Characterization of different substrates for Raman spectroscopic imaging of eukaryotic cells

For Raman spectroscopic analyses of the cells and other biological samples, the choice of the right substrate material is very important to avoid loss of information in characteristic spectral features because of competing background signals. In the current study, Raman spectroscopy is used to characterize several potential Raman substrates. Raman vibrational bands of the substrate material are discussed. The surface topography is analyzed by atomic force microscopy, and the root mean square surface roughness values are reported. Biocompatibility of the substrates is tested with Hep G2 cells evaluating cellular morphology as well as live/dead staining. Calcium fluoride, silicon, fused silica, borofloat glass, and silicon nitride membranes support cell growth and adherence. Silicon, borofloat glass, and fused silica give rise to Raman signals in the region of interest. Calcium fluoride substrate (UV grade) is suitable for Raman spectroscopic investigation of living cells. Nickel foil is suitable substrate for Raman spectroscopic investigation but cellular adherence and viability depend on the quality of the foil. Silicon nitride membranes coated with nickel chrome is a suitable Raman substrate in closed microfluidic systems. Copyright © 2016 John Wiley & Sons, Ltd.     

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal‐organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three‐step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal‐organic frameworks (MOFs), QuickFF is used to determine force fields for MIL‐53(Al) and MOF‐5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc.     

Late‐Stage Peptide Diversification by Bioorthogonal Catalytic CH Arylation at 23 °C in H2O

The step‐economical late‐stage diversification of tryptophan‐containing peptides was accomplished through chemo‐ and site‐selective palladium‐catalyzed C?H arylation under exceedingly mild reaction conditions. Thus, the C?H functionalization occurred efficiently at 23 °C with a catalyst loading as low as 0.5 mol %, and/or in H₂O.     

PPV Polymerization through the Gilch Route: Diradical Character of Monomers

Despite various studies on the polymerization of poly(p‐phenylene vinylene) (PPV) through different precursor routes, detailed mechanistic knowledge on the individual reaction steps and intermediates is still incomplete. The present study aims to gain more insight into the radical polymerization of PPV through the Gilch route. The initial steps of the polymerization involve the formation of a p‐quinodimethane intermediate, which spontaneously self‐initiates through a dimerization process leading to the formation of diradical species; chain propagation ensues on both sides of the diradical or chain termination occurs by the formation of side products, such as [2.2]paracyclophanes. Furthermore, different p‐quinodimethane systems were assessed with respect to the size of their aromatic core as well as the presence of heteroatoms in/on the conjugated system. The nature of the aromatic core and the specific substituents alter the electronic structure of the p‐quinodimethane monomers, affecting the mechanism of polymerization. The diradical character of the monomers has been investigated with several advanced methodologies, such as spin‐projected UHF, CASSCF, CASPT2, and DMRG calculations. It was shown that larger aromatic cores led to a higher diradical character in the monomers, which in turn is proposed to cause rapid initiation.     

Mesoporous‐Silica‐Functionalized Nanoparticles for Drug Delivery

The ever‐growing interest for finding efficient and reliable methods for treatment of diseases has set a precedent for the design and synthesis of new functional hybrid materials, namely porous nanoparticles, for controlled drug delivery. Mesoporous silica nanoparticles (MSNPs) represent one of the most promising nanocarriers for drug delivery as they possess interesting chemical and physical properties, thermal and mechanical stabilities, and are biocompatibile. In particular, their easily functionalizable surface allows a large number of property modifications further improving their efficiency in this field. This Concept article deals with the advances on the novel methods of functionalizing MSNPs, inside or outside the pores, as well as within the walls, to produce efficient and smart drug carriers for therapy.     

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

In the context of the SAMPL5 blinded challenge standard free energies of binding were predicted for a dataset of 22 small guest molecules and three different host molecules octa-acids (OAH and OAMe) and a cucurbituril (CBC). Three sets of predictions were submitted, each based on different variations of classical molecular dynamics alchemical free energy calculation protocols based on the double annihilation method. The first model (model A) yields a free energy of binding based on computed free energy changes in solvated and host-guest complex phases; the second (model B) adds long range dispersion corrections to the previous result; the third (model C) uses an additional standard state correction term to account for the use of distance restraints during the molecular dynamics simulations. Model C performs the best in terms of mean unsigned error for all guests (MUE \(3.2\,<\,3.4\,<\,3.6\,\text{kcal}\,\text{mol}^{-1}\)—95 % confidence interval) for the whole data set and in particular for the octa-acid systems (MUE \(1.7\,<\,1.9\,<\,2.1\,\text{kcal}\,\text{mol}^{-1}\)). The overall correlation with experimental data for all models is encouraging (\(R^2\, 0.65\,<\,0.70<0.75\)). The correlation between experimental and computational free energy of binding ranks as one of the highest with respect to other entries in the challenge. Nonetheless the large MUE for the best performing model highlights systematic errors, and submissions from other groups fared better with respect to this metric.