Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators

We present an approach to the estimate of the potential of mean force along a generic reaction coordinate based on maximum likelihood methods and path-ensemble averages in systems driven far from equilibrium. Following similar arguments, various free energy estimators can be recovered, all providing comparable computational accuracy. The method, applied to the unfolding process of the alpha-helix form of an alanine deca-peptide, gives results in good agreement with thermodynamic integration.Comment: 9 pages, 3 figures; important changes (figure 2, demonstration of Eq. 16, figure 3 and related discussion); style correction

Imidazole in Aqueous Solution: Hydrogen Bond Interactions and Structural Reorganization with Concentration

The structural and dynamic properties of imidazole in aqueous solution have been studied by means of classical and ab initio molecular dynamics simulations. We developed a new force field for the imidazole molecule with improved modeling of the electrostatic interactions, specifically tailored to address the well-known drawbacks of existing force fields based on the atomic fractional charge approach. To this end, we reparametrized the charge distribution on the heterocyclic ring, introducing an extra site accounting for the lone pair on the deprotonated nitrogen. The accuracy of the model in describing the hydrogen bond pattern in the aqueous solvent has been confirmed by comparing the classical results on imidazole–water interactions to accurate Car–Parrinello molecular dynamics simulations. It reproduces satisfactorily the experimental water/octanol partition coefficient of imidazole, as well as the structure of the imidazole molecular crystal. The force field has been finally applied to simulate aqueous solutions at various imidazole concentrations to obtain information on both imidazole–water and imidazole–imidazole interactions, providing a description of the different molecular arrangements in solution

Approximating nonequilibrium processes using a collection of surrogate diffusion models

The surrogate process approximation (SPA) is applied to model the nonequilibrium dynamics of a reaction coordinate (RC) associated with the unfolding and refolding processes of a deca-alanine peptide at 300 K. The RC dynamics, which correspond to the evolution of the end-to-end distance of the polypeptide, are produced by steered molecular dynamics (SMD) simulations and approximated using overdamped diffusion models. We show that the collection of (estimated) SPA models contain structural information "orthogonal" to the RC monitored in this study. Functional data analysis ideas are used to correlate functions associated with the fitted SPA models with the work done on the system in SMD simulations. It is demonstrated that the shape of the nonequilibrium work distributions for the unfolding and refolding processes of deca-alanine can be predicted with functional data analysis ideas using a relatively small number of simulated SMD paths for calibrating the SPA diffusion models.Comment: 13 pages, 7 figure

An updated checklist of the vascular flora of Montagna di Torricchio State Nature Reserve (Marche, Italy)

This study aims to increase floristic knowledge of Marche by means of a survey in the Montagna di Torricchio State Nature Reserve (central Italy). The Reserve, located in the central Apennines, covers about 3.2 km2 at altitudes ranging from 820 to 1,491 m a.s.l. It has been owned and managed as a strict reserve by the University of Camerino since 1970: all the anthropic activities ceased about 50 years ago, except for a minimal area where mowing and cattle grazing are still allowed. The floristic list consists of 789 specific and subspecific taxa belonging to 81 families and 352 genera. Two species are new for Italy (Taraxacum calocarpum and T. pulchrifolium) and 14 for Marche regional flora. Compared to previous floristic studies, we found 127 more taxa but we showed a certain stability in the life-form spectrum, suggesting limited effects of dynamic processes related to climate and land-use changes. The negligible number of alien species (11) is probably related to the limitations to anthropic activities in the Reserve. The occurrence of taxa never recorded for Italy and Marche highlights the floristic value of the Reserve for species conservation in the central Apennines

A Photochromic Azobenzene Peptidomimetic of a β-Turn Model Peptide Structure as a Conformational Switch

The insertion of azobenzene moiety in complex molecular protein or peptide systems can lead to molecular switches to be used to determine kinetics of folding/unfolding properties of secondary structures, such as α-helix, β-turn, or β-hairpin. In fact, in azobenzene, absorption of light induces a reversible trans ↔ cis isomerization, which in turns generates a strain or a structure relaxation in the chain that causes peptide folding/unfolding. In particular azobenzene may permit reversible conformational control of hairpin formation. In the present work a synthetic photochromic azobenzene amino acid derivative was incorporated as a turn element to modify the synthetic peptide [Pro7,Asn8,Thr10]CSF114 previously designed to fold as a type I β-turn structure in biomimetic HFA/water solution. In particular, the P-N-H fragment at positions 7–9, involved in a β-hairpin, was replaced by an azobenzene amino acid derivative (synthesized ad hoc) to investigate if the electronic properties of the novel peptidomimetic analog could induce variations in the isomerization process. The absorption spectra of the azopeptidomimetic analog of the type I β-turn structure and of the azobenzene amino acid as control were measured as a function of the irradiation time exciting into the respective first ππ* and nπ* transition bands. Isomerization of the azopeptidomimetic results strongly favored by exciting into the ππ* transition. Moreover, conformational changes induced by the cis↔ trans azopeptidomimetic switch were investigated by NMR in different solvents

Modelling of the Elementary Steps Involved in the Aluminum Electrochemical Deposition from Ionic Liquid Based Solution: The BMImCl/AlCl3 System

n/