Water molecules inside protein structure affect binding of monosaccharides with HIV‐1 antibody 2G12

Water molecules inside biomolecules constitute integral parts of their structure and participate in the functions of the proteins. Some of the X‐ray crystallographic data are insufficient for analyzing a series of ligand–protein complexes in the same condition. We theoretically investigated antibody binding abilities of saccharide ligands and the effects of the inner water molecules of ligand–antibody complexes. Classical molecular dynamics and quantum chemical simulations using a model with possible water molecules inside the protein were performed with saccharide ligands and Human Immunodeficiency Virus 1 neutralizing antibody 2G12 complexes to estimate how inner water molecules of the protein affect the dynamics of the complexes as well as the ligand–antibody interaction. Our results indicate the fact that d ‐fructose's strong affinity to the antibody was partly due to the good retentiveness of solvent water molecules of the ligand and its stability of the ligand's conformation and relative position in the active site. © 2016 Wiley Periodicals, Inc.     

Studies on the stereoselective selenolactonization, hydroxy and methoxy selenenylation of α- and β-hydroxy acids and esters. Synthesis of δ- and γ-lactones

The diastereoselective synthesis of hydroxy substituted γ- and δ-lactones was accomplished following two approaches. A 5- or 6-endo cyclization promoted by electrophilic selenium reagents of α- or β-hydroxy acids and a 5- or 6-exo cyclization of hydroxy esters obtained through a diastereoselective hydroxy selenenylation reaction of α- or β-hydroxy esters. Moreover, the diastereoselective methoxy selenenylation of the above compounds was investigated showing a case in which the compound that was unreactive in the hydroxy selenenylation conditions gave, in the methoxy selenenylation conditions, the deprotected diol. The usefulness of the methoxy selenenylation procedure was proven by the preparation of a symmetric compound unsymmetrically functionalized. Yields and selectivities were found to depend on substituents (Ph or alkyl groups at the carbon atom that undergoes the nucleophilic attack), mode of cyclization, kinetic or thermodynamic control conditions. In the latter case, silica gel played an important role.     

Substituent effect on oxidative cyclization of aldehyde thiosemicarbazones with ferric chloride

The reactivity of aldehyde thiosemicarbazones 1 with ferric chloride solutions was examined. When compounds 1 are not substituted on the N-2 nitrogen atom formation of 1,3,4-thiadiazole 3 heterocyclic ring was observed. In contrast 1,2,4-triazoline 4 and/or 1,3,4-thiadiazoline 5 heterocyclic rings were afforded when N-2 nitrogen atom carried a methyl or a phenyl group. The reaction mechanism is also discussed.     

Photoaddition of thienocoumarin derivatives to DNA: stoichiometry and kinetics of binding

Photoreaction of the 6,9-dimethyl-4-methoxymethyl-2H-thieno[3,2-g]-1-benzopyran-2-one (compound I) and 4-acetoxymethyl-6,9-dimethyl-2H-thieno[3,2-g]-1-benzopyran-2-one (compound II) to DNA was studied. The quantitative evaluation of the photobound molecules was performed by means of inductively coupled plasma atomic emission spectrometry (ICP-AES), exploiting the presence of the sulphur atom inside the tricyclic chromophore. The concurrent estimation of the phosphorus atom, present exclusively in the macromolecule, allowed possible intercalation sites to be identified and their involvement in the photoaddition reaction to be determined. The development of a kinetic model made it possible to discriminate and evaluate the single kinetic events that constitute the overall photoaddition process of I and II to DNA.     

Synthesis and structure of the adduct dichlorodiaquobis(ethylpropionate)magnesium(II)

The crystal and molecular structure of MgCl₂(H₂O)₂(ethylpropionate)₂ has been determined by single crystal X-ray diffraction analysis. The complex crystallizes in the triclinic system, space group (No. 2);a=5.912 (2),b=5.931 (3),c=12.792 (4) Å, =77.15°(3), =86.21°(3), =88.31°(3);Z=1. The metal lies at the center of a slightly distorted octahedron formed by two chlorine atoms and four oxygens, two from water molecules and two from the carbonyl groups of the ethylpropionate ligands in atrans configuration.     

Crystal structure of two cocrystallized complexes obtained from the reaction of magnesium chloride with 2,4-pentanedione

The crystal structures of two cocrystallized complexes of MgCl₂ with 2,4-pentanedione have been determined. The conglomerate crystallizes in the monoclinic system, space groupP 2₁/c (No. 14);a=7.835(2),b=18.169(4),c=13.303(3) Å, =90.70(2)°,Z=4. The former complex is a dimer which consists of two octahedra sharing one edge by two chlorine bridges between the metal atoms. The chelate ring in the equatorial plane and two apical water molecules realize the coordination polyhedron around each Mg atom. In the latter complex the metal lies at the center of a slightly distorted octahedron formed by six oxygens, four from two chelate ligands and two from apical water molecules.     

Mononuclear rearrangement of heterocycles in ionic liquids catalyzed by copper(II) salts

The reactivity of E- and Z-phenylhydrazones of 3-benzoyl-5-phenyl-1,2,4-oxadiazole in the presence of CuCl₂ and Cu(ClO₄)₂·6H₂O has been studied in four imidazolium ionic liquids [bmim][X] (X=BF₄⁻, PF₆⁻, SbF₆⁻ and CF₃SO₃⁻). The reaction may follow different mechanistic patterns, depending on the nature of the ionic liquid anion, accounting for both qualitative and kinetic data. In the presence of CuCl₂, two processes take place at the same time, i.e., the E?Z isomerization and the rearrangement of Z-isomer into the relevant 4-benzoylamino-2,5-diphenyl-1,2,3-triazole. In contrast, in the presence of Cu(ClO₄)₂·6H₂O, the rearrangement occurs only in solution of [bmim][BF₄] and [bmim][CF₃SO₃]. Collected data show that the effect of the ionic liquid on the isomerization and the rearrangement is different. In particular, a higher cross-linking degree seems to favour the triazole, but disfavour the E?Z isomerization.     

Supported proline and proline-derivatives as recyclable organocatalysts

In the last eight years, L-proline and L-proline derivatives, such as substituted prolinamides or pyrrolidines, have been successfully used as organocatalysts in several reactions. In this critical review we summarize the immobilization procedures of such organocatalysts highlighting their application, recoverability and reusability (86 references).