Combining the polarizable Drude force field with a continuum electrostatic Poisson–Boltzmann implicit solvation model

In this work, we have combined the polarizable force field based on the classical Drude oscillator with a continuum Poisson–Boltzmann/solvent‐accessible surface area (PB/SASA) model. In practice, the positions of the Drude particles experiencing the solvent reaction field arising from the fixed charges and induced polarization of the solute must be optimized in a self‐consistent manner. Here, we parameterized the model to reproduce experimental solvation free energies of a set of small molecules. The model reproduces well‐experimental solvation free energies of 70 molecules, yielding a root mean square difference of 0.8 kcal/mol versus 2.5 kcal/mol for the CHARMM36 additive force field. The polarization work associated with the solute transfer from the gas‐phase to the polar solvent, a term neglected in the framework of additive force fields, was found to make a large contribution to the total solvation free energy, comparable to the polar solute–solvent solvation contribution. The Drude PB/SASA also reproduces well the electronic polarization from the explicit solvent simulations of a small protein, BPTI. Model validation was based on comparisons with the experimental relative binding free energies of 371 single alanine mutations. With the Drude PB/SASA model the root mean square deviation between the predicted and experimental relative binding free energies is 3.35 kcal/mol, lower than 5.11 kcal/mol computed with the CHARMM36 additive force field. Overall, the results indicate that the main limitation of the Drude PB/SASA model is the inability of the SASA term to accurately capture non‐polar solvation effects. © 2018 Wiley Periodicals, Inc.     

Extension rate of the straight jet in electrospinning of poly(N‐isopropyl acrylamide) solutions in dimethylformamide: Influences of flow rate and applied voltage

In the electrospinning process, the measurement of extension rate of the straight jet is not an easy task. In this study, the diameter profile of the tapering straight jet is determined with a laser light‐scattering technique. Afterwards, the jet extension rate () is derived and used to compare with the solution‐intrinsic rates, for example, the terminal relaxation rate and the Rouse relaxation rate. The extension rate of the straight jet depends on position: it is highest near the cone apex (region I) and decays to a constant value in the major jet (region II) until approaching the jet end (region III), at which the extension rate abruptly drops to nearly zero, that is, _I >_II ≫_III ∼ 0. The jet diameter in region III is independent of solution concentration and applied voltage, but is scaled to the flow rate with an exponent of ∼0.37. The derived exponent is consistent with a simple prediction based on the counterbalance between the stretching electric force and the compressive force induced by the air drag force. Provided that air friction becomes overwhelming at the straight jet end, the long electrified jet is likely to buckle, thereby triggering the instability of jet whipping. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 319–329     

Synthesis of chromophores and polyimides with a green chemistry approach for second‐order nonlinear optical applications

This article presents the synthesis of nonlinear optical responsive chromophores by adopting a green chemistry approach by coupling N‐methyl‐N‐(2‐hydroxyethyl)‐4‐amino benzaldehyde with barbituric acid, 1,3‐indanedione, and 1,3‐diethyl‐2‐thiobarbituric acid as the acceptors through stilbene linkage. We performed the synthesis in less than 10 minutes at room temperature with water as a solvent without catalyst. Two different side‐chain polyimides were synthesized from poly(hydroxy‐imide)s with chromophores by Mitsunobu reaction. The chromophores were characterized by Fourier transform infrared, ¹H NMR, ¹³C NMR, and elemental analysis. However, the polyimides were characterized by Fourier transform infrared and ¹H NMR. The inherent viscosities (η_inh) of polyimides were determined by Ubbelohde viscometer, which ranged between 0.1793 and 0.1890 dL/g. The molecular weights of the polyimides were determined using gel permeation chromatography and were in range of 23 000 to 26 000. Polyimides demonstrated an excellent solubility in polar aprotic solvents, indicating good processability. Thermal behavior of these polyimides was studied by differential scanning calorimetry and thermogravimetric analysis. The T_g's were in the range of 185°C to 255°C. The change in the molecular orientation in the polymer films after electrical poling was ascertained using ultraviolet‐visible spectrophotometer and atomic force microscopy. The thicknesses and refractive indices of the thin films were determined by an ellipsometer. The second harmonic generation coefficients of the corona‐poled polymer films at T_opt's, determined by the Maker fringe technique, ranged between 59.33 and 77.82 pm/V. High thermal endurance observed for the polyimides is attributed to the extensive hydrogen bonds in the matrix. The developed polyimides showed no decay in second harmonic generation signals below 110°C, indicating the acceptance for nonlinear optical devices.     

The Narrowest Band Gap Ever Observed in Molecular Ferroelectrics: Hexane‐1,6‐diammonium Pentaiodobismuth(III)

Narrow band gaps and excellent ferroelectricity are intrinsically paradoxical in ferroelectrics as the leakage current caused by an increase in the number of thermally excited carriers will lead to a deterioration of ferroelectricity. A new molecular ferroelectric, hexane‐1,6‐diammonium pentaiodobismuth (HDA‐BiI₅), was now developed through band gap engineering of organic–inorganic hybrid materials. It features an intrinsic band gap of 1.89 eV, and thus represents the first molecular ferroelectric with a band gap of less than 2.0 eV. Simultaneously, low‐temperature solution processing was successfully applied to fabricate high‐quality ferroelectric thin films based on HDA‐BiI₅, for which high‐precision controllable domain flips were realized. Owing to its narrow band gap and excellent ferroelectricity, HDA‐BiI₅ can be considered as a milestone in the exploitation of molecular ferroelectrics, with promising applications in high‐density data storage and photovoltaic conversion.     

Perturbed structures generated using coordinates derived from compliance constants in internal vibrations for QTAIM dual functional analysis: Intrinsic dynamic nature of interactions

Perturbed structures for QTAIM dual functional analysis (QTAIM‐DFA) are proposed to generate using the coordinates corresponding to the compliance force constants in internal vibrations (CIV). In QTAIM‐DFA, total electron energy densities H_b( r _c) are plotted versus H_b( r _c) – V_b( r _c)/2 at bond critical points (BCPs) of interactions in question, where V_b( r _c) are potential energy densities at BCPs. Each plot of an interaction based on the data from both perturbed structures and fully optimized one takes the form (θ_p, κ_p), where θ_p corresponds to the tangent line of the plot and κ_p is the curvature. The θ_p values evaluated with CIV are equal to those obtained by partial optimizations with the interaction distance in question being fixed suitably, within the calculation errors. Very high applicability of CIV is demonstrated to generate the perturbed structures for QTAIM‐DFA. Dynamic nature of interactions based on (θ_p, κ_p) with CIV is called “intrinsic dynamic nature of interactions.”     

Influence of Coriolis force on thermal convection and impurity segregation during crystal growth under microgravity

In contrast with the generally accepted viewpoint, it is shown that the Coriolis force caused by rotation of an orbital station can appreciably affect natural convection and impurity distribution during the growth of crystals from a melt in orbital flight conditions. 2D and 3D steady and oscillatory convection in a rectangular enclosure is considered. The resonance phenomenon arising due to the interaction of the Coriolis force and harmonic oscillations of the gravity force is demonstrated. It is shown that for moderate values of the Ekman number the Coriolis force suppresses convection in one direction and amplifies it in the other, which in turn results in deformation of the impurity distribution over the cross-section of the crystal.     

Self-organization of a chiral D-EAK16 designer peptide into a 3D nanofiber scaffold

Self-assembling peptide nanofiber scaffolds are an excellent material for applications such as tissue repair, tissue regeneration, instant stopping of bleeding, and slow drug release. We report a new self-assembling peptide D-EAK16 consisting purely of D-amino acids. D-EAK16 and L-EAK16 display mirror-image CD spectra at 20 degrees C. Like L-EAK16, D-EAK16 self-assembles into nanofibers, thus demonstrating that chiral self-assembling peptide nanofiber scaffolds can be made from both L- and D-amino acids. We also show that D-peptide nanofibers are resistant to natural proteases and may thus be useful in biotechnology, nanobiotechnology, tissue repair and tissue regeneration as well as other medical applications.     

Towards chemical analysis of nanostructures in biofilms II: tip-enhanced Raman spectroscopy of alginates

This study examines the feasibility of using tip-enhanced Raman spectroscopy (TERS) for label-free chemical characterization of nanostructures in biological systems. For this purpose, a well-defined model system consisting of calcium alginate fibers is studied. In a companion paper, calcium alginate fibers and their network structures were shown to be a good model for the extracellular polysaccharides of biofilms at the nanoscale. TERS analysis of biological macromolecules, such as alginates, is complicated by heterogeneity in their sequence, molecular weight, and conformations, their small Raman cross-section, and the large number of functional groups, which can chemically interact with the silver surface of the tip and cause significant band shifts. Due to these effects, Raman frequencies in TERS spectra of biopolymers do not necessarily resemble band positions in the normal Raman spectrum of the bulk material, as is the case for less complex samples (e.g., dye molecules) studied so far. Additionally, analyte decomposition due to laser heating can have a significant influence, and carbon contamination signals can sometimes even overwhelm the weak analyte signals. Based on the investigation of alginates, strategies for spectra correction, choice of appropriate reference samples, and data interpretation are presented. With this approach, characteristic frequency ranges and specific marker bands can be found for biological macromolecules that can be employed for their identification in complex environments. Figure TERS spectrum of a calcium alginate fiber bundle     

Towards chemical analysis of nanostructures in biofilms I: imaging of biological nanostructures

Due to their direct influence on the stability of bacterial biofilms, a better insight into the nanoscopic spatial arrangement of the different extracellular polymeric substances (EPS), e.g., polysaccharides and proteins, is important for the improvement of biocides and for process optimization in wastewater treatment and biofiltration. Here, the first application of a combination of confocal laser-scanning microscopy (CLSM) and atomic force microscopy (AFM) to the investigation of river-water biofilms and related biopolymers is presented. AFM images collected at selected areas of CLS micrographs dramatically demonstrate the heterogeneity of biofilms at the nanometer scale and the need for a chemical imaging method with nanoscale resolution. The nanostructures (e.g., pili, flagella, hydrocolloids, and EPS) found in the extracellular matrix are classified according to shape and size, which is typically 50–150 nm in width and 1–10 nm in thickness, and sets the demands regarding spatial resolution of a potential chemical imaging method. Additionally, thin layers of the polysaccharide alginate were investigated. We demonstrate that calcium alginate is a good model for the EPS architecture at the nanometer scale, because of its similar network-like structure. Figure CLSM-AFM allows imaging of nanometer-sized extracellular structures