Packing modes in some mono- and disubstituted phenylpropiolic acids: repeated occurrence of the rare syn,anti catemer

Phenylpropiolic acid isolated in cryogenic nitrogen and xenon matrices: NIR and UV-induced study

Phenylpropiolic acid (C6H5C≡CCOOH, PPA) isolated in nitrogen and xenon cryogenic matrices was studied by infrared spectroscopy. The experimental studies were complemented by a series of quantum chemical calculations carried out at the density functional theory (B3LYP) and MP2 levels of theory (with different basis sets). The calculations predicted the existence of two planar PPA conformers, differing in the arrangement of the carboxylic group. The higher-energy trans-PPA conformer has a negligible population in the gas phase at room temperature and was prepared in situ in the N2 cryomatrix through vibrationally-induced rotamerization of the lower-energy cis-PPA conformer, achieved using selective narrowband infrared excitation of the OH stretching coordinate of the latter species. Broadband UV (λ > 235 nm) irradiation of matrix-isolated cis-PPA was also undertaken, leading to the observation of cis-PPA → trans-PPA isomerization. No other UV-induced photoreactions were observed. The in situ generated trans-PPA conformer was found to decay back to cis-PPA in the dark by tunneling, and its lifetimes under different experimental conditions were determined. The assignment of the infrared spectra of both conformers is presented, considerably extending the vibrational information available on this molecule.

Modulation of Weak Interactions in Structural Isomers: Positional Isomeric Effects on Crystal Packing and Physical Properties and Solid-State Thin-Film Fabrication

Selective formation of positional isomers and accordingly tuning the physicochemical properties of small conjugated organic molecules through structural isomers is an effective crystal engineering for a fascinating successful delivery of thermally stable and photophysically exciting compounds. By small structural skeleton changes, the single crystal of the naphthalenemaleonitrile isomers is found to exhibit a drastic change in crystal packing array, which in turn is found to tune the thermal and physicochemical properties. The α-isomer (A) forms the "herringbone packing" (HP) due to peri-interaction-sensitive C-H···(Ar)π (Ar = naphthalene ring) interactions, and the β-isomer (B) forms the "bricklayer packing" (BP) due to π(C≡N)···π(Ar) stacking interactions. These two positional isomers have revealed insight of molecular packing-dependent structure-property relationship. In this report, we show that a simple modification of relatively less common weak interactions, such as C-H···π(Ar) ↔ π(C≡N)···π(Ar), through the preparation of isomers, can lead to a drastic change in crystal packing (HP ↔ BP). Also, this report demonstrates that by a small structural diversity, one can obtain significant changes in the physicochemical properties like melting behavior, enthalpy, entropy, and electrical properties in the solid state. Therefore, it transpires from this study that structural isomer provides a useful complement to intermolecular nonbonding interactions as a tool to design new promising materials.

Not Your Usual Bioisostere: Solid State Study of 3D Interactions in Cubanes

Previous studies by Desiraju and co-workers have implicated the acidic hydrogen atoms of cubane as a support network for hydrogen bonding groups. Herein we report a detailed structural analysis of all currently available 1,4-disubstituted cubane structures with an emphasis on how the cubane scaffold interacts in its solid-state environment. In this regard, the interactions between the cubane hydrogen atoms and acids, ester, halogens, ethynyl, nitrogenous groups, and other cubane scaffolds were cataloged. The goal of this study was to investigate the potential of cubane as a substitute for phenyl. This could be achieved by analyzing all contacts that are directed by the cubane hydrogen atoms in the X-ray crystal structures. As a result, we have established several new cubane interaction profiles, such as the catemer formation seen in esters, the preferences of halogen-hydrogen contacts over direct halogen bonding, and the stabilizing effects caused by the cubane hydrogen atoms interacting with ethynyl groups. These interaction profiles can then be used as a guide for designing cubane bioisosteres of known materials and drugs containing phenyl moieties.

Affinity prediction computations and mechanosynthesis of carbamazepine based cocrystals

A combination of the excess enthalpy with the fusion entropy of the pure coformer is suggested to be of interest for coformers screening in order to form a multicomponent system with a given API (cocrystal/co-amorphous).

Exploring the role of ionic liquids to tune the polymorphic outcome of organic compounds

While molecular solvents are commonly used in the screening of polymorphs, the choices are often restricted. Ionic liquids (ILs) - also referred as designer solvents - have immense possibility in this regard because of their wide flexibility of tunability. More importantly, the interactions among the IL components are completely unique compared to those present in the molecular solvents. In this context, we have chosen tetrolic acid (TA) and isonicotinamide (INA), which showed solution-structure link in molecular solvents in the past, as probes to investigate the role of imidazolium based ionic liquids in the polymorphism of these two systems and whether the different solute-solvent interactions in ILs affect the polymorphic outcome. It is observed that the selected imidazolium-based ILs, with varying anion basicity have influenced the crystallization outcome by the interaction between ILs and model compounds. Later, we have utilized the concept of double salt ionic liquids (DSIL) for INA, a penta-morphic system, to investigate the variation in the polymorphic outcome. This approach helped to obtain the forms that were otherwise inaccessible in ILs.

Impact of chirality on peculiar ibuprofen molecular dynamics: hydrogen bonding organization and syn vs. anti carboxylic group conformations

Impact of chirality (R and S enantiomers) on syn vs. anti carboxylic group conformations, hydrogen bond dimers and peculiar ibuprofen molecular dynamics.

sp2CH⋯Cl hydrogen bond in the conformational polymorphism of 4-chloro-phenylanthranilic acid

Conformational flexibility and^sp2CH⋯Cl hydrogen bond lead to three polymorphs of 4-chloro-phenylanthranilic acid.

Color polymorphs of aldose reductase inhibitor epalrestat: configurational, conformational and synthon differences

We report five crystalline polymorphs and an amorphous phase of epalrestat together with configurational isomerism and color behavior: form I (deep red), form II (deep orange), form III (bright yellow), form IV (yellow), and form V (orange) are in the E,Z configuration of the drug, and a Z,Z isomer (bright yellow). Two pathways are identified for polymorph conversion: direct transformation of the E,Z isomer and another pathway via the Z,Z isomer to the E,Z polymorphs. From a pharmaceutical perspective, the stability of polymorphs was established under grinding, solvent slurry and thermal conditions: form I (thermodynamic) > form II > form V > form III > form IV (least stable).

Inclusion complexes of Cethyl-2-methylresorcinarene and pyridine N-oxides: breaking the C–I⋯−O–N+ halogen bond by host–guest complexation

C_ethyl-2-Methylresorcinarene and aromatic N-oxides manifest host–guest chemistry by C–H⋯π interactions and halogen bonding; the C–I⋯⁻O–N⁺ halogen bond with 2-iodopyridine N-oxide is broken by the in-cavity C–I⋯π interactions.

Z-effect reversal in carboxylic acid associates

The conformational preferences of carboxylic acids (Z-effect) can be reversed by H-bonding to anions due to the supramolecular stereoelectronic effect.

Bodipy recognizes polyaromatic hydrocarbons via C–H⋯F type weak H-bonding

Polycyclic aromatic hydrocarbons (PAHs) demonstrated unusual weak C–H⋯F type H-bonding interaction with meso-substituted Bodipy dyes (1–3) in ethanol medium.

A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems

Carboxyl and carboxylate groups form important supramolecular motifs (synthons). Besides carboxyl cyclic dimers, carboxyl and carboxylate groups can associate through a single hydrogen bond. Carboxylic groups can further form polymeric-like catemer chains within crystals. To date, no exhaustive classification of these motifs has been established. In this work, 17 association types were identified (13 carboxyl-carboxyl and 4 carboxyl-carboxylate motifs) by taking into account the syn and anti carboxyl conformers, as well as the syn and anti lone pairs of the O atoms. From these data, a simple rule was derived stating that only eight distinct catemer motifs involving repetitive combinations of syn and anti carboxyl groups can be formed. Examples extracted from the Cambridge Structural Database (CSD) for all identified dimers and catemers are presented, as well as statistical data related to their occurrence and conformational preferences. The inter-carboxyl(ate) and carboxyl(ate)-water hydrogen-bond properties are described, stressing the occurrence of very short (strong) hydrogen bonds. The precise characterization and classification of these supramolecular motifs should be of interest in crystal engineering, pharmaceutical and also biomolecular sciences, where similar motifs occur in the form of pairs of Asp/Glu amino acids or motifs involving ligands bearing carboxyl(ate) groups. Hence, we present data emphasizing how the analysis of hydrogen-containing small molecules of high resolution can help understand structural aspects of larger and more complex biomolecular systems of lower resolution.

Naphthyl groups in chiral recognition: structures of salts and esters of 2-methoxy-2-naphthylpropanoic acids

The crystal structures of salt 8, which was prepared from (R)-2-methoxy-2-(2-naphthyl)propanoic acid ((R)-MβNP acid, (R)-2) and (R)-1-phenylethylamine ((R)-PEA, (R)-6), and salt 9, which was prepared from (R)-2-methoxy-2-(1-naphthyl)propanoic acid ((R)-MαNP acid, (R)-1) and (R)-1-(p-tolyl)ethylamine ((R)-TEA, (R)-7), were determined by X-ray crystallography. The MβNP and MαNP anions formed ion-pairs with the PEA and TEA cations, respectively, through a methoxy-group-assisted salt bridge and aromatic CH⋅⋅⋅π interactions. The networks of salt bridges formed 2(1) columns in both salts. Finally, (S)-(2E,6E)-(1-(2) H(1) )farnesol ((S)-13) was prepared from the reaction of (2E,6E)-farnesal (11) with deuterated (R)-BINAL-H (i.e., (R)-BINAL-D). The enantiomeric excess of compound (S)-13 was determined by NMR analysis of (S)-MαNP ester 14. The solution-state structures of MαNP esters that were prepared from primary alcohols were also elucidated.

Synthesis, characterization, and molecular modeling of a pharmaceutical co-crystal: (2-chloro-4-nitrobenzoic acid):(nicotinamide)

The active pharmaceutical ingredient 2-chloro-4-nitrobenzoic acid (2c4n) is a potentially novel therapy for immunodeficiency diseases as an anti-viral and anti-cancer agent, and exists as a dimorph in the solid state. The Kofler hot stage contact method was employed to investigate the potential of preparing a co-crystal with nicotinamide (nic), a GRAS compound. The 1:1 co-crystal 1 was made using liquid-assisted grinding and solution crystallization experiments. The crystal structure determination of 1 reveals that the two molecules are associated via a carboxylic acid-pyridine hydrogen bond, while the nic forms a centrosymmetric R2(2)(8) dimer to ultimately form a ribbon architecture which is compared to other known co-crystals of nic. The melting point of the co-crystal is higher than the melting points of either of the pure components, indicating that the pharmaceutical co-crystal is thermally more stable than the pure pharmaceutical compound. The relative stability of the interactions in the co-crystal over the pure compounds is further supported by molecular modeling calculations.

Crystal engineering: a holistic view

Crystal engineering, the design of molecular solids, is the synthesis of functional solid-state structures from neutral or ionic building blocks, using intermolecular interactions in the design strategy. Hydrogen bonds, coordination bonds, and other less directed interactions define substructural patterns, referred to in the literature as supramolecular synthons and secondary building units. Crystal engineering has considerable overlap with supramolecular chemistry, X-ray crystallography, materials science, and solid-state chemistry and yet it is a distinct discipline in itself. The subject goes beyond the traditional divisions of organic, inorganic, and physical chemistry, and this makes for a very eclectic blend of ideas and techniques. The purpose of this Review is to highlight some current challenges in this rapidly evolving subject. Among the topics discussed are the nature of intermolecular interactions and their role in crystal design, the sometimes diverging perceptions of the geometrical and chemical models for a molecular crystal, the relationship of these models to polymorphism, knowledge-based computational prediction of crystal structures, and efforts at mapping the pathway of the crystallization reaction.