Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

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

Journal Article · · Faraday Discussions
DOI:https://doi.org/10.1039/c7fd00201g· OSTI ID:1539939
 [1];  [2];  [2];  [3];  [2];  [4];  [2];  [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
+ Show Author Affiliations

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.

Research Organization:
Univ. of California, Irvine, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
DOE Contract Number:
FG02-04ER15571
OSTI ID:
1539939
Journal Information:
Faraday Discussions, Vol. 207; ISSN 1359-6640
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English

References (60)

Using coherence to enhance function in chemical and biophysical systems journal March 2017
Ultrafast Excited-State Dynamics in Nucleic Acids journal April 2004
Fluorescence of DNA Duplexes: From Model Helices to Natural DNA journal October 2010
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
Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases journal November 2010
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
UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair journal December 2015
Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy journal February 2014
Two-dimensional sum-frequency generation (2D SFG) spectroscopy: summary of principles and its application to amyloid fiber monolayers journal January 2015
Probing Ultrafast Dynamics in Adenine With Mid-UV Four-Wave Mixing Spectroscopies journal August 2011
Two-Dimensional Electronic Spectroscopy in the Ultraviolet Wavelength Range journal August 2012
New Insights into the Photophysics of DNA Nucleobases journal October 2016
Ab initio simulations of two-dimensional electronic spectra: The SOS//QM/MM approach journal July 2013
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
Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate journal April 2016
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
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
Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy journal June 2015
Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table : Molcas 8 journal November 2015
The restricted active space self-consistent-field method, implemented with a split graph unitary group approach journal July 1990
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
Multiconfigurational Second-Order Perturbation Theory Restricted Active Space (RASPT2) Method for Electronic Excited States: A Benchmark Study journal December 2010
Unbiased auxiliary basis sets for accurate two-electron integral approximations journal September 2007
Low-cost evaluation of the exchange Fock matrix from Cholesky and density fitting representations of the electron repulsion integrals journal May 2007
Density fitting with auxiliary basis sets from Cholesky decompositions journal July 2009
Density matrix averaged atomic natural orbital (ANO) basis sets for correlated molecular wave functions: II. Second row atoms journal January 1991
Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate journal April 2015
Multiconfiguration perturbation theory with imaginary level shift journal August 1997
The IPEA dilemma in CASPT2 journal January 2017
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
Simulation of Multi-Dimensional Signals in the Optical Domain: Quantum-Classical Feedback in Nonlinear Exciton Propagation journal June 2016
Spectral lineshapes in nonlinear electronic spectroscopy journal January 2015
Surface hopping modeling of two-dimensional spectra journal April 2013
Calculating Two-Dimensional Spectra with the Mixed Quantum-Classical Ehrenfest Method journal February 2013
Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime journal September 2017
Ultrafast Excited-State Dynamics of Adenine and Monomethylated Adenines in Solution:  Implications for the Nonradiative Decay Mechanism journal November 2003
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
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
Resolving Ultrafast Photoinduced Deactivations in Water-Solvated Pyrimidine Nucleosides journal April 2017
Photophysics of Deoxycytidine and 5-Methyldeoxycytidine in Solution: A Comprehensive Picture by Quantum Mechanical Calculations and Femtosecond Fluorescence Spectroscopy journal June 2017
Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra journal April 2016
Intramolecular Base Stacking of Dinucleoside Monophosphate Anions in Aqueous Solution journal March 2012
Heterogeneous Exciton Dynamics Revealed by Two-Dimensional Optical Spectroscopy † journal October 2006
Two-Dimensional Electronic Spectroscopy of Molecular Aggregates journal September 2009
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
Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations journal January 2015
Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models journal August 2016
Simulation of photo-excited adenine in water with a hierarchy of equations of motion approach journal August 2017
Base-Stacking Disorder and Excited-State Dynamics in Single-Stranded Adenine Homo-oligonucleotides journal August 2012

Similar Records

Related Subjects

Chemistry