204
M. Ilchenko and I. Dubey
92. Schlund S, Schmuck C, Engels B (2005) Knock-out” analogues as a tool to quantify supramolecular processes: a theoretical study of molecular interactions in guanidiniocarbonyl
pyrrole carboxylate dimers J Am Chem Soc 127:11115–11124
93. Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Electronic structure calculations on
workstation computers: the program system turbomole. Chem Phys Lett 162:165–169.
94. Von Arnim M, Ahlrichs R (1998) Performance of parallel TURBOMOLE for density functional calculations. J Comput Chem 19:1746–1757
95. Miertus 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
96. Ilchenko MM, Dubey I Ya (2011) Density functional study of the structure of guanine octets
in aqueous medium. Int Rev Biophys Chem 2:82–86
97. Fonseca Guerra C, van der Wijst T, Poater J, Swart M, Bickelhaupt MF (2010) Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences
in π-π-stacking and hydrogen-bonding behavior. Theor Chem Acc 125:245–252
98. Mezzache S, Alves S, Paumard J-P, Pepe C, Tabet J-C (2007) Theoretical and gas-phase
studies of specific cationized purine base quartet. Rapid Commun Mass Spectrom 21:1075–
1082
99. Meyer M, Steinke T, Brandl M, Sühnel J (2001) Density functional study of guanine and
uracil quartets and of guanine quartet/metal ion complexes. J Comput Chem 22:109–124
100. Meng F, Wang F, Zhao X, Jalbout AF (2008) Guanine tetrad interacting with divalent metal
ions (M = Fe 2 + , Co
2 +
, Ni
2 +
, Cu
2 +
and Zn
2 +
): a density functional study. J Mol Struct: THEOCHEM 854:26–30.
101. Boys SF, Bernardi F (1970) Calculations of small molecular interaction by the difference of
separate total energies. Some procedures with reduced error. Mol Phys 19:553–566
102. Bader RFW (1990) Atoms in Molecules: A Quantum Theory. Clarendon Press, Oxford, UK
103. Rozas I, Alkorta I, Elguero J (1997) Unusual hydrogen bonds: H…π interactions. J Phys
Chem A 101:9457–9463
104. Deepa P, Kolandaivel P, Senthilkumar K (2011) Structural properties and the effect of interaction of alkali (Li
+
, Na
+
, K
+
) and alkaline earth (Be
2 +
, Mg
2 +
, Ca
2 +
) metal cations with G
and SG-tetrads. Comput Theor Chem 974:57–65
105. Meng F, Xu W, Liu C (2004) Theoretical study of incorporating 6-thioguanine into a guanine tetrad and their influence on the metal ion–guanine tetrad. Chem Phys Lett 389:421–
426
106. Yurenko YeP, Novotný J, Sklenář V, Marek R (2013) Exploring non-covalent interactions in
guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum
chemical approach. Phys. Chem Chem Phys DOI: 10.1039/C3CP53875C
107. Jissy AK, Datta A (2012) Effect of external electric field on H-bonding and π-stacking interactions in guanine aggregates. Chem Phys Chem 13:4163–4172
108. Gu J, Leszczynski J, Bansal M (1999) A new insight into the structure and stability of
Hoogsteen hydrogen-bonded G-tetrad: an ab initio SCF study. Chem Phys Lett 311:209–
314
109. Gu J, Leszczynski J (2000) A remarkable alteration in the bonding pattern: an HF and DFT
study on the interactions between the metal cations and the Hoogsteen hydrogen-bonded
G-tetrad. J Phys Chem A 104:6308–6313
110. van Mourik T, Dingley AJ (2005) Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters. Chem
Eur J 11:6064–6079
111. Becke AD (1997) Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals. J Chem Phys 107:8554–8560
112. NWChem (2003) Version 4.5, High Performance Computational Chemistry Group, Pacific
Northwest National Laboratory, Richland WA
M. Ilchenko and I. Dubey
92. Schlund S, Schmuck C, Engels B (2005) Knock-out” analogues as a tool to quantify supramolecular processes: a theoretical study of molecular interactions in guanidiniocarbonyl
pyrrole carboxylate dimers J Am Chem Soc 127:11115–11124
93. Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Electronic structure calculations on
workstation computers: the program system turbomole. Chem Phys Lett 162:165–169.
94. Von Arnim M, Ahlrichs R (1998) Performance of parallel TURBOMOLE for density functional calculations. J Comput Chem 19:1746–1757
95. Miertus 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
96. Ilchenko MM, Dubey I Ya (2011) Density functional study of the structure of guanine octets
in aqueous medium. Int Rev Biophys Chem 2:82–86
97. Fonseca Guerra C, van der Wijst T, Poater J, Swart M, Bickelhaupt MF (2010) Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences
in π-π-stacking and hydrogen-bonding behavior. Theor Chem Acc 125:245–252
98. Mezzache S, Alves S, Paumard J-P, Pepe C, Tabet J-C (2007) Theoretical and gas-phase
studies of specific cationized purine base quartet. Rapid Commun Mass Spectrom 21:1075–
1082
99. Meyer M, Steinke T, Brandl M, Sühnel J (2001) Density functional study of guanine and
uracil quartets and of guanine quartet/metal ion complexes. J Comput Chem 22:109–124
100. Meng F, Wang F, Zhao X, Jalbout AF (2008) Guanine tetrad interacting with divalent metal
ions (M = Fe 2 + , Co
2 +
, Ni
2 +
, Cu
2 +
and Zn
2 +
): a density functional study. J Mol Struct: THEOCHEM 854:26–30.
101. Boys SF, Bernardi F (1970) Calculations of small molecular interaction by the difference of
separate total energies. Some procedures with reduced error. Mol Phys 19:553–566
102. Bader RFW (1990) Atoms in Molecules: A Quantum Theory. Clarendon Press, Oxford, UK
103. Rozas I, Alkorta I, Elguero J (1997) Unusual hydrogen bonds: H…π interactions. J Phys
Chem A 101:9457–9463
104. Deepa P, Kolandaivel P, Senthilkumar K (2011) Structural properties and the effect of interaction of alkali (Li
+
, Na
+
, K
+
) and alkaline earth (Be
2 +
, Mg
2 +
, Ca
2 +
) metal cations with G
and SG-tetrads. Comput Theor Chem 974:57–65
105. Meng F, Xu W, Liu C (2004) Theoretical study of incorporating 6-thioguanine into a guanine tetrad and their influence on the metal ion–guanine tetrad. Chem Phys Lett 389:421–
426
106. Yurenko YeP, Novotný J, Sklenář V, Marek R (2013) Exploring non-covalent interactions in
guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum
chemical approach. Phys. Chem Chem Phys DOI: 10.1039/C3CP53875C
107. Jissy AK, Datta A (2012) Effect of external electric field on H-bonding and π-stacking interactions in guanine aggregates. Chem Phys Chem 13:4163–4172
108. Gu J, Leszczynski J, Bansal M (1999) A new insight into the structure and stability of
Hoogsteen hydrogen-bonded G-tetrad: an ab initio SCF study. Chem Phys Lett 311:209–
314
109. Gu J, Leszczynski J (2000) A remarkable alteration in the bonding pattern: an HF and DFT
study on the interactions between the metal cations and the Hoogsteen hydrogen-bonded
G-tetrad. J Phys Chem A 104:6308–6313
110. van Mourik T, Dingley AJ (2005) Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters. Chem
Eur J 11:6064–6079
111. Becke AD (1997) Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals. J Chem Phys 107:8554–8560
112. NWChem (2003) Version 4.5, High Performance Computational Chemistry Group, Pacific
Northwest National Laboratory, Richland WA