In this communication, we present the Jarzynski's Equality FREe Energy (JEFREE) library, an efficient and easy-to-use C++ library targeted to the calculation of the free energy profile along a selected generalized coordinate of a system, within the framework of the nonequilibrium steered transformations as introduced by Jarzynski [Phys. Rev. E, 1997, 56, 5018]. JEFREE can be readily integrated into any code, since both C and FORTRAN wrappers have been developed, and easily customizable by a user thanks to the object-oriented programming paradigm offered by the C++ language. Also, JEFREE implements the novel idea of making a total "morphing" of the system energy landscape before initiating the proper steering stage. This proves to be an efficient mean to overtake the problematic sampling of the initial equilibrium state when the number of degrees of freedom is high and the landscape owns many local minima separated by large energy barriers. The calculation of the free energy profile for the rotation along torsion angles in alkyl chains is presented as an example of application of our tool.

In this work, we develop a self-consistent route to inspect the conformational mobility of single chains in gold nanoparticles passivated with a monolayer of decanethiols. The approach is based on the match between a theoretical modeling under a coarse-grained level (i.e., system definition, buildup of the free energy profiles along relevant coordinates, modeling/parametrization of the friction, production of stochastic trajectories) and experimental spectroscopic investigations. The agreement between calculated and experimental values of 13 C NMR longitudinal relaxation times supports the theoretical assumptions and the model parametrization. On physical grounds, it emerges that the mobility of the single chains resembles that of an ideal chain made of connected n-butane-like bonds.

Using quantum chemical methods, we investigate the possible outcomes of reactions with acetylene and diacetylene molecules. We find both reactions to be exothermic reactions without barriers, yielding stable anions of the corresponding polyynes: and . We show in this work that the computed chemical rates in the case of the formation of the anion would be larger than those existing for the direct radiative electron attachment (REA) process, the main mechanism generally suggested for their formation. In the case of the anion, however, the present chemical rates of formation at low T are even lower than those known for its REA process, both mechanisms being inefficient for its formation under astrochemical conditions. The present results are discussed in view of their consequences on the issue of the possible presence of such anions in the ISM environments. They clearly indicate the present chemical route to formation to be inefficient at the expected temperatures of a dark molecular cloud, whereas this is found not to be the case for the , in line with the available experimental findings.

In this work we show that a non-equilibrium statistical tool based on Jarzynski's equality (JE) can be applied to achieve a sufficiently accurate mapping of the torsion free energy, bond-by-bond, for an alkyl thiol ligand tethered to a gold surface and sensing the presence of the surrounding cluster of similar chains. The strength of our approach is the employment of a strategy to let grow the internal energetics of the whole system (namely, the "energy morphing" stage recently presented by us in J. Comput. Chem., 2014, 35, 1865-1881) before initiating the rotational steering, which yields accurate results in terms of statistical uncertainties and bias on the free energy profiles. The work is mainly methodological and illustrates the feasibility of this kind of inspection on nanoscale molecular clusters with conformational flexibility. The outcomes for the archetype of self-assembled-monolayers considered here, a regular pattern of 10-carbon alkyl thiols on an ideal gold surface, give information on the conformational mobility of the ligands. Notably, such information is unlikely to be obtained by means of standard equilibrium techniques or by conventional molecular dynamics simulations.

We present a new general framework for solving the monodimensional Smoluchowski equation using a discrete variable representation (DVR) based on the so called sinc basis set. The reliability of our implementation is assessed by comparing the convergence of diffusive operator eigenvalues calculated using our method and using a simple finite difference scheme for some model diffusive problems. The results here presented open encouraging possibilities for dealing with more complicated systems, where additional coordinate dependent terms in the equation or multidimensional treatments are needed and traditional methods often become unfeasible.