Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study.

Terahertz (THz) spectra of DNA nucleobase crystals were experimentally studied by terahertz time domain spectroscopy (THz-TDS), Fourier transform infrared spectroscopy (FTIR), and computationally studied by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). We analyzed the vibrational spectra of solid-state DNA nucleobases and assigned the corresponding vibrational modes to the main peaks in the experimental spectra with the PBC-GEBF results. The computational results were verified to be in good accordance with the experimental data. Harmonic vibrational frequency results revealed that all the vibrational modes belong to collective vibrational modes, which involve complicated mixtures of inter- and intramolecular displacements, somewhere in the vicinity of 0.5-9THz.

[1]  Michael Nagel,et al.  Integrated THz technology for label-free genetic diagnostics , 2002 .

[2]  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.

[3]  S. Srivastava,et al.  Molecular interactions of 2'-deoxyguanosine 5'-monophosphate with glycine in aqueous media probed via concentration and pH dependent Raman spectroscopic investigations and DFT study. , 2012, Physical chemistry chemical physics : PCCP.

[4]  J L Hesler,et al.  Submillimeter-wave phonon modes in DNA macromolecules. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[5]  Wei Li,et al.  An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules. , 2005, Journal of the American Chemical Society.

[6]  Hui Yan,et al.  [Terahertz spectroscopy of DNA nucleobases: cytosine and thymine]. , 2013, Guang pu xue yu guang pu fen xi = Guang pu.

[7]  C. Beetz,et al.  The low frequency vibrations of pyrimidine and purine bases , 1980 .

[8]  A R Bishop,et al.  DNA Breathing Dynamics in the Presence of a Terahertz Field. , 2009, Physics letters. A.

[9]  Ieee Microwave Theory,et al.  Quasioptical systems : Gaussian beam quasioptical propagation and applications , 1998 .

[10]  B. Fischer,et al.  Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy , 2002, Physics in medicine and biology.

[11]  B. Gelmont,et al.  Sub-millimetre wave absorption spectra of artificial RNA molecules , 2003 .

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

[13]  W. Clegg,et al.  Anhydrous guanine: a synchrotron study. , 2006, Acta crystallographica. Section C, Crystal structure communications.

[14]  T. Row,et al.  Anhydrous Adenine: Crystallization, Structure, and Correlation with Other Nucleobases , 2008 .

[15]  Jun-ichi Nishizawa,et al.  THz transmittance measurements of nucleobases and related molecules in the 0.4- to 5.8-THz region using a GaP THz wave generator , 2005 .

[16]  Gerald J. Wilmink,et al.  Invited Review Article: Current State of Research on Biological Effects of Terahertz Radiation , 2011 .

[17]  Shuhua Li,et al.  Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods. , 2015, Journal of chemical theory and computation.

[18]  V. Krishnakumar,et al.  Spectroscopic, electronic structure and natural bond analysis of 2-aminopyrimidine and 4-aminopyrazolo[3,4-d]pyrimidine: a comparative study. , 2012, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[19]  J. Singh.  FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine). , 2015, Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy.

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

[21]  Shuhua Li,et al.  LSQC: Low scaling quantum chemistry program , 2015 .

[22]  Peter Uhd Jepsen,et al.  Precise ab-initio prediction of terahertz vibrational modes in crystalline systems , 2007 .

[23]  Lyubov V. Titova,et al.  Intense THz pulses cause H2AX phosphorylation and activate DNA damage response in human skin tissue , 2013, Biomedical optics express.

[24]  R. E. Marsh,et al.  The crystal structure of cytosine , 1964 .

[25]  Wei Li,et al.  Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates. , 2014, Accounts of chemical research.

[26]  Bao Liu,et al.  DNA cytosine methylation in plant development. , 2010, Journal of genetics and genomics = Yi chuan xue bao.

[27]  Yun-Shik Lee,et al.  Principles of Terahertz Science and Technology , 2008 .

[28]  J. Møller,et al.  The Effect of Hydrogen Bonding on the Structures of Uracil and Some Methyl Derivatives Studied by Experiment and Theory. , 1999 .

[29]  Wei Li,et al.  Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules. , 2007, The journal of physical chemistry. A.

[30]  J. Jia,et al.  Vibrational Spectra of Molecular Crystals with the Generalized Energy-Based Fragmentation Approach. , 2016, The journal of physical chemistry. A.

[31]  P. Mounaix,et al.  Broadband terahertz imaging of documents written with lead pencils , 2009 .

[32]  Alan R. Bishop,et al.  Mammalian Stem Cells Reprogramming in Response to Terahertz Radiation , 2010, PloS one.

[33]  Prashanth C. Upadhya,et al.  Temperature-dependent low-frequency vibrational spectra of purine and adenine , 2003 .