Metahybrid Density Functional Theory and Correlated ab Initio Studies on Microhydrated Adenine−Thymine Base Pairs

DFT STUDY OF THE PROTONATION AND DEPROTONATION ENTHALPIES OF BENZOXAZOLE, 1,2-BENZISOXAZOLE AND 2,1-BENZISOXAZOLE AND IMPLICATIONS FOR THE STRUCTURES AND ENERGIES OF THEIR ADDUCTS WITH EXPLICIT WATER MOLECULES

Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.

The electrostatic probe: a tool for the investigation of the Aβ(1-16) peptide deformations using the static modes

We investigate the conformational changes of the Amyloid β(1-16) peptide induced by moving Zn(2+) ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn(2+) ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.

Modeling the dissociative hydrolysis of the natural DNA nucleosides

Two-dimensional PCM-B3LYP/6-31+G(d) potential energy surfaces for the hydrolysis of the four natural 2'-deoxyribonucleosides (2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and thymidine) are characterized using a model that includes both implicit (bulk) solvent effects and (three or four) explicit water molecules in the optimization routine. For the first time, the experimentally predicted dissociative (S(N)1) mechanism is found to be favored over the synchronous (S(N)2) pathway for all nucleosides studied. Due to the success of our model in stabilizing the charge-separated intermediates along the S(N)1 pathway, it is proposed that the new model presented here is the smallest system capable of generating the experimentally predicted oxacarbenium cation intermediate. We therefore stress that dissociative mechanisms should be studied with methodologies that account for the (bulk) environment in the optimization routine, where these effects are often only included as a correction to the energy in the current literature. In addition to accounting for charge stabilization through implicit solvation, nucleophile activation and leaving group stabilization should also be explicitly introduced into the model to further stabilize the system. Our work also emphasizes the importance of studying the Gibbs surface, which in some cases provides a better description of chemically important regions of the reaction surface or changes the calculated trend in the magnitude of dissociative barriers. In addition, it is proposed that the methodology presented in this study can be used to calculate uncatalyzed deglycosylation barriers for a range of DNA nucleosides, which when compared to the corresponding enzyme-catalyzed reactions, will allow the prediction of the rate enhancement (barrier reduction) due to the enzyme.

Can the hybrid meta GGA and DFT-D methods describe the stacking interactions in conjugated polymers?

Newly developed hybrid meta density functionals and density functionals augmented by a classical London dispersion term have been systematically applied for the description of stacking energy and intermolecular distance of thiophene dimer and substituted thiophene dimer. The performance of the various approaches is compared with the benchmark ab-initio calculations done with CCSD(T) (Tsuzuki et al., JACS 2002, 124, 12200). Our results indicate that, contrary to the previous DFT methods which are not reliable, the new generation of DFT performs better the stacking interactions. These functionals, and especially those with an empirical correction, are suitable for general application in conducting polymers and, in particular, the modeling of solid state in which the overlap of Pi-Pi interactions between the conjugated chains is important.