Density function theory, nucleic acids

Bakalarski, G., P. Grochowski, J. S. Kwiatkowski, B. Lesyng, and J. Leszczynski. 1996. Molecular and electrostatic properties of the N-methylated nucleic acid bases by density functional theory. Chem. Phys. 204, 301. 

Li, J. Cramer, and Truhlar, D. G. 1999. Application of a Universal Solvation Model to Nucleic Acid Bases. Comparison of Semiempirical Molecular Orbital Theory, Ab Initio, Hartree-Fock Theory, and Density Functional Theory , Biophys. Chem.. 78, 147. 

Lewis FD, Letsinger RL, Wasielewski MR (2001) Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins. Acc Chem Res 34 159-170 Li Z, Cai Z, Sevilla MD (2001) Investigation of proton transfer within DNA base pair anion and cation radicals by density functional theory (DFT).J Phys Chem B 105 10115-10123 Li Z, Cai Z, Sevilla MD (2002) DFT calculations on the electron affinities of nucleic acid bases dealing with negative electron affinities. J Phys Chem A 106 1596-1603 Lillicrap SC, Fielden EM (1969) Luminescence kinetics following pulse irradiation. II. DNA. J Chem Phys 51 3503-3511... 

R. Cammi, B. Mennucci, Structure and properties of molecular solutes in electronic excited states A polarizable continuum model approach based on the time-dependent density functional theory, in Radiation Induced Molecular Phenomena in Nucleic Acids A Comprehensive Theoretical and Experimental Analysis, ed. by M.K. Shukla, J. Leszczynski. Series Challenges and Advances in Computational Chemistry and Physics, vol 5 (Springer, Netherlands 2008)... 

Because of the efficiency, the density functional theory also became an object of interest for the purpose of evaluation of intermolecular interaction energies for nucleic acid base complexes. Most standard functionals provide qualitatively a good picture of interactions in H-bonded nucleic acid base pairs. However, they completely fail for stacked complexes. This is due to the inability of current functionals to describe correctly the dispersion energy. Several routes were proposed to alleviate this deficiency with different rates of success [9-12],... 

M. Elstner, P. Hobza, T. Frauenheim, S. Suhai, E. Kaxiras, Hydrogen bonding and stacking interactions of nucleic acid base pairs A density-functional-theory based treatment. J. Chem. Phys. 114, 5149-5155 (2001)... 

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)1096-987X( 19980715)19 9<989 AID-JCC1 >3,0.CO 2-F... 

Hydrogen Bonding and Stacking Interactions of Nucleic Acid Base Pairs A Density-Functional-Theory Based Treatment. 

Circular Dichroism Vibrational Configuration Interaction Configuration Interaction PCI-X and Applications Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Magnetic Circular Dichroism of n Systems Molecular Magnetic Properties Nucleic Acid Conformation and Flexibility Modeling Using Molecular Mechanics Spectroscopy Computational Methods Stereochemistry Representation and Manipulation. 

One important class of integral equation theories is based on the reference interaction site model (RISM) proposed by Chandler [77]. These RISM theories have been used to smdy the confonnation of small peptides in liquid water [78-80]. However, the approach is not appropriate for large molecular solutes such as proteins and nucleic acids. Because RISM is based on a reduction to site-site, solute-solvent radially symmetrical distribution functions, there is a loss of infonnation about the tliree-dimensional spatial organization of the solvent density around a macromolecular solute of irregular shape. To circumvent this limitation, extensions of RISM-like theories for tliree-dimensional space (3d-RISM) have been proposed [81,82],... 

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