1
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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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2
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Asha H, Green JA, Esposito L, Martinez-Fernandez L, Santoro F, Improta R. Effect of the Thermal Fluctuations of the Photophysics of GC and CG DNA Steps: A Computational Dynamical Study. J Phys Chem B 2022; 126:10608-10621. [PMID: 36508709 DOI: 10.1021/acs.jpcb.2c05688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC)5 sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50-100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.
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Affiliation(s)
- Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438Frankfurt am Main, Germany
| | - Luciana Esposito
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autònoma de Madrid, Campus de Excelencia UAM-CSIC, 28049Madrid, Spain
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800Kongens Lyngby, Denmark
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3
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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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4
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Martínez-Fernández L, Esposito L, Improta R. Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives. Photochem Photobiol Sci 2020; 19:436-444. [DOI: 10.1039/d0pp00065e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química
- Facultad de Ciencias
- Modulo 13 Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC Cantoblanco
- 28049 Madrid
| | | | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini
- CNR
- I-80134 Napoli
- Italy
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5
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Rinkevicius Z, Li X, Vahtras O, Ahmadzadeh K, Brand M, Ringholm M, List NH, Scheurer M, Scott M, Dreuw A, Norman P. VeloxChem: A Python‐driven density‐functional theory program for spectroscopy simulations in high‐performance computing environments. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
- Department of Physics Kaunas University of Technology Kaunas Lithuania
| | - Xin Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Olav Vahtras
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Karan Ahmadzadeh
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Manuel Brand
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Magnus Ringholm
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Nanna Holmgaard List
- Department of Chemistry and the PULSE Institute Stanford University Stanford California
- SLAC National Accelerator Laboratory Menlo Park California
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing Ruprecht‐Karls University Heidelberg Germany
| | - Mikael Scott
- Interdisciplinary Center for Scientific Computing Ruprecht‐Karls University Heidelberg Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing Ruprecht‐Karls University Heidelberg Germany
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
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6
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Hognon C, Besancenot V, Gruez A, Grandemange S, Monari A. Cooperative Effects of Cytosine Methylation on DNA Structure and Dynamics. J Phys Chem B 2019; 123:7365-7371. [PMID: 31365827 DOI: 10.1021/acs.jpcb.9b05835] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The behavior of the structural parameters of DNA considering different levels of methylation in CpG islands is studied by means of full-atom molecular dynamics simulations and electronic circular dichroism, both in an artificial model system and in a gene promoter sequence. It is demonstrated that methylation although intrinsically brings quite local perturbations may, if its level is high enough, induce cooperative effects that strongly modify the DNA backbone torsional parameters altering the helicity as compared to the nonmethylated case. Because methylation of the CpG island is correlated with the regulation of gene expression, understanding the structural modifications induced in DNA is crucial to characterize all the fine equilibria into play in epigenetics phenomena.
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Affiliation(s)
- Cécilia Hognon
- Université de Lorraine and CNRS, UMR 7019 LPCT , F-54000 Nancy , France
| | | | - Arnaud Gruez
- Université de Lorraine and CNRS, UMR 7356 IMOPA , F-54000 Nancy , France
| | | | - Antonio Monari
- Université de Lorraine and CNRS, UMR 7019 LPCT , F-54000 Nancy , France
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7
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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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8
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Van Beeumen R, Williams-Young DB, Kasper JM, Yang C, Ng EG, Li X. Model Order Reduction Algorithm for Estimating the Absorption Spectrum. J Chem Theory Comput 2017; 13:4950-4961. [PMID: 28862869 DOI: 10.1021/acs.jctc.7b00402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ab initio description of the spectral interior of the absorption spectrum poses both a theoretical and computational challenge for modern electronic structure theory. Due to the often spectrally dense character of this domain in the quantum propagator's eigenspectrum for medium-to-large sized systems, traditional approaches based on the partial diagonalization of the propagator often encounter oscillatory and stagnating convergence. Electronic structure methods which solve the molecular response problem through the solution of spectrally shifted linear systems, such as the complex polarization propagator, offer an alternative approach which is agnostic to the underlying spectral density or domain location. This generality comes at a seemingly high computational cost associated with solving a large linear system for each spectral shift in some discretization of the spectral domain of interest. In this work, we present a novel, adaptive solution to this high computational overhead based on model order reduction techniques via interpolation. Model order reduction reduces the computational complexity of mathematical models and is ubiquitous in the simulation of dynamical systems and control theory. The efficiency and effectiveness of the proposed algorithm in the ab initio prediction of X-ray absorption spectra is demonstrated using a test set of challenging water clusters which are spectrally dense in the neighborhood of the oxygen K-edge. On the basis of a single, user defined tolerance we automatically determine the order of the reduced models and approximate the absorption spectrum up to the given tolerance. We also illustrate that, for the systems studied, the automatically determined model order increases logarithmically with the problem dimension, compared to a linear increase of the number of eigenvalues within the energy window. Furthermore, we observed that the computational cost of the proposed algorithm only scales quadratically with respect to the problem dimension.
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Affiliation(s)
- Roel Van Beeumen
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - David B Williams-Young
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Joseph M Kasper
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Chao Yang
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Esmond G Ng
- Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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9
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Gattuso H, García-Iriepa C, Sampedro D, Monari A, Marazzi M. Simulating the Electronic Circular Dichroism Spectra of Photoreversible Peptide Conformations. J Chem Theory Comput 2017; 13:3290-3296. [DOI: 10.1021/acs.jctc.7b00163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hugo Gattuso
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Cristina García-Iriepa
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
- Unidad
Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Diego Sampedro
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
| | - Antonio Monari
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Marco Marazzi
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
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10
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Padula D, Jurinovich S, Di Bari L, Mennucci B. Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum. Chemistry 2016; 22:17011-17019. [PMID: 27699878 DOI: 10.1002/chem.201602777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Indexed: 12/18/2022]
Abstract
We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.
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Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
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11
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Loco D, Jurinovich S, Di Bari L, Mennucci B. A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved? Phys Chem Chem Phys 2016; 18:866-77. [PMID: 26646952 DOI: 10.1039/c5cp06341h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties.
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Affiliation(s)
- Daniele Loco
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
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12
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Gattuso H, Spinello A, Terenzi A, Assfeld X, Barone G, Monari A. Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures. J Phys Chem B 2016; 120:3113-21. [DOI: 10.1021/acs.jpcb.6b00634] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hugo Gattuso
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Angelo Spinello
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
| | - Alessio Terenzi
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
- Institute
of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, Vienna, Austria
| | - Xavier Assfeld
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Giampaolo Barone
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
| | - Antonio Monari
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
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13
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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