Parallel implementation of the equation-of-motion coupled-cluster singles and doubles method and application for radical adducts of cytosine.

The equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) method has been implemented into the massively parallel ACES III program using two alternative strategies: (1) storing the entire EOM Hamiltonian matrix prior to diagonalization and (2) recomputing the four-virtual part of the matrix from integrals in a direct mode. The second is found to be far more efficient. EOM-CC shows virtually ideal scaling from 32 to 256 processors. With basis sets as large as 552 functions, the program was applied to determine vertical excitation energies for five cytosine radical adducts of -OH and -H at three sites C5, C6, and N3. These radicals are considered to play an important role in radiation induced DNA damage. The excitation energy spectrum shows two distinct patterns for the lowest transitions distinguishing the C6-OH, C6-H, and N3-H adducts from the C5-OH and C5-H. The results indicate that the two lowest transitions of the C6-OH isomer should contribute to the experimentally observed absorption maximum at 2.88 eV, while the third and fourth transitions of C6-OH and the two lowest transitions of C5-OH contribute to the 3.65 eV absorption maximum. We also report the CCSD with noniterative triples correction [CCSD(T)] relative energies of the C5-OH and C6-OH adducts using 1000 processors.

[1]  M. Head‐Gordon,et al.  A fifth-order perturbation comparison of electron correlation theories , 1989 .

[2]  So Hirata,et al.  Perturbative corrections to coupled-cluster and equation-of-motion coupled-cluster energies: A determinantal analysis , 2001 .

[3]  K. Hirao,et al.  A generalization of the Davidson's method to large nonsymmetric eigenvalue problems , 1982 .

[4]  B. Ames,et al.  The free radical theory of aging matures. , 1998, Physiological reviews.

[5]  R. Bartlett,et al.  Multiplicity of many-body wavefunctions using unrestricted Hartree-Fock reference functions , 1988 .

[6]  Olga Kennard,et al.  The molecular structures of nucleosides and nucleotides: Part 1. The influence of protonation on the geometries of nucleic acid constituents , 1982 .

[7]  J. Šponer,et al.  Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study , 1994 .

[8]  E. Hayon,et al.  Addition of hydroxyl radicals to pyrimidine bases and electron transfer reactions of intermediates to quinones. , 1973, Journal of the American Chemical Society.

[9]  Clifford E. Dykstra,et al.  Advanced theories and computational approaches to the electronic structure of molecules , 1984 .

[10]  R J Bartlett,et al.  Parallel implementation of electronic structure energy, gradient, and Hessian calculations. , 2008, The Journal of chemical physics.

[11]  T. Dunning,et al.  Electron affinities of the first‐row atoms revisited. Systematic basis sets and wave functions , 1992 .

[12]  R. J. Boyd,et al.  Effects of Ionizing Radiation on Crystalline Cytosine Monohydrate , 1998 .

[13]  K. Kowalski,et al.  On the electronically excited states of uracil. , 2008, Journal of Physical Chemistry A.

[14]  F. Peterson,et al.  Pulse radiolysis of nucleic acid constituents and related compounds. 3. Optical spectra and reactivity of organic free radicals formed by reaction of hydroxyl free radicals with pyrimidine bases. , 1970, Journal of the American Chemical Society.

[15]  F. Tureček,et al.  Proton and hydrogen atom adducts to cytosine. An experimental and computational study , 2007 .

[16]  J. Hüttermann,et al.  Reactions of water radiolysis intermediates with pyrimidine and purine bases in aqueous BeF2 glasses: an EPR study. , 1993, International journal of radiation biology.

[17]  S. Garte,et al.  Infrequent alterations of the p53 gene in rat skin cancers induced by ionizing radiation. , 1996, Carcinogenesis.

[18]  M. Sevilla,et al.  Protonation of nucleobase anions in gamma-irradiated DNA and model systems. Which DNA base is the ultimate sink for the electron? , 1994, Radiation research.

[19]  A. J. Sadlej,et al.  Medium-size polarized basis sets for high-level-correlated calculations of molecular electric properties , 1991 .

[20]  R. Bartlett,et al.  A full coupled‐cluster singles and doubles model: The inclusion of disconnected triples , 1982 .

[21]  F. Tureček,et al.  Hydrogen atom addition to cytosine, 1-methylcytosine, and cytosine-water complexes. a computational study of a mechanistic dichotomy , 2003 .

[22]  D. K. Hazra,et al.  Pattern of hydroxyl radical addition to cytosine and 1-, 3-, 5-, and 6-substituted cytosines. Electron transfer and dehydration reactions of the hydroxyl adducts , 1983 .

[23]  T. H. Dunning.  Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[24]  Anna I Krylov,et al.  Spin-conserving and spin-flipping equation-of-motion coupled-cluster method with triple excitations. , 2005, The Journal of chemical physics.

[25]  C. Sonntag,et al.  The chemical basis of radiation biology , 1987 .

[26]  Yueyuan Y. Xia,et al.  Theoretical study of the OH reaction with cytosine , 2005 .

[27]  R. Bartlett.  Many-Body Perturbation Theory and Coupled Cluster Theory for Electron Correlation in Molecules , 1981 .

[28]  H. Schaefer,et al.  Addition of hydrogen atom/hydride anion to the double bonds of cytosine tautomers: radical and anion structures and energetics , 2006 .

[29]  E. Davidson.  The iterative calculation of a few of the lowest eigenvalues and corresponding eigenvectors of large real-symmetric matrices , 1975 .

[30]  Marat Valiev,et al.  Hybrid coupled cluster and molecular dynamics approach: application to the excitation spectrum of cytosine in the native DNA environment. , 2006, The Journal of chemical physics.

[31]  Hideo Sekino,et al.  A linear response, coupled‐cluster theory for excitation energy , 1984 .