Despite of being ubiquitous in proteins, NHbackbone···S hydrogen bonds linking the sulfur atom of methionine or cysteine to backbone NH groups remain poorly documented. Here, we report vibrationally ...resolved IR NH stretch spectra of two methionine-containing dipeptides (Ac-Phe-Met-NH2 and Ac-Met-Phe-NH2). The conformations observed for both molecules, assigned with the help of DFT-D quantum chemistry, provide spectroscopic evidence for the formation of NHbackbone···S H-bonds, surprisingly strong enough to challenge the classical intrabackbone NH···OC H-bonds. The methionine side chain is found to fold locally, forming a H-bond with the neighboring amide groups (NH(i) or NH(i+1)). Comparison with protein data bank structural information shows that such a local folding is also common in proteins where it concerns 24% of the methionine residues that have a sulfur atom linked to a backbone NH group. This convergence between the strength of these NH···S H-bonds and protein structural data illustrates their contribution to the stability of protein chains.
The transesterification of phosphatidylcholine with methanol was successfully carried out using a promising solvent methyl tert-butyl ether instead of traditional ether, and the reaction was ...dramatically enhanced in the presence of tetrabutylammonium hydroxide as the phase-transfer catalyst. Kinetics of the reaction including the effects of the reaction conditions on the conversion of phosphatidylcholine and the apparent rate constant (kapp) were investigated in detail. On the basis of the experimental evidence, the transesterification mechanism was proposed and a kinetic model was developed, and the experimental data were well described by the pseudo-first-order equation. PUBLICATION ABSTRACT
An improved understanding of NOx formation at high pressures would be of considerable utility to efforts to develop advanced combustion devices. A combination of theoretical and modeling studies are ...implemented in an effort to improve the accuracy of models for the prompt NO process, which is the dominant source of NO under many conditions, and to improve our understanding of the role of this process at high pressures. The theoretical effort implements state-of-the-art treatments of NCN thermochemistry, the interrelated CH + N2 and NCN + H kinetics, and the kinetics of the NCN + OH reaction. For both reaction systems, we implement high level ab initio transition state theory based master equation simulations paying particular attention to the role of stabilization processes. For the NCN + H kinetics we include a treatment of inter-system crossing. The modeling effort focuses on exploring the role of pressure and prompt NO for premixed laminar flames at pressures ranging from 1 to 15 atm, via a comparison with the available experimental data. Additional simulations at higher pressures further explore the mechanistic changes at the pressures of relevance to applied combustion devices (e.g., 100 atm).
ABSTRACT
2,2,4‐Trimethylpentane, also known as isooctane, is used as one of the model fuel species on spark and homogeneous charge compression ignition engines. This study presents thermochemical and ...kinetic properties in the oxidation of the secondary isooctane radical, which includes the peroxy radical formed from the 3O2 association, the hydroperoxy alkyl radicals formed from the intramolecular hydrogen transfers, and the products formed from reactions of the hydroperoxy alkyl radicals. Geometries, vibration frequencies, internal rotor potentials, and thermochemical properties, ΔfH298∘, S°(T), and C°p(T) (5 K ≤ T ≤ 5000 K) were calculated at the individual B3LYP/6–31G(d,p) and the composite CBS‐QB3 calculation method. The standard enthalpies of formation at 298 K were evaluated using isodesmic reaction schemes with several work reactions for each species. Entropy and heat capacities were determined using geometric parameters and frequencies from the B3LYP/6–31G(d,p) calculations for the lowest energy conformer. Internal rotor barriers were determined. Application of group additivity with comparison to calculated values is also illustrated. Transition states and kinetic parameters for intramolecular hydrogen atom transfer and molecular elimination channels were characterized to evaluate reaction paths and kinetics. Kinetic parameters were determined versus pressure and temperature for the chemical activated formation and unimolecular dissociation of the peroxide adduct. Multifrequency quantum Rice–Ramsperger–Kassel analysis was used for k(E) with master equation analysis for falloff. The kinetic analysis shows that the main reaction channels are the formation of isooctene ((CH3)3CCH=C(CH3)2) + HO2•, and the formation of the cyclic: (CH3)2‐y(CCH2CHO)‐(CH3)2, (CH3)3C‐y(CHCO)‐(CH3)2, and (CH3)3C‐y(CHCHCH2O)‐(CH3).
Guided by the recent success of empirical model predicting the folding rates of small two‐state folding proteins from the relative contact order (CO) of their native structures, by a theoretical ...model of protein folding that predicts that logarithm of the folding rate decreases with the protein chain length L as L2/3, and by the finding that the folding rates of multistate folding proteins strongly correlate with their sizes and have very bad correlation with CO, we reexamined the dependence of folding rate on CO and L in attempt to find a structural parameter that determines folding rates for the totality of proteins. We show that the Abs_CO = CO × L, is able to predict rather accurately folding rates for both two‐state and multistate folding proteins, as well as short peptides, and that this Abs_CO scales with the protein chain length as L0.70 ± 0.07 for the totality of studied single‐domain proteins and peptides.
Interaction between light and matter results in new quantum states whose energetics can modify chemical kinetics. In the regime of ensemble vibrational strong coupling (VSC), a macroscopic number ...Formula: see text of molecular transitions couple to each resonant cavity mode, yielding two hybrid light-matter (polariton) modes and a reservoir of Formula: see text dark states whose chemical dynamics are essentially those of the bare molecules. This fact is seemingly in opposition to the recently reported modification of thermally activated ground electronic state reactions under VSC. Here we provide a VSC Marcus-Levich-Jortner electron transfer model that potentially addresses this paradox: although entropy favors the transit through dark-state channels, the chemical kinetics can be dictated by a few polaritonic channels with smaller activation energies. The effects of catalytic VSC are maximal at light-matter resonance, in agreement with experimental observations.
CRISPR-diagnostic assays have gained significant interest in the last few years. This interest has grown rapidly during the current COVID-19 pandemic, where CRISPR-diagnostics have been frontline ...contenders for rapid testing solutions. This surge in CRISPR-diagnostic research prompts the following question: what exactly are the achievable limits of detection and associated assay times enabled by the kinetics of enzymes such as Cas12 and Cas13? To explore this question, we here present a model based on Michaelis–Menten enzyme kinetics theory applied to CRISPR enzymes. We use the model to develop analytical solutions for reaction kinetics and develop back-of-the-envelope criteria to validate and check for consistency in reported enzyme kinetic parameters. We applied our analyses to all studies known to us, which report Michaelis–Menten-type kinetic data for CRISPR-associated enzymes. These studies include all subtypes of Cas12 and Cas13 and orthologs. We found all but one study clearly violate at least two of our three rules and therefore present data that violate basic physical limits. We performed an experimental study of reaction kinetics of LbCas12a with both ssDNA and dsDNA activators and use these data to validate our model and its predicted scaling. The validated model is used to explore CRISPR reaction time scales and the degree of reaction completion for practically relevant target concentrations applicable to CRISPR-diagnostic assays. The results have broad implications for achievable limits of detection and assay times of emerging, amplification-free CRISPR-detection methods.
Herein we address the factors controlling photocurrent generation in P3HT:PCBM blend films as a function of blend composition and annealing treatment. Absorption, photoluminescence, and transient ...absorption spectroscopy are used to distinguish the role of exciton dissociation, charge pair separation, and charge collection. Variations in blend film microstructure with composition and annealing treatment are studied using X-ray diffraction. While the trend in photocurrent generation with composition and annealing Muller, et al., Adv. Mater. 2008, 20, 3510 does not follow the trend in exciton dissociation, it closely follows the trend in charge pair generation. Moreover, charge pair generation efficiency is positively correlated to the degree of polymer crystallization and the appearance of large domains of both polymer and fullerene phases. We argue that larger domains assist charge pair separation by increasing the probability of escape from the P3HT:PCBM interface, thus reducing geminate charge recombination.
Rechargeable Li–O2 batteries are promising due to their superior high energy density but subject to sluggish oxygen reduction/evolution kinetics. Developing highly efficient catalysts to improve ...catalytic activity and alleviate oxidation–reduction overpotential of Li–O2 batteries is of great challenge and importance. Herein, a CO2‐assisted thermal‐reaction strategy is developed to fabricate isolated semi‐metallic selenium single‐atom‐doped Ti3C2 MXene catalyst (SASe‐Ti3C2) as cathodes for high‐performance Li–O2 batteries. The isolated moieties of single Se atom catalysis centers can function as active catalytic centers to drastically enhance the intrinsic LiO2‐absorption ability and thus fundamentally modulate the formation/decomposition mechanism of lithium peroxide (Li2O2) discharge product, thus demonstrating greatly enhanced redox kinetics and efficiently ameliorated overpotentials. Theoretical simulations reveal that the interaction between Se‐involved moieties and Ti3C2 substrate greatly enhances the intrinsic LiO2‐absorption ability and fundamentally promotes the charge transfer between electrode and Li2O2 product, deeply ameliorating the round‐trip overpotential. The well‐designed SASe–Ti3C2 electrode exhibits decreased charge/discharge polarization (1.10 V vs Li/Li+), ultrahigh discharge capacity (17 260 mAh g−1 at 100 mA g−1), and superior durability (170 cycles at 200 mA g−1) as cathode for Li–O2 batteries. The promising results will shed light on the design of highly efficient catalysts for oxygen‐involved systems of future investigation.
Ti3C2 MXene confining isolated semi‐metallic selenium atom (SASe–Ti3C2) catalysts, which are synthesized via a CO2‐assisted thermal‐reaction strategy, are first published in Li–O2 batteries as high‐performance cathodes. The SASe–Ti3C2 catalysts can drastically enhance the intrinsic LiO2‐absorption ability and thus fundamentally modulate the formation/decomposition mechanism of lithium peroxide discharge product, which could further demonstrate greatly enhanced redox kinetics and efficiently ameliorated overpotentials.
Nanozymes are nanomaterials exhibiting intrinsic enzyme-like characteristics that have increasingly attracted attention, owing to their high catalytic activity, low cost and high stability. This ...combination of properties has enabled a broad spectrum of applications, ranging from biological detection assays to disease diagnosis and biomedicine development. Since the intrinsic peroxidase activity of Fe
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nanoparticles (NPs) was first reported in 2007, >40 types of nanozymes have been reported that possess peroxidase-, oxidase-, haloperoxidase- or superoxide dismutase-like catalytic activities. Given the complex interdependence of the physicochemical properties and catalytic characteristics of nanozymes, it is important to establish a standard by which the catalytic activities and kinetics of various nanozymes can be quantitatively compared and that will benefit the development of nanozyme-based detection and diagnostic technologies. Here, we first present a protocol for measuring and defining the catalytic activity units and kinetics for peroxidase nanozymes, the most widely used type of nanozyme. In addition, we describe the detailed experimental procedures for a typical nanozyme strip-based biological detection test and demonstrate that nanozyme-based detection is repeatable and reliable when guided by the presented nanozyme catalytic standard. The catalytic activity and kinetics assays for a nanozyme can be performed within 4 h.
![Preparing L-[alpha]-Glycero...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/0538-8066/small "Preparing L-[alpha]-Glycerophosphocholine in a Phase-Transfer Catalytic Reaction: Kinetic Study")
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