179
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
79. Ebrahimi A, Habibi-Khorassani M, Bazzi S (2011) The impact of protonation and deprotonation of 3-methyl-2′-deoxyadenosine on N-glycosidic bond cleavage. Phys Chem Chem Phys:
PCCP 13:3334–3343. doi:10.1039/c0cp01279c
80. Berti PJ, Tanaka KSE (2002) No title. Adv Phys Org Chem 37:239–314.
81. Loverix S, Geerlings P, McNaughton M et al (2005) Substrate-assisted leaving group activation in enzyme-catalyzed N-glycosidic bond cleavage. J Biol Chem 280:14799–14802.
doi:10.1074/jbc.M413231200
82. Mol CD, Parikh SS, Putnam CD et al (1999) DNA repair mechanisms for the recognition
and removal of damaged DNA bases. Annu Rev Biophys and Biomol Struct 28:101–128.
doi:10.1146/annurev.biophys.28.1.101
83. Cao C, Kwon K, Jiang YL et al (2003) Solution structure and base perturbation studies reveal
a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I. J Biol
Chem 278:48012–48020. doi: 10.1074/jbc.M307500200
84. Palamarchuk GV, Shishkin OV, Gorb L, Leszczynski J (2013) Nucleic acid bases in anionic
2′-deoxyribonucleotides: a DFT/B3LYP study of structures, relative stability, and proton affinities. J Phys Chem B 117:2841–2849. doi:10.1021/jp311363c
85. Gonnella NC, Nakanishi H, Holtwick JB et al (1983) Studies of tautomers and protonation
of adenine and its derivatives by nitrogen-15 nuclear magnetic resonance spectroscopy. J Am
Chem Soc 105:2050–2055. doi:10.1021/ja00345a063
86. Brown RD, Godfrey PD, McNaughton D, Pierlot AP (1989) A study of the major gas-phase tautomer of adenine by microwave spectroscopy. Chem Phys Lett 156:61–63. doi:10.1016/00092614(89)87081-2
87. Lias SG, Liebman JF, Levin RD (1984) Evaluated gas phase basicities and proton affinities
of molecules; heats of formation of protonated molecules. J Phys Chem Ref Data 13:695.
doi:10.1063/1.555719
88. Greco F, Liguori A, Sindona G, Uccella N (1990) Gas-phase proton affinity of deoxyribonucleosides and related nucleobases by fast atom bombardment tandem mass spectrometry. J
the American Chem Soc 112:9092–9096. doi:10.1021/ja00181a009
89. Meot-Ner M (1979) Ion thermochemistry of low-volatility compounds in the gas phase. 2.
Intrinsic basicities and hydrogen-bonded dimers of nitrogen heterocyclics and nucleic bases.
J Am Chem Soc 101:2396–2403. doi:10.1021/ja00503a027
90. Kurinovich MA, Lee JK (2000) The acidity of uracil from the gas phase to solution: the coalescence of the N1 and N3 sites and implications for biological glycosylation. J Am Chem
Soc 122:6258–6262. doi:10.1021/ja000549y
91. Kurinovich MA, Lee JK (2002) The acidity of uracil and uracil analogs in the gas phase: four
surprisingly acidic sites and biological implications. J Am Soc Mass Spectrom 13:985–995.
doi:10.1016/S1044-0305(02)00410-5
92. Liu M, Li T, Amegayibor FS et al (2008) Gas-phase thermochemical properties of pyrimidine
nucleobases. J Org Chem 73:9283–9291. doi:10.1021/jo801822s
93. Bonaccorsi R, Pullman A, Scrocco E, Tomasi J (1972) The molecular electrostatic potentials for the nucleic acid bases: adenine, thymine, and cytosine. Theor Chim Acta 24:51–60.
doi:10.1007/BF00528310
94. Russo N, Toscano M, Grand A, Jolibois F (1998) Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: theoretical investigation into the framework
of density functional theory. J Comput Chem 19:989–1000. doi:10.1002/(SICI)1096987X(19980715)19:9<989::AID-JCC1>3.0.CO;2–F
95. Colominas C, Luque FJ, Orozco M (1996) Tautomerism and protonation of guanine and
cytosine. implications in the formation of hydrogen-bonded complexes. J Am Chem Soc
118:6811–6821. doi:10.1021/ja954293l
96. Podolyan Y, Gorb L, Leszczynski J (2000) Protonation of nucleic acid bases. A comprehensive post-Hartree–Fock study of the energetics and proton affinities. J Phys Chem A
104:7346–7352. doi:10.1021/jp000740u
97. Liguori A, Napoli A, Sindona G (2000) Survey of the proton affinities of adenine, cytosine,
thymine and uracil dideoxyribonucleosides, deoxyribonucleosides and ribonucleosides. J
Mass Spectrom: JMS 35:139–144. doi:10.1002/(SICI)1096-9888(200002)35:2<139::AIDJMS921>3.0.CO;2–A
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
79. Ebrahimi A, Habibi-Khorassani M, Bazzi S (2011) The impact of protonation and deprotonation of 3-methyl-2′-deoxyadenosine on N-glycosidic bond cleavage. Phys Chem Chem Phys:
PCCP 13:3334–3343. doi:10.1039/c0cp01279c
80. Berti PJ, Tanaka KSE (2002) No title. Adv Phys Org Chem 37:239–314.
81. Loverix S, Geerlings P, McNaughton M et al (2005) Substrate-assisted leaving group activation in enzyme-catalyzed N-glycosidic bond cleavage. J Biol Chem 280:14799–14802.
doi:10.1074/jbc.M413231200
82. Mol CD, Parikh SS, Putnam CD et al (1999) DNA repair mechanisms for the recognition
and removal of damaged DNA bases. Annu Rev Biophys and Biomol Struct 28:101–128.
doi:10.1146/annurev.biophys.28.1.101
83. Cao C, Kwon K, Jiang YL et al (2003) Solution structure and base perturbation studies reveal
a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I. J Biol
Chem 278:48012–48020. doi: 10.1074/jbc.M307500200
84. Palamarchuk GV, Shishkin OV, Gorb L, Leszczynski J (2013) Nucleic acid bases in anionic
2′-deoxyribonucleotides: a DFT/B3LYP study of structures, relative stability, and proton affinities. J Phys Chem B 117:2841–2849. doi:10.1021/jp311363c
85. Gonnella NC, Nakanishi H, Holtwick JB et al (1983) Studies of tautomers and protonation
of adenine and its derivatives by nitrogen-15 nuclear magnetic resonance spectroscopy. J Am
Chem Soc 105:2050–2055. doi:10.1021/ja00345a063
86. Brown RD, Godfrey PD, McNaughton D, Pierlot AP (1989) A study of the major gas-phase tautomer of adenine by microwave spectroscopy. Chem Phys Lett 156:61–63. doi:10.1016/00092614(89)87081-2
87. Lias SG, Liebman JF, Levin RD (1984) Evaluated gas phase basicities and proton affinities
of molecules; heats of formation of protonated molecules. J Phys Chem Ref Data 13:695.
doi:10.1063/1.555719
88. Greco F, Liguori A, Sindona G, Uccella N (1990) Gas-phase proton affinity of deoxyribonucleosides and related nucleobases by fast atom bombardment tandem mass spectrometry. J
the American Chem Soc 112:9092–9096. doi:10.1021/ja00181a009
89. Meot-Ner M (1979) Ion thermochemistry of low-volatility compounds in the gas phase. 2.
Intrinsic basicities and hydrogen-bonded dimers of nitrogen heterocyclics and nucleic bases.
J Am Chem Soc 101:2396–2403. doi:10.1021/ja00503a027
90. Kurinovich MA, Lee JK (2000) The acidity of uracil from the gas phase to solution: the coalescence of the N1 and N3 sites and implications for biological glycosylation. J Am Chem
Soc 122:6258–6262. doi:10.1021/ja000549y
91. Kurinovich MA, Lee JK (2002) The acidity of uracil and uracil analogs in the gas phase: four
surprisingly acidic sites and biological implications. J Am Soc Mass Spectrom 13:985–995.
doi:10.1016/S1044-0305(02)00410-5
92. Liu M, Li T, Amegayibor FS et al (2008) Gas-phase thermochemical properties of pyrimidine
nucleobases. J Org Chem 73:9283–9291. doi:10.1021/jo801822s
93. Bonaccorsi R, Pullman A, Scrocco E, Tomasi J (1972) The molecular electrostatic potentials for the nucleic acid bases: adenine, thymine, and cytosine. Theor Chim Acta 24:51–60.
doi:10.1007/BF00528310
94. Russo N, Toscano M, Grand A, Jolibois F (1998) Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: theoretical investigation into the framework
of density functional theory. J Comput Chem 19:989–1000. doi:10.1002/(SICI)1096987X(19980715)19:9<989::AID-JCC1>3.0.CO;2–F
95. Colominas C, Luque FJ, Orozco M (1996) Tautomerism and protonation of guanine and
cytosine. implications in the formation of hydrogen-bonded complexes. J Am Chem Soc
118:6811–6821. doi:10.1021/ja954293l
96. Podolyan Y, Gorb L, Leszczynski J (2000) Protonation of nucleic acid bases. A comprehensive post-Hartree–Fock study of the energetics and proton affinities. J Phys Chem A
104:7346–7352. doi:10.1021/jp000740u
97. Liguori A, Napoli A, Sindona G (2000) Survey of the proton affinities of adenine, cytosine,
thymine and uracil dideoxyribonucleosides, deoxyribonucleosides and ribonucleosides. J
Mass Spectrom: JMS 35:139–144. doi:10.1002/(SICI)1096-9888(200002)35:2<139::AIDJMS921>3.0.CO;2–A