RT-TDDFT study of hole oscillations in B-DNA monomers and dimers

References

• Binkley, J. S., Pople, J. A., & Hehre, W. J. (1980). Self-consistent molecular orbital methods. 21. Small split-valence basis sets for first-row elements. Journal of American Chemical Society, 102, 939–947.
   Web of Science ®Google Scholar
• Bolton, J. R., Mataga, N., & McLendon, G. (Eds.). (1991). Electron transfer in inorganic, organic and biological systems. Washington, DC: American Chemical Society.
   Google Scholar
• Burrows, C. J., & Muller, J. G. (1998). Oxidative nucleobase modifications leading to strand scission. Chemical Review, 98, 1109.
   PubMed Web of Science ®Google Scholar
• Cuniberti, G., Maci\’{a}, E., Rodriguez, A., & Römer, R. A. (2007). Tight-binding modeling of charge migration in DNA devices. In T. Chakraborty (Ed.), Charge migration in DNA: Perspectives from physics, chemistry, and biology. Berlin Heidelberg New York: Springer.
   Google Scholar
• Dandliker, P. J., Holmlin, R. E., & Barton, J. K. (1997). Oxidative thymine dimer repair in the DNA helix. Science, 275, 1465–1468.
   PubMed Web of Science ®Google Scholar
• Dunning, T. H. (1989). Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. The Journal of Chemical Physics, 90, 1007–1023.
   Web of Science ®Google Scholar
• Farazdel, A., Dupuis, M., & Clementi, E. (1990). Electric field induced intramolecular electron transfer in spiro π-electron systems and their suitability as molecular electronic devices. A theoretical study. Journal of American Chemical Society, 112, 4206–4214.
   Web of Science ®Google Scholar
• Genereux, J. C., & Barton, J. K. (2010). Mechanisms for DNA charge transport. Chemical Reviews, 110, 1642–1662.
   PubMed Web of Science ®Google Scholar
• Giese, B. (2002). Long-distance electron transfer through DNA. Annual Review of Biochemistry, 71, 51–70.
   PubMed Web of Science ®Google Scholar
• Giese, B. (2006). Electron transfer through DNA and peptides. Bioorganic & Medicinal Chemistry, 14, 6139–6143.
   PubMed Web of Science ®Google Scholar
• Grånäs, O., Kolesov, G., & Kaxiras, E. (2017). Impact of vibrations and electronic coherence on electron transfer in flat molecular wires. MRS Advances, 1–6. doi:10.1557/adv.2017.157
   Web of Science ®Google Scholar
• Hawke, L. G. D., Kalosakas, G., & Simserides, C. (2010). Electronic parameters for charge transfer along DNA. The European Physical Journal E, 32, 291.
   PubMed Web of Science ®Google Scholar
• Hehre, W. J., Ditchfield, R., & Pople, J. A. (1972). Self –consistent molecular orbital methods. XII. Further extensions of gaussian–type basis sets for use in molecular orbital studies of organic molecules. The Journal of Chemical Physics, 56, 2257–2261.
   Web of Science ®Google Scholar
• Hohenberg, P., & Kohn, W. (1964). Inhomogeneous electron gas. Physical Review, 136, B864.
   Web of Science ®Google Scholar
• Huang, M., Li, H., He, H., Zhang, X., & Wang, S. (2016). An electrochemical impedance sensor for simple and specific recognition of G-G mismatches in DNA. Analytical Methods, 8, 7413–7419.
   Web of Science ®Google Scholar
• ISO 20473 specifies: Near-Infrared (NIR) 0.78 - 3 μm, Mid-Infrared (MIR) 3–50 μm, Far-Infrared (FIR) 50–1000 μm. (2007).
   Google Scholar
• Kawai, K., & Majima, T. (2015). Increasing the hole transfer rate through DNA by chemical modification. In T. Akasaka, A. O. S. Fukuzumi, & H. K. Y. Aso (Eds.), Chemical science of π -electron systems. Tokyo Heidelberg New York Dordrecht London: Springer.
   Google Scholar
• Kohn, W., & Sham, L. J. (1965). Self-consistent equations including exchange and correlation effects. Physical Review, 140, A1133.
   Web of Science ®Google Scholar
• Lambropoulos, K., Chatzieleftheriou, M., Morphis, A., Kaklamanis, K., Lopp, R., Theodorakou, M., ... Simserides, C. (2016). Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model. Physical Review E, 94, 062403.
   PubMed Web of Science ®Google Scholar
• Lambropoulos, K., Chatzieleftheriou, M., Morphis, A., Kaklamanis, K., Theodorakou, M., & Simserides, C. (2015). Unbiased charge oscillations in B-DNA: Monomer polymers and dimer polymers. Physical Review E, 92, 032725.
   Web of Science ®Google Scholar
• Lambropoulos, K., Kaklamanis, K., Georgiadis, G., & Simserides, C. (2014). THz and above THz electron or hole oscillations in DNA dimers and trimers. Annalen der Physik (Berlin), 526, 249–258.
   Web of Science ®Google Scholar
• Lambropoulos, K., Kaklamanis, K., Morphis, A., Tassi, M., Lopp, R., Georgiadis, G., ... Simserides, C. (2016). Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers. Journal of Physics: Condensed Matter, 28, 495101.
   PubMed Web of Science ®Google Scholar
• Liang, W., Chapman, C. T., & Li, X. (2011). Efficient first-principles electronic dynamics. The Journal of Chemical Physics, 134, 184102.
   PubMed Web of Science ®Google Scholar
• Lopata, K., & Govind, N. (2011). Modeling fast electron dynamics with real-time time-dependent density functional theory: Application to small molecules and chromophores. Journal of Chemical Theory and Computation, 7, 1344–1355.
   PubMed Web of Science ®Google Scholar
• Löwdin, P.-O. (1950). On the non-orthogonality problem connected with the use of atomic wave functions in the theory of molecules and crystals. The Journal of Chemical Physics, 18, 365–375.
   Web of Science ®Google Scholar
• Maci\’{a}, E. (2009). Aperiodic stuctures in condensed matter: Fundamentals and applications. Boca Raton, FL: Taylor and Francis CRC.
   Google Scholar
• Marcus, R. A., & Sutin, N. (1985). Electron transfers in chemistry and biology. Biochimica et Biophysica Acta, 811, 265–322.
   Web of Science ®Google Scholar
• Marques, M. A. L. (2006). Time-dependent density functional theory. In M. A. L. Marques, C. Ullrich, F. Nogueira, A. Rubio, K. Burke, & E. K. U Gross (Eds.). Berlin: Springer.
   Google Scholar
• Newton, M. D., & Sutin, N. (1984). Electron transfer reactions in condensed phases. Annual Review of Physical Chemistry, 35, 437–480.
   Web of Science ®Google Scholar
• Partovi-Azar, P., & Kaghazchi, P. (2017). Time-dependent density functional theory study on direction-dependent electron and hole transfer processes in molecular systems. Journal of Computational Chemistry, 38, 698–703.
   PubMed Web of Science ®Google Scholar
• Provorse, M. R., & Isborn, C. M. (2016). Electron dynamics with real-time time-dependent density functional theory. International Journal of Quantum Chemistry, 116, 739–749.
   Web of Science ®Google Scholar
• Rajski, S. R., Jackson, B. A., & Barton, J. K. (2000). DNA repair: Models for damage and mismatch recognition. Mutation Research, 447, 49–72.
   PubMed Web of Science ®Google Scholar
• Runge, E., & Gross, E. K. U. (1984). Density-functional theory for time-dependent systems. Physical Review Letters, 52, 997.
   Web of Science ®Google Scholar
• Shih, C.-T., Cheng, Y.-Y., Wells, S. A., Hsu, C.-L., & Römer, R. A. (2011). Charge transport in cancer-related genes and early carcinogenesis. Computer Physics Communications, 182, 36–38.
   Web of Science ®Google Scholar
• Simserides, C. (2014). A systematic study of electron or hole transfer along DNA dimers, trimers and polymers. Chemical Physics, 440, 31–41.
   Web of Science ®Google Scholar
• Simserides, C. (2016). Quantum optics and lasers. ISBN: 978-960-603-073-4 . Athens: Hellenic Academic Libraries Link. http://hdl.handle.net/11419/2108. License: Attribution - Non-Commercial - No Derivatives. URI: http://hdl.handle.net/11419/2108 , http://repository.kallipos.gr/handle/11419/2108?locale=en
   Google Scholar
• Takimoto, Y., Vila, F. D., & Rehr, J. J. (2007). Real-time time-dependent density functional theory approach for frequency-dependent nonlinear optical response in photonic molecules. The Journal of Chemical Physics, 127, 154114.
   PubMed Web of Science ®Google Scholar
• Theilhaber, J. (1992). Ab initio simulations of sodium using time-dependent density-functional theory. Physical Review B, 46, 12990–13003.
   Web of Science ®Google Scholar
• Ullrich, C. (2012). Time-dependent density-functional theory: Concepts and applications. Oxford: Oxford University Press.
   Google Scholar
• Valiev, M., Bylaska, E. J., Govind, N., Kowalski, K., Straatsma, T. P., Van Dam, H. J. J., ... de Jong, W. A. (2010). NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations. Computer Physics Communications, 181, 1477–1489.
   Web of Science ®Google Scholar
• Wohlgamuth, C. H., McWilliams, M. A., & Slinker, J. D. (2013). DNA as a molecular wire: Distance and sequence dependence. Analytical Chemistry, 85, 8634–-8640.
   PubMed Web of Science ®Google Scholar
• Yabana, K., & Bertsch, G. F. (1996). Time-dependent local-density approximation in real time. Physical Review B, 54, 4484–4487.
   Web of Science ®Google Scholar
• Yanai, T., Tew, D. P., & Handy, N. C. (2004). A new hybrid exchange--correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chemical Physics Letters, 393, 51–57.
   Web of Science ®Google Scholar
• Yin, X., Ng, B. W. H., & Abbott, D. (2012). Terahertz sources and detectors. In Terahertz Imaging for Biomedical Applications: Pattern Recognition and Tomographic Reconstruction. New York, NY: Springer Science+Business Media, LLC. ISBN 978-1-4614-1820-7 e-ISBN 978-1-4614-1821-4. Retrieved from http://www.springer.com/978-1-4614-1820-7
   Google Scholar