Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

Recent hardware and software advances have enabled simulation studies of protein systems on biophysically-relevant timescales, often revealing the need for improved force fields. Although early force field development was limited by the lack of direct comparisons between simulation and experiment, recent work from several labs has demonstrated direct calculation of NMR observables from protein simulations. Here we quantitatively evaluate recent molecular dynamics force fields against a suite of 524 chemical shift and J coupling ((3)JH(N)H(α), (3)JH(N)C(β), (3)JH(α)C', (3)JH(N)C', and (3)JH(α)N) measurements on dipeptides, tripeptides, tetra-alanine, and ubiquitin. Of the force fields examined (ff96, ff99, ff03, ff03*, ff03w, ff99sb*, ff99sb-ildn, ff99sb-ildn-phi, ff99sb-ildn-nmr, CHARMM27, OPLS-AA), two force fields (ff99sb-ildn-phi, ff99sb-ildn-nmr) combining recent side chain and backbone torsion modifications achieve high accuracy in our benchmark. For the two optimal force fields, the calculation error is comparable to the uncertainty in the experimental comparison. This observation suggests that extracting additional force field improvements from NMR data may require increased accuracy in J coupling and chemical shift prediction. To further investigate the limitations of current force fields, we also consider conformational populations of dipeptides, which were recently estimated using vibrational spectroscopy.     

Galois extensions,plus closure,and maps on local cohomology

Given a local domain $(R,\mathfrak{m})$ of prime characteristic that is a homomorphic image of a Gorenstein ring, Huneke and Lyubeznik proved that there exists a module-finite extension domain S such that the induced map on local cohomology modules $H_{\mathfrak{m}}^i(R)\to H_{\mathfrak{m}}^i(S)$ is zero for each $i<\dim R$. We prove that the extension S may be chosen to be generically Galois, and analyze the Galois groups that arise.     

Effect of Cr doping on the ac electrical properties of MgAl<Subscript>2</Subscript>O<Subscript>4</Subscript> nanoparticles

Magnesium aluminate nanoparticles with different chromium concentration (0–12%) have been synthesized by a citrate–nitrate sol–gel route. X-ray diffraction studies confirmed the formation of single-phase cubic spinel structure excluding the presence of any secondary phase. Crystallite size of the synthesized nanoparticles was found to increase from 8.5 to 19.8 nm with the increase in Cr concentration. Fourier transformed infrared spectroscopic studies confirmed the presence of AlO₆ group which led to the formation of MgAl₂O₄ spinel structure. Surface morphology of the sintered pellets was investigated with the help of a field emission scanning electron microscope which revealed the existence of both grain and grain boundary along with their aggregates. The dielectric constant, dielectric loss and ac conductivity were studied as a function of frequency of the applied electric field for different composition and their nature of variation with frequency has been elucidated on the basis of Maxwell–Wagner interfacial model. Impedance spectroscopy technique has been used to study the effect of grain and grain boundary on the electrical properties of this spinel oxide. All the electrical parameters showed strong dependence on the nanostructural properties and were found to vary consistently with the increase of doping concentration.     

Superposition of Quantum Confinement Energy (SQCE) model for estimating shell thickness in core-shell quantum dots: validation and comparison

A novel theoretical model based on superposition of core and shell band-gaps, termed as SQCE model, is developed and reported here, which enables one to estimate the shell thickness in a core-shell quantum dot (QD), which is critically important in deciding its optical and electronic properties. We apply the model to two experimental core-shell QD systems, CdSe-CdS and CdSe-ZnS, which we synthesize by microemulsion method. We synthesize and study two series of samples, R and S to study the optical properties. The core size is varied in the R-series (by varying water-to-surfactant ratio, R) whereas the shell thickness is varied in the S-series (by varying the shell-to-core precursor molar ratio, S). The core and core-shell QDs from R-series and S-series are characterized for particle size, shape and crystallographic information. The shell thickness for all core-shell QD samples is estimated by SQCE model, and experimentally measured with TEM and SAXS. A close match is observed between experimental values and model predictions, thus validating the model. Further, the optimum shell thickness (corresponding to maximum quantum yield) values for CdS and ZnS over a 4.26 nm CdSe core have been estimated as 0.585 nm and 0.689 nm, respectively, from the SQCE model. The SQCE model developed in this work is applicable to other core-shell quantum dots also, such as CdTe-CdS, CdTe-CdSe and CdS-ZnS, and will serve as a useful complement to experimental measurement.     

Micro determination of olefinic unsaturation. Reaction of N-bromosuccinimide with olefins in polar medium

Summary A micro method for the determination of olefinic unsaturation in organic compounds has been developed. 2–10 mg sample dissolved in acetic acid is reacted with a known excess of N-bromosuccinimide at room temperature and the excess reagent is back titrated iodometrically. The maximum deviation in the results is ±2%. The compounds containing electron withdrawing groups close to the C=C site are not reactive and hence could not be determined by this procedure.

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Mikrobestimmung der Ungesättigtheit von Olefinen. Reaktion von N-Bromsuccinimid mit Olefinen in polarem Medium

Zusammenfassung 2–10mg der Probe werden in Essigsäure gelöst, mit überschüssigem Reagens versetzt und der Überschuß jodometrisch zurücktitriert. Der maximale Fehler der Ergebnisse beträgt ±2%. Verbindungen, die benachbart zur C=C-Doppelbindung elektronenentziehende Gruppen enthalten, können nicht analysiert werden.

     

Generalizing a two-conformation model for describing salt and temperature effects on protein retention and stability in hydrophobic interaction chromatography

A two-conformation adsorption model that includes the effects of salt concentration and temperature on both stability and adsorption has been developed to describe the effects of secondary protein unfolding on hydrophobic interaction chromatography (HIC). The model has been applied to a biotech protein and to beta-lactoglobulin on Phenyl Sepharose 6FF low sub HIC media. Thermodynamic property models for adsorption and protein stability with parameters obtained from experimental chromatographic data successfully describe observed chromatographic behavior over ranges of temperature and salt concentration, provide predictions of distribution among different conformers, and give a basis for calculating trends in retention strength and stability with changing conditions, that might prove useful in HIC process development.     

Working group report: Quantum chromodynamics

This is the report of the subgroup QCD of Working Group-4 at WHEPP-9. We present the activities that had taken place in the subgroup and report some of the partial results arrived at following the discussion at the working group meetings.     

Analysis of poly(amidoamine) dendrimer structure by UV-vis spectroscopy

We report a UV-vis spectroscopic study of four different types of poly(amidoamine) dendrimers. The results indicate that the degree of protonation of the interior tertiary amines of these dendrimers correlates directly to an absorption band with λ(max) in the range of 280-285 nm. Specifically, at low pH, the tertiary amines are protonated and the 280-285 nm band is absent. However, at elevated pH, when these groups are deprotonated, this band appears. Similar results were obtained for a simple model compound. The dependence of the 280-285 nm band on the chemical state of the tertiary amines of the dendrimers was confirmed by complexing them with Pd(2+) and Pt(2+). In this case the band disappears, and it only reappears when the metal ions are decomplexed following reduction with BH(4)(-). Finally, filtration experiments showed that the absorption band between 280-285 nm arises exclusively from intact, or nearly intact, dendrimers rather than low-molecular-weight fragments.     

Mathematical modelling of flow control in a tundish using electro-magnetic forces

The control of flow in a tundish is important for improving the quality of the steel. Dams, Wiers and Pouring chamber are some of the devices used for controlling the flow in the tundish. The investigation about the role of electromagnetic forces as a replacement for these devices is an objective for the present work. Thus, 3-D MHD simulation was performed to study the effect of electromagnetic forces on flow behaviour in the tundish. The MHD model developed for carrying out the simulation was validated with the analytical solution of the Hartman problem. The results obtained shows improvement in the desired characteristics for inclusion flotataion with magnetic flow modifier of optimum strength of magnetic field.