scholarly journals Quantum Mechanical Study of Protonation of Oxygen Ligands in the Laccase Active Site Based on X-Ray Structures of Subatomic Resolution

2022 ◽  
Author(s):  
Sergei Gavryushov ◽  
Nikolay Kuzmich ◽  
Konstantin Polyakov
Keyword(s):  
Oxygen Reduction ◽  
Molecular Oxygen ◽  
High Precision ◽  
Active Site ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Stable States ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Wide Range

Laccases are enzymes catalyzing oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Previously studies of oxygen reduction by laccases have recently been reported. They were based on single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution, As a result, coordinates of all non-hydrogen atoms of the active site have been determined with high precision for both oxidized and reduced states of the enzyme. Those data can be used to clarify the mechanism of molecular oxygen reduction by laccases. However, the X-ray data lack information about protonation states of the oxygen ligands involved. Applying quantum mechanical calculations, in the present work protonation of oxygen ligands in the active site of laccase was determined for both reduced and oxidized states of the enzyme (the stable states observed in experiments at reduction of molecular oxygen in laccase). The high precision of X-ray-determined atom coordinates allowed us to simplify preliminary calculations of molecular mechanics for models used in the quantum mechanical calculations.

scholarly journals Enzymatic control of dioxygen binding and functionalization of the flavin cofactor

2018 ◽  
Vol 115 (19) ◽  
pp. 4909-4914 ◽  
Author(s):  
Raspudin Saleem-Batcha ◽  
Frederick Stull ◽  
Jacob N. Sanders ◽  
Bradley S. Moore ◽  
Bruce A. Palfey ◽  
...  
Keyword(s):  
Active Site ◽  
Rational Design ◽  
Quantum Mechanical ◽  
Organic Substrates ◽  
Quantum Mechanical Calculations ◽  
Critical Transition ◽  
Precise Positioning ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fine Tune

The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O2) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O2, as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates. Here we employ O2-pressurized X-ray crystallography and quantum mechanical calculations to reveal how the precise positioning of O2 within a flavoenzyme’s active site enables the regiospecific formation of a covalent flavin–oxygen adduct and oxygenating species (i.e., the flavin-N5-oxide) by mimicking a critical transition state. This study unambiguously demonstrates how enzymes may control the O2 functionalization of an organic cofactor as prerequisite for oxidative catalysis. Our work thus illustrates how O2 reactivity can be harnessed in an enzymatic environment and provides crucial knowledge for future rational design of O2-reactive enzymes.

Crystal Forms of Semisynthetic Ergot Alkaloid Terguride

2002 ◽  
Vol 67 (4) ◽  
pp. 479-489 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Ladislav Cvak ◽  
Alexandr Jegorov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ergot Alkaloid ◽  
Simplified Model ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
Torsion Angles ◽  
Crystal Forms ◽  
X Ray ◽  
Independent Molecules

Two new structures of semisynthetic ergot alkaloid terguride created by unusual number of symmetry-independent molecules were determined by X-ray diffraction methods at 150 K. Form A (monoclinic, P212121, Z = 12) contains three symmetry-independent terguride molecules and two molecules of water in the asymmetric part of the unit cell. The form CA (monoclinic, P21, Z = 8) is an anhydrate remarkable by the presence of four symmetry-independent molecules in the crystal structure. Conformations of twelve symmetry-independent molecules that were found in four already described terguride structures are compared with torsion angles obtained by ab initio quantum-mechanical calculations for the simplified model of N-cyclohexyl-N'-diethylurea.

scholarly journals Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement

2020 ◽  
Vol 25 (6) ◽  
pp. 847-861
Author(s):  
Lili Cao ◽  
Octav Caldararu ◽  
Ulf Ryde
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Bound State ◽  
Real Space ◽  
Quantum Mechanical ◽  
Storage Site ◽  
Quantum Mechanical Calculations ◽  
Reaction Intermediate ◽  
Sulphide Ions ◽  
Vanadium Nitrogenase

Abstract Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum–mechanical calculations. This allows us to test various interpretations of the structure, employing quantum–mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH−-bound state, rather than an N2-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand. Graphic abstract

scholarly journals Design of Zeolite-Covalent Organic Frameworks for Methane Storage

Materials ◽  
2020 ◽  
Vol 13 (15) ◽  
pp. 3322
Author(s):  
Ha Huu Do ◽  
Soo Young Kim ◽  
Quyet Van Le ◽  
Nguyen-Nguyen Pham-Tran
Keyword(s):  
Quantum Mechanical ◽  
Methane Storage ◽  
Quantum Mechanical Calculations ◽  
Covalent Organic Frameworks ◽  
Grand Canonical Monte Carlo ◽  
Adsorption Ability ◽  
Wide Range ◽  
New Type ◽  
Ch4 Adsorption ◽  
Grand Canonical

A new type of zeolite-based covalent organic frameworks (ZCOFs) was designed under different topologies and linkers. In this study, the silicon atoms in zeolite structures were replaced by carbon atoms in thiophene, furan, and pyrrole linkers. Through the adoption of this strategy, 300 ZCOFs structures were constructed and simulated. Overall, the specific surface area of ZCOFs is in the range of 300–3500 m2/g, whereas the pore size is distributed from 3 to 27 Å. Furthermore, the pore volume exhibits a wide range between 0.01 and 1.5 cm3/g. Screening 300 ZCOFs with the criteria towards methane storage, 11 preliminary structures were selected. In addition, the Grand Canonical Monte Carlo technique was utilized to evaluate the CH4 adsorption ability of ZCOFs in a pressure ranging from 1 to 85 bar at a temperature of 298 K. The result reveals that two ZCOF structures: JST-S 183 v/v (65–5.8 bar) and NPT-S 177 v/v (35–1 bar) are considered as potential adsorbents for methane storage. Furthermore, the thermodynamic stability of representative structures is also checked base on quantum mechanical calculations.

Conformational Study of 2,4-Diaryl-3-azabicyclo[3.3.1]nonan-9-ones and Their 3-Methyl Derivatives by Quantum Mechanical Calculations, NMR, and X-ray Crystallography

1994 ◽  
Vol 59 (9) ◽  
pp. 2565-2569 ◽  
Author(s):  
Maria-Selma Arias ◽  
Yves G. Smeyers ◽  
Maria-Jose Fernandez ◽  
Nadine J. Smeyers ◽  
Enrique Galvez ◽  
...  
Keyword(s):  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Conformational Study ◽  
X Ray ◽  
X Ray Crystallography ◽  
Methyl Derivatives

The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism

2019 ◽  
Vol 75 (9) ◽  
pp. 804-816 ◽  
Author(s):  
Konstantin M. Polyakov ◽  
Sergei Gavryushov ◽  
Tatiana V. Fedorova ◽  
Olga A. Glazunova ◽  
Alexander N. Popov
Keyword(s):  
Molecular Oxygen ◽  
Enzymatic Reaction ◽  
Copper Ion ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Fluoride Ions ◽  
X Ray ◽  
Mechanism Of Inhibition ◽  
Wide Range ◽  
Oxygen Ligand

Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X-ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented. Three series of X-ray diffraction data sets were collected with increasing doses of absorbed X-ray radiation from a native S. murashkinskyi laccase crystal and from crystals of complexes of the laccase with chloride and fluoride ions. The data for the native laccase crystal confirmed the previously deduced enzymatic mechanism of molecular oxygen reduction. The structures of the complexes allowed the localization of chloride and fluoride ions in the channel near the T2 copper ion. These ions replace the oxygen ligand of the T2 copper ion in this channel and can play the role of this ligand in the enzymatic reaction. As follows from analysis of the structures from the increasing dose series, the inhibition of laccases by chloride and fluoride anions can be explained by the fact that the binding of these negatively charged ions at the position of the oxygen ligand of the T2 copper ion impedes the reduction of the T2 copper ion.

Molecular X-ray Spectra of Sulfur and Chlorine Bearing Substances

1970 ◽  
Vol 14 ◽  
pp. 453-486 ◽  
Author(s):  
G. Andermann ◽  
H. C. Whitehead
Keyword(s):  
Theoretical Models ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Molecular Models ◽  
X Ray ◽  
Starting Point ◽  
State Models ◽  
Basic Features ◽  
Photon Spectra ◽  
Molecular Bonding

AbstractThe interpretation and use of x-ray photon spectra of substances containing second row elements has utilized a number of theoretical models. These models may be divided into three basic categories, namely, the isolated atom model, various molecular models, and a number of solid state models, it is the purpose of this paper to examine critically the validity and limitations of molecular models for interpreting published x-ray photon spectra and spectra obtained by this group on chlorine and sulfur bearing substances.Chlorine and sulfur bearing substances were chosen for at least three important reasons. First, a great deal of published experimental data already exists on the Kα, Kβ, and L2, 3 transitions of these substances. Second, motivated in part by the long standing controversy concerning possible 3d orbital participation in the bonding of second row elements, there are extensive quantum mechanical calculations for ions containing sulfur and chlorine via simple molecular orbital concepts. Thirdj the availability of accurate photoelectron spectroscopic data on these substances now permits a detailed quantitative comparison of x-ray photon transitions with quantum mechanical calculations.Detailed evaluation along these lines indicates that for many substances the theoretically calculated energy values are frequently within a few electron volts (or less) of the experimentally observed energies. This study, therefore, tends to substantiate a viewpoint suggested by some recently; namely, that for many substances the starting point in interpreting most of the basic features of soft x-ray spectra should be based upon molecular bonding approaches.

Study of IrxMny(CO)n(DMF)z as Electrocatalyst for Oxygen Reduction and Hydrogen Oxidation in the Presence of Fuel Cell Contaminants

2016 ◽  
Vol 19 (4) ◽  
pp. 185-192 ◽  
Author(s):  
M.L. Barrios-Reyna ◽  
J. Uribe-Godínez ◽  
J.M. Olivares-Ramírez ◽  
O. Jiménez-Sandoval
Keyword(s):  
Oxygen Reduction ◽  
Hydrogen Oxidation ◽  
Rotating Disk ◽  
Pem Fuel Cells ◽  
Platinum Group Metals ◽  
The Novel ◽  
Hydrogen Oxidation Reaction ◽  
Acid Media ◽  
X Ray ◽  
Wide Range

The oxygen reduction reaction (ORR) and the hydrogen oxidation reaction (HOR) have been studied on a wide range of elec-trocatalysts, including bimetallic materials which are based solely on platinum group metals and their alloys. This work reports the synthe-sis and characterization of a novel bimetallic electrocatalyst, IrxMny(CO)n(DMF)z, for the ORR and HOR in acid media. The material was synthesized by reacting Ir4(CO)12 and MnCl2·4H2O in DMF. It was characterized structurally by FT-IR and micro-Raman spectroscopy, X-ray diffraction, SEM and energy-dispersive X-ray spectroscopy; the electrochemical characterization was made by the rotating disk elec-trode technique, at room temperature. The electrocatalytic activity of the new material for the ORR and HOR does not show appreciable variations due to the presence of methanol or carbon monoxide, respectively, even at high concentrations of these contaminants (2 mol L-1 methanol and 0.5% CO). This tolerance is a very important property with respect to platinum-based catalysts, which are poisoned by low concentrations of such contaminants. The kinetic parameters of the novel catalyst, such as Tafel slope (b), exchange current density (jo) and charge transfer coefficient (α), are reported as well. The results show that the novel electrocatalyst is attractive for evaluation as cath-ode/anode in PEM fuel cells.

scholarly journals Determination of the electron density in methyl (±)-(1S,2S,3R)-2-methyl-1,3-diphenylcyclopropanecarboxylate using refinements with X-ray scattering factors from wavefunction calculations of the whole molecule

2013 ◽  
Vol 69 (8) ◽  
pp. 910-914 ◽  
Author(s):  
John Bacsa ◽  
John Briones
Keyword(s):  
Electron Density ◽  
Title Compound ◽  
Cyclopropane Ring ◽  
Topological Analysis ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray ◽  
Compound C ◽  
X Ray Scattering

The molecule of the title compound, C18H18O2, is a substituted cyclopropane ring. The electron density in this molecule has been determined by refining single-crystal X-ray data using scattering factors derived from quantum mechanical calculations. Topological analysis of the electron densities in the three cyclopropane C—C bonds was carried out. The results show the effects of this substitution on these C—C bonds.

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