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1.  Chemical crystallography and crystal engineering 
IUCrJ  2014;1(Pt 6):380-381.
Today, there is very little doubt that chemistry owes as much to crystallography as crystallography does to chemistry. This mutual synergy defines modern chemical crystallography.
doi:10.1107/S2052252514021976
PMCID: PMC4224455  PMID: 25485117
Editorial; chemical crystallography; crystal engineering
2.  Combinatorial selection of molecular conformations and supramolecular synthons in quercetin cocrystal landscapes: a route to ternary solids 
IUCrJ  2015;2(Pt 4):402-408.
Crucial ‘purification’ steps inherent to the ‘selection’ of particular molecular conformations and supramolecular synthons in solution leads to a successful synthetic strategy for ternary solids, a normally difficult exercise in crystal engineering. This work also suggests a parallel between such strategies and combinatorial chemistry.
The crystallization of 28 binary and ternary cocrystals of quercetin with dibasic coformers is analyzed in terms of a combinatorial selection from a solution of preferred molecular conformations and supramolecular synthons. The crystal structures are characterized by distinctive O—H⋯N and O—H⋯O based synthons and are classified as nonporous, porous and helical. Variability in molecular conformation and synthon structure led to an increase in the energetic and structural space around the crystallization event. This space is the crystal structure landscape of the compound and is explored by fine-tuning the experimental conditions of crystallization. In the landscape context, we develop a strategy for the isolation of ternary cocrystals with the use of auxiliary template molecules to reduce the molecular and supramolecular ‘confusion’ that is inherent in a molecule like quercetin. The absence of concomitant polymorphism in this study highlights the selectivity in conformation and synthon choice from the virtual combinatorial library in solution.
doi:10.1107/S2052252515009884
PMCID: PMC4491312  PMID: 26175900
supramolecular synthons; polymorphism; quercetin; cocrystals; crystal structure landscape
3.  Intermolecular atom–atom bonds in crystals – a chemical perspective1  
IUCrJ  2015;2(Pt 2):159-160.
Short atom–atom distances between molecules are almost always indicative of specific intermolecular bonding. These distances may be used to assess the significance of all hydrogen bonds, including the C–H⋯O and even weaker C–H⋯F varieties.
doi:10.1107/S205225251500189X
PMCID: PMC4392408  PMID: 25866650
intermolecular atom–atom bonds; crystal binding
4.  Aniline–phenol recognition: from solution through supramolecular synthons to cocrystals 
IUCrJ  2014;1(Pt 4):228-239.
The Long-Range Synthon Aufbau Module (LSAM) concept is utilized in the crystal engineering of 1:1 cocrystals of trichlorophenols and halogen-substituted anilines. NMR studies show the presence of LSAMs in solution and also the sequence of association of hydrogen bonding and π⋯π stacking interations that constitute the LSAMs.
Aniline–phenol recognition is studied in the crystal engineering context in several 1:1 cocrystals that contain a closed cyclic hydrogen-bonded [⋯O—H⋯N—H⋯]2 tetramer supramolecular synthon (II). Twelve cocrystals of 3,4,5- and 2,3,4-trichlorophenol with one of eight halogenated anilines have been characterized. Ten of these cocrystals contain an extended octamer synthon that is assembled with hydrogen bonding and π⋯π stacking that defines a Long-Range Synthon Aufbau Module (LSAM). The design strategy is, therefore, based on the construction and transferability of the LSAM, which is a dimer of tetramers. Using the LSAM concept, two short cell axes in the crystal structures can be predicted. Whilst one of them is dictated by synthon II, the other one is dominated by π⋯π interactions. The third cell axis can also be predicted, in some cases, by systematic tuning of the halogen bonds. The design strategy is also verified in cocrystals of non-halogenated precursors. The observation of this large synthon in so many structures points to its stability and possible existence in solution. To this end, one-dimensional 1H and 15N NMR studies, performed on the 3,4,5-trichlorophenol–3,5-dichloroaniline cocrystal in CDCl3, show characteristic downfield shifts that point to a π⋯π stacked structure and to the robustness of the hydrogen-bonded aggregates. Nuclear Overhauser effects point to hydrogen bonding between aniline and phenol molecules in the aggregates. Diffusion-ordered spectroscopy and T 1 inversion recovery experiments show that stacking is present in concentrated solution and lost at a certain dilution. A sequence of events is therefore established: molecules of the aniline and the phenol associate via hydrogen bonding to form tetramers, and tetramers subsequently stack to form octamers.
doi:10.1107/S2052252514012081
PMCID: PMC4107923  PMID: 25075344
supramolecular synthon; crystal engineering; cocrystal; crystal structure prediction
5.  Halogen bonds in some dihalogenated phenols: applications to crystal engineering 
IUCrJ  2013;1(Pt 1):49-60.
The preference of Br to form type II contacts over type I is explored by various techniques. The mechanical properties of some dihalogenated phenols are correlated with their structures.
3,4-Dichlorophenol (1) crystallizes in the tetragonal space group I41/a with a short axis of 3.7926 (9) Å. The structure is unique in that both type I and type II Cl⋯Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C—Cl⋯Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinic P21/c packing of compound (3) is different; while the structure still has O—H⋯O hydrogen bonds, the tetramer O—H⋯O synthon seen in (1) and (2) is not seen. Rather than a type I Br⋯Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br⋯O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groups P21/c and I41/a with the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br⋯Br interaction in (2) is stronger than the corresponding type II Cl⋯Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.
doi:10.1107/S2052252513025657
PMCID: PMC4104968  PMID: 25075319
crystal engineering; crystal structure prediction; elastic deformation; intermolecular interaction
6.  Crystal landscape in the orcinol:4,4′-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters 
IUCrJ  2013;1(Pt 1):8-18.
The role of the supramolecular synthon as the operational structural unit in the late stages of the crystallization event is highlighted with reference to polymorphs and pseudopolymorphs in the orcinol–bipyridine cocrystal system.
Polymorphism in the orcinol:4,4′-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol⋯pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O—H⋯N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O—H⋯N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.
doi:10.1107/S2052252513024421
PMCID: PMC4104971  PMID: 25075315
cocrystal; supramolecular synthon; crystallization; crystal structure prediction; hydrogen bond
7.  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.
doi:10.1107/S160053681203437X
PMCID: PMC3435686  PMID: 22969557
8.  Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test 
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
doi:10.1107/S0108768111042868
PMCID: PMC3222142  PMID: 22101543
9.  Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test 
The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed.
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
doi:10.1107/S0108768111042868
PMCID: PMC3222142  PMID: 22101543
prediction; blind test; polymorph; crystal structure prediction
10.  Quinoxaline: Z′ = 1 form 
A new Z′ = 1 crystal structure of quinoxaline (or 1,4-diaza­naphthalene), C8H6N2, with one-fifth the volume of the earlier known Z′ = 5 structure was obtained by means of an in situ cryocrystallization technique.
doi:10.1107/S1600536810039905
PMCID: PMC3009138  PMID: 21588986
11.  1,3-Difluoro­benzene 
The weak electrostatic and dispersive forces between C(δ+)—F(δ−) and H(δ+)—C(δ−) are at the borderline of the hydrogen-bond phenomenon and are poorly directional and further deformed in the presence of other dominant inter­actions, e.g. C—H⋯π. The title compound, C6H4F2, Z′ = 2, forms one-dimensional tapes along two homodromic C—H⋯F hydrogen bonds. The one-dimensional tapes are connected into corrugated two-dimensional sheets by further bi- or trifrucated C—H⋯F hydrogen bonds. Packing in the third dimension is controlled by C—H⋯π inter­actions.
doi:10.1107/S1600536809038987
PMCID: PMC2971077  PMID: 21578278
12.  1,2,3-Trifluoro­benzene 
In the title compound, C6H3F3, weak electrostatic and dispersive forces between C(δ+)—F(δ−) and H(δ+)—C(δ−) groups are at the borderline of the hydrogen-bond phenomenon and are poorly directional and further deformed in the presence of π–π stacking inter­actions. The mol­ecule lies on a twofold rotation axis. In the crystal structure, one-dimensional tapes are formed via two anti­dromic C—H⋯F hydrogen bonds. These tapes are, in turn, connected into corrugated two-dimensional sheets by bifurcated C—H⋯F hydrogen bonds. Packing in the third dimension is furnished by π–π stacking inter­actions with a centroid–centroid distance of 3.6362 (14) Å.
doi:10.1107/S1600536809038975
PMCID: PMC2971369  PMID: 21578279

Results 1-12 (12)