scholarly journals The Structure of Oxalate Decarboxylase at its Active pH

2018 ◽  
Author(s):  
M. J. Burg ◽  
J. L. Goodsell ◽  
U. T. Twahir ◽  
S. D. Bruner ◽  
A. Angerhofer
Keyword(s):  
Active Site ◽  
Density Functional ◽  
Quaternary Structure ◽  
Density Functional Theory Calculations ◽  
Strong Hydrogen Bond ◽  
Binding Modes ◽  
Oxalate Decarboxylase ◽  
Direct Role ◽  
Closed Conformation ◽  
Loop Region

AbstractOxalate decarboxylase catalyzes the redox-neutral unimolecular disproportionation reaction of oxalic acid. The pH maximum for catalysis is ~4.0 and activity is negligible above pH7. Here we report on the first crystal structure of the enzyme in its active pH range at pH4.6, and at a resolution of 1.45 Å, the highest to date. The fundamental tertiary and quaternary structure of the enzyme does not change with pH. However, the low pH crystals are heterogeneous containing both a closed and open conformation of a flexible loop region which gates access to the N-terminal active site cavity. Residue E162 in the closed conformation points away from the active-site Mn ion owing to the coordination of a buffer molecule, acetate. Since the quaternary structure of the enzyme appears unaffected by pH many conclusions drawn from the structures taken at high pH remain valid. Density functional theory calculations of the possible binding modes of oxalate to the N-terminal Mn ion demonstrate that both mono- and bi-dentate coordination modes are possible in the closed conformation with an energetic preference for the bidentate binding mode. The simulations suggest that R92 plays an important role as a guide for positioning the substrate in its catalytically competent orientation. A strong hydrogen bond is seen between the bi-dentate bound substrate and E101, one of the coordinating ligands for the N-terminal Mn ion. This suggests a more direct role of E101 as a transient base during the first step of catalysis.

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 Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane

2018 ◽  
Vol 115 (18) ◽  
pp. 4565-4570 ◽  
Author(s):  
Benjamin E. R. Snyder ◽  
Lars H. Böttger ◽  
Max L. Bols ◽  
James J. Yan ◽  
Hannah M. Rhoda ◽  
...  
Keyword(s):  
Active Site ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Heme Iron ◽  
Zeolite Lattice ◽  
Non Heme Iron ◽  
Bonding Interaction ◽  
Lattice Density ◽  
X Ray Absorption

Iron-containing zeolites exhibit unprecedented reactivity in the low-temperature hydroxylation of methane to form methanol. Reactivity occurs at a mononuclear ferrous active site, α-Fe(II), that is activated by N2O to form the reactive intermediate α-O. This has been defined as an Fe(IV)=O species. Using nuclear resonance vibrational spectroscopy coupled to X-ray absorption spectroscopy, we probe the bonding interaction between the iron center, its zeolite lattice-derived ligands, and the reactive oxygen. α-O is found to contain an unusually strong Fe(IV)=O bond resulting from a constrained coordination geometry enforced by the zeolite lattice. Density functional theory calculations clarify how the experimentally determined geometric structure of the active site leads to an electronic structure that is highly activated to perform H-atom abstraction.

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.

Solvent effect on electron and proton transfer in the excited state of a hydrogen bonded phenol–imidazole complex

RSC Advances ◽  
2014 ◽  
Vol 4 (73) ◽  
pp. 38551-38557 ◽  
Author(s):  
Baotao Kang ◽  
Hu Shi ◽  
Shihai Yan ◽  
Jin Yong Lee
Keyword(s):  
Density Functional Theory ◽  
Excited State ◽  
Photosystem Ii ◽  
Ground State ◽  
Active Site ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Model System ◽  
Functional Theory ◽  
First Excited State

Density functional theory calculations have been carried out for the ground state (S0) and the first excited state (S1) of the H-bonded phenol and imidazole complex as a model system for the active site of photosystem II.

MERCURY ADSORPTION ON SULFURIC ACID-IMPREGNATED CARBONACEOUS SURFACE: THEORETICAL STUDY

2014 ◽  
Vol 21 (01) ◽  
pp. 1450018 ◽  
Author(s):  
PING HE ◽  
JIANG WU ◽  
XIUMIN JIANG ◽  
WEIGUO PAN ◽  
JIANXING REN
Keyword(s):  
Sulfuric Acid ◽  
Adsorption Capacity ◽  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Mercury Removal ◽  
Mercury Adsorption ◽  
Acid Effect ◽  
Negative Effect

Density functional theory calculations are performed to provide a molecular-level understanding of the mechanism of mercury adsorption on sulfuric acid-impregnated carbonaceous surface. The carbonaceous surface is modeled by a nine-fused benzene ring in which its edge carbon atoms on the upper side are unsaturated to simulate the active sites for reaction. SO 4 clusters with and without charge are examined to act as the representative species to model the sulfuric acid absorbed on the carbonaceous surface. All of the possible approaches of SO 4 clusters with and without charge on the carbonaceous surface are conduced to study their effects on mercury adsorption. The results suggest that sulfuric acid effect on the mercury adsorption capacity of the carbonaceous surface is very complicated, and it depends on a combination of concentration and charge of SO 4 cluster. SO 4 cluster presents a positive effect on mercury adsorption on the carbonaceous surface, but higher concentration of SO 4 cluster decreases the adsorption capacity of the carbonaceous surface for mercury removal because there is considerable competition for active sites between Hg and SO 4 cluster. Since all of the possible approaches of mercury on the carbonaceous surface with [Formula: see text] cluster, excluding one that mercury is adsorbed at bridge active site, can lead to the decrease in the adsorption energies of mercury on the carbonaceous surface, [Formula: see text] cluster presents a negative effect on the capacity of the carbonaceous surface for mercury adsorption regardless of the concentration of [Formula: see text] cluster. The results also indicate that SO 2 cluster and surface oxygen complex can be formed from SO 4 cluster with or without charge if mercury is adsorbed at bridge active site, which facilitates the mercury removal for the carbonaceous surface.

scholarly journals Theoretical Studies on the Binding Mode and Reaction Mechanism of TLP Hydrolase kpHIUH

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3884
Author(s):  
Xixi Wang ◽  
Jiankai Shan ◽  
Wei Liu ◽  
Jing Li ◽  
Hongwei Tan ◽  
...  
Keyword(s):  
Active Site ◽  
Density Functional ◽  
Catalytic Mechanism ◽  
Density Functional Theory Calculations ◽  
Binding Mode ◽  
Nucleophilic Attack ◽  
Hydrogen Bond Interactions ◽  
Binding Interface ◽  
Protein Dimer ◽  
Two Stages

In this work, we have investigated the binding conformations of the substrate in the active site of 5-HIU hydrolase kpHIUH and its catalytic hydrolysis mechanism. Docking calculations revealed that the substrate adopts a conformation in the active site with its molecular plane laying parallel to the binding interface of the protein dimer of kpHIUH, in which His7 and His92 are located adjacent to the hydrolysis site C6 and have hydrogen bond interactions with the lytic water. Based on this binding conformation, density functional theory calculations indicated that the optimal catalytic mechanism consists of two stages: (1) the lytic water molecule is deprotonated by His92 and carries out nucleophilic attack on C6=O of 5-HIU, resulting in an oxyanion intermediate; (2) by accepting a proton transferred from His92, C6–N5 bond is cleaved to completes the catalytic cycle. The roles of His7, His92, Ser108 and Arg49 in the catalytic reaction were revealed and discussed in detail.

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