scholarly journals Standard Gibbs Free Energy Change

2020 ◽  
Author(s):  
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Free Energy Change ◽  
Energy Change ◽  
Standard Gibbs Free Energy ◽  
Gibbs Free Energy Change

scholarly journals dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design

2021 ◽  
Author(s):  
Lin Wang ◽  
Vikas Upadhyay ◽  
Costas D. Maranas
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
De Novo ◽  
Free Energy Change ◽  
Energy Change ◽  
Easy Access ◽  
Standard Gibbs Free Energy ◽  
Gibbs Free Energy Change ◽  
Molecular Fingerprint ◽  
Metabolic Pathway Design

AbstractGroup contribution (GC) methods are conventionally used in thermodynamics analysis of metabolic pathways to estimate the standard Gibbs free energy change (ΔrG′o) of enzymatic reactions from limited experimental measurements. However, these methods are limited by their dependence on manually curated groups and inability to capture stereochemical information, leading to low reaction coverage. Herein, we introduce an automated molecular fingerprint-based thermodynamic analysis tool called dGPredictor that enables the consideration of stereochemistry within metabolite structures and thus increases reaction coverage. dGPredictor has a higher prediction accuracy as compared to existing GC methods and can capture free energy changes for isomerase and transferase reactions, which exhibit no overall group changes. We also demonstrate dGPredictor’s ability to predict the Gibbs free energy change for novel reactions and seamless integration within de novo metabolic pathway design tools such as novoStoic. This enables performing a thermodynamic analysis for synthetic pathways, thus safeguarding against the inclusion of reaction steps with infeasible directionalities. To facilitate easy access to dGPredictor, we developed a graphical user interface to predict the standard Gibbs free energy change for reactions at various pH and ionic strengths. The tool allows customized user input of known metabolites as KEGG IDs and novel metabolites as InChI strings (https://github.com/maranasgroup/dGPredictor).Author summaryThe genome-scale metabolic networks consist of a large number of biochemical reactions interconnected in a complex system. The standard Gibbs free energy change is commonly used to check for the feasibility of enzyme-catalyzed reactions as thermodynamics plays a crucial role in pathway design for biochemical synthesis. The group contribution methods using expert-defined functional groups have been extensively used for estimating standard Gibbs free energy change with limited experimental measurements. However, current methods using functional groups have major issues that limit its ability to cover all the metabolites and reactions as well as the inability to consider stereochemistry leads to erroneous estimation of free energy that undergoes only stereochemical change such as isomerases. Here, we introduce a molecular fingerprint-based thermodynamic tool dGPredictor that enables stereochemistry in metabolites and thus improves the reaction coverage with higher prediction accuracy compared to current GC methods. It also allows the ability to predict free energy change for novel reactions which can aid the de novo metabolic pathway design tool to ensure the reaction feasibility. We apply and test our method on reactions in the KEGG database and isobutanol synthesis pathway. In addition, we provide an open-source user-friendly web interface to facilitate easy access for standard Gibbs free energy change of reactions at different physiological states.

The standard gibbs free energy change of hydrolysis of α-d-ribose 1-phosphate

1980 ◽  
Vol 205 (1) ◽  
pp. 191-197 ◽  
Author(s):  
Marcella Camici ◽  
Francesco Sgarrella ◽  
Pier L. Ipata ◽  
Umberto Mura
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Free Energy Change ◽  
Energy Change ◽  
Standard Gibbs Free Energy ◽  
Gibbs Free Energy Change ◽  
Hydrolysis Of

Theoretical Thermodynamic Analysis and Phase Analysis of AZ91D/Flyash Composites

2014 ◽  
Vol 788 ◽  
pp. 604-607
Author(s):  
Hong Chao Chu ◽  
Si Rong Yu ◽  
Cui Xiang Wang ◽  
Qi Lou
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Minimum Principle ◽  
Solution Treatment ◽  
Entropy Change ◽  
Treatment Temperature ◽  
Free Energy Change ◽  
Energy Change ◽  
Solution Treatment Temperature ◽  
Gibbs Free Energy Change

The thermodynamic calculation is valuable for judging the feasibility of a reaction. In the present paper, the enthalpy change (∆HR), entropy change (∆SR) and Gibbs free energy change (∆GR) among various components in AZ91D Mg alloy-Cenosphere composites (FAC/AZ91D) were calculated. Through the calculation, we obtained the relationships between the Gibbs free energy changes and temperatures. The difficulty degree of every potential reaction could be directly reflected by the correlation curve between the temperature and the Gibbs free energy change. The analysis result provided the theoretical basis for the reaction temperature and the solution treatment temperature of the FAC/AZ91D system. At the same time, the analysis based on the minimum principle of the reaction free energy revealed the final components (MgO, Mg2Si and MgAl2O4), which was partially similar to the result of XRD analysis (MgO, Mg2Si and Mg17Al12).

Gibbs free energy change of a discrete chemical reaction event

2020 ◽  
Vol 152 (8) ◽  
pp. 084116
Author(s):  
Carlos Floyd ◽  
Garegin A. Papoian ◽  
Christopher Jarzynski
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Chemical Reaction ◽  
Free Energy Change ◽  
Energy Change ◽  
Gibbs Free Energy Change ◽  
Reaction Event

Behavior of Intermediate CaTiO3 in Reduction Process of TiO2 by Calcium Vapor

2013 ◽  
Vol 551 ◽  
pp. 25-31 ◽  
Author(s):  
Jin Gang Jia ◽  
Bao Qiang Xu ◽  
Bin Yang ◽  
Dong Sheng Wang ◽  
Heng Xiong ◽  
...  
Keyword(s):  
Free Energy ◽  
Titanium Oxide ◽  
Gibbs Free Energy ◽  
Reduction Process ◽  
Free Energy Change ◽  
Energy Change ◽  
Flow Sheet ◽  
Gibbs Free Energy Change ◽  
Crystal Water ◽  
Calcium Vapor

Preparing titanium powders by calcium vapor reduction of titanium oxide directly is a new way with short flow sheet and CaTiO3 is the very important intermediate compound in this process. In this paper, the behavior of intermediate CaTiO3 in the reduction process of TiO2 was investigated. The thermodynamic calculation indicated that the Gibbs free energy change of the reaction to produce CaTiO3 by CaO and TiO2 was always negative below 1000 °C; The reaction Gibbs free energy change of the calciothermic reduction of CaTiO3 was lower than that of TiO, which would be the most predominant step from TiO2 to Ti. The experimental results showed that CaTiO3 phase derived from the reaction between TiO2 and the reduction by-product CaO, and the reaction between TiO2 and the decomposition product CaO from the additive of CaCl2 with crystal water as well in the calcium vapor reduction process of titanium oxide. But CaTiO3 could be reduced to Ti much easier than that of TiO2 by calcium vapor.

Blinking Suppression in Highly Excited CdSe/ZnS Quantum Dots by Electron Transfer under Large Positive Gibbs (Free) Energy Change

ACS Nano ◽  
2018 ◽  
Vol 12 (9) ◽  
pp. 9060-9069 ◽  
Author(s):  
Elizabeth Mariam Thomas ◽  
Sushant Ghimire ◽  
Reiko Kohara ◽  
Ajith Nair Anil ◽  
Ken-ichi Yuyama ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Electron Transfer ◽  
Free Energy ◽  
Gibbs Free Energy ◽  
Free Energy Change ◽  
Energy Change ◽  
Gibbs Free Energy Change
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