Shobhana Krishnaswamy

Helical self-assembly of molecules in pseudopolymorphs of racemic 2,6-di-O-(4-halobenzoyl)-myo-inositol 1,3,5-orthoformates: clues for the construction of molecular assemblies for intermolecular acyl transfer reaction

The crystal structure of racemic 2,6-di-O-benzoyl-myo-inositol 1,3,5-orthoformate (1) which underwent a facile intermolecular benzoyl transfer reaction in the solid state, revealed a helical assembly of molecules along the two-fold screw axis via O–H⋯O hydrogen bond bringing the electrophile (CO) and the nucleophile (–OH) in close proximity along the helical axis. However, structurally related racemic 2,6-di-O-(p-halobenzoyl)-myo-inositol 1,3,5-orthoformates (bromo (2) and chloro (3)) produced triclinic dimorphs (both P) when crystallized from methanol and ethyl acetate. Molecules in either form did not assemble spirally (like 1), and instead exhibited a one-dimensional isostructurality, bridging O–H⋯O linked identical molecular strings via C–H⋯O interactions across the inversion center. However, the molecules of 2 and 3 assembled in a helical manner similar to 1 with inclusion of solvent molecules in the crystal lattice when crystallized from other common organic solvents. Remarkably, in all the solvates the host molecules formed strikingly similar helices around the crystallographic 21-screw axis through O–H⋯O bond involving the –OH group and carbonyl oxygen of the equatorial C2-O-benzoyl group. Comparison of the crystal structure of dimorphs and the solvatomorphs revealed that the solvent molecules, which interact with the orthoformate-bridge, trigger the helix formation of the host. The difference in the crystal structures of solvatomorphs arises in the interlinking of the neighbouring helices, which creates voids of different sizes to accommodate the solvent molecules. All the solvates crystallized in the monoclinic system distributed over three different space groups P21/n, P21/c and C2/c. In the P21/n system, the adjacent helices are linked via C–X⋯O contacts, in P21/c via C–H⋯X (X = Cl, Br) contacts and in C2/c via short X⋯X contacts (X = Cl). The helical organization achieved through solvent mediation and inclusion is of significance in creating molecular packing for intermolecular acyl transfer reactions in crystals.

cis-Protected palladium(II) based binuclear complexes as tectons in crystal engineering and the imperative role of the cis-protecting agent

A survey of the Cambridge Structural Database (CSD) for crystal structures of binuclear coordination complexes, formed by the combination of suitable ligand(s) and Pd(II) centres which are protected in a cis fashion by 2,2′-bipyridine (bpy), 1,10-phenanthroline (phen), tetramethylethylenediamine (tmeda) or ethylenediamine (en), was carried out. The structures of these binuclear complexes could be classified into five different categories – “opened jaws”, “helicate”, “plateau”, “step” and “bow-shaped” based on the relative spatial orientation of the Pd(II) square planes of the cations and the conformation of the ligand(s). Investigation of the molecular packing in these complexes revealed involvement of the cis-protected Pd(II) units in the self-assembly of the cations. Cations in the complexes that contained bpy and phen moieties often assembled via π⋯π stacking and C–H⋯π interactions between the aromatic rings of the cis-protecting Pd(II) units. In contrast, in the en and tmeda complexes, molecular self-organisation in most cases occurred through noncovalent interactions between the cis-protected Pd(II) units and the ligand, counteranion or included solvent molecules. Hence, the cations can be defined as ‘tectons’, each of which contains two cis-protecting units, which play the role of ‘supramolecular synthons’ in the self-assembly of these binuclear complexes. The study of these crystal structures provides information about preferred patterns of molecular association in these complexes, which is invaluable for the crystal engineering of pre-designed self-assembled coordination complexes for desired functions or properties.

Two modes of O--H...O hydrogen bonding utilized in dimorphs of racemic 6-O-acryloyl-2-O-benzoyl-myo-inositol 1,3,5-orthoformate.

The title compound, C(17)H(16)O(8), yields conformational dimorphs [forms (I) and (II)] at room temperature, separately or concomitantly, depending on the solvent of crystallization. The yield of crystals of form (I) is always much more than that of crystals of form (II). The molecule has one donor -OH group that can make intermolecular O-H...O hydrogen bonds with one of the two acceptor C=O groups, as well as with the hydroxyl O atom; interestingly, each of the options is utilized separately in the dimorphs. The crystal structure of form (I) contains one molecule in the asymmetric unit and is organized as a planar sheet of centrosymmetric dimers via O-H...O hydrogen bonds involving the OH group and the carbonyl O atom of the acryloyl group. In the crystal structure of form (II), which contains two independent molecules in the asymmetric unit, two different O-H...O hydrogen bonds, viz. hydroxyl-hydroxyl and hydroxyl-carbonyl (benzoyl), connect the molecules in a layered arrangement. Another notable feature is the transformation of form (II) to form (I) via melt crystallization upon heating to 411 K. The higher yield of form (I) during crystallization and the thermal transition of form (II) to form (I) suggest that the association in form (I) is more highly favoured than that in form (II), which is valuable in understanding the priorities of molecular aggregation during nucleation of various polymorphs.

Intramolecular Cyclization of Carbonate and Thiocarbonate Derivatives of myo-Inositol in the Solid State: Implications for Acyl Group Transfer Reactions in Molecular Crystals

Racemic 4-O-phenoxycarbonyl and 4-O-phenoxythiocarbonyl derivatives of myo-inositol orthoformate undergo thermal intramolecular cyclization in the solid state to yield the corresponding 4,6-bridged carbonates and thiocarbonates, respectively. The thermal cyclization also occurs in the solution and molten states, but less efficiently, suggesting that these cyclization reactions are aided by molecular pre-organization, although not strictly topochemically controlled. Crystal structures of two carbonates and a thiocarbonate clearly revealed that the relative orientation of the electrophile and the nucleophile in the crystal lattice facilitates the intramolecular cyclization reaction and forbids the intermolecular reaction. The correlation observed between the chemical reactivity and the non-covalent interactions in the crystal of the reactants provides a way to estimate the chemical stability of analogous molecules in the solid state.

Self-assembled molecular squares as supramolecular tectons

A concentration dependent equilibrating mixture of molecular squares [Pd4(L′)4(L)4](NO3)8 and triangles [Pd3(L′)3(L)3](NO3)6 was obtained when cis-protected Pd(II) units [Pd(L′)(NO3)2] (L′ = tmeda,[1] 2,2′-bpy,[2] phen) were combined in turn with 4,4′bipyridine (L) in water. The addition of AgOTs to the mixture led to a shift in the equilibrium, resulting in the disappearance of the triangles and exclusive formation of the squares in case of all the complexes. The crystal structures of the molecular squares [Pd4(L′)4(L)4](OTs)8 revealed a pair of tosylate anions encapsulated in the hydrophobic cavity of the square and the presence of several water molecules outside the cavity. The complexes [Pd4(bpy)4(L)4](OTs)8 and [Pd4(phen)4(L)4] (OTs)8 exhibited solvatomorphism and yielded two crystalline forms each, respectively. The cationic units in these crystals associate through π... π stacking interactions between the aromatic rings of the four bpy/phen units and form either one-dimensional arrays or twodimensional layers. The formation of a one-dimensional array occurs when one pair of bpy/phen units of the square engage in π...π stacking interactions with the tosylate anions instead of other adjacent bpy/phen units. Therefore, the cations in the bpy and phen squares may be considered as ‘tectons’ which contain four supramolecular ‘synthons’ apiece, i.e. the cis-protecting units bpy/phen. The knowledge of common patterns of molecular association and identification of supramolecular synthons in these structures can help in the crystal engineering of coordination compounds with desired solid-state properties/functions.

CCDC 902247: Experimental Crystal Structure Determination

Related Article: Rajendra C. Jagdhane, Madhuri T. Patil, Shobhana Krishnaswamy, Mysore S. Shashidhar|2013|Tetrahedron|69|5144|doi:10.1016/j.tet.2013.04.081

Comparison of racemic epi-inosose and (−)-epi-inosose

The conversion of myo-inositol to epi-inositol can be achieved by the hydride reduction of an intermediate epi-inosose derived from myo-inositol. (-)-epi-Inosose, (I), crystallized in the monoclinic space group P2(1), with two independent molecules in the asymmetric unit [Hosomi et al. (2000). Acta Cryst. C56, e584-e585]. On the other hand, (2RS,3SR,5SR,6SR)-epi-inosose, C(6)H(10)O(6), (II), crystallized in the orthorhombic space group Pca2(1). Interestingly, the conformation of the molecules in the two structures is nearly the same, the only difference being the orientation of the C-3 and C-4 hydroxy H atoms. As a result, the molecular organization achieved mainly through strong O-H···O hydrogen bonding in the racemic and homochiral lattices is similar. The compound also follows Wallachs rule, in that the racemic crystals are denser than the optically active form.