Nucleophilic properties of purine bases : inherent reactivity versus reaction conditions

In the present study, nucleophilic properties of adenine and guanine are examined by means of density functional theory. H+ is used as a model electrophile. Two modes of H+ attack on the bases are considered: on the neutral molecule and on the anion. Solvent effects are modeled by means of polarizable continuum model. Regioselectivity of attack is studied by analyzing two contributions. The first one is the energetic ordering of the tautomers. The second is the relative inherent reactivity of nucleophilic sites in the bases. Atomic softnesses calculated by means of charge sensitivity analysis are employed for this purpose. The most reactive sites in various tautomers are identified on the ground of Li–Evans model. For adenine, it is demonstrated that both in basic and in neutral pH N7 atom possesses the most nucleophilic character. In polar solvents, N7 substitution is also most favored energetically. In basic pH and nonpolar solvents as well as in the gas phase, N9 substitution is slightly more probable. For guanine, a mixture of N7- and N9-substituted products can be expected in basic pH. In neutral pH, inherent reactivity and energy trends are opposite to each other; therefore, the substitution does not occur. Experimentally observed products of reactions with various electrophiles and in various conditions confirm the results obtained in this study

Generalized charge sensitivity analysis

Charge sensitivity analysis was originally introduced in the trivial-atom resolution. Here, we extend this resolution into force-field atoms. The AMBERff99 force-field resolution was employed. The effective elec- tronegativities and hardnesses were derived for five dif- ferent population analyses (Mulliken, Hirschfeld, AIM, NPA and Voronoi charges) by applying evolutionary algorithms

Charge sensitivity approach to mutual polarization of reactants : molecular mechanics perspective

Charge sensitivity analysis (CSA) in force-field atoms resolution was applied to describe the mutual polarization of reactants as well as charge-transfer (CT) effects. An inclusion complex of β-cyclodextrin with salicylic acid was used as a model system. Three CSA models were taken into account and verified on a Born – Oppenheimer molecular dynamics (BOMD) trajectory. The models differed in terms of the equilibrium conditions imposed on the system. It was demonstrated that mutual polarization is an important source of stabilization, in contrast to the results obtained from static charge calculations. The energy lowering induced by CT was small and comparable to the CT stabilization that occurs in hydrogen-bonded systems. All models correctly described the main topological features of the BOMD energy surface. CSA in force-field atoms resolution qualitatively reproduced the charge reorganization accompanying hydrogen-bond formation. It was shown that CSA parameters are very sensitive to the bond formation process, which suggests that they could be applied in reactive force fields as detectors of newly formed chemical bonds

DFT studies of cation binding by β-cyclodextrin

Interactions of the β-cyclodextrin (β-CD) ligand with Na+, Cu+, Mg2+, Zn2+, and Al3+ cations were investigated using density functional theory modeling. The objective of this study was to give insight into the mechanism of cation complexation. Two groups of conformers were found. The first group preserved the initial orientation of glucopyranose residues inside the β-CD ligand. The mutual orientation of glucopyranose residues was strongly affected by the cation in the second group of conformers. The system interaction energy was decomposed into electrostatic (ES), Pauli and orbital contributions using the Ziegler–Rauk energy partitioning scheme. The total electrostatic energy, i.e., the sum of ES energy and polarization energy, is the dominating term in the interaction energy. In vacuum, the complexes formed with Al3+ were found to be more stable than with di- and monocations. The vacuum stability sequence was changed in aqueous solution

Formation of β-cyclodextrin complexes in an anhydrous environment

The formation of inclusion complexes of β-cyclodextrin was studied at the melting temperature of guest compounds by differential scanning calorimetry. The complexes of long-chain n-alkanes, polyaromatics, and organic acids were investigated by calorimetry and IR spectroscopy. The complexation ratio of β-cyclodextrin was compared with results obtained in an aqueous environment. The stability and structure of inclusion complexes with various stoichiometries were estimated by quantum chemistry and molecular dynamics calculations. Comparison of experimental and theoretical results confirmed the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds. This finding gives new insight into the mechanism of formation of host–guest complexes and shows that hydrophobic interactions play a secondary role in this case. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00894-016-3061-6) contains supplementary material, which is available to authorized users

Intermediate electrostatic field for the elongation method

A simple way to improve the accuracy of the fragmentation methods is proposed. The formalism was applied to the elongation (ELG) method at restricted open-shell Hartree-Fock (ROHF) level of theory. The α-helix conformer of polyglycine was taken as a model system. The modified ELG method includes a simplified electrostatic field resulting from point-charge distribution of the system’s environment. In this way the long-distance polarization is approximately taken into account. The field attenuates during the ELG process to eventually disappear when the final structure is reached. The point-charge distributions for each ELG step are obtained from charge sensitivity analysis (CSA) in force-field atoms resolution. The presence of the intermediate field improves the accuracy of ELG calculations. The errors in total energy and its kinetic and potential contributions are reduced by at least one-order of magnitude. In addition the SCF convergence of ROHF scheme is improved