X-ray structure refinement using aspherical atomic density functions obtained from quantum-mechanical calculations

Author(s):  
Dylan Jayatilaka ◽  
Birger Dittrich
2002 ◽  
Vol 67 (4) ◽  
pp. 479-489 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Ladislav Cvak ◽  
Alexandr Jegorov ◽  
...  

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.


1994 ◽  
Vol 59 (9) ◽  
pp. 2565-2569 ◽  
Author(s):  
Maria-Selma Arias ◽  
Yves G. Smeyers ◽  
Maria-Jose Fernandez ◽  
Nadine J. Smeyers ◽  
Enrique Galvez ◽  
...  

1970 ◽  
Vol 14 ◽  
pp. 453-486 ◽  
Author(s):  
G. Andermann ◽  
H. C. Whitehead

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.


Author(s):  
John Bacsa ◽  
John Briones

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.


2001 ◽  
Vol 56 (10) ◽  
pp. 1003-1008 ◽  
Author(s):  
H. Ünver ◽  
M. Kabak ◽  
D. M. Zengin ◽  
T. N. Durlu

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.


2019 ◽  
Vol 75 (4) ◽  
pp. 368-380 ◽  
Author(s):  
Octav Caldararu ◽  
Francesco Manzoni ◽  
Esko Oksanen ◽  
Derek T. Logan ◽  
Ulf Ryde

Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. A first validation of this method is provided by re-refining the structure of the galectin-3 carbohydrate-recognition domain in complex with lactose. The geometry is improved, in particular for water molecules, for which the method leads to better-resolved hydrogen-bonding interactions. The method has also been applied to the active copper site of lytic polysaccharide monooxygenase and shows that the protonation state of the amino-terminal histidine residue can be determined.


2022 ◽  
Author(s):  
Sergei Gavryushov ◽  
Nikolay Kuzmich ◽  
Konstantin Polyakov

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.


2015 ◽  
Vol 68 (10) ◽  
pp. 1599 ◽  
Author(s):  
Jingping Ou-Yang ◽  
Yu Zhao ◽  
Huailei Jiang ◽  
Lingxin Meng ◽  
Xingshu Li ◽  
...  

A simple, one-pot process for the construction of substituted spiro[5,5]undecane-1,5,9-triones using aromatic aldehydes and Meldrum’s acid, and aniline as a catalyst, is reported. Fifteen compounds were synthesized, and the trans/cis ratios were calculated based on 1H NMR analyses of the unpurified products. Quantum mechanical calculations and X-ray diffraction were undertaken to identify the configuration of compound 2a. The proposed mechanisms for these reactions are presented in this paper. In contrast to previous literature, this method endows excellent diastereoselectivity to a series of trans-substituted derivatives. The method is characterized by its simple operation, commercial availability of all materials, mild reaction conditions and moderate-to-good chemical yields.


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