The clathrate of tri-<i>o</i>-thymotide (TOT) and pyridine

Brunie, Simone; Navaza, A.; Tsoucaris, G.; Declercq, Jean‐Paul; Germain, G.

doi:10.1107/s0567740877009078

Cited by 20 publications

(11 citation statements)

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“…For the XRD analysis, this eliminates a common problem of locating the pyridine nitrogen that often is difficult to distinguish from C-H, such as in TOT‚pyridine in which the pyridine nitrogen position is not located unambiguously by diffraction. 23,27 iii. The ortho-and meta-Deuterons.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, any in-plane motion of the pyridine causes the nitrogen to be disordered over some (when restricted) or all (when unrestricted) of the aromatic atomic positions. 27 The TOT‚pyridine structure typifies the problems encountered with a dynamic pyridine guest.…”

Section: Discussionmentioning

confidence: 99%

“…In the XRD analysis, the highest peak in the electron diffraction map of the pyridine ring is attributed to the nitrogen atom, 27 but subsequent dynamic 2 H NMR work indicates that pyridine undergoes restricted in-plane motion which in fact partially disorders the nitrogen atom over three positions. 23 In the present case, the disordering of the pyridine guest over four symmetry-related positions in the calix cavity further complicates the identification of the pyridine nitrogen atom because the electron densities are reduced by a factor of 4.…”

Section: Discussionmentioning

confidence: 99%

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Weak Intermolecular Interactions and Molecular Recognition: Structure and Dynamics of the Benzene and Pyridine p-tert-Butylcalix[4]arene Inclusions

et al. 1999

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The host cavity of 1:1 host-guest compounds of p-tert-butylcalix [4]arene is well suited for the study of weak interactions in the solid state, as the motional freedom of the guests tests the weak intermolecular interactions in a very direct way. Benzene and pyridine are guests with a controlled number of similar (size, shape) as well contrasting (dipole moment, lone electron pair) properties that allow a meaningful comparative investigation of the structural and dynamic features. The 150 K single-crystal X-ray diffraction studies for the two host-guest compounds show that in both cases the guests occupy essentially the same orientation in the host cavity, with pyridine situated 0.11 Å deeper into the cavity than benzene. The complementarity of the diffraction and solid-state NMR techniques is illustrated, in particular, by incorporating the pyridine structural information obtained from 2 H NMR studies into the diffraction data, thus resolving the ambiguity of the nitrogen atom position. Despite similar structural environments, the guests exhibit quite different dynamic behavior. Variable temperature 2 H NMR spectra of the perdeuterated pyridine and benzene guests are interpreted in terms of specific motional models; benzene undergoes in-plane rotation followed by reorientation about the compound's 4-fold axis of symmetry. In contrast, pyridine reorients about the pyridine C 2 molecular symmetry axis (rather than in-plane rotation), followed by guest reorientation about the compound's C 4 axis of symmetry. A significant point is that the pyridine nitrogen has definite orientations in the cavity that cannot be explained by any specific directional electrostatic interactions between the host and guest. Both the dynamically averaged 15 N NMR chemical shift tensor components and the absence of short contacts rule out a C-H‚‚‚N hydrogen bonding interaction of the host to the guest. Despite the fact that the pyridine molecule is tightly docked in the host cavity, intermolecular interactions must be ascribed strictly to steric interactions acting in concert rather than specific directional interactions. Both guests are oriented in the host cavity such that the aromatic plane minimizes rather than maximizes contact with the host CH 3 groups. This result questions the ability to ascribe structural features in the solid state to isolated directional interactions, such as the importance and role of CH host ‚‚‚π guest interactions which have been suggested many times as having a stabilizing influence on this system.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Weak Intermolecular Interactions and Molecular Recognition: Structure and Dynamics of the Benzene and Pyridine p-tert-Butylcalix[4]arene Inclusions

et al. 1999

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“…For structure determination of C I /TOT using the measured &&h'' di!raction data, the average basic host structure determined for C I /TOT was used as the starting model, and the re"nement strategy described above for (2) 0.3003 (7) 0.5417 (7) 0.7116 (7) 0.6901 (7) 0.1279(4) 0.128(5) C (8) 0.3290 (7) 0.2892 (6) ? The carbon atoms (marked with asterisks) representing guest electron density do not correspond to real atoms in the crystal structure, as discussed in the text.…”

Section: Determination Of the Basic Host Structuresmentioning

confidence: 99%

Structural and Diffraction Properties of Incommensurate Solid Inclusion Compounds Formed between α,ω-Dihalogenoalkanes and Tri-ortho-thymotide

Serrano-González

Harris

1999

Journal of Solid State Chemistry

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“…As this determinant involves only the moduli of the structure factors and the stereochemistry of a fragment of the structure, we will compare our results with those of a Patterson search method. The calculations have been carried out for the structure of tri-o-thymotide, TOT, containing 40 atoms in the asymmetric unit (Brunie & Tsoucaris, 1974). The TOT molecule consists of three identical fragments which are stereochemically known (see Fig.…”

Section: Application To Real Structuresmentioning

confidence: 99%

New algebraic and probabilistic relations between structure factors and direct space information

Knossow¹,

Rango²,

Mauguen³

et al. 1977

Acta Cryst Sect A

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Further investigation of the Karle-Hauptman determinants leads to several new relations: the DN determinant is simply related to interatomic vectors; also obtained is a probabilistic restriction on the atomic positions inside the algebraically allowed regions, as defined by von Eller. On the other hand new Gram determinants are defined and shown to be useful in relating moduli, phases and interatomic vectors. A practical application is given of fitting a stereochemically known fragment in the unit cell.The aim of this paper is the study of useful properties of new Gram determinants (1) in connexion with probabilistic relations and with the notion of 'forbidden regions' introduced a few years ago by von Eller (1962Eller ( , 1964 and implicitly by Goedkoop (1952). These authors have shown that the use of the positivity of a Karle-Hauptman (K.H.) determinant associated with a partial structure can yield information about the atomic positions from the structure factors involved in the determinant. In this paper we report further results on probabilistic properties of K.H. determinants, as well as on new forms of determinants dealing with the following related topics: forbidden regions; use of stereochemical information. Indeed, (2) leads to a K.H. determinant which enables new phase restrictions to be deduced from the observed moduli.However, if one wants to introduce additional a priori information, the Vp set can be adapted accordingly to this information. This is the main idea underlying this paper.

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The clathrate of tri-o-thymotide (TOT) and pyridine

Cited by 20 publications

References 2 publications

Weak Intermolecular Interactions and Molecular Recognition: Structure and Dynamics of the Benzene and Pyridine p-tert-Butylcalix[4]arene Inclusions

Weak Intermolecular Interactions and Molecular Recognition: Structure and Dynamics of the Benzene and Pyridine p-tert-Butylcalix[4]arene Inclusions

Structural and Diffraction Properties of Incommensurate Solid Inclusion Compounds Formed between α,ω-Dihalogenoalkanes and Tri-ortho-thymotide

New algebraic and probabilistic relations between structure factors and direct space information

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