Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Solute–solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical–physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute–solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.     

Tin mediated Barbier type allylation in ionic liquids

The Barbier type allylation of carbonyl compounds is a useful organic transformation as the resultant homoallylic alcohols are important building blocks for many biologically active molecules. Tin mediated Barbier allylation of different carbonyl compounds in room temperature ionic liquid, [BMIM][BF₄] afforded the corresponding homoallylic alcohols in good to excellent yields. The ionic liquid was successfully recycled and reused in allylation reactions.     

Effectiveness of Photodynamic Therapy in Elimination of HPV‐16 and HPV‐18 Associated with CIN I in Mexican Women

This study aimed to determine the effectiveness of photodynamic therapy (PDT), using δ‐aminolevulinic acid (5‐ALA), in the elimination of premalignant cervical lesions in Mexican patients with human papillomavirus (HPV) infection and/or cervical intraepithelial neoplasia (CIN). Thirty women diagnosed with CIN I and/or positive for HPV participated in the study. Topical 6% 5‐ALA in gel form was applied to the uterine cervix; after 4 h, the lesion area was irradiated with a light dose of 200 J cm^?2 at 635 nm. This procedure was performed three times at 48‐h intervals. Clinical follow‐up was performed at 3, 6, and 12 months after the initial PDT administration, by colposcopy, cervical cytology, histopathological analysis, polymerase chain reaction, and hybrid capture. Of HPV‐infected patients without evidence of CIN I, 80% cleared the infection, while HPV associated with CIN I was eliminated in 83% of patients (P < 0.05). At 12 months, CIN I had regressed in 57% of patients, although this response was not statistically significant. PDT using 6% 5‐ALA is concluded to be effective in eliminating HPV infection associated or not with CIN I.     

Covalent selection of the thiol proteome on activated thiol sepharose: A robust tool for redox proteomics

Protein thiols contribute significantly to antioxidant defence and selective oxidation of cysteines is important in signal transduction even in sub-stress scenarios. However, cysteine is the second rarest residue in proteins and it can be difficult to target low-abundance thiol (-SH)-containing proteins in proteomic separations. Activated thiol sepharose (ATS) allows covalent selection of -SH-containing proteins which can then be recovered by reduction with mercaptoethanol or dithiothreitol. This is a robust method for enriching -SH-containing proteins. We have used ATS to estimate the percentage (by weight) of thiol-containing proteins in cell extracts from a range of biological sources: a bacterium, Escherichia coli; a fungus, Trichoderma harzianum; and a bivalve mollusc Mytilus edulis. -SH-containing proteins account for 2.52% (E. coli), 1.4% (T. harzianum) and 1.4% (M. edulis) of total protein. Exposure to pro-oxidants did not materially alter these values. On removal of low M_r thiols such as glutathione, the values for M. edulis did not significantly change but those for T. harzianum increased threefold. The two-dimensional electrophoresis profiles of ATS-selected proteins for each organism were compared in control and pro-oxidant-exposed preparations. This revealed that some proteins present in controls were absent in pro-oxidant-treated extracts which we attribute to thiol oxidation. ATS has significant potential in enrichment for -SH-containing proteins in redox proteomics.     

Vibrational analysis of x-ray absorption fine structure thermal factors by ab initio molecular dynamics: the Zn(II) ion in aqueous solution as a case study

In this work, we consider a new combination of vibrational analysis and normal-like mode decomposition of Debye-Waller factors of solvated ions entirely based on molecular dynamics data. Such a novel time-dependent analysis procedure provides a direct link between x-ray absorption fine structure parameters and normal mode contributions for an ion-solvent system. The potentialities of such a methodology rely on two fundamental aspects which distinguish it from already available tools. First, a general vibrational analysis that does not require any Gaussian or harmonic model for describing atomic fluctuations in liquids. Second, a very accurate sampling of the short range motions around the structural probe via the recently developed atom centered density matrix propagation/general liquid optimized boundary method. This novel molecular dynamics methodology is based on an integrated ab initio/classical potential using localized basis functions and nonperiodic boundary conditions. As a case study we have chosen the Zn(II) ion in aqueous solution. The consistency of our results and the observed good agreement with experiments show how the key support to advanced structural techniques from molecular dynamics can be further expanded and investigated.     

Light Electrospun Polyvinylpyrrolidone Blanket for Low Frequencies Sound Absorption

Light polymeric soundproofing materials(density = 63 kg/m~3) of interest for the transportation industry were fabricated through electrospinning. Blankets of electrospun polyvinylpyrrolidone(average fiber diameter =(1.6 ± 0.5) or(2.8 ± 0.5) μm) were obtained by stacking disks of electrospun mats. The sound absorption coefficients were measured using the impedance tube instrument based on ASTM E1050 and ISO 10534-2. For a given set of disks(from a minimum of 6) the sound absorption coefficient changed with the frequency(in the range 200–1600 Hz) following a bell shape curve with a maximum(where the coefficient is greater than 0.9) that shifts to lower frequencies at higher piled disks number and greater fiber diameter. This work showed that electrospinning produced sound absorbers with reduced thickness(2–3 cm) and excellent sound-absorption properties in the low and medium frequency range.     

On a notion of partially conditionally identically distributed sequences

A notion of conditionally identically distributed (c.i.d.) sequences has been studied as a form of stochastic dependence weaker than exchangeability, but equivalent to it in the presence of stationarity. We extend such notion to families of sequences. Paralleling the extension from exchangeability to partial exchangeability in the sense of de Finetti, we propose a notion of partially c.i.d. dependence, which is shown to be equivalent to partial exchangeability for stationary processes. Partially c.i.d. families of sequences preserve attractive limit properties of partial exchangeability, and are asymptotically partially exchangeable. Moreover, we provide strong laws of large numbers and two central limit theorems. Our focus is on the asymptotic agreement of predictions and empirical means, which lies at the foundations of Bayesian statistics. Natural examples of partially c.i.d. constructions are interacting randomly reinforced processes satisfying certain conditions on the reinforcement.     

Pd(0)‐Catalyzed Dearomative Diarylation of Indoles

We have developed a protocol for a Pd(0)‐catalyzed dearomative syn 1,2‐diarylation of indoles using readily available boroxines (dehydrated boronic acids) as coupling partners. This reaction proceeds efficiently using PtBu₃ as the ligand to divergently access to fused indolines while minimizing the extent of direct Suzuki coupling. The scope of the reaction is remarkably broad and all products are obtained as single diastereomers in moderate to excellent yields. We have also compiled data which parallels the steric and electronic properties of both substrate and boroxine with the propensity to undergo the desired dearomative process over direct Suzuki coupling.     

Caesium contamination in human milk and transfer factor from diet.

A study on caesium contamination in human milk, as a consequence of the Chernobyl fallout, was conducted in 1989 on a group of women from one of the areas of northern Italy most heavily affected by the radioactive fallout. Their diet was studied, and the caesium intake was calculated by using the mean food activity concentration in that area. The caesium transfer factor was evaluated both as the ratio of caesium concentration in mother's milk to the daily intake, and by using a simplified milk compartment model.