9-methylguanine and 1-methylthymine

The transition structures (TS) between H-bonded (H) and stacked (S) structures of 9-methyladenine...1-methylthymine and 9-methylguanine...1-methylcytosine base pairs were localized at the DFT-D/TZVP potential energy surface. The energy barrier between the S and TS structures is considerably higher for the former pair than for the latter, which makes localization of the stacked structure of this pair possible.

Topics: Adenine; Base Pairing; Cytosine; Guanine; Hydrogen Bonding; Models, Molecular; Thermodynamics; Thymine

Planar H-bonded and stacked structures of guanine...cytosine (G.C), adenine...thymine (A...T), 9-methylguanine...1-methylcytosine (mG...mC), and 9-methyladenine...1-methylthymine (mA...mT) were optimized at the RI-MP2 level using the TZVPP ([5s3p2d1f/3s2p1d]) basis set. Planar H-bonded structures of G...C, mG...mC, and A...T correspond to the Watson-Crick (WC) arrangement, in contrast to mA...mT for which the Hoogsteen (H) structure is found. Stabilization energies for all structures were determined as the sum of the complete basis set limit of MP2 energies and a (DeltaE(CCSD(T)) - DeltaE(MP2)) correction term evaluated with the cc-pVDZ(0.25,0.15) basis set. The complete basis set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and X = T and Q. This procedure is required since the convergency of the MP2 interaction energy for the present complexes is rather slow, and it is thus important to include the extrapolation to the complete basis set limit. For the MP2/aug-cc-pVQZ level of theory, stabilization energies for all complexes studied are already very close to the complete basis set limit. The much cheaper D-->T extrapolation provided a complete basis set limit close (by less than 0.7 kcal/mol) to the more accurate T-->Q term, and the D-->T extrapolation can be recommended for evaluation of complete basis set limits of more extended complexes (e.g. larger motifs of DNA). The convergency of the (DeltaE(CCSD(T)) - DeltaE(MP2)) term is known to be faster than that of the MP2 or CCSD(T) correlation energy itself, and the cc-pVDZ(0.25,0.15) basis set provides reasonable values for planar H-bonded as well as stacked structures. Inclusion of the CCSD(T) correction is essential for obtaining reliable relative values for planar H-bonding and stacking interactions; neglecting the CCSD(T) correction results in very considerable errors between 2.5 and 3.4 kcal/mol. Final stabilization energies (kcal/mol) for the base pairs studied are very substantial (A...T WC, 15.4; mA...mT H, 16.3; A...T stacked, 11.6; mA...mT stacked, 13.1; G...C WC, 28.8; mG...mC WC, 28.5; G...C stacked, 16.9; mG...mC stacked, 18.0), much larger than published previously. On the basis of comparison with experimental data, we conclude that our values represent the lower boundary of the true stabilization energies. On the basis of error analysis, we expect the present H-bonding energies to be fairly close to the true values, while

Topics: Adenine; Base Pairing; Cytosine; Guanine; Hydrogen Bonding; Models, Chemical; Models, Molecular; Thermodynamics; Thymine

Normal modes analyses for different molecules with biological interest have been performed and checked via the calculation of resonance Raman intensities. For this purpose, molecular orbital calculations were used to determine bond order changes in the lowest-lying electronic transitions. These bond order changes were used to calculate resonance Raman intensities in order to obtain correct vibrational assignments and reliable force fields.

Topics: Amino Acids; Base Pairing; Cresols; Cytosine; Electromagnetic Fields; Electrons; Guanine; Hydrocarbons, Aromatic; Imidazoles; Indoles; Molecular Structure; Nucleic Acids; Quantum Theory; Spectrum Analysis, Raman; Statistics as Topic; Thymine; Ultraviolet Rays; Uracil