Studying the hydrogen atom position in the strong-short intermolecular hydrogen bond of pure and 5-substituted 9-hydroxyphenalenones by invariom refinement and ONIOM cluster computations

The solid-state structures of three H-bonded enol forms of 5-substituted 9-hydroxyphenalenones were investigated to accurately determine the H atom positions of the intramolecular hydrogen bond. For this purpose, single-crystal X-ray diffraction (SC-XRD) data were evaluated by invariom-model refinement. In addition, QM/MM computations of central molecules in their crystal environment show that results of an earlier standard independent atom model refinement, which pointed to the presence of a resonance-assisted hydrogen bond in unsubstituted 9-hydroxyphenalone, are misleading: in all our three and the earlier solid-state structures the lowest energy form is that of an asymmetric hydrogen bond (CS form). Apparent differences of results from SC-XRD and other analytical methods are explained.

A resonance-assisted intramolecular hydrogen bond in compounds containing 2-hydroxy-3,5-dinitrobenzoic acid and its various deprotonated forms: redetermination of several related structures

A large number of structural determinations of compounds containing 2-hydroxy-3,5-dinitrobenzoic acid (I) and its various deprotonated forms, 2-hydroxy-3,5-dinitrobenzoate (II) or 2-carboxy-4,6-dinitrophenolate (III), are biased. The reason for the bias follows from incorrectly applied constraints or restraints on the bridging hydrogen, which is involved in the intramolecular hydrogen bond between the neighbouring carboxylic/carboxylate and oxo/hydroxy groups. This hydrogen bond belongs to the category of resonance-assisted hydrogen bonds. The present article suggests corrections for the following structure determinations that have been published in Acta Crystallographica: DUJZAK, JEVNAA, LUDFUL, NUQVEB, QIQJAD, SAFGUD, SEDKET, TIYZIM, TUJPEV, VABZIJ, WADXOR, YAXPOE [refcodes are taken from the Cambridge Structural Database [CSD; Groom et al. (2016). Acta Cryst. B72, 171–179]. The structural features of the title molecules in all the retrieved structures, together with structures that contain 3,5-dinitro-2-oxidobenzoate (IV), are discussed. Attention is paid to the localization of the above-mentioned bridging hydrogen, which can be situated closer to the O atom of the carboxylate/carboxylic group or that of the hydroxy/oxo group. In some cases, it is disordered between the two O atoms. The position of the bridging hydrogen seems to be dependent on the pK a (base) although with exceptions. A stronger basicity enhances the probability of the presence of a phenolate (III). The present article examines the problem of the refinement of such a bridging hydrogen as well as that of the hydrogen atoms involved in the hydroxy and primary and secondary amine groups. It appears that the best model, in many cases, is obtained by fixing the hydrogen-atom position found in the difference electron-density map while refining its isotropic displacement parameter.

Single crystal synchrotron X-ray diffraction for imaging hydrogen bond evolution

Hydrogen bonding is a valuable intermolecular interaction in "engineering" solid-state materials. This is because of the directionality and relative strength (1) of these bonds. Hydrogen bonds enable charge and energy transfer, via H-bond evolution, in a range of biological and chemical systems (2). Recent work has demonstrated that single crystal X-ray diffraction can be used to image the evolution of hydrogen bonds, including variable temperature proton migration and proton disorder processes. In particular, in a recent study of the temperature dependent proton disorder in hydrogen bonded 3,5-dinitrobenzoic acid (3,5-DNBA) dimers, the proton disorder deduced from data collected on an X-ray laboratory source is in agreement with that found from neutron data (3). This work focuses on variable temperature single crystal synchrotron X-ray diffraction, for the imaging of evolving hydrogen bonds. The development of appropriate methodology is important here, particularly as previous studies have involved laboratory X-ray sources only. Results will be presented from variable temperature data collections on I19, at the Diamond Light Source, and on beamline 11.3.1, at the Advanced Light Source (ALS), on systems such as 3,5-DNBA and co-crystals of benzimidazole, both exhibiting proton disorder across hydrogen bonding interactions. Synchrotron X-ray diffraction measurements have also been used to follow the change in the position of a proton within an intramolecular [N–H···N]+ hydrogen bond across a range of proton-sponge molecular complexes. Importantly, it has been possible to visualise the evolving hydrogen atom position in Fourier difference electron density maps generated from the synchrotron data. In particular, for the 35-DNBA study, the clearest picture of the evolving hydrogen atom position is observed in those generated from data collected at the ALS; even clearer than that observed in X-ray laboratory and neutron measurements on the same system.

Kyzylkumite, Ti2V3+O5(OH): new structure type, modularity and revised formula

The crystal structure of kyzylkumite, ideally Ti2V3+O5 (OH), from the Sludyanka complex in South Baikal, Russia was solved and refined (including the hydrogen atom position) to an agreement index, R1, of 2.34% using X-ray diffraction data collected on a twinned crystal. Kyzylkumite crystallizes in space group P21/c, with a = 8.4787(1), b = 4.5624(1), c = 10.0330(1) Å , β = 93.174(1)º, V = 387.51(1) Å3 and Z = 4. Tivanite, TiV3+O3OH, and kyzylkumite have modular structures based on hexagonal close packing of oxygen, which are made up of rutile [TiO2] and montroseite [V3+O(OH)] slices. In tivanite the rutile:montroseite ratio is 1:1, in kyzylkumite the ratio is 2:1. The montroseite module may be replaced by the isotypic paramontroseite V4+O2 module, which produces a phase with the formula Ti2V4+O6. In the metamorphic rocks of the Sludyanka complex, vanadium can be present as V4+ and V3+ within the same mineral (e.g.in batisivite, schreyerite and berdesinskiite). Kyzylkumite has a flexible composition with respect to the M4+/M3+ ratio. The relationship between kyzylkumite and a closely related Be-bearing kyzylkumite-like mineral with an orthorhombic norbergite-type structure from Byrud mine, Norway is discussed. Both minerals have similar X-ray powder diffraction patterns.

Syntheses, Crystal Structures and an Overview of Alkali Metal Maleates

The crystal structures of four alkali salts of maleic acid have been determined by single crystal X-ray diffraction: crystals of rubidium hydrogen maleate, RbH(C4H2O4), are very nearly centrosymmetrical, i. e., only one hydrogen atom position in the crystal structure violates the centrosymmetry. Thus, the space group is Pbc21 rather than Pbcm. The compound is isotypic with potassium hydrogen maleate, KH(C4H2O4), which has previously been described in space group Pbcm. It has been reinvestigated to prove that the correct space group is also Pbc21. The isotypic pair of rubidium hydrogen maleate maleic acid, RbH(C4H2O4) H2(C4H2O4), and caesium hydrogen maleate maleic acid, CsH(C4H2O4)H2(C4H2O4), crystallise in the triclinic space group P1̄. The geometry of the maleate units in these compounds corresponds well to data of other metal maleates. The only significant variation, concerning the intra-anionic hydrogen bond, is discussed. Furthermore, an overview of previously reported metal maleate structures is given, with special regard to the symmetry of the intramolecular hydrogen bond.