Cite this article as:
Bokarev A. N., Plastun I. L., Agandeeva K. E. Influence of the Hydrogen Bond on the IR-spectrum and Structure of Molecular Complex of Diamond Nanoparticles and DNA Bases. Izvestiya of Saratov University. New series. Series Physics, 2016, vol. 16, iss. 4, pp. 218-227. DOI: https://doi.org/10.18500/1817-3020-2016-16-4-218-227
Influence of the Hydrogen Bond on the IR-spectrum and Structure of Molecular Complex of Diamond Nanoparticles and DNA Bases
Background and Objectives: Using molecular modeling by the density functional theory method we analyze a hydrogen bonds formation and their influence on IR-spectrum and structure of molecular complex which is formed as the interaction of complementary couple of DNA nucleobases adenine and timin and nanodiamonds surrounded with carboxylic groups. As an example of nanodiamonds adamantine has been used. Intermolecular forces and structure of hydrogen bonds are investigated. In present time diamond-like nanoparticles are increasingly used in various fields of science and technology so investigations in that field of nanoparticle science is actual. In particular, active development of nanoparticles as adsorbents, biomarkers, drug delivery vehicles and in other biomedical applications can be clearly seen. Materials and Methods: Adenine-thymine-carboxylated adamantane complex spectra and optimization were obtained by numerical simulation using the Gaussian software. Obtained data meets experimental results well. Results: Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex were examined. Possibilities of interaction of diamond nanoparticles with DNA at the molecular level were considered.
1. Gonsalves K., Halberstadt C., Laurensin C., Nair L. Biomedical nanostructures. Hoboken, New Jersey, John Wiley & Sons, Inc., 2008. 515 p.
2. Dolmatov V. Yu. Detonation synthesis ultradispersed diamonds: properties and applications. Russian Chemical Reviews, 2001, vol. 70, no. 7, pp. 687–708.
3. Karpukhin A. V., Avkhacheva N. V., Yakovlev R. Yu., Kulakova I. I., Yashin V. A., Lisichkin G. V., Safronova V. G. Effect of detonation nanodiamonds on phagocyte activity. Cell Biology International, 2011, vol. 35, no. 7, pp. 727–733. DOI: https://doi.org/10.1042/CBI20100548
4. Samsonova Y. S., Petrova G. P., Gibizova V. V., Priezzhev A. V., Lugovtsov A. E., Ye Y. -S., Su T. -H., Perevedentseva E. V., Cheng C. -L. Investigation of interaction of albumin molecules with diamond nanoparticles in aqueous by dynamic light scattering. Quantum Electronics, 2012, vol. 42, no. 6, pp. 484–488.
5. Colarusso P., Zhang K.-Q., Guo B., Bernath P.F. The infrared spectra of uracil, thymine, and adenine in the gas phase. Chemical Physics Letters, 1997, vol. 269, pp. 39–48. DOI: https://doi.org/10.1016/S0009-2614(97)00245-5
6. Ten G. N., Nechaev V. V., Pankratov A. N., Berezin V. I., Baranov V. I. Effect of hydrogen bonding on the structure and vibrational spectra of complementary pairs of nucleic acid bases. II. adenine-thymine. Journal of Structural Chemistry, 2010, vol. 51, no. 5, pp. 854–861.
7. Bokarev A. N., Plastun I. L. Рolarizing properties of molecules ensembles - new approaches to calculations. Proceedings of SPIE, 2016, vol. 9917, pp. 99172C. DOI: https://doi.org/10.1117/12.2229801
8. Belenkov E. A., Ivanovskaya V. V., Ivanovsky A. L. Nanoalmazy i rodstvennye uglerodnye nanomaterialy. Komp’iuternoe materialovedenie [Nanodiamonds and related carbon nanomaterials. Computer materials science]. Ekaterinburg, UrO RAS, 2008. 169 p. (in Russian).
9. Bagrii E. I. Adamantany: Poluchenie, svoistva, primenenie [Adamantanes: synthesis, properties and application], Moscow, Science, 1989. 264 p. (in Russian).
10. Filik J., Harvey J. N., Allan N. L., May P. W., Dahl J. E. P., Shenggao L., Carlson R. M. K. Raman spectroscopy of diamondoids. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2006, vol. 64, pp. 681–692.
11. Baidakova M. V., Kukushkina Y. A., Sitnikova A. A., Yagovkina M. A., Kirilenko D. A., Sokolov V. V., Shestakov M. S., Vul’ A. Y., Zousman B., Levinson O. Structure of nanodiamonds prepared by laser synthesis. Physics of the Solid State, 2013, vol. 55, no. 8, pp. 1747–1753.
12. Kohn W. The electronic structure of matter: wave functions and density functionals. Physics-Uspekhi (Advances in Physical Sciences), 2002, vol. 172, no. 3, pp. 336–348.
13. Pople J. Quantum chemical models. Physics-Uspekhi (Advances in Physical Sciences), 2002, vol. 172, no. 3, pp. 349–356.
14. Frisch M. J., Trucks G. W., Cheeseman J. R., Scalmani G., Caricato M., Hratchian H. P., Li X., Barone V., Bloino J., Zheng G., Vreven T., Montgomery J. A., Petersson Jr. G. A., Scuseria G. E., Schlegel H. B., Nakatsuji H., Izmaylov A. F., Martin R. L., Sonnenberg J. L., Peralta J. E., Heyd J. J., Brothers E., Ogliaro F., Bearpark M., Robb M. A., Mennucci B., Kudin K. N., Staroverov V. N., Kobayashi R., Normand J., Rendell A., Gomperts R., Zakrzewski V. G., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H. Gaussian 09, Revision A.02. Wallingford CT, Gaussian Inc., 2009. 989 p.
15. Dolenko T. A., Burikov S. A., Laptinskiy K. A., Sarmanova O. E. Improvement of the fi delity of molecular DNA computations: control of DNA duplex melting using raman spectroscopy. Laser Physics, 2016, vol. 26, no. 2, 25206.
