Empirical force-field calculations on biological molecules represent an effective method to obtain atomic detail information on the relationship of their structure to their function. Results from those calculations depend on the quality of the force field. In this manuscript, optimization of the CHARMM27 all-atom empirical force field for nucleic acids is presented together with the resulting parameters. The optimization procedure is based on the reproduction of small molecule target data from both experimental and quantum mechanical studies and condensed phase structural properties of DNA and RNA. Via an iterative approach, the parameters were primarily optimized to reproduce macromolecular target data while maximizing agreement with small molecule target data. This approach is expected to ensure that the different contributions from the individual moieties in the nucleic acids are properly balanced to yield condensed phase properties of DNA and RNA, which are consistent with experiment. The quality of the presented force field in reproducing both crystal and solution properties are detailed in the present and an accompanying manuscript (MacKerell and Banavali, J Comput Chem, this issue). The resultant parameters represent the latest step in the continued development of the CHARMM all-atom biomolecular force field for proteins, lipids, and nucleic acids. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 86–104, 2000

All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations.

Tautomeric equilibria in relation to pi-electron delocalization.

The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorpti ...

On the structure and desorption dynamics of DNA bases adsorbed on gold: a temperature-programmed study.

The optimized geometries, harmonic vibrational frequencies, and energies of the three cyclic structures of the thymine−water complex are computed using density functional theory (B3LYP) combined with the 6-31++G(d,p) basis set. The proton affinity of the oxygen atoms and the deprotonation enthalpy of the NH bonds of thymine are computed at the same level and compared with recent data on uracil. In both uracil and thymine, the deprotonation enthalpies are lower (1391−1449 kJ mol-1) than those of the biological NH donors of the peptide links (1470−1485 kJ mol-1) (Mautner, M. J. Am. Chem. Soc. 1988, 110, 3075). Harmonic vibrational frequencies are also reported for the uracil−water complexes. In both uracil and thymine complexes, the most stable hydrogen bond is formed at the O site characterized by the smallest proton affinity and at the NH site characterized by the highest acidity. The intermolecular distances and the energies of the hydrogen bonds formed at the different sites of thymine and uracil depend...

http://quantchem.kuleuven.be/cmms/Articles/JPCA/jp981259v.pdf

Theoretical Study of the Interaction between Thymine and Water. Protonation and Deprotonation Enthalpies and Comparison with Uracil

Neutron Inelastic Scattering, Optical Spectroscopies and Scaled Quantum Mechanical Force Fields for Analyzing the Vibrational Dynamics of Pyrimidine Nucleic Acid Bases: 3. Cytosine

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Neutron Inelastic Scattering, Optical Spectroscopies and Scaled Quantum Mechanical Force Fields for Analyzing the Vibrational Dynamics of Pyrimidine Nucleic Acid Bases: 3. Cytosine