scholarly journals The influence of active site conformations on the hydride transfer step of the thymidylate synthase reaction mechanism

2015 ◽  
Vol 17 (46) ◽  
pp. 30793-30804 ◽  
Author(s):  
Katarzyna Świderek ◽  
Amnon Kohen ◽  
Vicent Moliner
Keyword(s):  
Reaction Mechanism ◽  
Thymidylate Synthase ◽  
Active Site ◽  
Hydride Transfer ◽  
Md Simulations ◽  
Concerted Mechanism ◽  
X Ray ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

QM/MM MD simulations from different X-ray structures support the concerted mechanism character in the rate limiting step of thymidylate synthase catalysis.

scholarly journals Understanding the reaction mechanism of Kolbe electrolysis on Pt anodes

2021 ◽  
Author(s):  
Sihang Liu ◽  
Nitish Govindarajan ◽  
Hector Prats ◽  
Karen Chan
Keyword(s):  
Reaction Mechanism ◽  
Potential Range ◽  
Microkinetic Model ◽  
Rate Determining Step ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Tafel Slopes ◽  
Kolbe Electrolysis ◽  
Kolbe Reaction ◽  
Rate Limiting

Kolbe electrolysis has been proposed an efficient electrooxidation process to synthesize (un)symmetrical dimers from biomass-based carboxylic acids. However, the reaction mechanism of Kolbe electrolysis remains controversial. In this work, we develop a DFT- based microkinetic model to study the reaction mechanism of Kolbe electrolysis of acetic acid (CH3COOH) on both pristine and partially oxidized Pt anodes. We show that the shift in the rate-determining step of oxygen evolution reaction (OER) on Pt(111)@α-PtO2 surface from OH* formation to H2O adsorption gives rise to the large Tafel slopes, i.e., the inflection zones, observed at high anodic potentials in experiments on Pt anodes. The activity passivation as a result of the inflection zone is further exacerbated in the presence of Kolbe species (i.e., CH3COO* and CH3*). Our simulations find the CH3COO* decarboxylation and CH3* dimerization steps determine the activity of Kolbe reaction during inflection zone. In contrast to the Pt(111)@α-PtO2 surface, Pt(111) shows no activity towards Kolbe products as the CH3COO* decarboxylation step is limiting throughout the considered potential range. This work resolves major controversies in the mechanistic analyses of Kolbe electrolysis on Pt anodes: the origin of the inflection zone, and the identity of the rate limiting step.

scholarly journals Beyond the Active Site: Mechanistic Investigations of the Role of the Secondary Coordination Sphere and Beyond on Multi-Electron Electrocatalytic Reactions and Their Relations Between Kinetics and Thermodynamics

2020 ◽  
Author(s):  
Vincent Wang
Keyword(s):  
Thermodynamic Parameters ◽  
Coordination Sphere ◽  
Active Site ◽  
Rate Constants ◽  
Reduction Reaction ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Secondary Coordination Sphere ◽  
Catalytic Rate ◽  
Rate Limiting

<p>The development of an electrocatalyst with a rapid turnover frequency, low overpotential and long-term stability is highly desired for fuel-forming reactions, such as water splitting and CO<sub>2</sub> reduction. The findings of the scaling relationships between the catalytic rate and thermodynamic parameters over a wide range of electrocatalysts in homogeneous and heterogeneous systems provide useful guidelines and predictions for designing better catalysts for those redox reactions. However, such relationships also suggest that a catalyst with a high catalytic rate is typically associated with a high overpotential for a given reaction. Inspired by enzymes, the introduction of additional interactions through the secondary coordination sphere beyond the active site, such as hydrogen-bonding or electrostatic interactions, have been shown to offer a promising avenue to disrupt these unfavorable relationships. Herein, we further investigate the influence of these cooperative interactions on the faster chemical steps, in addition to the rate-limiting step widely examined before, for molecular electrocatalysts with the structural and electronic modifications designed to facilitate the dioxygen reduction reaction, CO<sub>2</sub> reduction reaction and hydrogen evolving reaction. Based on the electrocatalytic kinetic analysis, the rate constants for faster chemical steps and their correlation with the corresponding thermodynamic parameters are evaluated. The results suggest that the effects of the secondary coordination sphere and beyond on these fuel-forming reactions are not necessarily beneficial for promoting all chemical steps and no apparent relation between rate constants and thermodynamic parameters are found in some cases studied here, which may implicate the design of electrocatalysts in the future. Finally, these analyses demonstrate that the characteristic features for voltammograms and foot-of-the-wave-analysis plots are associated with the specific kinetic phenomenon among these multi-electron electrocatalytic reactions, which provides a useful framework to probe the insights of chemical and electronic modifications on the catalytic steps quantitatively (i.e. kinetic rate constants) and to optimize some of critical steps beyond the rate-limiting step.</p>

scholarly journals Kinetic modelling of hydrogen transfer deoxygenation of a prototypical fatty acid over a bimetallic Pd60Cu40 catalyst: an investigation of the surface reaction mechanism and rate limiting step

2020 ◽  
Vol 5 (9) ◽  
pp. 1682-1693
Author(s):  
Kin Wai Cheah ◽  
Suzana Yusup ◽  
Martin J. Taylor ◽  
Bing Shen How ◽  
Amin Osatiashtiani ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Reaction Mechanism ◽  
Hydrogen Transfer ◽  
Surface Reaction ◽  
Kinetic Modelling ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Cu Catalyst ◽  
P Application ◽  
Rate Limiting

Application of tetralin as a source of hydrogen for catalytic conversion of oleic acid to diesel-like hydrocarbons using a bimetallic Pd–Cu catalyst.

scholarly journals Unveiling the Rate-Limiting Step of the Bc1 Complex Reaction Mechanism

2019 ◽  
Vol 116 (3) ◽  
pp. 419a
Author(s):  
Angela M. Barragan ◽  
Alexander V. Soudackov ◽  
Zaida Luthey-Schulten ◽  
Klaus Schulten ◽  
Sharon Hammes-Schiffer ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Complex Reaction ◽  
Bc1 Complex ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

Mechanism of the Ullmann condensation

1981 ◽  
Vol 46 (1) ◽  
pp. 92-100 ◽  
Author(s):  
Zdeněk Vrba
Keyword(s):  
Reaction Mechanism ◽  
Bifunctional Catalyst ◽  
Sulphonic Acid ◽  
Condensation Rate ◽  
Kinetic Relation ◽  
Bromide Anion ◽  
Reaction Intermediate ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

It has been found that the condensation rate of 1-amino-4-bromoanthraquinone-2-sulphonic acid (I) with 1,3-diaminobenzene-4-sulphonic acid (II) giving 1-amino-4-(3'-amino-4'-sulphoanilino)anthraquinone-2-sulphonic acid (III) in media of NaHCO3-CO2 and NaHCO3-Na2CO3 with catalysis by CuI obeys the kinetic relation *u = k[I][II][Cu+][CO2-3], being controlled by the kinetic relation *u = k[I][II][Cu+]2[PO3-4] in media of NaH2PO4-Na2HPO4 buffers. The suggested reaction mechanism presumes formation of a bifunctional catalyst CuCO-3 or Cu2PO-4 which splits off the proton and bromide anion from the reaction intermediate in the rate-limiting step.

A mathematical modelling of acid catalyzed decomposition of 3-methyl-1,3-diphenyltriazene

1987 ◽  
Vol 52 (10) ◽  
pp. 2492-2499 ◽  
Author(s):  
Oldřich Pytela ◽  
Petr Svoboda ◽  
Miroslav Večeřa
Keyword(s):  
Reaction Mechanism ◽  
Linear Regression ◽  
Organic Solvent ◽  
Mathematical Modelling ◽  
Aqueous Ethanol ◽  
Activation Parameters ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Acid Catalyzed ◽  
Rate Limiting

The effect of acids on the decomposition of 3-methyl-1,3-diphenyltriazene has been studied in aqueous ethanol (40% (v/v) ethanol). The dependences found between the rate constant and acid concentration have been analyzed by means of non-linear regression using models including the specific and general catalysis and formation of associates between the substrate and the buffer components. The substrate has been found to form electrostatic associates with the conjugated base of acid. The complex formed is decomposed with the assistance of the proton or a general acid in the rate-limiting step to form the product. The Bronsted coefficient α = 0.81 has been found. Investigation of the activation parameters supports the earlier conclusions, indicating a dependence between the reaction mechanism and composition of the aqueous organic solvent.

scholarly journals Observation of fast release of NO from ferrous d1 haem allows formulation of a unified reaction mechanism for cytochrome cd1 nitrite reductases

2011 ◽  
Vol 435 (1) ◽  
pp. 217-225 ◽  
Author(s):  
Serena Rinaldo ◽  
Katharine A. Sam ◽  
Nicoletta Castiglione ◽  
Valentina Stelitano ◽  
Alessandro Arcovito ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Turnover Number ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Nitrite Reductases ◽  
Cytochrome Cd1 ◽  
Paracoccus Pantotrophus ◽  
Rate Limiting ◽  
Fast Release ◽  
Present Experimental Evidence

Cytochrome cd1 nitrite reductase is a haem-containing enzyme responsible for the reduction of nitrite into NO, a key step in the anaerobic respiratory process of denitrification. The active site of cytochrome cd1 contains the unique d1 haem cofactor, from which NO must be released. In general, reduced haems bind NO tightly relative to oxidized haems. In the present paper, we present experimental evidence that the reduced d1 haem of cytochrome cd1 from Paracoccus pantotrophus releases NO rapidly (k=65–200 s−1); this result suggests that NO release is the rate-limiting step of the catalytic cycle (turnover number=72 s−1). We also demonstrate, using a complex of the d1 haem and apomyoglobin, that the rapid dissociation of NO is largely controlled by the d1 haem cofactor itself. We present a reaction mechanism proposed to be applicable to all cytochromes cd1 and conclude that the d1 haem has evolved to have low affinity for NO, as compared with other ferrous haems.

scholarly journals Revealing a hidden intermediate of rotatory catalysis with X-ray crystallography and Molecular simulations

2021 ◽  
Author(s):  
Mrinal Shekhar ◽  
Chitrak Gupta ◽  
Kano Suzuki ◽  
Abhishek Singharoy ◽  
Takeshi Murata
Keyword(s):  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Structural Information ◽  
Hydrolysis Product ◽  
X Ray ◽  
X Ray Crystallography ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Dynamics Simulations ◽  
Rate Limiting

The mechanism of rotatory catalysis in ATP-hydrolyzing molecular motors remain an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multi-step rotation process. Here, using Vacuolar or V1-type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using X-ray crystallography a new intermediate or 'dwell' is identified, which enables the release of an inorganic phosphate (or Pi) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transfor-mations, and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the sidechain level interactions transcend into larger scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. Inspection of all known rates encompassing the 4-step rotation mechanism implicates overcoming of the ADP interactions with V1-ATPase to be the rate-limiting step of motor action.

Formation and Decomposition of Nitrides on Iron Surfaces

1979 ◽  
Vol 34 (1) ◽  
pp. 30-39 ◽  
Author(s):  
G. Ertl ◽  
M. Huber ◽  
N. Thiele
Keyword(s):  
Photoelectron Spectroscopy ◽  
Electron Spectroscopy ◽  
Auger Electron ◽  
Thermal Desorption Spectroscopy ◽  
Iron Nitrides ◽  
Kcal Mole ◽  
X Ray ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

Abstract The formation (by interaction with ammonia) and decomposition of nitrides on clean Fe surfaces was studied by means of Auger electron spectroscopy, x-ray photoelectron spectroscopy, thermal desorption spectroscopy, and scanning electron microscopy. The N atoms may exist in various forms with quite similar electronic properties, viz. as chemisorbed layer (= "surface nitride"), dissolved in α-Fe or γ-Fe, as γ′-nitride (= Fe4N) or as e-nitride, depending on temperature as well as pressure and duration of interaction with NH3. There is no noticeable chemical shift of the ionization energies of the Fe core levels, indicating that the bond is essentially covalent. The activation energy for the decomposition of e-nitride into Fe4N + N2 is about 27 kcal/mole, that for the decomposition of Fe4N into Fe+N2 ranges between 51 and 57 kcal/mole, depending on the mode of preparation. The latter values are identical to those found previously for the desorption of N2 from various Fe single crystal planes and indicate that the decomposition of the chemisorbed "surface nitrides" is the rate-limiting step which prevents the spontaneous decom-position of the metastable bulk iron nitrides.

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