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 .     

Validating additive correction schemes against gradient-based extrapolations

The use of additive correction schemes to obtain structures and vibrational frequencies of increasingly larger molecules is becoming more common. Such approaches, based on the cubic extrapolation formula applied directly to the quantity of interest, have been successfully validated only at the highest levels of computational accuracy: for coupled cluster methods with comparably large basis sets. Here, a systematic validation of geometries and vibrational frequencies is carried out, including more affordable and relevant levels of theory, such as the Møller-Plesset perturbation theory applied with smaller basis sets. Comparisons of such additive schemes against the more rigorous gradient-based extrapolation are presented. The cbs () routine of the open-source quantum-chemistry package Psi4 has been extended for this purpose. The results confirm that geometries and frequencies of covalently bound species obtained with additive correction schemes are in an excellent agreement with the results of gradient-based extrapolations. However, when applied to systems involving noncovalent interactions, the errors due to such schemes are significantly larger. In general, we propose the application of gradient-based extrapolations, as they incur no extra cost compared to additive schemes.     

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.     

Benzyl Borane NHC Adducts: Beyond B−C Bond Scission

Benzyl-substituted boronates and borates are widely employed as mild sources in radical or anionic transfer reactions of benzyl entities. In this process the B−C bond to the benzyl moiety is essentially ruptured. In contrast, reactions with retention of the B−C bond are poorly investigated although several other reactive sites in benzyl–boron systems are clearly inherent. In this respect, the novel reactivity of the representative borane adduct IiPr−BH₂Bn [IiPr=:C{N(iPr)CH}₂, Bn=CH₂C₆H₅] is demonstrated. Dihalogenation of the BH₂ entity is observed with BCl₃ and BBr₃, whereas BI₃ either affords IiPr−BHI₂ or proceeds with borylation of the aromatic phenyl ring to give a hydride-bridged bisborylated species. The photochemical mono- and dihalogenation of the benzylic CH₂ group was demonstrated with elemental bromine Br₂. The brominated product IiPr−BBr₂−CHBr−C₆H₅ was borylated at the benzylic carbon atom in an umpolung event with BI₃ to afford the zwitterion IiPr−BI−CH(BI₃)−C₆H₅.     

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.     

Square‐Planar Ruthenium(II) Complexes: Control of Spin State by Pincer Ligand Functionalization

Functionalization of the PNP pincer ligand backbone allows for a comparison of the dialkyl amido, vinyl alkyl amido, and divinyl amido ruthenium(II) pincer complex series [RuCl{N(CH₂CH₂PtBu₂)₂}], [RuCl{N(CHCHPtBu₂)(CH₂CH₂PtBu₂)}], and [RuCl{N(CHCHPtBu₂)₂}], in which the ruthenium(II) ions are in the extremely rare square‐planar coordination geometry. Whereas the dialkylamido complex adopts an electronic singlet (S=0) ground state and energetically low‐lying triplet (S=1) state, the vinyl alkyl amido and the divinyl amido complexes exhibit unusual triplet (S=1) ground states as confirmed by experimental and computational examination. However, essentially non‐magnetic ground states arise for the two intermediate‐spin complexes owing to unusually large zero‐field splitting (D>+200 cm^?1). The change in ground state electronic configuration is attributed to tailored pincer ligand‐to‐metal π‐donation within the PNP ligand series.     

Interpenetrated Cage Structures

This Review covers design strategies, synthetic challenges, host–guest chemistry, and functional properties of interlocked supramolecular cages. Some dynamic covalent organic structures are discussed, as are selected examples of interpenetration in metal–organic frameworks, but the main focus is on discrete coordination architectures, that is, metal‐mediated dimers. Factors leading to interpenetration, such as geometry, flexibility and chemical makeup of the ligands, coordination environment, solvent effects, and selection of suitable counter anions and guest molecules, are discussed. In particular, banana‐shaped bis‐pyridyl ligands together with square‐planar metal cations have proven to be suitable building blocks for the construction of interpenetrated double‐cages obeying the formula [M₄L₈]. The peculiar topology of these double‐cages results in a linear arrangement of three mechanically coupled pockets. This allows for the implementation of interesting guest encapsulation effects such as allosteric binding and template‐controlled selectivity. In stimuli‐responsive systems, anionic triggers can toggle the binding of neutral guests or even induce complete structural conversions. The increasing structural and functional complexity in this class of self‐assembled hosts promises the construction of intelligent receptors, novel catalytic systems, and functional materials.