Solvate Suite: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling.

In this work, we introduce the Solvate Suite, a comprehensive and modular command-line interface designed for molecular simulation and microsolvation modeling. The suite interfaces with widely used scientific software, streamlining computational experiments for liquid systems through the automated creation of simulation boxes and topology with adjustable simulation parameters. Furthermore, it has features for graphical and statistical analysis of simulated properties and extraction of trajectory configurations with various filters. Additionally, it introduces innovative strategies for microsolvation modeling with a multiscale approach, employing equilibrated dynamics to identify favorable solute-solvent interactions and enabling full cluster optimization for free-energy calculations without imaginary frequency contamination.

Ab initio and DFT conformational study on N-nitrosodiethylamine, (C2H5)2N-N=O.

Ab initio (MP2) and DFT (B3LYP) calculations, using the cc-pVTZ and aug-cc-pVTZ basis sets, have been performed to characterize some stationary points on the ground state potential energy surface of the title molecules. Several properties as, for instance, relative energies, the barriers for NO rotation around the NN bond, NBO charges on O and amino N atoms, as well as the dipole moments, have been calculated and analyzed in the light of the structures found. Both computational levels here employed yield three minima, in which the C(2)NNO frame is 'planar' or 'quasi-planar'. Important correlations between NBO charges and geometric parameters, as well as between some structural features and dipole moments are also discussed. A total of 17 structures have been found for the (C(2)H(5))(2)N-N=O molecule. Two ranges of values have been obtained for the dipole moment, with the largest values occurring for the structures in which the nitrogen lone pair is parallel to the NO group π system. For instance, these two ranges are from ~4.1 to 4.5 D, and from ~1.6 to 2.1 D, at the MP2/cc-pVTZ level. These ranges are consistent with a larger and a smaller contribution of a dipolar resonance structure, respectively. As the method or basis set changes the values of the dipole moments change by at most ~0.23 D.

On the relative stabilities of the alkali cations 222 cryptates in the gas phase and in water-methanol solution.

The relative stabilities of the alkali [M subset 222]+ cryptates (M = Na, K, Rb and Cs) in the gas phase and in solution (80:20 v/v methanol:water mixture) at 298 K, are computed using a combination of ab initio quantum-chemical calculations (HF/6-31G and MP2/6-31+G*//HF/6-31+G*) and explicit-solvent Monte Carlo free-energy simulations. The results suggest that the relative stabilities of the cryptates in solution are due to a combination of steric effects (compression of large ions within the cryptand cavity), electronic effects (delocalization of the ionic charge onto the cryptand atoms) and solvent effects (dominantly the ionic dessolvation penalty). Thus, the relative stabilities in solution cannot be rationalized solely on the basis of a simple match or mismatch between the ionic radius and the cryptand cavity size as has been suggested previously. For example, although the [K subset 222]+ cryptate is found to be the most stable in solution, in agreement with experimental data, it is the [Na subset 222]+ cryptate that is the most stable in the gas phase. The present results provide further support to the notion that the solvent in which supramolecules are dissolved plays a key role in modulating molecular recognition processes.