Correction to: Investigation on the effect of cottonseed oil blended with different percentages of octanol and suspended MWCNT nanoparticles on diesel engine characteristics

Journal of Thermal Analysis and Calorimetry - In the original publication of the article, the affiliations of the third, fourth and fifth authors were incorrectly published.     

Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis

BioA catalyzes the second step of biotin biosynthesis, and this enzyme represents a potential target to develop new antitubercular agents. Herein we report the design, synthesis, and biochemical characterization of a mechanism-based inhibitor (1) featuring a 3,6-dihydropyrid-2-one heterocycle that covalently modifies the pyridoxal 5'-phosphate (PLP) cofactor of BioA through aromatization. The structure of the PLP adduct was confirmed by MS/MS and X-ray crystallography at 1.94 ? resolution. Inactivation of BioA by 1 was time- and concentration-dependent and protected by substrate. We used a conditional knock-down mutant of M. tuberculosis to demonstrate the antitubercular activity of 1 correlated with BioA expression, and these results provide support for the designed mechanism of action.     

Molecular Dynamics Simulations of a Cytochrome P450 from Tepidiphilus thermophilus (P450-TT) Reveal How Its Substrate-Binding Channel Opens

Cytochrome P450s (P450) are important enzymes in biology with useful biochemical reactions in, for instance, drug and xenobiotics metabolisms, biotechnology, and health. Recently, the crystal structure of a new member of the CYP116B family has been resolved. This enzyme is a cytochrome P450 (CYP116B46) from Tepidiphilus thermophilus (P450-TT) and has potential for the oxy-functionalization of organic molecules such as fatty acids, terpenes, steroids, and statins. However, it was thought that the opening to its hitherto identified substrate channel was too small to allow organic molecules to enter. To investigate this, we performed molecular dynamics simulations on the enzyme. The results suggest that the crystal structure is not relaxed, possibly due to crystal packing effects, and that its tunnel structure is constrained. In addition, the simulations revealed two key amino acid residues at the mouth of the channel; a glutamyl and an arginyl. The glutamyl’s side chain tightens and relaxes the opening to the channel in conjunction with the arginyl’s, though the latter’s side chain is less dramatically changed after the initial relaxation of its conformations. Additionally, it was observed that the effect of increased temperature did not considerably affect the dynamics of the enzyme fold, including the relative solvent accessibility of the amino acid residues that make up the substrate channel wall even as compared to the changes that occurred at room temperature. Interestingly, the substrate channel became distinguishable as a prominent tunnel that is likely to accommodate small- to medium-sized organic molecules for bioconversions. That is, P450-TT has the ability to pass appropriate organic substrates to its active site through its elaborate substrate channel, and notably, is able to control or gate any molecules at the opening to this channel.     

A High-Valent Non-Heme μ-Oxo Manganese(IV) Dimer Generated from a Thiolate-Bound Manganese(II) Complex and Dioxygen

This study deals with the unprecedented reactivity of dinuclear non-heme Mn^II–thiolate complexes with O₂, which dependent on the protonation state of the initial Mn^II dimer selectively generates either a di-μ-oxo or μ-oxo-μ-hydroxo Mn^IV complex. Both dimers have been characterized by different techniques including single-crystal X-ray diffraction and mass spectrometry. Oxygenation reactions carried out with labeled ¹⁸O₂ unambiguously show that the oxygen atoms present in the Mn^IV dimers originate from O₂. Based on experimental observations and DFT calculations, evidence is provided that these Mn^IV species comproportionate with a Mn^II precursor to yield μ-oxo and/or μ-hydroxo Mn^III dimers. Our work highlights the delicate balance of reaction conditions to control the synthesis of non-heme high-valent μ-oxo and μ-hydroxo Mn species from Mn^II precursors and O₂.     

Differences and Comparisons of the Properties and Reactivities of Iron(III)–hydroperoxo Complexes with Saturated Coordination Sphere

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high‐valent iron(IV)–oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)–hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)–hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)–hydroperoxo reacted directly with substrates or that an initial O?O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)–hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)–hydroperoxo complex with pentadentate ligand system (L₅²). Direct C?O bond formation by an iron(III)–hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L₅²)Fe^III(OOH)]²⁺ should be able to initiate an aromatic hydroxylation process, although a low‐energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)–hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O?O bond, whereas a heterolytic O?O bond breaking in heme iron(III)–hydroperoxo is found.     

Synthesis, structure and spectroscopic properties of calix[4]phloroglucinarene dodecamethyl ether and its trifluoroacetic acid complex

The action of trifluoroacetic acid (TFA) on 2,4,6-trimethoxybenzyl alcohol 3 affords the title tetrameric compound in high yield as a maroon TFA complex, 4; trituration of which with acetone gives the free, colorless, calix[4]phloroglucinarene (5) that can also be directly isolated by treating the reaction mixture with base. The novelty of compounds 4 and 5 is that they possess four additional methoxy groups, which occupy the cavity of the known calix[4]resorcinarene octamethyl ether (2). Ultraviolet-visible spectroscopic analysis shows that TFA-complex 4 exhibits transannular charge-transfer interactions between the opposite aromatic rings. The (1)H-NMR spectrum of the TFA-complex 4 does not change over a wide temperature range, strongly suggesting that it adopts a saddle (1,3-alternate) structure. The conformation of the free phloroglucinarene 5 is temperature-dependent, as determined by variable temperature (1)H NMR spectroscopy. Tetramer 5 adopts a partial cone conformation at low temperatures, but at elevated temperatures is similar to that of the TFA complex 4 (saddle). Tetramer 5 is conformationally mobile at ambient temperature, but generally has a flattened cone (boat) conformation. The ΔG(≠) for inversion in 5 between partial cone and boat conformation is 12.5 Kcal mol(-1), while that between boat and saddle conformation is 14.3 Kcal mol(-1). Conformational changes are also dependant on pH.     

Thermal explosion characteristics in a reduced kinetics model

The problem of thermal explosion arising from a spatially homogeneous reduced five steps reaction kinetic model, which comprises of the chain initiation, chain propagation/branching and chain termination steps is considered. By assuming realistic approximations, the pertubation technique was used to obtain expressions for thermal ignition time for the adiabatic system. In the non-adiabatic system, expressions for the critical heat loss parameter and the ignition temperature in the line of Semenov theory have been obtained. Analysis of the system involving some parameters, and the contributions of the heat released due to the termination reactions on the behaviour of the ignition times and Semenov parameters have been carried out and expressed graphically. Apart from confirming known results in literature, the results shed more light on hitherto unknown behaviour.     

Patient-specific model of lung deformation using spatially dependent constitutive parameters

Breathing-induced spatially dependent lung deformation is predicted using patient-specific elastic properties with the contact–impact analysis model. The lung geometry is derived from 4D CT scan data of real patients. The spatially varying Young’s modulus for the patient is obtained from a previous study that used inverse deformation of the lung. The compact–impact analysis is implemented using the finite element method. The predicted lung deformation is compared with the results based on linear elasticity. The results are consistent with physiology, indicating large deformations near the diaphragm and smaller values at remote locations on the lobe. The effect of non-linearity of elastic property is most significant at the remote locations where the diaphragm-induced deformation is significantly attenuated.