Journal articles: 'Catalytic reaction dynamics'

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Sun, Juan-Juan, Qi-Yuan Fan, Xin Jin, Jing-Li Liu, Tong-Tong Liu, Bin Ren, and Jun Cheng. "Size-dependent phase transitions boost catalytic activity of sub-nanometer gold clusters." Journal of Chemical Physics 156, no. 14 (April 14, 2022): 144304. http://dx.doi.org/10.1063/5.0084165.

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The characterization and identification of the dynamics of cluster catalysis are crucial to unraveling the origin of catalytic activity. However, the dynamical catalytic effects during the reaction process remain unclear. Herein, we investigate the dynamic coupling effect of elementary reactions with the structural fluctuations of sub-nanometer Au clusters with different sizes using ab initio molecular dynamics and the free energy calculation method. It was found that the adsorption-induced solid-to-liquid phase transitions of the cluster catalysts give rise to abnormal entropy increase, facilitating the proceeding of reaction, and this phase transition catalysis exists in a range of clusters with different sizes. Moreover, clusters with different sizes show different transition temperatures, resulting in a non-trivial size effect. These results unveil the dynamic effect of catalysts and help understand cluster catalysis to design better catalysts rationally.

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SA, Hosseini. "CFD Simulation of Catalytic Cracking of n-Heptane in a Fixed Bed Reactor." Petroleum & Petrochemical Engineering Journal 4, no. 2 (2020): 1–8. http://dx.doi.org/10.23880/ppej-16000220.

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This work aims to three-dimension computational fluid dynamics (CFD) simulation of n-heptane catalytic cracking in fixed bed reactor (L=0.80 m) and to promote the cracking model of n-heptane using CFD. The catalyst granules were located in middle section of the reactor. The reaction scheme of n-heptane catalytic cracking was involved one primary reaction and 24 secondary reactions. Catalytic cracking process with a model of 25 molecular reactions was simulated by Fluent 6.0 software. The ratio of tube-to-particle diameter was considered N=2. The contours of coke deposition rate, vorticity, velocity and coke precursors and their relations along the reactor were predicted and discussed.

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Dasgupta, Medhanjali, Dominik Budday, Saulo H. P. de Oliveira, Peter Madzelan, Darya Marchany-Rivera, Javier Seravalli, Brandon Hayes, et al. "Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis." Proceedings of the National Academy of Sciences 116, no. 51 (December 4, 2019): 25634–40. http://dx.doi.org/10.1073/pnas.1901864116.

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How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.

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Hazra, Jagadish P., Nisha Arora, Amin Sagar, Shwetha Srinivasan, Abhishek Chaudhuri, and Sabyasachi Rakshit. "Force-activated catalytic pathway accelerates bacterial adhesion against flow." Biochemical Journal 475, no. 16 (August 29, 2018): 2611–20. http://dx.doi.org/10.1042/bcj20180358.

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Mechanical cues often influence the factors affecting the transition states of catalytic reactions and alter the activation pathway. However, tracking the real-time dynamics of such activation pathways is limited. Using single-molecule trapping of reaction intermediates, we developed a method that enabled us to perform one reaction at one site and simultaneously study the real-time dynamics of the catalytic pathway. Using this, we showed single-molecule calligraphy at nanometer resolution and deciphered the mechanism of the sortase A enzymatic reaction that, counter-intuitively, accelerates bacterial adhesion under shear tension. Our method captured a force-induced dissociation of the enzyme–substrate bond that accelerates the forward reaction 100×, proposing a new mechano-activated catalytic pathway. In corroboration, our molecular dynamics simulations in the presence of force identified a force-induced conformational switch in the enzyme that accelerates proton transfer between CYS184 (acceptor) and HIS120 (donor) catalytic dyads by reducing the inter-residue distances. Overall, the present study opens up the possibility of studying the influence of factors affecting transition states in real time and paves the way for the rational design of enzymes with enhanced efficiency.

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Kristoffersen, Henrik H., Tejs Vegge, and Heine Anton Hansen. "OH formation and H2 adsorption at the liquid water–Pt(111) interface." Chemical Science 9, no. 34 (2018): 6912–21. http://dx.doi.org/10.1039/c8sc02495b.

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The liquid water–Pt(111) interface is studied with constant temperature ab initio molecular dynamics to explore the importance of liquid water dynamics on catalytic reactions such as the oxygen reduction reaction in PEM fuel cells.

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He, Yang, Jin-Cheng Liu, Langli Luo, Yang-Gang Wang, Junfa Zhu, Yingge Du, Jun Li, Scott X. Mao, and Chongmin Wang. "Size-dependent dynamic structures of supported gold nanoparticles in CO oxidation reaction condition." Proceedings of the National Academy of Sciences 115, no. 30 (July 9, 2018): 7700–7705. http://dx.doi.org/10.1073/pnas.1800262115.

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Gold (Au) catalysts exhibit a significant size effect, but its origin has been puzzling for a long time. It is generally believed that supported Au clusters are more or less rigid in working condition, which inevitably leads to the general speculation that the active sites are immobile. Here, by using atomic resolution in situ environmental transmission electron microscopy, we report size-dependent structure dynamics of single Au nanoparticles on ceria (CeO2) in CO oxidation reaction condition at room temperature. While large Au nanoparticles remain rigid in the catalytic working condition, ultrasmall Au clusters lose their intrinsic structures and become disordered, featuring vigorous structural rearrangements and formation of dynamic low-coordinated atoms on surface. Ab initio molecular-dynamics simulations reveal that the interaction between ultrasmall Au cluster and CO molecules leads to the dynamic structural responses, demonstrating that the shape of the catalytic particle under the working condition may totally differ from the shape under the static condition. The present observation provides insight on the origin of superior catalytic properties of ultrasmall gold clusters.

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WILLIAMS, G. S. BLAIR, AFTAB M. HOSSAIN, SHIYING SHANG, DAVID E. KRANBUEHL, and CAREY K. BAGDASSARIAN. "EVOLUTION OF A CATALYTICALLY EFFECTIVE MODEL ENZYME: THE IMPORTANCE OF TUNED CONFORMATIONAL FLUCTUATIONS." Journal of Theoretical and Computational Chemistry 02, no. 03 (September 2003): 323–34. http://dx.doi.org/10.1142/s0219633603000586.

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Possible causal connections between the dynamics of a thermally fluctuating model enzyme molecule and catalysis are explored. The model is motivated by observations from experiment and simulation that amino acid residues residing in different enzymatic domains may show markedly different degrees of conformational freedom. Consequently, we are interested in the catalytic efficacy of an enzyme as a function of long-range many-atom cooperative effects resulting from strong, moderate, and weak interactions between enzymatic residues. Here we show and quantify through molecular dynamics simulations how the number and distribution of these interactions affects an enzyme's conformational fluctuation dynamics and its effectiveness as a catalyst. For any given distribution of "stiff" and "loose" enzymatic domains, catalytic fitness is defined as the number of chemical events — specifically the number of times a catalytic residue and substrate surmount a chemical reaction barrier — during molecular dynamics simulation. Through mutation, recombination, and a selection procedure following the ideas of Darwinian evolution, a genetic algorithm drives a population of enzyme molecules to greater catalytic fitness by modifying the mix of stiff and loose interactions. Approximately 30,000 different enzyme molecules are generated by the genetic algorithm — each with a unique number and distribution of strong, moderate, and weak inter-residue interactions. While the catalytically least fit enzyme exhibits 16 chemical events, the fittest boasts 253. That point mutations far from the active-site chemistry in the fittest enzyme have a strong effect on the number of chemical events suggests that catalysis depends, in part, on long-range many-atom globally correlated dynamical fluctuations.

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Fan, Rong, Parsa Habibi, Johan T. Padding, and Remco Hartkamp. "Coupling mesoscale transport to catalytic surface reactions in a hybrid model." Journal of Chemical Physics 156, no. 8 (February 28, 2022): 084105. http://dx.doi.org/10.1063/5.0081829.

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In heterogeneous catalysis, reactivity and selectivity are not only influenced by chemical processes occurring on catalytic surfaces but also by physical transport phenomena in the bulk fluid and fluid near the reactive surfaces. Because these processes take place at a large range of time and length scales, it is a challenge to model catalytic reactors, especially when dealing with complex surface reactions that cannot be reduced to simple mean-field boundary conditions. As a particle-based mesoscale method, Stochastic Rotation Dynamics (SRD) is well suited for studying problems that include both microscale effects on surfaces and transport phenomena in fluids. In this work, we demonstrate how to simulate heterogeneous catalytic reactors by coupling an SRD fluid with a catalytic surface on which complex surface reactions are explicitly modeled. We provide a theoretical background for modeling different stages of heterogeneous surface reactions. After validating the simulation method for surface reactions with mean-field assumptions, we apply the method to non-mean-field reactions in which surface species interact with each other through a Monte Carlo scheme, leading to island formation on the catalytic surface. We show the potential of the method by simulating a more complex three-step reaction mechanism with reactant dissociation.

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Park, Jae-Hyun, Ji-Hye Yun, Yingchen Shi, Jeongmin Han, Xuanxuan Li, Zeyu Jin, Taehee Kim, et al. "Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers." International Journal of Molecular Sciences 20, no. 8 (April 20, 2019): 1943. http://dx.doi.org/10.3390/ijms20081943.

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HIV-1 integrase (HIV-1 IN) is an enzyme produced by the HIV-1 virus that integrates genetic material of the virus into the DNA of infected human cells. HIV-1 IN acts as a key component of the Retroviral Pre-Integration Complex (PIC). Protein dynamics could play an important role during the catalysis of HIV-1 IN; however, this process has not yet been fully elucidated. X-ray free electron laser (XFEL) together with nuclear magnetic resonance (NMR) could provide information regarding the dynamics during this catalysis reaction. Here, we report the non-cryogenic crystal structure of HIV-1 IN catalytic core domain at 2.5 Å using microcrystals in XFELs. Compared to the cryogenic structure at 2.1 Å using conventional synchrotron crystallography, there was a good agreement between the two structures, except for a catalytic triad formed by Asp64, Asp116, and Glu152 (DDE) and the lens epithelium-derived growth factor binding sites. The helix III region of the 140–153 residues near the active site and the DDE triad show a higher dynamic profile in the non-cryogenic structure, which is comparable to dynamics data obtained from NMR spectroscopy in solution state.

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10

Sekizawa, O., T. Uruga, Y. Takagi, K. Nitta, K. Kato, H. Tanida, K. Uesugi, et al. "SPring-8 BL36XU: Catalytic Reaction Dynamics for Fuel Cells." Journal of Physics: Conference Series 712 (May 2016): 012142. http://dx.doi.org/10.1088/1742-6596/712/1/012142.

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11

Echeverria, Carlos, and Raymond Kapral. "Autocatalytic reaction dynamics in systems crowded by catalytic obstacles." Physica D: Nonlinear Phenomena 239, no. 11 (June 2010): 791–96. http://dx.doi.org/10.1016/j.physd.2009.06.005.

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12

Min, Wei, X. Sunney Xie, and Biman Bagchi. "Two-Dimensional Reaction Free Energy Surfaces of Catalytic Reaction: Effects of Protein Conformational Dynamics on Enzyme Catalysis†." Journal of Physical Chemistry B 112, no. 2 (January 2008): 454–66. http://dx.doi.org/10.1021/jp076533c.

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13

Pineda, Miguel, and Michail Stamatakis. "Non-Equilibrium Thermodynamics and Stochastic Dynamics of a Bistable Catalytic Surface Reaction." Entropy 20, no. 11 (October 23, 2018): 811. http://dx.doi.org/10.3390/e20110811.

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Catalytic surface reaction networks exhibit nonlinear dissipative phenomena, such as bistability. Macroscopic rate law descriptions predict that the reaction system resides on one of the two steady-state branches of the bistable region for an indefinite period of time. However, the smaller the catalytic surface, the greater the influence of coverage fluctuations, given that their amplitude normally scales as the square root of the system size. Thus, one can observe fluctuation-induced transitions between the steady-states. In this work, a model for the bistable catalytic CO oxidation on small surfaces is studied. After a brief introduction of the average stochastic modelling framework and its corresponding deterministic limit, we discuss the non-equilibrium conditions necessary for bistability. The entropy production rate, an important thermodynamic quantity measuring dissipation in a system, is compared across the two approaches. We conclude that, in our catalytic model, the most favorable non-equilibrium steady state is not necessary the state with the maximum or minimum entropy production rate.

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Gregory, Mark T., Yang Gao, Qiang Cui, and Wei Yang. "Multiple deprotonation paths of the nucleophile 3′-OH in the DNA synthesis reaction." Proceedings of the National Academy of Sciences 118, no. 23 (June 4, 2021): e2103990118. http://dx.doi.org/10.1073/pnas.2103990118.

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DNA synthesis by polymerases is essential for life. Deprotonation of the nucleophile 3′-OH is thought to be the obligatory first step in the DNA synthesis reaction. We have examined each entity surrounding the nucleophile 3′-OH in the reaction catalyzed by human DNA polymerase (Pol) η and delineated the deprotonation process by combining mutagenesis with steady-state kinetics, high-resolution structures of in crystallo reactions, and molecular dynamics simulations. The conserved S113 residue, which forms a hydrogen bond with the primer 3′-OH in the ground state, stabilizes the primer end in the active site. Mutation of S113 to alanine destabilizes primer binding and reduces the catalytic efficiency. Displacement of a water molecule that is hydrogen bonded to the 3′-OH using the 2′-OH of a ribonucleotide or 2′-F has little effect on catalysis. Moreover, combining the S113A mutation with 2′-F replacement, which removes two potential hydrogen acceptors of the 3′-OH, does not reduce the catalytic efficiency. We conclude that the proton can leave the O3′ via alternative paths, supporting the hypothesis that binding of the third Mg2+ initiates the reaction by breaking the α–β phosphodiester bond of an incoming deoxyribonucleoside triphosphate (dNTP).

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Bukhavtsova, N. M., and N. M. Ostrovskii. "Catalytic reaction accompanied by capillary condensation, 3. Influence on reaction kinetics and dynamics." Reaction Kinetics and Catalysis Letters 65, no. 2 (November 1998): 321–29. http://dx.doi.org/10.1007/bf02475271.

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Filandr, Frantisek, Daniel Kavan, Daniel Kracher, Christophe V. F. P. Laurent, Roland Ludwig, Petr Man, and Petr Halada. "Structural Dynamics of Lytic Polysaccharide Monooxygenase during Catalysis." Biomolecules 10, no. 2 (February 5, 2020): 242. http://dx.doi.org/10.3390/biom10020242.

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Lytic polysaccharide monooxygenases (LPMOs) are industrially important oxidoreductases employed in lignocellulose saccharification. Using advanced time-resolved mass spectrometric techniques, we elucidated the structural determinants for substrate-mediated stabilization of the fungal LPMO9C from Neurospora crassa during catalysis. LPMOs require a reduction in the active-site copper for catalytic activity. We show that copper reduction in NcLPMO9C leads to structural rearrangements and compaction around the active site. However, longer exposure to the reducing agent ascorbic acid also initiated an uncoupling reaction of the bound oxygen species, leading to oxidative damage, partial unfolding, and even fragmentation of NcLPMO9C. Interestingly, no changes in the hydrogen/deuterium exchange rate were detected upon incubation of oxidized or reduced LPMO with crystalline cellulose, indicating that the LPMO-substrate interactions are mainly side-chain mediated and neither affect intraprotein hydrogen bonding nor induce significant shielding of the protein surface. On the other hand, we observed a protective effect of the substrate, which slowed down the autooxidative damage induced by the uncoupling reaction. These observations further complement the picture of structural changes during LPMO catalysis.

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Xu, Weilin, Jason S. Kong, Yun-Ting E. Yeh, and Peng Chen. "Single-molecule nanocatalysis reveals heterogeneous reaction pathways and catalytic dynamics." Nature Materials 7, no. 12 (November 9, 2008): 992–96. http://dx.doi.org/10.1038/nmat2319.

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Xin, Xin, Chen Li, Delu Gao, and Dunyou Wang. "Catalytic Descriptors to Investigate Catalytic Power in the Reaction of Haloalkane Dehalogenase Enzyme with 1,2-Dichloroethane." International Journal of Molecular Sciences 22, no. 11 (May 29, 2021): 5854. http://dx.doi.org/10.3390/ijms22115854.

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Enzymes play a fundamental role in many biological processes. We present a theoretical approach to investigate the catalytic power of the haloalkane dehalogenase reaction with 1,2-dichloroethane. By removing the three main active-site residues one by one from haloalkane dehalogenase, we found two reactive descriptors: one descriptor is the distance difference between the breaking bond and the forming bond, and the other is the charge difference between the transition state and the reactant complex. Both descriptors scale linearly with the reactive barriers, with the three-residue case having the smallest barrier and the zero-residue case having the largest. The results demonstrate that, as the number of residues increases, the catalytic power increases. The predicted free energy barriers using the two descriptors of this reaction in water are 23.1 and 24.2 kcal/mol, both larger than the ones with any residues, indicating that the water solvent hinders the reactivity. Both predicted barrier heights agree well with the calculated one at 25.2 kcal/mol using a quantum mechanics and molecular dynamics approach, and also agree well with the experimental result at 26.0 kcal/mol. This study shows that reactive descriptors can also be used to describe and predict the catalytic performance for enzyme catalysis.

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Ma, Huan, Klaudia Szeler, Shina C. L. Kamerlin, and Mikael Widersten. "Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA)." Chemical Science 7, no. 2 (2016): 1415–21. http://dx.doi.org/10.1039/c5sc03666f.

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Qi, Xin, and Tianbing Xia. "Structure, dynamics, and mechanism of the lead-dependent ribozyme." BioMolecular Concepts 2, no. 4 (August 1, 2011): 305–14. http://dx.doi.org/10.1515/bmc.2011.029.

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AbstractLeadzyme is a small catalytic RNA that was identified by in vitro selection for Pb2+-dependent cleavage from a tRNA library. Leadzyme employs a unique two-step Pb2+-specific mechanism to cleave within its active site. NMR and crystal structures of the active site revealed different folding patterns, but neither features the in-line alignment for attack by the 2′-OH nucleophilic group. These experimentally determined structures most likely represent ground states and are catalytically inactive. There are significant dynamics of the active site and the motif samples multiple conformations at the ground states. Various metal ion binding sites have been identified, including one that may be occupied by a catalytic Pb2+. Based on functional group analysis, a computational model of the transition state has been proposed. This model features a unique base triple that is consistent with sequence and functional group requirements for catalysis. This structure is likely only populated transiently, but imposing appropriate conformational constraints may significantly stabilize this state thereby promoting catalysis. Other ions may inhibit the cleavage by competing for the Pb2+ binding site, or by stabilizing the ground state thereby suppressing its transition to the catalytically active conformation. Some rare earth ions can enhance the reaction via an unknown mechanism. Because of its unique chemistry and dynamic behavior, leadzyme can continue to serve as an excellent model system for teaching us RNA biology and chemistry.

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Hanel, Rudolf, Manfred Pöchacker, and Stefan Thurner. "Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 368, no. 1933 (December 28, 2010): 5583–96. http://dx.doi.org/10.1098/rsta.2010.0267.

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Linearized catalytic reaction equations (modelling, for example, the dynamics of genetic regulatory networks), under the constraint that expression levels, i.e. molecular concentrations of nucleic material, are positive, exhibit non-trivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems, an inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity, which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems , their basic properties allow us to understand the fundamental dynamical properties of complex biological reaction networks. We analyse the Lyapunov spectrum, determine the probability of finding stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network , and study how the frequency distributions of oscillatory modes of such a system depend on the average connectivity.

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Stefanov, Plamen K., Yuichi Ohno, Toshiro Yamanaka, Yoshiyuki Seimiya, Kazushi Kimura, and Tatsuo Matsushima. "Reaction dynamics of catalytic CO oxidation on a Pt(113) surface." Surface Science 416, no. 1-2 (October 1998): 305–19. http://dx.doi.org/10.1016/s0039-6028(98)00616-5.

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23

Bao, Zhi Yong, Dang Yuan Lei, Ruibin Jiang, Xin Liu, Jiyan Dai, Jianfang Wang, Helen L. W. Chan, and Yuen Hong Tsang. "Bifunctional Au@Pt core–shell nanostructures for in situ monitoring of catalytic reactions by surface-enhanced Raman scattering spectroscopy." Nanoscale 6, no. 15 (2014): 9063–70. http://dx.doi.org/10.1039/c4nr00770k.

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Mehrabi, Pedram, Eike C. Schulz, Raison Dsouza, Henrike M. Müller-Werkmeister, Friedjof Tellkamp, R. J. Dwayne Miller, and Emil F. Pai. "Time-resolved crystallography reveals allosteric communication aligned with molecular breathing." Science 365, no. 6458 (September 12, 2019): 1167–70. http://dx.doi.org/10.1126/science.aaw9904.

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A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework’s dynamics and entropy constitute crucial components of the catalytic machinery.

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de Ruiter, Jessica M., and Francesco Buda. "Introducing a closed system approach for the investigation of chemical steps involving proton and electron transfer; as illustrated by a copper-based water oxidation catalyst." Physical Chemistry Chemical Physics 19, no. 6 (2017): 4208–15. http://dx.doi.org/10.1039/c6cp07454e.

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KING, DAVID A. "NONLINEAR EFFECTS IN ADSORPTION AND REACTION DYNAMICS AT SURFACES: KINETIC OSCILLATIONS UNDER SCRUTINY." Surface Review and Letters 01, no. 04 (December 1994): 435–42. http://dx.doi.org/10.1142/s0218625x94000400.

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A number of catalytic reactions exhibit complex dynamical behavior, including kinetic oscillations with both temporal and spatial characteristics. Attention has been focused on the CO+ NO and CO+O2 reactions on Pt{100}. Recent molecular beam studies conducted at Cambridge on the interaction of CO with Pt{100} have provided the basis for a new mechanism for oscillatory behavior. The rate of growth of (1×1) islands on the quasihexagonal reconstructed phase of Pt{100} is strongly nonlinear with respect to the local CO coverage on the hex-R phase at temperatures between 380 and 410 K, with a reaction order of 4. This strong nonlinearity results in a flux-dependent sticking probability for CO at this temperature, and detailed modeling also reproduces the major features in the oscillatory behavior observed for the CO+NO reaction. An important effect of the nonlinearity in both the CO+NO and CO+O2 oscillatory behavior at high temperatures is the maintenance of in-phase behavior across the surface during oscillations.

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Soumelidis, M. I., R. K. Stobart, and R. A. Jackson. "A chemically informed, control-oriented model of a three-way catalytic converter." Proceedings of the Institution of Mechanical Engineers, Part D: Journal of Automobile Engineering 221, no. 9 (September 1, 2007): 1169–82. http://dx.doi.org/10.1243/09544070jauto259.

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Chemical activity inside a three-way catalytic converter (TWC) is highly complex and usually is not taken into account when developing TWC control-oriented models. Such models still remain to a large extent empirical and do not perform satisfactorily under a wider range of operating conditions. This work demonstrates how a very simple model, based on the basic chemical processes that take place inside the catalytic converter, can successfully capture a large part of the strongly non-linear TWC dynamic behaviour. The proposed model is based on the reactions of ceria oxidation and carbon monoxide oxidation, which appear to dominate the fast dynamics of oxygen storage and release respectively. In addition, the water-gas shift reaction is incorporated into the model, which is responsible for the slower dynamic response of the catalyst under rich operating conditions. With some mild assumptions, a discrete-time version of the model was implemented in MATLAB. The model is sufficiently simple in structure for in-vehicle use and can be used for control and on-board diagnostic purposes.

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Parfenova, Lyudmila V., Pavel V. Kovyazin, Olesia V. Mukhamadeeva, Pavel V. Ivchenko, Ilya E. Nifant'ev, Leonard M. Khalilov, and Usein M. Dzhemilev. "Zirconocene dichlorides as catalysts in alkene carbo- and cyclometalation by AlEt₃: intermediate structures and dynamics." Dalton Transactions 50, no. 43 (2021): 15802–20. http://dx.doi.org/10.1039/d1dt03160k.

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Catalytic activity and chemoselectivity of zirconocenes in the reaction of alkenes with AlEt3 were evaluated. NMR study of the reaction between L2ZrCl2 and AlEt3 showed the formation of various bimetallic intermediates.

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Rosero Chicaíza, David Camilo, and Bibian A. Hoyos. "Reaction kinetic parameters for a distributed model of transport and reaction in Pd/Rh/CeZrO three-way catalytic converters." DYNA 86, no. 210 (July 1, 2019): 216–23. http://dx.doi.org/10.15446/dyna.v86n210.78596.

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This paper presents a two-dimensional distributed model for the transport and reaction of combustion gases in channels of three-way catalytic converters, considering a detailed reaction kinetics with 16 chemical reactions in palladium and rhodium catalysts, and taking into account diffusive effects within the coating, to obtain a new set of reaction kinetic parameters that do not depend on the thickness of the coating. The model was solved using a finite volume method with a first order upwind scheme and simulations were conducted using computational fluid dynamics. The model with the new distributed reaction kinetic parameters, produced an excellent agreement with the experimental data of concentration at the end of the channels. Also, the model reproduced the most important concentration changes for the gas components in the specified temperature range and allowed simulations with excess oxygen and different thicknesses.

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Piccini, GiovanniMaria, Mal-Soon Lee, Simuck F. Yuk, Difan Zhang, Greg Collinge, Loukas Kollias, Manh-Thuong Nguyen, Vassiliki-Alexandra Glezakou, and Roger Rousseau. "Ab initio molecular dynamics with enhanced sampling in heterogeneous catalysis." Catalysis Science & Technology 12, no. 1 (2022): 12–37. http://dx.doi.org/10.1039/d1cy01329g.

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Enhanced sampling ab initio simulations enable to study chemical phenomena in catalytic systems including thermal effects & anharmonicity, & collective dynamics describing enthalpic & entropic contributions, which can significantly impact on reaction free energy landscapes.

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Rossi, Kevin, Tzonka Mineva, Jean-Sebastien Filhol, Frederik Tielens, and Hazar Guesmi. "Realistic Modelling of Dynamics at Nanostructured Interfaces Relevant to Heterogeneous Catalysis." Catalysts 12, no. 1 (January 4, 2022): 52. http://dx.doi.org/10.3390/catal12010052.

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The focus of this short review is directed towards investigations of the dynamics of nanostructured metallic heterogeneous catalysts and the evolution of interfaces during reaction—namely, the metal–gas, metal–liquid, and metal–support interfaces. Indeed, it is of considerable interest to know how a metal catalyst surface responds to gas or liquid adsorption under reaction conditions, and how its structure and catalytic properties evolve as a function of its interaction with the support. This short review aims to offer the reader a birds-eye view of state-of-the-art methods that enable more realistic simulation of dynamical phenomena at nanostructured interfaces by exploiting resource-efficient methods and/or the development of computational hardware and software.

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Al-Najjar, Belal O. "Investigation of 15-hydroxyprostaglandin dehydrogenase catalytic reaction mechanism by molecular dynamics simulations." Journal of Molecular Graphics and Modelling 80 (March 2018): 190–96. http://dx.doi.org/10.1016/j.jmgm.2018.01.012.

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Liu, Ye, Youzhong Wan, Jingxuan Zhu, Muxin Li, Zhengfei Yu, Jiarui Han, Zuoming Zhang, and Weiwei Han. "Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations." International Journal of Molecular Sciences 20, no. 5 (March 8, 2019): 1188. http://dx.doi.org/10.3390/ijms20051188.

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The aminotransferase from Bacillus circulans (BtrR), which is involved in the biosynthesis of butirosin, catalyzes the pyridoxal phosphate (PLP)-dependent transamination reaction to convert valienone to β-valienamine (a new β-glycosidase inhibitor for the treatment of lysosomal storage diseases) with an optical purity enantiomeric excess value. To explore the stereoselective mechanism of valienamine generated by BtrR, multiple molecular dynamics (MD) simulations were performed for the BtrR/PLP/valienamine and BtrR/PLP/β-valienamine complexes. The theoretical results showed that β-valienamine could make BtrR more stable and dense than valienamine. β-valienamine could increase the hydrogen bond probability and decrease the binding free energy between coenzyme PLP and BtrR by regulating the protein structure of BtrR, which was conducive to the catalytic reaction. β-valienamine maintained the formation of cation-p interactions between basic and aromatic amino acids in BtrR, thus enhancing its stability and catalytic activity. In addition, CAVER 3.0 analysis revealed that β-valienamine could make the tunnel of BtrR wider and straight, which was propitious to the removal of products from BtrR. Steered MD simulation results showed that valienamine interacted with more residues in the tunnel during dissociation compared with β-valienamine, resulting in the need for a stronger force to be acquired from BtrR. Taken together, BtrR was more inclined to catalyze the substrates to form β-valienamine, either from the point of view of the catalytic reaction or product removal.

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Sarkar, Debarati, Snigdha Thakur, Yu-Guo Tao, and Raymond Kapral. "Ring closure dynamics for a chemically active polymer." Soft Matter 10, no. 47 (2014): 9577–84. http://dx.doi.org/10.1039/c4sm01941e.

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Our studies on ring closure of polymer showed how the long-range nature of the chemical concentration gradients, self-generated by the presence of a catalytic bead on which a chemical reaction occurs, could cause a distant bead to chemotactically move towards to the source of the gradient. Such chemically-active polymers hence undergo ring closure or loop formation more rapidly than inactive polymer chains.

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Boyes, Edward D., Alec P. LaGrow, Michael R. Ward, Thomas E. Martin, and Pratibha L. Gai. "Visualizing single atom dynamics in heterogeneous catalysis using analytical in situ environmental scanning transmission electron microscopy." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 378, no. 2186 (October 26, 2020): 20190605. http://dx.doi.org/10.1098/rsta.2019.0605.

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Progress is reported in analytical in situ environmental scanning transmission electron microscopy (ESTEM) for visualizing and analysing in real-time dynamic gas–solid catalyst reactions at the single-atom level under controlled reaction conditions of gas environment and temperature. The recent development of the ESTEM advances the capability of the established ETEM with the detection of fundamental single atoms, and the associated atomic structure of selected solid-state heterogeneous catalysts, in catalytic reactions in their working state. The new data provide improved understanding of dynamic atomic processes and reaction mechanisms, in activity and deactivation, at the fundamental level; and in the chemistry underpinning important technological processes. The benefits of atomic resolution-E(S)TEM to science and technology include new knowledge leading to improved technological processes, reductions in energy requirements and better management of environmental waste. This article is part of a discussion meeting issue ‘Dynamic in situ microscopy relating structure and function’.

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Legrand, Baptiste, Julie Aguesseau-Kondrotas, Matthieu Simon, and Ludovic Maillard. "Catalytic Foldamers: When the Structure Guides the Function." Catalysts 10, no. 6 (June 22, 2020): 700. http://dx.doi.org/10.3390/catal10060700.

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Enzymes are predominantly proteins able to effectively and selectively catalyze highly complex biochemical reactions in mild reaction conditions. Nevertheless, they are limited to the arsenal of reactions that have emerged during natural evolution in compliance with their intrinsic nature, three-dimensional structures and dynamics. They optimally work in physiological conditions for a limited range of reactions, and thus exhibit a low tolerance for solvent and temperature conditions. The de novo design of synthetic highly stable enzymes able to catalyze a broad range of chemical reactions in variable conditions is a great challenge, which requires the development of programmable and finely tunable artificial tools. Interestingly, over the last two decades, chemists developed protein secondary structure mimics to achieve some desirable features of proteins, which are able to interfere with the biological processes. Such non-natural oligomers, so called foldamers, can adopt highly stable and predictable architectures and have extensively demonstrated their attractiveness for widespread applications in fields from biomedical to material science. Foldamer science was more recently considered to provide original solutions to the de novo design of artificial enzymes. This review covers recent developments related to peptidomimetic foldamers with catalytic properties and the principles that have guided their design.

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Smolin, Alexander V., Мikhail N. Mikhailov, Aleksey F. Gadzaov, and Leonid M. Kustov. "Dynamics of Oxidation of Reduced Forms of CO2 under Electrochemical and Open-Сircuit Conditions on Polycrystalline Pt in H2CO3." Metals 11, no. 2 (February 5, 2021): 274. http://dx.doi.org/10.3390/met11020274.

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The problem of identifying correlations between catalytic and electrocatalytic processes is one of the fundamental problems of catalysis among “simple” organic substances, and the oxidation of CO and rCO2 is of great interest, since CO and CO2 are considered in pairs both during catalytic and electrocatalytic transformations. In the case of electrocatalysis, this analysis is important in the study of fuel cells. In this paper, we studied the correlation between the oxidation of reduced forms of CO2 (rCO2) under potentiodynamic-galvanoctatic electrochemical and open-circuit conditions of measurements on polycrystalline (pc)Pt in H2CO3. Periodic oscillations are revealed at the oxidation of Had and rCO2 on (pc)Pt. Quantum chemical calculations were carried out on the Pt13 cluster in order to identify the mechanisms of the rCO2 oxidation reaction. The correspondence in the energy parameters of the oxidation process of rCO2 under open-circuit conditions and electrochemical conditions is shown. The preliminary analysis of the system using density functional (DFT) calculations is carried out and the most stable systems that are based on Pt13 are found, namely rOH-Pt13-(CO)n, rOH-Pt13-(COH) and rOH-Pt13-(rCOOH). OH• species was chosen as the most likely candidate for the role of the oxidant for rCO2. Preliminary calculations for the expected reactions were carried out, and the optimal PES is revealed.

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Lian, Tianquan. "(Invited) In Situ Time-Resolved Probe of Charge Carrier Dynamics at Planar Semiconductor Photoelectrode/Liquid Interface." ECS Meeting Abstracts MA2022-01, no. 36 (July 7, 2022): 1579. http://dx.doi.org/10.1149/ma2022-01361579mtgabs.

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Photoelectrochemistry is a promising approach for converting solar energy to storable chemical energy in chemical fuels. The efficiency of photoelectrochemcial devices depends critically on efficient transfer of charge carrier across the electrode liquid interface and the efficiency and selectivity of the catalytic reaction on electrode surface. Although transient absorption spectroscopy is a powerful tool for probing interfacial dynamics in high surface area electrodes, it is often not applicable on planar electrodes because the observed signal is often dominated by carrier dynamics in the bulk. In this talk, we discuss our recent effort in developing in situ time-resolved linear and nonlinear spectroscopic tools that can be used to probe carrier dynamics and reactions at planar electrode/liquid interfaces, focusing on transient reflection spectroscopy and electric field induced second harmonic generation (EFISH) spectroscopy. Compared to transient absorption, transient reflection spectroscopy is more sensitive to surface carrier density that can be more directly correlated to catalysis. We showed that transient reflectance change can be used to follow charge carrier dynamics and their amplitude can be directly correlated to efficiency of initial interfacial charge separation on p-GaP single crystals protected by TiO2 ALD layer. Our finding suggests that IPCE is determined by the product of the efficiency of initial ultrafast (< hundreds of ps) charge separation across the GaP/TiO2 interface and the efficiency of water reduction reaction on the slower time scale. Key loss pathways that limit these efficiencies are discussed. In a second approach, we showed the EFISH signal in a n-doped single crystal TiO2 can be used to probe the accumulation of photogenerated carriers at surface states and these trapped carriers are responsible for the water oxidation reaction.

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Soren, Bini Chhetri, Jagadish Babu Dasari, Alessio Ottaviani, Beatrice Messina, Giada Andreotti, Alice Romeo, Federico Iacovelli, Mattia Falconi, Alessandro Desideri, and Paola Fiorani. "In Vitro and In Silico Characterization of an Antimalarial Compound with Antitumor Activity Targeting Human DNA Topoisomerase IB." International Journal of Molecular Sciences 22, no. 14 (July 12, 2021): 7455. http://dx.doi.org/10.3390/ijms22147455.

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Human DNA topoisomerase IB controls the topological state of supercoiled DNA through a complex catalytic cycle that consists of cleavage and religation reactions, allowing the progression of fundamental DNA metabolism. The catalytic steps of human DNA topoisomerase IB were analyzed in the presence of a drug, obtained by the open-access drug bank Medicines for Malaria Venture. The experiments indicate that the compound strongly and irreversibly inhibits the cleavage step of the enzyme reaction and reduces the cell viability of three different cancer cell lines. Molecular docking and molecular dynamics simulations suggest that the drug binds to the human DNA topoisomerase IB-DNA complex sitting inside the catalytic site of the enzyme, providing a molecular explanation for the cleavage-inhibition effect. For all these reasons, the aforementioned drug could be a possible lead compound for the development of an efficient anti-tumor molecule targeting human DNA topoisomerase IB.

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Chen, Qiang, Mingming Mao, Min Gao, Yongqi Liu, Junrui Shi, and Jia Li. "Design and Performance Investigation of a Compact Catalytic Reactor Integrated with Heat Recuperator." Energies 15, no. 2 (January 9, 2022): 447. http://dx.doi.org/10.3390/en15020447.

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The catalytic combustion has the advantage of lower auto-ignition temperature and helps to expand the combustible limit of lean premixed gas. However, the intake needs to be preheated to certain temperature commonly through an independent heat exchanger. Similar to the principles of non-catalytic RTO combustion, this paper presents a similar approach whereby the combustion chamber is replaced by a catalytic combustion bed. A new catalytic reactor integrated with a heat recuperator is designed to enhance the heat recirculation effect. Using a two-dimensional computational fluid dynamics model, the performance of the reactor is studied. The reaction performances of the traditional and compact reactors are compared and analyzed. Under the same conditions, the compact reactor has better reaction performance and heat recirculation effect, which can effectively decrease the ignition temperature of feed gas. The influences of the inlet velocity, the inlet temperature, the methane concentration, and the thermal conductivity of porous media on the reaction performance of integrated catalytic reactor are studied. The results show that the inlet velocity, inlet temperature, methane concentration, and thermal conductivity of porous media materials have important effects on the reactor performance and heat recirculation effect, and the thermal conductivity of porous media materials has the most obvious influence. Moreover, the reaction performance of multiunit integrated catalytic reactor is studied. The results show that the regenerative effect of multiunit integrated catalytic reactor is further enhanced. This paper is of great significance to the recycling of low calorific value gas energy and relieving energy stress in the future.

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Sementa, Luca, Oliviero Andreussi, William A. Goddard III, and Alessandro Fortunelli. "Catalytic activity of Pt38 in the oxygen reduction reaction from first-principles simulations." Catalysis Science & Technology 6, no. 18 (2016): 6901–9. http://dx.doi.org/10.1039/c6cy00750c.

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Modliński, Norbert J., Włodzimierz K. Kordylewski, and Maciej P. Jakubiak. "Numerical Simulation of O3 and NO Reacting in a Tubular Flow Reactor." Chemical and Process Engineering 34, no. 3 (September 1, 2013): 361–73. http://dx.doi.org/10.2478/cpe-2013-0029.

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Abstract A process capable of NOx control by ozone injection gained wide attention as a possible alternative to proven post combustion technologies such as selective catalytic (and non-catalytic) reduction. The purpose of the work was to develop a numerical model of NO oxidation with O3 that would be capable of providing guidelines for process optimisation during different design stages. A Computational Fluid Dynamics code was used to simulate turbulent reacting flow. In order to reduce computation expense a 11-step global NO - O3 reaction mechanism was implemented into the code. Model performance was verified by the experiment in a tubular flow reactor for two injection nozzle configurations and for two O3/NO ratios of molar fluxe. The objective of this work was to estimate the applicability of a simplified homogeneous reaction mechanism in reactive turbulent flow simulation. Quantitative conformity was not completely satisfying for all examined cases, but the final effect of NO oxidation was predicted correctly at the reactor outlet.

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Cai, Zhan Jun, Wei Min Kang, and Ya Bin Li. "Study on Characteristics of Gas Flow in Catalytic Converter with Different Outlet Diameters." Applied Mechanics and Materials 711 (December 2014): 16–19. http://dx.doi.org/10.4028/www.scientific.net/amm.711.16.

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. This paper studies the different diameters of tube outlet how to affect the gas flow pressure and velocity distribution in nanofiber catalytic converter by CFD (Computational Fluid Dynamics) method. Geometric model of the catalytic converter has been established and meshed by the pre-processing tool of FLUENT. The distribution of velocity and pressure in the converter which outlet diameter is 70 mm is more evenly than the converter which outlet diameter is 50 mm. It is conducive to reducing airflow static pressure in the catalytic converter that expanding the outlet diameter in the case of other conditions remains unchanged. Therefore, the larger outlet diameter is beneficial to exhaust catalytic reaction.

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Harrison, Ian. "Photochemical Exploration of Reaction Dynamics at Catalytic Metal Surfaces: From Ballistics to Statistics." Accounts of Chemical Research 31, no. 10 (October 1998): 631–39. http://dx.doi.org/10.1021/ar9700926.

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Yahya, Noorhana, Poppy Puspitasari, and Nor Hasifah Noordin. "Ammonia Synthesis Using Magnetically Induced Reaction." Defect and Diffusion Forum 334-335 (February 2013): 329–36. http://dx.doi.org/10.4028/www.scientific.net/ddf.334-335.329.

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Ammonia production is a high energy and capital intensive industry as it requires high temperature (400500°C) and high pressure (150300 bar) for its daily operations. By introducing nanocatalyst with the new concept of micro-reactor with applied magnetic field induction, the catalytic activity can be induced and the output can be enhanced. Magneto-dynamics will be introduced in the ammonia production process in order to replace the concept of thermodynamics in the Haber Bosch process. The nanocatalysts (Y3Fe5O12, Fe2O3, MnO, Mn0.8Zn0.2Fe2O4) have been reduced by using the temperature reduction method (TPR). The Y3Fe5O12(YIG) catalyst with magnetic induction produced242.56µmol/h.g-cat output of ammonia which is 2% much higher than ammonia synthesis without magnetic induction (237.52 µmol/g.h).The ammonia output based on the magnetic induction method at a temperature of 0°C is 242.56µmole/h.g-cat which is 0.90% higher than the synthesis at 25°C temperature (240.4 µmol/g.h). The ammonia output at 0.2Tesla is 249.04 µmole/h.g-cat which is higher 2.6% than the output at 0.1Tesla which is 242.56µmol/g.h. It is proven that the higher the applied magnetic field is, the more effective the catalytic activity will be as a better alignment of the electron spin of the catalyst occurs and enhances the adsorption and desorption process. Y3Fe5O12(YIG) shows the best catalytic reaction followed by Fe2O3(hematite) and MnO (manganese oxide). By this new route, synthesis of ammonia at low temperature is realized and offers ammonia producers an economic advantage compared to the classical routes.

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Lisitsa, Albert E., Lev A. Sukovatyi, Sergey I. Bartsev, Anna A. Deeva, Valentina A. Kratasyuk, and Elena V. Nemtseva. "Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction." International Journal of Molecular Sciences 22, no. 16 (August 17, 2021): 8827. http://dx.doi.org/10.3390/ijms22168827.

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Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial bioluminescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. Moreover, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important αGlu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis.

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Bricout, Hervé, Estelle Léonard, Christophe Len, David Landy, Frédéric Hapiot, and Eric Monflier. "Impact of cyclodextrins on the behavior of amphiphilic ligands in aqueous organometallic catalysis." Beilstein Journal of Organic Chemistry 8 (September 6, 2012): 1479–84. http://dx.doi.org/10.3762/bjoc.8.167.

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In this study, we showed that the addition of randomly modified β-cyclodextrin (RAME-β-CD) in aqueous medium could have a beneficial impact on the catalytic performances of phosphane-based aggregates in the Pd-catalyzed cleavage of allyl carbonates (Tsuji–Trost reaction). The RAME-β-CD/phosphane supramolecular interactions helped explain the catalytic results. The presence of RAME-β-CD in the aqueous compartment improved the phosphane-based aggregate dynamics. The exchanges between the hydrophobic substrate-containing aggregate core and the catalyst-containing aqueous phase were then greatly favored, resulting in an increase in the catalytic performances.

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Silva, Elisabete R., J. M. Silva, Fernando A. Costa Oliveira, M. Fatima Vaz, and M. Filipa Ribeiro. "Cordierite Foam Supports Washcoated with Zeolite-Based Catalysts for Volatile Organic Compounds (VOCs) Combustion." Materials Science Forum 636-637 (January 2010): 104–10. http://dx.doi.org/10.4028/www.scientific.net/msf.636-637.104.

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Reticulated cordierite foams produced by a direct foaming method were successfully washcoated with platinum-based zeolite catalysts. For comparison purposes, commercial cordierite monoliths were also washcoated. The effect of the structural properties on the fluid dynamics and catalytic behaviour for the toluene combustion were evaluated. Foam supports revealed highest performances, in terms of conversion into CO2, when compared to conventional honeycomb monoliths. The experimental results suggest that the catalytic behaviour is critically dependent on the fluid dynamics provided by structural characteristics of the supports, such as porosity, density and size of pores. The randomness and tortuosity of foams enhance reactant mixing, as it was evidenced by the higher axial and radial dispersions of the gas flow across the foam structure. This leads to better mass and heat transfers in the reaction system, thus improving the catalytic behaviour.

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Maksimovic, Tijana, Jelena Maksimovic, Pavle Tancic, Nebojsa Potkonjak, Zoran Nedic, Ljubinka Joksovic, and Maja Pagnacco. "A possible connection between phosphate tungsten bronzes properties and Briggs-Rauscher oscillatory reaction response." Science of Sintering 53, no. 2 (2021): 223–35. http://dx.doi.org/10.2298/sos2102223m.

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The calcium phosphate tungsten bronze (Ca-PWB) has been synthesized and characterized (TGA, DSC, XRPD, FTIR, SEM). The influence of solid insoluble materials Ca- PWB, as well as lithium doped (Li-PWB) and cation free phosphate tungsten (PWB) bronzes on the oscillatory Briggs-Rauscher (BR) reaction dynamics, is compared. The results show that doping with Li and Ca reduces sensitivity of the BR reaction towards bronzes addition. These findings suggest the usage of the BR reaction as an innovative method for testing of different properties of bronze material. The behavior of PWB in the BR reaction is significantly changed with divalent cation (Ca2+) doping. The reasons for the different bronzes behavior were found in their calculated unit cell volumes. Namely, the compressed Ca-PWB unit cell volume indicates the difficult availability of the active site for heterogeneous catalysis. Hence, the linear correlation (slope) of the BR oscillogram?s length (?osc) vs. mass of bronze in BR reaction might be considered as a new parameter for the evaluation of the bronzes catalytic activity.

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Misson, Laetitia E., Jeffrey T. Mindrebo, Tony D. Davis, Ashay Patel, J. Andrew McCammon, Joseph P. Noel, and Michael D. Burkart. "Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD." Proceedings of the National Academy of Sciences 117, no. 39 (September 14, 2020): 24224–33. http://dx.doi.org/10.1073/pnas.2009805117.

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Fatty acid synthases (FASs) and polyketide synthases (PKSs) iteratively elongate and often reduce two-carbon ketide units in de novo fatty acid and polyketide biosynthesis. Cycles of chain extensions in FAS and PKS are initiated by an acyltransferase (AT), which loads monomer units onto acyl carrier proteins (ACPs), small, flexible proteins that shuttle covalently linked intermediates between catalytic partners. Formation of productive ACP–AT interactions is required for catalysis and specificity within primary and secondary FAS and PKS pathways. Here, we use the Escherichia coli FAS AT, FabD, and its cognate ACP, AcpP, to interrogate type II FAS ACP–AT interactions. We utilize a covalent crosslinking probe to trap transient interactions between AcpP and FabD to elucidate the X-ray crystal structure of a type II ACP–AT complex. Our structural data are supported using a combination of mutational, crosslinking, and kinetic analyses, and long-timescale molecular dynamics (MD) simulations. Together, these complementary approaches reveal key catalytic features of FAS ACP–AT interactions. These mechanistic inferences suggest that AcpP adopts multiple, productive conformations at the AT binding interface, allowing the complex to sustain high transacylation rates. Furthermore, MD simulations support rigid body subdomain motions within the FabD structure that may play a key role in AT activity and substrate selectivity.

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Journal articles on the topic 'Catalytic reaction dynamics'

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