Follow:

Determination of a complex crystal structure in the absence of single crystals: Analysis of powder X-ray diffraction data, guided by solid-state NMR

https://doi.org/10.1039/C7SC00587C

This paper is focused on structure determination directly from powder XRD data in tandem with consideration of solid-state NMR data, specifically to elucidate the structure of 3′,5′-bis-O-decanoyl-2′-deoxyguanosine [denoted dG(C10)2Fig. 1]. This material is believed to be polymorphic, as two distinct solid forms have been identified on crystallization from ethanol. In previous work, Pham et al.28 referred to these two forms as 2q and 2r. The material studied in the present work corresponds to 2q, as the powder XRD data matches the powder XRD data for 2q published previously.29 We note that 2q appears to be more readily obtained, as 2r has only been reported once.28 In order to introduce a systematic nomenclature, we define polymorph I of dG(C10)2 as 2q and we define polymorph II of dG(C10)2 as 2r.

Fig. 1 Molecular structure of dG(C10)2 showing the atom numbering scheme. The green bracket indicates the Watson–Crick hydrogen-bonding groups. The non-hydrogen atoms of the guanine moiety are labelled 1 to 10 and the non-hydrogen atoms of the 2′-deoxyribose moiety are labelled 1′ to 6′ and 10′. Note that the atom labelled here as N10 was labelled N2 or NH2 in previous publications28–30 on dG(C10)2.

“Previous solid-state NMR studies of dG(C10)2 provide direct structural insights concerning the hydrogen-bonding between guanine moieties. Pham et al.28,30 determined the 15N chemical shifts and J-couplings for polymorph I of dG(C10)2 (see Table 1), including a 2hJN7N10 coupling of 5.9 Hz, while Webber et al.29 reported 1H and 13C chemical shifts and found evidence for several H⋯H short contacts. The value of 2hJN7N10 provides a strong indication that there is a relatively strong N–H⋯N hydrogen bond involving N7 and N10, which provided a robust criterion for acceptance or rejection of trial structures obtained in the structure solution from powder XRD data reported here (particularly as a basis for rejecting trial structures that clearly do not contain this hydrogen bond, as discussed in more detail below). Furthermore, comparison of the chemical shifts and J-couplings calculated for the final refined crystal structure with the chemical shifts and J-couplings measured experimentally provides additional scrutiny and validation of the crystal structure following the final Rietveld refinement.”

 

Leave a Comment