Carbonyl Bond Cleavage by Complementary Active Sites

2013 ◽  
Vol 117 (15) ◽  
pp. 7445-7450 ◽  
Author(s):  
W. Hunter Woodward ◽  
A. C. Reber ◽  
Jordan C. Smith ◽  
S. N. Khanna ◽  
A. W. Castleman
Keyword(s):  
Active Sites ◽  
Bond Cleavage ◽  
Carbonyl Bond

Kinetic Assessment of the Dry Reforming of Methane over a Solid Solution Ni–La Oxide Catalyst

2021 ◽  
Author(s):  
Victor Stivenson Sandoval-Bohorquez ◽  
Edgar M. Morales-Valencia ◽  
Carlos Omar Castillo-Araiza ◽  
Luz Marina Ballesteros Rueda ◽  
Víctor Gabriel Baldovino Medrano
Keyword(s):  
Solid Solution ◽  
Active Sites ◽  
Oxide Catalyst ◽  
Bond Cleavage ◽  
Scale Up ◽  
Active Surface ◽  
Dry Reforming ◽  
Dry Reforming Of Methane ◽  
Nickel Surface ◽  
Kinetics Of

The dry reforming of methane is a promising technology for the abatement of CH<sub>4</sub> and CO<sub>2</sub>. Solid solution Ni–La oxide catalysts are characterized by their long–term stability (100h) when tested at full conversion. The kinetics of dry reforming over this type of catalysts has been studied using both power law and Langmuir–Hinshelwood based approaches. However, these studies typically deal with fitting the net CH<sub>4</sub> rate hence disregarding competing and parallel surface processes and the different possible configurations of the active surface. In this work, we synthesized a solid solution Ni–La oxide catalyst and tested six Langmuir–Hinshelwood mechanisms considering both single and dual active sites for assessing the kinetics of dry reforming and the competing reverse water gas shift reaction and investigated the performance of the derived kinetic models. In doing this, it was found that: (1) all the net rates were better fitted by a single–site model that considered that the first C–H bond cleavage in methane occurred over a <a>metal−oxygen </a>pair site; (2) this model predicted the existence of a nearly saturated nickel surface with chemisorbed oxygen adatoms derived from the dissociation of CO<sub>2</sub>; (3) the dissociation of CO<sub>2</sub> can either be an inhibitory or an irrelevant step, and it can also modify the apparent activation energy for CH<sub>4</sub> activation. These findings contribute to a better understanding of the dry reforming reaction's kinetics and provide a robust kinetic model for the design and scale–up of the process.

scholarly journals The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms

2020 ◽  
Vol 21 (21) ◽  
pp. 8367
Author(s):  
Hannes M. Beyer ◽  
Salla I. Virtanen ◽  
A. Sesilja Aranko ◽  
Kornelia M. Mikula ◽  
George T. Lountos ◽  
...  
Keyword(s):  
Amino Acid ◽  
Active Sites ◽  
Bond Cleavage ◽  
Structural Basis ◽  
Protein Splicing ◽  
Active Site Residues ◽  
Class 1 ◽  
Characteristic Sequences ◽  
Dynamics Simulations ◽  
Esterification Reactions

Protein splicing catalyzed by inteins utilizes many different combinations of amino-acid types at active sites. Inteins have been classified into three classes based on their characteristic sequences. We investigated the structural basis of the protein splicing mechanism of class 3 inteins by determining crystal structures of variants of a class 3 intein from Mycobacterium chimaera and molecular dynamics simulations, which suggested that the class 3 intein utilizes a different splicing mechanism from that of class 1 and 2 inteins. The class 3 intein uses a bond cleavage strategy reminiscent of proteases but share the same Hedgehog/INTein (HINT) fold of other intein classes. Engineering of class 3 inteins from a class 1 intein indicated that a class 3 intein would unlikely evolve directly from a class 1 or 2 intein. The HINT fold appears as structural and functional solution for trans-peptidyl and trans-esterification reactions commonly exploited by diverse mechanisms using different combinations of amino-acid types for the active-site residues.

Infrared Spectroscopic Characterization of Sulfide Cluster-Derived Ensembles

1994 ◽  
Vol 368 ◽  
Author(s):  
James R. Brenner ◽  
Levi T. Thompson
Keyword(s):  
Transition Metal ◽  
Active Sites ◽  
Supported Catalysts ◽  
Bond Cleavage ◽  
Metal Sulfide ◽  
Spectroscopic Characterization ◽  
Incipient Wetness Impregnation ◽  
Late Transition Metals ◽  
Late Transition ◽  
Thiophene Hds

ABSTRACTThe transition metal sulfide clusters (MeCp)2Mo2(μ-SH)2(μ-S)2, (MeCp)2Mo2Co2(μ3-S)2(μ4-S)(CO)4 [MoCoS], and (MeCp)2Mo2 Fe2 (μ3-S)2(CO)8, (MeCp = methylcyclopentadienyl) were used to prepare γ-Al2O3-supported catalysts. For comparison, a series of supported materials was also prepared using conventional incipient wetness impregnation. Infrared spectroscopy of adsorbed species was used to characterize the sites in the clusterderived and conventionally prepared catalysts. Nitric oxide chemisorbed onto the MoCoS/A catalyst was associated initially only with Co sites and then upon gentle heating shifted to the Mo sites, indicating that Co and Mo were in close proximity. In contrast, NO adsorbed onto both Co and Mo sites in the conventionally prepared materials and desorbed independently from these two types of sites. Infrared spectra of adsorbed thiophene and pyridine were similar for the clusterderived and conventionally prepared catalysts. Thiophene reacted at 100 °C to produce both olefinic species. The most abundant products from thiophene HDS were 1-butene, cis-2-butene, and trans-2-butene. Displacement studies showed that thiophene, pyridine, and NO adsorbed to the same site. The most active sites for HDS and HDN contained both Mo and a late transition metal. The HDN product distributions suggested that Mo was selective for C=N bond cleavage while the late transition metals were more active for C=C hydrogenolysis.

scholarly journals Signal-Processing and Adaptive Prototissue Formation in Metabolic DNA Protocells

2021 ◽  
Author(s):  
Avik Samanta ◽  
Maximilian Hörner ◽  
Wei Liu ◽  
Wilfried Weber ◽  
Andreas Walther
Keyword(s):  
Signal Processing ◽  
Active Sites ◽  
Bond Cleavage ◽  
Soft Materials ◽  
Metabolic Reaction ◽  
Strand Displacement ◽  
Synthetic Cell ◽  
Displacement Reactions ◽  
Dna Strand

Abstract The fundamental life-defining processes in living cells, such as replication, division, adaptation, and tissue formation, take place via intertwined metabolic reaction networks orchestrating downstream signal processing in a confined, crowded environment with high precision. Hence, it is crucial to understand and reenact some of these functions in wholly synthetic cell-like entities (protocells) to envision designing soft-materials with life-like traits. Herein, we report on a programmable all-DNA protocell (PC) composed of a liquid DNA interior and a hydrogel-like shell, harboring DNAzyme active sites in the interior whose catalytic bond-cleaving activity leads to a downstream phenotype change in the protocells, as well as triggers prototissue formation. In this regard, we coupled several tools of DNA nanoscience, such as RNA cleavage, dynamic strand displacement reactions, and multivalent palindromic interactions, in a synchronize pathway so that the input signal can be processed inside the protocells and generate downstream cues giving rise to metabolic adaptive behavior. For example, the compartmentalized DNAzyme catalyzes the bond-cleavage of a substrate that releases a DNA strand in situ to trigger a strand displacement reaction at the shell of the protocells leading to a change in color resembling a “phenotype-like” change in cells, and finally to establish communication with other protocells via multivalent interactions.

scholarly journals Study on the cleavage of alkyl-O-aryl bonds by in situ generated hydroxyl radicals on an ORR cathode

RSC Advances ◽  
2017 ◽  
Vol 7 (81) ◽  
pp. 51419-51425 ◽  
Author(s):  
Lei Wang ◽  
Yongmei Chen ◽  
Shuangyan Liu ◽  
Haomin Jiang ◽  
Linan Wang ◽  
...  
Keyword(s):  
Hydroxyl Radicals ◽  
Active Sites ◽  
Bond Cleavage ◽  
Phenolic Hydroxyl ◽  
Hydroxyl Groups ◽  
Phenolic Hydroxyl Groups

˙OH selectively attacks the active sites opposite to phenolic hydroxyl groups and leads to bond-cleavage of ether bonds.

scholarly journals Signal-Processing and Adaptive Prototissue Formation in Metabolic DNA Protocells

2021 ◽  
Author(s):  
Avik Samanta ◽  
Maximilian Hörner ◽  
Wei Liu ◽  
Wilfried Weber ◽  
Andreas Walther
Keyword(s):  
Signal Processing ◽  
Active Sites ◽  
Bond Cleavage ◽  
Soft Materials ◽  
Metabolic Reaction ◽  
Strand Displacement ◽  
Synthetic Cell ◽  
Displacement Reactions ◽  
Dna Strand

The fundamental life-defining processes in living cells, such as replication, division, adaptation, and tissue formation, take place via intertwined metabolic reaction networks orchestrating downstream signal processing in a confined, crowded environment with high precision. Hence, it is crucial to understand and reenact some of these functions in wholly synthetic cell-like entities (protocells) to envision designing soft-materials with life-like traits. Herein, we report on a programmable all-DNA protocell (PC) composed of a liquid DNA interior and a hydrogel-like shell, harboring DNAzyme active sites in the interior whose catalytic bond-cleaving activity leads to a downstream phenotype change in the protocells, as well as triggers prototissue formation. In this regard, we coupled several tools of DNA nanoscience, such as RNA cleavage, dynamic strand displacement reactions, and multivalent palindromic interactions, in a synchronize pathway so that the input signal can be processed inside the protocells and generate downstream cues giving rise to metabolic adaptive behavior. For example, the compartmentalized DNAzyme catalyzes the bond-cleavage of a substrate that releases a DNA strand in situ to trigger a strand displacement reaction at the shell of the protocells leading to a change in color resembling a “phenotype-like” change in cells, and finally to establish communication with other protocells via multivalent interactions.

Human Plasminogen Variant Chicago III

1982 ◽  
Vol 48 (02) ◽  
pp. 146-152 ◽  
Author(s):  
R C Wohl ◽  
L Summaria ◽  
J Chediak ◽  
S Rosenfeld ◽  
K C Robbins
Keyword(s):  
Rate Constants ◽  
Active Sites ◽  
Bond Cleavage ◽  
Activation Parameters ◽  
Peptide Bond ◽  
Single Population ◽  
Homogeneous Population ◽  
Peptide Bond Cleavage ◽  
Michaelis Constants ◽  
Catalytic Rate

SummaryA new abnormal, variant, plasminogen Chicago III has been isolated from a patient with recurring deep vein thrombosis. Studies on the plasma fibrinolytic system of four family members showed no inheritance pattern. Kinetics of activation parameters of Chicago III plasminogen with different activators showed lowered catalytic rate constants from 159fold with urokinase, to 3fold with light (B) chain ‧ streptokinase complex, to 1.3fold with streptokinase. The Michaelis constants of activation of Chicago III plasminogen were 16fold higher with streptokinase, 6fold higher with light (B) chain ‧ streptokinase complex, and similar with urokinase. Each of the three activators exhibited different interaction characteristics with this variant zymogen, as they did with variant Chicago I and Chicago II plasminogens (previously reported). However, the latter variants were characterized by having normal catalytic rate constants of activation, with higher than normal apparent Michaelis constants of activation. Chicago III plasminogen, as well as Chicago I and II plasminogens, has a homogeneous population of molecules; the interpretation of the kinetic data was possible only in terms of a single population of molecules. The plasmins derived from Chicago I plasminogen, and also Chicago II and Chicago III plasminogens, have 100% active sites with normal amidase parameters. Basically, a single population of normal isoelectric forms were found in the Chicago III plasma, with three minor forms, about 11% of the total.The kinetic parameters have permitted us to classify the four known plasminogen variants into three different classes. The Class A homozygote (Tochigi) has both an active center defect and a charge mutation difference with normal cleavage of the Arg560-Val peptide bond; the Class B homozygote (Chicago I and Chicago II) has a Km of activation defect with impaired activator binding and normal cleavage of the Arg560-Val peptide bond; and, the Class C homozygote (Chicago III) has both a Km of activation defect with impaired activator binding and a kcat of activation defect, and impaired Arg560-Val peptide bond cleavage.

scholarly journals Tools for Prescreening the Most Active Sites on Ir and Rh Clusters toward C–H Bond Cleavage of Ethane: NBO Charges and Wiberg Bond Indexes

ACS Omega ◽  
2019 ◽  
Vol 4 (20) ◽  
pp. 18809-18819
Author(s):  
Yingbin Ge ◽  
Anna Le ◽  
Gregory J. Marquino ◽  
Phuc Q. Nguyen ◽  
Kollin Trujillo ◽  
...  
Keyword(s):  
Active Sites ◽  
Bond Cleavage ◽  
Nbo Charges

Kinetic Assessment of the Dry Reforming of Methane over a Solid Solution Ni–La Oxide Catalyst

2021 ◽  
Author(s):  
Victor Stivenson Sandoval-Bohorquez ◽  
Edgar M. Morales-Valencia ◽  
Carlos Omar Castillo-Araiza ◽  
Luz Marina Ballesteros Rueda ◽  
Víctor Gabriel Baldovino Medrano
Keyword(s):  
Solid Solution ◽  
Active Sites ◽  
Oxide Catalyst ◽  
Bond Cleavage ◽  
Scale Up ◽  
Active Surface ◽  
Dry Reforming ◽  
Dry Reforming Of Methane ◽  
Nickel Surface ◽  
Kinetics Of

The dry reforming of methane is a promising technology for the abatement of CH<sub>4</sub> and CO<sub>2</sub>. Solid solution Ni–La oxide catalysts are characterized by their long–term stability (100h) when tested at full conversion. The kinetics of dry reforming over this type of catalysts has been studied using both power law and Langmuir–Hinshelwood based approaches. However, these studies typically deal with fitting the net CH<sub>4</sub> rate hence disregarding competing and parallel surface processes and the different possible configurations of the active surface. In this work, we synthesized a solid solution Ni–La oxide catalyst and tested six Langmuir–Hinshelwood mechanisms considering both single and dual active sites for assessing the kinetics of dry reforming and the competing reverse water gas shift reaction and investigated the performance of the derived kinetic models. In doing this, it was found that: (1) all the net rates were better fitted by a single–site model that considered that the first C–H bond cleavage in methane occurred over a <a>metal−oxygen </a>pair site; (2) this model predicted the existence of a nearly saturated nickel surface with chemisorbed oxygen adatoms derived from the dissociation of CO<sub>2</sub>; (3) the dissociation of CO<sub>2</sub> can either be an inhibitory or an irrelevant step, and it can also modify the apparent activation energy for CH<sub>4</sub> activation. These findings contribute to a better understanding of the dry reforming reaction's kinetics and provide a robust kinetic model for the design and scale–up of the process.

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