Cooperativity in multiple unusual weak bonds

This review covers two aspects concerning cooperativity in multiple weak bonds: a summary of literature results and a theoretical study of a complete series of model complexes. All the 15 combination of five weak bonds were explored: hydrogen bonds, hydric bonds, dihydrogen bonds, halogen bonds and ion–π interactions. Since in several cases there were no examples reported, a systematic exploration has been carried out on simple models at the MP2/aug-cc-pVTZ level. The results thus obtained have been analyzed using the atoms in molecules methodology.     

Immobilization of α-amylase from Bacillus circulans GRS 313 on coconut fiber

A simple and inexpensive method for immobilizing alpha-amylase from Bacillus circulans GRS 313 on coconut fiber was developed. The immobilization conditions for highest efficiency were optimized with respect to immobilization pH of 5.5, 30 degrees C, contact time of 4 h, and enzyme to support a ratio of 1:1 containing 0.12 mg/mL of protein. The catalytic properties of the immobilized enzyme were compared with that of the free enzyme. The activity of amylase adsorbed on coconut fiber was 38.7 U/g of fiber at its optimum pH of 5.7 and 48 degrees C, compared with the maximum activity of 40.2 U/mL of free enzyme at the optimum pH of 4.9 and 48 degrees C. The reutilization capacity of the immobilized enzyme was up to three cycles.     

Reactions of oxidizing radicals with 2- and 3-aminopyridines: a pulse radiolysis study

Reactions of OH radicals and some one-electron oxidants with 2-aminopyridine (2-AmPy) and 3-aminopyridine (3-AmPy) were studied in aqueous solutions using pulse radiolysis technique. The OH adduct of 2-AmPy at pH 9 has an absorption maximum at 360 nm along with a weak absorption band in the visible region and was found to be reactive with oxygen. The rate constant for its reaction with O₂ was determined to be 1.0×10⁸ dm³ mol⁻¹ s⁻¹. At pH 4 also, the OH adduct of 2-AmPy has an absorption band at 360 nm. However, there are differences in the absorption at other wavelengths. From the plot of ΔOD vs. pH at 340 nm, the pK_a of the OH adduct was determined to be 6.5. Among the specific oxidants, only SO₄^−√ radicals were able to oxidize 2-AmPy. In the case of 3-aminopyridine (3-AmPy), the transient species formed by OH radical reaction at pH 9 has an absorption maximum at 410 nm with shoulder bands on both the sides. Its absorption spectrum at pH 4 was different indicating the existence of a pK value for the OH adduct. pK_a of 3-AmPy-OH radical adduct species was evaluated to be 5.7. This adduct species was also found to be reactive with oxygen (k=7.6×10⁶ dm³ mol⁻¹ s⁻¹). Specific one-electron oxidants like N₃^√, Br₂^−√ C₂^−√ and SO₄^−√ were able to oxidize 3-AmPy indicating that it is easier to oxidize 3-AmPy as compared to 2-AmPy.     

Activation of Nucleotide-Binding Oligomerization Domain 1 (NOD1) Receptor Signaling in Labeo rohita by iE-DAP and Identification of Ligand-Binding Key Motifs in NOD1 by Molecular Modeling and Docking

The nucleotide-binding oligomerization domain 1 (NOD1) receptor recognizes various pattern-associated structures of microbes through its leucine-rich repeat (LRR) domain and activates signaling cascades to induce innate immunity. This report describes the activation of NOD1 receptor signaling by gamma-d-glutamyl-meso-diaminopimelic acid (or γ-D-Glu-mDAP [iE-DAP]) in a commercially important fish species, rohu (Labeo rohita). It also described critical motifs in the NOD1-LRR domain that could be involved in binding iE-DAP, lipopolysaccharide (LPS), and polyinosinic:polycytidylic acid (poly I:C). The activation of NOD1 receptor signaling was studied by injecting iE-DAP, and analysis of tissue samples for NOD1 and receptor-interacting serine/threonine kinase (RICK) expression was done by quantitative real-time polymerase chain reaction (qRT-PCR) assay. To identify ligand-binding motifs in NOD1, the 3D model of NOD1-LRR was generated, followed by a 6-ns molecular dynamics simulation. Molecular docking of LPS with NOD1-LRR was executed at the Hex and PatchDock servers, and iE-DAP and poly I:C in the AutoDock 4.2, FlexX 2.1, Glide 5.5, and GOLD 4.1 programs. The results of qRT-PCR revealed significant (p?<?0.05) upregulation of NOD1 and RICK expression. Molecular docking revealed that the amino acid residues at LRR1–2, LRR3–7, and LRR8–9 could be involved in poly I:C, LPS, and iE-DAP binding, respectively. In fish, this is the first report describing the 3D structure of NOD1-LRR and its critical ligand-binding motifs.     

Porosity Switching in Polymorphic Porous Organic Cages with Exceptional Chemical Stability

Porous solids that can be switched between different forms with distinct physical properties are appealing candidates for separation, catalysis, and host–guest chemistry. In this regard, porous organic cages (POCs) are of profound interest because of their solution‐state accessibility. However, the application of POCs is limited by poor chemical stability. Synthesis of an exceptionally stable imine‐linked (4+6) porous organic cage ( TpOMe‐CDA ) is reported using 2,4,6‐trimethoxy‐1,3,5‐triformyl benzene (TpOMe) as a precursor aldehyde. Introduction of the ‐OMe functional group to the aldehyde creates significant steric and hydrophobic characteristics in the environment around the imine bonds that protects the cage molecules from hydrolysis in the presence of acids or bases. The electronic effect of the ‐OMe group also plays an important role in enhancing the stability of the reported POCs. As a consequence, TpOMe‐CDA reveals exceptional chemical stability in neutral, acidic and basic conditions, even in 12 m NaOH. Interestingly, TpOMe‐CDA exists in three different porous and non‐porous polymorphic forms (α, β, and γ) with respect to differences in crystallographic packing and the orientation of the flexible methoxy groups. All of the polymorphs retain their crystallinity even after treatment with acids and bases. All the polymorphs of TpOMe‐CDA differ significantly in their properties as well as morphology and could be reversibly switched in the presence of an external stimulus.