Accounting for the instantaneous disorder in the enzyme-substrate Michaelis complex to calculate the Gibbs free energy barrier of an enzyme reaction

2021 ◽  
Author(s):  
Sonia Romero-Téllez ◽  
Alejandro Cruz ◽  
Laura Masgrau ◽  
Àngels González-Lafont ◽  
José M Lluch
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Energy Barrier ◽  
Enzyme Reaction ◽  
Free Energy Barrier ◽  
Wide Spread ◽  
Energy Barriers ◽  
Enzyme Reactions ◽  
Enzyme Substrate

Many enzyme reactions present instantaneous disorder. These dynamic fluctuations in the enzyme-substrate Michaelis complexes generate a wide spread of energy barriers that cannot be experimentally observed, but that determines the...

Temperature-Dependent Micro-Crack Propagation

2004 ◽  
Author(s):  
Kazuhiro Kitamura ◽  
I. L. Maksimov
Keyword(s):  
Free Energy ◽  
Crack Propagation ◽  
Crack Length ◽  
Barrier Height ◽  
Finite Temperature ◽  
Energy Barrier ◽  
Free Energy Barrier ◽  
Energy Barriers ◽  
Equilibrium Crack ◽  
Environment Temperature

The crack-lattice trapping phenomenon introduce by R. Thomson et al[1] is studied for the conditions of the Frenkel-Kontrova-type experiment. By using a new method, which allows further model extension for a finite temperature case we are able to describe an equilibrium crack energetics for arbitrary externa conditions and ascertain the crack propagation conditions. Specifically, the system free energy F as a function of nonlinear bond displacement ul for an external forces P and for a finite temperature T is found. The equilibrium values for the displacement ul = ul* and for G* = G(ul*), are obtained. The free-energy barrier height G = Gmax − G* dependence upon P and T is determined. With the help of the exact solution of the equilibrium equations we obtained the free energy as function of crack length G(l,T,P). We found that local free energy barriers take place for every crack length l, which is in contrast to the Thomson model. From the microscopic viewpoint it means that crack advance is controlled by local free energy barriers. We found that near the equilibrium length the crack energy barrier is relatively high, while far from equilibrium crack position, energy barrier height decreases to a finite value. It is worth to note that the barrier height monotonically decrease with the increase of the environment temperature. On the basis of our model the temperature dependence of the crack surface energy will be found, the global energetics of the crack will be described.

Theoretical Investigation on Tautomerization Mechanism of 6-Thioguanine

2013 ◽  
Vol 690-693 ◽  
pp. 1418-1421 ◽  
Author(s):  
Hong Jiang Ren
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
Gibbs Free Energy ◽  
Rate Constants ◽  
Reaction Mechanisms ◽  
Energy Barrier ◽  
Intramolecular Proton Transfer ◽  
Transfer Reactions ◽  
Free Energy Barrier ◽  
Proton Transfer Reactions

The tautomerization reaction mechanisms between three stable 6-thioguanine tautomers were investigated theoretically using B3LYP/6-311+G(d,p) method. The results show that the pathway P(1) is to isomerize from TG(9,10,10,11) to TG(1,9,10,10) and the needed activation Gibbs free energy barrier is 112.7 kJ/mol with the rate constant of 1.12×10-7 s-1. Another two pathways P(2) and P(3) are to isomerize from TG(1,9,10,10) to TG(1,7,10,10) and the activation Gibbs free energy barriers of the rate-determining steps are 227.4 and 281.6 kJ/mol, respectively, with the related rate constants of 8.96×10-28 s-1 and 2.86×10-37 s-1, these results implying the intramolecular proton transfer reactions are infeasible in the gas phase.

DFT study on the hydrolysis of metsulfuron-methyl: A sulfonylurea herbicide

2018 ◽  
Vol 17 (08) ◽  
pp. 1850050 ◽  
Author(s):  
Qiuhan Luo ◽  
Gang Li ◽  
Junping Xiao ◽  
Chunhui Yin ◽  
Yahui He ◽  
...  
Keyword(s):  
Free Energy ◽  
Water Molecule ◽  
Carbonyl Group ◽  
Energy Barrier ◽  
Density Functional ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Metsulfuron Methyl ◽  
Catalytic Role ◽  
Hydrolysis Of

Sulfonylureas are an important group of herbicides widely used for a range of weeds and grasses control particularly in cereals. However, some of them tend to persist for years in environments. Hydrolysis is the primary pathway for their degradation. To understand the hydrolysis behavior of sulfonylurea herbicides, the hydrolysis mechanism of metsulfuron-methyl, a typical sulfonylurea, was investigated using density functional theory (DFT) at the B3LYP/6-31[Formula: see text]G(d,p) level. The hydrolysis of metsulfuron-methyl resembles nucleophilic substitution by a water molecule attacking the carbonyl group from aryl side (pathway a) or from heterocycle side (pathway b). In the direct hydrolysis, the carbonyl group is directly attacked by one water molecule to form benzene sulfonamide or heterocyclic amine; the free energy barrier is about 52–58[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. In the autocatalytic hydrolysis, with the second water molecule acting as a catalyst, the free energy barrier, which is about 43–45[Formula: see text]kcal[Formula: see text]mol[Formula: see text], is remarkably reduced by about 11[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is obvious that water molecules play a significant catalytic role during the hydrolysis of sulfonylureas.

COMPARING FOLDING MECHANISMS OF DIFFERENT PRION PROTEINS BY Gō MODEL

2013 ◽  
Vol 12 (08) ◽  
pp. 1341004
Author(s):  
XUE WU ◽  
TING FU ◽  
ZHI-LONG XIU ◽  
LIU YIN ◽  
JIN-GUANG WANG ◽  
...  
Keyword(s):  
Free Energy ◽  
Prion Protein ◽  
Energy Barrier ◽  
Prion Proteins ◽  
Coarse Grained ◽  
Transmissible Spongiform Encephalopathies ◽  
Free Energy Barrier ◽  
Spongiform Encephalopathies ◽  
Go Model ◽  
Folding Free Energy

Prions are associated with neurodegenerative diseases induced by transmissible spongiform encephalopathies. The infectious scrapie form is referred to as PrP Sc , which has conformational change from normal prion with predominant α-helical conformation to the abnormal PrP Sc that is rich in β-sheet content. Neurodegenerative diseases have been found from both human and bovine sources, but there are no reports about infected by transmissible spongiform encephalopathies from rabbit, canine and horse sources. Here we used coarse-grained Gō model to compare the difference among human, bovine, rabbit, canine, and horse normal (cellular) prion proteins. The denatured state of normal prion has relation with the conversion from normal to abnormal prion protein, so we used all-atom Gō model to investigate the folding pathway and energy landscape for human prion protein. Through using coarse-grained Gō model, the cooperativity of the five prion proteins was characterized in terms of calorimetric criterion, sigmoidal transition, and free-energy profile. The rabbit and horse prion proteins have higher folding free-energy barrier and cooperativity, and canine prion protein has slightly higher folding free-energy barrier comparing with human and bovine prion proteins. The results from all-atom Gō model confirmed the validity of C α-Gō model. The correlations of our results with previous experimental and theoretical researches were discussed.

scholarly journals DFT Investigation of Hydrogen Atom Abstraction from NHC-Boranes by Methyl, Ethyl and Cyanomethyl Radicals—Composition and Correlation Analysis of Kinetic Barriers

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4509
Author(s):  
Hong-jie Qu ◽  
Lang Yuan ◽  
Cai-xin Jia ◽  
Hai-tao Yu ◽  
Hui Xu
Keyword(s):  
Free Energy ◽  
Hydrogen Atom ◽  
Gibbs Free Energy ◽  
Density Functional ◽  
Vibrational Energy ◽  
Hydrogen Atom Abstraction ◽  
Reaction Energy ◽  
Energy Barriers ◽  
Energy Correction ◽  
Kinetic Barriers

Understanding the hydrogen atom abstraction (HAA) reactions of N-heterocyclic carbene (NHC)-boranes is essential for extending the practical applications of boron chemistry. In this study, density functional theory (DFT) computations were performed for the HAA reactions of a series of NHC-boranes attacked by •CH2CN, Me• and Et• radicals. Using the computed data, we investigated the correlations of the activation and free energy barriers with their components, including the intrinsic barrier, the thermal contribution of the thermodynamic reaction energy to the kinetic barriers, the activation Gibbs free energy correction and the activation zero-point vibrational energy correction. Furthermore, to describe the dependence of the activation and free energy barriers on the thermodynamic reaction energy or reaction Gibbs free energy, we used a three-variable linear model, which was demonstrated to be more precise than the two-variable Evans–Polanyi linear free energy model and more succinct than the three-variable Marcus-theory-based nonlinear HAA model. The present work provides not only a more thorough understanding of the compositions of the barriers to the HAA reactions of NHC-boranes and the HAA reactivities of the substrates but also fresh insights into the suitability of various models for describing the relationships between the kinetic and thermodynamic physical quantities.

Elucidating the role of solvents in acid catalyzed dehydration of biorenewable hydroxy-lactones

2020 ◽  
Vol 5 (4) ◽  
pp. 651-662 ◽  
Author(s):  
Gourav Shrivastav ◽  
Tuhin S. Khan ◽  
Manish Agarwal ◽  
M. Ali Haider
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Barrier ◽  
Free Energy Barrier ◽  
Activation Free Energy ◽  
Acid Catalyzed

Utilizing the differential stabilization of reactant and transition state in the polar and apolar solvents to lower the activation free energy barrier for acid-catalyzed dehydration of hydroxy lactones.

scholarly journals Free-Energy Barrier at Droplet Condensation

2010 ◽  
Vol 184 ◽  
pp. 400-414 ◽  
Author(s):  
Andreas Nußbaumer ◽  
Elmar Bittner ◽  
Wolfhard Janke
Keyword(s):  
Free Energy ◽  
Energy Barrier ◽  
Free Energy Barrier ◽  
Droplet Condensation
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