Bifunctional group participated nitrile group hydrolyzing enzyme model systems: Hydrolysis of the nitrile group of α-aminophenylacetonitrile to phenylglycineamide and phenylglycine by various thiol compounds

1988 ◽  
Vol 11 (4) ◽  
pp. 285-291 ◽  
Author(s):  
Young Bok Lee ◽  
Yang Mo Goo ◽  
Jae Keun Lee
Keyword(s):  
Nitrile Group ◽  
Model Systems ◽  
Thiol Compounds ◽  
Enzyme Model ◽  
Hydrolysis Of

Determination of the Photolysis Products of [FeFe]Hydrogenase Enzyme Model Systems using Ultrafast Multidimensional Infrared Spectroscopy

2010 ◽  
Vol 49 (20) ◽  
pp. 9563-9573 ◽  
Author(s):  
Andrew I. Stewart ◽  
Joseph A. Wright ◽  
Gregory M. Greetham ◽  
Spiridon Kaziannis ◽  
Stefano Santabarbara ◽  
...  
Keyword(s):  
Infrared Spectroscopy ◽  
Model Systems ◽  
Enzyme Model ◽  
Hydrogenase Enzyme

scholarly journals Towards a barrier height benchmark set for biologically relevant systems

2016 ◽  
Author(s):  
Jimmy C Kromann ◽  
Anders S Christensen ◽  
Qiang Cui ◽  
Jan H. Jensen
Keyword(s):  
Structural Model ◽  
Geometry Optimization ◽  
System Size ◽  
Model Systems ◽  
Maximum Deviation ◽  
Enzymatic Reactions ◽  
Data Set ◽  
Biologically Relevant ◽  
Enzyme Model ◽  
Reaction Energies

We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10-15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4-5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process.

scholarly journals Towards a barrier height benchmark set for biologically relevant systems

2016 ◽  
Author(s):  
Jimmy C Kromann ◽  
Anders S Christensen ◽  
Qiang Cui ◽  
Jan H. Jensen
Keyword(s):  
Structural Model ◽  
Geometry Optimization ◽  
System Size ◽  
Model Systems ◽  
Maximum Deviation ◽  
Enzymatic Reactions ◽  
Data Set ◽  
Biologically Relevant ◽  
Enzyme Model ◽  
Reaction Energies

We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10-15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4-5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process.

scholarly journals Multistage Chemical Recycling of Polyurethanes and Dicarbamates: A Glycolysis–Hydrolysis Demonstration

2021 ◽  
Vol 13 (6) ◽  
pp. 3583
Author(s):  
Pegah Zahedifar ◽  
Lukasz Pazdur ◽  
Christophe M.L. Vande Velde ◽  
Pieter Billen
Keyword(s):  
Bottom Layer ◽  
High Potential ◽  
Model Systems ◽  
Production Yield ◽  
Chemical Recycling ◽  
Reaction Conditions ◽  
Material Cycle ◽  
Hydrolysis Of

The use of polyurethanes and, therefore, the quantity of its scrap are increasing. Considering the thermoset characteristic of most polyurethanes, the most circular recycling method is by means of chemical depolymerization, for which glycolysis is finding its way into the industry. The main goal of polyurethane glycolysis is to recover the polyols used, but only limited attempts were made toward recovering the aromatic dicarbamate residues and derivates from the used isocyanates. By the split-phase glycolysis method, the recovered polyols form a top-layer phase and the bottom layer contain transreacted carbamates, excess glycol, amines, urea, and other side products. The hydrolysis of carbamates results in amines and CO2 as the main products. Consequently, the carbamates in the bottom layer of polyurethane split-phase glycolysis can also be hydrolyzed in a separate process, generating amines, which can serve as feedstock for isocyanate production to complete the polyurethane material cycle. In this paper, the full recycling of polyurethanes is reviewed and experimentally studied. As a matter of demonstration, combined glycolysis and hydrolysis led to an amine production yield of about 30% for model systems. With this result, we show the high potential for further research by future optimization of reaction conditions and catalysis.

Synthesis of dimeric estradiol enzyme model containing imidazolyl and study on its catalytic efficiency in hydrolysis of carboxylates and phosphates

2010 ◽  
Vol 15 (5) ◽  
pp. 438-442 ◽  
Author(s):  
Jia-Ming Yan ◽  
Ru-Gang Xie ◽  
Hua-Ming Zhao ◽  
De-Xian Wu ◽  
Ping-Fang Xia
Keyword(s):  
Catalytic Efficiency ◽  
Enzyme Model ◽  
Hydrolysis Of
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