d'Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Barcelona E-08028, Spain.
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Gassensmith JJ, Baumes JM, Smith BD. Discovery and early development of squaraine rotaxanes. Chem Commun (Camb) 2009:6329-38. [PMID: 19841772 PMCID: PMC2854661 DOI: 10.1039/b911064j] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chemical and photophysical properties of a fluorescent squaraine dye are greatly enhanced when it is mechanically encapsulated inside a tetralactam macrocycle. This feature article describes the synthesis, structure, and photophysical performance of first-generation squaraine rotaxanes, and shows how they can be used as fluorescent imaging probes and chemosensors.
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Affiliation(s)
- Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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46
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Hu B, Zhang J. Theoretical investigation on the white-light emission from a single-polymer system with simultaneous blue and orange emission. POLYMER 2009. [DOI: 10.1016/j.polymer.2009.10.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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47
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Labat F, Ciofini I, Hratchian HP, Frisch M, Raghavachari K, Adamo C. First Principles Modeling of Eosin-Loaded ZnO Films: A Step toward the Understanding of Dye-Sensitized Solar Cell Performances. J Am Chem Soc 2009; 131:14290-8. [DOI: 10.1021/ja902833s] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frédéric Labat
- Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05 France, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Ilaria Ciofini
- Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05 France, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Hrant P. Hratchian
- Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05 France, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Mike Frisch
- Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05 France, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Krishnan Raghavachari
- Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05 France, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Carlo Adamo
- Laboratoire d’Electrochimie, Chimie des Interfaces et Modélisation pour l’Energie, CNRS UMR-7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05 France, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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48
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Fu N, Baumes JM, Arunkumar E, Noll BC, Smith BD. Squaraine rotaxanes with boat conformation macrocycles. J Org Chem 2009; 74:6462-8. [PMID: 19639940 PMCID: PMC2847772 DOI: 10.1021/jo901298n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mechanical encapsulation of fluorescent, deep-red bis(anilino)squaraine dyes inside Leigh-type tetralactam macrocycles produces interlocked squaraine rotaxanes. The surrounding macrocycles are flexible and undergo rapid exchange of chair and boat conformations in solution. A series of X-ray crystal structures show how the rotaxane co-conformational exchange process involves simultaneous lateral oscillation of the macrocycle about the center of the encapsulated squaraine thread. Rotaxane macrocycles with 1,4-phenylene sidewalls and 2,6-pyridine dicarboxamide bridging units are more likely to adopt boat conformations in the solid state than analogous squaraine rotaxane systems with isophthalamide-containing macrocycles. A truncated squaraine dye, with a secondary amine attached directly to the central C(4)O(2) core, is less electrophilic than the extended bis(anilino)squaraine analogue, but it is still susceptible to chemical and photochemical bleaching. Its stability is greatly enhanced when it is encapsulated as an interlocked squaraine rotaxane. An X-ray crystal structure of this truncated squaraine rotaxane shows the macrocycle in a boat conformation, and NMR studies indicate that the boat is maintained in solution. Encapsulation as a rotaxane increases the dye's brightness by a factor of 6. The encapsulation process appears to constrain the dye and reduce deformation of the chromophore from planarity. This study shows how mechanical encapsulation as a rotaxane can be used as a rational design parameter to fine-tune the chemical and photochemical properties of squaraine dyes.
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Affiliation(s)
- Na Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46545, USA
| | - Jeffrey M. Baumes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46545, USA
| | - Easwaran Arunkumar
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46545, USA
| | - Bruce C. Noll
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46545, USA
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46545, USA
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49
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Jacquemin D, Wathelet V, Perpète EA, Adamo C. Extensive TD-DFT Benchmark: Singlet-Excited States of Organic Molecules. J Chem Theory Comput 2009; 5:2420-35. [DOI: 10.1021/ct900298e] [Citation(s) in RCA: 836] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Denis Jacquemin
- Groupe de Chimie-Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, and Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France
| | - Valérie Wathelet
- Groupe de Chimie-Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, and Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France
| | - Eric A. Perpète
- Groupe de Chimie-Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, and Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France
| | - Carlo Adamo
- Groupe de Chimie-Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, and Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France
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