Modeling the Active Sites in Metalloenzymes 5. The Heterolytic Bond Cleavage of H2in the [NiFe] Hydrogenase ofDesulfovibrio gigasby a Nucleophilic Addition Mechanism

2001 ◽  
Vol 40 (24) ◽  
pp. 6201-6203 ◽  
Author(s):  
Shuqiang Niu ◽  
Michael B. Hall
Keyword(s):  
Nucleophilic Addition ◽  
Active Sites ◽  
Bond Cleavage

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.

Synthesis of Potential Anticancer 1-(1H-Indol-3-yl)isoquinolines by Silver Nitrate Mediated Tandem Reactions of 2-Alkynyl­benzaldehyde Azines and Indoles

Synlett ◽  
2018 ◽  
Vol 29 (06) ◽  
pp. 773-778 ◽  
Author(s):  
Yun-Hui Zhao ◽  
Zhihua Zhou ◽  
Yong-Cheng Ma ◽  
Yueyang Luo ◽  
Yingli Zhu ◽  
...  
Keyword(s):  
Silver Nitrate ◽  
Nucleophilic Addition ◽  
Bond Cleavage ◽  
Domino Reaction ◽  
Reference Compound ◽  
Lead Compounds ◽  
Mild Conditions ◽  
Antitumor Compounds ◽  
Interesting Class

Novel antitumor compounds featuring isoquinoline and indole moieties were synthesized by a silver nitrate promoted domino reaction involving intramolecular cyclization, nucleophilic addition of indole, and subsequent N–N bond cleavage. The transformation from readily available starting materials into an interesting class of indole-substituted isoquinolines was completed under mild conditions and by simple operations in moderate to good yields. The antitumor activity of these compounds in vitro was significantly greater than that of a reference compound, 5-fluorouracil. The products might serve as new lead compounds for drugs for the treatment of cancer.

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.

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