Protein folding kinetics under force from molecular simulation

Despite a large number of studies on the mechanical unfolding of proteins, there are still relatively few successful attempts to refold proteins in the presence of a stretching force. We explore refolding kinetics under force using simulations of a coarse-grained model of ubiquitin. The effects of force on the folding kinetics can be fitted by a one-dimensional Kramers theory of diffusive barrier crossing, resulting in physically meaningful parameters for the height and location of the folding activation barrier. By comparing parameters obtained from pulling in different directions, we find that the unfolded state plays a dominant role in the refolding kinetics. Our findings explain why refolding becomes very slow at even moderate pulling forces and suggest how it could be practically observed in experiments at higher forces.     

Spectroscopic characterization of molybdenum dinitrogen complexes containing a combination of di- and triphosphine coligands: 31P NMR analysis of five-spin systems

The three molybdenum-N2 complexes [Mo(N2)(dpepp)(depe)] (1), [Mo(N2)(dpepp)(dppe)] (2), and [Mo(N2)(dpepp)(1,2-dppp)] (3), all of which contain a combination of a bi- and a tridentate phosphine ligand, were prepared and investigated by vibrational and (31)P NMR spectroscopy. As a tridentate ligand bis(2-diphenylphosphinoethyl)phenylphosphine (dpepp) has been employed. The three different bidentate ligands are 1,2-bis(diethylphosphino)ethane (depe), 1,2-bis(diphenylphosphino)ethane (dppe), and R-(+)-1,2-bis(diphenylphosphino)propane (1,2-dppp). N-N as well as metal-N vibrations of 1-3 are identified and interpreted in terms of the geometric and electronic structures of the complexes. (31)P NMR spectra are recorded and fully analyzed. Moreover, correlation spectroscopy (COSY)-45 measurements are performed to determine the relative signs of coupling constants. Special attention is directed to a detection of different isomers and their (31)P NMR, as well as vibrational spectroscopic properties. The implications of the results for the area of synthetic nitrogen fixation with phosphine complexes are discussed.     

Short-time transport properties in dense suspensions: from neutral to charge-stabilized colloidal spheres

We present a detailed study of short-time dynamic properties in concentrated suspensions of charge-stabilized and of neutral colloidal spheres. The particles in many of these systems are subject to significant many-body hydrodynamic interactions. A recently developed accelerated Stokesian dynamics (ASD) simulation method is used to calculate hydrodynamic functions, wave-number-dependent collective diffusion coefficients, self-diffusion and sedimentation coefficients, and high-frequency limiting viscosities. The dynamic properties are discussed in dependence on the particle concentration and salt content. Our ASD simulation results are compared with existing theoretical predictions, notably those of the renormalized density fluctuation expansion method of Beenakker and Mazur [Physica A 126, 349 (1984)], and earlier simulation data on hard spheres. The range of applicability and the accuracy of various theoretical expressions for short-time properties are explored through comparison with the simulation data. We analyze, in particular, the validity of generalized Stokes-Einstein relations relating short-time diffusion properties to the high-frequency limiting viscosity, and we point to the distinctly different behavior of de-ionized charge-stabilized systems in comparison to hard spheres.     

Maximum Caliber: a variational approach applied to two-state dynamics

We show how to apply a general theoretical approach to nonequilibrium statistical mechanics, called Maximum Caliber, originally suggested by E. T. Jaynes [Annu. Rev. Phys. Chem. 31, 579 (1980)], to a problem of two-state dynamics. Maximum Caliber is a variational principle for dynamics in the same spirit that Maximum Entropy is a variational principle for equilibrium statistical mechanics. The central idea is to compute a dynamical partition function, a sum of weights over all microscopic paths, rather than over microstates. We illustrate the method on the simple problem of two-state dynamics, A<-->B, first for a single particle, then for M particles. Maximum Caliber gives a unified framework for deriving all the relevant dynamical properties, including the microtrajectories and all the moments of the time-dependent probability density. While it can readily be used to derive the traditional master equation and the Langevin results, it goes beyond them in also giving trajectory information. For example, we derive the Langevin noise distribution rather than assuming it. As a general approach to solving nonequilibrium statistical mechanics dynamical problems, Maximum Caliber has some advantages: (1) It is partition-function-based, so we can draw insights from similarities to equilibrium statistical mechanics. (2) It is trajectory-based, so it gives more dynamical information than population-based approaches like master equations; this is particularly important for few-particle and single-molecule systems. (3) It gives an unambiguous way to relate flows to forces, which has traditionally posed challenges. (4) Like Maximum Entropy, it may be useful for data analysis, specifically for time-dependent phenomena.     

Influence of the remanent polarisation on the liquid crystal alignment in composite films of ferroelectric poly(vinylidene fluoride-trifluoroethylene) and a cyanobiphenyl-based liquid crystal

Polymer-dispersed liquid crystals (PDLCs) of ferroelectric poly(vinylidene fluoride-trifluoroethylene) and nematic 4-cyano-4?-n-hexylbiphenyl (6CB) or 4-cyano-4?-n-pentylbiphenyl (5CB) were prepared to study the effect of the remanent polarisation of the polymer on the liquid crystal alignment. We measured the macroscopic alignment of the liquid crystal molecules in the thickness direction by means of Infrared Transition-Moment Orientational Analysis. Electrical poling at 100 V/µm caused an increased order parameter up to 0.15. After subsequent annealing above the nematic-to-isotropic phase-transition temperature, the order parameter was reduced to 0.02. Nevertheless, the order parameter was still higher than for non-poled film indicating a slight orientation in thickness direction. Both values are lower than those expected from model calculations. In agreement with dielectric measurements, we attribute this result to the shielding effect of mobile charge carriers within the liquid crystal inclusions.     

Selective N,O‐Addition of the TEMPO Radical to Conjugated Boryldienes

B(C₆F₅)₂‐containing boryldienes 4 underwent the addition of two molar equivalents of TEMPO to give N,O‐bonded four‐membered heterocyclic products 7 . The reaction is a metal‐free example of the generation of reactive nitrogen‐centered TEMPO radical derivatives, in this case by the addition of TEMPO to the borane, followed by carbon–nitrogen bond formation and subsequent trapping of the resulting allyl radical by the second equivalent of TEMPO.     

Lung Cancer: EGFR Inhibitors with Low Nanomolar Activity against a Therapy‐Resistant L858R/T790M/C797S Mutant

The treatment of non‐small‐cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) inhibitors is made challenging by acquired resistance caused by somatic mutations. Third‐generation EGFR inhibitors have been designed to overcome resistance through covalent binding to the Cys 797 residue of the enzyme, and these inhibitors are effective against most clinically relevant EGFR mutants. However, the high dependence of these recent EGFR inhibitors on this particular interaction means that additional mutation of Cys 797 results in poor inhibitory activity, which leads to tumor relapse in initially responding patients. A new generation of irreversible and reversible mutant EGFR inhibitors was developed with strong noncovalent binding properties, and these compounds show high inhibitory activities against the cysteine‐mutated L858R/T790M/C797S EGFR.     

Harmonic Functions on Rank One Asymptotically Harmonic Manifolds

Asymptotically harmonic manifolds are simply connected complete Riemannian manifolds without conjugate points such that all horospheres have the same constant mean curvature \(h\). In this article we present results for harmonic functions on rank one asymptotically harmonic manifolds \(X\) with mild curvature boundedness conditions. Our main results are (a) the explicit calculation of the Radon–Nikodym derivative of the visibility measures, (b) an explicit integral representation for the solution of the Dirichlet problem at infinity in terms of these visibility measures, and (c) a result on horospherical means of bounded eigenfunctions implying that these eigenfunctions do not admit non-trivial continuous extensions to the geometric compactification \(\overline{X}\).     

Mechanochemical Synthesis of 3d Transition‐Metal–1,2,4‐Triazole Complexes as Precursors for Microwave‐Assisted and Thermal Conversion to Coordination Polymers with a High Influence on the Dielectric Properties

The complexes [MCl₂(TzH)₄] (M=Mn ( 1 ), Fe ( 2 ); TzH=1,2,4‐1H‐triazole) and [ZnCl₂(TzH)₂] ( 3 ) have been obtained by mechanochemical reactions of the corresponding divalent metal chloride and 1,2,4‐1H‐triazole. They were successfully used as precursors for the formation of coordination polymers either by a microwave‐assisted reaction or by thermal conversion. For manganese, the conversion directly yielded [MnCl₂TzH] ( 4 ), whereas for the iron‐containing precursor, [FeCl₂TzH] ( 6 ), was formed via the intermediate coordination polymer [FeCl(TzH)₂]Cl ( 5 ). For cobalt, the isotypic polymer [CoCl(TzH)₂]Cl ( 7 ) was obtained, but exclusively by a microwave‐induced reaction directly from CoCl₂. The crystal structures were resolved from single crystals and powders. The dielectric properties were determined and revealed large differences in permittivity between the precursor complexes and the rigid chain‐like coordination polymers. Whereas the monomeric complexes exhibit very different dielectric behaviour, depending on the transition metal, from “low‐k” to “high‐k” with the permittivity ranging from 4.3 to >100 for frequencies of up to 1000 Hz, the coordination polymers and complexes with strong intermolecular interactions are all close to “low‐k” materials with very low dielectric constants up to 50 °C. Therefore, the conversion procedures can be used to deliberately influence the dielectric properties from complex to polymer and for different 3d transition‐metal ions.     

Recent advances in capillary electrophoretic migration techniques for pharmaceutical analysis (2013–2015)

This review updates and follows‐up a previous review by highlighting recent advancements regarding capillary electromigration methodologies and applications in pharmaceutical analysis. General approaches such as quality by design as well as sample injection methods and detection sensitivity are discussed. The separation and analysis of drug‐related substances, chiral CE, and chiral CE‐MS in addition to the determination of physicochemical constants are addressed. The advantages of applying affinity capillary electrophoresis in studying receptor–ligand interactions are highlighted. Finally, current aspects related to the analysis of biopharmaceuticals are reviewed. The present review covers the literature between January 2013 and December 2015.