Biopolym. Cell. 1998; 14(5):419-427.
http://dx.doi.org/10.7124/bc.0004E6
Structure and Function of Biopolymers
How structural changeability of nitrogen bases affects macroscopic properties of their crystals
1Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

The author stands up for the idea accordingly to which uncommon optical and physical properties of nitrogen bases (unregularity of their anhydrous lattices which becomes essentially reduced under moistening and deuteration, temperature anomalies of dielectric permeability and tangent of loss angle, availability of defects – traps of charge carriers, violations of selection rules in polarized vibrational spectra etc.) are determined by stereochemical non-rigidity of the bases themselves. The nitrogen bases crystals with amino group and their hydrates are essentially John-Teller crystals with all the ensuing consequences. Such approach enables the author to explain macrostructural origing of the propeller configuration of the layer package of nitrogen bases with amino group in crystal slate by the increase of their inversion energy up to the values several times exceeding kT, under transition from the free state to the crystal one which is the result of the ρ-π-conjugation disturbance and specific electrostatic contacts of lone pair of amino nitrogen atom with positively charged hydrogen and carbon atoms from upper and lower molecular layers. Similar reason is based on the propeller configuration of Watson-Crick pairs in DNA and its wedge-like relative orientation. The evaluations of amino group inversion energies of nucleotide bases for crystals and in DNA were done.
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References

[1] Elinek O. Model systems nucleinic acids. Materials 2nd coordination. Workshop Mynvuzov USSR-Czechoslovakia. Vilnius: Mokslal, 1986;34-42.
[2] Shtepanek I, Baumruk V. Raman spectroscopy components of nucleic acids. Materials 2nd coordination. Workshop Mynvuzov USSR-Czechoslovakia. Vilnius: Mokslal, 1986; 84-92.
[3] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[4] Spackman MA, Weber HP, Craven BM. Energies of molecular interactions from Bragg diffraction data. J Am Chem Soc. 1988;110(3):775–82.
[5] Govorun DN, Mishchuk YaR, Zheltovsky NV. Low-frequency phonon Raman spectra of nucleic acid constituents: purine bases. Biopolym Cell. 1990; 6(3):24-31.
[6] Govorun DN, Mishchuk YaR, Zheltovsky NV. Low-frequency phonon raman spectra of nucleic acid constituents: pyrimidine bases. Biopolym Cell. 1990; 6(3):31-39.
[7] Maleev VIa, Semenov MA, Gasan AI, Kashpur VA. [Physical properties of the DNA-water system]. Biofizika. 1993;38(5):768-90.
[8] Babkov LM, Puchkovskaya GA, Makarenko SP, Gavrilko TA. IR spectroscopy of molecular hydrogen-bonded crystals. Kyiv, Naukova Dumka, 1989; 160 p.
[9] Sinsheimer RL, Scott JF, Loofbourrow JR. Use of thin films of sublimate for absorption spectroscopy. Nature. 1949;164(4175):796.
[10] Scott JF, Sinsheimer RL, Loofbourow JR. Factors Involved in the Sharpening of the Ultraviolet Absorption Spectrum of Guanine at Reduced Temperatures 1 . J Am Chem Soc. 1952;74(1):275–7.
[11] Gumanyuk VA, Sukhorukov BI, Khomenko VG. IR-spectroscopic and X-ray study of the effect of water vapour on the structure and transition amorphous state-crystal of nucleic acids pyrimidine bases. Biofizika. 1976; 21(4):597-602.
[12] Gumeniuk VA. [Effect of water on guanine crystallization: absorption spectra in the infrared and ultraviolet range]. Biofizika. 1980;25(5):793-5. Russian.
[13] Bogatina NI. Chmutov VM. Anomalies of doelectric properties of monocrystals of cytozm-monohydrate and textured polycrystals of nonaqueous cytozin. Biofizika. 1980; 25(4): 600-4.
[14] ?ubertov? E, Silinsh E, Prosser V. Some photoelectric properties of the nucleic acid bases in thin layers. Czech J Phys. 1973;23(3):356–67.
[15] Jel?nek O, T?le IA. Thermoluminescence and long afterglow of adenine in the solid state. J Lumin. 1975;10(6):371–9.
[16] Cherkasov YuA, Kiseleva MN, Dodonova NYa. The quantum yield of photogenerated charge carriers in anthracene and nucleic acid bases in the photon energy 3.10 eV. Optika i spektroskopiya. 1978; 45(6):1126-9.
[17] Ostapenko NI, Skryshevsky YuA, Kadashchuk AK, Rubin YuV. The nature of defective states in crystals of nucleic acid bases. Biopolym Cell. 1990; 6(3):65-9.
[18] Ostapenko YaI, Skryshevskiy YuA, Kadashchuk AK, Rubin YuV. [Thermally stimulated luminescence of nucleic acid bases crystals] . Izv Akad Nauk SSSR. Ser Fiz. 1990; 54(3):445-9.
[19] Skryshevskiy YuA, Ostapenko YaI, Kadashchuk AK, Shpak MT. [Manifestation tautomers crystals of nucleic acids]. Ukr Fiz Zh. 1992; 37(12): 1828-32.
[20] Zorkii PM, Razumaeva AE. The coexistence of molecules having different structures in organic crystals. J Struct Chem. 1979;20(3):390–3.
[21] Razumaeva AE, Zorkii PM. A quantitative comparison of organic molecular geometry. J Struct Chem. 1980;21(2):184–8.
[22] Sharma BD, McConnell JF. The crystal and molecular structure of isocytosine. Acta Crystallogr. 1965;19(5):797-806.
[23] Beetz CP, Ascarelli G. The low frequency vibrations of the nucleosides: Uridine, cytidine and inosine. Determination of vibrations associated with the ribose ring. Spectrochimica Acta Part A. 1980;36(6):525–34.
[24] Weber I, Kirin D. Low-frequency vibrational spectra of cytosine monohydrate single crystals. J Mol Struct. 1992;267:67–72.
[25] Govorun DM, Danchuk VD, Mishchuk YaR, Kondratyuk IV, Zheltovsky MV. About nonplanarity and dipole nonstability of canonical nucleotide bases methylated at the glycoside nitrogen. Dopovidi Nats Akad Nauk Ukrainy. 1995; (6):117-9.
[26] Hovorun DM, Mishchuk YaR, Kondratyuk IV. On a quantum-chemical nature of a stereochemical nonrigidity of canonical nucleotide bases. Biopolym Cell. 1996; 12(5):5-12.
[27] Bersuker IB. The Jahn-Teller effect and vibronic maymodeystvin in modern chemistry. M.: Nauka, 1987. 344.
[28] Hovorun DM, Mishchuk YaR, Kondratyuk IV. Topological features of potential energy hypersurface of canonical nucleotide bases. Biopolym Cell. 1996; 12(5):13-17.
[29] Govorun DM, Mischuk YaR, Kondratyuk IV, Zheltovs'kyi MV. Dynamic stereo isomerism of Watson-Crick nucleotide base pairs. Dopovidi Nats Akad Nauk Ukrainy. 1995;(11):121-3.
[30] Gol'danskii VI. M?ssbauer studies of tunnel phenomena in chemical and biological physics. Russ Chem Rev. 1987; 56(10):935–47.
[31] Krupianski? IuF, Sha?tan KV, Gol'danski? VI, Kurinov IV, Rubin AB. [Study of protein dynamics using M?ssbauer spectroscopy]. Biofizika. 1987;32(5):761-74.
[32] McMullan RK, Benci P, Craven BM. The neutron crystal structure of 9-methyladenine at 126 K. Acta Crystallogr B. 1980;36(6):1424–30.
[33] Riggs NV. An ab initio study of the stationary structures of the major gas-phase tautomer of adenine. Chem Phys Lett. 1991;177(4-5):447–50.
[34] Tretyak SM, Mitkevich VV. Adenin Structure. Kharkov, (Preprint Fiz-tekh. In-t Nizkih Temperatur AN UkrSSR N 9—89) 1989; 8 p.
[35] Barker DL, Marsh RE. The crystal structure of cytosine. Acta Cryst. 1964;17(12):1581–7.
[36] Bugg CE, Thewalt UT, Marsh RE. Base stacking in nucleic acid components: the crystal structures of guanine, guanosine and iosine. Biochem Biophys Res Commun. 1968;33(3):436-40.
[37] Tret'yak SM, Mitkevich VV, Sukhodub LF. Adenine structure, its alkyl derivatives and their crystalline hydrates. Abstracts of reports 7th All-Union. symp. Pushchino, 1986; 125-6.
[38] Tret'yak SM, Mitkevich VV, Sukhodub LF. Adenine trihydrate: structure at 295 K and 105 K. Kristallografiya. 1986; 32(5):1268-71.
[39] McClure RJ, Craven BM. New investigations of cytosine and its monohydrate. Acta Crystallogr. 1973;29(6):1234–8.
[40] Weber HP, Craven BM, McMullan RK. The structure of deuterated cytosine monohydrate at 82 K by neutron diffraction. Acta Crystallogr B. 1980;36(3):645–9.
[41] Pershin VK, Pershin VlK, Zorkiy PM. Mesophase - molecular systems with partial order: structure, mechanisms of polymorphism. Probl. crystal Chemistry. M.: Nauka, 1988;30-82.
[42] Klinger MI. Nizkotemperaturnye svoistva i lokalizovannye elektronnye sostoyaniya stekol. Uspekhi Fizicheskih Nauk. 1987;152(8):623-52.
[43] Shorygin PP. Raman scattering and conjugation. Russ Chem Rev. 1971; 40 (4):367–92. http://dx.doi.org/ 10.1070/RC1971v040n04ABEH001924
[44] Shorygin P, Burstein KYa. Pairing and periodic system of elements. Russ Chem Rev. 1991; 60(1):1-24.
[45] Romm IP, Guryanova EN p -Conjugation in Aromatic Compounds of Group V and VI Elements. Russ Chem Rev. 1986; 55(2):83-98.
[46] Govorun DM, Kondratyuk IV, Mishchuk YaR, Zheltovsky NV. The manifestation of Jahn-Teller effect in electronic absorption spectra of nucleic acids and their constituents. Int Sci conf. "Physics and Chemistry of org. phosphors" 95 (9—13 Oct 1995 ): Proc. Kharkov, 1995; 126.
[47] Mishra PC. Vibrational structures and intensity distributions in the electronic absorption spectra of nucleic acid bases: evidence for non-planarity of guanine. J Mol Struct. 1986;144(3-4):309–17.
[48] Chalyy AV. The influence of external electromagnetic fields on the ordering processes in environments with biochemical reactions. Investigation of the interaction of electromagnetic waves in the millimeter and submillimeter ranges with biological objects. Kiev: Naukova Dumka, 1989: 66-74.
[49] Govorun DM, Mishchuk YaR, Kondratyuk IV, Zheltovsky MV. Intramolecular cooperative hydrogen bonds in nucleotide bases. Dopovidi Nats Akad Nauk Ukrainy. 1996;(8):141-4.
[50] Smolyakov BP, Khaimovich EP. Dinamicheskie protsessy v dielektricheskikh steklakh pri nizkikh temperaturakh. Uspekhi Fizicheskih Nauk. 1982;136(2):317-43.
[51] Zorkiy PM. New view on the structure of an organic crystal. Zhurnal fizicheskoi khimii. 1994; 68(6):966-74.
[52] Iogansen AV. Infrared spectroscopy and spectral determination of the energy of the hydrogen bond. The hydrogen bond. M.: Nauka, 1981;112-55.
[53] Devyatykh GG, Sennikov PG. Spectroscopic determination and study of the molecular state of water in ultrapure volatile inorganic substances. Russ Chem Rev. 1995; 64 (9): 817–30.
[54] Govorun DM, Mishchuk YaR, Zheltovskiy MV. Research by calorimetry spectral energy of intermolecular bonds in crystals and spivkrystalizatah nucleotide bases. Theses. XI Ukr. Summer School "Spectroscopy of atoms and crystals" (Kharkiv, 10—16 May 1993). Kyiv, 1993; 70.
[55] Gabuda SP, Rzhavin AF. Nuclear magnetic resonance in crystallohydrates and hydrated proteins. Novosibirsk, Nauka. 1978; 160 p.
[56] Grimm H, Rupprecht A. Inelastic neutron scattering studies of oriented DNA. Nonlinear excitations in biomolecules (Les Houches School, May 30 to June 4, 1994).Ed. M. Peyrard. Berlin: Springer, 1994;101—115.
[57] Iakushevich LV. [Dynamics of DNA]. Mol Biol (Mosk). 1989;23(3):652-62.
[58] Frank-Kamenetski? MD. [Fluctuational mobility of DNA]. Mol Biol (Mosk). 1983;17(3):639-52.
[59] Zhurkin VB. [Local mobility of the DNA double helix. Comparison of conformational analysis with experiments]. Mol Biol (Mosk). 1983;17(3):622-38.