Elucidation of electron ionization induced fragmentations of adenine by semiempirical and density functional molecular dynamics.

The gas phase fragmentation pathways of the nucleobase adenine upon 70 eV electron ionization are investigated by means of a combined stochastic and first-principles based molecular dynamics approach. We employ no preconceived fragmentation channels in our calculations, which simulate standard electron ionization mass spectrometry (EI-MS) conditions. The reactions observed compare well to a wealth of experimental and theoretical data available for this important nucleic acid building block. All significant peaks in the experimental mass spectrum of adenine are reproduced. Additionally, the fragment ion connectivities obtained from our simulations at least partially concur with results from previous experimental studies on selectively isotope labeled adenines. Moreover, we are able to assign noncyclic structures that are entropically favored and have not been proposed in nondynamic quantum chemical studies before to the decomposition products, which result automatically from our molecular dynamics procedure. From simulations under various conditions it is evident that most of the fragmentation reactions even at low internal excess energy (<10 eV) occur very fast within a few picoseconds.

[1]  T. Henderson,et al.  Purine ring rearrangements leading to the development of cytokinin activity. Mechanism of the rearrangement of 3-benzyladenine to N6-benzyladenine. , 1975, Journal of the American Chemical Society.

[2]  Pierre Cloutier,et al.  Single, double, and multiple double strand breaks induced in DNA by 3-100 eV electrons. , 2003, Journal of the American Chemical Society.

[3]  N. Mermin.  Time-Dependent Correlations in a Solvable Ferromagnetic Model , 1964 .

[4]  B. Vojnovic,et al.  Measurement of DNA damage by electrons with energies between 25 and 4000 eV. , 1993, International journal of radiation biology.

[5]  J. Rice,et al.  Mass spectra of nucleic acid derivatives. II. Guanine, adenine, and related compounds. , 1967, Journal of the American Chemical Society.

[6]  J. Occolowitz.  Carbon-14 as a label in mass spectrometry , 1968 .

[7]  J. McCloskey,et al.  Collision-induced dissociation of adenine , 1992 .

[8]  D. Hunting,et al.  Resonant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons. , 2000, Science.

[9]  Stefan Grimme,et al.  First principles calculation of electron ionization mass spectra for selected organic drug molecules. , 2014, Organic & biomolecular chemistry.

[10]  Thomas Frauenheim,et al.  Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment , 2001 .

[11]  V. Barone,et al.  Toward reliable density functional methods without adjustable parameters: The PBE0 model , 1999 .

[12]  M. Elstner,et al.  Parametrization and Benchmark of DFTB3 for Organic Molecules. , 2013, Journal of chemical theory and computation.

[13]  Gustavo E. Scuseria,et al.  IMPROVING SELF-CONSISTENT FIELD CONVERGENCE BY VARYING OCCUPATION NUMBERS , 1999 .

[14]  L. Verlet.  Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[15]  R. Brédy,et al.  Fragmentation of adenine under energy control. , 2009, The Journal of chemical physics.

[16]  Walter Thiel,et al.  Orthogonalization corrections for semiempirical methods , 2000 .

[17]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[18]  H. Baumgärtel,et al.  Photoion mass spectrometry of adenine, thymine and uracil in the 6–22 eV photon energy range , 2005 .

[19]  D. Kingston,et al.  Intramolecular hydrogen transfer in mass spectra. I. Rearrangements in aliphatic hydrocarbons and aromatic compounds , 1973 .

[20]  T. Frauenheim,et al.  DFTB+, a sparse matrix-based implementation of the DFTB method. , 2007, The journal of physical chemistry. A.

[21]  Sándor Suhai,et al.  Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties , 1998 .

[22]  S. Bari,et al.  Interactions of neutral and singly charged keV atomic particles with gas-phase adenine molecules. , 2007, The Journal of chemical physics.

[23]  G. Baryshnikov,et al.  Fragmentation of the adenine and guanine molecules induced by electron collisions. , 2014, The Journal of chemical physics.

[24]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[25]  R. Weinkauf,et al.  Excited-state relaxation of protonated adenine. , 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.

[26]  V. Barone,et al.  Radical cations of DNA bases: some insights on structure and fragmentation patterns by density functional methods , 2000 .

[27]  T. Märk,et al.  Mass spectrometry (fragmentation ratios) of DNA base molecules following 80 keV proton impact with separation of direct ionization and electron capture processes , 2010 .

[28]  A. Becke,et al.  A density-functional model of the dispersion interaction. , 2005, The Journal of chemical physics.

[29]  K. Burke,et al.  Generalized Gradient Approximation Made Simple [Phys. Rev. Lett. 77, 3865 (1996)] , 1997 .

[30]  Stefan Grimme,et al.  Effect of the damping function in dispersion corrected density functional theory , 2011, J. Comput. Chem..

[31]  J. McCloskey,et al.  Mass spectrometry of nucleic acid constituents. Electron ionization spectra of selectively labeled adenines , 1982 .

[32]  R. W. Warren,et al.  Fractional occupation numbers and density functional energy gradients within the linear combination of Gaussian-type orbitals approach , 1996 .

[33]  Xiaohong Chen,et al.  Protonated adenine: Tautomers, solvated clusters, and dissociation mechanisms , 2005, Journal of the American Society for Mass Spectrometry.

[34]  Frank Neese,et al.  The ORCA program system , 2012 .

[35]  Stefan Grimme,et al.  Systematic quantum chemical study of DNA‐base tautomers , 2004, J. Comput. Chem..

[36]  D. Scott,et al.  Optimization and testing of mass spectral library search algorithms for compound identification , 1994, Journal of the American Society for Mass Spectrometry.

[37]  Stefan Grimme,et al.  Towards first principles calculation of electron impact mass spectra of molecules. , 2013, Angewandte Chemie.

[38]  J. Tully.  Mixed quantum–classical dynamics , 1998 .

[39]  J. Song,et al.  Photofragmentation in selected tautomers of protonated adenine. , 2011, Physical chemistry chemical physics : PCCP.

[40]  Hans W. Horn,et al.  Fully optimized contracted Gaussian basis sets for atoms Li to Kr , 1992 .

[41]  S. Grimme,et al.  A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems. , 2012, The Journal of chemical physics.