Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs:  NonempiricalAb InitioCalculations

Abstract

ContentsI. Introduction 3247 II. Calculations 3249 II.1. Interaction Energy 3249 II.2. Correlation Energy 3250 II.3. Density Functional Theory 3251 II.4. Vibrational Frequencies 3251 II.5. Gas-Phase Thermodynamic Characteristics of Nucleic Acid (NA) Base Pairs 3252 III. Structure and Properties of Isolated NA Bases 3252 III.1. Tautomeric Equilibria of Bases 3252 III.2. Protonization Energies of Bases 3253 III.3. Electrostatic Potential around NA Bases 3254 III.4. Polarizability 3255 III.5. Gas-Phase Electron Affinities (EA) and Ionization Potentials (IP) 3255 III.6. Nonplanarity of DNA Bases 3255 IV. Structure, Energetics, and Properties of NA Base Pairs 3257 IV.1. H-Bonded NA Base Pairs 3257 IV.2. Stacked NA Base Pairs 3262 IV.3. Reliability of MP2 Calculations 3267 IV.4. Application of the DFT Method 3269 IV.5. Performance of Empirical Potentials 3269 IV.6. Thermodynamic Characteristics 3270 V. Conclusions 3272 VI. Acknowledgments 3273 VII. References 3273

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

“…This is justified not only by economy Additionally, these tetramers belong to the less polar steps. On the contrary the d(GpG) is known [11,12] as the most polar system among all ten possible dinucleotide steps, what also is confirmed by mean values of dipole moment collected in Table 1. Besides, much lower values of SCF contribution are noticed in this case if compared to previously described set of dinucleotides.…”

“…A special example of system involving complicated interplay between many forces of different character [9][10][11] is found in the case of stabilization of polynucleotide chains. Many contributions are important for DNA involving contacts of its constituents as nucleobases, sugar moieties, phosphate backbones, surrounding water molecules, counter ions and diversity of ligands potentially present in solutions at physiological conditions.…”

“…Unfortunately, the level of theory used for characteristics of intermolecular interactions is a crucial factor determining magnitude of binding energies. This is related not only to level of electron correlation estimation [11][12][13][14][15][16][17][18][19], corrections of basis superposition errors (BSSE) [20] and quality of applied basis set [11][12][13][14] (or its extrapolation to complete one) but also to non-additive contributions to molecular cluster stabilizations [12][13][14][15][16]. As it was nowadays documented [16] accurate values for manybody effects require extensions of electron correlation beyond MP2 levels since this approximation can only encounter non-additivity via correlated exchange and induction components [21,22].…”

Dissociative multi-photon ionization of isolated uracil and uracil-adenine complexes

“…2a for conventional numbering of the ring atoms) [34,35]. MPI mass spectra of pure uracil clusters have previously been measured using 274 nm ns-timescale laser pulses but no information on fragment ions was reported [36].…”

Probing the Energetic and Structural Role of Amino Acid/Nucleobase Cation-π Interactions in Protein-Ligand Complexes

“…The basis set used is 6-31G**(0.2), which corresponds to the standard 6-31G** basis set where the Gaussian ␣ d -exponent of the d-polarization functions on the heavy atoms C, N, and O is equal to 0.8, with an additional ␣ d -exponent equal to 0.2. It has indeed been shown that this extended description of the d-polarization functions allows a more accurate description of cation-interactions (21,22). 1 The interaction energy ⌬E MP2 is calculated as the sum of the Hartree-Fock energy ⌬E HF and a correlation energy contribution ⌬E COR , evaluated here in Equation 1 as the second order term of the Møller-Plesset perturbation expansion.…”