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Shiv Nadar University

(SoNS) School of Natural Sciences

Cardanol, a sustainable origin phenol, was utilized as a reactive diluent to mediate solventless Mannich-type condensation reaction with para-formaldehyde and primary aromatic amines to form a homologous series of benzoxazine (Bz) monomers namely C-a, C-ddm, C-trisapm and C-tetraapm which differ in their degree of oxazine functionality as mono-, di-, tri- and tetra-oxazine respectively. A strong correlation is reflected between the number of oxazine rings in the monomer and the polymerization behavior, thermo-mechanical transitions, and properties of the polybenzoxazine synthesized. The monomer structure was confirmed by FTIR, 1H-, 13C-NMR spectroscopy and mass spectrometry. The curing, rheological, thermo-mechanical and thermal properties were determined using DSC, FTIR, rheometer, DMTA, LSS and TGA studies. The curing characteristic due to ROP of Bz monomers was supported both by DSC and FTIR studies. The presence of neighboring oxazine group in monomers (C-a to C-tetraapm) strongly attenuates the curing temperature (Ti = 225-140°C), enhances Tg, thermal stability, and mechanical properties. Interestingly, DFT calculations also supported the lowest curing temperature for highest oxazine functionality monomer (C-tetraapm). The interplay between the degree of oxazine functionality in the monomer; extent of H-bonding and crosslink density values in sustainable origin synthesized polybenzoxazines is suggested. The thermoset showed an increasing trend (PC-a < PC-ddm < PC-trisapm < PC-tetraapm) in Tg (58-109°C), thermal stability (355-391°C), char yield (13-37\%), LOI (23-31) and storage modulus (3.6-66.5 MPa) values. The monomers are liquid to semi-viscous paste at room temperature and showed potential for solventless processing in adhesive applications. © 2015 Royal Society of Chemistry.

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Chemistry

Fulltext

RSC Advances

Cardanol benzoxazines-interplay of oxazine functionality (mono to tetra) and properties

Here we described a natural product inspired modular DOS strategy for the synthesis of a library of hybrid systems that are structurally and stereochemically disparate. The main scaffold is a pyrroloisoquinoline motif, that is synthesized from tandem Pictet-Spengler lactamization. The structural diversity is generated via privileged scaffolds that are attached at the appropriate site of the motif. Screening of the library compounds for their antiplasmodial activity against chloroquine sensitive 3D7 cells indicated few compounds with moderate activity (20-50 μM). A systematic comparison of structural intricacy between the library members and a natural product dataset obtained from ZINC® revealed comparable complexity. © 2015 Elsevier Masson SAS.

European Journal of Medicinal Chemistry

A natural product based DOS library of hybrid systems

Furosemide (FS), a loop diuretic drug commonly used for the treatment of hypertension and edema, exhibited color cocrystal polymorphism with coformer 4,4′-bipyridine (4BPY) in the stoichiometry 2:1, albeit both the API and the cocrystal former are colorless. Crystallization from ethanol, isopropanol, ethanol-water (v/v, 1/1) mixture, and acetonitrile yielded pale yellow (form 1I, thin needles) and orange (form 1II, blocks) cocrystals concomitantly. Needles appeared from solution within a day, while the blocks were obtained after 1-2 days from the same flask, indicating that yellow needles were formed faster and the orange blocks were perhaps formed under thermodynamic conditions. Form 1I cocrystals could also be produced from the variety of common solvents. Cocrystallization of FS with 2,2′-bipyridine (2BPY) and 4-aminopyridine (4AP) gave colorless cocrystals 2 and 3, respectively, and did not exhibit polymorphism. The single-crystal X-ray structures, powder X-ray diffraction, photophysical characterization, differential scanning calorimetry, hot stage microscopy studies, and density functional theory (DFT) calculations provide insight into the structure-property relationship. The common structural features observed in all of the structures is the formation of sandwich motifs comprising FS and pyridines through π-stacking interactions. These motifs are linked differently through hydrogen bonding interactions in all three directions. The significant color difference between the two cocrystals dimorphs could be attributed to the different π-stacking patterns and hydrogen bonding interactions between molecules of FS and 4BPY in their cocrystal structures. Investigation on the origin of the color difference using DFT calculations revealed the decrease in HOMO-LUMO gap for form 1II cocrystals (orange) compared to form 1I crystals (light yellow). The crystal-to-crystal thermal transformation of form 1I crystals to form 1II crystals of 1 suggests the role of π-stacking assemblies in driving the self-assembly. © 2015 American Chemical Society.

Crystal Growth and Design

Furosemide Cocrystals with Pyridines: An Interesting Case of Color Cocrystal Polymorphism

We classify the combinations of parameters which lead three generations of quarks and leptons in the framework of magnetized twisted orbifolds on T2/Z2, T2/Z3, T2/Z4 and T2/Z6 with allowing nonzero discretized Wilson line phases and Scherk-Schwarz phases. We also analyze two actual examples with nonzero phases leading to one-pair Higgs and five-pair Higgses and discuss the difference from the results without nonzero phases studied previously. (Note: this article is registered under preprint number: arXiv:1501.02787 [hep-ph].). © 2015 The Authors.

Physics

Nuclear Physics B

Classification of three-generation models on magnetized orbifolds

Malaria, a leading parasitic killer, is caused by Plasmodium spp. The pathology of the disease starts when Plasmodium merozoites infect erythrocytes to form rings, that matures through a large trophozoite form and develop into schizonts containing multiple merozoites. The number of intra-erythrocytic merozoites is a key-determining factor for multiplication rate of the parasite. Counting of intraerythrocytic merozoites by classical 2-D microscopy method is error prone due to insufficient representation of merozoite in one optical plane of a schizont. Here, we report an alternative 3-D microscopy based automated method for counting of intraerythrocytic merozoites in entire volume of schizont. This method offers a considerable amount of advantages in terms of both, ease and accuracy. © 2015, Springer Science+Business Media Dordrecht.

Life Sciences

Systems and Synthetic Biology

Visualization and quantification of Plasmodium falciparum intraerythrocytic merozoites

In this study we introduce a rescoring method to improve the accuracy of docking programs against mPGES-1. The rescoring method developed is a result of extensive computational study in which different scoring functions and molecular descriptors were combined to develop consensus and rescoring methods. 127 mPGES-1 inhibitors were collected from literature and were segregated into training and external test sets. Docking of the 27 training set compounds was carried out using default settings in AutoDock Vina, AutoDock, DOCK6 and GOLD programs. The programs showed low to moderate correlation with the experimental activities. In order to introduce the contributions of desolvation penalty and conformation energy of the inhibitors various molecular descriptors were calculated. Later, rescoring method was developed as empirical sum of normalised values of docking scores, LogP and Nrotb. The results clearly indicated that LogP and Nrotb recuperate the predictions of these docking programs. Further the efficiency of the rescoring method was validated using 100 test set compounds. The accurate prediction of binding affinities for analogues of the same compounds is a major challenge for many of the existing docking programs; in the present study the high correlation obtained for experimental and predicted pIC50 values for the test set compounds validates the efficiency of the scoring method. © 2015 Gupta et al.

PLoS ONE

The augmenting effects of desolvation and conformational energy terms on the predictions of docking programs against mPGES-1

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2′-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5′-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5′-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase $\beta$ (hPol$\beta$). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg<sup>2+</sup> appeared during the process of phosphodiester bond formation and was located between the reacting $\alpha$- and $\beta$-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPol$\beta$ reopened its conformation, pyrophosphate was released and the newly incorporated primer 3′-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.

Journal of the American Chemical Society

Viewing human DNA polymerase $\beta$ faithfully and unfaithfully bypass an oxidative lesion by time-dependent crystallography

Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development. © 2015 Bhattacharjee et al.

Genome-wide analysis of homeobox gene family in legumes: Identification, gene duplication and expression profiling

Towards developing next generation scalable TiO2-based resistive switching (RS) memory devices, the efficacy of 50 keV Ar+-ion irradiation to achieve self-organized nano-channel based structures at a threshold fluence of 5 × 1016 ions/cm2 at ambient temperature is presented. Although x-ray diffraction results suggest the amorphization of as-grown TiO2 layers, detailed transmission electron microscopy study reveals fluence-dependent evolution of voids and eventual formation of self-organized nano-channels between them. Moreover, gradual increase of TiO/Ti2O3 in the near surface region, as monitored by x-ray photoelectron spectroscopy, establishes the upsurge in oxygen deficient centers. The impact of structural and chemical modification on local RS behavior has also been investigated by current-voltage measurements in conductive atomic force microscopy, while memory application is manifested by fabricating Pt/TiO2/Pt/Ti/SiO2/Si devices. Finally, the underlying mechanism of our experimental results has been analyzed and discussed in the light of oxygen vacancy migration through nano-channels. © 2015 AIP Publishing LLC.