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Title: Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

Abstract

A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry.

Authors:
ORCiD logo [1];  [2];  [2]; ORCiD logo [3];  [2];  [4]; ORCiD logo [2]; ORCiD logo [1]
  1. Univ Lyon, Ens de Lyon, CNRS; Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 5182; Lyon; France
  2. Dipartimento di Chimica Industriale “Toso Montanari”; Università di Bologna; Italy
  3. Department of Chemistry; University College London; London WC1H 0AJ; UK
  4. Department of Chemistry; University of California; Irvine; USA
Publication Date:
Research Org.:
Univ. of California, Irvine, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1539939
DOE Contract Number:  
FG02-04ER15571
Resource Type:
Journal Article
Journal Name:
Faraday Discussions
Additional Journal Information:
Journal Volume: 207; Journal ID: ISSN 1359-6640
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
Chemistry

Citation Formats

Segarra-Martí, Javier, Jaiswal, Vishal K., Pepino, Ana Julieta, Giussani, Angelo, Nenov, Artur, Mukamel, Shaul, Garavelli, Marco, and Rivalta, Ivan. Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates. United States: N. p., 2018. Web. doi:10.1039/c7fd00201g.
Segarra-Martí, Javier, Jaiswal, Vishal K., Pepino, Ana Julieta, Giussani, Angelo, Nenov, Artur, Mukamel, Shaul, Garavelli, Marco, & Rivalta, Ivan. Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates. United States. doi:10.1039/c7fd00201g.
Segarra-Martí, Javier, Jaiswal, Vishal K., Pepino, Ana Julieta, Giussani, Angelo, Nenov, Artur, Mukamel, Shaul, Garavelli, Marco, and Rivalta, Ivan. Mon . "Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates". United States. doi:10.1039/c7fd00201g.
@article{osti_1539939,
title = {Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates},
author = {Segarra-Martí, Javier and Jaiswal, Vishal K. and Pepino, Ana Julieta and Giussani, Angelo and Nenov, Artur and Mukamel, Shaul and Garavelli, Marco and Rivalta, Ivan},
abstractNote = {A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry.},
doi = {10.1039/c7fd00201g},
journal = {Faraday Discussions},
issn = {1359-6640},
number = ,
volume = 207,
place = {United States},
year = {2018},
month = {1}
}

Works referenced in this record:

Using coherence to enhance function in chemical and biophysical systems
journal, March 2017

  • Scholes, Gregory D.; Fleming, Graham R.; Chen, Lin X.
  • Nature, Vol. 543, Issue 7647
  • DOI: 10.1038/nature21425

Ultrafast Excited-State Dynamics in Nucleic Acids
journal, April 2004

  • Crespo-Hernández, Carlos E.; Cohen, Boiko; Hare, Patrick M.
  • Chemical Reviews, Vol. 104, Issue 4
  • DOI: 10.1021/cr0206770

Fluorescence of DNA Duplexes: From Model Helices to Natural DNA
journal, October 2010

  • Markovitsi, Dimitra; Gustavsson, Thomas; Vayá, Ignacio
  • The Journal of Physical Chemistry Letters, Vol. 1, Issue 22
  • DOI: 10.1021/jz101122t

Early Events of DNA Photodamage
journal, April 2015


Thymine Dimerization in DNA Is an Ultrafast Photoreaction
journal, February 2007


UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases
journal, July 2008

  • Takaya, T.; Su, C.; de La Harpe, K.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 30
  • DOI: 10.1073/pnas.0802079105

Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases
journal, November 2010

  • Barbatti, M.; Aquino, A. J. A.; Szymczak, J. J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 50
  • DOI: 10.1073/pnas.1014982107

Are the five natural DNA/RNA base monomers a good choice from natural selection?
journal, March 2009


Charge separation and charge delocalization identified in long-living states of photoexcited DNA
journal, March 2014

  • Bucher, D. B.; Pilles, B. M.; Carell, T.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 12
  • DOI: 10.1073/pnas.1323700111

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
journal, December 2015

  • Bucher, Dominik Benjamin; Kufner, Corinna Lucia; Schlueter, Alexander
  • Journal of the American Chemical Society, Vol. 138, Issue 1
  • DOI: 10.1021/jacs.5b09753

Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy
journal, February 2014

  • Buchanan, L. E.; Carr, J. K.; Fluitt, A. M.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 16
  • DOI: 10.1073/pnas.1401587111

Two-dimensional sum-frequency generation (2D SFG) spectroscopy: summary of principles and its application to amyloid fiber monolayers
journal, January 2015

  • Ghosh, Ayanjeet; Ho, Jia-Jung; Serrano, Arnaldo L.
  • Faraday Discussions, Vol. 177
  • DOI: 10.1039/C4FD00173G

Probing Ultrafast Dynamics in Adenine With Mid-UV Four-Wave Mixing Spectroscopies
journal, August 2011

  • West, Brantley A.; Womick, Jordan M.; Moran, Andrew M.
  • The Journal of Physical Chemistry A, Vol. 115, Issue 31
  • DOI: 10.1021/jp204416m

Two-Dimensional Electronic Spectroscopy in the Ultraviolet Wavelength Range
journal, August 2012

  • West, Brantley A.; Moran, Andrew M.
  • The Journal of Physical Chemistry Letters, Vol. 3, Issue 18
  • DOI: 10.1021/jz301048n

New Insights into the Photophysics of DNA Nucleobases
journal, October 2016

  • Prokhorenko, Valentyn I.; Picchiotti, Alessandra; Pola, Martina
  • The Journal of Physical Chemistry Letters, Vol. 7, Issue 22
  • DOI: 10.1021/acs.jpclett.6b02085

Ab initio simulations of two-dimensional electronic spectra: The SOS//QM/MM approach
journal, July 2013

  • Rivalta, Ivan; Nenov, Artur; Cerullo, Giulio
  • International Journal of Quantum Chemistry, Vol. 114, Issue 2
  • DOI: 10.1002/qua.24511

M ULTIDIMENSIONAL F EMTOSECOND C ORRELATION S PECTROSCOPIES OF E LECTRONIC AND V IBRATIONAL E XCITATIONS
journal, October 2000


Tracking the primary photoconversion events in rhodopsins by ultrafast optical spectroscopy
journal, January 2015

  • Polli, D.; Rivalta, I.; Nenov, A.
  • Photochemical & Photobiological Sciences, Vol. 14, Issue 2
  • DOI: 10.1039/C4PP00370E

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate
journal, April 2016

  • Li, Quansong; Giussani, Angelo; Segarra-Martí, Javier
  • Chemistry - A European Journal, Vol. 22, Issue 22
  • DOI: 10.1002/chem.201505086

Tracking Conformational Dynamics of Polypeptides by Nonlinear Electronic Spectroscopy of Aromatic Residues: A First-Principles Simulation Study
journal, August 2014


The Amber biomolecular simulation programs
journal, January 2005

  • Case, David A.; Cheatham, Thomas E.; Darden, Tom
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20290

Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
journal, June 2007


Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy
journal, June 2015

  • Nenov, Artur; Giussani, Angelo; Segarra-Martí, Javier
  • The Journal of Chemical Physics, Vol. 142, Issue 21
  • DOI: 10.1063/1.4921016

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table : Molcas 8
journal, November 2015

  • Aquilante, Francesco; Autschbach, Jochen; Carlson, Rebecca K.
  • Journal of Computational Chemistry, Vol. 37, Issue 5
  • DOI: 10.1002/jcc.24221

The restricted active space self-consistent-field method, implemented with a split graph unitary group approach
journal, July 1990

  • Malmqvist, Per Aake.; Rendell, Alistair.; Roos, Bjoern O.
  • The Journal of Physical Chemistry, Vol. 94, Issue 14
  • DOI: 10.1021/j100377a011

The restricted active space followed by second-order perturbation theory method: Theory and application to the study of CuO2 and Cu2O2 systems
journal, May 2008

  • Malmqvist, Per Åke; Pierloot, Kristine; Shahi, Abdul Rehaman Moughal
  • The Journal of Chemical Physics, Vol. 128, Issue 20
  • DOI: 10.1063/1.2920188

Multiconfigurational Second-Order Perturbation Theory Restricted Active Space (RASPT2) Method for Electronic Excited States: A Benchmark Study
journal, December 2010

  • Sauri, Vicenta; Serrano-Andrés, Luis; Shahi, Abdul Rehaman Moughal
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 1
  • DOI: 10.1021/ct100478d

Unbiased auxiliary basis sets for accurate two-electron integral approximations
journal, September 2007

  • Aquilante, Francesco; Lindh, Roland; Bondo Pedersen, Thomas
  • The Journal of Chemical Physics, Vol. 127, Issue 11
  • DOI: 10.1063/1.2777146

Low-cost evaluation of the exchange Fock matrix from Cholesky and density fitting representations of the electron repulsion integrals
journal, May 2007

  • Aquilante, Francesco; Pedersen, Thomas Bondo; Lindh, Roland
  • The Journal of Chemical Physics, Vol. 126, Issue 19
  • DOI: 10.1063/1.2736701

Density fitting with auxiliary basis sets from Cholesky decompositions
journal, July 2009

  • Pedersen, Thomas Bondo; Aquilante, Francesco; Lindh, Roland
  • Theoretical Chemistry Accounts, Vol. 124, Issue 1-2
  • DOI: 10.1007/s00214-009-0608-y

Density matrix averaged atomic natural orbital (ANO) basis sets for correlated molecular wave functions: II. Second row atoms
journal, January 1991

  • Widmark, Per-Olof; Persson, B. Joakim; Roos, Bj�rn O.
  • Theoretica Chimica Acta, Vol. 79, Issue 6
  • DOI: 10.1007/BF01112569

Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate
journal, April 2015

  • Altavilla, Salvatore F.; Segarra-Martí, Javier; Nenov, Artur
  • Frontiers in Chemistry, Vol. 3
  • DOI: 10.3389/fchem.2015.00029

Multiconfiguration perturbation theory with imaginary level shift
journal, August 1997


A modified definition of the zeroth-order Hamiltonian in multiconfigurational perturbation theory (CASPT2)
journal, September 2004


The CASSCF state interaction method
journal, February 1989


The restricted active space (RAS) state interaction approach with spin–orbit coupling
journal, May 2002


Sum-over-states versus quasiparticle pictures of coherent correlation spectroscopy of excitons in semiconductors: Femtosecond analogs of multidimensional NMR
journal, June 2007


Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule Perspectives
journal, June 2009

  • Abramavicius, Darius; Palmieri, Benoit; Voronine, Dmitri V.
  • Chemical Reviews, Vol. 109, Issue 6
  • DOI: 10.1021/cr800268n

Simulation of Multi-Dimensional Signals in the Optical Domain: Quantum-Classical Feedback in Nonlinear Exciton Propagation
journal, June 2016

  • Richter, Martin; Fingerhut, Benjamin P.
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 7
  • DOI: 10.1021/acs.jctc.6b00371

Spectral lineshapes in nonlinear electronic spectroscopy
journal, January 2015

  • Nenov, Artur; Giussani, Angelo; Fingerhut, Benjamin P.
  • Physical Chemistry Chemical Physics, Vol. 17, Issue 46
  • DOI: 10.1039/C5CP01167A

Surface hopping modeling of two-dimensional spectra
journal, April 2013

  • Tempelaar, Roel; van der Vegte, Cornelis P.; Knoester, Jasper
  • The Journal of Chemical Physics, Vol. 138, Issue 16
  • DOI: 10.1063/1.4801519

Calculating Two-Dimensional Spectra with the Mixed Quantum-Classical Ehrenfest Method
journal, February 2013

  • van der Vegte, C. P.; Dijkstra, A. G.; Knoester, J.
  • The Journal of Physical Chemistry A, Vol. 117, Issue 29
  • DOI: 10.1021/jp311668r

Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime
journal, September 2017

  • Kowalewski, Markus; Fingerhut, Benjamin P.; Dorfman, Konstantin E.
  • Chemical Reviews, Vol. 117, Issue 19
  • DOI: 10.1021/acs.chemrev.7b00081

Ultrafast Excited-State Dynamics of Adenine and Monomethylated Adenines in Solution:  Implications for the Nonradiative Decay Mechanism
journal, November 2003

  • Cohen, Boiko; Hare, Patrick M.; Kohler, Bern
  • Journal of the American Chemical Society, Vol. 125, Issue 44
  • DOI: 10.1021/ja035628z

Adenine, deoxyadenosine and deoxyadenosine 5′-monophosphate studied by femtosecond fluorescence upconversion spectroscopy
journal, April 2002


Relative Stability of the L a and L b Excited States in Adenine and Guanine: Direct Evidence from TD-DFT Calculations of MCD Spectra
journal, May 2014

  • Santoro, Fabrizio; Improta, Roberto; Fahleson, Tobias
  • The Journal of Physical Chemistry Letters, Vol. 5, Issue 11
  • DOI: 10.1021/jz500633t

Benchmark Studies on the Building Blocks of DNA. 1. Superiority of Coupled Cluster Methods in Describing the Excited States of Nucleobases in the Franck–Condon Region
journal, May 2012

  • Szalay, Péter G.; Watson, Thomas; Perera, Ajith
  • The Journal of Physical Chemistry A, Vol. 116, Issue 25
  • DOI: 10.1021/jp300977a

Resolving Ultrafast Photoinduced Deactivations in Water-Solvated Pyrimidine Nucleosides
journal, April 2017

  • Pepino, Ana Julieta; Segarra-Martí, Javier; Nenov, Artur
  • The Journal of Physical Chemistry Letters, Vol. 8, Issue 8
  • DOI: 10.1021/acs.jpclett.7b00316

Photophysics of Deoxycytidine and 5-Methyldeoxycytidine in Solution: A Comprehensive Picture by Quantum Mechanical Calculations and Femtosecond Fluorescence Spectroscopy
journal, June 2017

  • Martínez-Fernández, L.; Pepino, A. J.; Segarra-Martí, J.
  • Journal of the American Chemical Society, Vol. 139, Issue 23
  • DOI: 10.1021/jacs.7b01145

Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra
journal, April 2016

  • Giussani, Angelo; Segarra-Martí, Javier; Nenov, Artur
  • Theoretical Chemistry Accounts, Vol. 135, Issue 5
  • DOI: 10.1007/s00214-016-1867-z

Intramolecular Base Stacking of Dinucleoside Monophosphate Anions in Aqueous Solution
journal, March 2012

  • Jafilan, Salem; Klein, Leah; Hyun, Christian
  • The Journal of Physical Chemistry B, Vol. 116, Issue 11
  • DOI: 10.1021/jp209986y

Heterogeneous Exciton Dynamics Revealed by Two-Dimensional Optical Spectroscopy
journal, October 2006

  • Stiopkin, Igor; Brixner, Tobias; Yang, Mino
  • The Journal of Physical Chemistry B, Vol. 110, Issue 40
  • DOI: 10.1021/jp062882f

Two-Dimensional Electronic Spectroscopy of Molecular Aggregates
journal, September 2009

  • Ginsberg, Naomi S.; Cheng, Yuan-Chung; Fleming, Graham R.
  • Accounts of Chemical Research, Vol. 42, Issue 9
  • DOI: 10.1021/ar9001075

Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back
journal, January 2015

  • Conti, Irene; Nenov, Artur; Höfinger, Siegfried
  • Phys. Chem. Chem. Phys., Vol. 17, Issue 11
  • DOI: 10.1039/C4CP05546B

Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations
journal, January 2015

  • Nenov, Artur; Segarra-Martí, Javier; Giussani, Angelo
  • Faraday Discussions, Vol. 177
  • DOI: 10.1039/C4FD00175C

Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models
journal, August 2016

  • Martínez-Fernández, L.; Pepino, A. J.; Segarra-Martí, J.
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 9
  • DOI: 10.1021/acs.jctc.6b00518

Simulation of photo-excited adenine in water with a hierarchy of equations of motion approach
journal, August 2017

  • Dijkstra, Arend G.; Prokhorenko, Valentyn I.
  • The Journal of Chemical Physics, Vol. 147, Issue 6
  • DOI: 10.1063/1.4997433

Base-Stacking Disorder and Excited-State Dynamics in Single-Stranded Adenine Homo-oligonucleotides
journal, August 2012

  • Su, Charlene; Middleton, Chris T.; Kohler, Bern
  • The Journal of Physical Chemistry B, Vol. 116, Issue 34
  • DOI: 10.1021/jp305350t