Unusual Weiss–Cook condensation of dimethyl 2,3-dioxobutanedioate and dimethyl 3-oxoglutarate

1994 ◽  
Vol 72 (4) ◽  
pp. 1162-1164 ◽  
Author(s):  
Ghislain Deslongchamps ◽  
Daniel Mink ◽  
Paul D. Boyle ◽  
Nina Singh
Keyword(s):  
Sodium Chloride ◽  
Dimethyl Sulfoxide ◽  
Reaction Pathway ◽  
Quantitative Yield ◽  
X Ray ◽  
X Ray Crystallography ◽  
Kinetically Controlled

The Weiss–Cook condensation of dimethyl 2,3-dioxobutanedioate with two equivalents of dimethyl 3-oxoglutarate in aqueous bicarbonate produces an "abnormal" product, pentamethyl cis-3-(carbomethoxymethyl)-3,7-dihydroxy-2-oxabicyclo-[3.3.0]oct-7-ene-1,4,5,6,8-pentacarboxylate 7, whose structure has been determined by X-ray crystallography. Rrapcho decarbomethoxylation (sodium chloride, aqueous dimethyl sulfoxide, 140 °C) of this compound produces dimethyl cis-3,7-dioxobi-cyclo[3.3.0]octane-1,5-dicarboxylate 4 in quantitative yield. These results suggest that compound 7 may be the product of a kinetically controlled reaction pathway involving 4-hydroxypent-2-en-1-one intermediate 5. Heating of 7 in dimethyl sulfoxide may have promoted thermodynamic equilibration to a Weiss–Cook product, which then decarbomethoxylated to produce 4.

scholarly journals Reactions of Titanocene- and Zirconocene-Bis(trimethylsilyl)acetylene Complexes with Selected Heterocyclic and Aromatic NH and OH Acid Compounds

2007 ◽  
Vol 72 (4) ◽  
pp. 475-491 ◽  
Author(s):  
Perdita Arndt ◽  
Vladimir V. Burlakov ◽  
Ulrike Jäger-Fiedler ◽  
Marcus Klahn ◽  
Anke Spannenberg ◽  
...  
Keyword(s):  
Bond Activation ◽  
Reaction Pathway ◽  
Reaction Products ◽  
X Ray ◽  
X Ray Crystallography

The titanocene complexes Cp'2Ti(η2-Me3SiC2SiMe3) (Cp' = Cp (1), Cp* (2)) react with pyrrole under the formation of the titanium(III) mono-N-pyrrolides Cp'2Ti(NC4H4) (Cp' = Cp (6), Cp* (7)); whereas the corresponding zirconocene system Cp2Zr(η2-Me3SiC2SiMe3)(thf) (3) forms in a different reaction pathway first the Cp2Zr(NC4H4)[C(SiMe3)=CH(SiMe3)] (8) and then the zirconium(IV) bis-N-pyrrolide Cp2Zr(NC4H4)2 (11). With Cp*2Zr(η2-Me3SiC2SiMe3) (4) and pyrrole, the zirconium(IV) mono-N-pyrrolide with an agostic alkenyl group Cp*2Zr(NC4H4)[C(SiMe3)=CH(SiMe3)] (9) was obtained. In the reaction of the ethylenebistetrahydroindenyl (ebthi) complex rac-(ebthi)Zr(η2-Me3SiC2SiMe3) (5) with 2,3,5,6-tetrafluoroaniline under N-H bond activation, a complex with an agostic alkenyl group rac-(ebthi)Zr(NH-C6HF4)[C(SiMe3)=CH(SiMe3)] (10) was formed. Compound 10 reacts with additional 2,3,5,6-tetrafluoroaniline to give the bisanilide rac-(ebthi)Zr(NH-C6HF4)2 (12) which was obtained directly from 5 with two equivalents of 2,3,5,6-tetrafluoroaniline. In reactions of complex 5 with unsubstituted aniline to rac-(ebthi)Zr(NH-C6H5)2 (13) and with pentafluorophenol to bisphenolate rac-(ebthi)Zr(O-C6F5)2 (14), no intermediates could be isolated. The new reaction products 6, 9, 10, 12, 13 and 14 were investigated by X-ray crystallography.

Effects of solvents on the crystal structure of cross-linked lysozyme crystals

2018 ◽  
Vol 32 (19) ◽  
pp. 1840041
Author(s):  
Yohei Yamada ◽  
Shota Toyama ◽  
Tomoki Yabutani
Keyword(s):  
Crystal Structure ◽  
Acetic Acid ◽  
Hydrochloric Acid ◽  
Dimethyl Sulfoxide ◽  
Optical Microscopy ◽  
Immersion Test ◽  
X Ray ◽  
Lattice Constants ◽  
X Ray Crystallography ◽  
Lysozyme Crystals

The effects of solvents on the structural stability of cross-linked lysozyme crystals were investigated by an immersion test using alkaline (0.1 M ammonia [NH3] and 0.1 M sodium hydroxide [NaOH]), acidic (0.1 M acetic acid [CH3COOH] and 0.1 M hydrochloric acid [HCl]) and organic (50% [v/v] and undiluted ethanol, acetone, 2-propanol and dimethyl sulfoxide [DMSO]) solvents. The morphology and lattice constants were monitored by optical microscopy and X-ray crystallography. The cross-linked crystals exhibited good stability against NH3, CH3COOH, HCl, ethanol, acetone and 2-propanol. However, samples preserved in DMSO and NaOH were severely degraded.

Mapping the conformational itinerary of β-glycosidases by X-ray crystallography

2003 ◽  
Vol 31 (3) ◽  
pp. 523-527 ◽  
Author(s):  
G.J. Davies ◽  
V.M.-A. Ducros ◽  
A. Varrot ◽  
D.L. Zechel
Keyword(s):  
Transition State ◽  
Reaction Pathway ◽  
Tight Binding ◽  
Three Dimensional ◽  
Intermediate Structure ◽  
Active Centre ◽  
X Ray ◽  
Solution Structures ◽  
X Ray Crystallography ◽  
Covalent Intermediate

The conformational agenda harnessed by different glycosidases along the reaction pathway has been mapped by X-ray crystallography. The transition state(s) formed during the enzymic hydrolysis of glycosides features strong oxocarbenium-ion-like character involving delocalization across the C-1–O-5 bond. This demands planarity of C-5, O-5, C-1 and C-2 at or near the transition state. It is widely, but incorrectly, assumed that the transition state must be 4H3 (half-chair). The transition-state geometry is equally well supported, for pyranosides, by both the 4H3 and 3H4 half-chair and 2,5B and B2,5 boat conformations. A number of retaining β-glycosidases acting on gluco-configured substrates have been trapped in Michaelis and covalent intermediate complexes in 1S3 (skew-boat) and 4C1 (chair) conformations, respectively, pointing to a 4H3-conformed transition state. Such a 4H3 conformation is consistent with the tight binding of 4E- (envelope) and 4H3-conformed transition-state mimics to these enzymes and with the solution structures of compounds bearing an sp2 hybridized anomeric centre. Recent work reveals a 1S5 Michaelis complex for β-mannanases which, together with the 0S2 covalent intermediate, strongly implicates a B2,5 transition state for β-mannanases, again consistent with the solution structures of manno-configured compounds bearing an sp2 anomeric centre. Other enzymes may use different strategies. Xylanases in family GH-11 reveal a covalent intermediate structure in a 2,5B conformation which would also suggest a similarly shaped transition state, while 2S0-conformed substrate mimics spanning the active centre of inverting cellulases from family GH-6 may also be indicative of a 2,5B transition-state conformation. Work in other laboratories on both retaining and inverting α-mannosidases also suggests non-4H3 transition states for these medically important enzymes. Three-dimensional structures of enzyme complexes should now be able to drive the design of transition-state mimics that are specific for given enzymes, as opposed to being generic or merely fortuitous.

Syntheses and Structures of Thorium(IV) Complexes with Bis(diphenylphosphino)ethane Dioxide, Ph2P(O)CH2CH2P(O)Ph2, and Bis(diphenylphosphoryl)amide, [Ph2P(O)NP(O)Ph2]

2000 ◽  
Vol 55 (3-4) ◽  
pp. 285-290 ◽  
Author(s):  
Élida Bonfada ◽  
Ernesto Schulz-Lang ◽  
Renato André Zan ◽  
Ulrich Abram
Keyword(s):  
Dimethyl Sulfoxide ◽  
Coordination Sphere ◽  
Phosphine Oxide ◽  
X Ray ◽  
Bond Lengths ◽  
X Ray Crystallography ◽  
Oxygen Atoms

Abstract The cationic thorium(IV) complexes [Th{Ph2P(O)CH2CH2P(O)Ph2}2(NO3)3]NO3 and [Th{Ph2P(O)NP(O)Ph2}3(dmso)2]NO3 have been synthesized by reactions of Th(NO3)4 · 5H2O with bis(diphenylphosphino)ethane dioxide, Ph2P(O)CH2CH2P(O)Ph2 (L1), or ammonium bis(diphenylphosphoryl)amide, (NH4)[Ph2P(O)NP(O)Ph2] (NH4L2), and subsequent recrystallization from dimethyl sulfoxide. The products have been studied spectroscopically and by X-ray crystallography. The thorium atom is ten-co-ordinate in the [Th(L1)2(NO3)3]+ cation with a coordination sphere which does not match one of the idealized polyhedra for ten-coordination. Th-O bonds have been found in the range between 2.342(3) (phosphine oxide) and 2.599(4) A (nitrate). An eight-coordinate thorium atom is found in the [Th(L2)3(dmso)2]+ cation. The almost ideal square-antiprismatic environment of the metal is occupied by oxygen atoms with Th-0 bond lengths between 2.363(6) and 2.392(11) Å

Combining X-ray crystallography and single-crystal spectroscopy to probe enzyme mechanisms

2009 ◽  
Vol 37 (2) ◽  
pp. 378-381 ◽  
Author(s):  
Arwen R. Pearson ◽  
Robin L. Owen
Keyword(s):  
Data Collection ◽  
Single Crystal ◽  
Diffraction Data ◽  
Reaction Pathway ◽  
X Ray ◽  
X Ray Crystallography ◽  
Enzyme Systems ◽  
Catalytic Intermediates ◽  
Trapping Methods ◽  
Induced Changes

The combination of X-ray crystallography and rapid cryo-trapping methods has enabled the visualization of catalytic intermediates in a variety of enzyme systems. However, the resolution of the X-ray experiment is not always sufficient to precisely place the structure on the reaction pathway. In addition, many trapped intermediates are X-ray-sensitive and can decay during diffraction data collection, resulting in a final structure that may not be representative of the initial trapped species. Complementary methods, such as single-crystal spectroscopy, provide a means to precisely identify the cryo-trapped species as well as detect any X-ray-induced changes during diffraction data collection.

Conformation of a Fluorochrome from Aniline Blue

1997 ◽  
Vol 50 (10) ◽  
pp. 987
Author(s):  
Maureen F. Mackay, ◽  
Michael J. McTigue ◽  
Maruse Sadek
Keyword(s):  
Solid State ◽  
Single Crystal ◽  
Dimethyl Sulfoxide ◽  
Chemical Shifts ◽  
Deuterium Oxide ◽  
Sodium Ion ◽  
Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Solid State Conformation

The solid-state conformation of the fluorochrome sodium 4,4′-[carbonylbis(benzene-4,1-diyl)bis(imino)]-bisbenzenesulfonate has been defined by single-crystal X-ray crystallography. Monoclinic crystals belong to the space group C 2/c with a 11·732(1), b 6·185(1), c 37·179(3) Å, β 94·40(1)° and Z 8. The structure was refined to a final R0·042 for all 2271 unique terms. In the crystal six oxygen atoms form an octahedral grouping around the sodium ion and these octahedra are linked into layers sandwiched between the layers of organic anions which adopt an extended conformation. The n.m.r. spectra indicate that in solution the fluorochrome is flexible and averages to an extended structure that maintains symmetry about its longitudinal and carbonyl axes. Chemical shifts have been measured in water, deuterium oxide and (D6)dimethyl sulfoxide

Synthesis of 1,8,8-Trimethyl-6,10-dioxaspiro[4.5]dec-2-ene-1-ethanol; X-Ray Crystallography of (1RS,2SR)-1,8,8-Trimethyl-1-(prop-2'-enyl)-6,10-dioxaspiro[4.5]dec-2-yl Benzoate

1994 ◽  
Vol 47 (4) ◽  
pp. 739 ◽  
Author(s):  
DJ Collins ◽  
GD Fallon ◽  
RP Mcgeary
Keyword(s):  
Oxidative Cleavage ◽  
Quantitative Yield ◽  
Borohydride Reduction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Flash Vacuum Pyrolysis ◽  
Hydride Reduction ◽  
Tetrabutylammonium Fluoride ◽  
Vacuum Pyrolysis ◽  
Relative Stereochemistry

Reaction of 2-methyl-2-(prop-2′-enyl)cyclopentane-1,3-dione (2) with 2,2-dimethylpropane-1,3-diol gave 1,8,8-trimethyl-1-(prop-2′-enyl)-6,10-dioxaspiro[4.5]decan-2-one (3), hydride reduction of which afforded a 1:1 epimeric mixture of the corresponding alcohols (4a) and (4b). They were separated, and the derived benzoates (5a) and (5b) were each subjected to a three-step sequence of oxidative cleavage, borohydride reduction and silylation to give the pure epimers (8a) and (8b) of 1,8,8-trimethyl-1-(2′-t-butyldimethylsilyloxyethyl)-6,10-dioxaspiro[4.5]dec-2-yl benzoate. Flash vacuum pyrolysis of a mixture of these epimeric benzoates (8a,b) gave an almost quantitative yield of 1,8,8-trimethyl-1-(2′-t-butyldimethylsilyloxyethyl)-6,10-dioxaspiro[4.5]dec-2-ene (9a), treatment of which with tetrabutylammonium fluoride afforded the corresponding alcohol (9b). The relative stereochemistry of (1RS,2SR)-1,8,8-trimethyl-1-(prop-2′-enyl)-6,10-dioxaspiro [4.5]dec-2-yl benzoate (5b) was established by X-ray crystallography.

Structural verification of a tetrahydrotetrazole compound

2019 ◽  
Vol 75 (9) ◽  
pp. 1208-1212
Author(s):  
Gary W. Breton ◽  
Lauren A. Hahn ◽  
Kenneth L. Martin
Keyword(s):  
Half Life ◽  
Reaction Pathway ◽  
Membered Ring ◽  
Crystal Phase ◽  
Previous Attempt ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Spectral Evidence

Tetrahydrotetrazoles are five-membered-ring heterocycles containing four contiguous saturated nitrogen atoms. Very few examples of such compounds have been reported in the literature. Our previous attempt at the synthesis of a member of this class of compound suggested that the N—N bonds may be more labile than expected. This finding raised the question as to whether the structures of any of the previously reported tetrahydrotetrazoles had been properly assigned. We have reproduced the synthesis of a reported tetrahydrotetrazole, namely 1,2-di-tert-butyl 3-phenyl-1H,2H,3H,10bH-[1,2,3,4]tetrazolo[5,1-a]isoquinoline-1,2-dicarboxylate, C25H30N4O4, and have now confidently confirmed its structure via X-ray crystallography. However, while sufficiently stable in the crystal phase, we discovered that it remains very labile in solution (having a half-life of only 15 min at 20 °C in CDCl3). A tentative reaction pathway for its dissociation based on 1H NMR spectral evidence is provided.

Reaction pathway of ADP-ribose pyrophosphatase, revealed by time-resolved X-ray crystallography

2008 ◽  
Vol 64 (a1) ◽  
pp. C271-C272
Author(s):  
N. Kamiya ◽  
K. Kai ◽  
N. Nakagawa ◽  
S. Kuramitsu ◽  
I. Miyahara
Keyword(s):  
Reaction Pathway ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Conformational and structural diversity of iridium dimethyl sulfoxide complexes

2017 ◽  
Vol 73 (6) ◽  
pp. 1032-1042 ◽  
Author(s):  
Benjamin M. Ridgway ◽  
Ana Foi ◽  
Rodrigo S. Corrêa ◽  
Damian E. Bikiel ◽  
Javier Ellena ◽  
...  
Keyword(s):  
Dimethyl Sulfoxide ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Structural Diversity ◽  
Stable Form ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Crystallography ◽  
Conformational Preferences ◽  
Clinically Significant

Transition metal complexes containing dimethyl sulfoxide (DMSO) are important precursors in catalysis and metallodrugs. Understanding the solid-state supramolecular structure is crucial for predicting the properties and biological activity of the material. Several crystalline phases of DMSO-coordinated iridium anions with different cations, potassium (1a) and n-butylammonium (1b), were obtained and their structures determined by X-ray crystallography. Compound (1a) is present in two solvatomorphic forms: α and β; the β form contains disordered solvent water. In addition, the structures exhibit different rotamers of the trans-[IrCl4(DMSO)2]− anion with the trans-DMSO ligands being oriented in anti and gauche conformations. In consideration of these various conformers, the effects of the crystallized solvent and intermolecular interactions on the conformational preferences of the anion are discussed. In addition, density functional theory calculations were used to investigate the energies of the anions in the different conformations. It was found that hydrogen bonds between water and the DMSO complex stabilize the gauche conformation which is the least stable form of the trans-DMSO complex. Consequently, by controlling the number of hydrogen-bond donors and acceptors and the amount of water, it may be possible to obtain different solvatomorphs of clinically significant metallodrugs.

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