Using the<i>t</i>-distribution to improve the absolute structure assignment with likelihood calculations

Hooft, Rob; Straver, Leo; Spek, Anthony L.

doi:10.1107/s0021889810018601

Cited by 98 publications

(78 citation statements)

References 4 publications

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“…Furthermore, the Baysian statistical analysis of Hooft, Straver, and Spek, implemented in PLATON [18], also predicts that the structure has the correct absolute configuration (P3 true = 1.000) and that there is no probability of the structure being a racemic twin (P3 rac-twin = 0.000). Similar results are obtained regardless of whether a Gaussian or a Student’s t -distribution is used [20]. For the sake of completeness, the structure was also fully refined in P2 1 /m.…”

Section: Methodssupporting

confidence: 71%

The crystal structure of oxaliplatin: A case of overlooked pseudo symmetry

Johnstone

2014

Polyhedron

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The crystal structure of the anticancer drug oxaliplatin, [Pt(R,R-DACH)(oxalate)] (DACH = diaminocyclohexane), was first reported in the non-centrosymmetric space group P21, confirming the sole presence of the R,R enantiomer of the DACH ligand [M. A. Bruck et al., Inorg. Chim. Acta, 92 (1984) 279–284]. It was later proposed that the crystal structure is better described in the centrosymmetric space group P21/m, signifying the presence of the compound as a racemic mixture [A. S. Abu-Surrah et al., Polyhedron, 22 (2003) 1529–1534]. Herein is presented a reinvestigation of this crystal structure, which shows that the discrepancy between the two proposed space group assignments arises from overlooked pseudo symmetry. The crystal structures of the synthetic precursor to oxaliplatin, Pt(R,R-DACH)I2, and a platinum(IV) derivative, trans-[Pt(R,R-DACH)(oxalate)(OH)2], were also determined, and the absolute configuration of the DACH ligand in each was confirmed to be R,R. A spectroscopic investigation of the optical rotatory dispersion (ORD) of the oxaliplatin crystals was carried out to further confirm the lack of the true crystallographic mirror plane required for a P21/m solution. The ORD was theoretically simulated, in one instance, by applying the Kramers-Kronig transform to the computed circular dichroism spectrum and was found to corroborate the spectroscopic and crystallographic findings. Finally, a brief discussion is given of the importance of discussing the details of nuanced crystal structures and of providing evidence in addition to X-ray structure determination if chemically unexpected results are obtained.

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Section: Methodssupporting

confidence: 71%

The crystal structure of oxaliplatin: A case of overlooked pseudo symmetry

Johnstone

2014

Polyhedron

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“…Calculations using PLATON (Spek, 2009) yielded values for the Hooft (Hooft et al, 2010) and Parsons parameters (intensity quotients) (Parsons et al, 2013) of 0.19 (11) and 0.18 (8), respectively. Though the values of the Flack, Hooft and Parsons parameters rather point to the absolute structure determination, the standard uncertainties are too high for the unequivocal assignment of the absolute structure.…”

Section: Refinementmentioning

confidence: 99%

A study of the planarity of the pyrrolone fragment in 2-isopropyl-2,3-dihydro-1H-isoindol-1-one

et al. 2016

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Orthophthalaldehyde (o-phthalaldehyde, OPA) is an aromatic dialdehyde bearing two electron-withdrawing carbonyl groups. The reactions of OPA with primary amines are broadly applied for the synthesis of important heterocyclic compounds with biological relevance. A number of such reactions have been investigated recently and several structures of condensation products have been reported, however, the complex reaction mechanism is still not fully understood and comprises concurrent as well as consecutive reactions. The reaction products depend on the primary amine which reacts with OPA, the reaction environment (solvent) and the proportion of the reactants. The title molecule, C11H13NO, the product of the reaction of OPA with isopropylamine, contains a five-membered pyrrole C4N ring with a carbonyl substituent, which forms part of the isoindolinone unit. Though this pyrrole ring contains one C atom in the sp(3)-hybridized state, it is fairly planar. The title molecule has been compared with similar structures retrieved from the Cambridge Structural Database in order to study this phenomenon. The planarity of this fragment has been explained by the presence of partially delocalized C-C, C-N and C-O bonds, and by an inner angle in the planar pentagonal ring (∼108°), which is close to the ideal tetrahedral value for the sp(3)-hybridized state of the constituent C atom. Due to this propitious angle, this C atom can be present in states intermediate between sp(3)- and sp(2)-hybridized in different structures, while still maintaining the planarity of the ring. There are only weak intermolecular C-H...O hydrogen bonds and C-H...π-electron ring interactions in the structure. In particular, it is the pyrrole ring which is involved in these interactions.

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“…All H atoms were located in difference maps. The correct absolute configuration for the molecules of compound (V) in the crystal selected for data collection was determined by the Flack x parameter (Flack, 1983) of 0.11 (15), calculated using 1344 quotients of the type [(I + ) À (I À )]/[(I + ) + (I À )] (Parsons et al, 2013); the corresponding Hooft y parameter (Hooft et al, 2010) of 0.10 (13) was calculated using 1392 Bijvoet pairs (97% coverage). For compound (III), the low-angle reflection 002, which had been partially attenuated by the beam stop, was omitted from the final refinements.…”

Section: Refinementmentioning

confidence: 99%

“…For the crystal of (V) selected for data collection, the values of the Flack x parameter (Flack, 1983) and the Hooft y parameter (Hooft et al, 2010), calculated for the R configuration, were x = 0.11 (15) and y = 0.10 (13). 1-6).…”

Section: Figurementioning

confidence: 99%

Six polycyclic pyrimidoazepine derivatives: syntheses, molecular structures and supramolecular assembly

et al. 2016

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A versatile synthetic method has been developed for the formation of variously substituted polycyclic pyrimidoazepine derivatives, formed by nucleophilic substitution reactions on the corresponding chloro-substituted compounds; the reactions can be promoted either by conventional heating in basic solutions or by microwave heating in solvent-free systems. Thus, (6RS)-6,11-dimethyl-3,5,6,11-tetrahydro-4H-benzo[b]pyrimido[5,4-f]azepin-4-one, C14H15N3O, (I), was isolated from a solution containing (6RS)-4-chloro-8-hydroxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepine and benzene-1,2-diamine; (6RS)-4-butoxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-8-ol, C18H23N3O2, (II), was formed by reaction of the corresponding 6-chloro compound with butanol, and (RS)-4-dimethylamino-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-8-ol, C16H20N4O, (III), was formed by reaction of the chloro analogue with alkaline dimethylformamide. (6RS)-N-Benzyl-8-methoxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-4-amine, C22H24N4O, (IV), (6RS)-N-benzyl-6-methyl-1,2,6,7-tetrahydropyrimido[5',4':6,7]azepino[3,2,1-hi]indol-8-amine, C22H22N4, (V), and (7RS)-N-benzyl-7-methyl-2,3,7,8-tetrahydro-1H-pyrimido[5',4':6,7]azepino[3,2,1-ij]quinolin-9-amine, C23H24N4, (VI), were all formed by reaction of the corresponding chloro compounds with benzylamine under microwave irradiation. In each of compounds (I)-(IV) and (VI), the azepine ring adopts a conformation close to the boat form, with the C-methyl group in a quasi-equatorial site, whereas the corresponding ring in (V) adopts a conformation intermediate between the twist-boat and twist-chair forms, with the C-methyl group in a quasi-axial site. No two of the structures of (I)-(VI) exhibit the same range of intermolecular hydrogen bonds: different types of sheet are formed in each of (I), (II), (V) and (VI), and different types of chain in each of (III) and (IV).

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Using thet-distribution to improve the absolute structure assignment with likelihood calculations

Cited by 98 publications

References 4 publications

The crystal structure of oxaliplatin: A case of overlooked pseudo symmetry

The crystal structure of oxaliplatin: A case of overlooked pseudo symmetry

A study of the planarity of the pyrrolone fragment in 2-isopropyl-2,3-dihydro-1H-isoindol-1-one

Six polycyclic pyrimidoazepine derivatives: syntheses, molecular structures and supramolecular assembly

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