Aspherical scattering factors for<i>SHELXL</i>– model, implementation and application

Lübben, Jens; Wandtke, Claudia M.; Hübschle, Christian B.; Ruf, Michael; Sheldrick, George M.; Dittrich, Birger

doi:10.1107/s2053273318013840

Cited by 59 publications

(40 citation statements)

References 91 publications

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“…The structure solution and refinements were carried out using the Yadokari-XG [32] graphical interface. The positions of the non-hydrogen atoms were determined using the SHELXT-2014/ 5 [33] program and refined on F 2 by full-matrix least-squares techniques using the SHELXL-2014/7 [34] program. All non-hydrogen atoms were refined with anisotropic thermal parameters, while all hydrogen atoms were placed using AFIX instructions.…”

Section: X-ray Diffraction Studiesmentioning

confidence: 99%

Synthesis and Systematic Structural Analysis of Cationic Half‐Sandwich Ruthenium Chalcogenocarbonyl Complexes

Suzuki

Mutoh

Tsuchida

et al. 2020

Chemistry A European J

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Although the chemistry of transition‐metal complexes with carbonyl (CO) and thiocarbonyl (CS) ligands has been well developed, their heavier analogues, namely selenocarbonyl (CSe) and tellurocarbonyl (CTe) complexes remain scarce. The limited availability of such CSe and CTe complexes has so far hampered our understanding of the differences between such chalcogenocarbonyl (CE: E=O, S, Se, Te) ligands. Herein, we report the synthesis and properties of a series of cationic half‐sandwich ruthenium CE complexes of the type [CpRu(CE)(H2IMes)(CNCH2Ts)][BArF4] (Cp=η5‐C5H5−; H2IMes=1,3‐dimesitylimidazolin‐2‐ylidene; ArF=3,5‐(CF3)2C6H3). A combination of X‐ray diffraction analyses, NMR spectroscopic analyses, and DFT calculations revealed an increasing π‐accepting ability of the CE ligands in the order O

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Section: X-ray Diffraction Studiesmentioning

confidence: 99%

Synthesis and Systematic Structural Analysis of Cationic Half‐Sandwich Ruthenium Chalcogenocarbonyl Complexes

Suzuki

Mutoh

Tsuchida

et al. 2020

Chemistry A European J

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“…However, the computational cost of HARs and even of ELMO-DB HARs (when very large macromolecules are investigated) are still much higher compared to TAAM refinements. Another recent approach is the use of Bond Oriented Deformation Density (BODD) and Lone Pair Electron Density (LONE) via a tool called IDEAL (Lü bben et al, 2019). This approach refines data as fast as IAM alone but does not reach the same sophistication in representing electron density as TAAM (including Invarioms) or HAR (Lü bben et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

Jha

Gruza

Kumar

et al. 2020

Acta Crystallogr Sect B

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Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min 0.83 Å ) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

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“…[20] The structure was solved by direct methods using SHELXT [21] and refined on F 2 using SHELXL-2018. [22] Aspherical scattering factors [23] have been applied at the final refinement steps for compound 3a. The SHELXTL program suite [19] was used for molecular graphics.…”

Section: General Informationmentioning

confidence: 99%

Reversed steric order of reactivity for tert‐butyl and adamantyl‐3‐cyanomethylene‐1,2,4‐triazines

Иванов

2021

Journal of Heterocyclic Chem

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Reactions of 2-(6-tert-butyl-5-oxo-4,5-dihydro-1,2,4-triazin-3(2H)-ylidene)-3-oxo-3-R-propanenitriles (R = t-Bu, Ad-1) with tert-butyl bromoacetate gave the corresponding N(2), C(5) O bis-alkylation products. Treatment of the latter with t-BuLi, in the case of R = t-Bu, led to intramolecular condensation at the exocyclic nitrile group. However, in the case of R = Ad-1, the condensation with the sterically more hindered carbonyl group was observed to give diastereomerically pure 8-cyanopyrrolo [1,2-b][1,2,4]triazine-6-carboxylate derivatives. The structures of the isolated products were confirmed by spectral methods and X-ray singlecrystal diffraction.

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Aspherical scattering factors forSHELXL– model, implementation and application

Cited by 59 publications

References 91 publications

Synthesis and Systematic Structural Analysis of Cationic Half‐Sandwich Ruthenium Chalcogenocarbonyl Complexes

Synthesis and Systematic Structural Analysis of Cationic Half‐Sandwich Ruthenium Chalcogenocarbonyl Complexes

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

Reversed steric order of reactivity for tert‐butyl and adamantyl‐3‐cyanomethylene‐1,2,4‐triazines

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