An evaluation of resolution, accuracy, and precision in FT-IR spectroscopy

Infrared spectroscopy is a foundational technique for the elucidation of chemical structures. The advancements in interferometric spectroscopy, and specifically the development of Fourier transform infrared (FT-IR) spectroscopy, are responsible for the widespread usage of IR spectrometers ranging from teaching labs to pharmaceutical quality control. FT-IR affords an excellent signal-to-noise ratio that permits sensitive sampling with quantitative accuracy and high wavenumber precision based on well documented advantages (Jacquinot, Fellgett, Connes). However, the effect of resolution and instrument-to-instrument variation on wavenumber accuracy is not well understood, with previous work grossly overestimating error. Here, a recommendation of wavenumber accuracy as a function of spectral resolution, accounting for instrument variation among leading manufacturers, is given based on an experimental study of polystyrene and acetaminophen. For peaks that are well resolved and not saturated, the position can be known within 1.1 cm-1 at a spectral resolution of 4 cm-1 or higher, and within 2.2 cm-1 at 8 cm-1 resolution. Other sources of variation are also discussed (e.g., poorly resolved peaks, peak saturation, water interference, spectral noise) to give general recommendations on when IR peak positions can be considered significantly different. Such guidelines are critical for interpreting subtle positional variations, as are often present in different crystal forms of pharmaceuticals.

Gauging the Strength of the Molecular Halogen Bond via Experimental Electron Density and Spectroscopy

Strong and weak halogen bonds (XBs) in discrete aggregates involving the same acceptor are addressed by experiments in solution and in the solid state. Unsubstituted and perfluorinated iodobenzenes act as halogen donors of tunable strength; in all cases, quinuclidine represents the acceptor. NMR titrations reliably identify the strong intermolecular interactions in solution, with experimental binding energies of approx. 7 kJ/mol. Interaction of the σ hole at the halogen donor iodine leads to a redshift in the symmetric C-I stretching vibration; this shift reflects the interaction energy in the halogen-bonded adducts and may be assessed by Raman spectroscopy in condensed phase even for weak XBs. An experimental picture of the electronic density for the XBs is achieved by high-resolution X-ray diffraction on suitable crystals. Quantum theory of atoms in molecules (QTAIM) analysis affords the electron densities and energy densities in the bond critical points of the halogen bonds and confirms stronger interaction for the shorter contacts. For the first time, the experimental electron density shows a significant effect on the atomic volumes and Bader charges of the quinuclidine N atoms, the halogen-bond acceptor: strong and weak XBs are reflected in the nature of their acceptor atom. Our experimental findings at the acceptor atom match the discussed effects of halogen bonding and thus the proposed concepts in XB activated organocatalysis.

Uracil Derivatives for Halogen-Bonded Cocrystals

Among non-covalent interactions, halogen bonding is emerging as a new powerful tool for supramolecular self-assembly. Here, along with a green and effective method, we report three new halogen-bonded cocrystals containing uracil derivatives and 1,2,4,5-tetrafluoro-3,6-diiodobenzene as X-bond donor coformer. These multicomponent solids were prepared both by solvent-drop grinding and solution methods and further characterized by powder and single-crystal X-ray diffraction, Fourier-transformed infrared spectroscopy, and thermal methods (TGA-DSC). In order to study the relative importance of hydrogen versus halogen bonds in the crystal packing, computational methods were applied.

Controlling the molecular arrangement of racemates through weak interactions: the synergy between π-interactions and halogen bonds

POX and NX halogen bonds in combination with π-stacking interactions lead to the sorting of π-extended R- and S-isomers. Theoretical calculations point to a positive synergistic effect between the π-interactions and the halogen bonds to be the origin of such phenomena. As a result, enantiomeric building blocks form homoleptically connected quadrangular structures.

Identification of an Overlooked Halogen-Bond Synthon and Its Application in Designing Fluorescent Materials

Research on new supramolecular synthons facilitates the progress of materials design. Herein, the ability of sp² carbonyl oxygen atoms to act as halogen-bond acceptors was established through cocrystallization. Four sets of carbonyl compounds, including aldehydes, ketones, esters, and amides, were selected as halogen-bond acceptors. In the absence of strong hydrogen bonds, 14 out of 16 combinations of halogen-bond donors and acceptors could form cocrystals, whereby the supramolecular synthon C=O⋅⋅⋅X acts as the main interaction. Further, the geometric parameters of the C=O⋅⋅⋅X interaction were statistically revealed on the basis of the crystallographic database. The bifurcated interaction mode that has been observed in other halogen-bond synthons rarely occurs in the case of C=O⋅⋅⋅X. The robustness of C=O⋅⋅⋅X makes its application in crystal engineering possible and opens up new opportunities in designing multicomponent fluorescent materials, as indicated by multicolor emission of cocrystals D through C=O⋅⋅⋅X interactions.

New Crystal Forms for Biologically Active Compounds. Part 1: Noncovalent Interactions in Adducts of Nevirapine with XB Donors

Stabilization of specific crystal polymorphs of an active pharmaceutical ingredient is crucial for preventing uncontrollable interconversion of various crystalline forms, which affects physicochemical properties as well as physiological activity. Co-crystallization with various excipients is an emerging productive way of achieving such stabilization in the solid state. In this work, we identified an opportunity for co-crystallization of antiviral drug nevirapine (NVP) with a classical XB donor, 1,2,4,5-tetrafluoro-3,6-diiodobenzene (1,4-FIB), as well as 1,3-diiodobenzene (1,3-DIB), which has been seldom employed as an XB donor to date. In the X-ray structures of NVP·1,4-FIB and NVP·1,3-DIB co-crystals, different hydrogen and halogen bonding modes were detected and further investigated via DFT calculations as well as topological analysis of the electron density distribution within the framework of the QTAIM method at the M06/DZP-DKH level of theory. Estimated energies of these supramolecular contacts vary from 0.6 to 5.7 kcal/mol.

The diiodomethyl-sulfonyl moiety: an unexplored halogen bond-donor motif

The α-iodosulfone moiety acts as a new and effective halogen bond donor system in the solid state and in solution.

Non-covalent interactions observed in nevirapinium pentaiodide hydrate which include the rare I4–I−···O=C halogen bonding

In the course of screening for novel crystalline forms of antiviral drug nevirapine, co-crystallization of the latter with molecular iodine was attempted. This resulted in the formation of a hydrate salt form composed of the protonated nevirapinium cation and pentaiodide anion. In the X-ray structure of NVPH+I5 −·H2O, halogen and hydrogen bonding interactions were identified and studied by DFT calculations and topological analysis of the electron density distribution within the framework of QTAIM method at the B3LYP/DZP-DKH and M06/DZP-DKH levels of theory. Estimated energies of these contacts are 1.3–9.4 kcal/mol.

Halogen bonding driven crystal engineering of iodophthalonitrile derivatives

Various halogen bonding driven crystal structures can be obtained by simple modifications of iodophthalonitrile derivatives.

Cooperative intermolecular S–Cl⋯O and F⋯F associations in the crystal packing of α,ω-di(sulfonyl chloride) perfluoroalkanes, ClSO2(CF2)nSO2Cl, where n = 4, 6

Halogen bonding between neighboring sulfonyl chloride groups and short fluorine–fluorine contacts supports crystal formation in the title compounds.

Assembly and dichroism of a four-component halogen-bonded metal–organic cocrystal salt solvate involving dicyanoaurate(I) acceptors

We describe the use of dicyanoaurate ions as linear ditopic metal–organic acceptors for the halogen bond-driven assembly of a dichroic metal–organic cocrystal based on azobenzene chromophores. Structural analysis by single crystal X-ray diffraction revealed that the material is a four-component solid, consisting of anticipated anionic metal–organic halogen-bonded chains based on dicyanoaurate ions, as well as complex potassium-based cations and discrete molecules of the crown ether 15-crown-5. Importantly, the structural analysis revealed the parallel alignment of the halogen-bonded chains required for dichroic behaviour, confirming that crystal engineering principles developed for the design of halogen-bonded dichroic organic cocrystals are also applicable to metal-based structures. In the broader context of crystal engineering, the structure of the herein reported dichroic material is additionally interesting as the presence of an ion pair, a neutral azobenzene and a molecule of a room-temperature liquid make it an example of a solid that simultaneously conforms to definitions of a salt, a cocrystal, and a solvate.

Structural characterization of the aquaporin inhibitor 2-nicotinamido-1,3,4-thiadiazole

Nicotinamides are a class of compounds with a wide variety of applications, from use as antimicrobial agents to inhibitors of biological processes. These compounds are also cofactors, which are necessary components of metabolic processes. Structural modification gives rise to the activities observed. Similarly, 1,3,4-thiadiazoles have been shown to possess antioxidant, antimicrobial, or anti-inflammatory biological activity. To take advantage of each of the inherent characteristics of the two aforementioned functional groups, 2-nicotinamido-1,3,4-thiadiazole, C8H6N4OS, was synthesized. Since defining chemical connectivity is paramount in understanding biological activity, in this report, the structural characterization of 2-nicotinamido-1,3,4-thiadiazole has been carried out using X-ray crystallographic methods. The NMR-derived assignments were made possible by utilizing one- (1D) and two-dimensional (2D) NMR techniques. In addition, UV-Visible and IR spectroscopies, and elemental analysis were used to fully characterize the product synthesized by the one-step reaction between nicotinoyl chloride hydrochloride and 2-amino-1,3,4-thiadiazole. Computational parameters related to blood-brain barrier permeability are also presented.

Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano-halogen interactions

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano-halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013). RSC Adv. 3, 12955-12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C-H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic-aromatic interactions and cyano-halogen interactions, further stabilizing the molecular packing. A database analysis of cyano-halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53, 662-671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano-halogen interactions in their packing. Three geometric parameters for the C-X...N[triple-bond]C interaction (X = F, Cl, Br or I), viz. the N...X distance and the C-X...N and C-N...X angles, were analysed. The results indicate that all the short cyano-halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.

Stabilizing volatile liquid chemicals using co-crystallization

A convenient, effective, and scalable protocol for stabilizing volatile liquid chemicals is reported.