Comparative Molecular Mechanics and Quantum Mechanics Study of Monohydration of Nucleic Acid Bases

DNA is the most important biological molecule and its hydration contributes essentially to the structure and functions of the double helix. We analyze the monohydration of the individual bases of nucleic acids and their methyl derivatives using methods of Molecular Mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values obtained with QM. For Adenine and Thymine the QM local minima energy values are closer to those obtained by the PM potential (average of 0.72 kcal/mol) than by the AMBER force field (1.86 kcal/mol). The differences in energy between MM and QM results are more pronounced for Guanine and Cytosine, especially for minima with the water molecule forming H-bonds with two proton-acceptor centers of the base. Such minima are the deepest ones obtained via MM methods while QM calculations result in the global minima corresponding to water molecule H-bonded to one acceptor and one donor site of the base. Calculations for trimethylated bases with a water molecule corroborate the MM results. The energy profiles were obtained with some degrees of freedom of the water molecule being frozen. This data will contribute to the improvement of the molecular mechanics force fields.

Thermodynamic Consistency Test for Binary Gas ＋ Water Equilibrium Data at Low and High Pressures

Phase equilibrium in binary gas + water mixtures over wide ranges of temperatures and pressures are modeled and tested for thermodynamic consistency. For modeling, the Peng-Robinson equation of state was used and the Wong-Sandler mixing rules were incorporated into the equation of state parameters. In the Wong-Sandler mixing rules the van Laar model for the excess Gibbs energy was applied. In addition, a reasonable and flexible method is applied to test the thermodynamic consistency of pressure-temperature-concentration(P-T-x) data of these binary mixtures.Modeling is found acceptable in all cases, meaning that deviations in correlating the pressure and the gas phase concentration are low. For all cases the thermodynamic consistency method gives a clear conclusion about consistency or inconsistency of a set of experimental P-T-x data.

Colloidal synthesis and characterization of Cu_2ZnSnS_4 nanoplates

Synthesis of copper zinc tin sulphide(Cu_2ZnSnS_4/ with nanoplate morphology was achieved through colloidal method using oleic acid as capping agent and solvent with 1-octadecene(1-ODE) at 240°C.X-ray diffraction(XRD) analysis shows that the synthesized nanoplates possessed pure kesterite phase.SEM analysis clearly shows the formation of nanoplates having the size of about 50–100 nm.Electron spin resonance(ESR) spectrum analysis of the prepared nanoplates shows that the valence state of copper(II) which indicates the strong coupling with other metal ions.Thermo gravimetric/differential thermal analysis(TG/DTA) analysis shows the weight loss of sample at 450°C predicting the loss of capping ligands on the surface of the nanoparticles.The possible mechanism for the conversion of nanoplate-like structures during synthesis was discussed.The results are discussed in detail.