Bioligninolysis: Recent Updates for Biotechnological Solution

Bioligninolysis involves living organisms and/or their products in degradation of lignin, which is highly resistant, plant-originated polymer having three-dimensional network of dimethoxylated (syringyl), monomethoxylated (guaiacyl), and non-methoxylated (p-hydroxyphenyl) phenylpropanoid and acetylated units. As a major repository of aromatic chemical structures on earth, lignin bears paramount significance for its removal owing to potential application of bioligninolytic systems in industrial production. Early reports illustrating the discovery and cloning of ligninolytic biocatalysts in fungi was truly a landmark in the field of enzymatic delignification. However, the enzymology for bacterial delignification is hitherto poorly understood. Moreover, the lignin-degrading bacterial genes are still unknown and need further exploration. This review deals with the current knowledge about ligninolytic enzyme families produced by fungi and bacteria, their mechanisms of action, and genetic regulation and reservations, which render them attractive candidates in biotechnological applications.     

CuII Coordination Chemistry of Patellamide Derivatives: Possible Biological Functions of Cyclic Pseudopeptides

Two synthetic derivatives of the naturally occurring cyclic pseudooctapeptides patellamide A–F and ascidiacyclamide, that is, H₄pat², H₄pat³, as well as their Cu^II complexes are described. These cyclic peptide derivatives differ from the naturally occurring macrocycles by the variation of the incorporated heterocyclic donor groups and the configuration of the amino acids connecting the heterocycles. The exchange of the oxazoline and thiazole groups by dimethylimidazoles or methyloxazoles leads to more rigid macrocycles, and the changes in the configuration of the side chains leads to significant differences in the folding of the cyclic peptides. These variations allow a detailed study of the various possible structural changes on the chemistry of the Cu^II complexes formed. The coordination of Cu^II with these macrocyclic species was monitored by high‐resolution electrospray mass spectrometry (ESI‐MS), spectrophotometric (UV/Vis) and circular dichroic (CD) titrations, and electron paramagnetic resonance (EPR) spectroscopy. Density functional theory (DFT) calculations and molecular mechanics (MM) simulations have been used to model the structures of the Cu^II complexes and provide a detailed understanding of their geometric preferences and conformational flexibility. This is related to the Cu^II coordination chemistry and the reactivity of the dinuclear Cu^II complexes towards CO₂ fixation. The variation observed between the natural and various synthetic peptide systems enables conclusions about structure–reactivity correlations, and our results also provide information on why nature might have chosen oxazolines and thiazoles as incorporated heterocycles.     

Charge transfer in polypeptides: effect of secondary structures on charge-transfer integral and site energies

We have theoretically studied the charge transfer in glycine polypeptide using quantum mechanical models based on a tight-binding Hamiltonian approach. The charge-transfer integrals and site energies involved in the transport of positive charge through the peptide bond in glycine polypeptide have been calculated. The charge-transfer integrals and site energies have been calculated directly from the matrix elements of the Kohn-Sham Hamiltonian defined in terms of the molecular orbitals of the individual fragments of the glycine polypeptide. In addition to this, we have calculated the rate of charge transfer between a neighboring amino acid subgroup through the Marcus rate equation. These calculations have been performed for the different secondary structures of the glycine model peptide such as linear, alpha-helix, 3(10)-helix, and antiparallel beta-sheet by varying the dihedral angles omega, varphi, and psi along the Calpha-carbon of amino acid subgroup. Present theoretical results confirm that the charge transfer through the peptide bond is strongly affected by the conformations of the oligopeptide.     

An efficient one-pot construction of substituted pyrimidinones

A concise, scaleable synthesis of building block 10 for p38 kinase inhibitor B is described. The key step is the one-pot construction of 5-aryl-3-methyl-2-methylsulfanyl-6-pyridin-4-yl-3H-pyrimidin-4-one 4 from arylacetic acid ethyl ester 1. Subsequent hydrolysis of the thiomethyl group to the hydroxy group and chlorination provided the key intermediate, 2-chloro-3-methyl-6-pyridin-4-yl-5-aryl-3H-pyrimidin-4-one 10. This class of reactive building blocks enabled the rapid evaluation of a variety of side chains at the 2-position of the pyrimidinone in SAR studies of inhibitors of p38 MAP kinase.     

How are the ready and unready states of nickel-iron hydrogenase activated by H2? A density functional theory study

We have explored possible mechanisms for the formation of the catalytically active Ni(a)-S state of the enzyme, nickel iron hydrogenase, from the Ni*(r) (ready) or Ni*(u) (unready) state, by reaction with H(2), using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an -OH bridge, the rate determining step is the cleavage of H(2) at the Ni(3+) centre with a barrier of approximately 15 kcal mol(-1). We take the unready state to have a -OOH bridge, and find that reaction with H(2) to form the Ni(r)-S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of approximately 19 kcal mol(-1). The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.     

Metal chelates in vinyl polymerization. I. Ferric dipivaloylmethide as an initiator

The behavior of the chelate, ferric dipivaloylmethide, Fe(DPM)₃, in vinyl polymerization systems was investigated. The polymerization was found to be of free-radical nature. The rate of polymerization was proportional to the square root of the concentration of the chelate. The monomer exponent was close to 1.5 for the Fe(DPM)₃-initiated polymerization of styrene and methyl methacrylate. The kinetic and transfer constants and activation energies for these systems have been evaluated. Spectral studies revealed the possibility of a complex formation between the chelate and the monomer. A kinetic scheme for the Fe(DPM)₃-initiated polymerization is derived based on this initial complex formation.     

Theoretical investigation on intramolecular electron transfer in polypeptides

Theoretical investigations on the intramolecular electron transfer between the intermediate residues of different secondary structures of an oligopeptide have been carried out. Density functional theory calculations have been performed to calculate the charge transfer integral, spatial overlap integral and site-energies for the optimized secondary structures of the glycine oligopeptide by varying the dihedral angles ( and ψ) along the -carbon atom of amino acid subgroups. The reorganization energy has been calculated in the presence of an excess negative charge. The electron transfer rates for the model peptide have been estimated and the dependence of the rate on secondary structures is discussed.     

Structure,conformation and NMR studies on 1,2-dioxane and halogen substituted 1,2-dioxane molecules

Molecular structure and conformational stability of chair and twist conformers of 1,2-dioxane and halogen substituted compounds of the 1,2-dioxane have been studied using ab initio and density functional theory (DFT) methods. The molecular geometries of 1,2-dioxane, 3,6-difluoro, 3,6-dichloro, 3,3,6,6-tetrafluoro and 3,3,6,6-tetrachloro 1,2-dioxane compounds were optimized at HF, MP2, B3LYP and B3PW91 levels of theory by implementing 6-31G* basis set. To study the effect of polar medium, self-consistent reaction field theory is used to optimize the conformers at B3LYP/6-31G* level of theory. The geometrical parameters of chair and twist conformers have been discussed in the light of interaction between lone pair electrons present in the oxygen and substituted halogen atoms. The relative stability of the conformers have been studied using relative energy, maximum hardness principle and thermodynamical quantities. The 13C-NMR chemical shift study for carbon atoms in the title compounds are calculated and the results have been discussed.