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

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.

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.

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.

Crystal Structure and Tautomerism of 1-[N-(4-Iodophenyl)]aminomethylidene-2(1H)naphthalenone

2001 ◽  
Vol 56 (10) ◽  
pp. 1003-1008 ◽  
Author(s):  
H. Ünver ◽  
M. Kabak ◽  
D. M. Zengin ◽  
T. N. Durlu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Quantum Mechanical ◽  
Monoclinic Space Group ◽  
Quantum Mechanical Calculations ◽  
X Ray ◽  
H Nmr ◽  
Mechanical Methods ◽  
Intramolecular Hydrogen ◽  
Semi Empirical

1-[N-(4-Iodophenyl)]aminomethylidene-2(1H)naphthalenone (1) (C17H12NOI) has been studied by X-ray analysis, IR, 1H NMR, UV and AM1 semi-empirical quantum mechanical methods. It crystallises in the monoclinic space group P21/n with a = 4.844(3), b = 21.428(2), c = 13.726(2) Å, ß = 93.07(2)° (R1 =0.032 for 4132 reflections [I > 2σ(I)]). The title compound is not planar and an intramolecular hydrogen bond connects O1 and N1 [2.530(4) Å]. Complementary IR, 1H NMR and UV measurements out. Tautomerism and conformations of the title semi-empirical quantum mechanical calculations and the results are compared with the X-ray data.

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 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.

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