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Fusè M, Mazzeo G, Ghidinelli S, Evidente A, Abbate S, Longhi G. Experimental and theoretical aspects of magnetic circular dichroism and magnetic circularly polarized luminescence in the UV, visible and IR ranges: A review. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124583. [PMID: 38850611 DOI: 10.1016/j.saa.2024.124583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/21/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
A historical sketch of the MCD (magnetic circular dichroism) spectroscopy is reported in its experimental and theoretical aspects. MCPL (magnetic circularly polarized luminescence) is also considered. The main studies are presented encompassing porphyrinoid systems, aggregates and materials, as well as simple organic molecules useful for the advancement of the interpretation. The MCD of chiral systems is discussed with special attention to new studies of natural products with potential pharmaceutical valence, including Amaryllidaceae alkaloids and related isocarbostyrils. Finally, the vibrational form of MCD, called MVCD, which is recorded in the IR part of the spectrum is also discussed. A final brief note on perspectives is given.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Simone Ghidinelli
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Antonio Evidente
- Institute of Sciences of Food Production, National Research Council, Via Amendola 122/O, 70185 Bari, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy; Istituto Nazionale di Ottica, INO-CNR, Research Unit of Brescia, c/o CSMT, Via Branze 35, 25123 Brescia, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy; Istituto Nazionale di Ottica, INO-CNR, Research Unit of Brescia, c/o CSMT, Via Branze 35, 25123 Brescia, Italy
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2
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Choutka J, Parkan K, Pohl R, Kaminský J. On the origin of the electronic and magnetic circular dichroism of naphthyl C-glycosides: Anomeric configuration. Carbohydr Res 2024; 535:109021. [PMID: 38171193 DOI: 10.1016/j.carres.2023.109021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Aryl C-glycosides, in which the glycosidic bond is changed to a carbon-carbon bond, are an important family of biologically-active compounds. They often serve as secondary metabolites or exhibit antibiotic and cytostatic activities. Their stability to hydrolysis has made them attractive targets for new drugs. Their conformational behavior often strongly influences the resulting function. Their detailed structural and conformational description is thus highly desirable. This work studies the structure of three different naphthyl C-glycosides using UV-vis absorption as well as electronic and magnetic circular dichroism. It also describes their conformational preferences using a combination of molecular dynamics and DFT calculations. The reliability of these preferences has been verified by simulations of spectral properties and a comparison with their measured spectra. In particular, ECD spectroscopy has been shown to distinguish easily between α- and β-pseudoanomers of aryl C-glycosides. Computer simulations and spectral decomposition have revealed how the resulting ECD patterns of the naphthyl glycosides studied are influenced by different conformer populations. In conclusion, reliable ECD patterns cannot be calculated by separating the naphthyl rotation from other conformational motions. MCD patterns have been similar for all the naphthyl C-glycosides studied. No clear diagnostic features have been found for either the pseudoanomeric configuration or the preferred hydroxymethyl rotamer. Nevertheless, the work has demonstrated the potential of MCD for the study of aryl glycosides interacting with proteins.
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Affiliation(s)
- Jan Choutka
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic
| | - Kamil Parkan
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic; Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic.
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3
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Andersen JH, Coriani S, Hättig C. Efficient Protocol for Computing MCD Spectra in a Broad Frequency Range Combining Resonant and Damped CC2 Quadratic Response Theory. J Chem Theory Comput 2023; 19:5977-5987. [PMID: 37650779 DOI: 10.1021/acs.jctc.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Coupled cluster response theory offers a path to high-accuracy calculations of spectroscopic properties, such as magnetic circular dichroism (MCD). However, divergence or slow convergence issues are often encountered for electronic transitions in high-energy regions with a high density of states. This is here addressed for MCD by an implementation of damped quadratic response theory for resolution-of-identity coupled cluster singles-and-approximate-doubles (RI-CC2), along with an implementation of the MCD A term from resonant response theory. Combined, damped and resonant response theory calculations provide an efficient strategy to obtain MCD spectra over a broad frequency range and for systems that include highly symmetric molecules with degenerate excited states. The protocol is illustrated by application to zinc tetrabenzoporphyrin in the energy region of 2-8 eV and comparison to experimental data. Timings are reported for the resonant and damped approaches, showing that a greater part of the calculation time is consumed by the construction of the building blocks for the final MCD ellipticity. A recommendation on how to use the procedure is outlined.
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Affiliation(s)
- Josefine H Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Christof Hättig
- Arbeitsgruppe Quantenchemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Cerezo J, Santoro F. FCclasses3: Vibrationally-resolved spectra simulated at the edge of the harmonic approximation. J Comput Chem 2023; 44:626-643. [PMID: 36380723 PMCID: PMC10100349 DOI: 10.1002/jcc.27027] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/03/2022] [Accepted: 10/16/2022] [Indexed: 11/17/2022]
Abstract
We introduce FCclasses3, a code to carry out vibronic simulations of electronic spectra and nonradiative rates, based on the harmonic approximation. Key new features are: implementation of the full family of vertical and adiabatic harmonic models, vibrational analysis in curvilinear coordinates, extension to several electronic spectroscopies and implementation of time-dependent approaches. The use of curvilinear valence internal coordinates allows the adoption of quadratic model potential energy surfaces (PES) of the initial and final states expanded at arbitrary configurations. Moreover, the implementation of suitable projectors provides a robust framework for defining reduced-dimensionality models by sorting flexible coordinates out of the harmonic subset, so that they can then be treated at anharmonic level, or with mixed quantum classical approaches. A set of tools to facilitate input preparation and output analysis is also provided. We show the program at work in the simulation of different spectra (one and two-photon absorption, emission and resonance Raman) and internal conversion rate of a typical rigid molecule, anthracene. Then, we focus on absorption and emission spectra of a series of flexible polyphenyl molecules, highlighting the relevance of some of the newly implemented features. The code is freely available at http://www.iccom.cnr.it/en/fcclasses/.
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Affiliation(s)
- Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de MadridMadridSpain
- Consiglio Nazionale delle RicercheIstituto di Chimica dei Composti Organo Metallici (ICCOM‐CNR)PisaItaly
| | - Fabrizio Santoro
- Consiglio Nazionale delle RicercheIstituto di Chimica dei Composti Organo Metallici (ICCOM‐CNR)PisaItaly
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5
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Kaminský J, Andrushchenko V, Bouř P. Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment. RSC Adv 2021; 11:8411-8419. [PMID: 35423314 PMCID: PMC8695171 DOI: 10.1039/d1ra00076d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/30/2022] Open
Abstract
Chiroptical spectroscopic methods are excellent tools to study structure and interactions of biomolecules. However, their sensitivity to different structural aspects varies. To understand the dependence of absorption, electronic and magnetic circular dichroism (ECD, MCD) intensities on the structure, dynamics and environment, we measured and simulated spectra of nucleosides and other nucleic acid model components. The conformation space was explored by molecular dynamics (MD), the electronic spectra were generated using time dependent density functional theory (TDDFT). The sum over state (SOS) method was employed for MCD. The results show that accounting for the dynamics is crucial for reproduction of the experiment. While unpolarized absorption spectroscopy is relatively indifferent, ECD reflects the conformation and geometry dispersion more. MCD spectra provide variable response dependent on the wavelength and structural change. In general, MCD samples the structure more locally than ECD. Simple computational tests suggest that the optical spectroscopies coupled with the computational tools provide useful information about nucleic acid components, including base pairing and stacking.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Valery Andrushchenko
- 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
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6
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Ghidinelli S, Abbate S, Mazzeo G, Paoloni L, Viola E, Ercolani C, Donzello MP, Longhi G. Characterization of tetrakis(thiadiazole)porphyrazine metal complexes by magnetic circular dichroism and magnetic circularly polarized luminescence. Chirality 2020; 32:808-816. [PMID: 32189418 DOI: 10.1002/chir.23221] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/11/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
The magnetic circular dichroism (MCD) spectra of metal complexes of tetrakis(thiadiazole)porphyrazines ([TTDPzM] with M = 2HI , ZnII , MgII (H2 O), and CdII ) have been recorded in dimethyl formamide solution. Together with the UV-Vis spectra, the MCD spectra provide useful information about the structure and electronic properties of the complexes. The experimental UV-Vis and MCD spectra compare pretty well with DFT calculations of two sorts, based either on the sum-over-states (SOS) approach or on the complex polarization propagator approach. They further corroborate the findings and interpretation of MCD spectra of porphyrazines based on the model of Michl for peripheral molecular orbitals. Magnetic circularly polarized luminescence (MCPL) spectra, quite uncommon in the literature, have been recorded for [TTDPzM] (M = 2HI , ZnII , MgII (H2 O)).
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Affiliation(s)
- Simone Ghidinelli
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy.,Unit of Brescia, Consiglio Nazionale delle Ricerche-I.N.O. c/o CSMT, Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | | | - Elisa Viola
- Dipartimento di Chimica, Università di Roma Sapienza, Rome, Italy
| | - Claudio Ercolani
- Dipartimento di Chimica, Università di Roma Sapienza, Rome, Italy
| | | | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy.,Unit of Brescia, Consiglio Nazionale delle Ricerche-I.N.O. c/o CSMT, Brescia, Italy
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7
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Hashimoto S, Tahara K. Theoretical Study on the Geometry, Aromaticity, and Electronic Properties of Benzo[3,4]cyclobutathiophenes and Their Homologues. J Org Chem 2019; 84:9850-9858. [PMID: 31310116 DOI: 10.1021/acs.joc.9b00661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The geometry, aromaticity, and electronic properties of benzo[3,4]cyclobutathiophenes (BCTs) and their homologues have been examined theoretically using density functional theory calculations. The harmonic oscillator measure of aromaticity and nucleus-independent chemical shift analyses revealed the aromaticity characteristics of the two regioisomers benzo[3,4]cyclobuta[1,2-b]thiophene and benzo[3,4]cyclobuta[1,2-c]thiophene. When the aromaticity of one of the six-π-electron rings increases, it concomitantly decreases in the other ring. The anti-aromaticity of the four-membered ring varies depending on the π-electron density of the shared bond with the thiophene ring. This leads to a large difference of the highest occupied molecular orbital-lowest unoccupied molecular orbital gap between the isomers. Linear BCT homologues show medium diradical characters and the smallest EGap values. In the angular and branched homologues, the π-electrons of central benzene rings are localized avoiding the shared bonds, which results in a nonaromatic character. These data were compared to those of the parent hydrocarbons. Because of the diene character of the thiophene ring, the number and position of annulated thiophenocyclobutadieno moieties significantly influence the aromaticity and EGap values of BCT homologues. The present study does not only provide insight into the aromaticity and the properties of organic compounds containing four-membered rings but also affords helpful design guidelines of novel organic semiconductors.
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Affiliation(s)
- Shingo Hashimoto
- Department of Applied Chemistry, School of Science and Technology , Meiji University , 1-1-1 Higashimita , Tama-ku, Kawasaki , Kanagawa 214-8571 , Japan
| | - Kazukuni Tahara
- Department of Applied Chemistry, School of Science and Technology , Meiji University , 1-1-1 Higashimita , Tama-ku, Kawasaki , Kanagawa 214-8571 , Japan
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8
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Heit YN, Sergentu DC, Autschbach J. Magnetic circular dichroism spectra of transition metal complexes calculated from restricted active space wavefunctions. Phys Chem Chem Phys 2019; 21:5586-5597. [DOI: 10.1039/c8cp07849a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Multiconfigurational restricted active space (RAS) self-consistent field (SCF) or configuration interaction (CI) approaches, augmented with a treatment of spin–orbit coupling by state interaction, were used to calculate the magnetic circular dichroism , , and/or for closed- and open-shell transition metal complexes.
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Affiliation(s)
- Yonaton N. Heit
- Department of Chemistry
- University at Buffalo, State University of New York
- Buffalo
- USA
| | | | - Jochen Autschbach
- Department of Chemistry
- University at Buffalo, State University of New York
- Buffalo
- USA
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9
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Keiderling TA, Bouř P. Theory of Molecular Vibrational Zeeman Effects as Measured with Circular Dichroism. PHYSICAL REVIEW LETTERS 2018; 121:073201. [PMID: 30169061 DOI: 10.1103/physrevlett.121.073201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 06/08/2023]
Abstract
We present a general theory that enables the first nonempirical computation of molecular vibrational Zeeman effects as are detectable with magnetic vibrational circular dichroism spectroscopy (MVCD). In this method, the second derivatives of the molecular magnetic moment appear to be essential to determine the observable MVCD intensities. Using a quasiharmonic approximation, computations based on our method allowed a band-to-band comparison of simulated to measured spectra. Given this new possibility of its reliable interpretation, MVCD spectroscopy may develop as a useful tool to yield detailed information on molecular vibrational states and structure, including achiral systems.
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Affiliation(s)
- Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, USA
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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10
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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.
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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
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11
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Kaminský J, Kříž J, Bouř P. On the magnetic circular dichroism of benzene. A density-functional study. J Chem Phys 2017; 146:144301. [PMID: 28411621 DOI: 10.1063/1.4979570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Spectroscopy of magnetic circular dichroism (MCD) provides enhanced information on molecular structure and a more reliable assignment of spectral bands than absorption alone. Theoretical modeling can significantly enhance the information obtained from experimental spectra. In the present study, the time dependent density functional theory is employed to model the lowest-energy benzene transitions, in particular to investigate the role of the Rydberg states and vibrational interference in spectral intensities. The effect of solvent is explored on model benzene-methane clusters. For the lowest-energy excitation, the vibrational sub-structure of absorption and MCD spectra is modeled within the harmonic approximation, providing a very good agreement with the experiment. The simulations demonstrate that the Rydberg states have a much stronger effect on the MCD intensities than on the absorption, and a very diffuse basis set must be used to obtain reliable results. The modeling also indicates that the Rydberg-like states and associated transitions may persist in solutions. Continuum-like solvent models are thus not suitable for their modeling; solvent-solute clusters appear to be more appropriate, providing they are large enough.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo Náměstí 2, 16610 Prague, Czech Republic
| | - 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
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12
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Martinez-Fernandez L, Fahleson T, Norman P, Santoro F, Coriani S, Improta R. Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution. Photochem Photobiol Sci 2017; 16:1415-1423. [DOI: 10.1039/c7pp00105c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The excited electronic states of thiouracils, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the TD-DFT level of theory.
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Affiliation(s)
| | - T. Fahleson
- KTH Royal Institute of Technology
- SE-10044 Stockholm
- Sweden
| | - P. Norman
- KTH Royal Institute of Technology
- SE-10044 Stockholm
- Sweden
| | - F. Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR)
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
| | - S. Coriani
- Department of Chemistry
- Technical University of Denmark
- Denmark
| | - R. Improta
- Istituto di Biostrutture e Bioimmagini-CNR
- I-80134 Napoli
- Italy
- LIDYL
- CEA
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13
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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.
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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.
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14
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Santoro F, Jacquemin D. Going beyond the vertical approximation with time-dependent density functional theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1260] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche; Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR); Pisa Italy
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230; Université de Nantes; Nantes France
- Institut Universitaire de France; Paris France
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15
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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]
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16
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Fahleson T, Kauczor J, Norman P, Santoro F, Improta R, Coriani S. TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids. J Phys Chem A 2015; 119:5476-89. [DOI: 10.1021/jp512468k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Tobias Fahleson
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Joanna Kauczor
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Patrick Norman
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM−CNR), Area della Ricerca del CNR, Via
Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 6, I-80134 Napoli, Italy
| | - Sonia Coriani
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy
- Aarhus Institute of Advanced Studies, Aarhus University, DK-8000 Aarhus C, Denmark
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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
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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]
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