The whole range of hydrogen bonds in one crystal structure: neutron diffraction and charge-density studies of N,N-dimethylbiguanidinium bis(hydrogensquarate)

How to get maximum structure information from anisotropic displacement parameters obtained by three-dimensional electron diffraction: an experimental study on metal-organic frameworks

Three-dimensional electron diffraction (3D ED) has been used for ab initio structure determination of various types of nanocrystals, such as metal-organic frameworks (MOFs), zeolites, metal oxides and organic crystals. These crystals are often obtained as polycrystalline powders, which are too small for single-crystal X-ray diffraction (SCXRD). While it is now possible to obtain accurate atomic positions of nanocrystals by adopting kinematical refinement against 3D ED data, most new structures are refined with isotropic displacement parameters (U _eq), which limits the detection of possible structure disorders and atomic motions. Anisotropic displacement parameters (ADPs, U^ij ) obtained by anisotropic structure refinement, on the other hand, provide information about the average displacements of atoms from their mean positions in a crystal, which can provide insights with respect to displacive disorder and flexibility. Although ADPs have been obtained from some 3D ED studies of MOFs, they are seldom mentioned or discussed in detail. We report here a detailed study and interpretation of structure models refined anisotropically against 3D ED data. Three MOF samples with different structural complexity and symmetry, namely ZIF-EC1, MIL-140C and Ga(OH)(1,4-ndc) (1,4-ndcH₂ is naphthalene-1,4-dicarboxylic acid), were chosen for the studies. We compare the ADPs refined against individual data sets and how they are affected by different data-merging strategies. Based on our results and analysis, we propose strategies for obtaining accurate structure models with interpretable ADPs based on kinematical refinement against 3D ED data. The ADPs of the obtained structure models provide clear and unambiguous information about linker motions in the MOFs.

Weaving a 2D net of hydrogen and halogen bonds: cocrystal of a pyrazolium bromide with tetrafluorodiiodobenzene

Hydrohalides of Lewis bases may act as halogen bond (XB) acceptors and combine two directional interactions, namely, hydrogen bonds (HB) and XBs in the same solid. 3-(1,3,5-Trimethyl-1H-pyrazol-4-yl)acetylacetone (C11H16N2O2, HacacMePz) was protonated with HX (X = Cl or Br) to afford the hydrohalides, C11H17N2O2 +·X − or H2acacMePz+·X − (1, X = Cl; 2, X = Br). Hydrohalides 1 and 2 are isomorphous and adopt a classical dipole packing. Consistent with the observation for most β-diketones, the enol form with an intramolecular HB is observed. Additional noteworthy interactions are HBs of the protonated pyrazolium towards the X − anion at donor–acceptor distances of 2.9671 (17) Å for 1 and 3.159 (4) Å for 2. Cocrystallization of hydrobromide 2 with the XB donor tetrafluorodiiodobenzene (TFDIB) leads to the adduct C11H17N2O2 +·Br−·0.5C6F4I2·H2O or (H2acacMePz+·Br−)2·(H2O)2·TFDIB (3), in which the XB donor TFDIB is situated on a crystallographic centre of inversion. Classical HBs link organic cations, water molecules and Br− anions into chains along [010]. Almost orthogonal to this interaction, XBs with Br...I = 3.2956 (4) Å connect neighbouring chains along [102] into two-dimensional sheets in the (10\overline{2}) plane. Assisted by their negative charge, halide anions represent particularly good nucleophiles towards XB donors.

Estimating electron density at the bond critical point through atomic Hirshfeld surfaces

Interatomic surfaces often carry information related to the electron distribution in a molecule or crystal, not only being a visual aid but also enabling quantitative analyses. Under certain conditions, atomic Hirshfeld surfaces present a high resemblance to the interatomic surfaces obtained through the quantum theory of atoms in molecules (QTAIM), with the advantage of being easily calculated, even for crystal structures determined at low resolutions (i.e. when a charge-density refinement is not performed). Here an empirical relation between the curvedness property of the Hirshfeld surfaces and the electron density at the bond critical point for certain types of covalent and coordination interactions involving carbon atoms has been obtained. The exponential function was tested to estimate the electron density in different crystalline systems, and the highest deviation from reference values obtained through QTAIM was just 16%. Additionally, fine details of this fit may be salient to the difference in electronegativity of the atoms involved in the bond.

Synthesis, structure and magnetocaloric properties of a new two-dimensional gadolinium(III) coordination polymer based on azobenzene-2,2',3,3'-tetracarboxylic acid

A new Gd3+ coordination polymer (CP), namely, poly[diaqua[μ4-1'-carboxy-3,3'-(diazene-1,2-diyl)dibenzene-1,2,2'-tricarboxylato]gadolinium(III)], [Gd(C16H7N2O8)(H2O)2]n, (I), has been synthesized hydrothermally from Gd(NO3)3·6H2O and azobenzene-2,2',3,3'-tetracarboxylic acid (H4abtc). The target solid has been characterized by single-crystal and powder X-ray diffraction, elemental analysis, IR spectroscopy and susceptibility measurements. CP (I) crystallizes in the monoclinic space group C2/c. The structure features a 4-connected topology in which Gd3+ ions are connected by carboxylate groups into a linear chain along the monoclinic symmetry direction. Adjacent one-dimensional aggregates are bridged by Habtc3- ligands to form a two-dimensional CP in the (10-1) plane. A very short hydrogen bond [O...O = 2.4393 (4) Å] links neighbouring layers into a three-dimensional network. A magnetic study revealed antiferromagnetic Gd...Gd coupling within the chain direction. CP (I) displays a significant magnetocaloric effect (MCE), with a maximum -ΔSm of 27.26 J kg-1 K-1 for ΔH = 7 T at 3.0 K. As the MCE in (I) exceeds that of the commercial magnetic refrigerant GGG (Gd3Ga5O12, -ΔSm = 24 J kg-1 K-1, ΔH = 30 kG), CP (I) can be regarded as a potential cryogenic material for low-temperature magnetic refrigeration.

Biguanides: Species with versatile therapeutic applications

Biguanides are compounds in which two guanidine moieties are fused to form a highly conjugated system. Biguanides are highly basic and hence they are available as salts mostly hydrochloride salts, these cationic species have been found to exhibit many therapeutic properties. This review covers the research and development carried out on biguanides and accounts the various therapeutic applications of drugs containing biguanide group-such as antimalarial, antidiabetic, antiviral, anticancer, antibacterial, antifungal, anti-tubercular, antifilarial, anti-HIV, as well as other biological activities. The aim of this review is to compile all the medicinal chemistry applications of this class of compounds so as to pave way for the accelerated efforts in finding the drug action mechanisms associated with this class of compounds. Importance has been given to the organic chemistry of these biguanide derivatives also.

Weak yet Decisive: Molecular Halogen Bond and Competing Weak Interactions of Iodobenzene and Quinuclidine

The halogen bonded adduct between the commonly used constituents quinuclidine and iodobenzene is based on a single weak nitrogen-iodine contact, and the isolation of this adduct was initially unexpected. Iodobenzene does not contain any electron-withdrawing group and therefore represents an unconventional halogen bond donor. Based on excellent diffraction data of high resolution, an electron density study was successfully accomplished and confirmed one of the longest N···I molecular halogen bonds with a distance of 2.9301(4) Å. The topological analysis identified the XB as a directional but weak σ hole interaction and revealed secondary contacts between peripheral regions of opposite charge. These additional contacts and their competition with a nitrogen-based interaction were confirmed by NOESY experiments in solution. Integration enabled us to determine the relative NOE ratios and provided insight regarding the existing interactions.

Displacement parameters from density-functional theory and their validation in the experimental charge density of tartaric acid

Advanced theory matches advanced experiment: anisotropic displacement parameters for tartaric acid have been calculated in the quasi-harmonic approximation and determined experimentally based on a charge density study.

The many flavours of halogen bonds - message from experimental electron density and Raman spectroscopy

Experimental electron-density studies based on high-resolution diffraction experiments allow halogen bonds between heavy halogens to be classified. The topological properties of the electron density in Cl...Cl contacts vary smoothly as a function of the interaction distance. The situation is less straightforward for halogen bonds between iodine and small electronegative nucleophiles, such as nitrogen or oxygen, where the electron density in the bond critical point does not simply increase for shorter distances. The number of successful charge-density studies involving iodine is small, but at least individual examples for three cases have been observed. (a) Very short halogen bonds between electron-rich nucleophiles and heavy halogen atoms resemble three-centre-four-electron bonds, with a rather symmetric heavy halogen and without an appreciable σ hole. (b) For a narrow intermediate range of halogen bonds, the asymmetric electronic situation for the heavy halogen with a pronounced σ hole leads to rather low electron density in the (3,-1) critical point of the halogen bond; the properties of this bond critical point cannot fully describe the nature of the associated interaction. (c) For longer and presumably weaker contacts, the electron density in the halogen bond critical point is only to a minor extent reduced by the presence of the σ hole and hence may be higher than in the aforementioned case. In addition to the electron density and its derived properties, the halogen-carbon bond distance opposite to the σ hole and the Raman frequency for the associated vibration emerge as alternative criteria to gauge the halogen-bond strength. We find exceptionally long C-I distances for tetrafluorodiiodobenzene molecules in cocrystals with short halogen bonds and a significant red shift for their Raman vibrations.

Proton disorder in a short intramolecular hydrogen bond investigated by single-crystal neutron diffraction at 2.5 and 170 K

The substituted acetylacetone 3-[2-(pyridin-4-yl)ethyl]pentane-2,4-dione, C₁₂H₁₅NO₂, (1), with an ethylene bridge between the acetylacetone moiety and the heteroaromatic ring, represents an attractive linker for mixed-metal coordination polymers. In the crystal, (1) adopts an antiperiplanar conformation with respect to the C-C bond in the central ethylene group and almost coplanar acetylacetone and pyridyl groups. The ditopic molecule exists as the enol tautomer, with proton disorder in the short intramolecular hydrogen bond. Single-crystal neutron diffraction at 2.5 K indicated site occupancies of 0.602 (17) and 0.398 (17). The geometry of the acetylacetone moiety is in agreement with such a site preference of the bridging hydrogen: the O atom associated with the preferred H-atom site subtends the longer [1.305 (2) Å] and the more carbonyl-like O atom the shorter [1.288 (2) Å] C-O bond. Based on structure-factor calculations for the alternative H-atom sites, reflections particularly sensitive for proton distribution were identified and measured in a second neutron data collection at 170 K. At this temperature, 546 independent neutron intensities were used to refine positional and isotropic displacement parameters for a structure model in which parameters for C and O atoms were constrained to those obtained by single-crystal X-ray diffraction at the same temperature. The site occupancies for the disordered proton do not significantly differ from those at 2.5 K.

Short is strong: experimental electron density in a very short N···I halogen bond

2,3,5,6-Tetrafluoro-1,4-diiodobenzene and 4-(dimethylamino)pyridine co-crystallize in 1:2 stoichiometry. A diffraction experiment at standard resolution was already conducted in 2010 and revealed one of the shortest N···I contacts ever reported. We collected X-ray intensities at 100 K up to a very high resolution of 1.23 Å−1. These experimental data allowed to refine a structure model based on atom-centered multipoles according to the Hansen-Coppens approach and provided an experimental electron density. A subsequent analysis with the help of Bader’s atoms in molecules theory showed a strong interaction between the pyridine N atom and the σ hole of its closest iodine neighbor on the halogenated benzene. This contact is characterized by a distance of 2.6622(4) Å and associated with a remarkably large electron density of 0.359(5) e⋅Å−3 in the (3, −1) critical point, unprecedented for a secondary interaction. This bona fide shortest halogen bond ever investigated by an experimental charge density study is associated with a significantly negative total energy density in the bond critical point and thus can reliably be classified as strong. Both the electron density and the position of the bond critical point suggest to compare the short N···I contact to coordinative or covalent bonds rather than to σ hole interactions.

A whole zoo of hydrogen bonds in one crystal structure: tris(isonicotinium) hydrogensulfate sulfate monohydrate

Depending on the reaction partner, the organic ditopic molecule isonicotinic acid (Hina) can act either as a Brønsted acid or base. With sulfuric acid, the pyridine ring is protonated to become a pyridinium cation. Crystallization from ethanol affords the title compound tris(4-carboxypyridinium) hydrogensulfate sulfate monohydrate, 3C₆H₆NO₂⁺·HSO₄^-·SO₄^2-·H₂O or [(H₂ina)₃(HSO₄)(SO₄)(H₂O)]. This solid contains 11 classical hydrogen bonds of very different flavour and nonclassical C-H...O contacts. All N-H and O-H donors find at least one acceptor within a suitable distance range, with one of the three pyridinium H atoms engaged in bifurcated N-H...O hydrogen bonds. The shortest hydrogen-bonding O...O distance is subtended by hydrogensulfate and sulfate anions, viz. 2.4752 (19) Å, and represents one of the shortest hydrogen bonds ever reported between these residues.

Plane-Wave Density Functional Theory Meets Molecular Crystals: Thermal Ellipsoids and Intermolecular Interactions

Molecular compounds, organic and inorganic, crystallize in diverse and complex structures. They continue to inspire synthetic efforts and "crystal engineering", with implications ranging from fundamental questions to pharmaceutical research. The structural complexity of molecular solids is linked with diverse intermolecular interactions: hydrogen bonding with all its facets, halogen bonding, and other secondary bonding mechanisms of recent interest (and debate). Today, high-resolution diffraction experiments allow unprecedented insight into the structures of molecular crystals. Despite their usefulness, however, these experiments also face problems: hydrogen atoms are challenging to locate, and thermal effects may complicate matters. Moreover, even if the structure of a crystal is precisely known, this does not yet reveal the nature and strength of the intermolecular forces that hold it together. In this Account, we show that periodic plane-wave-based density functional theory (DFT) can be a useful, and sometimes unexpected, complement to molecular crystallography. Initially developed in the solid-state physics communities to treat inorganic solids, periodic DFT can be applied to molecular crystals just as well: theoretical structural optimizations "help out" by accurately localizing the elusive hydrogen atoms, reaching neutron-diffraction quality with much less expensive measurement equipment. In addition, phonon computations, again developed by physicists, can quantify the thermal motion of atoms and thus predict anisotropic displacement parameters and ORTEP ellipsoids "from scratch". But the synergy between experiment and theory goes much further than that. Once a structure has been accurately determined, computations give new and detailed insights into the aforementioned intermolecular interactions. For example, it has been debated whether short hydrogen bonds in solids have covalent character, and we have added a new twist to this discussion using an orbital-based theory that once more had been developed for inorganic solids. However, there is more to a crystal structure than a handful of short contacts between neighboring residues. We hence have used dimensionally resolved analyses to dissect crystalline networks in a systematic fashion, one spatial direction at a time. Initially applied to hydrogen bonding, these techniques can be seamlessly extended to halogen, chalcogen, and pnictogen bonding, quantifying bond strength and cooperativity in truly infinite networks. Finally, these methods promise to be useful for (bio)polymers, as we have recently exemplified for α-chitin. At the interface of increasingly accurate and popular DFT methods, ever-improving crystallographic expertise, and new challenging, chemical questions, we believe that combined experimental and theoretical studies of molecular crystals are just beginning to pick up speed.

Charge density of the biologically active molecule (2-oxo-1,3-benzoxazol-3(2H)-yl)acetic acid

(2-Oxo-1,3-benzoxazol-3(2H)-yl)acetic acid is a member of a biologically active class of compounds. Its molecular structure in the crystal has been determined by X-ray diffraction, and its gas phase structure was obtained by quantum chemical calculations at the B3LYP/6-311++G(d,p) level of theory. In order to understand the dynamics of the molecule, two presumably soft degrees of freedom associated with the relative orientation of the planar benzoxazolone system and its substituent at the N atom were varied systematically. Five conformers have been identified as local minima on the resulting two-dimensional potential energy surface within an energy window of 27 kJ mol(-1). The energetically most favourable minimum closely matches the conformation observed in the crystal. Based on high-resolution diffraction data collected at low temperature, the experimental electron density of the compound was determined. Comparison with the electron density established by theory for the isolated molecule allowed the effect of intermolecular interactions to be addressed, in particular a moderately strong O-H...O hydrogen bond with a donor...acceptor distance of 2.6177 (9) Å: the oxygen acceptor is clearly polarized in the extended solid. The hydrogen bond connects consecutive molecules to chains, and the pronounced charge separation leads to stacking between neighburs with antiparallel dipole moments perpendicular to the chain direction.

Anisotropic thermal motion in transition-metal carbonyls from experiments and ab initio theory

This proof-of-concept study extends the ab initio computation of anisotropic displacement parameters to complexes with transition metal centres.

N-(6-Methylpyridin-2-yl)mesitylenesulfonamide and acetic acid--a salt, a cocrystal or both?

In the solid obtained from N-(6-methylpyridin-2-yl)mesitylenesulfonamide and acetic acid, the constituents interact via two N-H···O hydrogen bonds. The H atom situated in one of these short contacts is disordered over two positions: one of these positions is formally associated with an adduct of the neutral sulfonamide molecule and the neutral acetic acid molecule, and corresponds to a cocrystal, while the alternative site is associated with salt formation between a protonated sulfonamide molecule and deprotonated acetic acid molecule. Site-occupancy refinements and electron densities from difference Fourier maps suggest a trend with temperature, albeit of limited significance; the cocrystal is more relevant at 100 K, whereas the intensity data collected at room temperature match the description as cocrystal and salt equally well.

Vibrational properties and bonding nature of Sb2Se3 and their implications for chalcogenide materials

There is more to chemical bonding in chalcogenides than the shortest, strongest bonds, as revealed by microscopic quantum-chemical descriptors.

Antimony selenide (antimonselite, Sb₂Se₃) is a versatile functional material with emerging applications in solar cells. It also provides an intriguing prototype to study different modes of bonding in solid chalcogenides, all within one crystal structure. In this study, we unravel the complex bonding nature of crystalline Sb₂Se₃ by using an orbital-based descriptor (the crystal orbital Hamilton population, COHP) and by analysing phonon properties and interatomic force constants. We find particularly interesting behaviour for the medium-range Sb···Se contacts, which still contribute significant stabilisation but are much softer than the “traditional” covalent bonds. These results have implications for the assembly of Sb₂Se₃ nanostructures, and bond-projected force constants appear as a useful microscopic descriptor for investigating a larger number of chalcogenide functional materials in the future.

Systematic experimental charge density analysis of anion receptor complexes

The first systematic electronic resolution study of a series of urea-based anion receptor complexes is presented and shows the binding strength to be greater for more basic anion–receptor pairs in the solid state.

Biguanide and squaric acid as pH-dependent building blocks in crystal engineering

Biguanides and squaric acid are attractive partners for crystal engineering: they incorporate multiple sites that can donate or accept hydrogen bonds. Protonation equilibria in their solutions and the outcome of crystallization experiments are pH dependent: 10 different salts have been obtained from N,N-dimethylbiguanide, N-phenylbiguanide and N-o-tolylbiguanide.

The halogen bond made visible: experimental charge density of a very short intermolecular Cl···Cl donor-acceptor contact

[ZnCl(2)(3,4,5-trichloropyridine)(2)] features short intermolecular Cl···Cl contacts between halogen atoms of different nature, and a charge density study provides experimental evidence for the accepted model of the halogen bonds: an arene-bonded Cl atom acts as a donor of electron density towards the "sigma hole" of a chlorido ligand attached to a neighbouring Zn(II) cation.