Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Fast sample preparation involving MASE and coupled column normal phase liquid chromatography for the rapid trace analysis of dioxins in air-dust samples from fire catastrophe emissions

A new approach has been developed and tested for the urgent analysis of dioxins in samples of air-dust filters originating from catastrophe emissions. The procedure consists of a fast extraction of the sample with microwave solvent extraction (MASE) and acetone as solvent followed by a fast cleanup of the extract with normal phase coupled column liquid chromatography (LC/LC).

The multi-dimensional LC/LC system employs a 50 mm×4.6 mm i.d. column packed with 3 μm silica and a 150 mm×4.6 mm i.d. column packed with 5 μm PYE as the first and second analytical column, respectively. Iso-hexane is used on both columns to perform cleanup and dichloromethane to perform efficient back-flush elution of the compounds from the second column. The obtained polarity-based separation in the first dimension and molecular-structure based separation in the second dimension provides a fast and powerful cleanup.

Validation was done by analysing samples of homemade RIVM air-dust with aged residues (n=8, spiking level about 15 pg mg⁻¹ per compound) of dioxins/furans and samples of reference Urban Dust SRM 1649a (n=4) with both the new approach and the existing conventional procedure and were instrumentally analyzed with capillary gas chromatography and high resolution mass spectrometric detection (GC/HRMS).

In comparison to the existing conventional procedure, the new approach reduces sample processing from several days to several hours per sample.

As regards the aged-residue air-dust samples, the new method shows a good accuracy, precision and high selectivity providing a performance in good agreement with the existing procedure. In SRM air-dust, the concentration of a few compounds obtained by the new method was below (10–50%) the certified value.     

Structure elucidation of the unprecedented asymmetric bis-chelate complex [Pd(1,3-bis(di(o-methoxy-m-methylphenyl)phosphino)propane)2]2+ in the solid state and in solution

Complexes of the type [Pd(ligand)(2)](anion)(2) were prepared with a series of bidentate di(o-methoxyphenyl)phosphine ligands with increasing steric bulk on the meta position of the phenyl groups: m-H (L1); m-MeO (L2); and m-Me (L3). The solid-state structure of [Pd(L2)(2)](OTs)(2) revealed that the two ligands are symmetrically coordinated to Pd(2+). In the solid state structure of [Pd(L3)(2)](OTs)(2) however, the two ligands are unsymmetrically coordinated to Pd(2+), yielding an unprecedented conformation of this bis-chelate P(4)Pd(2+) complex. (1)H-(1)H-COSY and NOESY analysis and a (31)P-NMR simulation showed that the asymmetric structure of [Pd(L3)(2)](OTs)(2) is retained in solution.     

Carbonylation of nitrobenzene in methanol with palladium bidentate phosphane complexes: an unexpectedly complex network of catalytic reactions, centred around a Pd-imido intermediate

The reactivity of palladium complexes of bidentate diaryl phosphane ligands (P₂) was studied in the reaction of nitrobenzene with CO in methanol. Careful analysis of the reaction mixtures revealed that, besides the frequently reported reduction products of nitrobenzene [methyl phenyl carbamate (MPC), N,N′‐diphenylurea (DPU), aniline, azobenzene (Azo) and azoxybenzene (Azoxy)], large quantities of oxidation products of methanol were co‐produced (dimethyl carbonate (DMC), dimethyl oxalate (DMO), methyl formate (MF), H₂O, and CO). From these observations, it is concluded that several catalytic processes operate simultaneously, and are coupled via common catalytic intermediates. Starting from a P₂Pd⁰ compound formed in situ, oxidation to a palladium imido compound P₂Pd^II?NPh, can be achieved by de‐oxygenation of nitrobenzene 1) with two molecules of CO, 2) with two molecules of CO and the acidic protons of two methanol molecules, or 3) with all four hydrogen atoms of one methanol molecule. Reduction of P₂Pd^II?NPh to P₂Pd⁰ makes the overall process catalytic, while at the same time forming Azo(xy), MPC, DPU and aniline. It is proposed that the Pd–imido species is the central key intermediate that can link together all reduction products of nitrobenzene and all oxidation products of methanol in one unified mechanistic scheme. The relative occurrence of the various catalytic processes is shown to be dependent on the characteristics of the catalysts, as imposed by the ligand structure.     

π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures

Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called “π-hole interactions” are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about −5 kcal mol⁻¹ for ligand–protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand–protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.     

Platform Synthetic Lectins for Divalent Carbohydrate Recognition in Water

Biomimetic carbohydrate receptors (“synthetic lectins”) have potential as agents for biological research and medicine. However, although effective strategies are available for “all‐equatorial” carbohydrates (glucose, etc.), the recognition of other types of saccharide under natural (aqueous) conditions is less well developed. Herein we report a new approach based on a pyrene platform with polar arches extending from aryl substituents. The receptors are compatible with axially substituted carbohydrates, and also feature two identical binding sites, thus mimicking the multivalency observed for natural lectins. A variant with negative charges forms 1:2 host/guest complexes with aminosugars, with K₁>3000 m ^?1 for axially substituted mannosamine, whereas a positively charged version binds the important α‐sialyl unit with K₁≈1300 m ^?1.     

Computational Evaluation of Me2TCCP as Lewis Acid

Supramolecular adducts between dimethyl-2,2,3,3-tetracyanocyclopropane (Me₂TCCP) with 21 small (polar) molecules and 10 anions were computed with DFT (B3LYP-D3/def2-TZVP). Their optimized geometries were used to obtain interaction energies, and perform energy decomposition and ‘atoms-in-molecules’ analyses. A set of 38 other adducts were also evaluated for comparison purposes. Selected examples were further scrutinized by inspection of the molecular electrostatic potential maps, Noncovalent Interaction index plots, the Laplacian, the orbital interactions, and by estimating the Gibbs free energy of complexation in hexane solution. These calculations divulge the thermodynamic feasibility of Me₂TCCP adducts and show that complexation is typically driven by dispersion with less polarized partners, but by orbital interactions when more polarized or anionic guests are deployed. Most Me₂TCCP adducts are more stable than simple hydrogen bonding with water, but less stable than traditional Lewis adducts involving Me₃B, or a strong halogen bond such as with Br₂. Several bonding analyses showed that the locus of interaction is found near the electron poor sp³-hydridized (NC)₂C−C(CN)₂ carbon atoms. An empty hybrid σ*/π* orbital on Me₂TCCP was identified that can be held responsible for the stability of the most stable adducts due to donor-acceptor interactions.     

Small Cycloalkane (CN)2CC(CN)2 Structures Are Highly Directional Non‐covalent Carbon‐Bond Donors

High‐level calculations (RI‐MP2/def2‐TZVP) disclosed that the σ‐hole in between two C atoms of cycloalkane X₂C?CX₂ structures (X=F, CN) is increasingly exposed with decreasing ring size. The interacting energy of complexes of F^?, HO^?, N≡C^?, and H₂CO with cyclopropane and cyclobutane X₂C?CX₂ derivatives was calculated. For X=F, these energies are small to positive, while for X=CN they are all negative, ranging from ?6.8 to ?42.3 kcal mol^?1. These finding are corroborated by a thorough statistical survey of the Cambridge Structural Database (CSD). No clear evidence could be found in support of non‐covalent carbon bonding between electron‐rich atoms (El.R.) and F₂C?CF₂ structures. In marked contrast, El.R.???(CN)₂C?C(CN)₂ interactions are abundant and highly directional. Based on these findings, the hydrophobic electrophilic bowl formed by 1,1′,2,2′‐tetracyano cyclopropane or cyclobutane derivatives is proposed as a new and synthetically accessible supramolecular synthon.     

σ‐Hole Opposite to a Lone Pair: Unconventional Pnicogen Bonding Interactions between ZF3 (Z=N,P, As,and Sb) Compounds and Several Donors

The ability of several pnicogen sp³ derivatives ZF₃ (Z=N, P, As, Sb) to interact with electron‐rich entities by means of the opposite face to the lone pair (lp) is investigated at the RI‐MP2/aug‐cc‐pVQZ level of theory. The strength of the interaction ranges from ?1 to ?87 kJ mol^?1, proving its favorable nature, especially when the lp is coordinated to a metal center, whereby the strength of the interaction is significantly enhanced. NBO analysis showed that orbital effects are modest contributors to the global stabilization of the pnicogen σ‐hole bonded complexes studied. Finally, a selection of Cambridge Structural Database examples are shown that demonstrate the impact of this counterintuitive binding mode in the solid state.