scholarly journals Probing the Structure of [NiFeSe] Hydrogenase with QM/MM Computations

2020 ◽  
Vol 10 (3) ◽  
pp. 781 ◽  
Author(s):  
Samah Moubarak ◽  
N. Elghobashi-Meinhardt ◽  
Daria Tombolelli ◽  
Maria Andrea Mroginski
Keyword(s):  
Iron Oxidation ◽  
Structural Models ◽  
Oxidation States ◽  
Quantum Mechanical ◽  
Desulfovibrio Vulgaris ◽  
X Ray ◽  
X Ray Crystallography ◽  
Desulfovibrio Vulgaris Hildenborough ◽  
Optimized Geometries ◽  
Good Agreement

The geometry and vibrational behavior of selenocysteine [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough have been investigated using a hybrid quantum mechanical (QM)/ molecular mechanical (MM) approach. Structural models have been built based on the three conformers identified in the recent crystal structure resolved at 1.3 Å from X-ray crystallography. In the models, a diamagnetic Ni2+ atom was modeled in combination with both Fe2+ and Fe3+ to investigate the effect of iron oxidation on geometry and vibrational frequency of the nonproteic ligands, CO and CN-, coordinated to the Fe atom. Overall, the QM/MM optimized geometries are in good agreement with the experimentally resolved geometries. Analysis of computed vibrational frequencies, in comparison with experimental Fourier-transform infrared (FTIR) frequencies, suggests that a mixture of conformers as well as Fe2+ and Fe3+ oxidation states may be responsible for the acquired vibrational spectra.

scholarly journals The influence of exocyclic lone pairs on the bonding and geometry of type A mesoionic rings

2021 ◽  
Author(s):  
Christopher Antony Ramsden ◽  
Wojciech Piotr Oziminski
Keyword(s):  
Ab Initio ◽  
Type A ◽  
Nbo Analysis ◽  
Ring Systems ◽  
X Ray ◽  
X Ray Crystallography ◽  
Bond Model ◽  
Lone Pairs ◽  
Mp2 Calculations ◽  
Good Agreement

AbstractBased on structures determined by X-ray crystallography, ab initio MP2 calculations on type A mesoionic rings give geometries in good agreement with observed values. A study of four mesoionic ring systems, each with exocyclic oxygen, nitrogen or carbon groups, shows that the presence and configuration of exocyclic lone pairs significantly influences the geometry and configurational preference. Using a localised bond model and NBO analysis, these effects are rationalised in terms of an anomeric interaction of lone pairs with the antibonding orbitals of adjacent σ bonds. In agreement with experiment, similar effects are calculated for pyran-2-imines.

scholarly journals Structure of the manganese complex in photosystem II: insights from X–ray spectroscopy

2002 ◽  
Vol 357 (1426) ◽  
pp. 1347-1358 ◽  
Author(s):  
Vittal K. Yachandra
Keyword(s):  
Fine Structure ◽  
Emission Spectroscopy ◽  
Structural Models ◽  
Oxidation States ◽  
X Ray ◽  
X Ray Scattering ◽  
Raman Process ◽  
Mn Cluster ◽  
X Ray Absorption ◽  
S States

We have used Mn K–edge absorption and Kβ emission spectroscopy to determine the oxidation states of the Mn complex in the various S states. We have started exploring the new technique of resonant inelastic X–ray scattering spectroscopy; this technique can be characterized as a Raman process that uses K–edge energies (1s to 4p, ca . 6550 eV) to obtain L–edge–like spectra (2p to 3d, ca . 650 eV). The relevance of these data to the oxidation states and structure of the Mn complex is presented. We have obtained extended X–ray absorption fine structure data from the S 0 and S 3 states and observed heterogeneity in the Mn–Mn distances leading us to conclude that there may be three rather than two di– μ –oxo–bridged units present per tetranuclear Mn cluster. In addition, we have obtained data using Ca and Sr X–ray spectroscopy that provide evidence for a heteronuclear Mn1Ca cluster. The possibility of three di– μ –oxo–bridged Mn–Mn moieties and the proximity of Ca is incorporated into developing structural models for the Mn cluster. The involvement of bridging and terminal O ligands of Mn in the mechanism of oxygen evolution is discussed in the context of our X–ray spectroscopy results.

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

Vapour growth, morphology, absolute structure and pyroelectric coefficient of meta-nitroaniline single crystals

2019 ◽  
Vol 52 (3) ◽  
pp. 564-570 ◽  
Author(s):  
Rolf Hesterberg ◽  
Michel Bonin ◽  
Martin Sommer ◽  
Matthias Burgener ◽  
Bernhard Trusch ◽  
...  
Keyword(s):  
Room Temperature ◽  
Vapour Phase ◽  
Pyroelectric Coefficient ◽  
Growth Speed ◽  
Published Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Absolute Structure ◽  
Good Agreement

The growth speed of (hkl) faces in the vapour phase, the absolute structure obtained by X-ray crystallography, and the value and the sign of the pyroelectric coefficient of meta-nitroaniline (mNA) were analysed in detail. The in situ observation of morphologically well developed faces of several mNA crystals growing in evacuated ampoules reveals no pronounced growth speed anisotropy for polar faces defining the unique axis 2 of the mm2 group. Scanning pyroelectric microscopy confirms mono-domain mNA crystals. X-ray measurements in the space group Pca21 show that the molecular planes coincide with the {\bar 211} and {\bar 2\bar 1\bar 1} faces, and the nitro groups cover the {201} face in the opposite direction to the crystal tip, characterizing the polar habitus studied here. At room temperature, the sign of the pyroelectric coefficient is positive for a measured effective value of 6.3 µC m−2 K−1, in good agreement with values reported by other authors. From previous elastic and piezoelectric published data, the secondary pyroelectric effect was calculated to be positive and far greater than the effective one, yielding a negative value for the primary pyroelectric coefficient.

scholarly journals The influence of exocyclic lone pairs on the bonding and geometry of type A mesoionic rings

2021 ◽  
Author(s):  
Christopher Antony Ramsden ◽  
Wojciech Piotr Oziminski
Keyword(s):  
Ab Initio ◽  
Type A ◽  
Ring Systems ◽  
X Ray ◽  
X Ray Crystallography ◽  
Bond Model ◽  
Lone Pairs ◽  
Mp2 Calculations ◽  
Good Agreement

Abstract Based on structures determined by X-ray crystallography, ab initio MP2 calculations on type A mesoionic rings give geometries in good agreement with observed values. A study of four mesoionic ring systems, each with exocyclic oxygen, nitrogen or carbon groups, shows that the presence and configuration of exocyclic lone pairs significantly influences the geometry and configurational preference. Using a localised bond model, these effects are rationalised in terms of an anomeric interaction of lone pairs with the antibonding orbitals of adjacent σ bonds. In agreement with experiment, similar effects are calculated for pyran-2-imines.

Crystal Structure Optimization and Semi-Empirical Quantum Chemical Calculations of N-(3,4-Dichlorophenyl)-3-Oxo-Butanamide

2012 ◽  
Vol 620 ◽  
pp. 82-86
Author(s):  
Mukesh M. Jotani
Keyword(s):  
Crystal Structure ◽  
Molecular Electrostatic Potential ◽  
Crystal Packing ◽  
Empirical Method ◽  
Molecular Orbital Calculations ◽  
X Ray ◽  
Semi Empirical ◽  
Packing Interactions ◽  
Optimized Geometries ◽  
Good Agreement

The crystal structure of N-(3,4-Dichlorophenyl)-3-oxobutanamide (I) is optimized by semi-empirical methods using MOPAC2009 program. The optimized geometries from both Austin Model 1 (AM1) and Parametrization Model 6 (PM6) describe the conformational discrepancy and crystal packing. The energy minimized structures from both the models are in good agreement with X-ray crystal data. The intramolecular charge transfer interactions are studied from the molecular orbital calculations. The parametric molecular electrostatic potential (PMEP) calculated by AM1 semi-empirical method shows the involvement of oxygen and chlorine atoms in the crystal packing interactions. The aromaticity of phenyl ring in the structure is determined using HOMED calculations.

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