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.     

Reactivity of urethanes at high temperature: Transurethanization and side reactions

The reactivity of urethanes based on 1,6‐hexamethylene diisocyanate (HDI) and 4,4′‐methylene diphenyl diisocyanate (MDI) was investigated at temperatures between 190 °C and 235 °C. Diurethane model compounds end‐capped with either 1‐dodecanol (D‐core‐D) or 1‐hexadecanol (H‐core‐H) were mixed and annealed at high temperature. The core was either MDI or HDI. The transurethanization reaction was followed based on the formation of the compounds (H‐core‐D). The amount of H‐core‐D and of side products, which had formed after variable annealing times, were identified with ¹H NMR, FTIR, SEC, and MALDI‐TOF. Transurethanization was considerably faster for MDI‐based urethanes than for HDI‐based urethanes. Only traces of side products were formed during annealing of MDI‐based urethanes, whereas a significant amount of allophanates was formed from HDI‐based urethanes under the same conditions. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 621–629     

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     

In situ ultrasonic measurements: a powerful tool to control the synthesis of zeolites from coal fly ash

An in situ ultrasonic diagnostic technique was applied to monitoring the hydrothermal synthesis of zeolite A and X of clear solution extracted from alkaline fused class F coal fly ash. In this context, kinetic evaluations based on in situ ultrasonic diagnostic data displayed an important approach to study the synthesis process. The impact on nucleation and crystal growth was demonstrated by variation of a few relevant parameters such as reaction temperature, amount of water, Na₂O and ageing time, including templated colloidal synthesis mixtures as model solution. To complement the kinetic analysis, ex situ techniques such as ICP, X-ray diffraction, scanning electron microscopy and dynamic light scattering were used to investigate liquid phase and reaction products extracted from the reaction mixture during the synthesis.