205
6 Quantum Chemical Approaches in Modeling the Structure of DNA …
113. Szolomájer J, Paragi G, Batta G, Fonseca Guerra C, Bickelhaupt FM, Kele Z, Pádár P, Kupihára Z, Kovács L (2011) 3-Substituted xanthines as promising candidates for quadruplex
formation: computational, synthetic and analytical studies. New J Chem 35:486–482
114. Meyer M, Hocquet A, Sühnel J (2005) Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. J Comput Chem 26:352–364
115. Meyer M, Steinke T, Sühnel J (2007) Density functional study of isoguanine tetrad and
pentad sandwich complexes with alkali metal ions. J Mol Model 13:335–345
116. Hua Y, Changenet-Barret P, Improta R, Vaya I, Gustavsson T, Kotlyar AB, Zikich D, Šket P,
Plavec J, Markovitsi D (2012) Cation effect on the electronic excited states of guanine nanostructures studied by time-resolved fluorescence spectroscopy. J Phys Chem C 116:14682–
14689
117. Liu H, Gauld JW (2009) Protonation of guanine quartets and quartet stacks: insights from
DFT studies. Phys Chem Chem Phys 11:278–287
118. Lech CJ, Heidi B, Phan AT (2013) Guanine base stacking in G-quadruplex nucleic acids.
Nucl Acids Res 41:2034–2046
119. Šponer J, Mládek A, Špačková N, Cang X, Cheatham TE, Grimme S (2013) Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantumchemical computations. J Am Chem Soc 135:9785–9796
120. Fonseca Guerra C, Zijlstra H, Paragi G, Bickelhaupt FM (2011) Telomere structure and
stability: Covalency in hydrogen bonds, not resonance assistance, causes cooperativity in
guanine quartets. Chem Eur J 17:12612–12622
121. Warshel A. (1991). Computer Modeling of Chemical Reactions in Enzymes and Solutions.
John Wiley, New York.
122. Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/
MM) simulations for organic and enzymatic reactions. Acc Chem Res 43:142–151
123. Banáš P, Jurečka P, Walter NG, Šponer J, Otyepka M (2009) Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods 49:202–
216
124. Clay EH, Gould IR (2005) A combined QM and MM investigation into guanine quadruplexes J Mol Graph Model 24:138–146
125. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE III, DeBolt S, Ferguson D,
Seibel G, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to
simulate the structural and energetic properties of molecules. Comput Phys Comm 91:1–41
126. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox
T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of
proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179–5197
127. Ferreira R, Artali R, Benoit A, Gargallo R, Eritja R, Ferguson DM, Sham YY, Mazzini S
(2013) Structure and stability of human telomeric G-quadruplex with preclinical 9-amino
acridines. PLOS One, 8, e57701. doi: 10.1371/journal.pone.0057701
128. Subramanian AK, Cardin CJ (2012) Molecular modelling studies of binding of DACD derivatives into G-quadruplex DNA: comparison of force field and quantum polarized ligand
docking methods. Int J Pharm Pharm Sci 4:509–514
129. Glide (2009) version 5.5, Schrodinger, Inc, New York
130. Jaguar (2011) version 7.8, Schrodinger, Inc, New York
131. Dubey LV, Ilchenko MM, Zozulya VN, Ryazanova OA, Pogrebnoy PV, Dubey IYa (2011)
Synthesis, structure and antiproliferative activity of cationic porphyrin-imidazophenazine
conjugate. Int Rev Biophys Chem 2:147–152
132. Zhao Y, Truhlar DG (2006) Comparative DFT study of van der Waals complexes: raregas dimers, alkaline-earth dimers, zinc dimer, and zinc-rare-gas dimers. J Phys Chem A
110:5121–5129
133. 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 117:43–54
6 Quantum Chemical Approaches in Modeling the Structure of DNA …
113. Szolomájer J, Paragi G, Batta G, Fonseca Guerra C, Bickelhaupt FM, Kele Z, Pádár P, Kupihára Z, Kovács L (2011) 3-Substituted xanthines as promising candidates for quadruplex
formation: computational, synthetic and analytical studies. New J Chem 35:486–482
114. Meyer M, Hocquet A, Sühnel J (2005) Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. J Comput Chem 26:352–364
115. Meyer M, Steinke T, Sühnel J (2007) Density functional study of isoguanine tetrad and
pentad sandwich complexes with alkali metal ions. J Mol Model 13:335–345
116. Hua Y, Changenet-Barret P, Improta R, Vaya I, Gustavsson T, Kotlyar AB, Zikich D, Šket P,
Plavec J, Markovitsi D (2012) Cation effect on the electronic excited states of guanine nanostructures studied by time-resolved fluorescence spectroscopy. J Phys Chem C 116:14682–
14689
117. Liu H, Gauld JW (2009) Protonation of guanine quartets and quartet stacks: insights from
DFT studies. Phys Chem Chem Phys 11:278–287
118. Lech CJ, Heidi B, Phan AT (2013) Guanine base stacking in G-quadruplex nucleic acids.
Nucl Acids Res 41:2034–2046
119. Šponer J, Mládek A, Špačková N, Cang X, Cheatham TE, Grimme S (2013) Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantumchemical computations. J Am Chem Soc 135:9785–9796
120. Fonseca Guerra C, Zijlstra H, Paragi G, Bickelhaupt FM (2011) Telomere structure and
stability: Covalency in hydrogen bonds, not resonance assistance, causes cooperativity in
guanine quartets. Chem Eur J 17:12612–12622
121. Warshel A. (1991). Computer Modeling of Chemical Reactions in Enzymes and Solutions.
John Wiley, New York.
122. Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/
MM) simulations for organic and enzymatic reactions. Acc Chem Res 43:142–151
123. Banáš P, Jurečka P, Walter NG, Šponer J, Otyepka M (2009) Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods 49:202–
216
124. Clay EH, Gould IR (2005) A combined QM and MM investigation into guanine quadruplexes J Mol Graph Model 24:138–146
125. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE III, DeBolt S, Ferguson D,
Seibel G, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to
simulate the structural and energetic properties of molecules. Comput Phys Comm 91:1–41
126. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox
T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of
proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179–5197
127. Ferreira R, Artali R, Benoit A, Gargallo R, Eritja R, Ferguson DM, Sham YY, Mazzini S
(2013) Structure and stability of human telomeric G-quadruplex with preclinical 9-amino
acridines. PLOS One, 8, e57701. doi: 10.1371/journal.pone.0057701
128. Subramanian AK, Cardin CJ (2012) Molecular modelling studies of binding of DACD derivatives into G-quadruplex DNA: comparison of force field and quantum polarized ligand
docking methods. Int J Pharm Pharm Sci 4:509–514
129. Glide (2009) version 5.5, Schrodinger, Inc, New York
130. Jaguar (2011) version 7.8, Schrodinger, Inc, New York
131. Dubey LV, Ilchenko MM, Zozulya VN, Ryazanova OA, Pogrebnoy PV, Dubey IYa (2011)
Synthesis, structure and antiproliferative activity of cationic porphyrin-imidazophenazine
conjugate. Int Rev Biophys Chem 2:147–152
132. Zhao Y, Truhlar DG (2006) Comparative DFT study of van der Waals complexes: raregas dimers, alkaline-earth dimers, zinc dimer, and zinc-rare-gas dimers. J Phys Chem A
110:5121–5129
133. 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 117:43–54