Shakir Ali Siddiqui

Designing redox proteins with predictable and tunable electron transfer properties is a major goal in de novo bioenergetics. Here we show that replacing heme B with a series of structurally conservative non-natural metalloporphyrins enables broad modulation of redox potentials over 400 mV in the de novo designed monoheme m4D2 and diheme 4D2 T19D. The non-natural porphyrins bind with high affinity and do not compromise either the heme binding site or global protein structure, as evidenced by X-ray crystallography and NMR spectroscopy. We also report the native-like NMR structure of m4D2 loaded with the non-natural and symmetric iron 2,4-dimethyldeuteroporphyrin IX, confirming our modular approach to tetrahelical redox protein design. This work establishes a versatile platform for constructing tunable electron carriers for engineered bioenergetic pathways and bioelectronic applications.

Methane is a generic chemical feedstock, and its conversion to methanol can provide an alternative fuel. We herein provide a first-principles-based strategy for designing a catalyst that operates in a synchronized catalytic cycle and efficiently converts methane into methanol. In so doing, we designed an earlier, experimentally synthesized, porphyrin-based supramolecular cage based on a designed local electric field (D-LEF) by strategically substituting charged groups. We show that the negatively charged substitutions at the porphyrin destabilize the transition state, which, in turn, inhibits the active oxidant formation (Fe═O) as well as the methanol production. In contrast, the positively charged substitution efficiently forms the active oxidant cage and catalyzes the methanol formation. As such, we propose that D-LEF acts as a switch for the methane-to-methanol conversion, and one can readily enhance or inhibit it by switching between different charge states of the molecular cages. As such, this conceptual study will guide experimentalists in designing highly efficient, switchable supramolecular cages.

Here, we report on the chemistry of electrofreezing of water near -0.5 °C as induced by aluminum and magnesium electrodes. We suggest that the processes are triggered by the action of hydrated Al³⁺ and Mg²⁺ ions or their hydrated hydroxides, as created by electrolysis and the electric field. The uniqueness of octahedral hydrated Al³⁺ and Mg²⁺ ions lies in their high polarizing power, which acidifies the coordinated water that interacts with the bulk water to create hexagonal ice-like architectures. The aluminum electrodes induce icing when used as an anode (+50 V), while magnesium electrodes induce icing either as an anode or cathode at the same voltage, where the formation of the hydroxide ions is plausible. Furthermore, molecular dynamic simulations suggest that these species induce in their surroundings, under the influence of the electric field, "ice-like" assemblies that trigger the icing process. Those simulations suggest that the order in which the species lower the entropy of the system is Al(OH)₃ > Mg(OH)₂ > Al³⁺ > Mg²⁺.

The active sites of heme enzymes have evolved to control the formation of highly reactive intermediates in oxidative catalysis. Proton delivery to the heme is essential, yet the mechanisms of proton delivery remain poorly understood. Here, we identify routes and drivers of proton delivery in a heme peroxidase (ascorbate peroxidase) using computational approaches that combine classical, quantum, and hybrid methods with enhanced sampling and local electric field (LEF) analyses. Our results show that networks of active‐site water molecules facilitate proton exchange with Arg38, which may act as a transient proton carrier at the γ‐heme edge where the substrate binds. The distal His42 residue aids proton transfer into the active site via solvent at the δ‐edge. Molecular dynamics simulations of three heme peroxidases identify hydrated channels leading to both γ‐ and δ‐edges, allowing solvent protons to reach the active site. Comparison with eight other heme peroxidases shows that these channels are conserved. LEF analyses reveal a continuous electrostatic funnel drawing protons toward the heme from the γ‐ and δ‐edges, a feature that is broadly conserved across other peroxidases. These results suggest that nature pre‐organizes electrostatic funnels and solvent channels to provide multiple well‐defined routes for proton delivery in peroxidase catalysis.

The active sites of heme enzymes have evolved to control the formation of highly reactive intermediates in oxidative catalysis. Proton delivery to the heme is essential, yet the mechanisms of proton delivery remain poorly understood. Here, we identify routes and drivers of proton delivery in a heme peroxidase (ascorbate peroxidase) using computational approaches that combine classical, quantum, and hybrid methods with enhanced sampling and local electric field (LEF) analyses. Our results show that networks of active‐site water molecules facilitate proton exchange with Arg38, which may act as a transient proton carrier at the γ‐heme edge where the substrate binds. The distal His42 residue aids proton transfer into the active site via solvent at the δ‐edge. Molecular dynamics simulations of three heme peroxidases identify hydrated channels leading to both γ‐ and δ‐edges, allowing solvent protons to reach the active site. Comparison with eight other heme peroxidases shows that these channels are conserved. LEF analyses reveal a continuous electrostatic funnel drawing protons toward the heme from the γ‐ and δ‐edges, a feature that is broadly conserved across other peroxidases. These results suggest that nature pre‐organizes electrostatic funnels and solvent channels to provide multiple well‐defined routes for proton delivery in peroxidase catalysis.

The active site architecture of heme enzymes has evolved to control the formation of highly reactive intermediates for oxidative catalysis. Finely tuned proton delivery to heme is essential, yet the mechanisms of proton delivery and the sources of protons are poorly understood. Here, we identify routes and drivers of proton delivery in a heme peroxidase enzyme (ascorbate peroxidase) employing a range of computational molecular modeling approaches, including molecular dynamics (MD) simulations, density functional theory (DFT) and combined quantum mechanics/molecular mechanics (QM/MM) calculations, enhanced sampling techniques, and local electric field (LEF) analyses. Our results show that networks of active site water molecules facilitate proton ex-change with Arg38, which may serve as a transient proton carrier at the γ-edge of the heme, where the substrate (ascorbate) binds. The distal His42 residue aids proton transfer into the active site via solvent from the δ-heme edge. MD simulations of three peroxidases identify hydrated channels in the structure – pointing towards both the γ- and δ-edges of the heme – through which protons from solvent can access the active site. Comparison with structures of 8 other heme peroxidases shows that these channels are conserved features. LEF calculations show a continuous electrostatic funnel, running from positive to negative, that pulls protons from the protein surface along the channels towards the heme iron from both the γ- and δ-heme edges. This electric field is also found to be a conserved feature in several peroxidases; its direction and shape is conserved but the gradient varies between differ-ent enzymes, suggesting that nature preorganises the electric field as a determinant of relative activity. Rather than a simplistic model for proton delivery (in which a single substrate provides a single proton (and an electron) to the heme) the data instead show conserved solvent channels and electrostatic funnels, which provide multiple well defined routes for proton delivery in peroxidase catalysis.

Divalent carbodicationic synthon has attracted significant attention due to its unique reactivity and bonding. The application of this synthon in synthetic settings is still fancy owing to its super‐electrophilicity. Generation of this reactive intermediate in a catalytic fashion is challenging. For the first time, the reactivity of the chemical equivalent of divalent dication synthon has been proposed via Lewis acid‐catalysed heterolytic ionisation of ynone via sequential conjugate addition to ynone followed by C─C bond cleavage to afford heteroarenes. A library of quinazolinones and 2‐substituted quinazolinones has been synthesised with good to excellent yields having a wide range of functional group tolerance and broad substrate scope using 2‐amino benzamides as a nucleophilic partner. Furthermore, 1,2‐diaminobenzenes afforded the corresponding benzimidazole in synthetically good yield. The generality of this strategy has been demonstrated by the successful synthesis of 6‐mono and 2,6‐di‐substituted quinazolinones and 2,4,6‐tri‐substituted quinazoline with very high efficiency. The mechanistic study confirmed the role of the cooperative effect and secondary orbital interaction in Grob‐type fragmentation and not the involvement of any radical intermediate in the catalytic cycle.