Solvent effects on the rate of the keto-enol interconversion of 2-nitrocyclohexanone

The rates of tautomerization of 2-nitrocyclohexanone (2-NCH) have been measured spectrophotometrically at 25.0 +/- 0.1 degrees C in several organic aprotic solvents and their binary mixtures. In cyclohexane the reaction is effectively catalyzed by bases and inhibited by acids while the so-called "spontaneous reaction" appears essentially due to autocatalysis. Apparent second order rate constants (k(app)(B)) for the reaction catalyzed by triethylamine (TEA) and pyridine (Pyr) have been obtained. From the experimental k(app)(B) values rate constants for the enolization (k(1)(B)) and ketonization (k(-1)(B)) reactions have been calculated. A Kamlet-Taft type linear solvation energy relationship (LSER) adequately accounts for the observed solvent effects. Activation parameters for both reactions show that solvent effects are mainly entropic in origin and that there is a shift of the transition state from a ketone-like to an enol-like structure on passing from less to more polar solvents.     

On the behaviour of the (Z)-phenylhydrazones of some 5-alkyl-3-benzoyl-1,2,4-oxadiazoles in solution and in the gas phase: kinetic and spectrometric evidence in favour of self-assembly

Rate constants, k_A,R, for the rearrangement of the (Z)-phenylhydrazones (1a-e) of a series of 5-alkyl-3-benzoyl-1,2,4-oxadiazoles substituted at C(5) with linear alkyl chains of different length (from C₄ up to C₁₂) into the relevant 4-acylamino-2,5-diphenyl-1,2,3-triazoles (2a-e) have been measured in dioxan/water in the base-catalyzed region (pS⁺ 10.5-12.6). For each substrate log k_A,R are linearly related to pS⁺. The significant decrease of the slopes of these straight lines (from 0.96 down to 0.78) upon increasing the length of the linear alkyl chain at C(5) and that of the reactivity (down to 14-26%) upon increasing the substrate concentration suggest a decrease of the polarity of the ‘actual’ reaction medium and provide indirect evidence of the tendency of the substrates (Z)-1a-e to self-assemble. To confirm the above outcome direct evidence of the formation of self-assemblies in solution were obtained from ¹H NMR and spectrofluorimetry measurements while ESI-MS experiments point out the presence of aggregated substrates also in the gas phase.     

The role of attractive van der Waals forces in the catalysis of Michael addition by a phenyl decorated uranyl-salophen complex

The Et(3)N-assisted addition of beta-ketoester 3 to MVK in chloroform is catalyzed with high turnover efficiency by the phenyl-substituted uranyl-salophen compound 2b but not by the parent compound 1b. A plausible mechanism is suggested, involving concomitant nucleophilic attack at the beta-carbon and hydrogen bonding between the Et(3)NH(+) countercation and the carbonyl oxygen of the s-cis conformation of the enone reactant. The role of the van der Waals interactions with the aromatic side arm of 2b as a crucial driving force for catalysis is discussed.     

Evidence for Multiple Binding Modes in the Initial Contact Between SARS-CoV-2 Spike S1 Protein and Cell Surface Glycans**

Infection of host cells by SARS-CoV-2 begins with recognition by the virus S (spike) protein of cell surface heparan sulfate (HS), tethering the virus to the extracellular matrix environment, and causing the subunit S1-RBD to undergo a conformational change into the ‘open’ conformation. These two events promote the binding of S1-RBD to the angiotensin converting enzyme 2 (ACE2) receptor, a preliminary step toward viral-cell membrane fusion. Combining ligand-based NMR spectroscopy with molecular dynamics, oligosaccharide analogues were used to explore the interactions between S1-RBD of SARS CoV-2 and HS, revealing several low-specificity binding modes and previously unidentified potential sites for the binding of extended HS polysaccharide chains. The evidence for multiple binding modes also suggest that highly specific inhibitors will not be optimal against protein S but, rather, diverse HS-based structures, characterized by high affinity and including multi-valent compounds, may be required.     

Differentiation of Vitis vinifera varieties by MALDI-MS analysis of the grape seed proteins

Until now the study of pathogenic related proteins in grape juice and wine, performed by ESI-MS, LC/ESI-MS, and MALDI/MS, has been proposed for differentiation of varieties. In fact, chitinases and thaumatin-like proteins persist through the vinification process and cause hazes and sediments in bottled wines. An additional instrument, potentially suitable for the grape varieties differentiation, has been developed by MALDI/MS for the grape seed protein analysis. The hydrosoluble protein profiles of seeds extract from three different Vitis vinifera grape (red and white) varieties were analyzed and compared. In order to evaluate the environmental conditions and harvest effects, the seed protein profiles of one grape variety from different locations and harvests were studied.     

Polymerized mixed aggregates containing gadolinium complex and CCK8 peptide

Two novel amphiphilic unimers containing an aliphatic hydrophobic chain (PDA) with two C≡C triple bonds and hydrophilic heads presenting the chelating agent DTPAGlu and the CCK8 bioactive peptide, respectively, have been prepared by solid phase synthesis. Aggregates obtained by mixing together PDA-DTPAGlu, or its Gd(III) complex, and PDA-L2-CCK8 in 70/30 molar ratio before and after a polymerization process carried out by UV irradiation have been structurally characterized by means of small angle neutron scattering. The relaxivity properties of aggregates containing Gadolinium complexes have also been investigated. Elongated mixed micelles have been observed, in which the relaxivity value r _1p for each Gadolinium complex, measured at 20 MHz and 298 K, is around 12 mM^–1 s^–1.     

Gold(I)-dithioether supramolecular polymers: synthesis, characterization, and luminescence

A series of discrete compounds and supramolecular polymers were synthesized by self-assembly of dithioether building blocks and HAuCl4.3H2O. In complexes 1 {[AuL(1-Me)Cl], where L(1-Me) is bis(methylthio)methane} and 2 {[Au2L(2-Ph)Cl2], where L(2-Ph) is 1,2-bis(phenylthio)ethane}, adjacent units are connected via aurophilic interactions. Complex 1, a one-dimensional (1D) supramolecular polymer, and complex 2, a two-dimensional supramolecular network, both feature nearly linear [Au-Au-](infinity) chains. Complexes 4a, 4b, and 4c, all of which contain 1,3-bis(phenylthio)propane (L(3-Ph)), are polymorphs having the composition [Au2L(3-Ph)Cl2]. Complex 3 {[Au2L(1-Ph)Cl2], where L(1-Ph) is bis(phenylthio)methane}and complexes 4a and 4b consist of nearly identical 1D supramolecular polymers formed through Au-Au interactions. The third polymorph, 4c, is a molecular complex, as it does not have metal-metal interactions. Complex 5 {[Au2L(4-Ph)Cl2], where L(4-Ph) is 1,4-bis(phenylthio)butane} is also molecular. UV-vis spectra showed that the absorption bands of these complexes are allowed ligand-centered transitions between 230 and 260 nm. Complexes 1, 2, and 6 {[AuL(3-Me)Cl], where L(3-Me) is 1,3-bis(methylthio)propane} exhibited solid-state luminescence at 5 K with vibronic progressions and band maxima at approximately 570 nm. It is suggested that complex 6 contains [Au-Au-](infinity) chains.     

CE assay of methylmalonyl-coenzyme-a mutase activity

Methylmalonyl-coenzyme A mutase (MCM) is a 5'-deoxyadenosylcobalamin-linked mitochondrial enzyme that catalyzes the isomerization of L-methylmalonyl-coenzyme A to succinyl-coenzyme A. We described a method for methylmalonyl-CoA and succinyl-CoA separation by CE, suitable for the evaluation of MCM activity. The working conditions for optimal separation were obtained in order to achieve the best resolution in the shortest analysis time. The optimization of buffer composition together with other variables, such as injection time, separation voltage, migration time, and capillary temperature, resulted in a solution of 30 mM NaH2PO4 containing 15 mM SDS, pH 3.2. Separations were carried out in an uncoated fused-silica capillary (55 cm, 50 microm id) at -25 kV, reading at 254 nm. The method performance was evaluated by measuring total and holo-MCM activity in biological matrices such as rat liver and human peripheral blood lymphocytes (PBL). The mean MCM activity was expressed in nmol/h/mg protein of tissue/cell extract and was calculated from the amount of reaction product formed. The rapidity of analysis and utmost precision (repeatability and within-laboratory reproducibility) point out the potentialities of the proposed method for the differential diagnosis of methylmalonic acidemia, in relation to protein or coenzyme defects.     

Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4

The complex between distamycin A and the parallel DNA quadruplex [d(TGGGGT)]4 has been studied by 1H NMR spectroscopy and isothermal titration calorimetry (ITC). To unambiguously assert that distamycin A interacts with the grooves of the quadruplex [d(TGGGGT)]4, we have analyzed the NMR titration profile of a modified quadruplex, namely [d(TGGMeGGT)]4, and we have applied the recently developed differential frequency-saturation transfer difference (DF-STD) method, for assessing the ligand-DNA binding mode. The three-dimensional structure of the 4:1 distamycin A/[d(TGGGGT)]4 complex has been determined by an in-depth NMR study followed by dynamics and mechanics calculations. All results unequivocally indicate that distamycin molecules interact with [d(TGGGGT)]4 in a 4:1 binding mode, with two antiparallel distamycin dimers that bind simultaneously two opposite grooves of the quadruplex. The affinity between distamycin A and [d(TGGGGT)]4 enhances ( approximately 10-fold) when the ratio of distamycin A to the quadruplex is increased. In this paper we report the first three-dimensional structure of a groove-binder molecule complexed to a DNA quadruplex structure.     

Ion pair recognition of quaternary ammonium and iminium salts by uranyl-salophen compounds in solution and in the solid state

Efficient ditopic receptors for quaternary ammonium and iminium salts have been obtained upon functionalization of the uranyl-salophen unit with conformationally flexible side arms bearing phenyl or beta-naphthyl substituents. Binding affinities in chloroform solution have been measured for a large number of quaternary salts comprising tetramethylammonium (TMA), tetrabutylammonium (TBA), acetylcholine (ACh), N-methylpyridinium (NMP), and N-methylisoquinolinium (NmiQ) cations. Recognition of the anion partner is ensured by coordination to the hard Lewis acidic uranyl center, whereas cation-pi/CH-pi interactions of the quaternary ions are established with the aromatic pendants. The role of the cation-anion interactions on the dynamics of exchange between the free and complexed species is discussed. Solid-state structures have been obtained for a few salt-receptor combinations. In the solid state, side-armed receptor molecules form assemblies that enclose ion pair aggregates of varying composition and structure, including AChCl dimers, two different kinds of tetrameric (TMA)Cl clusters, and unidimentional salt strips of (NMP)Br. The lack of side arms as preferential binding sites for the polar quaternary cations prevents association patterns of the kinds formed with the side-armed receptors, as shown by the crystal structure of the complex of (TMA)Cl with the parent uranyl-salophen receptor.