DFT exploration of active site motifs in methane hydroxylation by Ni-ZSM-5 zeolite

2018 ◽  
Vol 8 (22) ◽  
pp. 5875-5885 ◽  
Author(s):  
Muhammad Haris Mahyuddin ◽  
Kazunari Yoshizawa
Keyword(s):  
Dft Calculations ◽  
Active Site ◽  
Active Sites ◽  
Zeolite P

DFT calculations suggest [Ni2(μ-O)2]2+ and [Ni3(μ-O)3]2+ species as two possible active sites in methane hydroxylation by Ni-ZSM-5 zeolite. Both of them are predicted to activate methane and desorb the formed methanol with low activation and desorption energies.

Catalytic Resonance Theory: Parallel Reaction Pathway Control

2019 ◽  
Author(s):  
M. Alexander Ardagh ◽  
Manish Shetty ◽  
Anatoliy Kuznetsov ◽  
Qi Zhang ◽  
Phillip Christopher ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
Active Site ◽  
Active Sites ◽  
Reaction Pathway ◽  
Control Strategies ◽  
Oscillation Amplitude ◽  
Catalytic Performance ◽  
Parallel Reaction ◽  
Resonance Theory ◽  
Static Conditions

Catalytic enhancement of chemical reactions via heterogeneous materials occurs through stabilization of transition states at designed active sites, but dramatically greater rate acceleration on that same active site is achieved when the surface intermediates oscillate in binding energy. The applied oscillation amplitude and frequency can accelerate reactions orders of magnitude above the catalytic rates of static systems, provided the active site dynamics are tuned to the natural frequencies of the surface chemistry. In this work, differences in the characteristics of parallel reactions are exploited via selective application of active site dynamics (0 < ΔU < 1.0 eV amplitude, 10<sup>-6</sup> < f < 10<sup>4</sup> Hz frequency) to control the extent of competing reactions occurring on the shared catalytic surface. Simulation of multiple parallel reaction systems with broad range of variation in chemical parameters revealed that parallel chemistries are highly tunable in selectivity between either pure product, even when specific products are not selectively produced under static conditions. Two mechanisms leading to dynamic selectivity control were identified: (i) surface thermodynamic control of one product species under strong binding conditions, or (ii) catalytic resonance of the kinetics of one reaction over the other. These dynamic parallel pathway control strategies applied to a host of chemical conditions indicate significant potential for improving the catalytic performance of many important industrial chemical reactions beyond their existing static performance.

Nonlinear Vibrations in a 2-Dimensional Protein Cluster Model with Linear Bonds

2000 ◽  
Vol 214 (1) ◽  
Author(s):  
E.G. Shidlovskaya ◽  
L. Schimansky-Geier ◽  
Yu.M. Romanovsky
Keyword(s):  
Active Site ◽  
Internal Resonance ◽  
Cluster Model ◽  
Active Sites ◽  
Nonlinear Vibrations ◽  
Nonlinear Phenomena ◽  
Two Dimensional ◽  
Dimensional Model ◽  
Two Dimensional Model

A two dimensional model for the substrate inside a pocket of an active site of an enzyme is presented and investigated as a vibrational system. The parameters of the system are evaluated for α-chymotrypsin. In the case of internal resonance it is analytically and numerically shown that the energy concentrated on a certain degree of freedom might be several times larger than in the non-resonant case. Additionally, the system is driven by harmonic excitations and again energy due to nonlinear phenomena is redistributed inhomogeneously. These results may be of importance for the determination of the rates of catalytic events of substrates bound in pockets of active sites.

Effect of Modifiers on the Hydrolysis of Basic and Neutral Peptides by Carboxypeptidase B

1975 ◽  
Vol 53 (7) ◽  
pp. 747-757 ◽  
Author(s):  
Graham J. Moore ◽  
N. Leo Benoiton
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Kinetic Behavior ◽  
Carboxypeptidase A ◽  
Phenyllactic Acid ◽  
Carboxypeptidase B ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Basic Peptides ◽  
Hydrolysis Of

The initial rates of hydrolysis of Bz-Gly-Lys and Bz-Gly-Phe by carboxypeptidase B (CPB) are increased in the presence of the modifiers β-phenylpropionic acid, cyclohexanol, Bz-Gly, and Bz-Gly-Gly. The hydrolysis of the tripeptide Bz-Gly-Gly-Phe is also activated by Bz-Gly and Bz-Gly-Gly, but none of these modifiers activate the hydrolysis of Bz-Gly-Gly-Lys, Z-Leu-Ala-Phe, or Bz-Gly-phenyllactic acid by CPB. All modifiers except cyclohexanol display inhibitory modes of binding when present in high concentration.Examination of Lineweaver–Burk plots in the presence of fixed concentrations of Bz-Gly has shown that activation of the hydrolysis of neutral and basic peptides by CPB, as reflected in the values of the extrapolated parameters, Km(app) and keat, occurs by different mechanisms. For Bz-Gly-Gly-Phe, activation occurs because the enzyme–modifier complex has a higher affinity than the free enzyme for the substrate, whereas activation of the hydrolysis of Bz-Gly-Lys derives from an increase in the rate of breakdown of the enzyme–substrate complex to give products.Cyclohexanol differs from Bz-Gly and Bz-Gly-Gly in that it displays no inhibitory mode of binding with any of the substrates examined, activates only the hydrolysis of dipeptides by CPB, and has a greater effect on the hydrolysis of the basic dipeptide than on the neutral dipeptide. Moreover, when Bz-Gly-Lys is the substrate, cyclohexanol activates its hydrolysis by CPB by increasing both the enzyme–substrate binding affinity and the rate of the catalytic step, an effect different from that observed when Bz-Gly is the modifier.The anomalous kinetic behavior of CPB is remarkably similar to that of carboxypeptidase A, and is a good indication that both enzymes have very similar structures in and around their respective active sites. A binding site for activator molecules down the cleft of the active site is proposed for CPB to explain the observed kinetic behavior.

scholarly journals Photolabelling of Salmonella typhimurium LT2 sialidase. Identification of a peptide with a predicted structural similarity to the active sites of influenza-virus sialidases

1992 ◽  
Vol 285 (3) ◽  
pp. 957-964 ◽  
Author(s):  
T G Warner ◽  
R Harris ◽  
R McDowell ◽  
E R Vimr
Keyword(s):  
Salmonella Typhimurium ◽  
Active Site ◽  
Influenza A ◽  
Active Sites ◽  
Enzyme Inhibitors ◽  
Structural Similarity ◽  
Competitive Inhibitor ◽  
Beta Sheets ◽  
Sialidase Inhibitor ◽  
Active Site Cavity

The sialidase from Salmonella typhimurium LT2 was characterized by using photoaffinity-labelling techniques. The well-known sialidase inhibitor 5-acetamido-2,6-anhydro-3,5-dideoxy-D-glycero-D-galacto-non- 2-enonic acid (Neu5Ac2en) was modified to contain an amino group at C-9, which permitted the incorporation of 4-azidosalicylic acid in amide linkage at this position. Labelling of the purified protein with the radioactive (125I) photoprobe was determined to be highly specific for a region within the active-site cavity. This conclusion was based on the observation that the competitive inhibitor Neu5Ac2en in the photolysis mixture prevented labelling of the protein. In contrast, compounds with structural and chemical features similar to the probe and Neu5Ac2en, but which were not competitive enzyme inhibitors, did not affect the photolabelling of the protein. The peptide interacting with the probe was identified by CNBr treatment of the labelled protein, followed by N-terminal sequence analysis. Inspection of the primary structure of the protein, predicted from the cloned structural gene for the sialidase [Hoyer, Hamilton, Steenbergen & Vimr (1992) Mol. Microbiol. 6, 873-884] revealed that the label was incorporated into a 9.6 kDa fragment situated within the terminal third of the molecule near the C-terminal end. Secondary-structural predictions using the Garnier-Robson algorithm [Garnier, Osguthorpe & Robson (1978) J. Mol. Biol. 120, 97-120] of the labelled peptide revealed a structural similarity to the active site of influenza-A- and Sendai-HN-virus sialidases with a repetitive series of alternating beta-sheets connected with loops.

scholarly journals Multiplicity of Active-Site in Heterogeneous Ziegler-Natta Catalyst and Its Correlation with Polymer Microstructure

1970 ◽  
Vol 46 (4) ◽  
pp. 487-494
Author(s):  
ATM Kamrul Hasan
Keyword(s):  
Molecular Weight ◽  
Computer Simulation ◽  
Active Site ◽  
Photoelectron Spectroscopy ◽  
Active Sites ◽  
Chain Structure ◽  
Surface Complexes ◽  
Polymer Microstructure ◽  
Natta Catalyst ◽  
Ziegler Natta Catalyst

Multiplicity of active-site in heterogeneous Ziegler-Natta catalysts and its correlation with polymer microstructure was studied through the surface structure analysis of catalyst by computer simulation of X-ray Photoelectron Spectroscopy (XPS) data and microstructure investigation of polypropylene chains based on the deconvolution of the molecular weight distribution curves by multiple Flory most probable distributions using Gel Permeation Chromatography (GPC) method. The number and relative intensities of these peaks were found correlated to the distribution of multiple active sites. In this investigation, four individual categories of active sites were identified, each of which yields polypropylene with unique properties of molecular weight and chain structure different from other active sites. The reason of the multiplicity of active sites was determined by the presence of different locations of surface titanium species coordinated with other surface atoms or molecules. These different surface complexes of active species determine the multiple active site nature of catalyst which replicates the microtacticity, molecular weight and chain microstructure distribution of polymer. Keywords: Ziegler-Natta catalyst; Multiple active sites; Flory components; Computer simulation; Deconvolution; MWD. DOI: http://dx.doi.org/10.3329/bjsir.v46i4.9596 BJSIR 2011; 46(4): 487-494

scholarly journals Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites

2018 ◽  
Vol 115 (48) ◽  
pp. 12124-12129 ◽  
Author(s):  
Benjamin E. R. Snyder ◽  
Max L. Bols ◽  
Hannah M. Rhoda ◽  
Pieter Vanelderen ◽  
Lars H. Böttger ◽  
...  
Keyword(s):  
High Activity ◽  
Active Site ◽  
Active Sites ◽  
High Performance ◽  
Density Functional ◽  
Catalyst Deactivation ◽  
Density Functional Theory Calculations ◽  
Oxidation Catalysis ◽  
Spectroscopic Techniques ◽  
Benzene Hydroxylation

A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates.

scholarly journals Computational Investigation of the Role of Active Site Heterogeneity for a Supported Organovanadium(III) Hydrogenation Catalyst

2021 ◽  
Author(s):  
Prajay Patel ◽  
Robert Wells ◽  
David Kaphan ◽  
Massimiliano Delferro ◽  
Rex T. Skodje ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Computational Models ◽  
Surface Heterogeneity ◽  
Reaction Pathways ◽  
Spectroscopic Techniques ◽  
Organometallic Catalysts ◽  
Heterolytic Cleavage ◽  
Styrene Hydrogenation

<div> <div> <p></p><p><a>A crucial consideration for supported heterogeneous catalysts is the non-uniformity of the active sites, particularly for Supported Organometallic Catalysts (SOMCs). Standard spectroscopic techniques, such as X-ray absorption spectroscopy (XAS), reflect the nature of the most populated sites, which are often intrinsically structurally distinct from the most catalytically active sites. With computational models, often only a few representative structures are used to depict catalytic active sites on a surface, even though there are numerous observable factors of surface heterogeneity that contribute to the kinetically favorable active species. A previously reported study on the mechanism of a surface organovanadium(III) catalyst [(SiO)V<sup>III</sup>(Mes)(THF)] for styrene hydrogenation yielded two possible mechanisms: heterolytic cleavage and redox cycling. These two mechanistic scenarios are challenging to differentiate experimentally based on the kinetic readouts of the catalyst are identical. To showcase the importance of modeling surface heterogeneity and its effect on catalytic activity, density functional theory (DFT) computational models of a series of potential active sites of [(SiO)V<sup>III</sup>(Mes)(THF)] for the reaction pathways are applied in combination with kinetic Monte Carlo (kMC) simulations. Computed results were t then compared to the previously reported experimental kinetic study</a><a>.: 1) DFT free energy reaction pathways indicated the likely active site and pathway for styrene hydrogenation; a heterolytic cleavage pathway requiring a bare tripodal vanadium site. 2) From the kMC simulations, a mixture of the different bond lengths from the support oxygen to the metal center was required to qualitatively describe the experimentally observed kinetic aspects of a supported organovanadium(III) catalyst for olefin hydrogenation. </a>This work underscores the importance of modeling surface heterogeneity in computational catalysis.</p><p></p></div></div>

scholarly journals Short hydrogen bonds in the catalytic mechanism of serine proteases

2008 ◽  
Vol 73 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Vladimir Leskovac ◽  
Svetlana Trivic ◽  
Draginja Pericin ◽  
Mira Popovic ◽  
Julijan Kandrac
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Active Site ◽  
Serine Proteases ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Data Bank ◽  
Ground State Structure ◽  
Low Barrier Hydrogen Bonds ◽  
Short Hydrogen Bonds

The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 ? revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 ? long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 ? long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

Understanding condensation domain selectivity in non-ribosomal peptide biosynthesis: structural characterization of the acceptor bound state

2021 ◽  
Author(s):  
Max Cryle ◽  
Thierry Izore ◽  
Y. T. Ho ◽  
Joe Kaczmarski ◽  
Athina Gavriilidou ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Peptide Bond ◽  
Bound State ◽  
Modular Assembly ◽  
Central Function ◽  
Acceptor Substrate ◽  
Peptide Synthetases ◽  
Peptide Biosynthesis ◽  
Condensation Domain

Abstract Non-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report the first structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this previously uncharacterized complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.

Energy Distribution of Active Sites in Heterogeneous Ziegler-Natta Catalysts. Method of Study of Active Site Non-Uniformity

1999 ◽  
pp. 89-96 ◽  
Author(s):  
L. A. Novokshonova ◽  
N. Yu Kovaleva ◽  
Yu A. Gavrilov ◽  
V. G. Krasheninnikov ◽  
T. A. Ladygin ◽  
...  
Keyword(s):  
Energy Distribution ◽  
Active Site ◽  
Active Sites ◽  
Ziegler Natta Catalysts
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