Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable ¹⁹F chemical-shift predictions to deduce ligand-binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the ¹⁹F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of ¹⁹F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.     

NIFTy 3 – Numerical Information Field Theory: A Python Framework for Multicomponent Signal Inference on HPC Clusters

NIFTy , “Numerical Information Field Theory,” is a software framework designed to ease the development and implementation of field inference algorithms. Field equations are formulated independently of the underlying spatial geometry allowing the user to focus on the algorithmic design. Under the hood, NIFTy ensures that the discretization of the implemented equations is consistent. This enables the user to prototype an algorithm rapidly in 1D and then apply it to high‐dimensional real‐world problems. This paper introduces NIFTy  3, a major upgrade to the original NIFTy  framework. NIFTy  3 allows the user to run inference algorithms on massively parallel high performance computing clusters without changing the implementation of the field equations. It supports n‐dimensional Cartesian spaces, spherical spaces, power spaces, and product spaces as well as transforms to their harmonic counterparts. Furthermore, NIFTy  3 is able to handle non‐scalar fields, such as vector or tensor fields. The functionality and performance of the software package is demonstrated with example code, which implements a mock inference inspired by a real‐world algorithm from the realm of information field theory. NIFTy  3 is open‐source software available under the GNU General Public License v3 (GPL‐3) at https://gitlab.mpcdf.mpg.de/ift/NIFTy/tree/NIFTy_3 .     

Synthesis of μ2-Oxo-Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations

Iron(III) porphyrins have the propensity to form μ₂-oxo-dimers, the structures of which resemble two wheels on an axle. Whereas their crystal structure is known, their solution structure and internal dynamics is not. In the present work, the structure and dynamics of such dimers were studied by means of electron paramagnetic resonance (EPR) spectroscopy and quantum chemistry based molecular dynamics (MD) simulations by using the semiempirical tight-binding method (GFN-xTB). To enable EPR investigation of the dimers, a nitroxide was attached to each of the tetraphenylporphyrin cores through a linear and a bent linker. The inter-nitroxide distance distributions within the dimers were determined by continuous-wave (cw)-EPR and pulsed electron–electron double resonance (PELDOR or DEER) experiments and, with the help of MD, interpreted in terms of the rotation of the porphyrin planes with respect to each other around the Fe–O–Fe axis. It was found that such rotation is restricted to the four registers defined by the phenyl substituents. Within the registers, the rotation angle swings between 30° and 60° in the proximal and between 125° and 145° in the distal register. With EPR, all four angles were found to be equally populated, whereas the 30° and 145° angles are strongly favored to the expense of the 60° and 125° angles in the MD simulation. In either case, the internal dynamics of these dimers thus resemble the motion of a step motor.     

Tuning the phase behavior of semicrystalline hydrogenated polynorbornene via epimerization

Hydrogenated polynorbornene (hPN) synthesized by ring‐opening metathesis polymerization (ROMP) exhibits a thermoreversible change in crystal polymorph at a temperature T _cc below its melting point, T _m. The polymorphic transition corresponds to a sharp increase in rotational disorder around the chain axis as the temperature is increased above T _cc. Saturation of ROMP polynorbornene (PN) to hPN can be achieved through both catalytic and noncatalytic approaches. Here, three different hydrogenation routes were employed on the same precursor polymer: catalytic routes over either supported Pd⁰ or a Ni/Al complex, and noncatalytic saturation with diimide. The different hydrogenation routes result in hPNs with varying degrees of epimerization of the cyclopentylene ring (from cis to trans); these epimerized units are included in the hPN crystals. The crystal structure of the rotationally ordered hPN polymorph, observed below T _cc, changes sharply at low levels of epimerization and then is weakly influenced by further increases in trans content. The stability of the rotationally ordered hPN polymorph decreases with increasing epimerization, as reflected in a reduction of T _cc from 134 °C to 92 °C at 22% epimerization. T _cc is less affected by epimerization than by the inclusion of a similar content of 5‐methylnorbornene units, reflecting the smaller size of the trans defect. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1188–1195     

Melt spinning of propylene carbonate‐plasticized poly(acrylonitrile)‐co‐poly(methyl acrylate)

The primary use of poly(acrylonitrile) (PAN) fibers, commonly referred to as acrylic fibers, is in textile applications like clothing, furniture, carpets, and awnings. All commercially available PAN fibers are processed by solution spinning; however, alternative, more cost‐effective processes like melt spinning are still highly desired. Here, the melt spinning of PAN‐co‐poly(methyl acrylate) (PMA) plasticized with propylene carbonate (PC) at 175°C is reported. The use of methyl acrylate (MA) as comonomer and PC as an external plasticizer renders the approach a combination of internal and external plasticization. Various mixtures of PAN and PC used in this work were examined by rheology, subjected to melt spinning, followed by discontinuous and continuous washing, respectively. The best fibers were derived from a PAN‐co‐PMA copolymer containing 8.1 mol‐% of MA having a number‐average molecular weight M _n of 34 000 g/mol, spun in the presence of 22.5 wt.‐% of PC. The resulting fibers were analyzed by scanning electron microscopy and wide‐angle X‐ray scattering (WAXS), and were subjected to mechanical testing.     

Comparison of monomethoxy‐, dimethoxy‐, and trimethoxysilane anchor groups for surface‐initiated RAFT polymerization from silica surfaces

The immobilization of reversible addition–fragmentation chain transfer (RAFT) agents on silica for surface‐initiated RAFT polymerizations (SI‐RAFT) via the Z‐group approach was studied systematically in dependence of the functionality of the RAFT‐agent anchor group. Monoalkoxy‐, dialkoxy‐, and trialkoxy silyl ether groups were incorporated into trithiocarbonate‐type RAFT agents and bound to planar silica surfaces as well as to silica nanoparticles. The immobilization efficiency and the structure of the bound RAFT‐agent film varied strongly in dependence of the used solvent (toluene vs. 1,2‐dimethoxyethane) and the anchor group functionality, as evidenced by atomic force microscopy, transmission electron microscopy, dynamic light scattering, and UV/Vis spectroscopy. Surface‐initiated RAFT polymerizations using functionalized silica nanoparticles revealed that grafted oligomers, which often occur in SI‐RAFT, are not formed within the crosslinked structures that originate from the immobilization, and that RAFT‐agent films that show less aggregation during the immobilization are more efficient during SI‐RAFT in terms of polymer grafting density. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 103–113