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 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 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 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.

On the role of lysine in the active site Ser-X-X-Lys region of penicillin-recognizing enzymes

2010 ◽  
Vol 88 (1) ◽  
pp. 1-4
Author(s):  
Saul Wolfe ◽  
Kiyull Yang
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Basis Set ◽  
Penicillin G ◽  
Hydroxyl Group ◽  
Functional Theory ◽  
One Step ◽  
Optimized Geometries

Using Autodock, docking of penicillin G to the crystal structures of penicillin-recognizing enzymes leads to an alignment in the active site Ser-X-X-Lys region consisting of the serine hydroxyl group, the terminal amino group of lysine, a second hydroxyl group, and the N–C=O of the β-lactam. This alignment is consistent with the notion that acylation of the serine hydroxyl group proceeds by a one-step cooperative mechanism in which C–O bond formation and proton transfer to the β-lactam nitrogen take place through a heteroatom bridge. For the cooperative ring opening of penam by two molecules of methanol and one molecule of methylamine or one molecule of water, density functional theory with the B3LYP DFT gradient-corrected functional and the 6–31G(d) basis set reproduces the alignment seen in the docked structures. Methylamine lowers the barrier calculated at MP2/6–31G(d) from the DFT-optimized geometries by 3 kcal/mol; water increases the barrier by 4 kcal/mol. The function of the conserved lysine in the active sites of penicillin-recognizing enzymes is therefore to catalyze the formation of an acyl enzyme by a cooperative mechanism.

Effects of particle size and edge structure on the electronic structure, spectroscopic features, and chemical properties of Au(111)-supported MoS2 nanoparticles

2016 ◽  
Vol 188 ◽  
pp. 323-343 ◽  
Author(s):  
Albert Bruix ◽  
Jeppe V. Lauritsen ◽  
Bjørk Hammer
Keyword(s):  
Electronic Structure ◽  
Active Sites ◽  
Density Functional ◽  
Computational Models ◽  
Chemical Properties ◽  
Structural Motif ◽  
Edge Structure ◽  
Catalytically Active ◽  
Level Shifts ◽  
And Chemical Properties

Materials based on MoS2 are widely used as catalysts and their structure usually consists of single-layered MoS2 nanoparticles whose edges are known to constitute the catalytically active sites. Methods based on density functional theory are used in this work to calculate the electronic structure of representative computational models of MoS2 nanoparticles supported on Au(111). By considering nanoparticles with different edge-terminations, compositions, and sizes, we describe how the electronic structure, Mo3d core-level shifts, and chemical properties (i.e. H adsorption and S vacancy formation) depend on the MoS2 nanoparticle size and structure. In addition, site-specific properties, largely inaccessible when using only slab models of MoS2 edges, are reported, which reveal that the edge sites are not uniform along the nanoparticle and largely depend on the proximity to the corners of the triangular NPs, especially when interacting with a metallic support. Furthermore, a structural motif where H atoms adsorb favourably in a bridging position between two Mo atoms is proposed as an active site for the hydrogen evolution reaction.

What causes iron-sulphur bonds in active sites of one-iron superoxide reductase and two-iron superoxide reductase to differ?

2011 ◽  
Vol 65 (4) ◽  
Author(s):  
Radu Silaghi-Dumitrescu
Keyword(s):  
Vibrational Spectroscopy ◽  
Vibrational Spectra ◽  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Superoxide Reductase ◽  
Vibrational Properties ◽  
Nir Absorption ◽  
Semi Empirical ◽  
Ci Calculations

AbstractThe electronic and vibrational properties of [Fe(NHis)4(SCys)] sites responsible for the catalysis of superoxide reduction in two types of superoxide reductase (SOR), one-iron superoxide reductase (1Fe-SOR) and two-iron superoxide reductase (2Fe-SOR), were compared previously (Clay et al., 2003); the differences between these two classes of SOR, examined by UV-VIS and NIR absorption, VTMCD, and vibrational spectroscopy techniques, were interpreted as being indicative of weaker Fe-S bonds in 2Fe-SOR in comparison with 1Fe-SOR. Here, we report on density functional (DFT) and semi-empirical (ZINDO/S-CI) calculations exploring the extent of this difference in bonding between the two classes of SOR. The differences observed experimentally between the electronic spectra of the two SORs are shown to probably arise either from different degrees of torsion between the Fe—ligand bonds or from differences in length of the Fe—carboxylate bond, but are shown to be incompatible with any significant differences in Fe—S bond lengths. The differences observed in the vibrational spectra between the two SORs are shown to correlate with differences in the Fe-S bond length of no more than 0.01 Å, which in turn arise from slight differences in the polarity of the medium surrounding the iron active site in the two proteins.

scholarly journals A Unique Ru-N4-P Coordinated Structure Synergistically Waking Up the Nonmetal P Active Site for Hydrogen Production

Research ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Chuanqiang Wu ◽  
Shiqing Ding ◽  
Daobin Liu ◽  
Dongdong Li ◽  
Shuangming Chen ◽  
...  
Keyword(s):  
Hydrogen Evolution ◽  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Highly Efficient ◽  
Catalytic Sites ◽  
Catalytically Active ◽  
Doped Graphene ◽  
Waking Up

Numerous experiments have demonstrated that the metal atom is the active center of monoatomic catalysts for hydrogen evolution reaction (HER), while the active sites of nonmetal doped atoms are often neglected. By combining theoretical prediction and experimental verification, we designed a unique ternary Ru-N4-P coordination structure constructed by monodispersed Ru atoms supported on N,P dual-doped graphene for highly efficient hydrogen evolution in acid solution. The density functional theory calculations indicate that the charge polarization will lead to the most charge accumulation at P atoms, which results in a distinct nonmetallic P active sites with the moderate H∗ adsorption energy. Notably, these P atoms mainly supply highly efficient catalytic sites with ultrasmall absorption energy of 0.007 eV. Correspondingly, the Ru-N4-P demonstrated outstanding HER performance not only in an acidic condition but also in alkaline environment. Notably, the performance of Ru-NPC catalyst at high current is even superior to the commercial Pt/C catalysts, whether in acidic or alkaline medium. Our in situ synchrotron radiation infrared spectra demonstrate that a P-Hads intermediate is continually emerging on the Ru-NPC catalyst, actively proving the nonmetallic P catalytically active site in HER that is very different with previously reported metallic sites.

Molecular Orbital Studies of Enzyme Catalysed Reactions. Rearrangement of Chorismate to Prephenate

1979 ◽  
Vol 32 (9) ◽  
pp. 1921 ◽  
Author(s):  
PR Andrews ◽  
RC Haddon
Keyword(s):  
Aqueous Solution ◽  
Transition State ◽  
Molecular Orbital ◽  
Active Site ◽  
Active Sites ◽  
Transition States ◽  
Reaction Pathways ◽  
Carboxyl Groups ◽  
Molecular Orbital Calculations ◽  
Charge Delocalization

Molecular orbital calculations are used to describe the reaction surface for the non-enzymic Claisen rearrangement of chorismate to prephenate, which may proceed through either a boat-like or a chair-like transition state. Detailed molecular geometries are obtained for the neutral and dianionic forms of chorismate, prephenate, and the alternative transition states. The transition states are asymmetric structures in which the breaking C-O bond (c. 1.45 A) is significantly shorter than the making C-C bond (c. 1.95 A). The alternative reaction pathways have almost identical enthalpies of activation (chair, 277.4 kJ/mol ; boat, 282.8 kJ/mol; dianionic forms) which result partly from a loss of internal bond strength and partly from repulsive interactions between the polar carboxyl groups. Protonation stabilizes the transition states (chair, 247.3 kJ/mol; boat, 248.5 kJ/mol ; diacid forms) by delocalization of charge in the carboxyl groups, and a similar mechanism is proposed for the greatly reduced enthalpy of activation in aqueous solution (86.6 kJ/mol). The enthalpy difference between the alternative reaction pathways is insufficient to define a preferred transition state structure, and either pathway may be favoured for the non-enzymic reaction in aqueous solution. For the enzyme-catalysed reaction the chair pathway is used, and the calculated transition state structures and enthalpy barriers provide information relevant to the catalytic mechanism. They indicate that an active site comprising only two essential binding groups is sufficient to account for catalysis; the orientation of these groups within the active site should allow simultaneous bond formation, accompanied by charge delocalization, to both carboxyl groups of the transition state, but not to those of substrate or product. The calculated structure for the chair transition state, taken in conjunction with those for chorismate and prephenate, thus provides a template for the active sites of chorismate mutases.

scholarly journals Spectroscopic ruler for measuring active-site distortions based on Raman optical activity of a hydrogen out-of-plane vibration

2018 ◽  
Vol 115 (35) ◽  
pp. 8671-8675 ◽  
Author(s):  
Shojiro Haraguchi ◽  
Takahito Shingae ◽  
Tomotsumi Fujisawa ◽  
Noritaka Kasai ◽  
Masato Kumauchi ◽  
...  
Keyword(s):  
Dihedral Angle ◽  
Optical Activity ◽  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Water Soluble ◽  
Plane Vibration ◽  
Raman Optical Activity ◽  
Out Of Plane ◽  
Halorhodospira Halophila

Photoactive yellow protein (PYP), from the phototrophic bacterium Halorhodospira halophila, is a small water-soluble photoreceptor protein and contains p-coumaric acid (pCA) as a chromophore. PYP has been an attractive model for studying the physical chemistry of protein active sites. Here, we explore how Raman optical activity (ROA) can be used to extract quantitative information on distortions of the pCA chromophore at the active site in PYP. We use 13C8-pCA to assign an intense signal at 826 cm−1 in the ROA spectrum of PYP to a hydrogen out-of-plane vibration of the ethylenic moiety of the chromophore. Quantum-chemical calculations based on density functional theory demonstrate that the sign of this ROA band reports the direction of the distortion in the dihedral angle about the ethylenic C=C bond, while its amplitude is proportional to the dihedral angle. These results document the ability of ROA to quantify structural deformations of a cofactor molecule embedded in a protein moiety.

scholarly journals Atomic Control of Active Site Ensembles in Ordered Alloys to Enhance Hydrogenation Selectivity

2021 ◽  
Author(s):  
Anish Dasgupta ◽  
Hoaran He ◽  
Rushi Gong ◽  
Shun-Li Shang ◽  
Eric Zimmerer ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Functional Theory ◽  
Ethane Conversion ◽  
Precise Control ◽  
Atom Manipulation ◽  
Catalytic Sites ◽  
Ordered Alloys ◽  
Ethylene Selectivity

Abstract Intermetallic compounds offer unique opportunities for atom-by-atom manipulation of catalytic ensembles through precise stoichiometric control. The [Pd, (M), Zn] γ-brass phase allows for controlled synthesis of Pd-M-Pd catalytic sites (M = Zn, Pd, Cu, Ag and Au) isolated in an inert Zn matrix. These multi-atom heteronuclear active sites are catalytically distinct from Pd single atoms and fully coordinated Pd. We quantify the unexpectedly large effect of active site composition (i.e., identity of M atom in Pd-M-Pd sites) on ethylene selectivity during acetylene semi-hydrogenation. Subtle stoichiometric control demonstrates Pd-Pd-Pd sites are active for ethylene hydrogenation, whereas Pd-Zn-Pd sites show no measurable ethylene to ethane conversion. Agreement between experimental and density functional theory predicted activities and selectivities demonstrates precise control of Pd-M-Pd active site composition. The diversity and well-defined structure of intermetallics can be utilized to design active sites assembled with atomic-level precision.

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