Charge density in crystalline citrinin from X-ray diffraction at 19 K

Abstract

For the fungal metabolite citrinin, CI3Hl4O5, the total experimental electron distribution p(r) and its Laplacian V2p(r) have been obtained from an extensive set (36 564 measurements) of single-crystal X-ray diffracted intensities at a temperature of 19 f 2 K. Relevant steps in data collection and processing are reported. The resulting 7698 independent intensity data have been analysed with a multipole (pseudoatoms) formalism. The topological properties of p(r) have been determined according to the quantum theory of atoms in molecules. CC and CO bond path lengths have been obtained by numerical integration; their values are found to be well correlated with those of the electron density at the bond critical points. Topological features have been used to characterize the extension of the conjugated system of the molecule, and to confirm the stability of its rings, particularly the two formed by intramolecular H bonds. Maps of V2p(r) are presented, showing details in the valence charge distribution and providing a very sensitive tool for analysing dependence of the density on the model adopted to interpret X-ray data. The known chemical reactivity of the molecule towards nucleophiles at a csp2 atom is confirmed by the shape of the molecular reactive surface (the zero envelope of V2p(r)).Key words: experimental electron density, low-temperature X-ray diffraction, topological analysis, Laplacian of p.Resume : En se basant sur un ensemble extensif (36 564 mesures) d'intensitks de diffraction des rayons X par un cristal unique obtenues i une tempkrature de 19 + 2 K, on a obtenu la distribution expkrimentale totale, p(r), ainsi que son laplacien, v2p(r), pour le mCtabolite de champignon citrinine, CI,H,,O5. On a ensuite analyst les 7698 donnCes indkpendantes d'intensitt k I'aide du formalisme multipble (pseudoatomes). On a determink les propriCtCs topologiques de p(r) suivant la thCorie quantique des atomes dans les molCcules. On a dCterminC les longueurs des liaisons CC et CO par leur inttgration numCrique; on a trouvt que leurs valeurs donnent une bonne corrilation avec celles obtenues i partir de la densite Clectronique des points critiques de liaison. On a utilisC des caractkristiques topologiques pour caractkriser l'extension du systtme conjuguC de la molCcule et pour confirmer la stabilitC de ses noyaux, particulibrement les deux formCs par les liaisons hydrogbnes intramoliculaires. On prisente des cartes de VZp(r) qui montrent les details de la distribution de charge de valence et qui fournissent un outil trbs sensible pour analyser la dtpendance de la densitC sur le modble adopt6 pour interpriter les donnCes de diffraction des rayons X. En se basant sur la forme de la surface molCculaire rCactive (l'enveloppe zCro du V2p(r)), on a confirm6 la rCactivitC connue de la molCcule vis-i-vis des nuclCophiles au niveau d'un atome de carbone sp2.Mots clis : densit6 klectronique expkrimentale, diffraction des rayons X ? I basse temptrature, diffraction, analyse topologique, laplacien de p.[Traduit par la rtdacti...

Electron Density Investigation of a Push–Pull Ethylene (C14H24N2O2⋅H2O) by X‐ray Diffraction atT= 21 K

“…Finally, the 18 CÀH bond lengths in the methyl groups, ranging from 1.041(18) to 1.124 (14) ä, are comparable with the neutron average value of 1.059(30) ä. In this connection, it was noted [29] that when only very low temperature neutron measurements are considered, larger methyl CÀH distances are usually observed, approaching our average value.…”

“…The existence of a correlation between 1 b values and bond lengths has been extensively investigated. [29,37,38] Generally, both experimental and theoretical data fit a simple linear model, 1 b = aR AB + b, very well, giving similar slopes and only slightly different intercepts depending on the method used to obtain the data. To reduce the systematic differences due to the methodological approach (experimental apparatus, data treatment, etc.…”

“…To reduce the systematic differences due to the methodological approach (experimental apparatus, data treatment, etc. ), the properties of the CC bonds of PPE were compared with those of two organic molecules analyzed in our laboratory at T < 25 K, namely citrinin [29] and syn-1,6:8,13-bis-carbonyl [14]annulene (BCA).…”

Accurate Charge-Density Studies as an Extension of Bayesian Crystal Structure Determination

“…Structurefactor phases, which cannot be measured, are treated as Non-uniform prior-prejudice distribution UP Uniform prior-prejudice distribution NNM Non-nuclear density maximum ² Similar evidence of the inability of single-exponential deformation functions to account for all the information present in the observations have also been found in studies of organic (Howard et al, 1995;Roversi, Barzaghi, Merati & Destro, 1996) and inorganic (Souhassou et al, 1995) molecular crystals. constants at each cycle of re®nement and assumed equal to the calculated values at the previous cycle, but do undergo changes from one cycle to the next. This problem has recently been brought to general attention in the context of re®nement of macromolecular structures, where inappropriate treatment of phases can result in a signi®cant source of variance being absent from the least-squares variance±covariance matrix and in phase bias being locked in by the use of an incomplete model .…”

Atoms in crystals – from experimental charge densities

“…This de®nition is ®rmly based on quantum-mechanical methods. Recently, the QTAM has been successfully applied to experimentally determined electron densities derived from X-ray singlecrystal diffraction data (Flensburg et al, 1995;Howard et al, 1995;Bianchi et al, 1996;Espinosa et al, 1996;Roversi et al, 1996;Koritsa  nszky et al, 1998;Madsen, Flensburg & Larsen, 1998;Madsen, Iversen et al, 1998). These analyses have been based on the location and characterization of critical points [r&r c 0] for intramolecular and hydrogen-bond interactions in the electron density.…”