175
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
puter time. The support from computational facilities of joint computational cluster of SSI “Institute for Single Crystals” and Institute for Scintillation Materials of National Academy of Science
of Ukraine incorporated into Ukrainian National Grid is gratefully acknowledged.
References
1. Saenger W (1988) Principles of nucleic acid structures. Springer, New York
2. Neidle S (1994) DNA Structure and recognition. Oxford University Press, Oxford
3. Sinden RSR (1994) DNA structure and function. Academic Press, San Diego
4. Hecht SM (1996) Bioorganic chemistry: nucleic acids. Oxford University Press, Oxford
5. Chu CK, Baker DC (1993) Nucleosides and nucleotides as antitumor and antiviral agents.
Plenum Press, New York
6. Sato T (1984) Structure of calcium thymidine 5′-phosphate dihydrate, Ca2+.C10H13N2O8P2–
.2H2O. Acta Crystallogr Sect C Cryst Struct Commun 40:736–738. doi:10.1107/
S0108270184005539
7. Trueblood KN, Horn P, Luzzati V (1961) The crystal structure of calcium thymidylate. Acta
Crystallogr 14:965–982. doi:10.1107/S0365110X61002801
8. Lalitha HN, Ramakumar S, Viswamitra MA (1989) Structure of 5-methyl-2′-deoxycytidine
5′-monophosphate dihydrate. Acta Crystallogr Sect C Cryst Struct Commun 45:1652–1655.
doi:10.1107/S0108270189005445
9. Jardetsky O, Roberts GCK (1981) NMR in molecular biology. Academic Press, New York
10. Sundaralingam M (1973) Conformation of biological molecules and polymers. Jerus Symp
Quant Chem Biochem 5:417.
11. Sundaralingam M (1975) Structure and conformation of nucleic acid and protein–nucleic acid
interactions. University of Baltimore, Baltimore
12. Foloppe N, Hartmann B, Nilsson L, MacKerell AD (2002) Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophysical J
82:1554–1569. doi:10.1016/S0006-3495(02)75507-0
13. Leulliot N, Ghomi M, Scalmani G, Berthier G (1999) Ground state properties of the nucleic
acid constituents studied by density functional calculations. I. Conformational features of
ribose, dimethyl phosphate, uridine, cytidine, 5′-methyl phosphate-uridine, and 3′-methyl
phosphate-uridine. J Phys Chem A 103:8716–8724. doi: 10.1021/jp9915634
14. Leulliot N, Ghomi M, Jobic H et al (1999) Ground state properties of the nucleic acid constituents studied by density functional calculations. 2. Comparison between calculated and
experimental vibrational spectra of uridine and cytidine. J Phys Chem B 103:10934–10944.
doi:10.1021/jp9921147
15. Hocquet A, Leulliot N, Ghomi M (2000) Ground-state properties of nucleic acid constituents
studied by density functional calculations. 3. Role of sugar puckering and base orientation on
the energetics and geometry of 2′-deoxyribonucleosides and ribonucleosides. J Phys Chem B
104:4560–4568. doi:10.1021/jp994077p
16. Foloppe N, MacKerell AD (1999) Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA.
Biophysical J 76:3206–3218. doi:10.1016/S0006-3495(99)77472-2
17. Gaigeot M-P, Leulliot N, Ghomi M et al (2000) Analysis of the structural and vibrational
properties of RNA building blocks by means of neutron inelastic scattering and density functional theory calculations. Chem Phys 261:217–237. doi:10.1016/S0301-0104(00)00224-X
18. 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
19. Shishkin O V, Gorb L, Zhikol OA, Leszczynski J (2004) Conformational analysis of canonical 2-deoxyribonucleotides. 1. Pyrimidine nucleotides. J Biomol Struct Dyn 21:537–554. doi
:10.1080/07391102.2004.10506947
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
puter time. The support from computational facilities of joint computational cluster of SSI “Institute for Single Crystals” and Institute for Scintillation Materials of National Academy of Science
of Ukraine incorporated into Ukrainian National Grid is gratefully acknowledged.
References
1. Saenger W (1988) Principles of nucleic acid structures. Springer, New York
2. Neidle S (1994) DNA Structure and recognition. Oxford University Press, Oxford
3. Sinden RSR (1994) DNA structure and function. Academic Press, San Diego
4. Hecht SM (1996) Bioorganic chemistry: nucleic acids. Oxford University Press, Oxford
5. Chu CK, Baker DC (1993) Nucleosides and nucleotides as antitumor and antiviral agents.
Plenum Press, New York
6. Sato T (1984) Structure of calcium thymidine 5′-phosphate dihydrate, Ca2+.C10H13N2O8P2–
.2H2O. Acta Crystallogr Sect C Cryst Struct Commun 40:736–738. doi:10.1107/
S0108270184005539
7. Trueblood KN, Horn P, Luzzati V (1961) The crystal structure of calcium thymidylate. Acta
Crystallogr 14:965–982. doi:10.1107/S0365110X61002801
8. Lalitha HN, Ramakumar S, Viswamitra MA (1989) Structure of 5-methyl-2′-deoxycytidine
5′-monophosphate dihydrate. Acta Crystallogr Sect C Cryst Struct Commun 45:1652–1655.
doi:10.1107/S0108270189005445
9. Jardetsky O, Roberts GCK (1981) NMR in molecular biology. Academic Press, New York
10. Sundaralingam M (1973) Conformation of biological molecules and polymers. Jerus Symp
Quant Chem Biochem 5:417.
11. Sundaralingam M (1975) Structure and conformation of nucleic acid and protein–nucleic acid
interactions. University of Baltimore, Baltimore
12. Foloppe N, Hartmann B, Nilsson L, MacKerell AD (2002) Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophysical J
82:1554–1569. doi:10.1016/S0006-3495(02)75507-0
13. Leulliot N, Ghomi M, Scalmani G, Berthier G (1999) Ground state properties of the nucleic
acid constituents studied by density functional calculations. I. Conformational features of
ribose, dimethyl phosphate, uridine, cytidine, 5′-methyl phosphate-uridine, and 3′-methyl
phosphate-uridine. J Phys Chem A 103:8716–8724. doi: 10.1021/jp9915634
14. Leulliot N, Ghomi M, Jobic H et al (1999) Ground state properties of the nucleic acid constituents studied by density functional calculations. 2. Comparison between calculated and
experimental vibrational spectra of uridine and cytidine. J Phys Chem B 103:10934–10944.
doi:10.1021/jp9921147
15. Hocquet A, Leulliot N, Ghomi M (2000) Ground-state properties of nucleic acid constituents
studied by density functional calculations. 3. Role of sugar puckering and base orientation on
the energetics and geometry of 2′-deoxyribonucleosides and ribonucleosides. J Phys Chem B
104:4560–4568. doi:10.1021/jp994077p
16. Foloppe N, MacKerell AD (1999) Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA.
Biophysical J 76:3206–3218. doi:10.1016/S0006-3495(99)77472-2
17. Gaigeot M-P, Leulliot N, Ghomi M et al (2000) Analysis of the structural and vibrational
properties of RNA building blocks by means of neutron inelastic scattering and density functional theory calculations. Chem Phys 261:217–237. doi:10.1016/S0301-0104(00)00224-X
18. 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
19. Shishkin O V, Gorb L, Zhikol OA, Leszczynski J (2004) Conformational analysis of canonical 2-deoxyribonucleotides. 1. Pyrimidine nucleotides. J Biomol Struct Dyn 21:537–554. doi
:10.1080/07391102.2004.10506947