The Crystal Packing of Organic Molecules: Challenge and Fascination Below 1000 Da

Gas Storage in Porous Molecular Materials

Molecules with permanent porosity in the solid state have been studied for decades. Porosity in these systems is governed by intrinsic pore space, as in cages or macrocycles, and extrinsic void space, created through loose, intermolecular solid-state packing. The development of permanently porous molecular materials, especially cages with organic or metal-organic composition, has seen increased interest over the past decade, and as such, incredibly high surface areas have been reported for these solids. Despite this, examples of these materials being explored for gas storage applications are relatively limited. This minireview outlines existing molecular systems that have been investigated for gas storage and highlights strategies that have been used to understand adsorption mechanisms in porous molecular materials.

J-dimer emission in interwoven metal-organic frameworks

J-dimer emission is an emergent property that occurs when pairs of ground state fluorophores associate, typically in a dilute solution medium. The resulting fluorescence is shifted with respect to the monomer. J-dimer emission, however, has never been observed in concentrated dispersions or in the solid state. We posited that multivariate (MTV) MOFs with double interwoven structures would help to isolate these dimers within their crystalline matrix. Using this strategy, J-aggregate density was controlled during crystallization by following a substitutional solid solution approach. Here, we identified the presence of J-dimers over the entire composition range for interwoven PIZOF-2/NNU-28 structures with variable amounts of a diethynyl-anthracene aggregate-forming link. We produced bulk crystals that systematically shifted their fluorescence from green to red with lifetimes (up to 13 ns) and quantum yields (up to 76%) characteristic of π–π stacked aggregates. Photophysical studies also revealed an equilibrium constant of dimerization, K_D = 1.5 ± 0.3 M⁻¹, enabling the first thermodynamic quantification of link–link interactions that occur during MOF assembly. Our findings elucidate the role that supramolecular effects play during crystallization of MTV MOFs, opening pathways for the preparation of solid-state materials with solution-like properties by design.

J-dimer emission is an emergent property that occurs when pairs of ground-state fluorophores associate within multivariate MOFs producing tunable red shifted emission.

Intermolecular Interactions in Functional Crystalline Materials: From Data to Knowledge

Intermolecular interactions of organic, inorganic, and organometallic compounds are the key to many composition–structure and structure–property networks. In this review, some of these relations and the tools developed by the Cambridge Crystallographic Data Center (CCDC) to analyze them and design solid forms with desired properties are described. The potential of studies supported by the Cambridge Structural Database (CSD)-Materials tools for investigation of dynamic processes in crystals, for analysis of biologically active, high energy, optical, (electro)conductive, and other functional crystalline materials, and for the prediction of novel solid forms (polymorphs, co-crystals, solvates) are discussed. Besides, some unusual applications, the potential for further development and limitations of the CCDC software are reported.

The solid-state structure of the β-blocker metoprolol: a combined experimental and in silico investigation

Metoprolol {systematic name: (RS)-1-isopropylamino-3-[4-(2-methoxyethyl)phenoxy]propan-2-ol}, C15H25NO3, is a cardioselective β1-adrenergic blocking agent that shares part of its molecular skeleton with a large number of other β-blockers. Results from its solid-state characterization by single-crystal and variable-temperature powder X-ray diffraction and differential scanning calorimetry are presented. Its molecular and crystal arrangements have been further investigated by molecular modelling, by a Cambridge Structural Database (CSD) survey and by Hirshfeld surface analysis. In the crystal, the side arm bearing the isopropyl group, which is common to other β-blockers, adopts an all-trans conformation, which is the most stable arrangement from modelling data. The crystal packing of metoprolol is dominated by an O-H...N/N...H-O pair of hydrogen bonds (as also confirmed by a Hirshfeld surface analysis), which gives rise to chains containing alternating R and S metoprolol molecules extending along the b axis, supplemented by a weaker O...H-N/N-H...O pair of interactions. In addition, within the same stack of molecules, a C-H...O contact, partially oriented along the b and c axes, links homochiral molecules. Amongst the solid-state structures of molecules structurally related to metoprolol deposited in the CSD, the β-blocker drug betaxolol shows the closest analogy in terms of three-dimensional arrangement and interactions. Notwithstanding their close similarity, the crystal lattices of the two drugs respond differently on increasing temperature: metoprolol expands anisotropically, while for betaxolol, an isotropic thermal expansion is observed.

Evaluating the Energetic Driving Force for Cocrystal Formation

We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol^-1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems-hydrogen-bonded, halogen-bonded, and weakly bound cocrystals-finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition-more densely packed cocrystals with stronger hydrogen bonding tend to be more stable-but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems.

Solid state characterization and theoretical study of non-linear optical properties of a Fluoro-N-Acylhydrazide derivative

In this work we determine the linear and non-linear optical properties of a Fluoro-N-Acylhydrazide derivative (FBHZ), using a combined supermolecule approach and an iterative scheme of electrostatic polarization, where the atoms of neighbouring molecules are represented by point charges. Our results for non-linear optics (NLO) are comparable to those found experimentally, suggesting that FBHZ constitutes an attractive object for future studies and for use as an interesting material for third-order NLO applications. The dynamic electrical properties of FBHZ in different solvent media are reported. Its molecular properties are closely related to supramolecular features; accordingly, we analysed all its crystal structure properties via intermolecular interactions in the solid state, using X-ray crystallography data and Hirshfeld surface (HS), including thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and hot-stage microscopy (HSM), where the results reveal crystal stability in respect to temperature variation.

WinPSSP: a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

The direct-space methods software Powder Structure Solution Program (PSSP) [Pagola & Stephens (2010). J. Appl. Cryst. 43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.

Isomorphism and solid solution as shown by an accurate high-resolution diffraction experiment

High-resolution crystal structure determination and spherical and multipolar refinement enabled an organic solid solution of 1-(4'-chlorophenyl)-2-methyl-4-nitro-1H-imidazole-5-carbonitrile and 5-bromo-1-(4'-chlorophenyl)-2-methyl-4-nitro-1H-imidazole to be found, which would not normally be revealed using only standard resolution data (ca 0.8 Å), as the disordered part is only visible at high resolution. Therefore, this new structure would have been reported as just another polymorphic form, even more reasonably as isostructural with other derivatives. To the best of our knowledge this is the first example of organic solid solution modelled via charge density Hansen-Coppens formalism and analysed by means of quantum theory of atoms in molecules (QTAIM) theory.

Design of Clathrate Compounds that Use Only Weak Intermolecular Attractions

Intermolecular attractive forces that are considerably weaker than hydrogen bonding and coordination complexation may be used in the design of new molecules that function as host molecules in the solid-state. Known literature examples of accidentally discovered hosts (clathrands), which do not involve strong interactions in their crystals, are identified and discussed. Their molecular symmetry and supramolecular interactions are analysed in order to identify structural features that facilitate and promote molecular inclusion. The solid-state properties of a family of designed compounds that embody these principles are then described. Prediction of their inclusion behaviour was 95 % successful and a wide variety of crystal packing arrangements were encountered. This is an inevitable consequence of competition between many different molecular interactions of comparable energy during the crystallisation process. The lowest energy combination of these host–host and host–guest associations generates the observed outcome. One consequence of this behaviour is that detailed prediction of a new clathrate crystal packing arrangement is extremely difficult. However, a second consequence is that crystal structure analysis provides a rich source of information about weak intermolecular forces and new supramolecular synthons that previously had remained hidden.

Calculation of lattice energies of organic crystals: the PIXEL integration method in comparison with more traditional methods

The lattice energies of 47 crystal structures of organic compounds spanning a wide range of chemical functionalities are calculated using simple atom-atom potential energy functions, using coulombic terms with point-charge parameters, and using the PIXEL formulation, which is based on integral sums over the molecular electron density to obtain coulombic, polarization, dispersion and repulsion lattice energies. Comparisons among the different formulations, and the sensitivity and significance of the results against convenience, ease of application and number of parameters, are discussed. Improvements in the treatment of overlap repulsion in PIXEL are described, as well as a scheme for the minimization of the crystal lattice energy, based on the Symplex algorithm, which although computationally demanding, is shown to be feasible even with comparatively modest computing resources. The reproduction of experimental heats of sublimation is only marginally better with the PIXEL method, which however has great advantages in its being generally applicable in principle throughout the periodic table, at the expense of a minimal number of parameters, and in the fact that it sees the intermolecular interaction as the effect of the whole molecular electron density, in a physically more justifiable approach. This latter view in turn suggests a transition from a consideration of atom-atom bonds to a consideration of molecule-molecule bonding, opening a new view of packing factors in molecular crystals.

Crystal structure of carnidazole form II from synchrotron X-ray powder diffraction: structural comparison with form I, the hydrated form and the low energy conformations in vacuo

The crystal structure of carnidazole form II, O-methyl [2-(2-methyl-5-nitro-1H-imidazole-1-yl)ethyl]thiocarbamate, has been determined using synchrotron X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined by the Rietveld method. For structure solution, 12 degrees of freedom were defined: one motion group and six torsions. Form II crystallizes in space group P2(1)/n, Z=4, with unit cell parameters after Rietveld refinement: a=13.915(4), b=8.095(2), c=10.649(3) A, beta=110.83(1) degrees, and V=1121.1(5) A3. The two polymorphic forms, as well as the hydrate, crystallize in the monoclinic space group P2(1)/n having four molecules in the cell. In form II, the molecules are held together by forming two infinite zig-zag chains via hydrogen bonds of the type N--H...N, the same pattern as in form I. A conformational study of carnidazole, at semiempirical PM3 level, was performed using stochastic approaches based on modification of the flexible torsion angles. The values of the torsion angles for the molecules of the two polymorphic forms and the hydrate of carnidazole are compared to those obtained from the conformational search. Form I and form II are enantiotropic polymorphic pairs this agrees with the fact that the two forms are conformational polymorphs.

Abundant Polymorphism in a System with Multiple Hydrogen-Bonding Opportunities: Oxalyl Dihydrazide

To date, only one crystal structure has been reported in the literature for oxalyl dihydrazide [H(2)N.NH.CO.CO.NH.NH(2)]. In the present paper, we report the discovery of four new polymorphs of oxalyl dihydrazide, obtained by crystallization from solution under different conditions, including the use of different crystallization solvents. All polymorphs have the trans-trans-trans conformation of the N-N-C-C-N-N backbone, but the positions of the hydrogen atoms of the NH(2) groups relative to this backbone differ between the different polymorphs through variation of the torsion angle around each NH-NH(2) bond. The different polymorphs display a range of different hydrogen-bonding arrangements, constructed from different types of hydrogen-bonded array. The existence of several different potential hydrogen-bond donor and hydrogen-bond acceptor groups in the oxalyl dihydrazide molecule, together with the fact that the N-H bonds of the NH(2) groups adopt different orientations with respect to the molecular plane, leads to several possible geometric permutations for hydrogen-bonding arrangements in the solid state. It would not be surprising if even more polymorphs of oxalyl dihydrazide are discovered in the future.

Tunable N-substitution in Zwitterionic Benzoquinonemonoimine Derivatives: Metal Coordination, Tandemlike Synthesis of Zwitterionic Metal Complexes, and Supramolecular Structures

Full details on a very efficient transamination reaction for the synthesis of zwitterionic N,N-dialkyl-2-amino-5-alcoholate-1,4-benzoquinonemonoiminium derivatives [C6H2(=NHR)2(=O)2] 5-16 are reported. The molecular structures of zwitterions 5 (R=CH3) in 5.H2O, 13 (R=CH2CH2OMe), 15 (R=CH2CH2NMe2), and of the parent, unsubstituted system [C6H2(=NH2)2(=O)2] 4 in 4.H2O have been established by single-crystal X-ray diffraction. This one-pot preparation can be carried out in water, MeOH, or EtOH and allows access to new zwitterions with N-substituents bearing functionalities such as -OMe (13), -OH (9-12), NR1R2 with R1 = or not equal R2 (14-16) or an alkene (8), leading to a rich coordination chemistry and allowing fine-tuning of the supramolecular arrangements in the solid state. As previously described for 15, which reacted with Zn(acac)2 to afford the octahedral Zn(II) complex [Zn[C6H2(NCH2CH2NMe2)O(O)(NHCH2CH2NMe2)]2] (20), ligands 13 and 16 with coordinating "arms" afforded with Zn(acac)2 the 2:1 adducts [Zn[C6H2(NCH2CH2X)O(=O)(NHCH2CH2NX)]2] 19 (X=OMe) and 21 (X=NHEt), with N2O4 and N4O2 donor sets around the octahedral Zn(II) center, respectively. Furthermore, zwitterions 15 and 16 reacted with ZnCl2 to give the stable, crystallographically characterized Zn(II) zwitterionic complexes [ZnCl2[C6H2(NCH2CH2NR1R2)O(=O)(NHCH2CH2NHR1R2)]] 22 (R1=R2=Me) and 23 (R1=Et, R2=H) by means of an unprecedented, tandemlike synthesis in which 1) the two pendant amino groups of the organic benzoquinonemonoimine zwitterionic precursor favor metal coordination and proton transfer and 2) the saturated linker prevents pi-conjugation between the charges. The nature of the structural arrangements in the solid state for both inorganic (20, 22, 23) and organic (5, 9, 13, and 15) molecules is determined by subtle variations in the nature of the N-substituent on the zwitterion precursor.

Hydrogen Bonding Patterns of Calix[4]arenes with Thiourea Functionalities in Solution and in the Solid State

[structure: see text] We have synthesized a number of calix[4]arene derivatives presenting thiourea functional groups at their upper rims by the condensation of a 1,3-di(p-amino)calix[4]arene with alkyl isothiocyanates. Mono- and dithiourea-substituted calix[4]arenes were prepared selectively in good yields, and homocoupling of the former led to calix[4]arene dimers with a thiourea linker. X-ray crystallography revealed interesting intra- and intermolecular hydrogen bonding patterns. (1)H NMR data and computational studies also provided some insight into the hydrogen bonding patterns.

Noncovalent Self-Assembly of Bicyclo[4.2.2]diketopiperazines: Influence of Saturation in the Bridging Carbacyclic Ring

[structure: see text] We have prepared 7,9-diazabicyclo[4.2.2]dec-3-ene-8,10-dione (3) and 7,9-diazabicyclo[4.2.2]decane-8,10-dione (4), which differ by virtue of the degree of unsaturation in the bridging carbacyclic tether on a 2,5-diketopiperazine. Remarkably different self-assembly patterns were observed in the solid state for the two compounds, attributed to subtle variations in the conformational constraints imposed by the tether.

Polymorphism of a Novel Sodium Ion Channel Blocker

2-[[4-(4-Fluorophenoxy)phenyl]-methylene]-hydrazinecarboxamide, a member of the semicarbazone family which has shown potential therapeutic use as anticonvulsants, has been found to exist in two polymorphic forms denoted A and B. In addition to reporting aspects of the physical characterization of both forms, the crystal structure of polymorph A has been determined directly from powder X-ray diffraction data using the Genetic Algorithm technique for structure solution, followed by Rietveld refinement. This structure is compared with that of polymorph B, which was determined previously from single crystal X-ray diffraction data. Knowledge of the crystal structures of the two polymorphs provides the opportunity for establishing structure-property relationships. This work further emphasizes the scope and utility of ab initio structure solution from powder X-ray diffraction data in the pharmaceuticals field.

Solid-State Supramolecular Organization, Established Directly from Powder Diffraction Data, and Photoluminescence Efficiency of Rigid-Core Oligothiophene-S,S-dioxides

The "rigid-core" material 3,5-dimethyl-2,3'-bis(3-methylthiophene)-dithieno[3,2-b:',3'-d]thiophene-4,4-dioxide (DTTOMe4) has the highest photoluminescence ever reported for thiophene-based molecules in the solid state. We report the structure of this material, determined directly from powder X-ray diffraction data using the Genetic Algorithm method for structure solution, followed by Rietveld refinement, and the structural properties are discussed in relation to the structures of the corresponding subsystems DTTO and DTTOMe. While the crystal structures of the latter compounds contain cofacial dimers, the crystal structure of DTTOMe4 comprises layers of molecules aligned in an antiparallel fashion. Intermediate neglect of differential overlap with single configuration interaction (INDO/SCI) calculations on the intermolecular interactions in the three crystal structures show that the different solid-state photoluminescence efficiencies of DTTOMe4, DTTOMe, and DTTO cannot be correlated with the different types of dipole-dipole alignment in the solid state. Instead, photoluminescence efficiencies correlate well with the rate of formation of nonradiatively decaying charge-transfer pairs upon photoexcitation. Because of larger intermolecular distances in DTTOMe4, the photoluminescence is less effectively quenched by charge-transfer processes than in DTTOMe and DTTO.

Physicochemical aspects of host-guest compounds

The macro properties of crystalline inclusion compounds depend on their structures. Their thermal stabilities are a function of the strength and the directionality of the various nonbonded interactions occurring in the host-guest assembly. Their lattice energies, as measured by the method of atom-atom potentials, correlate with the thermodynamics of the guest-release reactions and the selectivity that a given host displays for a particular guest. The kinetics of solid-host:vapor-guest reactions and of guest exchange are important in our understanding of catalytic processes. Crystal engineering, in which materials of predetermined properties may be synthesized, is still at the empirical stage.

Solution and solid-state models of peptide CH...O hydrogen bonds

Fumaramide derivatives were analyzed in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography in order to characterize the formation of CH...O interactions under each condition and to thereby serve as models for these interactions in peptide and protein structure. Solutions of fumaramides at 10 mM in CDCl(3) were titrated with DMSO-d(6), resulting in chemical shifts that moved downfield for the CH groups thought to participate in CH...O=S(CD(3))(2) hydrogen bonds concurrent with NH...O=S(CD(3))(2) hydrogen bonding. In this model, nonparticipating CH groups under the same conditions showed no significant change in chemical shifts between 0.0 and 1.0 M DMSO-d(6) and then moved upfield at higher DMSO-d(6) concentrations. At concentrations above 1.0 M DMSO-d(6), the directed CH...O=S(CD(3))(2) hydrogen bonds provide protection from random DMSO-d(6) contact and prevent the chemical shifts for participating CH groups from moving upfield beyond the original value observed in CDCl(3). X-ray crystal structures identified CH...O=C hydrogen bonds alongside intermolecular NH...O=C hydrogen bonding, a result that supports the solution (1)H NMR spectroscopy results. The solution and solid-state data therefore both provide evidence for the presence of CH...O hydrogen bonds formed concurrent with NH...O hydrogen bonding in these structures. The CH...O=C hydrogen bonds in the X-ray crystal structures are similar to those described for antiparallel beta-sheet structure observed in protein X-ray crystal structures.