First-principles-informed energetic span and microkinetic analysis of ethanol catalytic conversion to 1,3-butadiene on MgO

Kinetic modeling of single-step catalytic conversion of ethanol to 1,3-butadiene is necessary to inform accurate process design. This paper considers the synthesis of 1,3-butadiene on an MgO (100) step-edge using first-principles-informed energetic span and microkinetic analysis to explore the reaction free energy landscapes and kinetic limitations of competing reaction pathways. Previous studies have observed mechanisms proceeding via both dehydrogenation and dehydration of ethanol, and highlighted sensitivity to conditions and catalyst composition. Here, we use the energetic span concept to characterize the theoretical maximum turnover and degree of rate control for states in each reaction pathway, finding dehydrogenation to be more active than dehydration for producing 1,3-butadiene, and suggesting states in the dehydrogenation, dehydration, and condensation steps to be rate-determining. The influence of temperature on the relative rate contribution of each state is quantified and explained through the varying temperature sensitivity of the free energy landscape. A microkinetic model is developed to explore the impact of competition between pathways, interaction with gas-phase species, and high surface coverage of stable reaction intermediates. This suggests that the turnover obtained may be significantly lower than predicted from the free energy landscape alone. The theoretical rate-determining states were found to contribute to high surface coverage of adsorbed ethanol and longer, oxygenated hydrocarbons. The combined energetic span and microkinetic analysis permits investigation of a complex system from two perspectives, each with inherent advantages, and helps elucidate conflicting observations of rate determining steps and product distribution by considering the interplay between the different pathways and the equilibrium with gas-phase products.

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First-principles-informed energy span and microkinetic analysis of ethanol catalytic conversion to 1,3-butadiene on MgO

10.26434/chemrxiv.13118420.v2 ◽

2021 ◽

Author(s):

Astrid Boje ◽

William E. Taifan ◽

Henrik Ström ◽

Tomas Bucko ◽

Jonas Baltrusaitis ◽

...

Keyword(s):

Free Energy ◽

First Principles ◽

Surface Coverage ◽

Reaction Pathway ◽

Relative Rate ◽

Energy Landscape ◽

Catalytic Conversion ◽

Turnover Frequency ◽

Catalyst Composition ◽

The Impact

Kinetic modeling of single-step catalytic conversion of ethanol to 1,3-butadiene is necessary to inform accurate process design. This paper uses first-principles-informed energy span and microkinetic analysis to explore the reaction free energy landscapes and kinetic limitations of competing reaction pathways on a MgO (100) step-edge. Previous studies suggested mechanisms proceeding via both dehydrogenation and dehydration of ethanol, and highlighted sensitivity to conditions and catalyst composition. Here, we use the energy span concept to characterize the theoretical maximum turnover and degree of turnover frequency control for states in each reaction pathway, finding the dehydration route to be less active for 1,3-butadiene, and suggesting rate-determining states in the dehydrogenation, dehydration, and condensation steps. The influence of temperature on the relative rate contribution of each state is quantified and explained through the varying temperature sensitivity of the free energy landscape. A microkinetic model is developed to explore competition between pathways, interaction with gas-phase species, and surface coverage limitations. This suggests that the turnover may be significantly lower than predicted solely based on energetics. Turnover frequency determining states found to have high surface coverage include adsorbed ethanol and two longer, oxygenated hydrocarbons. The combined energy span and microkinetic analysis permits investigation of a complex system from two perspectives and helps elucidate conflicting observations of rate determining steps and product distribution by considering both energetic and kinetic limitations. The impact of uncertainty in the energy landscape is quantified using a correlated error model. While the range of predictions is large, the average performance and trends are similar.

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The Trajectory Taken by Dimeric Cu/Zn Superoxide Dismutase Through the Protein Unfolding and Dissociation Landscape Is Modulated by Salt-Bridge Formation

10.26434/chemrxiv.7898246 ◽

2019 ◽

Author(s):

Luke McAlary ◽

Julian Harrison ◽

J. Andrew Aquilina ◽

Steven Fitzgerald ◽

Celine Kelso ◽

...

Keyword(s):

Superoxide Dismutase ◽

Free Energy ◽

Gas Phase ◽

Protein Unfolding ◽

Energy Landscape ◽

Salt Bridge ◽

Native Mass Spectrometry ◽

Free Energy Landscape ◽

Related Point ◽

Macromolecular Protein

Native mass spectrometry (MS) is a powerful means for studying macromolecular protein assemblies, including accessing activated states. However, much remains to be understood about what governs which regions of the protein (un)folding funnel are explored by activation of protein ions in vacuum. Here we examine the trajectory that dimeric Cu/Zn superoxide dismutase (SOD1) dimers take over the unfolding and dissociation free energy landscape in vacuum. We examined wild-type SOD1 and six disease-related point-mutants by using tandem MS and ion-mobility MS (MS/MS-IMMS) coupled with increasing collisional activation potentials. For six of the seven SOD1 variants, increasing activation promoted dimers to transition through two unfolding events to access three gas-phase conformers before dissociating symmetrically into monomers with (as near as possible) equal charges. The exception was G37R, which proceeded only through the first unfolding transition, and displayed a much higher abundance of asymmetric products. We localise this effect to the formation of a new salt-bridge in the first activated conformation. To examine the data quantitatively, we generated a model of SOD1 gas phase unfolding and dissociation, and applied Arrhenius-type analysis to estimate the barriers on the corresponding free energy landscape. This reveals an increase in the barrier height to unfolding in G37R to be >5 kJ/mol-1 higher than for the other variants, consistent with expectations for the strength of a salt-bridge. Our work demonstrates the importance of bond formation during the unfolding of proteins in vacuum, and provides a framework for comparing quantitatively the free energy landscape they explore upon activation.

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The Trajectory Taken by Dimeric Cu/Zn Superoxide Dismutase Through the Protein Unfolding and Dissociation Landscape Is Modulated by Salt-Bridge Formation

10.26434/chemrxiv.7898246.v2 ◽

2019 ◽

Author(s):

Luke McAlary ◽

Julian Harrison ◽

J. Andrew Aquilina ◽

Steven Fitzgerald ◽

Celine Kelso ◽

...

Keyword(s):

Superoxide Dismutase ◽

Free Energy ◽

Gas Phase ◽

Protein Unfolding ◽

Energy Landscape ◽

Salt Bridge ◽

Native Mass Spectrometry ◽

Free Energy Landscape ◽

Related Point ◽

Macromolecular Protein

Native mass spectrometry (MS) is a powerful means for studying macromolecular protein assemblies, including accessing activated states. However, much remains to be understood about what governs which regions of the protein (un)folding funnel are explored by activation of protein ions in vacuum. Here we examine the trajectory that dimeric Cu/Zn superoxide dismutase (SOD1) dimers take over the unfolding and dissociation free energy landscape in vacuum. We examined wild-type SOD1 and six disease-related point-mutants by using tandem MS and ion-mobility MS (MS/MS-IMMS) coupled with increasing collisional activation potentials. For six of the seven SOD1 variants, increasing activation promoted dimers to transition through two unfolding events to access three gas-phase conformers before dissociating symmetrically into monomers with (as near as possible) equal charges. The exception was G37R, which proceeded only through the first unfolding transition, and displayed a much higher abundance of asymmetric products. We localise this effect to the formation of a new salt-bridge in the first activated conformation. To examine the data quantitatively, we generated a model of SOD1 gas phase unfolding and dissociation, and applied Arrhenius-type analysis to estimate the barriers on the corresponding free energy landscape. This reveals an increase in the barrier height to unfolding in G37R to be >5 kJ/mol-1 higher than for the other variants, consistent with expectations for the strength of a salt-bridge. Our work demonstrates the importance of bond formation during the unfolding of proteins in vacuum, and provides a framework for comparing quantitatively the free energy landscape they explore upon activation.

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Unraveling the mechanism of biomimetic hydrogen fuel production – a first principles molecular dynamics study

Physical Chemistry Chemical Physics ◽

10.1039/c9cp06770a ◽

2020 ◽

Vol 22 (19) ◽

pp. 10447-10454 ◽

Cited By ~ 1

Author(s):

Rakesh C. Puthenkalathil ◽

Mihajlo Etinski ◽

Bernd Ensing

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

First Principles ◽

Molecular Hydrogen ◽

Energy Landscape ◽

Free Energy Landscape ◽

Hydrogen Fuel ◽

Fuel Production ◽

Hydrogenase Enzyme ◽

First Principles Molecular Dynamics

The Fe2(bdt)(CO)6 [bdt = benzenedithiolato] complex, a synthetic mimic of the [FeFe] hydrogenase enzyme can electrochemically convert protons into molecular hydrogen. The free energy landscape reveals a different mechanism for the biomimetic cycle.

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REFOLDING OF HOMOPOLYMER UNDER QUENCHED FORCE

Vietnam Journal of Science and Technology ◽

10.15625/2525-2518/55/6a/12360 ◽

2018 ◽

Vol 55 (6A) ◽

pp. 1

Author(s):

Maksim Kouza

Keyword(s):

Free Energy ◽

Single Molecule ◽

Energy Landscape ◽

Coarse Grain ◽

Free Energy Landscape ◽

Single Molecule Force Spectroscopy ◽

Denatured State ◽

Dna And Rna ◽

Go Model ◽

The Impact

Recently single molecule force spectroscopy has become an useful tool to study protein, DNA and RNA. However, very little attention was paid to homopolymer which plays an important role in many domains of science. In this paper we make the first attempt to decipher the free energy landscape of homopolymer using the external force as reaction coordinate. The impact of the quenched force on the free energy landscape was studied using simplified coarse-grain Go model. Similar to protein, we have obtained a clear switch from the thermal regime to force-driven regime. The distance between the denatured state and transition state in the temperature-driven regime is smaller than in the force-driven one. Having a rugged free energy landscape without a pronounced funnel the homopolymer folding is much slower than that of protein making study of homopolymer very time consuming.

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