Advancements in biocatalysis: From computational to metabolic engineering

Through several waves of technological research and un-matched innovation strategies, bio-catalysis has been widely used at the industrial level. Because of the value of enzymes, methods for producing value-added compounds and industrially-relevant fine chemicals through biological methods have been developed. A broad spectrum of numerous biochemical pathways is catalyzed by enzymes, including enzymes that have not been identified. However, low catalytic efficacy, low stability, inhibition by non-cognate substrates, and intolerance to the harsh reaction conditions required for some chemical processes are considered as major limitations in applied bio-catalysis. Thus, the development of green catalysts with multi-catalytic features along with higher efficacy and induced stability are important for bio-catalysis. Implementation of computational science with metabolic engineering, synthetic biology, and machine learning routes offers novel alternatives for engineering novel catalysts. Here, we describe the role of synthetic biology and metabolic engineering in catalysis. Machine learning algorithms for catalysis and the choice of an algorithm for predicting protein-ligand interactions are discussed. The importance of molecular docking in predicting binding and catalytic functions is reviewed. Finally, we describe future challenges and perspectives.     

Asymmetric Oxygen Bridged Copper(II) Carboxylate: Synthesis,Complete Characterization,and Crystal Structure

Binuclear centrosymmetric copper(II) complex of the formula bipyCu(L)₄Cubipy, where bipy = 2,2′- bipyridine and L = 4-methoxy-2-phenyl acetate, is synthesized and characterized by FT-IR, UV-Visible, ESR and mass spectroscopy, electrochemical, thermogravimetric, and single crystal XRD techniques. The complex contains two differently oriented molecules per unit cell stabilized via intermolecular interactions. Geometry around each Cu(II) was found to be square pyramidal affected by asymmetrically bridging oxygen atoms occupying the apical position of one square pyramid and the axial position of another in the same binuclear molecule. The square base is formed by two oxygen atoms from two carboxylate ligands and two nitrogen atoms from the bipyridine moiety. TGA shows that the complex is stable up to 170 °C followed by stepwise loss of coordinated ligands, which was supported by GC-MS data as well. A broad absorption spectrum indicated ²B_1g as the ground state and single electron occupancy of the dx²–y² orbital, which was confirmed by the ESR spectrum. The electrochemical study gives two oxidation curves corresponding to Cu(II)/Cu(III) and Cu(I)/Cu(II) and a reduction signal corresponding to the Cu(II)/Cu(I) process. The robust complex represents an interesting contribution to the understanding of coordination chemistry.     

Synthesis,characterization and bioactivity of mixed-ligand Cu(II) complexes containing Schiff bases derived from S-benzyldithiocarbazate and saccharinate ligand and the X-ray crystal structure of the copper-saccharinate complex containing S-benzyl-β-N-(acetylpyrid-2-yl)methylenedithiocarbazate

Mixed-ligand complexes of general formula, [Cu(NNS)(sac)] (NNS′ = S-benzyl-β-N-(2-acetylpyrid-2-yl)methylenedithiocarbazate, NNS″ = S-benzyl-β-N-(2-benzoylpyrid-2-yl)methylenedithiocarbazate and NNS? = S-benzyl-β-N-(6-methylpyrid-2-yl)methylenedithio-carbazate, sac = the saccharinate anion) have been synthesized by reacting [Cu(sac)₂(H₂O)₄] · 2H₂O with the appropriate ligands in ethanol and characterized by various physico-chemical techniques. Magnetic and spectral evidence indicate that the complexes are four-coordinate in which the Schiff bases coordinate as NNS ligands and the sac- anion coordinates as a unidentate N-donor ligand. An X-ray crystallographic structural analysis of [Cu(NNS′)(sac)] shows that the complex has a distorted square-planar geometry with the Schiff base coordinated to the copper (II) ion as a uninegatively charged tridentate chelating agent via the pyridine nitrogen atom, the azomethine nitrogen atom and the thiolate sulphur atom while the fourth coordination position is occupied by the N-bonded saccharinate anion. The complexes have been evaluated for their biological activities against selected pathogens and cancer cell lines. They display weak activity against the pathogenic bacteria and fungi. The complexes were highly active against the leukemic cell line (HL-60) but only [Cu(NNS′)(sac)] was found to exhibit strong cytotoxicity against the ovarian cancer cell line (Caov-3). All complexes were inactive against the breast cancer cell line (MCF-7).     

A method for modeling icosahedral virions: Rotational symmetry boundary conditions

We present two techniques for implementing a new method of simulating an entire virion. Earlier computer simulations of a capsid protein revealed large edge effects due to the use of free standing boundaries. Because of the size of a given protomer, conventional three-dimensional periodic boundary conditions would be extremely wasteful. This would require an extremely large number of solvent molecules, and therefore would be computationally feasible for only a fragment of the entire virion. The new method employs non-space-filling computational cells in molecular modeling and molecular dynamics with the boundary conditions based on the icosahedral group. The method is general and could be used for any molecular system with a point group symmetry. With this method, the dynamical and spatial intra and interprotomer correlations can be studied at atomic levels. The technique is applicable to any virion with icosahedral symmetry. A sample calculation involving a geometry optimization of the human rhinovirus coat proteins is given to demonstrate the technique.     

Synthesis,XRD, spectral (IR,UV–Vis,NMR) characterization and quantum chemical exploration of benzoimidazole‐based hydrazones: A synergistic experimental‐computational analysis

Present study advocates the joint experimental and computational studies of two potent benzoimidazole‐based hydrazones with chemical formula C₂₃H₁₈F₂N₄O ( 5a ) and C₂₅H₂₂FN₅O₃ ( 5b ). Both 5a and 5b were synthesized and resolved into their crystal structures using SC‐XRD for the assessment of bond lengths, bond angles, unit cells and space groups. The structures of 5a and 5b were chemically characterized using infrared (FT‐IR), UV–Visible, nuclear magnetic resonance (¹H‐NMR and ¹³C‐NMR), EIMS and elemental analysis. DFT at M06‐2X/6‐31G(d,p) level of theory was performed to get optimized structures and countercheck the experimental findings. Overall, DFT findings show excellent concurrence with the experimental data which confirms the purity of both compounds. FMO, NBO analysis, MEP surfaces and nonlinear optical (NLO) properties were explored at same level of theory. UV–Vis analysis at TDDFT/M06‐2X/6‐31G(d,p) level of theory showed that 5b is red shifted with λ_max 331.69 nm as compared to 5a with λ_max 240.25 nm. Global reactivity parameters were estimated using energy of FMOs indicated the greater harness value than the softness values of 5a and 5b . NBO analysis confirmed that the presence of non‐covalent interactions, hydrogen bonding and hyper conjugative interactions are pivotal cause for the existence of 5a and 5b in the solid‐state. NLO results of 5a and 5b were observed better than standard molecule recommended the NLO activity of said molecules for optoelectronic applications.     

Application of intense ion beams to planetary physics research at the Facility for Antiprotons and Ion Research facility

This paper presents detailed 2D hydrodynamic simulations of implosion of a multi‐layered cylindrical target that is driven by an intense uranium beam. The target is comprised of a thick, high‐Z, high‐ρ cylindrical shell that encloses a sample material (Fe in the present case). Two options have been used for the focal spot geometry: an annular form and a circular form. The purpose of this work is to show that an intense heavy‐ion beam can induce the extreme physical conditions in the sample material similar to those that exist in the planetary cores. In this study, we use parameters of the beam that will be generated at the Facility for Antiprotons and Ion Research (FAIR), Darmstadt, in a few years' time. Production of these high‐energy‐density (HED) samples will allow us to study planetary physics in the laboratory. It is to be noted that planetary physics research is an important part of the FAIR HED physics program. A dedicated experiment named LAboratory PLAnetary Sciences (LAPLAS) has been proposed for this purpose. These simulations show that in such experiments an Fe sample can be imploded to the Earth's core conditions and to those in more massive rocky planets called Super‐Earths. Similarly, implosion of hydrogen and water samples will generate the core conditions of solar and extrasolar hydrogen‐rich gas giants and water‐rich icy planets, respectively. The LAPLAS experiments will thus provide very valuable information on the equation of state and transport properties of matter under extreme physical conditions, which will help scientists understand the structure and evolution of the planets in our solar system as well as of the extrasolar planets.     

Preparation of primary arylamines via arylzinc chlorides in good yields

Primary arylamines can be prepared easily by electrophilic amination of arylzinc chlorides with acetone O-(2,4,6-trimethylphenylsulfonyl)oxime in the presence of DMPU as additive and CuCN as catalyst in good yields.     

Rational design of a BiFeWO6 nanostructure for supercapacitor applications

Journal of Solid State Electrochemistry - Scientists are increasingly interested in improving electroactive technologies for supercapacitor applications, since energy storage devices have improved...