177
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
38. Sponer J, Leszczynski J, Hobza P (2002) Electronic properties, hydrogen bonding, stacking,
and cation binding of DNA and RNA bases. Biopolymers 61:3–31. doi:10.1002/1097-0282
(2001) 61:1 < 3::AID-BIP10048>3.0.CO;2–4
39. Svozil D, Kalina J, Omelka M, Schneider B (2008) DNA conformations and their sequence
preferences. Nucleic acids res 36:3690–3706. doi:10.1093/nar/gkn260
40. Schneider B, Neidle S, Berman HM (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42:113–124. doi:10.1002/(SICI)10970282(199707)42:1 < 113::AID-BIP10 > 3.0.CO;2–O
41. Drew HR, Wing RM, Takano T et al (1981) Structure of a B-DNA dodecamer: conformation
and dynamics. PNAS 78:2179.
42. Grzeskowiak K, Yanagi K, Privé GG, Dickerson and RE (1991) The structure of B-helical CG-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair
reversals. J Biol Chem 266:8861.
43. Shishkin OV, Gorb L, Luzanov AV 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
44. Bader RFW (1990) Atoms in molecules. A quantum theory. Clarendon, Oxford
45. Popelier PLA (1998) Characterization of a dihydrogen bond on the basis of the electron density. J Phys Chem A 102:1873–1878. doi: 10.1021/jp9805048
46. Koch U, Popelier PLA (1995) Characterization of C–H–O hydrogen bonds on the basis of the
charge density. J Phys Chem 99:9747–9754. doi:10.1021/j100024a016
47. Cremer D, Kraka E, Slee TS et al (1983) Description of homoaromaticity in terms of electron
distributions. J Am Chem Soc 105:5069–5075. doi:10.1021/ja00353a036
48. Hocquet A (2001) Intramolecular hydrogen bonding in 2′-deoxyribonucleosides: an AIM topological study of the electronic density. Phys Chem Chem Phys 3:3192–3199. doi:10.1039/
b101781k
49. Zefirov YV., Zorky PM (1989) No title. Uspekhi Khimii (Russian Chemical Rev) 58:713.
50. Thomas Steiner (2002) The hydrogen bond in the solid state. Angew Chem Int Ed 41:48.
doi:10.1002/1521-3773(20020104)41:1<48::AID-ANIE48>3.0.CO;2–U
51. Hocquet A, Ghomi M (2000) The peculiar role of cytosine in nucleoside conformational behaviour: hydrogen bond donor capacity of nucleic bases. Phys Chem Chem Phys 2:5351–
5353. doi:10.1039/b007246j
52. Shishkin OV, Palamarchuk GV, 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+
53. Palamarchuk GV, Shishkin OV, Gorb L, Leszczynski J (2009) Dependence of deformability
of geometries and characteristics of intramolecular hydrogen bonds in canonical 2′-deoxyribonucleotides on DNA conformations. J Biomol Struct Dyn 26:653–662. doi:10.1080/07391
102.2009.10507279
54. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789. doi:10.1103/PhysRevB.37.785
55. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098–3100. doi: 10.1103/PhysRevA.38.3098
56. Parr RG, Yang W (1989) Density functional theory of atoms and molecules. Oxford University Press, New York
57. Cammi R, Mennucci B, Tomasi J (2000) Fast evaluation of geometries and properties of
excited molecules in solution: a Tamm-Dancoff model with application to 4-dimethylaminobenzonitrile. J Phys Chem A 104:5631–5637. doi:10.1021/jp000156l
58. Cossi M, Scalmani G, Rega N, Barone V (2002) New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution. J
Chem Phys 117:43. doi: 10.1063/1.1480445
59. Miertuš S, Scrocco E, Tomasi J (1981) Electrostatic interaction of a solute with a continuum.
A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects. Chem
Phys 55:117–129. doi:10.1016/0301-0104(81)85090-2
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
38. Sponer J, Leszczynski J, Hobza P (2002) Electronic properties, hydrogen bonding, stacking,
and cation binding of DNA and RNA bases. Biopolymers 61:3–31. doi:10.1002/1097-0282
(2001) 61:1 < 3::AID-BIP10048>3.0.CO;2–4
39. Svozil D, Kalina J, Omelka M, Schneider B (2008) DNA conformations and their sequence
preferences. Nucleic acids res 36:3690–3706. doi:10.1093/nar/gkn260
40. Schneider B, Neidle S, Berman HM (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42:113–124. doi:10.1002/(SICI)10970282(199707)42:1 < 113::AID-BIP10 > 3.0.CO;2–O
41. Drew HR, Wing RM, Takano T et al (1981) Structure of a B-DNA dodecamer: conformation
and dynamics. PNAS 78:2179.
42. Grzeskowiak K, Yanagi K, Privé GG, Dickerson and RE (1991) The structure of B-helical CG-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair
reversals. J Biol Chem 266:8861.
43. Shishkin OV, Gorb L, Luzanov AV 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
44. Bader RFW (1990) Atoms in molecules. A quantum theory. Clarendon, Oxford
45. Popelier PLA (1998) Characterization of a dihydrogen bond on the basis of the electron density. J Phys Chem A 102:1873–1878. doi: 10.1021/jp9805048
46. Koch U, Popelier PLA (1995) Characterization of C–H–O hydrogen bonds on the basis of the
charge density. J Phys Chem 99:9747–9754. doi:10.1021/j100024a016
47. Cremer D, Kraka E, Slee TS et al (1983) Description of homoaromaticity in terms of electron
distributions. J Am Chem Soc 105:5069–5075. doi:10.1021/ja00353a036
48. Hocquet A (2001) Intramolecular hydrogen bonding in 2′-deoxyribonucleosides: an AIM topological study of the electronic density. Phys Chem Chem Phys 3:3192–3199. doi:10.1039/
b101781k
49. Zefirov YV., Zorky PM (1989) No title. Uspekhi Khimii (Russian Chemical Rev) 58:713.
50. Thomas Steiner (2002) The hydrogen bond in the solid state. Angew Chem Int Ed 41:48.
doi:10.1002/1521-3773(20020104)41:1<48::AID-ANIE48>3.0.CO;2–U
51. Hocquet A, Ghomi M (2000) The peculiar role of cytosine in nucleoside conformational behaviour: hydrogen bond donor capacity of nucleic bases. Phys Chem Chem Phys 2:5351–
5353. doi:10.1039/b007246j
52. Shishkin OV, Palamarchuk GV, 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+
53. Palamarchuk GV, Shishkin OV, Gorb L, Leszczynski J (2009) Dependence of deformability
of geometries and characteristics of intramolecular hydrogen bonds in canonical 2′-deoxyribonucleotides on DNA conformations. J Biomol Struct Dyn 26:653–662. doi:10.1080/07391
102.2009.10507279
54. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789. doi:10.1103/PhysRevB.37.785
55. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098–3100. doi: 10.1103/PhysRevA.38.3098
56. Parr RG, Yang W (1989) Density functional theory of atoms and molecules. Oxford University Press, New York
57. Cammi R, Mennucci B, Tomasi J (2000) Fast evaluation of geometries and properties of
excited molecules in solution: a Tamm-Dancoff model with application to 4-dimethylaminobenzonitrile. J Phys Chem A 104:5631–5637. doi:10.1021/jp000156l
58. Cossi M, Scalmani G, Rega N, Barone V (2002) New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution. J
Chem Phys 117:43. doi: 10.1063/1.1480445
59. Miertuš S, Scrocco E, Tomasi J (1981) Electrostatic interaction of a solute with a continuum.
A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects. Chem
Phys 55:117–129. doi:10.1016/0301-0104(81)85090-2