The Advantages of Flexibility: The Role of Entropy in Crystal Structures Containing C-H···F Interactions

Molecular crystal structures are often interpreted in terms of strong, structure directing, intermolecular interactions, especially those with distinct geometric signatures such as H-bonds or π-stacking interactions. Other interactions can be overlooked, perhaps because they are weak or lack a characteristic geometry. We show that although the cumulative effect of weak interactions is significant, their deformability also leads to occupation of low energy vibrational energy levels, which provides an additional stabilizing entropic contribution. The entropies of five fluorobenzene derivatives have been calculated by periodic DFT calculations to assess the entropic influence of C-H···F interactions in stabilizing their crystal structures. Calculations reproduce inelastic neutron scattering data and experimental entropies from heat capacity measurements. C-H···F contacts are shown to have force constants which are around half of those of more familiar interactions such as hydrogen bonds, halogen bonds, and C-H···π interactions. This feature, in combination with the relatively high mass of F, means that the lowest energy vibrations in crystalline fluorobenzenes are dominated by C-H···F contributions. C-H···F contacts occur much more frequently than would be expected from their enthalpic contributions alone, but at 150 K, the stabilizing contribution of entropy provides, at -10 to -15 kJ mol-1, a similar level of stabilization to the N-H···N hydrogen bond in ammonia and O-H···O hydrogen bond in water.

Performance of Dispersion-Inclusive Density Functional Theory Methods for Energetic Materials

Molecular crystals of energetic materials (EMs) are denser than typical molecular crystals and are characterized by distinct intermolecular interactions between nitrogen-containing moieties. To assess the performance of dispersion-inclusive density functional theory (DFT) methods, we have compiled a data set of experimental sublimation enthalpies of 31 energetic materials. We evaluate the performance of three methods: the semilocal Perdew-Burke-Ernzerhof (PBE) functional coupled with the pairwise Tkatchenko-Scheffler (TS) dispersion correction, PBE with the many-body dispersion (MBD) method, and the PBE-based hybrid functional (PBE0) with MBD. Zero-point energy contributions and thermal effects are described using the quasi-harmonic approximation (QHA), including explicit treatment of thermal expansion, which we find to be non-negligible for EMs. The lattice energies obtained with PBE0+MBD are the closest to experimental sublimation enthalpies with a mean absolute error of 9.89 kJ/mol. However, the state-of-the-art treatment of vibrational and thermal contributions makes the agreement with experiment worse. Pressure-volume curves are also examined for six representative materials. For pressure-volume curves, all three methods provide reasonable agreement with experimental data with mean absolute relative errors of 3% or less. Most of the intermolecular interactions typical of EMs, namely nitro-amine, nitro-nitro, and nitro-hydrogen interactions, are more sensitive to the choice of the dispersion method than to the choice of the exchange-correlation functional. The exception is π-π stacking interactions, which are also very sensitive to the choice of the functional. Overall, we find that PBE+TS, PBE+MBD, and PBE0+MBD do not perform as well for energetic materials as previously reported for other classes of molecular crystals. This highlights the importance of testing dispersion-inclusive DFT methods for diverse classes of materials and the need for further method development.

New Screening Protocol for Effective Green Solvents Selection of Benzamide, Salicylamide and Ethenzamide

New protocol for screening efficient and environmentally friendly solvents was proposed and experimentally verified. The guidance for solvent selection comes from computed solubility via COSMO-RS approach. Furthermore, solute-solvent affinities computed using advanced quantum chemistry level were used as a rationale for observed solvents ranking. The screening protocol pointed out that 4-formylomorpholine (4FM) is an attractive solubilizer compared to commonly used aprotic solvents such as DMSO and DMF. This was tested experimentally by measuring the solubility of the title compounds in aqueous binary mixtures in the temperature range between 298.15 K and 313.15 K. Additional measurements were also performed for aqueous binary mixtures of DMSO and DMF. It has been found that the solubility of studied aromatic amides is very high and quite similar in all three aprotic solvents. For most aqueous binary mixtures, a significant decrease in solubility with a decrease in the organic fraction is observed, indicating that all systems can be regarded as efficient solvent-anti-solvent pairs. In the case of salicylamide dissolved in aqueous-4FM binary mixtures, a strong synergistic effect has been found leading to the highest solubility for 0.6 mole fraction of 4-FM.

High-Pressure Polymorphism in Hydrogen-Bonded Crystals: A Concise Review

High-pressure polymorphism is a developing interdisciplinary field. Pressure up to 20 GPa is a powerful thermodynamic parameter for the study and fabrication of hydrogen-bonded polymorphic systems. This review describes how pressure can be used to explore polymorphism and surveys the reports on examples of compounds that our group has studied at high pressures. Such studies have provided insight into the nature of structure–property relationships, which will enable crystal engineering to design crystals with desired architectures through hydrogen-bonded networks. Experimental methods are also briefly surveyed, along with two methods that have proven to be very helpful in the analysis of high-pressure polymorphs, namely, the ab initio pseudopotential plane–wave density functional method and using Hirshfeld surfaces to construct a graphical overview of intermolecular interactions.

A first-order phase transition in Blatter's radical at high pressure

The crystal structure of Blatter's radical (1,3-diphenyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl) has been investigated between ambient pressure and 6.07 GPa. The sample remains in a compressed form of the ambient-pressure phase up to 5.34 GPa, the largest direction of strain being parallel to the direction of π-stacking interactions. The bulk modulus is 7.4 (6) GPa, with a pressure derivative equal to 9.33 (11). As pressure increases, the phenyl groups attached to the N1 and C3 positions of the triazinyl moieties of neighbouring pairs of molecules approach each other, causing the former to begin to rotate between 3.42 to 5.34 GPa. The onset of this phenyl rotation may be interpreted as a second-order phase transition which introduces a new mode for accommodating pressure. It is premonitory to a first-order isosymmetric phase transition which occurs on increasing pressure from 5.34 to 5.54 GPa. Although the phase transition is driven by volume minimization, rather than relief of unfavourable contacts, it is accompanied by a sharp jump in the orientation of the rotation angle of the phenyl group. DFT calculations suggest that the adoption of a more planar conformation by the triazinyl moiety at the phase transition can be attributed to relief of intramolecular H...H contacts at the transition. Although no dimerization of the radicals occurs, the π-stacking interactions are compressed by 0.341 (3) Å between ambient pressure and 6.07 GPa.

Coexistence of Intra- and Intermolecular Hydrogen Bonds: Salicylic Acid and Salicylamide and Their Thiol Counterparts

The ωB97-XD/6-311++G(d,p) calculations were carried out on dimers and monomers of salicylic acid and salicylamide as well as on their thiol counterparts; different conformations of these species were considered. The searches through the Cambridge Structural Database were performed to find related structures; thus the analysis of results of these searches is presented. Various approaches were applied to analyze inter- and intramolecular hydrogen bonds occurring in the above-mentioned species: natural bond orbital (NBO) method, symmetry-adapted perturbation theory (SAPT) approach, the quantum theory of atoms in molecules (QTAIM), and the electron localization function (ELF) method. The results of calculations indicate a slight mutual influence of inter- and intramolecular hydrogen bonds. However, the frequent occurrence of both interactions in crystal structures indicates the importance of their coexistence. The occurrence of intramolecular chalcogen bonds for trans conformations of species analyzed is also discussed.

Suppression of isotopic polymorphism

Crystallisation at pressure overcomes the effect of isotopic polymorphism in the methylpyridine pentachlorophenol co-crystal. Though the hydrogenated Cc polymorph can only be obtained at pressure, it is stable on recovery to ambient conditions.

A new high-pressure benzocaine polymorph - towards understanding the molecular aggregation in crystals of an important active pharmaceutical ingredient (API)

Benzocaine (BZC), an efficient and highly permeable anaesthetic and an active pharmaceutical ingredient of many commercially available drugs, was studied under high pressure up to 0.78 GPa. As a result, new BZC polymorph (IV) was discovered. The crystallization of polymorph (IV) can be initiated by heating crystals of polymorph (I) at a pressure of at least 0.45 GPa or by their compression to 0.60 GPa. However, no phase transition from polymorph (I) to (IV) was observed. Although polymorph (IV) exhibits the same main aggregation motif as in previously reported BZC polymorphs (I)-(III), i.e. a hydrogen-bonded ribbon, its molecular packing and hydrogen-bonding pattern differ considerably. The N-H...N hydrogen bonds joining parallel BZC ribbons in crystals at ambient pressure are eliminated in polymorph (IV), and BZC ribbons become positioned at an angle of about 80°. Unfortunately, crystals of polymorph (IV) were not preserved on pressure release, and depending on the decompression protocol they transformed into polymorph (II) or (I).

A Short Review of Current Computational Concepts for High-Pressure Phase Transition Studies in Molecular Crystals

High-pressure chemistry of organic compounds is a hot topic of modern chemistry. In this work, basic computational concepts for high-pressure phase transition studies in molecular crystals are described, showing their advantages and disadvantages. The interconnection of experimental and computational methods is highlighted, showing the importance of energy calculations in this field. Based on our deep understanding of methods’ limitations, we suggested the most convenient scheme for the computational study of high-pressure crystal structure changes. Finally, challenges and possible ways for progress in high-pressure phase transitions research of organic compounds are briefly discussed.

Highly selective and sensitive simultaneous nanomolar detection of Cs(i) and Al(iii) ions using tripodal organic nanoparticles in aqueous media: the effect of the urea backbone on chemosensing

Chemosensing plays a very important role in the detection of essential/pollutant ions in aqueous media. In this manuscript, two tripodal ligands, i.e., 1-(2-hydroxybenzyl)-3-(4-nitrophenyl)-1-phenylurea (ligand 1) and 1-(2-hydroxybenzyl)-3-(4-nitrophenyl)-1-phenylthiourea (ligand 2) have been synthesised, which differ in the linker molecule, i.e., urea and thiourea in ligand 1 and ligand 2, respectively. The ligands were characterised by NMR, IR and mass spectroscopic techniques. Ligands 1 and 2 (2 mM) were further employed for the generation of their organic nanoparticles (ONPs) (0.01 mM) of size 20–25 nm and 30–35 nm, respectively, by the reprecipitation method. The chemosensing properties of 1-ONP and 2-ONP solutions were investigated. 1-ONP showed simultaneous recognition behaviour towards Cs(i) and Al(iii) with the limits of detection of ∼220 and ∼377 nM, respectively, in an aqueous medium, while 2-ONP did not show any recognition behaviour towards any ion.

Two ligands 1 and 2 are synthesized and their organic nanoparticles (1-ONP and 2-ONP) are generated. 1-ONP has shown the chemosensing of Cs(i) (∼220 nm) and Al(iii) (∼377 nm) in aqueous medium while 2-ONP has not shown any chemosensing behaviour.

Crystal nucleation of salicylamide and a comparison with salicylic acid

Nucleation behaviour of salicylamide in different solvents was determined and compared with salicylic acid, attempting to progress the rationalization of the influence of the solvent and solute on crystal nucleation of organic compounds in solution.

Intramolecular Hydrogen Bonds in Selected Aromatic Compounds: Recent Developments

A review of intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl Mannich bases, dipyrrins, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, and 4-Bora-3a,4a-diaza-s-indacene (BODIPY) dyes with tautomeric sensors as substituents is presented in this paper. Ortho-hydroxy Schiff and Mannich base derivatives are known as model molecules for analysing the properties of intramolecular hydrogen bonding. The compounds under discussion possess physicochemical features modulated by the presence of strong intramolecular hydrogen bonds. The equilibrium between intra- and inter-molecular hydrogen bonds in BODIPY is discussed. Therefore, the summary can serve as a knowledge compendium of the influence of the hydrogen bond on the molecular properties of aromatic compounds.

Face indexing and shape analysis of salicylamide crystals grown in different solvents

The effect of solvent on salicylamide's crystal habit was investigated. It is deduced that ethyl acetate is adsorbed more strongly on the faces, the increased size of which, can explain the shape change.

A thermodynamically consistent phase diagram of a trimorphic pharmaceutical, l-tyrosine ethyl ester, based on limited experimental data

Crystalline polymorphs possess different physical properties, and phase changes between those polymorphs may affect the properties of engineered materials such as drugs. This is very well illustrated by the large effort that is put into the capability to predict phase behaviour of pharmaceuticals to avoid the unexpected appearance of different crystal forms. Much progress has been made, but one of the remaining challenges is (the accuracy in) the prediction of phase behaviour as a function of temperature. Obviously, predictions should at a certain point be verified against experimental data; however, it may not always be easy to elucidate the phase behaviour of a given compound experimentally, because thermodynamically and kinetically controlled phenomena occur in a convoluted fashion in experimental data. The present paper discusses the trimorphism of l-tyrosine ethyl ester as an example case of how experimental data in combination with the thermodynamic tenets lead to a consistent phase diagram, which can be used as the basis for pharmaceutical formulations and for comparison with polymorph predictions by computer. The positions of the two-phase equilibria I-II, I-III, and I-L have been obtained experimentally. Using the Clapeyron equation and the alternation rule, it has been shown how the positions of the other equilibria II-L, III-L, and II-III can be deduced in combination with the stability rankings of the phases and the phase equilibria. The experimental data have been obtained by synchrotron X-ray diffraction, Raman spectroscopy, and thermal analysis as a function of pressure and temperature. Furthermore, laboratory X-ray diffraction as a function of temperature and differential scanning calorimetry have been used. At room temperature, form II is the most stable phase, which remains stable with increasing pressure, as it possesses the smallest specific volume. Form I becomes stable above 33 °C (306 K), but with increasing pressure it turns into form III. On thermodynamic grounds, form III is expected to have a stable domain at very low temperatures.

Pressure-induced phase transition of 4-aminobenzonitrile: the formation and enhancement of N–H⋯N weak hydrogen bonds

A reversible pressure-induced structural phase transition of 4-aminobenzonitrile was found at about 0.3 GPa by conducting in situ high-pressure synchrotron angle-dispersive X-ray diffraction (ADXRD) experiments. The discontinuous changes of Raman modes at 0.2 GPa confirmed the occurrence of phase transition. In situ high-pressure Raman spectra indicated that the molecular arrangement and intermolecular interactions changed abruptly. The process of this phase transition continued up to about 1.0 GPa. When the pressure reached 1.1 GPa, the initial N–H⋯N interaction transformed into a new weak hydrogen bond, which was enhanced by further compression. The ab initio calculations and Hirshfeld surfaces were used to illustrate the above views. This study gives an example that demonstrates that the pressure can induce the formation of hydrogen bonds, which contributes to the development of supramolecular chemistry.

The initial N–H⋯N interactions in 4-aminobenzonitrile crystals are enhanced and changed into weak hydrogen bonds by high pressure.

Pressure-induced phase transition in N–H⋯O hydrogen-bonded crystalline malonamide

In this study, malonamide (C₃H₆N₂O₂) was compressed under up to 10.4 GPa of pressure in a diamond anvil cell at room temperature.

Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding

A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.

Tunable trimers: using temperature and pressure to control luminescent emission in gold(I) pyrazolate-based trimers

A systematic investigation into the relationship between the solid-state luminescence and the intermolecular Au⋅⋅⋅Au interactions in a series of pyrazolate-based gold(I) trimers; tris(μ2 -pyrazolato-N,N')-tri-gold(I) (1), tris(μ2 -3,4,5- trimethylpyrazolato-N,N')-tri-gold(I) (2), tris(μ2 -3-methyl-5-phenylpyrazolato-N,N')-tri-gold(I) (3) and tris(μ2 -3,5-diphenylpyrazolato-N,N')-tri-gold(I) (4) has been carried out using variable temperature and high pressure X-ray crystallography, solid-state emission spectroscopy, Raman spectroscopy and computational techniques. Single-crystal X-ray studies show that there is a significant reduction in the intertrimer Au⋅⋅⋅Au distances both with decreasing temperature and increasing pressure. In the four complexes, the reduction in temperature from 293 to 100 K is accompanied by a reduction in the shortest intermolecular Au⋅⋅⋅Au contacts of between 0.04 and 0.08 Å. The solid-state luminescent emission spectra of 1 and 2 display a red shift with decreasing temperature or increasing pressure. Compound 3 does not emit under ambient conditions but displays increasingly red-shifted luminescence upon cooling or compression. Compound 4 remains emissionless, consistent with the absence of intermolecular Au⋅⋅⋅Au interactions. The largest pressure induced shift in emission is observed in 2 with a red shift of approximately 630 cm(-1) per GPa between ambient and 3.80 GPa. The shifts in all the complexes can be correlated with changes in Au⋅⋅⋅Au distance observed by diffraction.

Structure of organic solids at low temperature and high pressure

This tutorial review summarises the current state of the art in low temperature and high pressure crystallography of molecular organic and coordination compounds.

Polymorphism of felodipine co-crystals with 4,4′-bipyridine

The calcium-channel blocking agent felodipine forms co-crystals with 4,4′-bipyridine with 1 : 1 and 2 : 1 molar ratios. The co-crystal with 1 : 1 molar ratio exists in two polymorphic forms. The co-crystals polymorphism was investigated by X-ray diffraction, DSC, solution calorimetry and Hirshfeld surfaces analysis.

Compression studies of face-to-face π-stacking interaction in sodium squarate salts: Na2C4O4 and Na2C4O4●3H2O

High-pressure Raman scattering and synchrotron X-ray diffraction measurements of sodium squarate (Na(2)C(4)O(4), SS) are performed in a diamond anvil cell. SS possesses a rare, but typical structure, which can show the effect of face-to-face π-stacking without interference of other interactions. At ~11 GPa, it undergoes a phase transition, identified as a symmetry transformation from P2(1)/c to P2(1). From high-pressure Raman patterns and the calculated model of SS, it can be proved that the phase transition results from the distorted squarate rings. We infer it is the enhancement of π-stacking that dominates the distortion. For comparison, high-pressure Raman spectra of sodium squarate trihydrate (Na(2)C(4)O(4)●3H(2)O, SST) are also investigated. The structure of SST is determined by both face-to-face π-stacking and hydrogen bonding. SST can be regarded as a deformation of SS. A phase transition, with the similar mechanism as SS, is observed at ~10.3 GPa. Our results can be well supported by the previous high-pressure studies of ammonium squarate ((NH(4))(2)C(4)O(4), AS), and vice versa. High-pressure behaviors of the noncovalent interactions in SS, SST, and AS are compared to show the impacts of hydrogen bonding and the role of electrostatic interaction in releasing process.

2-propoxybenzamide

In the title mol-ecule, C(10)H(13)NO(2), the amide -NH(2) group is oriented toward the prop-oxy substituent and an intra-molecular N-H⋯O hydrogen bond is formed between the N-H group and the prop-oxy O atom. The benzene ring forms dihedral angles of 12.41 (2) and 3.26 (2)° with the amide and prop-oxy group mean planes, respectively. In the crystal, N-H⋯O hydrogen bonds order pairs of mol-ecules with their mol-ecular planes parallel, but at an offset of 0.73 (2) Å to each other. These pairs are ordered into two types of symmetry-related columns extended along the a axis with the mean plane of a pair in one column approximately parallel to (-122) and in the other to (-1-22). The two planes form dihedral angle of 84.40 (1)°. Overall, in a three-dimensional network, the hydrogen-bonded pairs of mol-ecules are either located in (-1-22) or (-122) layers. In one layer, each pair is involved in four C-H⋯O contacts, twice as a donor and twice as an acceptor. Additionally, there is a short C-H⋯C contact between a benzene C-H group and the amide π-system.

Pressure-induced phase transition in N-H···O hydrogen-bonded molecular crystal oxamide

The effect of high pressure on the structural stability of oxamide has been investigated in a diamond anvil cell by Raman spectroscopy up to ∼14.6 GPa and by angle-dispersive X-ray diffraction (ADXRD) up to ∼17.5 GPa. The discontinuity in Raman shifts around 9.6 GPa indicates a pressure-induced structural phase transition. This phase transition is confirmed by the change of ADXRD spectra with the symmetry transformation from P1 to P1. On total release of pressure, the diffraction pattern returns to its initial state, implying this transition is reversible. We discuss the pressure-induced variations in N-H stretching vibrations and the amide modes in Raman spectra and propose that this phase transition is attributed to the distortions of the hydrogen-bonded networks.

Effect of pressure on crystalline L- and DL-serine: revisited by a combined single-crystal X-ray diffraction at a laboratory source and polarized Raman spectroscopy study

Information on the effect of pressure on hydrogen bonds, which could be derived from single-crystal X-ray diffraction at a laboratory source and polarized Raman spectroscopy, has been compared. L-Serine and DL-serine were selected for this case study. The role of hydrogen bonds in pressure-induced phase transitions in the first system and in the structural stability of the second one are discussed. Non-monotonic distortion of selected hydrogen bonds in the pressure range below ∼ 1–2 GPa, a change in the compression mechanism at ∼ 2–3 GPa, and the evidence of formation of bifurcated N—H...O hydrogen bonds in DL-serine at ∼ 3–4 GPa are considered.