Chemistry

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Shiv Nadar University

World University root node

(SoNS) School of Natural Sciences

Macromolecular Chemistry and Physics

Macromol. Chem. Phys. 12/2016

The iron(IV)-oxo (ferryl) intermediate has been amply established as the principal oxidant in nonheme enzymes and the key player in C-H bond activations and functionalizations. In contrast to this status, our present QM/MM calculations of the mechanism of fosfomycin biosynthesis (a broad range antibiotic) by the nonheme HppE enzyme rule out the iron(IV)-oxo as the reactive species in the hydrogen abstraction (H-abstraction) step of the pro-R hydrogen from the (S)-2-hydroxypropylphosphonic substrate. Moreover, the study reveals that the ferryl species is bypassed in HppE, while the actual oxidant is an HO• radical hydrogen-bonded to a ferric-hydroxo complex, resulting via the homolytic dissociation of the hydrogen peroxide complex, Fe(II)-H2O2. The computed energy barrier of this pathway is 12.0 kcal/mol, in fair agreement with the experimental datum of 9.8 kcal/mol. An alternative mechanism involves the iron-complexed hydroxyl radical (FeIII-(HO•)) that is obtained by protonation of the iron(IV)-oxo group via the O-H group of the substrate. The barrier for this pathway, 23.0 kcal/mol, is higher than the one in the first mechanism. In both mechanisms, the HO• radical is highly selective; its H-abstraction leading to the final cis-fosfomycin product. It appears that HppE is prone to usage of HO• radicals for C-H bond activation, because the ferryl oxidant requires a specific H-abstraction trajectory (-FeOH ∼ 180°) that cannot be met for intramolecular H-abstraction. Thus, this work broadens the landscape of nonheme iron enzymes and makes a connection to Fenton chemistry, with implications on new potential biocatalysts that may harness hydroxyl radicals for C-H bond functionalizations. © 2016 American Chemical Society.

Journal of the American Chemical Society

How do Enzymes Utilize Reactive OH Radicals? Lessons from Nonheme HppE and Fenton Systems

This work uses combined quantum mechanical/molecular mechanical and molecular dynamics simulations to investigate the mechanism and selectivity of H2O2-dependent hydroxylation of fatty acids by the P450SPα class of enzymes. H2O2 is found to serve as the surrogate oxidant for generating the principal oxidant, Compound I (Cpd I), in a mechanism that involves homolytic O-O bond cleavage followed by H-abstraction from the Fe-OH moiety. Our results rule out a substrate-assisted heterolytic cleavage of H2O2 en route to Cpd I. We show, however, that substrate binding stabilizes the resultant Fe-H2O2 complex, which is crucial for the formation of Cpd I in the homolytic pathway. A network of hydrogen bonds locks the HO· radical, formed by the O-O homolysis, thus directing it to exclusively abstract the hydrogen atom from Fe-OH, thereby forming Cpd I, while preventing the autoxoidative reaction, with the porphyrin ligand, and the substrate oxidation. The so formed Cpd I subsequently hydroxylates fatty acids at their α-position with S-enantioselectivity. These selectivity patterns are controlled by the active site: substrate's binding by Arg241 determines the α-regioselectivity, while the Pro242 residue locks the prochiral α-CH2, thereby leading to hydroxylation of the pro-S C-H bond. Our study of the mutant Pro242Ala sheds light on potential modifications of the enzyme's active site in order to modify reaction selectivity. Comparisons of P450SPα to P450BM3 and to P450BSβ reveal that function has evolved in these related metalloenzymes by strategically placing very few residues in the active site. © 2016 American Chemical Society.

Emergence of function in p450-proteins: A combined quantum mechanical/molecular mechanical and molecular dynamics study of the reactive species in the H2O2-dependent cytochrome P450SPα and its regio- and enantioselective hydroxylation of fatty acids

A sulfur-rich copolymer, poly(S-r-C-a) has been synthesized via a sustainable route, showing the utility of two major industrial wastes- elemental sulfur (petroleum waste) and cardanol (agro waste), to explore its potential as cathode material for Li-S batteries. The sulfur-rich copolymer exhibited a reduction in the active material dissolution into the electrolyte and a low self-discharge rate behavior during the rest time compared to an elemental sulfur cathode, indicating the chemical confinement of sulfur units. The presence of organosulfur moieties in copolymer suppress the irreversible deposition of end-discharge products on electrode surfaces and thus improve the electrochemical performances of Li-S batteries. This sulfur copolymer offered a reversible capacity of 892 mA h g-1 at 2nd cycle and maintained the capacity of 528 mA h g-1 after 50 cycles at 200 mA g-1. Reduced graphene oxide (rGO) prepared via a sustainable route was used as a conductive filler to extract the better electrochemical performances from this sulfur copolymer. Such sustainable origin batteries prepared via economically viable showed an improved specific capacity of ∼975 mA h g-1 after 100 cycles at 200 mA g-1 current rate with capacity fading of 0.15\% per cycle and maintained a stable performance over 500 cycles at 2000 mA g-1.

Fulltext

Scientific Reports

Sustainable Sulfur-rich Copolymer/Graphene Composite as Lithium-Sulfur Battery Cathode with Excellent Electrochemical Performance

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.

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

Systems and Synthetic Biology

Erratum to: Diversity oriented synthesis for novel anti-malarials [Syst Synth Biol, DOI 10.1007/s11693-015-9171-0]

A 241-membered cyanine-based library was constructed by the combinatorial chemistry strategy. Combined with high-throughput screening, we successfully discovered a novel fluorescent probe (CyC-M716) capable of identifying a subset of parallel G-quadruplexes with propeller loops stretching across three tetrad layers with high sensitivity and selectivity. © The Royal Society of Chemistry 2015.

Chemical Communications

Development of fluorescent probes specific for parallel-stranded G-quadruplexes by a library approach

Quantum mechanical/molecular mechanical calculations address the longstanding-question of a "second oxidant" in P450 enzymes wherein the proton-shuttle, which leads to formation of the "primary-oxidant" Compound I (Cpd I), was severed by mutating the crucial residue (in P450cam: Threonine-252-to-Alanine, hence T252A). Investigating the oxidant candidates Cpd I, ferric hydroperoxide, and ferric hydrogen peroxide (FeIII(O2H2)), and their reactions, generates reactivity networks which enable us to rule out a "second oxidant" and at the same time identify an additional coupling pathway that is responsible for the epoxidation of 5-methylenylcamphor by the T252A mutant. In this "second-coupling pathway", the reaction starts with the FeIII(O2H2) intermediate, which transforms to Cpd I via a O-O homolysis/H-abstraction mechanism. The persistence of FeIII(O2H2) and its oxidative reactivity are shown to be determined by interplay of substrate and protein. The substrate 5-methylenylcamphor prevents H2O2 release, while the protein controls the FeIII(O2H2) conversion to Cpd I by nailing-through hydrogen-bonding interactions-the conformation of the HO• radical produced during O-O homolysis. This conformation prevents HO• attack on the porphyrins meso position, as in heme oxygenase, and prefers H-abstraction from FeIVOH thereby generating H2O + Cpd I. Cpd I then performs substrate oxidations. Camphor cannot prevent H2O2 release and hence the T252A mutant does not oxidize camphor. This "second pathway" transpires also during H2O2 shunting of the cycle of wild-type P450cam, where the additional hydrogen-bonding with Thr252 prevents H2O2 release, and contributes to a successful Cpd I formation. The present results lead to a revised catalytic cycle of Cytochrome P450cam. © 2015 American Chemical Society.

Quantum Mechanical/Molecular Mechanical Calculated Reactivity Networks Reveal How Cytochrome P450cam and Its T252A Mutant Select Their Oxidation Pathways