FACTS: Fast analytical continuum treatment of solvation

An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation of the volume and spatial symmetry of the solvent that is displaced from around a solute atom by its neighboring atoms. The two measures of solvent displacement are combined in empirical equations to approximate the atomic (or self) electrostatic solvation energy and the solvent accessible surface area. The former directly yields the effective Born radius, which is used in the generalized Born (GB) formula to calculate the solvent-screened electrostatic interaction energy. A comparison with finite-difference Poisson data shows that atomic solvation energies, pair interaction energies, and their sums are evaluated with a precision comparable to the most accurate GB implementations. Furthermore, solvation energies of a large set of protein conformations have an error of only 1.5%. The solvent accessible surface area is used to approximate the nonpolar contribution to solvation. The empirical approach, called FACTS (Fast Analytical Continuum Treatment of Solvation), is only four times slower than using the vacuum energy in molecular dynamics simulations of proteins. Notably, the folded state of structured peptides and proteins is stable at room temperature in 100-ns molecular dynamics simulations using FACTS and the CHARMM force field.     

Physico-chemical study of norfloxacin and metronidazole binary mixtures

Journal of Thermal Analysis and Calorimetry - The physico-chemical characterization of norfloxacin commercial sample (NF), norfloxacin anhydrous form A (NFanhA), norfloxacin pentahydrate...     

Estimation of protein folding probability from equilibrium simulations

The assumption that similar structures have similar folding probabilities (p(fold)) leads naturally to a procedure to evaluate p(fold) for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide or protein. The procedure utilizes a structurally homogeneous clustering and does not require any additional simulation. It can be used to detect multiple folding pathways as shown for a three-stranded antiparallel beta-sheet peptide investigated by implicit solvent molecular dynamics simulations.     

Chemistry at the Edge of Graphene

The selective functionalization of graphene edges is driven by the chemical reactivity of its carbon atoms. The chemical reactivity of an edge, as an interruption of the honeycomb lattice of graphene, differs from the relative inertness of the basal plane. In fact, the unsaturation of the p_z orbitals and the break of the π conjugation on an edge increase the energy of the electrons at the edge sites, leading to specific chemical reactivity and electronic properties. Given the relevance of the chemistry at the edges in many aspects of graphene, the present Review investigates the processes and mechanisms that drive the chemical functionalization of graphene at the edges. Emphasis is given to the selective chemical functionalization of graphene edges from theoretical and experimental perspectives, with a particular focus on the characterization tools available to investigate the chemistry of graphene at the edge.     

Iron(II) complexes of new hexadentate 1,1,1-tris-(iminomethyl)ethane podands, and their 7-methyl-1,3,5-triazaadamantane rearrangement products

New iron(II) podand complexes have been prepared, by condensation of 2-(aminomethyl)-2-methyl-1,3-diaminopropane with 3 equiv of a heterocyclic aldehyde in the presence of hydrated Fe[BF(4)](2) or Fe[ClO(4)](2) as templates. The 2-(aminomethyl)-2-methyl-1,3-diaminopropane is prepared in situ by deprotonation of its trihydrochloride salt. The chloride must be removed from these reactions by precipitation with silver, to avoid the formation of the alternative 2,4,6-trisubstituted-7-methyl-1,3,5-triazaadamantane condensation products, or their FeCl(2) adducts. The crystal structures of two 2,4,6-tri(pyridyl)-7-methyl-1,3,5-triazaadamantane-containing species are presented, and contain two different geometric isomers of this tricyclic ring with three equatorial, or two equatorial and one axial, pyridyl substituents. Both structures feature strong C-HX (X = Cl or F) hydrogen bonding from the aminal C-H groups in the triazaadamantane ring. Five iron(II) podand complexes were successfully obtained, all of which contain low-spin iron centres.     

Piecewise-linear programming: The compact (CPLP) algorithm

A compact algorithm is presented for solving the convex piecewise-linear-programming problem, formulated by means of a separable convex piecewise-linear objective function (to be minimized) and a set of linear constraints. This algorithm consists of a finite sequence of cycles, derived from the simplex method, characteritic of linear programming, and the line search, characteristic of nonlinear programming. Both the required storage and amount of calculation are reduced with respect to the usual approach, based on a linear-programming formulation with an expanded tableau. The tableau dimensions arem×(n+1), wherem is the number of constraints andn the number of the (original) structural variables, and they do not increase with the number of breakpoints of the piecewise-linear terms constituting the objective function.     

Real-time cosmology

In recent years, improved astrometric and spectroscopic techniques have opened the possibility of measuring the temporal change of radial and transverse position of sources in the sky over relatively short time intervals. This has made at least conceivable to establish a novel research domain, which we dub “real-time cosmology”. We review for the first time most of the work already done in this field, analysing the theoretical framework as well as some foreseeable observational strategies and their capability to constrain models. We first focus on real-time measurements of the overall redshift drift and angular separation shift in distant sources, which allows the observer to trace the background cosmic expansion and large scale anisotropy, respectively. We then examine the possibility of employing the same kind of observations to probe peculiar and proper accelerations in clustered systems, and therefore their gravitational potential. The last two sections are devoted to the future change of the cosmic microwave background on “short” time scales, as well as to the temporal shift of the temperature anisotropy power spectrum and maps. We conclude revisiting in this context the usefulness of upcoming experiments (like CODEX and Gaia) for real-time observations.     

Drug-excipient compatibility studies in binary and ternary mixtures by physico-chemical techniques

This work is part of a systematic study undertaken to find and optimize a general method of detecting the drug-excipient interactions, with the aim of predicting rapidly and inexpensively the long term stability of a pharmaceutical product and speed up its marketing. Here, in particular, the compatibility of haloperidol with several excipients (PVP, magnesium stearate and α-lactose) in binary and ternary mixtures, both as prepared and ball-milled, has been assessed by thermal methods, electron microscopy, IR spectroscopy and X-ray diffraction. The differences between the experimental behaviour of the systems and that expected as weighted average of similarly treated pure components are interaction indicators. The DSC has proven to be, among the selected analytical techniques, the most sensitive and specific in assessing the compatibility. A strong interaction has been observed between PVP and haloperidol. It is favoured by the mechanical stress and is more evident in the composition 20:80. On the contrary, α-lactose and magnesium stearate were found to be compatible with the drug.     

Mechanical Properties of 3-Glycidoxypropyltrimethoxysilane Based Hybrid Organic-Inorganic Materials

Hybrid organic-inorganic materials were synthesized from acid catalysed sols of tetraethyl orthosilicate, 3-glycidoxypropyltrimethoxysilane and titanium or zirconium alkoxides. The mechanical properties of these materials were measured in different conditions of preparation. The elastic modulus E was determined by a resonance method and by Knoop microindentation. After a thermal treatment at 125°C for 120 h, E was around 3–5 and 1–2 GPa for the samples synthesized with titanium butoxide or zirconium butoxide, respectively. An increase in E in the samples cured for longer times was observed. Knoop microhardness also increased with the heating time and was larger in samples synthesized from titanium alkoxides than zirconium alkoxides. The two methods gave results in good agreement when applied to samples treated for shorter times. In the other samples Knoop microindentation gave a larger value of E compared to the resonance vibration method. Hardness to elastic modulus ratio, H/E, was evaluated by Knoop microindentation. The elastic recovery at the longest heat treatment time was similar to that of soda-lime glasses. Fracture toughness was measured by three points flexural test, a _KIc in the range of 0.4–0.5 MPa m^1/2 was evaluated for samples treated during 168 h.