Protonation Equilibrium in the Active Site of the Photoactive Yellow Protein

The role and existence of low-barrier hydrogen bonds (LBHBs) in enzymatic and protein activity has been largely debated. An interesting case is that of the photoactive yellow protein (PYP). In this protein, two short HBs adjacent to the chromophore, p-coumaric acid (pCA), have been identified by X-ray and neutron diffraction experiments. However, there is a lack of agreement on the chemical nature of these H-bond interactions. Additionally, no consensus has been reached on the presence of LBHBs in the active site of the protein, despite various experimental and theoretical studies having been carried out to investigate this issue. In this work, we perform a computational study that combines classical and density functional theory (DFT)-based quantum mechanical/molecular mechanical (QM/MM) simulations to shed light onto this controversy. Furthermore, we aim to deepen our understanding of the chemical nature and dynamics of the protons involved in the two short hydrogen bonds that, in the dark state of PYP, connect pCA with the two binding pocket residues (E46 and Y42). Our results support the existence of a strong LBHB between pCA and E46, with the H fully delocalized and shared between both the carboxylic oxygen of E46 and the phenolic oxygen of pCA. Additionally, our findings suggest that the pCA interaction with Y42 can be suitably described as a typical short ionic H-bond of moderate strength that is fully localized on the phenolic oxygen of Y42.

Synthesis and physicochemical studies of a series of mixed-ligand transition metal complexes and their molecular docking investigations against Coronavirus main protease

A novel series of mixed-ligand complexes of the type, [M(L1)(L2)Cl]·2H2O [L1 = 2-(α-methyl salicylidene hydrazine) benzimidazole (primary ligand), L2 = 2,2′-bipyridine (bipy; secondary ligand), M = Co(ii), Ni(ii), Cu(ii) and Zn(ii)], were based on the physicoanalytical studies. The spectroscopic findings revealed tridentate nature of the Schiff base ligand (L1) and its coordination to the metal ions via azomethine nitrogen, ring nitrogen and the deprotonated phenolic oxygen atoms. Furthermore, the synthesized compounds were evaluated for antimicrobial activity against Bacillus subtilis, Escherichia coli and Salmonella typhi microorganisms. In addition, molecular docking studies were carried out against Middle East respiratory syndrome coronavirus (PDB ID: 4ZS6) and severe acute respiratory syndrome coronavirus 2 main protease (PDB ID: 6W63).

Meso-pyrrolyl BODIPY based colorimetric optical sensor for Cu2+ ions

A simple meso-pyrrolyl BODIPY-Schiff base conjugate was synthesized by reacting ([Formula: see text]-formylpyrrolyl) BODIPY with 2-aminophenol in ethanol at reflux followed by recrystallization from CH2Cl2/petroleum ether, affording the conjugate in 72% yield. The conjugate was thoroughly characterized by HR-MS, 1D and 2D NMR and X-ray crystallographic techniques. The X-ray structure of the meso-pyrrolyl BODIPY-Schiff base conjugate revealed that the meso-pyrrole and the phenyl substituents were deviated by an angle of [Formula: see text] and [Formula: see text], respectively, from the plane of the BF2-dipyrrin core. The absorption spectrum of the conjugate was similar to the ([Formula: see text]-formylpyrrolyl) BODIPY with a strong absorption band at 508 nm, whereas the fluorescence of the ([Formula: see text]-formylpyrrolyl) BODIPY was completely quenched in the BODIPY-Schiff base conjugate. Furthermore, cation sensing studies revealed that the conjugate has a specific sensing ability for the Cu(II) ion even in the presence of the other metal ions, as verified by the visual, absorption and mass spectral studies. The DFT optimized structure revealed that the Cu(II) ion was bound to pyrrolic nitrogen, imine nitrogen, phenolic oxygen and two water molecules in a distorted square pyramidal fashion. TD-DFT studies accounted well for the absorption spectra of the BODIPY-Schiff base conjugate and its Cu[Formula: see text] bound complex.

Total Synthesis of Putative Structure of Asperipin-2a and Stereochemical Reassignment

The total synthesis of the putative structure of asperipin-2a is described. The synthesis features ether cross-links between the phenolic oxygen of Tyr6 and β position of Tyr3 and the phenolic oxygen of Tyr3 and the β position of Hpp1 in the unique 17- and 14-membered bicyclic structure of asperipin-2a, respectively. The synthesized putative structure does not match the natural product and a stereochemical reassignment is postulated.

Total Synthesis of Putative Structure of Asperipin-2a and Stereochemical Reassignment

The total synthesis of the putative structure of asperipin-2a is described. The synthesis features ether cross-links between the phenolic oxygen of Tyr6 and β position of Tyr3 and the phenolic oxygen of Tyr3 and the β position of Hpp1 in the unique 17- and 14-membered bicyclic structure of asperipin-2a, respectively. The synthesized putative structure does not match the natural product and a stereochemical reassignment is postulated.

Synthesis and structures of diaryloxystannylenes and -plumbylenes embedded in 1,3-diethers of thiacalix[4]arene

Monomeric stannylenes and plumbylenes embedded in 1,3-diethers of thiacalix[4]arene, whose structures are highly dependent on the substituents on the phenolic oxygen atoms, have been synthesized.

The Cycle Destruction during Complex Formation of 4-salicylideneamino-3-hydrazino-5-mercapto-1,2,4-triazole with Ni (II) ions

Using single crystal X-ray diffraction method, it was shown that the interaction of 4-salicylideneamino-3-hydrazino-5-mercapto-1,2,4-triazole with Ni (II) acetate yields a complex of nickel with salicylidene-thiosemicarbazone instead of the expected complex with the corresponding Schiff base. A possible mechanism of hydrolysis of the thiotriazole ring is proposed. The N- (salicylidene) thiosemicarbazone is a tridentate and almost flat structure ligand coordinates to the nickel (II) cation through thiosemicarbazone sulphur, phenolic oxygen, and azomethine nitrogen atoms. The nickel (II) ion in the complex is four-coordinated in distorted square-planar geometry. The intermolecular hydrogen bonds N─H∙∙∙N, as well as hydrogen bonds N─H∙∙∙O, O─H∙∙∙O and O─H∙∙∙S through the solvate water molecules, give rise to the 3-D network of the complex [Ni(TSC)((NH2)2CS)]•H2O.

“SYNTHESIS, CHARACTERIZATION AND MICROBIAL STUDY OF Cu(II), Ni(II), Co(II) AND Zn(II) COMPLEXESES WITH 2-HYDROXY-4,5-DIIODO-BENZYLIDENE-4-NITRO-ANILINE”

Schiff base ligand 2-Hydroxy-4,5-diiodo-benzylidene-4-nitro-aniline (L) and its complexes with Cu (II), Ni (II), Co (II) and Zn (II) were prepared and characterized by analytical, spectroscopic (IR, UV-Vis) techniques, electrical conductivity and magnetic measurements. The results indicate that the ligand coordinate through azomithine nitrogen and phenolic oxygen to the metal ions. The complexes were further screened for microbial activity.

Dependence of tautomerism on substituent type in o-hydroxy Schiff bases

Quantum computational methods were used to elucidate the structures of the o-hydroxy Schiff bases with different substituents. It is possible for a Schiff base to have different tautomeric structures depending on intramolecular proton transfer from the phenolic oxygen atom to the nitrogen atom. Proton transfer results in two tautomeric structures known as the phenol-imine and keto-amine forms. To explain the substituent effect on the proton transfer process in five o-hydroxy-Schiff bases, possible geometric structures in gas phase were optimized using density functional theory (DFT) at the B3LYP/6-311G(d,p) level. To describe tautomerism including intramolecular proton transfer, potential energy surface (PES) scans were performed starting from the optimized geometry of the phenol-imine form. HOMA indices were calculated in order to estimate p-electron delocalization. In addition, the substituent effect on the tautomerization rate was examined using Hammett substituent constants and calculating the activation energies.