scholarly journals Circular Dichroism and UV Resonance Raman Study of the Impact of Alcohols on the Gibbs Free Energy Landscape of an α-Helical Peptide

Biochemistry ◽  
2010 ◽  
Vol 49 (15) ◽  
pp. 3336-3342 ◽  
Author(s):  
Kan Xiong ◽  
Sanford A. Asher
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Energy Landscape ◽  
Resonance Raman ◽  
Free Energy Landscape ◽  
Helical Peptide ◽  
Uv Resonance Raman ◽  
Raman Study ◽  
The Impact ◽  
Circular Dichroïsm

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

2020 ◽  
Author(s):  
Astrid Boje ◽  
William E. Taifan ◽  
Henrik Ström ◽  
Tomas Bucko ◽  
Jonas Baltrusaitis ◽  
...  
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
First Principles ◽  
Surface Coverage ◽  
Energy Landscape ◽  
High Surface ◽  
Catalytic Conversion ◽  
Free Energy Landscape ◽  
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 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.

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

2020 ◽  
Author(s):  
Astrid Boje ◽  
William E. Taifan ◽  
Henrik Ström ◽  
Tomas Bucko ◽  
Jonas Baltrusaitis ◽  
...  
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
First Principles ◽  
Surface Coverage ◽  
Energy Landscape ◽  
High Surface ◽  
Catalytic Conversion ◽  
Free Energy Landscape ◽  
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 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.

scholarly journals REFOLDING OF HOMOPOLYMER UNDER QUENCHED FORCE

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.

scholarly journals 1J1400 Folding and unfolding mechanisms of helical peptide through free energy landscape

2002 ◽  
Vol 42 (supplement2) ◽  
pp. S56
Author(s):  
S. Ono ◽  
N. Kamiya ◽  
N. Ito ◽  
J. Higo ◽  
H. Nakamura
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Helical Peptide

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

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