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

Peng, Bo; Kowalski, Karol; Panyala, Ajay; Krishnamoorthy, Sriram

doi:10.1063/1.5138658

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

Authors:

^[1];

^[2]; Panyala, Ajay ^[3]; Krishnamoorthy, Sriram ^[3]

Advanced Computing, Mathematics, and Data Division, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
High Performance Computing, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA

Publication Date:: 2020-01-07

Sponsoring Org.:: USDOE

OSTI Identifier:: 1580783

Grant/Contract Number:: AC06-76RLO-1830; AC05-00OR22725

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Journal of Chemical Physics

Additional Journal Information:: Journal Name: Journal of Chemical Physics Journal Volume: 152 Journal Issue: 1; Journal ID: ISSN 0021-9606

Publisher:: American Institute of Physics

Country of Publication:: United States

Language:: English

Citation Formats


                    Peng, Bo, Kowalski, Karol, Panyala, Ajay, 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.

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                    Peng, Bo, Kowalski, Karol, Panyala, Ajay, & Krishnamoorthy, Sriram. Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments.  United States.  https://doi.org/10.1063/1.5138658

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                    Peng, Bo, Kowalski, Karol, Panyala, Ajay, and Krishnamoorthy, Sriram. Tue .  
"Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments".  United States.  https://doi.org/10.1063/1.5138658.

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@article{osti_1580783,

  title        = {Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments},

  author       = {Peng, Bo and Kowalski, Karol and Panyala, Ajay and Krishnamoorthy, Sriram},

  abstractNote = {},

  doi          = {10.1063/1.5138658},

  journal      = {Journal of Chemical Physics},

  number       = 1,

  volume       = 152,

  place        = {United States},

  year         = {2020},

  month        = {1}

}

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

Citation Formats

Coupled-cluster theory in quantum chemistry journal, February 2007

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

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

Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair journal, January 2019

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

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

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

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

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

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

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

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

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

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

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

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

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

Generalized Gradient Approximation Made Simple journal, October 1996

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

Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects journal, February 1981

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

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

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

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

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

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

The equation of motion coupled‐cluster method. A systematic biorthogonal approach to molecular excitation energies, transition probabilities, and excited state properties journal, May 1993

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

Long-Distance Electron Transfer Through DNA journal, June 2002

Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations journal, April 2013

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

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

Hole Transfer Kinetics of DNA journal, June 2013

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

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

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

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

Photoelectron spectroscopy of some biological molecules journal, January 1978

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

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

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

Electronic properties of DNA journal, August 2001

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

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

Theoretical Studies of GG-Specific Photocleavage of DNA via Electron Transfer: Significant Lowering of Ionization Potential and 5‘-Localization of HOMO of Stacked GG Bases in B-Form DNA journal, January 1996

Spectral functions of the uniform electron gas via coupled-cluster theory and comparison to the G W and related approximations journal, June 2016

Coupled-cluster theory in quantum chemistry
journal, February 2007

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

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

Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair
journal, January 2019

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

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

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

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

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

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

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

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

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

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

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

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

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

Generalized Gradient Approximation Made Simple
journal, October 1996

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

Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects
journal, February 1981

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

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

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

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

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

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

The equation of motion coupled‐cluster method. A systematic biorthogonal approach to molecular excitation energies, transition probabilities, and excited state properties
journal, May 1993

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

Long-Distance Electron Transfer Through DNA
journal, June 2002

Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations
journal, April 2013

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

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

Hole Transfer Kinetics of DNA
journal, June 2013

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

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

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

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

Photoelectron spectroscopy of some biological molecules
journal, January 1978

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

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

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

Electronic properties of DNA
journal, August 2001

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

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

Theoretical Studies of GG-Specific Photocleavage of DNA via Electron Transfer: Significant Lowering of Ionization Potential and 5‘-Localization of HOMO of Stacked GG Bases in B-Form DNA
journal, January 1996

Spectral functions of the uniform electron gas via coupled-cluster theory and comparison to the $G W$ and related approximations
journal, June 2016