reaction initiation
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2021 ◽  
Vol 77 (10) ◽  
pp. 1218-1232
Author(s):  
Diana C. F. Monteiro ◽  
Emmanuel Amoah ◽  
Cromarte Rogers ◽  
Arwen R. Pearson

Careful selection of photocaging approaches is critical to achieve fast and well synchronized reaction initiation and perform successful time-resolved structural biology experiments. This review summarizes the best characterized and most relevant photocaging groups previously described in the literature. It also provides a walkthrough of the essential factors to consider in designing a suitable photocaged molecule to address specific biological questions, focusing on photocaging groups with well characterized spectroscopic properties. The relationships between decay rates (k in s−1), quantum yields (φ) and molar extinction coefficients (ɛmax in M −1 cm−1) are highlighted for different groups. The effects of the nature of the photocaged group on these properties is also discussed. Four main photocaging scaffolds are presented in detail, o-nitrobenzyls, p-hydroxyphenyls, coumarinyls and nitrodibenzofuranyls, along with three examples of the use of this technology. Furthermore, a subset of specialty photocages are highlighted: photoacids, molecular photoswitches and metal-containing photocages. These extend the range of photocaging approaches by, for example, controlling pH or generating conformationally locked molecules.


2021 ◽  
Author(s):  
Michelle Ting ◽  
Lars Yunker ◽  
Ian Chagunda ◽  
Katherine Hatlelid ◽  
Meghan Vieweg ◽  
...  

<p>Understanding catalytic reactions is inherently difficult because not only is the catalyst the least abundant component in the mixture, but it also takes many different forms as the reaction proceeds. Precatalyst is converted into active catalyst, short-lived intermediates, resting states, and decomposition products. Polymerization catalysis is harder yet to study, because as the polymer grows the identities of these species change with every turnover as monomers are added to the chain. Modern mass spectrometric methods have proved to be up to the challenge, with multiple reaction monitoring (MRM) in conjunction with pressurized sample infusion (PSI) used to continuously probe all stages of the Suzuki polycondensation (SPC) reaction. Initiation, propagation, and termination steps were tracked in real time, and the outstanding sensitivity and low signal-to-noise of the approach has real promise with respect to the depth with which this reaction and others like it can be studied.</p>


2021 ◽  
Author(s):  
Michelle Ting ◽  
Lars Yunker ◽  
Ian Chagunda ◽  
Katherine Hatlelid ◽  
Meghan Vieweg ◽  
...  

<p>Understanding catalytic reactions is inherently difficult because not only is the catalyst the least abundant component in the mixture, but it also takes many different forms as the reaction proceeds. Precatalyst is converted into active catalyst, short-lived intermediates, resting states, and decomposition products. Polymerization catalysis is harder yet to study, because as the polymer grows the identities of these species change with every turnover as monomers are added to the chain. Modern mass spectrometric methods have proved to be up to the challenge, with multiple reaction monitoring (MRM) in conjunction with pressurized sample infusion (PSI) used to continuously probe all stages of the Suzuki polycondensation (SPC) reaction. Initiation, propagation, and termination steps were tracked in real time, and the outstanding sensitivity and low signal-to-noise of the approach has real promise with respect to the depth with which this reaction and others like it can be studied.</p>


2021 ◽  
Vol 11 (7) ◽  
pp. 2361-2368
Author(s):  
Nicolas Alfonso ◽  
Van K. Do ◽  
Anthony J. Chavez ◽  
Yuhao Chen ◽  
Travis J. Williams

This minireview documents cases where catalyst carbonylation can be detrimental, beneficial, or even essential in the activation and lifecycle of catalysis for hydrogen transfer reactions.


2020 ◽  
Vol 75 (4) ◽  
pp. 285-291
Author(s):  
Jiao-Nan Yuan ◽  
Hai-Chao Ren ◽  
Yong-Kai Wei ◽  
Wei-Sen Xu ◽  
Guang-Fu Ji ◽  
...  

AbstractMicroscopic electron properties of α-hexahydro-1,3,5-trinitro-1,3,5-triazine (α-RDX) with different shock wave velocities have been investigated based on molecular dynamics together with multi-scale shock technique. The studied shock wave velocities are 8, 9 and 10 km ⋅ s−1. It has been said that the shock sensitivity and reaction initiation of explosives are closely relevant with their microscopic electron properties. The reactions, including the reaction products, which are counted from the trajectory during the simulations are analysed first. The results showed that the number of the products strictly rely on shock wave velocities. The reaction rates and decomposition rates are also studied, which showed the differences between the different shock velocities. The results of electron properties show that α-RDX is a wide-gap insulator in the ground state and the metallisation conditions of shocked RDX are determined, which are lower than under-static high pressure.


2020 ◽  
Vol 27 (2) ◽  
pp. 360-370 ◽  
Author(s):  
Pedram Mehrabi ◽  
Henrike M. Müller-Werkmeister ◽  
Jan-Philipp Leimkohl ◽  
Hendrik Schikora ◽  
Jelena Ninkovic ◽  
...  

Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.


Crystals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 116 ◽  
Author(s):  
Marius Schmidt

Ever since the first structure of an enzyme, lysozyme, was solved, scientists have been eager to explore how these molecules perform their catalytic function. There has been an overwhelmingly large body of publications that report the X-ray structures of enzymes determined after substrate and ligand binding. None of them truly show the structures of an enzyme working freely through a sequence of events that range from the formation of the enzyme–substrate complex to the dissociation of the product. The technical difficulties were too severe. By 1969, Sluyterman and de Graaf had pointed out that there might be a way to start a reaction in an enzyme crystal by diffusion and following its catalytic cycle in its entirety with crystallographic methods. The crystal only has to be thin enough so that the diffusion is not rate limiting. Of course, the key questions are as follows: How thin should the crystal be? Will the existing X-ray sources be able to collect data from a thin enough crystal fast enough? This review shines light on these questions.


2020 ◽  
Vol 62 (4) ◽  
pp. 621
Author(s):  
Р.Р. Алтунин ◽  
Е.Т. Моисеенко ◽  
С.М. Жарков

Based on the study of a solid-state reaction process in Al/Ag thin films (the atomic ratio being Al:Ag=1:3) carried out by in situ electron diffraction method and electrical resistivity measurements, the reaction initiation temperature has been determined and a model of structural phase transitions occurring during the solid-state reaction has been proposed. The solid-state reaction begins at 70°C with the formation of an Al-Ag solid solution at the interface of aluminum and silver nanolayers. It has been found that in the reaction process intermetallic compounds γ-Ag2Al => µ-Ag3Al are successively formed. It has been established that for the formation of the µ-Ag3Al phase in thin films (up to 100 nm) the following is necessary: first, significant excess of silver over aluminum in the atomic composition, second, the formation of the µ-Ag3Al phase begins only after all the FCC aluminum has reacted. The work was supported by the Russian Science Foundation (grant #18-13-00080).


2020 ◽  
Author(s):  
Dihia Idrici ◽  
Michael J. Soo ◽  
Samuel Goroshin ◽  
Andrew J. Higgins ◽  
David L. Frost

Nanomaterials ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 1251 ◽  
Author(s):  
Lei Zhang ◽  
Yi Yu ◽  
Meizhen Xiang

Understanding the reaction initiation of energetic single crystals under external stimuli is a long-term challenge in the field of high energy density materials. Herewith, we developed an ab initio molecular dynamics method based on the multiscale shock technique (MSST) and reported the reaction initiation mechanism by performing large-scale simulations for the sensitive explosive benzotrifuroxan (BTF), insensitive explosive triaminotrinitrobenzene (TATB), four polymorphs of hexanitrohexaazaisowurtzitane (CL-20) pristine crystals and five novel CL-20 cocrystals. A theoretical indicator, tinitiation, the delay of decomposition reaction under shock, was proposed to characterize the shock sensitivity of energetic single crystal, which was proved to be reliable and satisfactorily consistent with experiments. We found that it was the coupling of heat and pressure that drove the shock reaction, wherein the vibrational spectra, the specific heat capacity, as well as the strength of the trigger bonds were the determinants of the shock sensitivity. The intermolecular hydrogen bonds were found to effectively buffer the system from heating, thereby delaying the decomposition reaction and reducing the shock sensitivity of the energetic single crystal. Theoretical rules for synthesizing novel energetic materials with low shock sensitivity were given. Our work is expected to provide a useful reference for the understanding, certifying and adjusting of the shock sensitivity of novel energetic materials.


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