The Structures and Stabilities of the Complexes of Biologically Available Ligands with Fe(II) Porphine: An Ab Initio Study

Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations

Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.

Theoretical Study on Electronic Structural Properties of Catalytically Reactive Metalloporphyrin Intermediates

Metalloporphyrins have attracted great attention in the potential application of biomimetic catalysis. Especially, they were widely investigated as green catalysts in the chemical oxidation of various hydrocarbons through the catalytic activation of molecular oxygen. The structural properties of active central metal ions were reported to play a decisive role in catalytic activity. However, those delicate structural changes are difficult to be experimentally captured or elucidated in detail. Herein, we explored the electronic structural properties of metalloporphyrins (metal porphyrin (PMII, PMIIICl)) and their corresponding catalytically active intermediates (metal(III)-peroxo(PMIII-O2), metal(III)-hydroperoxo(PMIII-OH), and metal(IV)-oxo(PMIV=O), (M=Fe, Mn, and Co)) through the density functional theory method. The ground states of these intermediates were determined based on the assessment of relative energy and the corresponding geometric structures of ground states also further confirmed the stability of energy. Furthermore, our analyses of Mulliken charges and frontier molecular orbitals revealed the potential catalytic behavior of reactive metalloporphyrin intermediates.

Replacement of the heme axial lysine as a test of conformational adaptability in the truncated hemoglobin THB1

Amino acid replacement is a useful strategy to assess the roles of axial heme ligands in the function of native heme proteins. THB1, the protein product of the Chlamydomonas reinhardtii THB1 gene, is a group 1 truncated hemoglobin that uses a lysine residue in the E helix (Lys53, at position E10 by reference to myoglobin) as an iron ligand at neutral pH. Phylogenetic evidence shows that many homologous proteins have a histidine, methionine or arginine at the same position. In THB1, these amino acids would each be expected to convey distinct reactive properties if replacing the native lysine as an axial ligand. To explore the ability of the group 1 truncated Hb fold to support alternative ligation schemes and distal pocket conformations, the properties of the THB1 variants K53A as a control, K53H, K53M, and K53R were investigated by electronic absorption, EPR, and NMR spectroscopies. We found that His53 is capable of heme ligation in both the Fe(III) and Fe(II) states, that Met53 can coordinate only in the Fe(II) state, and that Arg53 stabilizes a hydroxide ligand in the Fe(III) state. The data illustrate that the group 1 truncated Hb fold can tolerate diverse rearrangement of the heme environment and has a strong tendency to use two protein side chains as iron ligands despite accompanying structural perturbations. Access to various redox pairs and different responses to pH make this protein an excellent test case for energetic and dynamic studies of heme ligation.

Silyl diol ester as a new selectivity control agent in MgCl2-supported Ziegler-Natta systems for propylene polymerization: catalyst structure and polymer properties

In this study, bis(benzoyloxy)dimethylsilane (SDE) was developed as a non-phthalate selectivity control agent (internal donor (ID) and external donor (ED)) in MgCl₂-supported Ziegler–Natta (ZN) systems. The impact of SDE as an ID was investigated in regards to chemical composition, morphology, adsorption behavior (using FTIR spectroscopy, WAXD and SEM studies) and the propylene polymerization performance of the catalyst. The results of the adsorption behavior of SDE revealed that SDE, while able to stabilize the electronically unsaturated surfaces of MgCl₂ [(104) and (110)], has a rather high tendency to be absorbed on strongly acidic Mg ions at the corners of these crystals. The catalyst with optimum SDE content as an ID afforded a system with reasonable activity and isotacticity (even in the absence of ED) along with broader molecular weight distribution (PDI: 6.2–10) and greater flexural modulus than phthalate-based ZN systems. SDE was also used as a new ED in most widely used fourth- and fifth-generation catalyst systems. The results revealed that in fifth-generation catalyst systems, there was an increase in hydrogen response (>40%) along with an increase of activity without any change in the thermal properties of the final polymer in comparison to a conventional ED (alkoxy silane).

In this study, bis(benzoyloxy)dimethylsilane (SDE) was developed as a non-phthalate selectivity control agent (internal donor (ID) and external donor (ED)) in MgCl₂-supported Ziegler–Natta (ZN) systems for polypropylene polymerization.

Computational electrochemistry: prediction of liquid-phase reduction potentials

This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

A computational study of ligand binding affinities in iron(iii) porphine and protoporphyrin IX complexes

In the context of antimalarial drug development, density functional theory has been used to model the interactions between a diverse set of 31 small ligands and the iron(iii) centre of ferriprotoporphyrin IX, as well as key events in the crystallization of this molecule by the malaria parasite.

Synthesis, coordination chemistry, and physico-chemical properties of the 2-chloroethoxy-iron(III)(ethylthio) porphyrazine

Reaction of octakis(ethylthio)porphyrazine ( H 2 OESPz ) with FeBr 2 in ClCH 2 CH 2 OH at 135 °C affords the 2-chloroethoxy-iron(III)-(ethylthio)porphyrazine, ( ClCH 2 CH 2 O ) Fe III OESPz , ( LFe III OESPz ) in good yield. The spectroscopic, redox, and coordination properties of the complex and its μ-oxo dimer derivative, [ Fe III OESPz ]2 O , are investigated and compared to those of the iron(III)porphyrin analogs.