Srinu Tothadi

Halogen Bonds in Crystal Engineering: Like Hydrogen Bonds yet Different

The halogen bond is an attractive interaction in which an electrophilic halogen atom approaches a negatively polarized species. Short halogen atom contacts in crystals have been known for around 50 years. Such contacts are found in two varieties: type I, which is symmetrical, and type II, which is bent. Both are influenced by geometric and chemical considerations. Our research group has been using halogen atom interactions as design elements in crystal engineering, for nearly 30 years. These interactions include halogen···halogen interactions (X···X) and halogen···heteroatom interactions (X···B). Many X···X and almost all X···B contacts can be classified as halogen bonds. In this Account, we illustrate examples of crystal engineering where one can build up from previous knowledge with a focus that is provided by the modern definition of the halogen bond. We also comment on the similarities and differences between halogen bonds and hydrogen bonds. These interactions are similar because the protagonist atoms-halogen and hydrogen-are both electrophilic in nature. The interactions are distinctive because the size of a halogen atom is of consequence when compared with the atomic sizes of, for example, C, N, and O, unlike that of a hydrogen atom. Conclusions may be drawn pertaining to the nature of X···X interactions from the Cambridge Structural Database (CSD). There is a clear geometric and chemical distinction between type I and type II, with only type II being halogen bonds. Cl/Br isostructurality is explained based on a geometric model. In parallel, experimental studies on 3,4-dichlorophenol and its congeners shed light on the nature of halogen···halogen interactions and reveal the chemical difference between Cl and Br. Variable temperature studies also show differences between type I and type II contacts. In terms of crystal design, halogen bonds offer a unique opportunity in the strength, atom size and interaction gradation; this may be used in the design of ternary cocrystals. Structural modularity in which an entire crystal structure is defined as a combination of modules is rationalized on the basis of the intermediate strength of a halogen bond. The specific directionality of the halogen bond makes it a good tool to achieve orthogonality in molecular crystals. Mechanical properties can be tuned systematically by varying these orthogonally oriented halogen···halogen interactions. In a further development, halogen bonds are shown to play a systematic role in organization of LSAMs (long range synthon aufbau module), which are bigger structural units containing multiple synthons. With a formal definition in place, this may be the right time to look at differences between halogen bonds and hydrogen bonds and exploit them in more subtle ways in crystal engineering.

Salt and Cocrystals of Sildenafil with Dicarboxylic Acids: Solubility and Pharmacokinetic Advantage of the Glutarate Salt

Sildenafil is a drug used to treat erectile dysfunction and pulmonary arterial hypertension. Because of poor aqueous solubility of the drug, the citrate salt, with improved solubility and pharmacokinetics, has been marketed. However, the citrate salt requires an hour to reach its peak plasma concentration. Thus, to improve solubility and bioavailability characteristics, cocrystals and salts of the drug have been prepared by treating aliphatic dicarboxylic acids with sildenafil; the N-methylated piperazine of the drug molecule interacts with the carboxyl group of the acid to form a heterosynthon. Salts are formed with oxalic and fumaric acid; salt monoanions are formed with succinic and glutaric acid. Sildenafil forms cocrystals with longer chain dicarboxylic acids such as adipic, pimelic, suberic, and sebacic acids. Auxiliary stabilization via C-H···O interactions is also present in these cocrystals and salts. Solubility experiments of sildenafil cocrystal/salts were carried out in 0.1N HCl aqueous medium and compared with the solubility of the citrate salt. The glutarate salt and pimelic acid cocrystal dissolve faster than the citrate salt in a two hour dissolution experiment. The glutarate salt exhibits improved solubility (3.2-fold) compared to the citrate salt in water. Solubilities of the binary salts follow an inverse correlation with their melting points, while the solubilities of the cocrystals follow solubilities of the coformer. Pharmacokinetic studies on rats showed that the glutarate salt exhibits doubled plasma AUC values in a single dose within an hour compared to the citrate salt. The high solubility of glutaric acid, in part originating from the strained conformation of the molecule and its high permeability, may be the reason for higher plasma levels of the drug.

Designing ternary cocrystals with hydrogen bonds and halogen bonds

A graded selection of hydrogen bonds and halogen bonds allows for the isolation of 2 : 1 : 1 ternary cocrystals of the general form 4-nitrobenzamide : diacid : 1,4-dihalogenated benzene, which are mediated by the amide-acid and I···O2N supramolecular synthons.

Synthon identification in co-crystals and polymorphs with IR spectroscopy. Primary amides as a case study

IR spectroscopy has been widely employed to distinguish between different crystal forms such as polymorphs, clathrates, hydrates and co-crystals. IR has been used to monitor co-crystal formation and single synthon detection. In this work, we have developed a strategy to identify multiple supramolecular synthons in polymorphs and co-crystals with this technique. The identification of multiple synthons in co-crystals with IR is difficult for several reasons. In this paper, a four step method involving well assigned IR spectral markers that correspond to bonds in a synthon is used. IR spectra of three forms of the co-crystal system, 4-hydroxybenzoic acid:4,4′-bipyridine (2 : 1), show clear differences that may be attributed to differences in the synthon combinations existing in the forms (synthon polymorphism). These differences were picked out from the three IR spectra and the bands analysed and assigned to synthons. Our method first identifies IR marker bands corresponding to (covalent) bonds in known/model crystals and then the markers are mapped in known co-crystals having single synthons. Thereafter, the IR markers are queried in known co-crystals with multiple synthons. Finally they are queried in unknown co-crystals with multiple synthons. In the last part of the study, the N–H stretching absorptions of primary amides that crystallize with the amide dimers linked in a ladder like chain show two specific absorptions which are used as marker absorptions and all variations of this band structure have been used to provide details on the environment around the dimer. The extended dimer can accordingly be easily distinguished from the isolated dimer.

Unusual co-crystal of isonicotinamide: the structural landscape in crystal engineering.

The idea of a structural landscape is based on the fact that a large number of crystal structures can be associated with a particular organic molecule. Taken together, all these structures constitute the landscape. The landscape includes polymorphs, pseudopolymorphs and solvates. Under certain circumstances, it may also include multi-component crystals (or co-crystals) that contain the reference molecule as one of the components. Under still other circumstances, the landscape may include the crystal structures of molecules that are closely related to the reference molecule. The idea of a landscape is to facilitate the understanding of the process of crystallization. It includes all minima that can, in principle, be accessed by the molecule in question as it traverses the path from solution to the crystal. Isonicotinamide is a molecule that is known to form many co-crystals. We report here a 2:1 co-crystal of this amide with 3,5-dinitrobenzoic acid, wherein an unusual N−H⋯N hydrogen-bonded pattern is observed. This crystal structure offers some hints about the recognition processes between molecules that might be implicated during crystallization. Also included is a review of other recent results that illustrate the concept of the structural landscape.

Polymorphism in cocrystals of urea:4,4′-bipyridine and salicylic acid:4,4′-bipyridine

Polymorphic cocrystals of urea:4,4′-bipyridine and salicylic acid:4,4′-bipyridine were obtained by crystallization from different solvents. The urea tape is a rare phenomenon in cocrystals but it is consistent in urea:4,4′-bipyridine polymorphic cocrystals. The polymorph obtained from MeCN has symmetrical N–H⋯N hydrogen bond distances on either side of the urea tape. However, the other form obtained from MeOH has unsymmetrical N–H⋯N hydrogen bond lengths. In the polymorphic cocrystals of salicylic acid:4,4′-bipyridine, the basic supramolecular synthon acid–pyridine is the same but the 3D packing is different. Both the polymorphic pairs of cocrystals come under the category of packing polymorphs. All polymorphs were characterized by single-crystal X-ray diffraction (SCXRD), PXRD, DSC, FT-IR and HSM. N–H⋯N and the acid–pyridine supramolecular synthons were insulated by FT-IR vibrational spectroscopy.

Combinatorial crystal synthesis of ternary solids based on 2-methylresorcinol

Cocrystallization experiments of 2-methylresorcinol with several N-bases were performed to identify selective and preferred crystallization routes in relevant structural landscapes. These preferred supramolecular synthon-based crystallization routes were further enhanced by using carefully chosen coformer combinations to synthesize stoichiometric ternary solids. The exercise consists of modular selection and amplification of supramolecular synthons from single through two- to three-component molecular solids, and is equivalent to solid state combinatorial synthesis.

4-Hy­droxy­benzamide 1,4-dioxane hemisolvate

The asymmetric unit of the title compound, C7H7NO2·0.5C4H8O2, is composed of one 4-hydroxybenzamide molecule and half of a 1,4-dioxane molecule. The complete dioxin molecule is generated by crystallographic inversion symmetry. The crystal has an extensive system of hydrogen bonds, in which the three donor H atoms are fully utilized: these result in amide–amide homodimers, and N—H⋯O(dioxane) and O—H⋯O(amide) links.