Search results for "Reaction coordinate"

The transition state and cognate concepts

2019

Abstract This review aims firstly to clarify the meanings of key terms and concepts associated with the idea of the transition state, as developed by theoreticians and applied by experimentalist, and secondly to provide an update to the meaning and significance of the transition state in an era when computational simulation, in which complexity is being increasingly incorporated, is commonly employed as a means by which to bridge the realms of theory and experiment. The relationship between the transition state and the potential-energy surface for an elementary reaction is explored, with discussion of the following terms: saddle point, minimum-energy reaction path, reaction coordinate, acti…

Adaptive Finite Temperature String Method in Collective Variables.

2017

Here we present a modified version of the on-the-fly string method for the localization of the minimum free energy path in a space of arbitrary collective variables. In the proposed approach the shape of the biasing potential is controlled by only two force constants, defining the width of the potential along the string and orthogonal to it. The force constants and the distribution of the string nodes are optimized during the simulation, improving the convergence. The optimized parameters can be used for umbrella sampling with a path CV along the converged string as the reaction coordinate. We test the new method with three fundamentally different processes: chloride attack to chloromethane…

Direct Visualization of the Conformational Dynamics of Single Influenza Hemagglutinin Trimers

2018

Influenza hemagglutinin (HA) is the canonical type I viral envelope glycoprotein and provides a template for the membrane-fusion mechanisms of numerous viruses. The current model of HA-mediated membrane fusion describes a static "spring-loaded" fusion domain (HA2) at neutral pH. Acidic pH triggers a singular irreversible conformational rearrangement in HA2 that fuses viral and cellular membranes. Here, using single-molecule Förster resonance energy transfer (smFRET)-imaging, we directly visualized pH-triggered conformational changes of HA trimers on the viral surface. Our analyses reveal reversible exchange between the pre-fusion and two intermediate conformations of HA2. Acidification of p…

2018

The origin of substrate preference in promiscuous enzymes was investigated by enzyme isotope labelling of the alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH). At physiological temperature, protein dynamic coupling to the reaction coordinate was insignificant. However, the extent of dynamic coupling was highly substrate-dependent at lower temperatures. For benzyl alcohol, an enzyme isotope effect larger than unity was observed, whereas the enzyme isotope effect was close to unity for isopropanol. Frequency motion analysis on the transition states revealed that residues surrounding the active site undergo substantial displacement during catalysis for sterically bulky alcohol…

A kinetic study of the cracking, isomerization, and disproportionation of n-heptane on a chromium-exchanged Y zeolite

1982

The kinetic rate constants for the cracking, isomerization, and disproportionation of n-heptane over a CrHNaY (32% chromium exchanged) zeolite catalyst at 400, 450, and 470 °C have been calculated. The interaction of n-heptane with a model Lewis acid such as BF3 and progress along the reaction coordinate have been studied by means of molecular orbital calculations. From the kinetic results, i.e., activation energies and frequency factors, and the theoretical calculations, it can be concluded that the controlling step in these reactions is not the formation of the carbonium ion, but the subsequent transformation of this carbonium ion. In addition, the theoretical calculations show that the a…

Exploring chemical reactivity of complex systems with path-based coordinates: role of the distance metric.

2014

Path-based reaction coordinates constitute a valuable tool for free-energy calculations in complex processes. When a reference path is defined by means of collective variables, a nonconstant distance metric that incorporates the nonorthonormality of these variables should be taken into account. In this work, we show that, accounting for the correct metric tensor, these kind of variables can provide iso-hypersurfaces that coincide with the iso-committor surfaces and that activation free energies equal the value that would be obtained if the committor function itself were used as reaction coordinate. The advantages of the incorporation of the variable metric tensor are illustrated with the an…

Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane.

2015

Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio-and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light - chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference mult…

Nucleation in suspensions of anisotropic colloids

2005

We report Monte Carlo studies of liquid crystal nucleation in two types of anisotropic colloidal systems: hard rods and hard ellipsoids. In both cases we find that nucleation pathways differ strongly from the pathways in systems of spherical particles. Short hard rods show an effect of self-poisoning. This part of the article is based on a previous publication [T. Schilling, D. Frenkel, Self-poisoning of crystal nuclei in hard-rod liquids, Phys. Rev. Lett. 92 (2004) 085505]. When a crystallite forms, its surfaces are covered preferentially by rods which align perpendicular to the surface. Therefore subsequent growth is stunted. Hard, almost spherical ellipsoids can be compressed to very hig…

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

2013

Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy ((15)N, (13)C, (2)H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy e…

Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach

2008

We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6'-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction in aqueous solution and the reaction catalyzed by Chalcone Isomerase. By means of rare event simulations of trajectories started at the transition state, we have computed the transmission coefficients, obtaining 0.76 +/- 0.04 and 0.87 +/- 0.03, in water and in the enzyme, respectively. According to these simulations, the Michael addition can be seen as a formation of a new intramolecular carbon-oxygen bond accompanied by a charge transfer essentially taking place from the nu…