176
T. A. Zubatiuk et al.
20. Shishkin OV, Gorb L, Zhikol OA, Leszczynski J (2004) Conformational analysis of canonical
2-deoxyribonucleotides. 2. Purine nucleotides. J Biomol Struct Dyn 22:227–244. doi:10.108
0/07391102.2004.10506998
21. Gorb L, Shishkin O, Leszczynski J (2005) Charges of phosphate groups. A role in stabilization of 2′-deoxyribonucleotides. A DFT investigation. J Biomol Struct Dyn 22:441–454. doi:
10.1080/07391102.2005.10507015
22. Šponer J, Leszczynski J, Hobza P (1996) Structures and energies of hydrogen-bonded
DNA base pairs. A nonempirical study with Inclusion of electron correlation. J Phys Chem
100:1965–1974. doi:10.1021/jp952760f
23. Šponer J, Leszczyński J, Hobza P (1996) Nature of nucleic acid–base stacking: nonempirical
ab initio and empirical potential Characterization of 10 stacked base dimers. comparison of
stacked and h-bonded base pairs. J Phys Chem 100:5590–5596. doi:10.1021/jp953306e
24. Šponer J, Burda J V., Sabat M et al (1998) Interaction between the guanine–cytosine Watson–
Crick DNA base pair and hydrated group IIa (Mg 2+, Ca 2+, Sr 2+, Ba 2+ ) and group IIb (Zn
2+, Cd 2+, Hg 2+ ) metal cations. J Phys Chem A 102:5951–5957. doi:10.1021/jp980769m
25. Řeha D, KabelácÌ M, RyjácÌek F et al (2002) Intercalators. 1. nature of stacking interactions
between intercalators (ethidium, daunomycin, ellipticine, and 4′,6-diaminide-2-phenylindole)
and DNA base pairs. Ab initio quantum chemical, Density functional theory, and empirical
potential study. J American Chem Soc 124:3366–3376. doi:10.1021/ja011490d
26. Spacková N, Cheatham TE, Ryjácek F et al (2003) Molecular dynamics simulations and
thermodynamics analysis of DNA–drug complexes. Minor groove binding between 4′,6-diamidino-2-phenylindole and DNA duplexes in solution. J Am Chem Soc 125:1759–1769.
doi:10.1021/ja025660d
27. Shishkin O V, Gorb L, Luzanov A V et al (2003) Structure and conformational flexibility of
uracil:a comprehensive study of performance of the MP2, B3LYP and SCC-DFTB methods.
J Mol Struct: Theochem 625:295–303. doi:10.1016/S0166-1280(03)00032-0
28. Gorb L, Kaczmarek A, Gorb A et al (2005) Thermodynamics and kinetics of intramolecular proton transfer in guanine. Post Hartree-Fock study. J Phys Chem B 109:13770–13776.
doi:10.1021/jp050394m
29. Isayev O, Furmanchuk A, Shishkin O V et al (2007) Are isolated nucleic acid bases really planar? A Car-Parrinello molecular dynamics study. J phys chem B 111:3476–3480. doi:10.1021/
jp070857j
30. Samijlenko SP, Yurenko YP, Stepanyugin A V, Hovorun DM (2010) Tautomeric equilibrium
of uracil and thymine in model protein–nucleic acid contacts. Spectroscopic and quantum
chemical approach. J phys chem B 114:1454–1461. doi:10.1021/jp909099a
31. Shishkin O V, Palamarchuk G V, Gorb L, Leszczynski J (2006) Intramolecular hydrogen
bonds in canonical 2′-deoxyribonucleotides: an atoms in molecules study. J phys chem B
110:4413–4422. doi:10.1021/jp056902+
32. Slavícek P, Winter B, Faubel M et al (2009) Ionization energies of aqueous nucleic acids:
photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations. J Am Chem
Soc 131:6460–6467. doi:10.1021/ja8091246
33. Sapse DS, Champeil É, Maddaluno J et al (2008) An ab initio study of the interaction of DNA
fragments with methyllithium. C R Chim 11:1262–1270. doi:10.1016/j.crci.2008.04.009
34. Yurenko YP, Zhurakivsky RO, Ghomi M et al (2007) How many conformers determine the
thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical
study. J Phys Chem B 111:9655–9663. doi:10.1021/jp073203j
35. Yurenko YP, Zhurakivsky RO, Ghomi M et al (2007) Comprehensive conformational analysis
of the nucleoside analogue 2′-beta-deoxy-6-azacytidine by DFT and MP2 calculations. J Phys
Chem B 111:6263–6271. doi:10.1021/jp066742h
36. Shishkin OV, Pelmenschikov A, Hovorun DM, Leszczynski J (2000) Molecular structure of
free canonical 2′-deoxyribonucleosides: a density functional study. J Mol Struct 526:329–
341. doi:10.1016/S0022-2860(00)00497-X
37. Hobza P, Šponer J (1999) Structure, energetics, and dynamics of the nucleic acid base pairs:
nonempirical ab initio calculations. Chem Rev 99:3247–3276. doi:10.1021/cr9800255
T. A. Zubatiuk et al.
20. Shishkin OV, Gorb L, Zhikol OA, Leszczynski J (2004) Conformational analysis of canonical
2-deoxyribonucleotides. 2. Purine nucleotides. J Biomol Struct Dyn 22:227–244. doi:10.108
0/07391102.2004.10506998
21. Gorb L, Shishkin O, Leszczynski J (2005) Charges of phosphate groups. A role in stabilization of 2′-deoxyribonucleotides. A DFT investigation. J Biomol Struct Dyn 22:441–454. doi:
10.1080/07391102.2005.10507015
22. Šponer J, Leszczynski J, Hobza P (1996) Structures and energies of hydrogen-bonded
DNA base pairs. A nonempirical study with Inclusion of electron correlation. J Phys Chem
100:1965–1974. doi:10.1021/jp952760f
23. Šponer J, Leszczyński J, Hobza P (1996) Nature of nucleic acid–base stacking: nonempirical
ab initio and empirical potential Characterization of 10 stacked base dimers. comparison of
stacked and h-bonded base pairs. J Phys Chem 100:5590–5596. doi:10.1021/jp953306e
24. Šponer J, Burda J V., Sabat M et al (1998) Interaction between the guanine–cytosine Watson–
Crick DNA base pair and hydrated group IIa (Mg 2+, Ca 2+, Sr 2+, Ba 2+ ) and group IIb (Zn
2+, Cd 2+, Hg 2+ ) metal cations. J Phys Chem A 102:5951–5957. doi:10.1021/jp980769m
25. Řeha D, KabelácÌ M, RyjácÌek F et al (2002) Intercalators. 1. nature of stacking interactions
between intercalators (ethidium, daunomycin, ellipticine, and 4′,6-diaminide-2-phenylindole)
and DNA base pairs. Ab initio quantum chemical, Density functional theory, and empirical
potential study. J American Chem Soc 124:3366–3376. doi:10.1021/ja011490d
26. Spacková N, Cheatham TE, Ryjácek F et al (2003) Molecular dynamics simulations and
thermodynamics analysis of DNA–drug complexes. Minor groove binding between 4′,6-diamidino-2-phenylindole and DNA duplexes in solution. J Am Chem Soc 125:1759–1769.
doi:10.1021/ja025660d
27. Shishkin O V, Gorb L, Luzanov A V et al (2003) Structure and conformational flexibility of
uracil:a comprehensive study of performance of the MP2, B3LYP and SCC-DFTB methods.
J Mol Struct: Theochem 625:295–303. doi:10.1016/S0166-1280(03)00032-0
28. Gorb L, Kaczmarek A, Gorb A et al (2005) Thermodynamics and kinetics of intramolecular proton transfer in guanine. Post Hartree-Fock study. J Phys Chem B 109:13770–13776.
doi:10.1021/jp050394m
29. Isayev O, Furmanchuk A, Shishkin O V et al (2007) Are isolated nucleic acid bases really planar? A Car-Parrinello molecular dynamics study. J phys chem B 111:3476–3480. doi:10.1021/
jp070857j
30. Samijlenko SP, Yurenko YP, Stepanyugin A V, Hovorun DM (2010) Tautomeric equilibrium
of uracil and thymine in model protein–nucleic acid contacts. Spectroscopic and quantum
chemical approach. J phys chem B 114:1454–1461. doi:10.1021/jp909099a
31. Shishkin O V, Palamarchuk G V, Gorb L, Leszczynski J (2006) Intramolecular hydrogen
bonds in canonical 2′-deoxyribonucleotides: an atoms in molecules study. J phys chem B
110:4413–4422. doi:10.1021/jp056902+
32. Slavícek P, Winter B, Faubel M et al (2009) Ionization energies of aqueous nucleic acids:
photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations. J Am Chem
Soc 131:6460–6467. doi:10.1021/ja8091246
33. Sapse DS, Champeil É, Maddaluno J et al (2008) An ab initio study of the interaction of DNA
fragments with methyllithium. C R Chim 11:1262–1270. doi:10.1016/j.crci.2008.04.009
34. Yurenko YP, Zhurakivsky RO, Ghomi M et al (2007) How many conformers determine the
thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical
study. J Phys Chem B 111:9655–9663. doi:10.1021/jp073203j
35. Yurenko YP, Zhurakivsky RO, Ghomi M et al (2007) Comprehensive conformational analysis
of the nucleoside analogue 2′-beta-deoxy-6-azacytidine by DFT and MP2 calculations. J Phys
Chem B 111:6263–6271. doi:10.1021/jp066742h
36. Shishkin OV, Pelmenschikov A, Hovorun DM, Leszczynski J (2000) Molecular structure of
free canonical 2′-deoxyribonucleosides: a density functional study. J Mol Struct 526:329–
341. doi:10.1016/S0022-2860(00)00497-X
37. Hobza P, Šponer J (1999) Structure, energetics, and dynamics of the nucleic acid base pairs:
nonempirical ab initio calculations. Chem Rev 99:3247–3276. doi:10.1021/cr9800255