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.     

Contingent derivatives and regularization for noncoercive inverse problems

Abstract

We study the inverse problem of parameter identification in noncoercive variational problems that commonly appear in applied models. We examine the differentiability of the set-valued parameter-to-solution map using the first-order and the second-order contingent derivatives. We explore the inverse problem using the output least-squares and the modified output least-squares objectives. By regularizing the noncoercive variational problem, we obtain a single-valued regularized parameter-to-solution map and investigate its smoothness and boundedness. We also consider optimization problems using the output least-squares and the modified output least-squares objectives for the regularized variational problem. We give a complete convergence analysis showing that for the output least-squares and the modified output least-squares, the regularized minimization problems approximate the original optimization problems suitably. We also provide the first-order and the second-order adjoint method for the computation of the first-order and the second-order derivatives of the output least-squares objective. We provide discrete formulas for the gradient and the Hessian calculation and present numerical results.     

A Carbene‐Extended ATRA Reaction

Atom‐transfer radical addition (ATRA) reactions have gained a strong foothold in organic synthesis by virtue of their operational simplicity, synthetic versatility, and perfect atom economy. A rich chemical space can be accessed through clever combinations of the simple starting materials. Many variations of this general motif have been reported. However, the vast majority involve the addition of an organic halide across a C=C double bond, resulting in the formation of 1,2‐bifunctional products. This report introduces a significant expansion of this general reactivity concept to give 1,3‐bifunctional adducts through the combination of 1,1‐ATRA to a carbenoid and 1,2‐ATRA to an alkyne. Both processes operate under mild conditions (RT, 5 h) with the same commercial catalyst (CoBr₂, dppbz).     

Hyperpolarization of Amino Acids in Water Utilizing Parahydrogen on a Rhodium Nanocatalyst

NMR offers many possibilities in chemical analysis, structural investigations, and medical diagnostics. Although it is broadly used, one of NMR spectroscopies main drawbacks is low sensitivity. Hyperpolarization techniques enhance NMR signals by more than four orders of magnitude allowing the design of new contrast agents. Parahydrogen induced polarization that utilizes the para-hydrogen's singlet state to create enhanced signals is of particular interest since it allows to produce molecular imaging agents within seconds. Herein, we present a strategy for signal enhancement of the carbonyl ¹³C in amino acids by using parahydrogen, as demonstrated for glycine and alanine. Importantly, the hyperpolarization step is carried out in water and chemically unmodified canonical amino acids are obtained. Our approach thus offers a high degree of biocompatibility, which is crucial for further application. The rapid sample hyperpolarization (within seconds) may enable the continuous production of biologically useful probes, such as metabolic contrast agents or probes for structural biology.     

The h-SbxWO3+2x Oxygen Excess Antimony Tungsten Bronze

We describe the previously unreported oxygen excess hexagonal antimony tungsten bronze with composition Sb_0.5W₃O₁₀, in the following denoted as h-Sb_xWO_3+2x with x=0.167, to demonstrate its analogy to classical A_xWO₃ tungsten bronzes. This compound forms in a relatively narrow temperature range between 580 °C<T<620 °C. It was obtained as a dark-blue polycrystalline powder, and as thin, needle-shaped, blue single crystals. h-Sb_xWO_3+2x crystallizes in the hexagonal space group P6/mmm with the cell parameters a=7.4369(4) Å and c=3.7800(2) Å. The antimony and excess oxygen occupy the hexagonal channels within the network of corner-sharing WO₆ octahedra. h-Sb_xWO_3+2x has a resistivity of ρ_{300 K}≈1.28 mΩ cm at room temperature, with little if any temperature-dependence on cooling. DFT calculations on a simplified model for this compound find a metallic-like electronic structure with the Fermi level falling within rather flat bands, especially around the Γ point.     

Cover Feature: How Many O-Donor Groups in Enterobactin Does It Take to Bind a Metal Cation? (Chem. Eur. J. 28/2019)

The E. coli siderophore enterobactin, the strongest Fe^III chelator known to date, forms hexacoordinate complexes with Si^IV, Ge^IV, and Ti^IV. Synthetic protocols have been developed to prepare non-symmetric enterobactin analogues with varying denticities. Various benzoic acid residues were coupled to the macrocyclic lactone to afford a diverse library of ligands. These enterobactin analogues were bound to Si^IV, Ge^IV, and Ti^IV, and the complexes were investigated through experimental and computational techniques. The binding behavior of the synthesized chelators enabled assessment of the contribution of each of the phenolic hydroxy groups in enterobactin to metal-ion complexation. It was found that at least four O-donors are needed for enterobactin derivatives to act as metal binders. Density functional theory calculations indicate that the strong binding behavior of enterobactin can be ascribed to a diminished translational entropy penalty, a common feature of the chelate effect, coupled with the structural arrangement of the three catechol moieties, which allows the triseryl base to be installed without distorting the preferred local metal-binding geometry of the catecholate ligands.     

IR Tools: a MATLAB package of iterative regularization methods and large-scale test problems

Numerical Algorithms - This paper describes a new MATLAB software package of iterative regularization methods and test problems for large-scale linear inverse problems. The software package, called...     

On the distribution of the sum of digits of sums $$a+b$$ a + b

The Ramanujan Journal - Let $${\mathcal {A}}$$ , $${\mathcal {B}}$$ be large subsets of $$\{1,\ldots ,N\}$$ . We study the distribution of the sum of binary digits of the sums $$a+b$$ with...     

Sustainable challenges on the moon

For a permanently manned outpost on the moon – a moon village – a first holistic concept of a sustainable material flow has been established. From this context three dedicated topics have been investigated to more depth: Additive manufacturing (AM) of Al from disused space crafts, AM of structural elements with local resources, and resource extraction from regolith via thermal processes.     

Compactness and convergence rates in the combinatorial integral approximation decomposition

The combinatorial integral approximation decomposition splits the optimization of a discrete-valued control into two steps: solving a continuous relaxation of the discrete control problem, and computing a discrete-valued approximation of the relaxed control. Different algorithms exist for the second step to construct piecewise constant discrete-valued approximants that are defined on given decompositions of the domain. It is known that the resulting discrete controls can be constructed such that they converge to a relaxed control in the \(\hbox {weak}^*\) topology of \(L^\infty \) if the grid constant of this decomposition is driven to zero. We exploit this insight to formulate a general approximation result for optimization problems, which feature discrete and distributed optimization variables, and which are governed by a compact control-to-state operator. We analyze the topology induced by the grid refinements and prove convergence rates of the control vectors for two problem classes. We use a reconstruction problem from signal processing to demonstrate both the applicability of the method outside the scope of differential equations, the predominant case in the literature, and the effectiveness of the approach.