A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins

Peptides bind to class II major histocompatibility complex (MHC) proteins in an extended conformation. Pockets in the peptide binding site spaced to accommodate peptide side chains at the P1, P4, P6, and P9 positions have been previously characterized and help to explain the obtained peptide binding specificity. However, two peptides differing only at P10 have significantly different binding affinities for HLA-DR1. The structure of HLA-DR1 in complex with the tighter binding peptide shows that the peptide binds in the usual polyproline type II conformation, but with the P10 residue accommodated in a shallow pocket at the end of the binding groove. HLA-DR1 variants with polymorphic residues at these positions were produced and found to exhibit different side chain specificity at the P10 position. These results define a new specificity position in HLA-DR proteins.     

Dynamic Light Scattering and NMR Studies of Napin

We analyze the structure of napin (BngNAP1), a storage protein (m.w. 14.5 kDa) from Brassica napus. On the basis of the results of ¹H NMR spectroscopy and dynamic light scattering (DLS) studies, the overall shape and secondary structure of the molecule are estimated.     

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

Pentafluorophenyl Esters as Exchangeable Stoppers for the Construction of Photoactive [2]Rotaxanes

Stable pillar[5]arene-containing [2]rotaxane building blocks with pentafluorophenyl ester stoppers have been efficiently prepared on a multi-gram scale. Reaction of these building blocks with various nucleophiles gave access to a wide range of [2]rotaxanes with amide, ester or thioester stoppers in good to excellent yields. The rotaxane structure is fully preserved during these chemical transformations. Actually, the addition-elimination mechanism at work during these transformations totally prevents the unthreading of the axle moiety of the mechanically interlocked system. The stopper exchange reactions were optimized both in solution and under mechanochemical solvent-free conditions. While amide formation is more efficient in solution, the solvent-free conditions are more powerful for the transesterification reactions. Starting from a fullerene-functionalized pillar[5]arene derivative, this new strategy gave easy access to a photoactive [2]rotaxane incorporating a C₆₀ moiety and two Bodipy stoppers. Despite the absence of covalent connectivity between the Bodipy and the fullerene moieties in this photoactive molecular device, efficient through-space excited state interactions have been evidenced in this rotaxane.     

Synthesis of the four enantiomers of diethyl 1,2-di(N-Boc-amino)propylphosphonates

A simple and efficient synthetic strategy to all four enantiomerically pure diethyl 1,2-di(N-Boc-amino)propylphosphonates has been elaborated starting from the corresponding N-[(R)-(1-phenylethyl)]aziridine-(2S)- and N-[(S)-(1-phenylethyl)]aziridine-(2R)-carboxaldehydes, employing a one-pot three-components Kabachnik-Fields reaction followed by the hydrogenolytic removal of the chiral auxiliary and aziridine ring opening with simultaneous protection of the amino groups as the N-Boc derivatives.     

Effectiveness of the Oxygenation over Classical Protonolysis Reactions: A Case of Alkylzinc Complexes Incorporating an Aminoalcoholate Ligand

Alkylzinc aminoalcoholates have emerged as powerful catalysts in organic synthesis and polymerization processes. Despite extensive research, difficulties in the rational design of these catalytic systems and in-depth understanding of their modes of action have hitherto been encountered. Most of the major obstacles stem largely from the relatively limited knowledge of the structure-activity relationship of zinc catalysts. In fact, the key active species are often generated in situ via the protonolysis of the alkylzinc precursors, which precludes their isolation and detailed characterization. Herein, the effectiveness of the oxygenation over the classical protonolysis in the synthesis of zinc alkylperoxides stabilized by an aminoalcoholate ligand is demonstrated. The controlled oxygenation of a tert-butylzinc complex incorporating a pridinolum (prinol) ligand leads to well-defined a dinuclear adduct of a (prinol)ZnOOtBu moiety with the parent tBuZn(prinol) complex and a novel dimer [tBuOOZn(prinol)]₂ with terminal alkylperoxide groups. The observed reaction outcomes strongly depend on the reaction conditions. Although sparse examples of heteroleptic adducts of the [RZn(L)]_x[ROOZn(L)]_y-type are known, the herein reported homoleptic [ROOZn(L)]_x aggregate is unprecedented. Strikingly, comparative studies involving reactions between tBuZn(prinol) and tert-butylhydroperoxide or ethanol revealed that the respective seemingly simple zinc alkylperoxides, or zinc alkoxides, respectively, are not accessible via the classical alcoholysis. We believe that these game-changing results concerning multifaceted chemistry of organozinc aminoalcoholates should pave the way for more rational development of various Zn-based catalytic systems.