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Journal articles on the topic 'Molecular reaction mechanism'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 February 2022

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1

Stack, Andrew G., and Paul R. C. Kent. "Geochemical reaction mechanism discovery from molecular simulation." Environmental Chemistry 12, no. 1 (2015): 20. http://dx.doi.org/10.1071/en14045.

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Environmental context Computational simulations are providing an increasingly useful way to isolate specific geochemical and environmental reactions and to test how important they are to the overall rate. In this review, we summarise a few ways that one can simulate a reaction and discuss each technique’s overall strengths and weaknesses. Selected case studies illustrate how these techniques have helped to improve our understanding for geochemical and environmental problems. Abstract Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile and ro

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2

Ardèvol, Albert, Javier Iglesias-Fernández, Víctor Rojas-Cervellera, and Carme Rovira. "The reaction mechanism of retaining glycosyltransferases." Biochemical Society Transactions 44, no. 1 (2016): 51–60. http://dx.doi.org/10.1042/bst20150177.

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The catalytic mechanism of retaining glycosyltransferases (ret-GTs) remains a controversial issue in glycobiology. By analogy to the well-established mechanism of retaining glycosidases, it was first suggested that ret-GTs follow a double-displacement mechanism. However, only family 6 GTs exhibit a putative nucleophile protein residue properly located in the active site to participate in catalysis, prompting some authors to suggest an unusual single-displacement mechanism [named as front-face or SNi (substitution nucleophilic internal)-like]. This mechanism has now received strong support, fro

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3

Nagaoka, Masataka, Yoshishige Okuno, Tokio Yamabe, and Kenichi Fukui. "Abinitio calculations and the chemical reaction molecular dynamics simulation." Canadian Journal of Chemistry 70, no. 2 (1992): 377–87. http://dx.doi.org/10.1139/v92-054.

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To clarify the mechanism of chemical reactions in solution, each solvent molecule was classified as either a reactive-solvent molecule or a medium-solvent molecule in accordance with its role in the reaction. The proton transfer reaction of formamidine in water was treated as a model reaction. Abinitio molecular orbital calculations were performed for the complex made up of a formamidine, a reactive-water molecule, and a medium-water molecule. The optimized geometries and the solvation energies were obtained and the orbital interaction analysis carried out along the intrinsic reaction coordina

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4

Cremer, Dieter, and Elfi Kraka. "From Molecular Vibrations to Bonding, Chemical Reactions, and Reaction Mechanism." Current Organic Chemistry 14, no. 15 (2010): 1524–60. http://dx.doi.org/10.2174/138527210793563233.

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5

Tolosa, S., A. Hidalgo, and J. A. Sansón. "Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution fromAb InitioPotential and Molecular Dynamics Simulations." Journal of Chemistry 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/265958.

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A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described usingab initiosolute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3) via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activati

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6

Tachikawa, Hiroto. "SN2 and SN2′ reaction dynamics of cyclopropenyl chloride with halide ion A direct ab initio molecular dynamics (MD) study." Canadian Journal of Chemistry 83, no. 9 (2005): 1597–605. http://dx.doi.org/10.1139/v05-176.

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Direct ab initio molecular dynamics (MD) calculations have been carried out for the reaction of cyclopropenyl chloride with halide ion (F) (F + (CH)3Cl → F(CH)3 + Cl) in gas phase. Both SN2 and SN2′ channels were found as product channels. These channels are strongly dependent on the collision angle of F to the target (CH)3Cl molecule. The collision at one of the carbon atoms of the C=C double bond leads to the SN2′ reaction channel; whereas the collision at the methylene carbon atom leads to the SN2 reaction channel. The reactions proceed via a direct mechanism without long-lived complexe

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7

Bissaro, Bastien, Bennett Streit, Ingvild Isaksen, et al. "Molecular mechanism of the chitinolytic peroxygenase reaction." Proceedings of the National Academy of Sciences 117, no. 3 (2020): 1504–13. http://dx.doi.org/10.1073/pnas.1904889117.

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Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of monocopper enzymes broadly distributed across the tree of life. Recent reports indicate that LPMOs can use H2O2 as an oxidant and thus carry out a novel type of peroxygenase reaction involving unprecedented copper chemistry. Here, we present a combined computational and experimental analysis of the H2O2-mediated reaction mechanism. In silico studies, based on a model of the enzyme in complex with a crystalline substrate, suggest that a network of hydrogen bonds, involving both the enzyme and the substrate, brings H2

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De Wispelaere, Kristof, Simon Bailleul, and Veronique Van Speybroeck. "Towards molecular control of elementary reactions in zeolite catalysis by advanced molecular simulations mimicking operating conditions." Catalysis Science & Technology 6, no. 8 (2016): 2686–705. http://dx.doi.org/10.1039/c5cy02073e.

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9

Mestdagh, J. M., C. Alcaraz, J. Berlande, et al. "Reaction Dynamics of Electronically Excited Barium Atoms With Free Molecules and Molecular Clusters." Laser Chemistry 10, no. 5-6 (1990): 389–403. http://dx.doi.org/10.1155/1990/36585.

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In this review article we describe some recent results obtained in our laboratory. The successful combination of crossed molecular beam techniques and various laser excitation schemes has been used to study chemiluminescent reactions of ground and excited electronic states of barium with free molecules and molecular clusters. Studies include the identification of reaction products in cases where many chemiluminescent reaction channels are opened. The case of Ba(6sp1P1,6s5d1D2,6s5d3Dj) reacting with H20, methanol, ethanol, propanol-1, propanol-2, methyl-2, propanol-2, butanol-l, allyl alcohol

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10

MURRAY, A. W. "ChemInform Abstract: Molecular Rearrangements (Organic Reaction Mechanism)." ChemInform 25, no. 21 (2010): no. http://dx.doi.org/10.1002/chin.199421287.

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11

Alfonso-Prieto, Mercedes, Xevi Biarnés, Pietro Vidossich, and Carme Rovira. "The Molecular Mechanism of the Catalase Reaction." Journal of the American Chemical Society 131, no. 33 (2009): 11751–61. http://dx.doi.org/10.1021/ja9018572.

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12

Wang, Zhi-Xiang, Ming-Bao Huang. та Ruo-Zhuang Liu. "Theoretical study on the insertion reaction of CH(X2Π) with CH4". Canadian Journal of Chemistry 75, № 7 (1997): 996–1001. http://dx.doi.org/10.1139/v97-119.

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The CH + CH4 reaction has been studied by means of ab initio molecular orbital calculations incorporating electron correlation with Møller–Plesset perturbation theory up to second and fourth orders with the 6-31G(d,p) and 6-311++G(2d,p) basis sets. An energetically feasible insertion reaction path has been found in the potential energy surface that confirms the experimental proposal for the mechanism of the CH + CH4 reaction. The feature of the mechanism for the CH + CH4 insertion reaction is found to be different from the feature of the mechanisms for the CH + NH3, CH + H2O, and CH + HF inser

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13

Suhail, Mohammad, Sofi Danish Mukhtar, Imran Ali, Ariba Ansari, and Saiyam Arora. "Theoretical DFT study of Cannizzaro reaction mechanism: A mini perspective." European Journal of Chemistry 11, no. 2 (2020): 139–44. http://dx.doi.org/10.5155/eurjchem.11.2.139-144.1975.

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In regards to the Cannizzaro reaction and its peculiar mechanism, some researchers have presented a free radical mechanism for the Cannizzaro reaction, while others have found that it is feasible through an ionic mechanism, but the actual mechanism has not been finalized yet. The researchers have given the proof of both the mechanisms through their papers published. Actually, Cannizzaro reaction may occur through both mechanisms depending on both molecular structure and different conditions which are yet to be explained. Recently published papers describe that free radical mechanism occurs onl

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14

Sun, Hong, Chuang Liu, Xiao Jia Gao, and Yu Lan Tang. "Oxygen Reduction in PEM Fuel Cell Based on Molecular Simulation." Advanced Materials Research 156-157 (October 2010): 432–38. http://dx.doi.org/10.4028/www.scientific.net/amr.156-157.432.

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The electrochemical reaction in the cathode plays an important role on the performance and application of PEM fuel cell. In this paper, mechanism of oxygen reduction reaction in the cathode of PEM fuel cell is simulated based on molecule dynamics and quantum mechanics. The most probable electrochemical reaction process in the cathode is obtained by analyzing transition state and free energy of oxygen reduction reaction with the catalysis of Pt. Simulation results show that 2e reaction mechanism is more applicable to oxygen reduction reaction in the cathode than 4e reaction mechanism; according

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15

Kulakova, A. M., M. G. Khrenova, and A. V. Nemukhin. "Molecular mechanism of chromogenic substrate hydrolysis in the active site of human carboxylesterase-1." Biomeditsinskaya Khimiya 67, no. 3 (2021): 300–305. http://dx.doi.org/10.18097/pbmc20216703300.

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Human carboxylesterases are involved in the protective processes of detoxification during the hydrolytic metabolism of xenobiotics. Knowledge of the molecular mechanisms of substrates hydrolysis in the enzymes active site is necessary for the rational drug design. In this work, the molecular mechanism of the hydrolysis reaction of para-nitrophenyl acetate in the active site of human carboxylesterase was determined using modern methods of molecular modeling. According to the combined method of quantum mechanics/molecular mechanics calculations, the chemical reaction occurs within four elementar

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16

Long, Fengqin, Zheng Chen, Keli Han, Lu Zhang, and Wei Zhuang. "Differentiation between Enamines and Tautomerizable Imines Oxidation Reaction Mechanism using Electron-Vibration-Vibration Two Dimensional Infrared Spectroscopy." Molecules 24, no. 5 (2019): 869. http://dx.doi.org/10.3390/molecules24050869.

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Intermediates lie at the center of chemical reaction mechanisms. However, detecting intermediates in an organic reaction and understanding its role in reaction mechanisms remains a big challenge. In this paper, we used the theoretical calculations to explore the potential of the electron-vibration-vibration two-dimensional infrared (EVV-2DIR) spectroscopy in detecting the intermediates in the oxidation reactions of enamines and tautomerizable imines with 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO). We show that while it is difficult to identify the intermediates from their infrared and Raman

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17

Almatarneh, Mansour H., Shefa’ F. Alrebei, Mohammednoor Altarawneh, Yuming Zhao, and Abd Al-Aziz Abu-Saleh. "Computational Study of the Dissociation Reactions of Secondary Ozonide." Atmosphere 11, no. 1 (2020): 100. http://dx.doi.org/10.3390/atmos11010100.

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This contribution presents a comprehensive computational study on the reactions of secondary ozonide (SOZ) with ammonia and water molecules. The mechanisms were studied in both a vacuum and the aqueous medium. All the molecular geometries were optimized using the B3LYP functional in conjunction with several basis sets. M06-2X, APFD, and ωB97XD functionals with the full basis set were also used. In addition, single-point energy calculations were performed with the G4MP2 and G3MP2 methods. Five different mechanistic pathways were studied for the reaction of SOZ with ammonia and water molecules.

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18

Fu, Yu-Wei, Wei-Feng Sun, and Xuan Wang. "UV-Initiated Crosslinking Reaction Mechanism and Electrical Breakdown Performance of Crosslinked Polyethylene." Polymers 12, no. 2 (2020): 420. http://dx.doi.org/10.3390/polym12020420.

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The ultraviolet (UV) irradiation crosslinking reactions of polyethylene and the electronic properties of photo-initiators and reaction products are theoretically investigated by the first-principles calculations. The crosslinked polyethylene (XLPE) materials are prepared in experiments that employ the UV-initiated crosslinking technique with different photon-initiation systems. Infrared spectrum and the alternating current dielectric breakdown strength of UV-initiated XLPE are tested to explore the effect of reaction products on the breakdown characteristics in combination with the electron st

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19

Nhan, N. T. T., P. H. Kien, P. K. Hung, N. V. Hong, and L. T. San. "About the diffusion mechanism in the silica liquid." International Journal of Modern Physics B 30, no. 10 (2016): 1650059. http://dx.doi.org/10.1142/s0217979216500594.

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In this paper, we have numerically studied the diffusion mechanism in silica liquid based on the idea that the collective movement of particles is controlled by reactions [Formula: see text] and [Formula: see text]. Four models at temperatures from 2600 K to 3500 K have been constructed by molecular dynamic simulation. The simulation shows that the liquid has a small amount of defect-cells which are of importance for the diffusion. In particular, the majority of reactions happen via defect-cells SiO5 and OSi3. Moreover, the defect-cells do not uniformly distribute in the liquid, but they have

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20

Bravaya, Ksenia, Anastasia Bochenkova, Bella Grigorenko, Igor Topol, Stanley Burt, and Alexander Nemukhin. "Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases." Journal of Chemical Theory and Computation 2, no. 4 (2006): 1168–75. http://dx.doi.org/10.1021/ct6000686.

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21

Rice, Betsy M., William Mattson, John Grosh, and S. F. Trevino. "Molecular-dynamics study of detonation. II. The reaction mechanism." Physical Review E 53, no. 1 (1996): 623–35. http://dx.doi.org/10.1103/physreve.53.623.

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22

Inano, Hiroshi, та Bun-Ichi Tamaoki. "Testicular 17β-hydroxysteroid dehydrogenase: Molecular properties and reaction mechanism". Steroids 48, № 1-2 (1986): 1–26. http://dx.doi.org/10.1016/0039-128x(86)90038-3.

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23

Tsona, Narcisse Tchinda, and Lin Du. "A potential source of atmospheric sulfate from O<sub>2</sub><sup>−</sup>-induced SO<sub>2</sub> oxidation by ozone." Atmospheric Chemistry and Physics 19, no. 1 (2019): 649–61. http://dx.doi.org/10.5194/acp-19-649-2019.

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Abstract. It was formerly demonstrated that O2SOO− forms at collisions rate in the gas phase as a result of SO2 reaction with O2-. Here, we present a theoretical investigation of the chemical fate of O2SOO− by reaction with O3 in the gas phase, based on ab initio calculations. Two main mechanisms were found for the title reaction, with fundamentally different products: (i) formation of a van der Waals complex followed by electron transfer and further decomposition to O2 + SO2 + O3- and (ii) formation of a molecular complex from O2 switching by O3, followed by SO2 oxidation to SO3- within the c

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24

Jez, Joseph M., and Joseph P. Noel. "Reaction Mechanism of Chalcone Isomerase." Journal of Biological Chemistry 277, no. 2 (2001): 1361–69. http://dx.doi.org/10.1074/jbc.m109224200.

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25

Critchley, C. "The Molecular Mechanism of Photoinhibition — Facts and Fiction." Functional Plant Biology 15, no. 2 (1988): 27. http://dx.doi.org/10.1071/pp9880027.

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In this paper, the evidence supporting two different models for the molecular mechanism of photoinhibition is discussed. One hypothesis centres around the suggestion that photoinhibition is due to the loss of the herbicide-binding Dl polypeptide of photosystem II. The other model suggests that damage to a functional group in the reaction centre is the primary cause of photoinhibition. In order to put the apparent controversy into context, recent developments in our understanding of the structure and function of the photosystem II reaction centre are described. Interpretation and judgement of a

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26

Paajanen, Antti, Aleksi Rinta-Paavola, and Jukka Vaari. "High-temperature decomposition of amorphous and crystalline cellulose: reactive molecular simulations." Cellulose 28, no. 14 (2021): 8987–9005. http://dx.doi.org/10.1007/s10570-021-04084-2.

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AbstractWe study the thermal decomposition of cellulose using molecular simulations based on the ReaxFF reactive force field. Our analysis focuses on the mechanism and kinetics of chain scission, and their sensitivity on the condensed phase environment. For this purpose, we simulate the thermal decomposition of amorphous and partially crystalline cellulose at various heating rates. We find that thermal degradation begins with depolymerization via glycosidic bond cleavage, and that the order of events corresponds to a randomly initiated chain reaction. Depolymerization is followed by ring fragm

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27

Li, Guifa, and Hui Wang. "Mechanism of Oxygen Reduction Reaction for Sulfur-Doped Graphene Catalyst: First-principles research." E3S Web of Conferences 290 (2021): 01017. http://dx.doi.org/10.1051/e3sconf/202129001017.

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The mechanism of oxygen reduction reaction for surfur-doped graphene catalyst was investigated by first-principles calculation. Several parameters, such geometry structure, reaction energy and electronic structure were used to analyze the reaction process. The results show that the OOH molecule absorbed on S-graphene with pyridine structure exhibits chemical adsorption. But the OOH molecule on S-graphene with pyrrole structure performs physical adsorption. The adsorbed energies of OOH molecule on S-graphene prove such phenomenon. The electronic structure shows that the excellent ORR of OOH mol

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28

Mlostoń, Grzegorz, Karolina Kula, and Radomir Jasiński. "A DFT Study on the Molecular Mechanism of Additions of Electrophilic and Nucleophilic Carbenes to Non-Enolizable Cycloaliphatic Thioketones." Molecules 26, no. 18 (2021): 5562. http://dx.doi.org/10.3390/molecules26185562.

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The molecular mechanisms of addition of dihalocarbenes and dimethoxycarbene to thioketones derived from 2,2,4,4-tetrmethylcyclobutane-1,3-dione were examined on the basis of the DFT wb97xd/6-311g(d,p)(PCM) calculations. Obtained results demonstrated that the examined processes exhibit polar nature and in the case of electrophilic dichloro-, and dibromocarbenes are initiated by the attack of carbene species onto the sulfur atom of the C=S group. Remarkably, reactions involving more electrophilic carbenes (dichloro-, and dibromocarbene) proceeds via stepwise mechanism involving thiocarbonyl ylid

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29

Shoji, Mitsuo, Yukihiro Abe, Mauro Boero, Yasuteru Shigeta, and Yoshiaki Nishiya. "Reaction mechanism of N-cyclopropylglycine oxidation by monomeric sarcosine oxidase." Physical Chemistry Chemical Physics 22, no. 29 (2020): 16552–61. http://dx.doi.org/10.1039/d0cp01679a.

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30

Cao, Le, Simeng Li, Ziwei Yi, and Mengmeng Gao. "Simplification of Carbon Bond Mechanism IV (CBM-IV) under Different Initial Conditions by Using Concentration Sensitivity Analysis." Molecules 24, no. 13 (2019): 2463. http://dx.doi.org/10.3390/molecules24132463.

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Carbon Bond Mechanism IV (CBM-IV) is a widely used reaction mechanism in which VOCs are grouped according to the molecular structure. In the present study, we applied a sensitivity analysis on the CBM-IV mechanism to clarify the importance of each reaction under two different initial conditions (urban and low-NO scenarios). The reactions that exert minor influence on the reaction system are then screened out from the mechanism, so that a reduced version of the CBM-IV mechanism under specific initial conditions can be obtained. We found that in a typical urban condition, 11 reactions can be rem

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31

Sugishima, Masakazu, Kei Wada, and Keiichi Fukuyama. "Recent Advances in the Understanding of the Reaction Chemistries of the Heme Catabolizing Enzymes HO and BVR Based on High Resolution Protein Structures." Current Medicinal Chemistry 27, no. 21 (2020): 3499–518. http://dx.doi.org/10.2174/0929867326666181217142715.

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In mammals, catabolism of the heme group is indispensable for life. Heme is first cleaved by the enzyme Heme Oxygenase (HO) to the linear tetrapyrrole Biliverdin IXα (BV), and BV is then converted into bilirubin by Biliverdin Reductase (BVR). HO utilizes three Oxygen molecules (O2) and seven electrons supplied by NADPH-cytochrome P450 oxidoreductase (CPR) to open the heme ring and BVR reduces BV through the use of NAD(P)H. Structural studies of HOs, including substrate-bound, reaction intermediate-bound, and several specific inhibitor-bound forms, reveal details explaining substrate binding to

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32

Khenkin, Alexander M., Irena Efremenko, Jan M. L. Martin, and Ronny Neumann. "The kinetics and mechanism of oxidation of reduced phosphovanadomolybdates by molecular oxygen: theory and experiment in concert." Physical Chemistry Chemical Physics 20, no. 11 (2018): 7579–87. http://dx.doi.org/10.1039/c7cp08610e.

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33

Ohori, T., S. Nakamura, and K. Shimizu. "Semiempirical molecular orbital study of the reaction mechanism of RNase." Seibutsu Butsuri 41, supplement (2001): S105. http://dx.doi.org/10.2142/biophys.41.s105_3.

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34

Watanabe, Yoshihito, Takafumi Ueno, Shunichi Fukuzumi, and Shigeru Kato. "Molecular mechanism of the catalase reaction studied by myoglobin mutants." Journal of Inorganic Biochemistry 96, no. 1 (2003): 51. http://dx.doi.org/10.1016/s0162-0134(03)80491-9.

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35

MURAKI, Norifumi. "Molecular Mechanism of Heme Transport and Uptake Reaction in Corynebacteria." Nihon Kessho Gakkaishi 62, no. 2 (2020): 78–79. http://dx.doi.org/10.5940/jcrsj.62.78.

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36

Gnaim, Samer, and Doron Shabat. "Chemiluminescence molecular probe with a linear chain reaction amplification mechanism." Organic & Biomolecular Chemistry 17, no. 6 (2019): 1389–94. http://dx.doi.org/10.1039/c8ob03042a.

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37

Hamada, Yojiro, Yusuke Kanematsu, and Masanori Tachikawa. "Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism." Biochemistry 55, no. 40 (2016): 5764–71. http://dx.doi.org/10.1021/acs.biochem.6b00267.

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38

Bacaloglu, Radu, and Michael H. Fisch. "Reaction mechanism of poly(vinyl chloride) degradation. Molecular orbital calculations." Journal of Vinyl and Additive Technology 1, no. 4 (1995): 241–49. http://dx.doi.org/10.1002/vnl.730010410.

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Yuan, Wentao, Beien Zhu, Xiao-Yan Li, et al. "Visualizing H2O molecules reacting at TiO2 active sites with transmission electron microscopy." Science 367, no. 6476 (2020): 428–30. http://dx.doi.org/10.1126/science.aay2474.

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Imaging a reaction taking place at the molecular level could provide direct information for understanding the catalytic reaction mechanism. We used in situ environmental transmission electron microscopy and a nanocrystalline anatase titanium dioxide (001) surface with (1 × 4) reconstruction as a catalyst, which provided highly ordered four-coordinated titanium “active rows” to realize real-time monitoring of water molecules dissociating and reacting on the catalyst surface. The twin-protrusion configuration of adsorbed water was observed. During the water–gas shift reaction, dynamic changes in

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Wallin, Göran, and Johan Åqvist. "The transition state for peptide bond formation reveals the ribosome as a water trap." Proceedings of the National Academy of Sciences 107, no. 5 (2010): 1888–93. http://dx.doi.org/10.1073/pnas.0914192107.

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Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculat

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41

Cannistraro, Vincent J., and David Kennell. "The Processive Reaction Mechanism of Ribonuclease II." Journal of Molecular Biology 243, no. 5 (1994): 930–43. http://dx.doi.org/10.1006/jmbi.1994.1693.

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42

Shute, Janis K., Raymond Baker, David C. Billington, and David Gani. "Mechanism of the myo-inositol phosphatase reaction." Journal of the Chemical Society, Chemical Communications, no. 6 (1988): 422. http://dx.doi.org/10.1039/c39880000422.

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Shute, Janis K., Raymond Baker, David C. Billington, and David Gani. "Mechanism of the myo-inositol phosphatase reaction." Journal of the Chemical Society, Chemical Communications, no. 9 (1988): 626. http://dx.doi.org/10.1039/c39880000626.

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O'Boyle, Noel M., Gemma L. Holliday, Daniel E. Almonacid, and John B. O. Mitchell. "Using Reaction Mechanism to Measure Enzyme Similarity." Journal of Molecular Biology 368, no. 5 (2007): 1484–99. http://dx.doi.org/10.1016/j.jmb.2007.02.065.

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Bresien, Jonas, Thomas Kröger-Badge, Stefan Lochbrunner, et al. "A chemical reaction controlled by light-activated molecular switches based on hetero-cyclopentanediyls." Chemical Science 10, no. 12 (2019): 3486–93. http://dx.doi.org/10.1039/c8sc04893b.

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46

Caplow, M., and J. Shanks. "Mechanism of the microtubule GTPase reaction." Journal of Biological Chemistry 265, no. 15 (1990): 8935–41. http://dx.doi.org/10.1016/s0021-9258(19)38978-1.

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47

Mizuguchi, Hiroyuki, Paul F. Cook, Chia-Hui Tai, Charles A. Hasemann, and Kosaku Uyeda. "Reaction Mechanism of Fructose-2,6-bisphosphatase." Journal of Biological Chemistry 274, no. 4 (1999): 2166–75. http://dx.doi.org/10.1074/jbc.274.4.2166.

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48

Zhao, Xiaodong, Jianquan Liu, David S. Hsu, Shaying Zhao, John-Stephen Taylor, and Aziz Sancar. "Reaction Mechanism of (6-4) Photolyase." Journal of Biological Chemistry 272, no. 51 (1997): 32580–90. http://dx.doi.org/10.1074/jbc.272.51.32580.

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49

Watanabe, Kenji, Takashi Mie, Akitami Ichihara, Hideaki Oikawa, and Mamoru Honma. "Detailed Reaction Mechanism of Macrophomate Synthase." Journal of Biological Chemistry 275, no. 49 (2000): 38393–401. http://dx.doi.org/10.1074/jbc.m003119200.

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Du, Songjian, Tingting Li, Xinwei Wang, et al. "Molecular simulation on mechanism of thiophene hydrodesulfurization on surface of Ni2P." Energy Exploration & Exploitation 39, no. 3 (2021): 975–92. http://dx.doi.org/10.1177/0144598721994950.

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Abstract:

Hydrodesulfurization reaction, as the last step of hydrothermal cracking reaction, is of great significance for the reduction of viscosity and desulfurization of heavy oil. Based on Density Functional Theory and using Dmol3 module of Materials Studio, this research simulated the adsorption and hydrodesulfurization of thiophene on Ni2P (001) surface, and discussed the hydrodesulfurization reaction mechanism of thiophene on Ni2P (001) surface. It was found that the direct hydrodesulfurization of thiophene had more advantages than the indirect hydrodesulfurization of thiophene. Finally, the optim

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