Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine

We propose a generic method to model polarization in the context of high‐rank multipolar electrostatics. This method involves the machine learning technique kriging, here used to capture the response of an atomic multipole moment of a given atom to a change in the positions of the atoms surrounding this atom. The atoms are malleable boxes with sharp boundaries, they do not overlap and exhaust space. The method is applied to histidine where it is able to predict atomic multipole moments (up to hexadecapole) for unseen configurations, after training on 600 geometries distorted using normal modes of each of its 24 local energy minima at B3LYP/apc‐1 level. The quality of the predictions is assessed by calculating the Coulomb energy between an atom for which the moments have been predicted and the surrounding atoms (having exact moments). Only interactions between atoms separated by three or more bonds (“1, 4 and higher” interactions) are included in this energy error. This energy is compared with that of a central atom with exact multipole moments interacting with the same environment. The resulting energy discrepancies are summed for 328 atom–atom interactions, for each of the 29 atoms of histidine being a central atom in turn. For 80% of the 539 test configurations (outside the training set), this summed energy deviates by less than 1 kcal mol^?1. © 2013 Wiley Periodicals, Inc.     

High speed CO-OFDM-FSO transmission system

This work is focused to carry out the investigation of fading resistant coherent detected OFDM-FSO system using a simulated test-bed employing OSSB- and ODSB-schemes under clear weather conditions. The data rate transmission is enhanced to 1 Tbps range by employing the coherent detection scheme over a prolonged FSO link as compared to direct detection based OFDM-FSO system (Sharma [18]). Further, the simulated work is also demonstrated for OSSB- and ODSB-schemes to report the best scheme to be used in CO-OFDM-FSO systems to achieve acceptable BER at high data rate transmission (up to1 Tbps).     

Spectroscopic signatures of nitrogen-substituted zeolites

Nanoporous acid catalysts such as zeolites form the backbone of catalytic technologies for refining petroleum. With the promise of a biomass economy, new catalyst systems will have to be discovered, making shape-selective base catalysts especially important because of the high oxygen content in biomass-derived feedstocks. Strongly basic zeolites are attractive candidates, but such materials are notoriously difficult to make due to the strong inherent acidity of aluminosilicates. Several research groups have endeavored to produce strongly basic zeolites by treating zeolites with amines, but to date there is no compelling evidence that nitrogen is incorporated into zeolite frameworks. In this communication, we detail synthesis, NMR spectroscopy, and quantum mechanical calculations showing that nitrogen adds onto both surface and interior sites while preserving the framework structure of zeolites. This finding is crucial for the rational design of new biomass-refinement catalysts, allowing 50 years of zeolite science to be brought to bear on the catalytic synthesis of biofuels.     

Copper bis(2,2,6,6-tetramethyl-3,5-heptanedionate) catalyzed synthesis of N-substituted ferrocenes

An efficient catalytic protocol for the Ulmann-type coupling reaction of both bromo and iodoferrocene with heterocyclic amines using a stable and well defined copper bis(2,2,6,6-tetramethyl-3,5-heptanedionate) complex has been developed. The protocol was applicable for the synthesis of wide variety of N-substituted ferrocenes and the desired products were obtained in good to excellent yields.     

Visible light-mediated photocatalyzed synthesis of oxazole via intermolecular C?N and C?O bond formation

An efficient visible light-mediated, eosin Y-catalyzed synthesis of oxazole has been developed from benzil with primary amines, that providing a straightforward, green, and environmentally benign access to a wide variety of substituted oxazole-2-amines under mild reaction conditions.     

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X‐ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra‐molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.     

Hepatitis C Virus NS3/4A Inhibition and Host Immunomodulation by Tannins from Terminalia chebula: A Structural Perspective

Terminalia chebula Retz. forms a key component of traditional folk medicine and is also reported to possess antihepatitis C virus (HCV) and immunomodulatory activities. However, information on the intermolecular interactions of phytochemicals from this plant with HCV and human proteins are yet to be established. Thus, by this current study, we investigated the HCV NS3/4A inhibitory and host immune-modulatory activity of phytocompounds from T. chebula through in silico strategies involving network pharmacology and structural bioinformatics techniques. To start with, the phytochemical dataset of T. chebula was curated from biological databases and the published literature. Further, the target ability of the phytocompounds was predicted using BindingDB for both HCV NS3/4A and other probable host targets involved in the immune system. Further, the identified targets were docked to the phytochemical dataset using AutoDock Vina executed through the POAP pipeline. The resultant docked complexes with significant binding energy were subjected to 50 ns molecular dynamics (MD) simulation in order to infer the stability of complex formation. During network pharmacology analysis, the gene set pathway enrichment of host targets was performed using the STRING and Reactome pathway databases. Further, the biological network among compounds, proteins, and pathways was constructed using Cytoscape 3.6.1. Furthermore, the druglikeness, side effects, and toxicity of the phytocompounds were also predicted using the MolSoft, ADVERpred, and PreADMET methods, respectively. Out of 41 selected compounds, 10 were predicted to target HCV NS3/4A and also to possess druglike and nontoxic properties. Among these 10 molecules, Chebulagic acid and 1,2,3,4,6-Pentagalloyl glucose exhibited potent HCV NS3/4A inhibitory activity, as these scored a lowest binding energy (BE) of −8.6 kcal/mol and −7.7 kcal/mol with 11 and 20 intermolecular interactions with active site residues, respectively. These findings are highly comparable with Asunaprevir (known inhibitor of HCV NS3/4A), which scored a BE of −7.4 kcal/mol with 20 key intermolecular interactions. MD studies also strongly suggest that chebulagic acid and 1,2,3,4,6-Pentagalloyl glucose as promising leads, as these molecules showed stable binding during 50 ns of production run. Further, the gene set enrichment and network analysis of 18 protein targets prioritized 10 compounds and were predicted to potentially modulate the host immune system, hemostasis, cytokine levels, interleukins signaling pathways, and platelet aggregation. On overall analysis, this present study predicts that tannins from T. chebula have a potential HCV NS3/4A inhibitory and host immune-modulatory activity. However, further experimental studies are required to confirm the efficacies.     

Synthesis,Properties and Reactivity Studies of a Hetero-dicopper Complex Consisting of a Porphyrin and a Bispyridylamine Moiety Connected by a Xanthene Backbone

Synthesis, characterization and reactivity studies of a hetero-dicopper complex, particularly towards oxygen reduction are presented. A bischlorido copper(II) trishistidine-type coordination unit is positioned directly above a copper porphyrin unit. The close distance between the two coordination fragments is secured by a rigid xanthene backbone. Surprisingly, the dinuclear complex is not active towards oxygen reduction unlike the earlier published mononuclear analogues with a bispyridylamine copper center. However, the compound architecture of this multinuclear metal complex is interesting and can play an important role in the development of new catalysts for ORR.     

Making and Breaking of C−N Bonds: Applications in the Synthesis of Unsymmetric Tertiary Amines and α-Amino Carbonyl Derivatives

An operationally simple process has been developed for the synthesis of unsymmetrical amines and α-amino carbonyl derivatives in the absence of a catalyst, ligand, oxidant, or any additives. Contrary to known reductive amination methods, this protocol is amenable to substrates containing other reducible groups. This process effectively results in consecutive cleavage and formation of C−N bonds. DFT studies and Hammett analysis provide useful insight into the mechanism. The role of noncovalent interactions as a stabilizing factor have been examined in the protocol. A wide range of alkyl-bromides have been coupled efficiently with a variety of dimethyl anilines to get unsymmetric tertiary amines with yields up to 90%. This methodology was further extended to the synthesis of α-amino carbonyl derivatives with yields up to 93%.