Effects of structural variations on the hydrogen bond pairing between adenine derivatives and thymine
DOI:
https://doi.org/10.20450/mjcce.2015.644Keywords:
DNA base pair, adenine, thymine, hydrogen bonding, electrostatic potential, atomic chargesAbstract
Abstract: The hydrogen bonding between substituted adenines and thymine was investigated by density functional theory computations at the B3LYP/6-311+G(2d,2p) level. The effect of 20 different polar substituents at position 8 in adenine was examined in detail. Three different theoretical parameters, reflecting the electrostatics at the atoms involved in hydrogen bonding, were applied. An excellent correlation between electrostatic potentials at the bonding atoms in the monomer adenines and interaction energies was derived (Eqn. 2). It can be employed in designing bioactive adenine derivatives that are able to bind with a finely adjusted strength to thymine bioreceptor sites. NBO and Hirshfeld atomic charges are found to be less successful as reactivity predictors in these interactions.
References
G. C. Pimental, A. L. McClellan, The Hydrogen Bond, Freeman, San Francisco, 1960.
G. A. Jeffrey, An Introduction to Hydrogen Bonding, Oxford University Press: Oxford, 1997.
J. D. Watson, F. H. Crick, Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid, Nature, 171, 737–738 (1953).
G. A. Jeffrey, W. Saenger, Hydrogen Bonding in Biological Structures. Springer, Berlin, 1991.
J. Sponer, J. Leszczynski, P. Hobza, Electronic proper-ties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases, Biopolymers, 61, 3–31 (2001/2002).
J. Sponer, J. Leszczynski, P. Hobza, Hydrogen Bond-ing and Stacking of DNA Bases: A Review of Quantum-chemical ab initio Studies, J. Biomol. Struct. Dynamics, 14, 117–135 (1996).
R. L. Baldwin, Energetics of protein folding, J. Mol. Biol., 371, 283–301 (2007).
K. A. Dill, S. B. Ozkan, M. S. Shell, T. R. Weikl, The protein folding problem, Annu. Rev. Biophys. Biomol. Struct., 37, 289–316 (2008).
T. N. C. Wells, A. R. Fersht, Hydrogen bonding in enzymatic catalysis analyzed by protein engineering, Nature, 316, 566–657 (1985).
K. B. Schowen, H. H. Limbach, G. S. Denisov, R. L. Schowen, Hydrogen bonds and proton transfer in gen-eral-catalytic transition-state stabilization in enzyme catalysis, Biochim. Biophys. Acta, 1458, 43–62 (2000).
H. Kubinyi, Hydrogen bonding: the last mystery in drug design?, in Pharmacokinetic optimization in drug research: biological, physicochemical, and computational strategies, B. Testa, H. v. Waterbeemd, G. Folkers, R. Guy, Eds., Helvetica Chimica Acta and Wiley-VCH, Zürich, 2001, pp. 513–524.
M. H. Abraham, P. L. Grellier, D. V. Prior, J. J. Morris, P. J. Taylor, Hydrogen bonding. Part 10. A scale of so-lute hydrogen-bond basicity using log K values for complexation in tetrachloromethane. J. Chem. Soc. Perkin Trans., 2, 521–529 (1990).
S. P. Williams, P. B. Sigler, Atomic structure of progesterone complexed with its receptor, Nature, 393, 392–396 (1998).
M. H. Abraham, A. Ibrahim, A.M. Zissimos, Y. H. Zhao, J. Comer, Application of hydrogen bonding calculations in property based drug design., Drug Discov. Today., 7, 1056–1063 (2002).
H. Bohm, G. Schneider, Protein-Ligand Interactions: From Molecular Recognition to Drug Design, WILEY-VCH Verlag, 2003, pp. 262–266.
W. Saenger, Principles of nucleic acid structure, Springer, New York, 1984.
W. Arber, S. Linn, DNA modification and restriction, Ann. Rev. Biochem., 38, 467–500 (1969).
C. J. Leumann, DNA Analogues: From supramolecular principles to biological properties, Bioorg.&Med. Chem., 10, 841–854 (2002).
A. Moser, R. Guza, N. Tretyakova, D. M. York, Density functional study of the influence of C5 cytosine substitution in base pairs with guanine, Theor Chem Acc, 122, 179–188 (2009).
S. M. Morris, The genetic toxicology of 5-fluoro-pyrim¬idines and 5-chlorouracil, Mutat. Res., 297, 39–51, (1993).
S. Kawahara, T. Uchimaru, Computer-Aided molecular design of hydrogen bond equivalents of nucleobases: theoretical study of substituent effects on the hydrogen bond energies of nucleobase pairs, Eur. J. Org. Chem., 2577–2584 (2003).
P. Hozba, J. Sponer, Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical Ab-Initio calculations, Chem. Rev., 99, 3247–3276 (1999).
P. Hozba, R. Zahradnik, K. Mueller-Dethlefs, The world of non-covalent interactions, Coll. Czech. Chem. Com., 71, 443–531 (2006).
J. Sponer, P. Jureska, P. Hobza, Accurate interaction energies of hydrogen-bonded nucleic acid base pairs, J. Am. Chem. Soc., 126, 10142–10151 (2004).
E. Bergmann, B. Pullman, Molecular and quantum pharmacology, Springer, Berlin, 1974.
W. Saenger, Principles of nucleic acid structure; Springer: New York, 1984.
A. K. Chandra, M. T. Nguyen, T. Uchimaru, T. Zeegers-Huyskens, Protonation and deprotonation enthalpies of guanine and adenine and implications for the structure and energy of their complexes with water: Comparison with uracil, thymine and cytosine, J. Phys. Chem. A, 103, 8853–8860 (1999).
S. Sharma, J. K. Lee, The acidity of adenine and adenine derivatives and biological implications. A computational and experimental gas phase study, J. Org. Chem., 67, 8360–8365 (2002).
K. Morokuma, Why do molecules interact? The origin of electron donor acceptor complexes, hydrogen bonding and proton affinity, Acc. Chem. Res., 10, 294–300 (1977).
P. Gilli, V. Ferretti, V. Bertolasi, G. Gilli, A novel approach to hydrogen bonding theory, in Adv. Mol. Struct. Res., M. Hargittai, I. Hargittai, Eds.; JAI Press, Greenwich, CT, 2, 1996, pp. 67–102.
G. R. Desiraju, T. Steiner, The weak hydrogen bond in structural chemistry and biology; Oxford University Press: New York, 2001.
G. Naray-Szabo, in Molecular electrostatic potentials: concepts and applications; J. S. Murray, K. Sen, Eds.; Elsevier: Berlin, 1996, pp. 333–365.
C. F. Guerra, F. M. Bickelhaupt, J. G. Snijders, E. J. Baerends, The nature of the hydrogen bond in DNA base pairs: the role of charge transfer and resonance assistance, Chem. Eur. J., 5, 3581–3594 (1991).
F. C. Guerra, F. M. Bickelhaupt, Charge transfer and environment effects responsible for characteristics of DNA base pairing, Angew. Chem. Int. Ed., 38, 2942–2945 (1999).
C. F. Guerra, T. van der Wijst, F. M. Bickelhaupt, Substituent Effects on Hydrogen Bonding in Watson-Crick Base Pairs. A Theoretical Study, Struct. Chem., 16, 211–221 (2005).
B. Jeziorski, R. Moszynski, K. Szalewicz, Perturbation theory approach to intermolecular potential energy surfaces of Van der Waals complexes, Chem. Rev., 94, 1887−1930 (1994).
M. O. Sinnokrot, C. D. Sherrill, Unexpected substituent effects in face-to-face π-stacking interactions, J. Phys. Chem. A, 107, 8377−8379 (2003).
M. O. Sinnokrot, C. D. Sherrill, Substituent effects in π-π interactions: sandwich and T-shaped configurations, J. Am. Chem. Soc., 126, 7690−7697 (2004).
C. F. Guerra, T. van der Wijst, F. M. Bickelhaupt, Supramolecular switches based on the GC Watson-Crick pair. Effect of neutral and ionic substituents, Chem. Eur. J., 12, 3032–3042 (2006).
F. Meng, C. Lui, W. Xu, Substituent effects of R (R = CH3, CH3O, F, and NO2) on the A:T and C:G base pairs: A theoretical study, Chem. Phys. Lett., 373, 72–78 (2003).
F. Meng, H. Wang, W. Xu, C. Lui, Substituent effect of large conjugate groups on the DNA base pair derivatives: density functional study, Int. J. Quant. Chem., 104, 79–86 (2005).
F. Meng, H. Wang, W. Xu, C. Lui, H. Wang, Theoreti-cal study of GC+/GC base derivatives, Chem. Phys. 308, 117–123 (2005).
C. Xue, P. L. A. Popelier, Computational study of substituents effects on the interaction energies of hydrogen-bonded Watson-Crick Cytosine:Guanine base pairs, J. Phys. Chem. B, 112, 5257–5256 (2008).
C. Xue, P. L. A. Popelier, Prediction of interaction energies of substituted hydrogen- bonded Watson-Crick Cytosine:Guanine 8X base pair, J. Phys. Chem. B, 113, 3245–3250 (2009).
(a) A. D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior, Phys. Rev. A, 38, 3098–3100 (1998); (b) A. D. Becke, A new mixing of Hartree-Fock and local density-functional theories, J. Chem. Phys., 98, 1372–1377 (1993).
Y. W. Lee Yang, R. G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B, 37, 785–789 (1988).
(a) A. D. McLean, G. S. Chandler, Contracted Gaussian basis sets for molecular calculation. I. Second raw atoms, Z=11–18, J. Chem. Phys., 72, 5639–5649 (1980); (b) A. Krishnan, J. S. Binkley, R. Seeger, J. A. Pople, Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions, J. Chem. Phys., 72, 650–655 (1980); (c) Clark T., Chandrasekhar J.; Spitznagel G. W.; Schleyer P. v. R.; Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li–F, J. Comp. Chem,. 4, 294–301 (1983).
M. J. Frisch et al. Gaussian 09 (Revision-A.02); Gaussian, Inc., Wallingford CT, 2009.
S. E. F. Boys, F. Bernardi, Calculation of small molecular interactions by differences of separate total energies–some procedures with reduced errors, Mol. Phys., 19, 553–566 (1970).
E. B. Wilson , Four–dimensional electron density function, J. Phys. Chem., 36, 2232–2233 (1962).
P. Politzer, D. G. Truhlar, Chemical applications of atomic and molecular electrostatic potentials, Plenum Press: New York, 1981.
J. S. Murray, K. Sen, Eds.; Molecular electrostatic po-tentials: concepts and applications; Elsevier: Amster-dam, 1996.
P. Bobadova-Parvanova, B. Galabov, Ab initio molecular-orbital study of hydrogen-bonded complexes of carbonyl aliphatic compounds with hydrogen fluoride, J. Phys. Chem. A, 102, 1815–1819 (1998).
B. Galabov, P. Bobadova-Parvanova, Molecular electrostatic potential as reactivity index in hydrogen bonding: an initio molecular orbital study of complexes of nitrile and carbonyl compounds with hydrogen fluoride, J. Phys. Chem. A, 103, 6793–6799 (1999).
B. Galabov, P. Bobadova-Parvanova, Molecular electrostatic potential as reactivity index in hydrogen bond formation: an HF/6-31+G(d) study of hydrogen-bonded (HCN)n clusters, n = 2,3,4,5,6,7, J. Mol. Struct., 550–551, 93–98 (2000).
V. Dimitrova, S. Ilieva, B. Galabov, Electrostatic potential at atomic sites as a reactivity descriptor for hydrogen bonding. Complexes of monosubstituted acetylenes and ammonia, J. Phys. Chem. A, 106, 11801–11805 (2002).
B. Galabov, P. Bobadova-Parvanova, S. Ilieva, V. Dimitrova, The electrostatic potential at atomic sites as a reactivity index in the hydrogen bond formation, J. Mol. Struct. Theochem, 630, 101–112 (2003).
B. Galabov, D. Cheshmedzhieva, S. Ilieva, B. Hadjieva, Computational study of the reactivity of N-phenyl¬acetamides in the alkaline hydrolysis reaction, J. Phys. Chem. A, 108, 11457–11462 (2004).
B. Galabov, S. Ilieva, H. F. Schaefer, An efficient computational approach for the evaluation of substituent constants, J. Org. Chem., 71, 6382–6387 (2006).
B. Galabov, S. Ilieva, B. Hadjieva, Y. Atanasov, H. F. Schaefer, Predicting reactivities of organic molecules. Theoretical and experimental studies on the aminolysis of phenyl acetates, J. Phys. Chem. A, 112, 6700–6707 (2008).
B. Galabov, V. Nikolova, J. J. Wilke, H. F. Schaefer, W. D. Allen, Origin of the SN2 benzylic effect, J. Am. Chem. Soc., 130, 9887–9896 (2008).
B. Galabov, S. Ilieva, G. Koleva, W. D. Allen, H. F. Schaefer, P. v. R. Schleyer, Structure-reactivity relationships for Aromatic molecules: Application of the electrostatic potential at nuclei and electrophile affinity electronic indices, WIREs Comput. Mol. Sci., 3, 37–55 (2013).
B. Galabov, V. Nikolova, S. Ilieva, Does the molecular electrostatic potential reflect the effects of substituents in aromatic systems?, Chem.-Eur. J., 19, 5149–5155 (2013).
V. Nikolova, S. Ilieva, B. Galabov, H. F. Schaefer III, Experimental Measurement and Theory of substituent effects on π-hydrogen bonding: Complexes of substituted phenols with benzene, J. Org. Chem., 79, 6823–6831 (2014).
C.-H. Wu, B. Galabov, J. I.-C. Wu, S. Ilieva, P. v. R. Schleyer, W. D. Allen, Do π-Conjugative Effects facilitate SN2 reactions?, J. Am. Chem. Soc., 136, 3118–3126 (2014).
K. Kitaura, K. Morokuma, A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation, Int. J. Quant. Chem., 10, 325–340 (1976).
K. Morokuma, Molecular-orbital studies of hydrogen bonds. 3. C-O.....H-O hydrogen bond in H2CO....H2O and H2CO...2H2O, J. Chem. Phys., 55, 1236–1248 (1971).
H. Umeyama, K. Morokuma, The origin of hydrogen bonding: An energy decomposition study, J. Am. Chem. Soc., 99, 1316–1332 (1977).
(a) A. E. Reed, L. A. Curtiss, F. Weinhold, Natural population analysis, Chem. Rev., 88, 899–926 (1988); (b) J. E. Carpenter, F. Weinhold, Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint, J. Mol. Struct. (Theochem), 169, 41–62 (1988).
F. L. Hirshfeld, Bonded-atom fragments for describing molecular charge densities, Theor. Chem. Acc., 44, 129–138 (1977).
R. M. Badger, S. H. Bauer, Spectroscopic studies of the hydrogen bond. II. The shift of the O[single bond]H vibrational frequency in the formation of the hydrogen bond, J. Chem. Phys., 5, 839–841 (1939).
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