skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments

Abstract

Accurate description of the ionization process in DNA is crucial to the understanding of the DNA damage under exposure to ionizing radiation, as well as to the exploration of the potential application of DNA strands in nano-electronics. During the last years, relevant studies have been focused on the lowest ($i.e.$ the first) valence ionization energies (VIE) of DNA bases-related species, while a clear picture of a broader ionization spectrum of longer sequence is still missing. Theoretically, this requires applying highly accurate and predictable methods on a relatively large system size ($e.g.$ several base pairs), of which the computational complexity prohibits most of the practices. In this work, by employing our recently developed Green's function coupled-cluster (GFCC) library on supercomputing facilities, we have studied the spectral functions of several guanine$-$cytosine (G$-$C) base pair structures ([G$-$C]$$_n$$, $n=1-3$) in a relatively broad near-valence regime ($$-25\sim-5$$ eV) in the coupled-cluster with singles and doubles (CCSD) level. Our focus is to give a many-body understanding of the spectral profile and feature change as the system size expands in this regime. The results show that, for the considered G$-$C base pairs, even though the lowest VIE keeps reducing as the system size expands, the spectral function profiles of all three G$-$C base pairs are very much alike in the considered regime, and the relative peak positions didn't vary by more than 0.2 eV. Further analysis of the second ionized state for each G$-$C base pair shows the total 2$h$$-$1$p$ components could contribute up to $$\sim$$9\% of the corresponding ionized state as more G$-$C base pairs being stacked, of which the leading 2$h$$-$1$p$ components feature a transition from the intra-base-pair cytosine $$\pi\rightarrow\pi^\ast$$ excitation in single layer [G$-$C]$$_1$$ to the inter-base-pair electron excitation in multi-layer [G$-$C]$$_2$$ and [G$-$C]$$_3$$.

Authors:
 [1];  [1]; ORCiD logo [1];  [1]
  1. BATTELLE (PACIFIC NW LAB)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1599991
Report Number(s):
PNNL-SA-148915
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 152; Journal Issue: 1
Country of Publication:
United States
Language:
English

Citation Formats

Peng, Bo, Kowalski, Karol, Panyala, Ajay R., and Krishnamoorthy, Sriram. Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments. United States: N. p., 2020. Web. doi:10.1063/1.5138658.
Peng, Bo, Kowalski, Karol, Panyala, Ajay R., & Krishnamoorthy, Sriram. Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments. United States. doi:10.1063/1.5138658.
Peng, Bo, Kowalski, Karol, Panyala, Ajay R., and Krishnamoorthy, Sriram. Tue . "Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments". United States. doi:10.1063/1.5138658.
@article{osti_1599991,
title = {Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments},
author = {Peng, Bo and Kowalski, Karol and Panyala, Ajay R. and Krishnamoorthy, Sriram},
abstractNote = {Accurate description of the ionization process in DNA is crucial to the understanding of the DNA damage under exposure to ionizing radiation, as well as to the exploration of the potential application of DNA strands in nano-electronics. During the last years, relevant studies have been focused on the lowest ($i.e.$ the first) valence ionization energies (VIE) of DNA bases-related species, while a clear picture of a broader ionization spectrum of longer sequence is still missing. Theoretically, this requires applying highly accurate and predictable methods on a relatively large system size ($e.g.$ several base pairs), of which the computational complexity prohibits most of the practices. In this work, by employing our recently developed Green's function coupled-cluster (GFCC) library on supercomputing facilities, we have studied the spectral functions of several guanine$-$cytosine (G$-$C) base pair structures ([G$-$C]$_n$, $n=1-3$) in a relatively broad near-valence regime ($-25\sim-5$ eV) in the coupled-cluster with singles and doubles (CCSD) level. Our focus is to give a many-body understanding of the spectral profile and feature change as the system size expands in this regime. The results show that, for the considered G$-$C base pairs, even though the lowest VIE keeps reducing as the system size expands, the spectral function profiles of all three G$-$C base pairs are very much alike in the considered regime, and the relative peak positions didn't vary by more than 0.2 eV. Further analysis of the second ionized state for each G$-$C base pair shows the total 2$h$$-$1$p$ components could contribute up to $\sim$9\% of the corresponding ionized state as more G$-$C base pairs being stacked, of which the leading 2$h$$-$1$p$ components feature a transition from the intra-base-pair cytosine $\pi\rightarrow\pi^\ast$ excitation in single layer [G$-$C]$_1$ to the inter-base-pair electron excitation in multi-layer [G$-$C]$_2$ and [G$-$C]$_3$.},
doi = {10.1063/1.5138658},
journal = {Journal of Chemical Physics},
number = 1,
volume = 152,
place = {United States},
year = {2020},
month = {1}
}

Works referenced in this record:

DNA-Mediated Charge Transport in Redox Sensing and Signaling
journal, January 2010

  • Genereux, Joseph C.; Boal, Amie K.; Barton, Jacqueline K.
  • Journal of the American Chemical Society, Vol. 132, Issue 3
  • DOI: 10.1021/ja907669c

Long-Distance Electron Transfer Through DNA
journal, June 2002


Hole Transfer Kinetics of DNA
journal, June 2013

  • Kawai, Kiyohiko; Majima, Tetsuro
  • Accounts of Chemical Research, Vol. 46, Issue 11
  • DOI: 10.1021/ar400079s

Electronic properties of DNA
journal, August 2001


Modeling Photoionization of Aqueous DNA and Its Components
journal, March 2015

  • Pluhařová, Eva; Slavíček, Petr; Jungwirth, Pavel
  • Accounts of Chemical Research, Vol. 48, Issue 5
  • DOI: 10.1021/ar500366z

Ionization Energies of Aqueous Nucleic Acids: Photoelectron Spectroscopy of Pyrimidine Nucleosides and ab Initio Calculations
journal, May 2009

  • Slavíček, Petr; Winter, Bernd; Faubel, Manfred
  • Journal of the American Chemical Society, Vol. 131, Issue 18
  • DOI: 10.1021/ja8091246

Ionization of Purine Tautomers in Nucleobases, Nucleosides, and Nucleotides: From the Gas Phase to the Aqueous Environment
journal, February 2011

  • Pluhařová, Eva; Jungwirth, Pavel; Bradforth, Stephen E.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 5
  • DOI: 10.1021/jp110388v

The effect of sequence on the ionization of guanine in DNA
journal, January 2016

  • Chakraborty, Rahul; Ghosh, Debashree
  • Physical Chemistry Chemical Physics, Vol. 18, Issue 9
  • DOI: 10.1039/c5cp07804k

Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent
journal, December 2009

  • Yokojima, Satoshi; Yoshiki, Norifumi; Yanoi, Wataru
  • The Journal of Physical Chemistry B, Vol. 113, Issue 51
  • DOI: 10.1021/jp9054582

Unexpectedly Small Effect of the DNA Environment on Vertical Ionization Energies of Aqueous Nucleobases
journal, October 2013

  • Pluhařová, Eva; Schroeder, Christi; Seidel, Robert
  • The Journal of Physical Chemistry Letters, Vol. 4, Issue 21
  • DOI: 10.1021/jz402106h

First-Principles Photoemission Spectroscopy of DNA and RNA Nucleobases from Koopmans-Compliant Functionals
journal, July 2016

  • Nguyen, Ngoc Linh; Borghi, Giovanni; Ferretti, Andrea
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 8
  • DOI: 10.1021/acs.jctc.6b00145

Self-interaction correction to density-functional approximations for many-electron systems
journal, May 1981


Ab initio determination of the ionization potentials of DNA and RNA nucleobases
journal, August 2006

  • Roca-Sanjuán, Daniel; Rubio, Mercedes; Merchán, Manuela
  • The Journal of Chemical Physics, Vol. 125, Issue 8
  • DOI: 10.1063/1.2336217

Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra
journal, November 2010

  • Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav
  • The Journal of Physical Chemistry A, Vol. 114, Issue 46
  • DOI: 10.1021/jp1063726

Four Bases Score a Run: Ab Initio Calculations Quantify a Cooperative Effect of H-Bonding and π-Stacking on the Ionization Energy of Adenine in the AATT Tetramer
journal, September 2012

  • Bravaya, Ksenia B.; Epifanovsky, Evgeny; Krylov, Anna I.
  • The Journal of Physical Chemistry Letters, Vol. 3, Issue 18
  • DOI: 10.1021/jz3011139

Zooming into π-Stacked Manifolds of Nucleobases: Ionized States of Dimethylated Uracil Dimers
journal, February 2010

  • Zadorozhnaya, Anna A.; Krylov, Anna I.
  • The Journal of Physical Chemistry A, Vol. 114, Issue 4
  • DOI: 10.1021/jp910440d

The effect of π-stacking, H-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine–adenine, thymine–thymine and adenine–thymine dimers
journal, January 2010

  • Bravaya, Ksenia B.; Kostko, Oleg; Ahmed, Musahid
  • Physical Chemistry Chemical Physics, Vol. 12, Issue 10
  • DOI: 10.1039/b919930f

Ab Initio Study of the Ionization of the DNA Bases:  Ionization Potentials and Excited States of the Cations
journal, July 2006

  • Cauët, Emilie; Dehareng, Dominique; Liévin, Jacques
  • The Journal of Physical Chemistry A, Vol. 110, Issue 29
  • DOI: 10.1021/jp0617625

Photoelectron Spectra of Some Important Biological Molecules: Symmetry-Adapted-Cluster Configuration Interaction Study
journal, May 2013

  • Farrokhpour, Hossein; Ghandehari, Maryam
  • The Journal of Physical Chemistry B, Vol. 117, Issue 20
  • DOI: 10.1021/jp311213c

Base and Phosphate Electron Detachment Energies of Deoxyribonucleotide Anions
journal, October 2006

  • Zakjevskii, Viatcheslav V.; King, Samuel J.; Dolgounitcheva, Olga
  • Journal of the American Chemical Society, Vol. 128, Issue 41
  • DOI: 10.1021/ja064621p

Coupled cluster approach to the single-particle Green's function
journal, March 1992

  • Nooijen, Marcel; Snijders, Jaap G.
  • International Journal of Quantum Chemistry, Vol. 44, Issue S26
  • DOI: 10.1002/qua.560440808

Electron propagator theory with the ground state correlated by the coupled-cluster method
journal, March 1993

  • Meissner, Leszek; Bartlett, Rodney J.
  • International Journal of Quantum Chemistry, Vol. 48, Issue S27
  • DOI: 10.1002/qua.560480810

Coupled cluster Green's function method: Working equations and applications
journal, October 1993

  • Nooijen, Marcel; Snijders, Jaap G.
  • International Journal of Quantum Chemistry, Vol. 48, Issue 1
  • DOI: 10.1002/qua.560480103

Second order many‐body perturbation approximations to the coupled cluster Green’s function
journal, January 1995

  • Nooijen, Marcel; Snijders, Jaap G.
  • The Journal of Chemical Physics, Vol. 102, Issue 4
  • DOI: 10.1063/1.468900

Green’s Function Coupled-Cluster Approach: Simulating Photoelectron Spectra for Realistic Molecular Systems
journal, June 2018


Green’s function coupled cluster formulations utilizing extended inner excitations
journal, December 2018

  • Peng, Bo; Kowalski, Karol
  • The Journal of Chemical Physics, Vol. 149, Issue 21
  • DOI: 10.1063/1.5046529

Quasiparticle energy spectra of isolated atoms from coupled-cluster singles and doubles (CCSD): Comparison with exact CI calculations
journal, July 2018

  • Nishi, Hirofumi; Kosugi, Taichi; Furukawa, Yoritaka
  • The Journal of Chemical Physics, Vol. 149, Issue 3
  • DOI: 10.1063/1.5029536

Comparison of Green’s functions for transition metal atoms using self-energy functional theory and coupled-cluster singles and doubles (CCSD)
journal, June 2018

  • Kosugi, Taichi; Nishi, Hirofumi; Furukawa, Yoritaka
  • The Journal of Chemical Physics, Vol. 148, Issue 22
  • DOI: 10.1063/1.5029535

Band structures in coupled-cluster singles-and-doubles Green’s function (GFCCSD)
journal, May 2018

  • Furukawa, Yoritaka; Kosugi, Taichi; Nishi, Hirofumi
  • The Journal of Chemical Physics, Vol. 148, Issue 20
  • DOI: 10.1063/1.5029537

Approximate Green’s Function Coupled Cluster Method Employing Effective Dimension Reduction
journal, April 2019

  • Peng, Bo; Van Beeumen, Roel; Williams-Young, David B.
  • Journal of Chemical Theory and Computation, Vol. 15, Issue 5
  • DOI: 10.1021/acs.jctc.9b00172

Toward generalized tensor algebra for ab initio quantum chemistry methods
conference, January 2019

  • Mutlu, Erdal; Kowalski, Karol; Krishnamoorthy, Sriram
  • Proceedings of the 6th ACM SIGPLAN International Workshop on Libraries, Languages and Compilers for Array Programming - ARRAY 2019
  • DOI: 10.1145/3315454.3329958

Molecular properties in solution described with a continuum solvation model
journal, October 2002

  • Tomasi, Jacopo; Cammi, Roberto; Mennucci, Benedetta
  • Physical Chemistry Chemical Physics, Vol. 4, Issue 23
  • DOI: 10.1039/b207281p

Ionization potentials and donor properties of nucleic acid bases and related compounds
journal, July 1975


Photoelectron spectroscopy of some biological molecules
journal, January 1978

  • Dougherty, D.; Younathan, E. S.; Voll, R.
  • Journal of Electron Spectroscopy and Related Phenomena, Vol. 13, Issue 3
  • DOI: 10.1016/0368-2048(78)85042-7

Vacuum-Ultraviolet Photoionization Studies of the Microhydration of DNA Bases (Guanine, Cytosine, Adenine, and Thymine)
journal, August 2007

  • Belau, Leonid; Wilson, Kevin R.; Leone, Stephen R.
  • The Journal of Physical Chemistry A, Vol. 111, Issue 31
  • DOI: 10.1021/jp0705929

Experimental Observation of Guanine Tautomers with VUV Photoionization
journal, April 2009

  • Zhou, Jia; Kostko, Oleg; Nicolas, Christophe
  • The Journal of Physical Chemistry A, Vol. 113, Issue 17
  • DOI: 10.1021/jp811107x

An EOM-CCSD-PCM Benchmark for Electronic Excitation Energies of Solvated Molecules
journal, December 2016

  • Ren, Sijin; Harms, Joseph; Caricato, Marco
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 1
  • DOI: 10.1021/acs.jctc.6b01053

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
journal, September 2010

  • Valiev, M.; Bylaska, E. J.; Govind, N.
  • Computer Physics Communications, Vol. 181, Issue 9, p. 1477-1489
  • DOI: 10.1016/j.cpc.2010.04.018