X-ray and Solid State NMR Studies of Bis(5,5-dimethyl-2-thioxo-1,3,2-dioxaphosphorinan-2-yl) Disulfide and Diselenide

Potrzebowski, Marek J.; Großmann, G.; Błaszczyk, Jarosław; Wieczorek, Michał W.; Sieler, Joachim; Knopik, P.; Komber, Hartmut

doi:10.1021/ic00099a019

Cited by 22 publications

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“…They do not share even such crystallographic features like crystal symmetry or space group [36]. The overall threedimensional shape of both molecules (conformation) is also quite different [36]. The bond lengths, which involve selenium, are, similarly like in the previous observation for compounds 1a and 1b, much longer than the respective bonds that involve sulfur ( Table 1).…”

Section: Compound P-s P-se P=s S-s Se-se C-s C-se Refmentioning

confidence: 52%

“…In fact, the Se-and S-containing analogs do not have any obstacles preventing them from being structurally non isomorphous. For example, see crystal structures of compounds 3a and 3b (Table 1) [36]. The performed refinement of a small molecule with intentionally altered atom type (Figure 1) yielded strange thermal mobility and very bad refinement statistics.…”

Section: Resultsmentioning

confidence: 99%

Section: Compound P-s P-se P=s S-s Se-se C-s C-se Refmentioning

confidence: 95%

“…bis(5,5-dimethyl-2-thioxo-1,3,2-dioxaphosphorinan-2-yl) disulfide [36] 3b: bis(5,5-dimethyl-2-thioxo-1,3,2-dioxaphosphorinan-2-yl) diselenide [36] 4-42: for compound names, please see supplementary material .…”

Section: Compound P-s P-se P=s S-s Se-se C-s C-se Refmentioning

confidence: 99%

“…Table 1 contains collection of interatomic distances, which involve S or Se atoms, and shows that the distances which involve Se atoms are much longer from the distances which involve S atoms. All examples, which are provided in Table 1, have been selected from author's previous work on X-ray structure determination of small-molecular organic compounds such as phosphoroorganic disulfides and diselenides [35][36][37][38][39][40][41], selenides [42], dithianes, dithiolanes, oxathiaphospholanes, dithiaphospholanes and oxaselenaphospholanes [43][44][45][46][47][48][49][50][51][52][53], phosphoramidothioates [44], phosphoramidoselenoates [54], sulfoxides [55][56][57][58][59] and thiophosphoryl compounds [60]. For full listing of compounds 1-42 included in that comparison, please see supplementary material.…”

Section: Introductionmentioning

confidence: 99%

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Handling of Selenomethionines in Macromolecular Refinement

Błaszczyk¹

2014

Biochem Anal Biochem

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In the Protein Data Bank, we can find X-ray structures which were determined from selenium-derivatized proteins, but the deposited coordinates, to our surprise, contain native methionines. The problem is likely due to not complete substitution of native methionines with selenomethionines during chemical reaction. When the crystal grows from such sample, and later is subjected for X-ray analysis, it may show partial presence of native sulfur. This paper is a voice in discussion how to handle the refinement of selenomethionines. The purpose of this work is to explain why selenomethionines can't be refined purely as native methionines, particularly in macromolecular structures determined at high resolution. It is important because selenium and sulfur are different chemical elements. To explain the importance of refinement of correct atom type, author provides evidence, collected mainly from his previously reported small organic structures containing sulfur or selenium. Author emphasizes that the Xray structures, which contain selenium, are never identical with their sulfur-containing analogs. They differ at least in the respective bond lengths. Two available publicly X-ray structures have been re-refined, one small molecule and one macromolecule, in which the atom type was intentionally changed. Refinement of chemically incorrect atom type yielded non-natural behavior of atomic displacement parameters. Author concludes that the structures which contain incorrect atom types can't represent the experimental data but can serve only as models. There are examples, in the PDB, which show that selenomethionines in not fully Se-Met derivatized proteins can be refined with arbitrarily assumed fractional, less than 100%, occupancies. This inspired the author to perform various re-refinements, of the above mentioned Se-Met structure that contained S atoms in coordinates. In these re-refinements, selenomethionines are handled in different manners, and the results are compared. Author suggests refinement of chemical identities, selenium and sulfur, with fractional occupancies, as a method.

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Section: Compound P-s P-se P=s S-s Se-se C-s C-se Refmentioning

confidence: 52%

Section: Resultsmentioning

confidence: 99%

Section: Compound P-s P-se P=s S-s Se-se C-s C-se Refmentioning

confidence: 95%

Section: Compound P-s P-se P=s S-s Se-se C-s C-se Refmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Handling of Selenomethionines in Macromolecular Refinement

Błaszczyk¹

2014

Biochem Anal Biochem

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Alkali Metal Thioselenophosphinates, M[SeSPR₂]: One‐Pot Multicomponent Synthesis, DFT Study, and Synthetic Application

et al. 2012

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Diverse alkali metal thioselenophosphinates, M[SeSPR 2 ] (M = Li, Na, K, Rb, and Cs; R = alkyl, aryl, aralkyl, and hetaralkyl), have been synthesized in 78-94 % yields by means of a one-pot multicomponent reaction between secondary phosphanes, sulfur, selenium, and alkali metal hydroxides under mild conditions (room temperature, -50°C, 0.5 h, EtOH). The molecular and electronic structure of the [SeSPPh 2 ]anion and its coordination behavior towards Li + , Na + , and K + cations have been investigated at the B3LYP level of theory. The alkylation of the alkali metal thioselenophosphinates with various organic halides proceeds regiosecifically at the selenium center to form Se-organyl thioselenophosphinates, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Str., 664033 Irkutsk, Russian Federation

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Unexpected One‐Electron Oxidation of a Secondary Phosphite Selenide Cp(CO)₂FeP(Se)(OiPr)₂ by GaCl₃ and InCl₃ – Rare Examples of Di‐ and Triselenide Formation

et al. 2013

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The reactions of the neutral phosphonoselenoate [Cp(CO)2FeP(Se)(OiPr)2] (1) with Lewis acids (GaCl3, InCl3) produce dicationic complexes [{Cp(CO)2FeP(OiPr)2}2Sen][GaCl4]2, [n = 2 (2), 3 (3)] and [{Cp(CO)2FeP(OiPr)2}2Sen][InCl4]2 [n = 2 (4), 3 (5)] in good yields; the complexes comprise an Se3 (or Se2) chain that bridges two FpP(OiPr)2 groups [Fp = Cp(CO)2Fe]. These compounds are the one‐electron oxidation products of secondary phosphite selenide 1 by group 13 (Ga, In) trichlorides. On the other hand, the reaction of GaCl3 with (iPrO)2PSe2– (dsep) yields only the Lewis adduct tris(O,O‐diisopropyldiselenophosphate)gallium (6). The 31P NMR spectrum of 6 at 183 K reveals that the gallium(III) center is surrounded by one chelating and two pendant dsep ligands, which is in line with the obtained X‐ray structure. In addition, the two‐electron oxidation of 1 leads to phosphite [Cp(CO)2FeP(O)(OiPr)2] formation.

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X-ray and Solid State NMR Studies of Bis(5,5-dimethyl-2-thioxo-1,3,2-dioxaphosphorinan-2-yl) Disulfide and Diselenide

Cited by 22 publications

References 0 publications

Handling of Selenomethionines in Macromolecular Refinement

Handling of Selenomethionines in Macromolecular Refinement

Alkali Metal Thioselenophosphinates, M[SeSPR₂]: One‐Pot Multicomponent Synthesis, DFT Study, and Synthetic Application

Unexpected One‐Electron Oxidation of a Secondary Phosphite Selenide Cp(CO)₂FeP(Se)(OiPr)₂ by GaCl₃ and InCl₃ – Rare Examples of Di‐ and Triselenide Formation

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X-ray and Solid State NMR Studies of Bis(5,5-dimethyl-2-thioxo-1,3,2-dioxaphosphorinan-2-yl) Disulfide and Diselenide

Cited by 22 publications

References 0 publications

Handling of Selenomethionines in Macromolecular Refinement

Handling of Selenomethionines in Macromolecular Refinement

Alkali Metal Thioselenophosphinates, M[SeSPR2]: One‐Pot Multicomponent Synthesis, DFT Study, and Synthetic Application

Unexpected One‐Electron Oxidation of a Secondary Phosphite Selenide Cp(CO)2FeP(Se)(OiPr)2 by GaCl3 and InCl3 – Rare Examples of Di‐ and Triselenide Formation

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Product

Resources

About

Alkali Metal Thioselenophosphinates, M[SeSPR₂]: One‐Pot Multicomponent Synthesis, DFT Study, and Synthetic Application

Unexpected One‐Electron Oxidation of a Secondary Phosphite Selenide Cp(CO)₂FeP(Se)(OiPr)₂ by GaCl₃ and InCl₃ – Rare Examples of Di‐ and Triselenide Formation