Physical Chemistry Chemical Physics

doi: 10.1039/d4cp90034kpmid: N/A

doi: 10.1039/d4cp90035apmid: N/A

doi: 10.1039/d4cp90036gpmid: N/A

Barati, Farzaneh; Hosseini, Fakhrisadat; Vafaee, Rayeheh; Sabouri, Zahra; Ghadam, Parinaz; Arab, Seyed Shahriar; Shadfar, Najmeh; Piroozmand, Firoozeh

doi: 10.1039/d3cp03989gpmid: 38294035

Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.

Guo, Chenxi; Xia, Shiyu; Tian, Yu; Li, Fenghua; Xu, Guobao; Wu, Fengxia; Niu, Wenxin

doi: 10.1039/d3cp05624dpmid: 38314869

CO-stripping experiments are employed as a highly structure-sensitive and in situ strategy to explore the mechanisms of plasmon-enhanced electrooxidation reactions. By using Pt–Au heterodimers as a model catalyst, the plasmon-induced current and potential changes on Pt and Au sites can be identified and explained.

Shahpouri, Elham; Abavi-Torghabeh, Naghmeh; Kalantarian, Mohammad Mahdi; Mustarelli, Piercarlo

doi: 10.1039/d3cp04815bpmid: 38314849

It is vital to comprehend the charge/discharge behaviors of batteries to improve their properties. In this paper, we normalize the electrode materials’ behaviors according to the time of the process to allow a rational comparison between different materials and batteries.

Paul, Anirban; Nandi, Dhananjay; Slaughter, Daniel S.; Fedor, Juraj; Nag, Pamir

doi: 10.1039/d3cp04834apmid: 38231029

Bond-breaking in CCl4via dissociative electron attachment (DEA) has been studied using a velocity map imaging (VMI) spectrometer. A number of effects related to the dissociation dynamics have been revealed. The near-zero eV s-wave electron attachment, which leads to the production of Cl− anions, is accompanied by a very efficient intramolecular vibrational redistribution. This is manifested by a small fraction of the excess energy being released in the form of the fragments' translation energy. A similar effect is observed for higher-lying electronic resonances with one exception: the resonance centered around 6.2 eV leads to the production of fast Cl2− fragments and their angular distribution is forward peaking. This behavior could not be explained with a single-electronic-state model in the axial recoil approximation and is most probably caused by bending dynamics initiated by a Jahn–Teller distortion of the transient anion. The CCl2− fragment has a reverse backward-peaking angular distribution, suggesting the presence of a long-distance electron hopping mechanism between the fragments.

Das, Sukanta; Prabhudesai, Vaibhav S.

doi: 10.1039/d3cp05456jpmid: 38261379

Dissociative electron attachment (DEA) shows functional group-dependent site selectivity in H− ion channels. In this context, thiol functional groups have yet to be studied in great detail, although they carry importance in radiation damage studies where low-energy secondary electrons are known to induce damage through the DEA process. In this context, we report detailed measurements of absolute cross-sections and momentum images of various anion fragments formed in the DEA process in simple aliphatic thiols. We also compare the observed dynamics with that reported earlier in hydrogen sulphide, the precursor molecule for this functional group, and with that in aliphatic alcohols. Our findings show substantial resemblance in the underlying dynamics in these compounds and point to a possible generalisation of these features in the DEA to thiols. In addition, we identify various pathways that contribute to the S− and SH− channels.

Brás, Elisa M.; Zimmermann, Charlotte; Fausto, Rui; Suhm, Martin A.

doi: 10.1039/d3cp05668fpmid: 38314587

Two simple nitroxyl radicals, di-tert-butyl nitroxyl (DTBN) and 2,2,6,6-tetramethylpiperidinyloxyl (TEMPO) are solvated by one or two water, methanol, tert-butyl alcohol or phenol molecules. The resulting low temperature IR spectra of the vacuum-isolated microsolvates in the OH stretching range are assigned based on harmonic DFT predictions for closed shell solvent dimers and trimers and their offset from experiment, to minimise theory-guided assignment bias. Systematic conformational preferences for the first and second solvent molecule are observed, depending on the conformational rigidity of the radical. These assignments are collected into an experimental benchmark data set and used to assess the spectral predicting power of different DFT approaches. The goal is to find inexpensive computational methods which provide reliable spectral predictions for this poorly explored class of microsolvates.

Ablyasova, Olesya S.; Zamudio-Bayer, Vicente; Flach, Max; da Silva Santos, Mayara; Lau, J. Tobias; Hirsch, Konstantin

doi: 10.1039/d3cp05468cpmid: 38305255

The spin state of metal centers in many catalytic reactions has been demonstrated to be a rate limiting factor when high-valent metal centers such as manganese are involved. Although numerous manganese(v) complexes, including a few manganese(v) oxo complexes, have been identified, thus far only one of these, [MnVH3 buea(O)], has been directly confirmed to exist in a high spin state. Such a high-spin manganese(v) center may play a crucial role in the dioxygen formation process in the elusive S4 state of the Kok cycle in photosystem II. In this study, we provide direct experimental evidence, using X-ray magnetic circular dichroism (XMCD) and X-ray absorption spectroscopy (XAS), of gas phase [OMnO]+ as the second known high-spin manganese(v) oxo complex. We conclusively assign the ground state as 3B1 (C2v). Additionally, we provide fingerprint spectra not only for [OMnV O]+, but also for the high-spin hydroxidooxidomanganese(iv) ion [OMnIV OH]+ in its 4A′′ (Cs) ground state that is expected to exhibit similar XAS and XMCD spectral signatures to neutral dioxidomanganese(iv).