A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

First example of the C-alkylation of indoles with Baylis-Hillman acetates

Baylis-Hillman acetates undergo S_N2′ allylic substitution with indoles in the presence of 20 mol % of indium tribromide under mild conditions to afford a new class of substituted indoles in high yields with (E)-stereoselectivity. The stereochemistry of the products was assigned by various NMR experiments.     

Characterization of N‐methylated amino acids by GC‐MS after ethyl chloroformate derivatization

Methylation is an essential metabolic process in the biological systems, and it is significant for several biological reactions in living organisms. Methylated compounds are known to be involved in most of the bodily functions, and some of them serve as biomarkers. Theoretically, all α‐amino acids can be methylated, and it is possible to encounter them in most animal/plant samples. But the analytical data, especially the mass spectral data, are available only for a few of the methylated amino acids. Thus, it is essential to generate mass spectral data and to develop mass spectrometry methods for the identification of all possible methylated amino acids for future metabolomic studies. In this study, all N‐methyl and N,N‐dimethyl amino acids were synthesized by the methylation of α‐amino acids and characterized by a GC‐MS method. The methylated amino acids were derivatized with ethyl chloroformate and analyzed by GC‐MS under EI and methane/CI conditions. The EI mass spectra of ethyl chloroformate derivatives of N‐methyl ( 1–18 ) and N,N‐dimethyl amino acids ( 19–35 ) showed abundant [M‐COOC₂H₅]⁺ ions. The fragment ions due to loss of C₂H₄, CO₂, (CO₂ + C₂H₄) from [M‐COOC₂H₅]⁺ were of structure indicative for 1–18 . The EI spectra of 19–35 showed less number of fragment ions when compared with those of 1–18 . The side chain group (R) caused specific fragment ions characteristic to its structure. The methane/CI spectra of the studied compounds showed [M + H]⁺ ions to substantiate their molecular weights. The detected EI fragment ions were characteristic of the structure that made easy identification of the studied compounds, including isomeric/isobaric compounds. Fragmentation patterns of the studied compounds ( 1–35 ) were confirmed by high‐resolution mass spectra data and further substantiated by the data obtained from ¹³C₂‐labeled glycines and N‐ethoxycarbonyl methoxy esters. The method was applied to human plasma samples for the identification of amino acids and methylated amino acids. Copyright © 2016 John Wiley & Sons, Ltd.     

Pyrolysis of sorghum bagasse biomass into bio-char and bio-oil products

The transformation of renewable biomass into valuable products as alternatives to fossil fuels is essential for sustainable energy in sustainable society. This work systematically investigates the pyrolysis of sorghum bagasse biomass into bio-char and bio-oil products and studies the effect of temperature (623–823 K) on the conversion of sorghum bagasse and products yields. The physicochemical properties of bio-char were thoroughly studied using powder X-ray diffraction, elemental analysis (CHNSO), scanning electronic microscope, calorific value (CV), and Fourier transform infrared (FTIR) spectroscopy techniques. Also, gas chromatography–mass spectrometry (GC–MS), CV, and FTIR were used to understand the properties of bio-oil. The results obtained indicate that an increase in the pyrolysis temperature from 623 to 823 K leads to a decrease in the bio-char yield from 42.55 to 30.38%. On the other hand, the maximum bio-oil yield of 15.94% was obtained at 723 K. The bio-char obtained at 673 and 773 K was found by FTIR analysis to be composed of a highly ordered aromatic carbon structure. The calorific value of bio-oil, which contains a greater amount of acidic compounds, was found to be 6740 kcal/kg. The GC–MS analyses revealed the presence of octadecenoic acid, p-cresol, 2,6-dimethoxy phenol, 4-ethyl 2-methoxy phenol, phenol, o-guaiacol, and octadecanoic acid in the bio-oil obtained from the pyrolysis of sorghum bagasse biomass. The present study provides useful information for understanding the quality of bio-oil and bio-char obtained from high biomass sorghum bagasse.     

Ultrafast Excited State Relaxation Dynamics of New Fuchsine- a Triphenylmethane Derivative Dye

An all-inclusive investigation of the ultrafast excited state relaxation dynamics of a triphenylmethane derivative molecule, New Fuchsine (NF), using a combined approach of density functional theory (DFT), femtosecond transient absorption spectroscopy (fs-TAS), and photoluminescence spectroscopy is presented in this work. The DFT calculations confirmed the formation of twisted molecular structure in the excited state of NF in ethanol solution with bond rotation of ≈86°. TAS measurements of NF solution exhibited ultrafast ground state-recovery pathway via a conical intersection confirming an ultrafast structural reorientation. On the contrary, TAS measurements of NF thin-film exhibited a longer excited-state lifetime suggesting a hindered molecular twisted state formed as an intermediate step. Photophysical kinetic models are proposed to globally fit the fs-TAS data establishing the twisted intramolecular charge transfer (TICT) state mediated ground state recovery for NF in solution and thin film, respectively. Temperature-dependent photoluminescence study of NF film provided a clear insight into the effect of rotational motion of phenyl rings in NF molecules over the TICT mediated emission.     

Randomized broadcast in networks

In this paper we study the rate at which a rumor spreads through an undirected graph. This study has two important applications in distributed computation: in simple, robust and efficient broadcast protocols, and in the maintenance of replicated databases.     

Mass spectral study of substituted allyl aryl and allyl alkyl selenides and some analogous sulfides

The electron impact (EI) mass spectra of allyl aryl selenides showed abundant molecular ions and many fragment ions containing the selenium atom. alpha-Cleavage is the dominant process in the fragmentation of selenides, and cleavage product ions are characteristic of the substituents. In the case of 3-methyl allyl and related aryl selenides, characteristic delta-hydrogen migration to the selenium atom is observed. A McLafferty-type rearrangement is found in benzyl allyl selenides and substituted alkyl allyl selenides. The charge on the rearrangement products preferably remains on the fragments containing the phenyl group. The [M - SeH](+), [M - CH(3)](+) and [M - C(2)H(4)](+) ions are found only in the EI mass spectrum of allyl phenyl selenide, and are attributed to a Claisen rearrangement in the source of the mass spectrometer. All structurally informative fragmentation processes are supported by collision induced dissociation spectra of molecular ions. The fragmentation patterns found in methane chemical ionization (CI) spectra of the selenides were significantly different from those observed in EI. The EI and CI mass spectra of analogous sulfides showed similar behaviour to that observed in the corresponding selenides. Copyright 1999 John Wiley & Sons, Ltd.