A Novel Homoconjugated Propellane Triimide: Synthesis, Structural Analyses, and Gas Separation

Rigid three-dimensional (3D) polycyclic propellanes have garnered interest due to their unique conformational spaces, which display great potential use in selectivity, separation and as models to study through-space electronic interactions. Herein we report the synthesis of a novel rigid propellane, trinaphtho[3.3.3]propellane triimide, which comprises three imide groups embedded on a trinaphtho[3.3.3]propellane. This propellane triimide exhibits large bathochromic shift, amplified molar absorptivity, enhanced fluorescence, and lower reduction potential when compared to the subunits. Computational and experimental studies reveal that the effective through-space π-orbitals interacting (homoconjugation) occurs between the subunits. Single-crystal XRD analysis reveals that the propellane triimide has a highly quasi-D3h symmetric skeleton and readily crystallizes into different superstructures by changing alkyl chains at the imide positions. In particular, the porous 3D superstructure with S-shaped channels is promising for taking up ethane (C2H6) with very good selectivity over ethylene (C2H4), which can purify C2H4 from C2H6/C2H4 in a single separation step. This work showcases a new class of rare 3D polycyclic propellane with intriguing electronic and supramolecular properties.

α-D-2'-Deoxyadenosine, an irradiation product of canonical DNA and a component of anomeric nucleic acids: crystal structure, packing and Hirshfeld surface analysis

α-D-2'-Deoxyribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited. Herein, the single-crystal X-ray structure of α-D-2'-deoxyadenosine (α-dA), C10H13N5O3, and its conformational parameters were determined. In the crystalline state, α-dA forms two conformers in the asymmetric unit which are connected by hydrogen bonds. The sugar moiety of each conformer is arranged in a `clamp'-like fashion with respect to the other conformer, forming hydrogen bonds to its nucleobase and sugar residue. For both conformers, a syn conformation of the nucleobase with respect to the sugar moiety was found. This is contrary to the anti conformation usually preferred by α-nucleosides. The sugar conformation of both conformers is C2'-endo, and the 5'-hydroxyl groups are in a +sc orientation, probably due to the hydrogen bonds formed by the conformers. The formation of the supramolecular assembly of α-dA is controlled by hydrogen bonding and stacking interactions, which was verified by a Hirshfeld and curvedness surface analysis. Chains of hydrogen-bonded nucleobases extend parallel to the b direction and are linked to equivalent chains by hydrogen bonds involving the sugar moieties to form a sheet. A comparison of the solid-state structures of the anomeric 2'-deoxyadenosines revealed significant differences of their conformational parameters.

Deciphering the driving forces in crystal packing by analysis of electrostatic energies and contact enrichment ratios

Hirshfeld surface analysis is a widely used tool for identifying the types of intermolecular contacts that contribute most significantly to crystal packing stabilization. One useful metric for analyzing these contacts is the contact enrichment descriptor, which indicates the types of contacts that are over- or under-represented. In this statistical study, enrichment ratios were combined with electrostatic energy (Eelec) data for a variety of compound families. To compute the electrostatic interaction energy between atoms, charge density models from the ELMAM2 database of multipolar atoms were used. As expected, strong hydrogen bonds such as O/N-H...N and O/N-H...O typically display large enrichment values and have the most negative (i.e. favorable) electrostatic energies. Conversely, contacts that are repulsive from an electrostatic perspective are usually the most under-represented. Analyzing the enrichment ratio and electrostatic energy indicators was shown to help identify which favorable contacts are the most competitive with each other. For weaker interactions, such as hydrophobic contacts, the behavior is less clear cut and can depend on other factors such as the chemical content of the molecule. The anticorrelation between contact enrichment and Eelec is generally lost for weaker contacts. However, we observed that C...C contacts are often enriched in crystal structures containing heterocycles, despite the low electrostatic attraction. For molecules with only weak hydrogen bond donors/acceptors and hydrophobic groups, the correlation between contact enrichment and Eelec is still evident for the strongest of these interactions. However, there are some exceptions where the most favorable contacts from an electrostatic perspective are not the most over-represented. This can occur in cases where the shape of the molecule is complex or elongated, favoring dispersion forces and shape complementarity in the packing.

Uri Shmueli (1928-2023)

Obituary for Uri Shmueli.

Perfluoroalkyl Chain Length Effect on Crystal Packing and [LnO8] Coordination Geometry in Lanthanide-Lithium β-Diketonates: Luminescence and Single-Ion Magnet Behavior

Functionalized perfluoroalkyl lithium β-diketonates (LiL) react with lanthanide(III) salts (Ln = Eu, Gd, Tb, Dy) in methanol to give heterobimetallic Ln-Li complexes of general formula [(LnL₃)(LiL)(MeOH)]. The length of fluoroalkyl substituent in ligand was found to affect the crystal packing of complexes. Photoluminescent and magnetic properties of heterobimetallic β-diketonates in the solid state are reported. The effect of the geometry of the [LnO₈] coordination environment of heterometallic β-diketonates on the luminescent properties (quantum yields, phosphorescence lifetimes for Eu, Tb, Dy complexes) and single-ion magnet behavior (U_eff for Dy complexes) is revealed.

Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone

Structure determination of G-protein-coupled receptors (GPCRs) is key for the successful development of efficient drugs targeting GPCRs. BRIL is a thermostabilized apocytochrome b₅₆₂ (with M7W/H102I/R106L mutations) from Escherichia coli and is often used as a GPCR fusion protein for expression and crystallization. SRP2070Fab, an anti-BRIL antibody Fab fragment, has been reported to facilitate and enhance the crystallization of BRIL-fused GPCRs as a crystallization chaperone. This study was conducted to characterize the high-resolution crystal structure of the BRIL-SRP2070Fab complex. The structure of the BRIL-SRP2070Fab complex was determined at 2.1 Å resolution. This high-resolution structure elucidates the binding interaction between BRIL and SRP2070Fab. When binding to BRIL, SRP2070Fab recognizes conformational epitopes, not linear epitopes, on the surface of BRIL helices III and IV, thereby binding perpendicularly to the helices, which indicates stable binding. Additionally, the packing contacts of the BRIL-SRP2070Fab co-crystal are largely due to SRP2070Fab rather than BRIL. The accumulation of SRP2070Fab molecules by stacking is remarkable and is consistent with the finding that stacking of SRP2070Fab is predominant in known crystal structures of BRIL-fused GPCRs complexed with SRP2070Fab. These findings clarified the mechanism of SRP2070Fab as a crystallization chaperone. Moreover, these data will be useful in the structure-based drug design of membrane-protein drug targets.

Synthesis and crystal structure of a new copper(II) complex based on 5-ethyl-3-(pyridin-2-yl)-1,2,4-triazole

The title compound, bis-[μ-3-ethyl-5-(pyridin-2-yl)-1H-1,2,4-triazol-1-ido]bis[acetato-(di-methyl-formamide)-copper(II)], [Cu₂(C₉H₉N₄)₂(C₂H₃O₂)₂(C₃H₇NO)₂] or [Cu₂(L ^Et)₂(OAc)₂(dmf)₂], is a triazolate complex, which contains two 3-(2-pyrid-yl)-5-ethyl-triazolates (L ^Et)^- in bidentate-bridged coordination modes. Both copper atoms are involved in the formation of a planar six-membered metallocycle Cu-[N-N]₂-Cu. The inversion center of the complex is located at the mid-point of the Cu⋯Cu vector. Each Cu^II atom has a distorted trigonal-bipyramidal environment formed by the three nitro-gen atoms of the deprotonated bridging 3-(2-pyrid-yl)-5-ethyl-triazolate unit, oxygen atoms of the OAc^- group and dmf mol-ecule. In the crystal, C-H⋯O hydrogen bonds link the mol-ecules into chains running along the c-axis direction.

Hybrid Cycloalkyl-Alkyl Chain-Based Symmetric/Asymmetric Acceptors with Optimized Crystal Packing and Interfacial Exciton Properties for Efficient Organic Solar Cells

Hybrid cycloalkyl-alkyl side chains are considered a unique composite side-chain system for the construction of novel organic semiconductor materials. However, there is a lack of fundamental understanding of the variations in the single-crystal structures as well as the optoelectronic and energetic properties generated by the introduction of hybrid side chains in electron acceptors. Herein, symmetric/asymmetric acceptors (Y-C10ch and A-C10ch) bearing bilateral and unilateral 10-cyclohexyldecyl are designed, synthesized, and compared with the symmetric acceptor 2,2'-((2Z,2'Z)-((12,13-bis(2-butyloctyl)-3,9 bis(ethylhexyl)-12,13-dihydro-[1,2,5]thiadiazolo[3,4-e]thieno[2″,3″':4',5']thieno[2',3':4,5] pyrrolo[3,2-g]thieno[2',3':4,5]thieno[3,2-b]indole-2,10- diyl)bis(methanylylidene))bis(5,6-difluoro-3-oxo-2,3-dihydro-1H-indene-2,1-diylidene))dimalononitrile (L8-BO). The stepwise introduction of 10-cyclohexyldecyl side chains decreases the optical bandgap, deepens the energy level, and enables the acceptor molecules to pack closely in a regular manner. Crystallographic analysis demonstrates that the 10-cyclohexyldecyl chain endows the acceptor with a more planar skeleton and enforces more compact 3D network packing, resulting in an active layer with higher domain purity. Moreover, the 10-cyclohexyldecyl chain affects the donor/acceptor interfacial energetics and accelerates exciton dissociation, enabling a power conversion efficiency (PCE) of >18% in the 2,2'-((2Z,2'Z)-((12,13-bis(2-ethylhexyl)-3,9-diundecyl12,13-dihydro-[1,2,5]thiadiazolo[3,4-e]thieno[2″,3″':4',5']thieno[2',3':4,5]pyrrolo[3,2-g]thieno[2',3':4,5]thieno[3,2-b]indole-2,10-diyl)bis(methanylylidene))bis(5,6-difluoro-3-oxo-2,3-dihydro-1H-indene-2,1-diylidene))dimalononitrile (Y6) (PM6):A-C10ch-based organic solar cells (OSCs). Importantly, the incorporation of Y-C10ch as the third component of the PM6:L8-BO blend results in a higher PCE of 19.1%. The superior molecular packing behavior of the 10-cyclohexyldecyl side chain is highlighted here for the fabrication of high-performance OSCs.

Progressive alignment of crystals: reproducible and efficient assessment of crystal structure similarity

During in silico crystal structure prediction of organic molecules, millions of candidate structures are often generated. These candidates must be compared to remove duplicates prior to further analysis (e.g. optimization with electronic structure methods) and ultimately compared with structures determined experimentally. The agreement of predicted and experimental structures forms the basis of evaluating the results from the Cambridge Crystallographic Data Centre (CCDC) blind assessment of crystal structure prediction, which further motivates the pursuit of rigorous alignments. Evaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a flexible algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration (R _g) as a metric to quantify the shape of the superimposed clusters. It is shown that the absence of metrics to describe cluster shape adds ambiguity to the results of the CCDC blind assessments because it is not possible to determine whether the superposition algorithm has prioritized tightly packed molecular clusters (i.e. to minimize R _g) or prioritized reduced RMSD (i.e. via possibly elongated clusters with relatively larger R _g). For example, it is shown that when the PAC algorithm described here uses single linkage to prioritize molecules for inclusion in the superimposed clusters, the results are nearly identical to those calculated by the widely used program COMPACK. However, the lower R _g values obtained by the use of average linkage are favored for molecule prioritization because the resulting RMSDs more equally reflect the importance of packing along each dimension. It is shown that the PAC algorithm is faster than COMPACK when using a single process and its utility for biomolecular crystals is demonstrated. Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.

Polymorphic transition due to grinding: the case of 3-[1-(tert-butoxycarbonyl)azetidin-3-yl]-1,2-oxazole-4-carboxylic acid

A polymorphic transition as a result of grinding was found for 3-[1-(tert-butoxycarbonyl)azetidin-3-yl]-1,2-oxazole-4-carboxylic acid. The thorough study of polymorphic structures before and after crystal structure transformation has revealed some pre-conditions for a polymorphic transition and regularities of changes in molecular and crystal structure. In metastable polymorph 1a, the conformationally flexible molecule adopts a conformation with the higher energy and forms a less preferable linear supramolecular synthon. Additional energy imparted to a crystal structure during the grinding process proved to be enough to overcome low energy barriers for the nitrogen inversion and rotation of the oxazole ring around the sp³-sp² single bond. As a result, polymorph 1b with a molecule adopting conformation with lower energy and forming a more preferable centrosymmetric supramolecular synthon was obtained. The study of pairwise interaction energies in the two polymorphs has shown that metastable polymorph 1a is organized by molecular building units and has a columnar-layered structure. A centrosymmetric dimer should be recognized as a complex building unit in more stable polymorph 1b, which has a layered structure.

Crystal structures of human glyoxalase I and its complex with TLSC702 reveal inhibitor binding mode and substrate preference

Human glyoxalase I (hGLO I) is an enzyme for detoxification of methylglyoxal (MG), and has been considered an attractive target for the development of new anti-cancer drugs. In our previous report, the GLO I inhibitor TLSC702 induced apoptosis in tumor cells. Here, we determined the crystal structures of hGLO I and its complex with TLSC702. In the complex, the carboxy O atom of TLSC702 is coordinated to Zn²⁺ , and TLSC702 mainly shows van der Waals interaction with hydrophobic residues. In the inhibitor-unbound structure, glycerol, which has similar functional groups to MG, was bound to Zn²⁺ , indicating that GLO I can easily bind to MG. This study provides a structural basis to develop better anticancer drugs.

Synthesis and Structural Characterization of Pyridine-2,6-dicarboxamide and Furan-2,5-dicarboxamide Derivatives

Derivatives based on pyridine-2-6- and furan-2,5-dicarboxamide scaffolds reveal numerous chemical properties and biological activities. This fact makes them an exciting research topic in supramolecular and coordination chemistry and in discovering new pharmacologically-active compounds. This work aimed to obtain a series of symmetrical pyridine-2-6- and furan-2,5-dicarboxamides through a condensation reaction of the appropriate acyl chlorides and aromatic amides. Successful syntheses were confirmed with NMR spectroscopy. We solved their crystal structures for seven compounds; two pyridine and five furan derivatives. Based on our crystallographic studies, we were able to indicate supramolecular features of the crystals under investigation. Additionally, Hirshfeld surface analysis allowed us to calculate a distribution of intermolecular contacts in the dicarboxamide crystals.

Structural Characterization of Multicomponent Crystals Formed from Diclofenac and Acridines

Multicomponent crystals containing diclofenac and acridine (1) and diclofenac and 6,9-diamino-2-ethoxyacridine (2) were synthesized and structurally characterized. The single-crystal XRD measurements showed that compound 1 crystallizes in the triclinic P-1 space group as a salt cocrystal with one acridinium cation, one diclofenac anion, and one diclofenac molecule in the asymmetric unit, whereas compound 2 crystallizes in the triclinic P-1 space group as an ethanol solvate monohydrate salt with one 6,9-diamino-2-ethoxyacridinium cation, one diclofenac anion, one ethanol molecule, and one water molecule in the asymmetric unit. In the crystals of the title compounds, diclofenac and acridines ions and solvent molecules interact via N–H⋯O, O–H⋯O, and C–H⋯O hydrogen bonds, as well as C–H⋯π and π–π interactions, and form heterotetramer bis[⋯cation⋯anion⋯] (1) or heterohexamer bis[⋯cation⋯ethanol⋯anion⋯] (2). Moreover, in the crystal of compound 1, acridine cations and diclofenac anions interact via N–H⋯O hydrogen bond, C–H⋯π and π–π interactions to produce blocks, while diclofenac molecules interact via C–Cl⋯π interactions to form columns. In the crystal of compound 2, the ethacridine cations interact via C–H⋯π and π–π interactions building blocks, while diclofenac anions interact via π–π interactions to form columns.

Comparison of Proton Acceptor and Proton Donor Properties of H2O and H2O2 in Organic Crystals of Drug-like Compounds: Peroxosolvates vs. Crystallohydrates

Two new peroxosolvates of drug-like compounds were synthesized and studied by a combination of X-ray crystallographic, Raman spectroscopic methods, and periodic DFT computations. The enthalpies of H-bonds formed by hydrogen peroxide (H₂O₂) as a donor and an acceptor of protons were compared with the enthalpies of analogous H-bonds formed by water (H₂O) in isomorphic (isostructural) hydrates. The enthalpies of H-bonds formed by H₂O₂ as a proton donor turned out to be higher than the values of the corresponding H-bonds formed by H₂O. In the case of H₂O₂ as a proton acceptor in H-bonds, the ratio appeared reversed. The neutral O∙∙∙H-O/O∙∙∙H-N bonds formed by the lone electron pair of the oxygen atom of water were the strongest H-bonds in the considered crystals. In the paper, it was found out that the low-frequency Raman spectra of isomorphous crystalline hydrate and peroxosolvate of N-(5-Nitro-2-furfurylidene)-1-aminohydantoin are similar. As for the isostructural hydrate and peroxosolvate of the salt of protonated 2-amino-nicotinic acid and maleic acid monoanion, the Raman spectra are different.

Drastic Modulation of Molecular Packing and Intrinsic Dissolution Rates by Meniscus-Guided Coating of Extremely Confined Pharmaceutical Thin Films

Nanosizing has emerged as one of the most effective formulation strategies for enhancement of dissolution properties of active pharmaceutical ingredients (APIs). In addition to enhancing the specific area of the dissolving solids, nanosizing can also capture and stabilize the metastable form of the API, which can further enhance the solubility by drastic modulation of surface energies. Herein, we employ meniscus-guided coating to fabricate nanothin films of three APIs that show anticancer properties and are poorly soluble:10-HCPT, SN-38, and amonafide. By modulating the coating speed, we systematically deposited the APIs in films ranging from ∼200 nm thickness to extreme confinement of ∼10 nm (<10 molecular layers). In all three APIs, we observe a general order-to-disorder transition with semicrystalline (10-HCPT and amonafide) or amorphous (SN-38) form of API solids trapped in thin films when the thickness decreases below a critical value of ∼25-30 nm. The existence of a critical thickness highlights the importance of nanoconfinement in tuning molecular packing. In the case of 10-HCPT, we demonstrate that the disordered form of the API occurs largely due to lack of incorporation of water molecules in thinner films below the critical thickness, thereby disrupting the three-dimensional hydrogen-bonded network held by water molecules. We further developed a dissolution model that predicts variation of the intrinsic dissolution rate (IDR) with API film thickness, which also closely matched with experimental results. We achieved drastic improvement in the IDR of ∼240% in 10-HCPT by decreasing film thickness alone. Further leveraging the order-to-disorder transition led to 2570% modulation of the IDR for amonafide. Our work demonstrates, for the first time, opportunities to largely modulate API dissolution by precisely controlling the dimensionality of thin films.

3D Hexagonal Arrangement of DNA Tensegrity Triangles

The tensegrity triangle motif utilizes Watson-Crick sticky end cohesion to self-assemble into a rhombohedral crystal lattice using complementary 5'-GA and 5'-TC sticky ends. Here, we report that using noncanonical 5'-AG and 5'-TC sticky ends in otherwise isomorphic tensegrity triangles results in crystal self-assembly in the P6₃ hexagonal space group as revealed by X-ray crystallography. In this structure, the DNA double helices bend at the crossover positions, a feature that was not observed in the original design. Instead of propagating linearly, the tilt between base pairs of each right-handed helix results in a left-handed superstructure along the screw axis, forming a microtubule-like structure composed of three double helices with an unbroken channel at the center. This hexagonal lattice has a cavity diameter of 11 nm and a unit cell volume of 886 000 ų-far larger than the rhombohedral counterpart (5 nm, 330 000 ų).

Diastereomeric resolution of 3-chloromandelic acid with threo-(1S,2S)-2-amino-l-p-nitrophenyl-1,3-propanediol

An optical resolution of 3-chloromandelic acid (3-ClMA) using threo-(1S,2S)-2-amino-l-p-nitrophenyl-1,3-propanediol ([S,S]-SA) as a resolving agent was presented. The effects of the type of solvents, the amount of solvent, molar ratio of the resolving agent to racemate and filtration temperature on resolution were investigated. Under the optimal resolution conditions, the content of less soluble salt reached 98%, and the resolution efficiency was as high as 94%. The weak intermolecular interactions (such as hydrogen bond, halogen bond, CH/π and van der Waals interactions) and molecular packing mode in crystal structure of the less soluble salt (R)-3-ClMA(S,S)-SA were investigated. A wall-like 2-D hydrogen-bonding network and hydrophobic structure between hydrogen-bonding walls were revealed. (S,S)-SA was also used to resolve 2-ClMA and 4-ClMA respectively and the corresponding less soluble salts (R)-2-ClMA·(R,R)-SA and (R)-4-ClMA·(R,R)-SA were obtained using threo-(1R,2R)-2-amino-l-p-nitrophenyl-1,3-propanediol ((R,R)-SA) as a resolving agent. In addition, two other resolving agents, (R)-ɑ-phenethylamine ((R)-PEA) and (R)-N-benzyl phenethylamine ((R)-BPA) reported in the literature for the resolution of 3-ClMA were examined along with the newly proposed resolving agent, (S,S)-SA. The crystal structures of the resulting less soluble salts (R)-3-ClMA·(S,S)-SA, (R)-3-ClMA·(R)-PEA and (R)-3-ClMA·(R)-BPA were compared and examined.

The α-D-anomer of 2'-deoxycytidine: crystal structure, nucleoside conformation and Hirshfeld surface analysis

β-2'-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of α-2'-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of α-2'-deoxycytidine, C9H13N3O4 (1), and the conformational parameters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with χ = 173.4 (2)°, and the sugar residue adopts an almost symmetrical C2'-endo-C3'-exo twist (23T; S-type), with P = 179.7°. Both values lie outside the conformational range usually preferred by α-nucleosides. In addition, the amino group at the nucleobase shows partial double-bond character. This is supported by two separated signals for the amino protons in the 1H NMR spectrum, indicating a hindered rotation around the C4-N4 bond and a relatively short C-N bond in the solid state. Crystal packing is controlled by N-H...O and O-H...O contacts between the nucleobase and sugar moieties. Moreover, two weak C-H...N contacts (C1'-H1' and C3'-H3'A) are observed. A Hirshfeld surface analysis was carried out and the results support the intermolecular interactions observed by the X-ray analysis.

C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening

The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a broad pH range and in the presence of a wide variety of precipitants and additives. Remarkably, the crystal dimensions vary from a few micrometres, as used in serial crystallography, to several hundred micrometres, with a very diverse crystal morphology. More than 100 unique single-crystal X-ray diffraction data sets were collected from randomly selected crystals and analysed. The addition of small-molecule additives revealed three new crystal packings of C-PC, which are discussed in detail. The high propensity of this protein to crystallize, combined with its natural blue colour and its fluorescence characteristics, make it an excellent candidate as a superior and highly adaptable model system in crystallography. C-PC can be used in technical and methods development approaches for X-ray and neutron diffraction techniques, and as a system for comprehending the fundamental principles of protein crystallography.

The Influence of Solvent on the Crystal Packing of Ethacridinium Phthalate Solvates

The synthesis, structural characterization and influence of solvents on the crystal packing of solvated complexes of ethacridine with phthalic acid: 6,9-diamino-2-ethoxyacridinium phthalate methanol solvate (1), 6,9-diamino-2-ethoxyacridinium phthalate ethanol solvate (2), 6,9-diamino-2-ethoxyacridinium phthalate isobutanol solvate (3), and 6,9-diamino-2-ethoxyacridinium phthalate tert-butanol solvate monohydrate (4) are described in this article. Single-crystal XRD measurements revealed that the compounds 1–4 crystallized in the triclinic P-1 space group, and the 6,9-diamino-2-ethoxyacridinium cations, phthalic acid anions and solvent molecules interact via strong N–H···O, O–H···O, C–H···O hydrogen bonds, and C–H···π and π–π interactions to form different types of basic structural motifs, such as: heterotetramer bis[···cation···anion···] in compound 1 and 2, heterohexamer bis[···cation···alcohol···anion···] in compound 3, and heterohexamer bis[···cation···water···anion···] in compound 4. Presence of solvents molecule(s) in the crystals causes different supramolecular synthons to be obtained and thus has an influence on the crystal packing of the compounds analyzed.

Noble Gas Bonding Interactions Involving Xenon Oxides and Fluorides

Noble gas (or aerogen) bond (NgB) can be outlined as the attractive interaction between an electron-rich atom or group of atoms and any element of Group-18 acting as an electron acceptor. The IUPAC already recommended systematic nomenclature for the interactions of groups 17 and 16 (halogen and chalcogen bonds, respectively). Investigations dealing with noncovalent interactions involving main group elements (acting as Lewis acids) have rapidly grown in recent years. They are becoming acting players in essential fields such as crystal engineering, supramolecular chemistry, and catalysis. For obvious reasons, the works devoted to the study of noncovalent Ng-bonding interactions are significantly less abundant than halogen, chalcogen, pnictogen, and tetrel bonding. Nevertheless, in this short review, relevant theoretical and experimental investigations on noncovalent interactions involving Xenon are emphasized. Several theoretical works have described the physical nature of NgB and their interplay with other noncovalent interactions, which are discussed herein. Moreover, exploring the Cambridge Structural Database (CSD) and Inorganic Crystal Structure Database (ICSD), it is demonstrated that NgB interactions are crucial in governing the X-ray packing of xenon derivatives. Concretely, special attention is given to xenon fluorides and xenon oxides, since they exhibit a strong tendency to establish NgBs.

7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization

The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson-Crick proton donor site N3-H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-deazaguanosine, C<sub>10</sub>H<sub>12</sub>IN<sub>5</sub>O<sub>5</sub> (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4'-endo) for the ribose moiety, with an antiperiplanar orientation of the 5'-hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2' of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O-H...O and N-H...O). The concept of pK-value differences to evaluate base-pair stability was applied to purine-purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.

Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport

The transmembrane intracellular lectin ER-Golgi intermediate compartment protein 53 (ERGIC-53) and the soluble EF-hand multiple coagulation factor deficiency protein 2 (MCFD2) form a complex that functions as a cargo receptor, trafficking various glycoproteins between the endoplasmic reticulum (ER) and the Golgi apparatus. It has been demonstrated that the carbohydrate-recognition domain (CRD) of ERGIC-53 (ERGIC-53CRD) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53CRD complexed with MCFD2 and mannosyl oligosaccharides have revealed protein-protein and protein-sugar binding modes. In contrast, the polypeptide-recognition mechanism of MCFD2 remains largely unknown. Here, a 1.60 Å resolution crystal structure of the ERGIC-53CRD-MCFD2 complex is reported, along with three other crystal forms. Comparison of these structures with those previously reported reveal that MCFD2, but not ERGIC-53-CRD, exhibits significant conformational plasticity that may be relevant to its accommodation of various polypeptide ligands.

Mercury 4.0: from visualization to analysis, design and prediction

The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

Interplay between Charge Carrier Mobility, Exciton Diffusion, Crystal Packing, and Charge Separation in Perylene Diimide-Based Heterojunctions

Two of the key parameters that characterize the usefulness of organic semiconductors for organic or hybrid organic/inorganic solar cells are the mobility of charges and the diffusion length of excitons. Both parameters are strongly related to the supramolecular organization in the material. In this work we have investigated the relation between the solid-state molecular packing and the exciton diffusion length, charge carrier mobility, and charge carrier separation yield using two perylene diimide (PDI) derivatives which differ in their substitution. We have used the time-resolved microwave photoconductivity technique and measured charge carrier mobilities of 0.32 and 0.02 cm2/(Vs) and determined exciton diffusion lengths of 60 and 18 nm for octyl- and bulky hexylheptyl-imide substituted PDIs, respectively. This diffusion length is independent of substrate type and aggregate domain size. The differences in charge carrier mobility and exciton diffusion length clearly reflect the effect of solid-state packing of PDIs on their optoelectronic properties and show that significant improvements can be obtained by effectively controlling the solid-state packing.

A novel crystal form of metacetamol: the first example of a hydrated form

We report the crystal structure and crystallization conditions of a first hydrated form of metacetamol (a hemihydrate), C₈H₉NO₂·0.5H₂O. It crystallizes from metacetamol-saturated 1:1 (v/v) water-ethanol solutions in a monoclinic structure (space group P2₁/n) and contains eight metacetamol and four water molecules per unit cell. The conformations of the molecules are the same as in polymorph II of metacetamol, which ensures the formation of hydrogen-bonded dimers and R₂²(16) ring motifs in its crystal structure similar to those in polymorph II. Unlike in form II, however, these dimers in the hemihydrate are connected through water molecules into infinite hydrogen-bonded molecular chains. Different chains are linked to each other by metacetamol-water and metacetamol-metacetamol hydrogen bonds, the latter type being also present in polymorph I. The overall noncovalent network of the hemihydrate is well developed and several types of hydrogen bonds are responsible for its formation.

Influence of ortho-substituent on the molecular and crystal structures of 2-(N-arylimino)coumarin-3-carboxamide: isotypic and polymorphic structures

During a comprehensive study of a series of 2-(N-arylimino)coumarin-3-carboxamides with the aryl group substituted in the ortho-position by either a halogen atom, a methyl group or a methoxy group, the existence of three groups of isotypic crystal structures has been revealed. The similarity of crystal structures belonging to the same groups was confirmed by the analysis based on the comparison of pairwise interactions energies obtained from quantum chemical calculations. Group I includes unsubstituted, methyl-substituted and polymorphic modification 1 of fluoro-substituted 2-(N-arylimino)coumarin-3-carboxamide. Structures of polymorphic modification 2 of fluoro-substituted derivative, chloro-substituted and polymorphic modification 1 of bromo-substituted 2-(N-arylimino)coumarin-3-carboxamide may represent group II. Group III contains structures of polymorphic modification 2 of bromo-substituted derivative, iodine- and methoxy-substituted 2-(N-arylimino)coumarin-3-carboxamides. Structures of the same type group have extremely close parameters of the unit cell as well as those of molecular and crystal structures. But they are not identical. Polymorphic modifications of fluoro- and bromo-substituted 2-(N-arylimino)coumarin-3-carboxamides belong to different crystal types mainly due to different arrangement of basic structural motifs separated out using quantum chemical calculations.

Crystal structure of 1-anilino-5-methyl-1H-1,2,3-triazole-4-carb-oxy-lic acid monohydrate

The water mol­ecule connects the mol­ecules in the crystal packing. The crystal structure exhibits N—H⋯O, O—H⋯O and O—H⋯N inter­actions, resulting in the formation of a three-dimensional framework.

In the mol­ecular structure of the title compound, C₁₀H₁₀N₄O₂·H₂O, the angle between the triazole and arene rings is 87.39 (5)°. The water of crystallization connects the mol­ecules in the crystal packing. The crystal structure exhibits N—H⋯O, O—H⋯O and O—H⋯N inter­actions, resulting in the formation of a three-dimensional framework. The inter­molecular inter­actions were identified and qu­anti­fied using Hirshfeld surface analysis.

Crystal structure of N,N'-bis-[3-(methyl-sulfan-yl)prop-yl]-1,8:4,5-naphthalene-tetra-carb-oxy-lic di-imide

The title compound, C22H22N2O4S2, was synthesized by the reaction of 1,4,5,8-naphthalene-tetra-carb-oxy-lic dianhydride with 3-(methyl-sulfan-yl)propyl-amine. The whole mol-ecule is generated by an inversion operation of the asymmetric unit. This mol-ecule has an anti form with the terminal methyl-thio-propyl groups above and below the aromatic di-imide plane, where four intra-molecular C-H⋯O and C-H⋯S hydrogen bonds are present and the O⋯H⋯S angle is 100.8°. DFT calculations revealed slight differences between the solid state and gas phase structures. In the crystal, C-H⋯O and C-H⋯S hydrogen bonds link the mol-ecules into chains along the [2 direction. adjacent chains are inter-connected by π-π inter-actions, forming a two-dimensional network parallel to the (001) plane. Each two-dimensional layer is further packed in an ABAB sequence along the c-axis direction. Hirshfeld surface analysis shows that van der Waals inter-actions make important contributions to the inter-molecular contacts. The most important contacts found in the Hirshfeld surface analysis are H⋯H (44.2%), H⋯O/O⋯H (18.2%), H⋯C/C⋯H (14.4%), and H⋯S/S⋯H (10.2%).

DFT Computed Dielectric Response and THz Spectra of Organic Co-Crystals and Their Constituent Components

Terahertz (THz) spectroscopy has been put forth as a non-contact, analytical probe to characterize the intermolecular interactions of biologically active molecules, specifically as a way to understand, better develop, and use active pharmaceutical ingredients. An obstacle towards fully utilizing this technique as a probe is the need to couple features in the THz regions to specific vibrational modes and interactions. One solution is to use density functional theory (DFT) methods to assign specific vibrational modes to signals in the THz region, coupling atomistic insights to spectral features. Here, we use open source planewave DFT packages that employ ultrasoft pseudopotentials to assess the infrared (IR) response of organic compounds and complex co-crystal formulations in the solid state, with and without dispersion corrections. We compare our DFT computed lattice parameters and vibrational modes to experiment and comment on how to improve the agreement between theory and modeling to allow for THz spectroscopy to be used as an analytical probe in complex biologically relevant systems.

Far-Infrared Spectroscopy as a Probe for Polymorph Discrimination

Pharmaceutical crystalline polymorph and amorphous form detection and quantification is a standard requirement in the pharmaceutical industry. Infrared (IR) spectroscopy provides an important probe for the characterization of polymorphs. Nonetheless, characterization and discrimination among polymorphs using mid-IR spectroscopy is not always possible in part because the technique mainly probes vibrational modes arising from functional groups in the sample. In the present work, far-IR spectroscopy is demonstrated for the discrimination of polymorphs. This region is influenced by delocalized lattice vibrational modes derived from intermolecular forces and packing arrangements in the crystal structure. A total of 10 polymorphic pharmaceuticals were prepared to conduct a critical evaluation of the question, does this far-IR region add value for polymorph differentiation? It is demonstrated that the far-IR region offers high discriminating power for polymorphs compared to the mid-IR spectral region. In addition, structural similarity and dissimilarity in polymorphic packing arrangements can be derived from this analysis.

The crystal structure of the N-acetylglucosamine 2-epimerase from Nostoc sp. KVJ10 reveals the true dimer

The N-acetylglucosamine 2-epimerase (AGE) from Nostoc sp. KVJ10 (nAGE10) was crystallized in a different space group to other AGEs. The nAGE10 dimer, while different from the proposed AGE dimers in previously published structures, can also be found in these structures and is probably the biological dimer.

N-Acetylglucosamine 2-epimerases (AGEs) catalyze the interconversion of N-acetylglucosamine and N-acetylmannosamine. They can be used to perform the first step in the synthesis of sialic acid from N-acetylglucosamine, which makes the need for efficient AGEs a priority. This study presents the structure of the AGE from Nostoc sp. KVJ10 collected in northern Norway, referred to as nAGE10. It is the third AGE structure to be published to date, and the first one in space group P4₂2₁2. The nAGE10 monomer folds as an (α/α)₆ barrel in a similar manner to that of the previously published AGEs, but the crystal did not contain the dimers that have previously been reported. The previously proposed ‘back-to-back’ assembly involved the face of the AGE monomer where the barrel helices are connected by small loops. Instead, a ‘front-to-front’ dimer was found in nAGE10 involving the long loops that connect the barrel helices at this end. This assembly is also present in the other AGE structures, but was attributed to crystal packing, even though the ‘front’ interface areas are larger and are more conserved than the ‘back’ interface areas. In addition, the front-to-front association allows a better explanation of the previously reported observations considering surface cysteines. Together, these results indicate that the ‘front-to-front’ dimer is the most probable biological assembly for AGEs.

Comparison of computationally cheap methods for providing insight into the crystal packing of highly bromomethylated azobenzenes

For five bromomethylated azobenzenes, namely (E)-[4-(bromomethyl)phenyl][4-(dibromomethyl)phenyl]diazene, C₁₄H₁₁Br₃N₂, (E)-1,2-bis[4-(dibromomethyl)phenyl]diazene, C₁₄H₁₀Br₄N₂, (E)-[3-(bromomethyl)phenyl][3-(dibromomethyl)phenyl]diazene, C₁₄H₁₁Br₃N₂, (E)-[3-(dibromomethyl)phenyl][3-(tribromomethyl)phenyl]diazene, C₁₄H₁₀Br₄N₂, and (E)-1,2-bis[3-(dibromomethyl)phenyl]diazene, C₁₄H₉Br₅N₂, the computationally cheap CLP PIXEL approach and CrystalExplorer were used for calculating lattice energies and performing Hirshfeld surface analysis via the enrichment ratios of atomic contacts. The procedures and caveats are discussed in detail. The findings from these tools are contrasted with the results of geometric analysis of the structures. We conclude that an energy-based discussion of the crystal packing provides substantially more insight than one based purely on geometry, as has so long been the custom in crystallography. In addition, we find a surprising shortage of halogen-halogen interactions in these highly bromomethylated compounds.

On the helical arrangements of protein molecules

Helical structures are prevalent in biology. In the PDB, there are many examples where protein molecules are helically arranged, not only according to strict crystallographic screw axes but also according to approximate noncrystallographic screws. The preponderance of such screws is rather striking as helical arrangements in crystals must preserve an integer number of subunits per turn, while intuition and simple packing arguments would seem to favor fractional helices. The article provides insights into such questions, based on stereochemistry, trigonometry, and topology, and illustrates the findings with concrete PDB structures. Updated statistics of Sohncke space groups in the PDB are also presented.

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.

Structural parameters of dimethyl sulfoxide, DMSO, at 100 K, based on a redetermination by use of high-quality single-crystal X-ray data

Accurate structural parameters (bond lengths and angles) of dimethyl sulfoxide, DMSO, have been obtained from the redetermination of its crystal structure by single-crystal X-ray diffraction at 100 K using CCD data in order to get a reference point for the deformation of the chemically bonded mol­ecule. In addition, the new data show that mol­ecule approximates C_s symmetry in the solid state where all atoms occupy general positions.

The title compound, C₂H₆OS, is a high melting, polar and aprotic solvent widely used in organic and inorganic chemistry. It serves as a H-atom acceptor in hydrogen bonding and is used as an ambidentate ligand in coordination chemistry. The evaluation of the influence of inter­molecular inter­actions on the inter­nal structural parameters of the chemically bonded DMSO mol­ecules affords precise structural data of the free mol­ecule as a point of reference. So far, valid data have been obtained only by use of neutron powder diffraction [Ibberson (2005 ▸). Acta Cryst. C61, o571–o573]. In the present redetermination, structural data have been obtained from a single-crystal X-ray diffraction experiment at 100 K, revealing a better comparison with DMSO mol­ecules in other crystal structures. In the solid state, the pyramidal mol­ecule exhibits a nearly perfect C_s symmetry [including H atoms, which are eclipsed with respect to the C⋯C axis], with a C—S—C bond angle of 97.73 (7)° and an S—O bond length of 1.5040 (10) Å, corresponding very well with an S=O double bond, and with almost equal S—C bond lengths [mean value = 1.783 (4) Å] and O—S—C bond angles [mean value = 106.57 (4)°]. The crystal packing is influenced by C—H⋯O inter­actions (2.42–2.47 Å) between all three H atoms of only one methyl group with the O atoms of three neighbouring DMSO mol­ecules. The inter­actions of the O atom with H atoms (or Lewis acids, or hydrogen-donor groups) of adjacent mol­ecules in relation to the orientation of the complete DMSO mol­ecule are described in terms of the angle ω and the distance d_norm; ω is the angle between the pseudo-mirror plane of the mol­ecule and the plane defined through the S=O bond and the inter­acting atom, and d_norm is the distance of the inter­acting atom from the plane perpendicular to the S=O bond.

Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids

An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP). Six single-site mutations were examined: Ala138 on the surface of a β-sheet was mutated to Ile, Tyr, Arg, Gln, Val and Lys. In agreement with prediction, it was observed that the two mutants (A138I and A138Y) harbouring the residues with the highest crystal-packing propensities for β-sheet at position 138 provided better crystallization scores relative to those of other constructs, including the wild type, and that the crystal-packing propensity for β-sheet provided the best correlation with the ratio of obtaining crystals. Two new crystal forms of these mutants were obtained that diffracted to high resolution, generating novel packing interfaces with the mutated residues (Ile/Tyr). The mutations introduced did not affect the overall structures, indicating that a β-sheet can accommodate a successful mutation if it is carefully selected so as to avoid intramolecular steric hindrance. A significant negative correlation between the ratio of obtaining amorphous precipitate and the crystal-packing propensity was also found.

A new solvate of furosemide with dimethylacetamide

The loop diuretic furosemide is used widely in the treatment of congestive heart failure and edema, and is practically insoluble in water. The physicochemical and pharmacokinetic properties of drugs can be modified by preparing the drug in an appropriate solid-state form. A new solvate of furosemide with dimethylacetamide (DMA) {systematic name: 4-chloro-2-[(furan-2-yl)methylamino]-5-sulfamoylbenzoic acid N,N-dimethylacetamide disolvate}, C₁₂H₁₁ClN₂O₅S·2C₄H₉NO, (I), is reported. The channeled structure formed on slow crystallization contains DMA solvent molecules in its channels. This structure adds to the evidence of varied conformations observed across all known structures, so supporting the idea that this flexible molecule has conformational lability. The current structure also differs from those of other previously known furosemide solvates in the number of solvent molecules per furosemide molecule, viz. 2:1 instead of 1:1. Desolvation of (I) gives the most stable form of furosemide, i.e. Form I.

Accurate hydrogen parameters for the amino acid L-leucine

The structure of the primary amino acid L-leucine has been determined for the first time by neutron diffraction. This was made possible by the use of modern neutron Laue diffraction to overcome the previously prohibitive effects of crystal size and quality. The packing of the structure into hydrophobic and hydrophilic layers is explained by the intermolecular interaction energies calculated using the PIXEL method. Variable-temperature data collections confirmed the absence of phase transitions between 120 and 300 K in the single-crystal form.

Revisiting antibody modeling assessment for CDR-H3 loop

The antigen-binding site of antibodies, also known as complementarity-determining region (CDR), has hypervariable sequence properties. In particular, the third CDR loop of the heavy chain, CDR-H3, has such variability in its sequence, length, and conformation that ordinary modeling techniques cannot build a high-quality structure. At Stage 2 of the Second Antibody Modeling Assessment (AMA-II) held in 2013, the model structures of the CDR-H3 loops were submitted by the seven modelers and were critically assessed. After our participation in AMA-II, we rebuilt one of the long CDR-H3 loops with 13 residues (A52 antibody) by a more precise method, using enhanced conformational sampling with the explicit water model, as compared to our previous method employed at AMA-II. The current stable models obtained from the free energy landscape at 300 K include structures similar to the X-ray crystal structures. Those models were not built in our previous work at AMA-II. The current free energy landscape suggested that the CDR-H3 loop structures in the crystal are not stable in solution, but they are stabilized by the crystal packing effect.

Manipulation of an existing crystal form unexpectedly results in interwoven packing networks with pseudo-translational symmetry

A nonribosomal peptide synthetase di-domain construct was produced using known crystal packing as a guide, and the resulting crystal has an unanticipated packing.

Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes that synthesize a myriad of diverse molecules. Tailoring domains have been co-opted into NRPSs to introduce further variety into nonribosomal peptide products. Linear gramicidin synthetase contains a unique formylation-tailoring domain in its initiation module (F-A-PCP). The structure of the F-A di-domain has previously been determined in a crystal form which had large solvent channels and no density for the minor A_sub subdomain. An attempt was made to take advantage of this packing by removing the A_sub subdomain from the construct (F-A_Δsub) in order to produce a crystal that could accommodate the PCP domain. In the resulting crystal the original packing network was still present, but a second network with the same packing and almost no contact with the original network took the place of the solvent channels and changed the space group of the crystal.

Cryoannealing-induced space-group transition of crystals of the carbonic anhydrase psCA3

Cryoannealing has been demonstrated to improve the diffraction quality and resolution of crystals of the β-carbonic anhydrase psCA3 concomitant with a change in space group. After initial flash-cooling in a liquid-nitrogen cryostream an X-ray diffraction data set from a psCA3 crystal was indexed in space group P21212 and was scaled to 2.6 Å resolution, but subsequent cryoannealing studies revealed induced protein rearrangements in the crystal contacts, which transformed the space group to I222, with a corresponding improvement of 0.7 Å in resolution. Although the change in diffraction resolution was significant, only minor changes in the psCA3 structure, which retained its catalytic `open' conformation, were observed. These findings demonstrate that cryoannealing can be successfully utilized to induce higher diffraction-quality crystals while maintaining enzymatically relevant conformations and may be useful as an experimental tool for structural studies of other enzymes where the initial diffraction quality is poor.

The Suppression of Columnar π-Stacking in 3-Adamantyl-1-phenyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl

3-Adamantyl-1-phenyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl (4) crystallizes as chains of radicals where the spin bearing benzotriazinyl moieties are isolated from each other. Magnetic susceptibility studies in the 5–300 K temperature region indicate that radical 4 demonstrates typical paramagnetic behavior stemming from non-interacting S = ½ spins.

Nobiletin: a citrus flavonoid displaying potent physiological activity

Nobiletin [systematic name: 2-(3,4-dimethoxyphenyl)-5,6,7,8-tetramethoxy-4H-chromen-4-one; C21H22O8] is a flavonoid found in citrus peels, and has been reported to show a wide range of physiological properties, including anti-inflammatory, anticancer and antidementia activities. We have solved the crystal structure of nobiletin, which revealed that the chromene and arene rings of its flavone moiety, as well as the two methoxy groups bound to its arene ring, were coplanar. In contrast, the C atoms of the four methoxy groups bound to the chromene ring are out of the plane, making the molecule conformationally chiral. A comparison of the crystal structures of nobiletin revealed that it could adopt a variety of different conformations through rotation of the covalent bond between the chromene and arene rings, and the orientations of methoxy groups bound to the chromene ring.

Two new isatin derivatives: 1-benzyl-4,5,6-trimethoxyindoline-2,3-dione and 1-benzyl-5-fluoroindoline-2,3-dione

Isatin (1H-indole-2,3-dione) derivatives represent synthetically useful substrates which can be used to prepare a broad range of heterocyclic compounds. In the title compounds, C18H17NO5, (I), and C15H10FNO2, (II), the isatin ring systems are planar and form a dihedral angle of 73.04 (7)° in (I) and 76.82 (11)° in (II) with the benzyl groups. The bicyclic scaffolds in both compounds are almost superimposable, with an r.m.s. deviation of 0.061 Å. The crystal structures of both derivatives are stabilized by C-H···O interactions. These contacts generate an R(1)2(7) ring motif in (I) and a C(7) chain motif in (II).

Synthesis and Crystallographic Insight into the Structural Aspects of Some Novel Adamantane-Based Ester Derivatives

Adamantyl-based compounds are commercially important in the treatments for neurological conditions and type-2 diabetes, aside from their anti-viral abilities. Their values in drug design are chronicled as multi-dimensional. In the present study, a series of 2-(adamantan-1-yl)-2-oxoethyl benzoates, 2(a–q), and 2-(adamantan-1-yl)-2-oxoethyl 2-pyridinecarboxylate, 2r, were synthesized by reacting 1-adamantyl bromomethyl ketone with various carboxylic acids using potassium carbonate in dimethylformamide medium at room temperature. Three-dimensional structures studied using X-ray diffraction suggest that the adamantyl moiety can serve as an efficient building block to synthesize 2-oxopropyl benzoate derivatives with synclinal conformation with a looser-packed crystal packing system. Compounds 2a, 2b, 2f, 2g, 2i, 2j, 2m, 2n, 2o, 2q and 2r exhibit strong antioxidant activities in the hydrogen peroxide radical scavenging test. Furthermore, three compounds, 2p, 2q and 2r, show good anti-inflammatory activities in the evaluation of albumin denaturation.

Likelihood of atom-atom contacts in crystal structures of halogenated organic compounds

The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen⋯halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C⋯C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C-H⋯Cl and O-H⋯O are the preferred interactions in compounds containing both O and Cl.

Low solubility in drug development: de-convoluting the relative importance of solvation and crystal packing

OBJECTIVES

An increasing trend towards low solubility is a major issue for drug development as formulation of low solubility compounds can be problematic. This paper presents a model which de-convolutes the solubility of pharmaceutical compounds into solvation and packing properties with the intention to understand the solubility limiting features.

METHODS

The Cambridge Crystallographic Database was the source of structural information. Lattice energies were calculated via force-field based approaches using Materials Studio. The solvation energies were calculated applying quantum chemistry models using Cosmotherm software.

KEY FINDINGS

The solubilities of 54 drug-like compounds were mapped onto a solvation energy/crystal packing grid. Four quadrants were identified were different balances of solvation and packing were defining the solubility. A version of the model was developed which allows for the calculation of the two features even in absence of crystal structure.

CONCLUSION

Although there are significant number of in-silico models, it has been proven very difficult to predict aqueous solubility accurately. Therefore, we have taken a different approach where the solubility is not predicted directly but is de-convoluted into two constituent features.

Crystallization and preliminary crystallographic analysis of human aquaporin 1 at a resolution of 3.28 Å

Aquaporin water channels (AQPs) are found in almost every organism from humans to bacteria. In humans, 13 classes of AQPs control water and glycerol homeostasis. Knockout studies have suggested that modulating the activity of AQPs could be beneficial for the treatment of several pathologies. In particular, aquaporin 1 is a key factor in cell migration and angiogenesis, and constitutes a possible target for anticancer compounds and also for the treatment of glaucoma. Here, a preliminary crystallographic analysis at 3.28 Å resolution of crystals of human aquaporin 1 (hAQP1) obtained from protein expressed in Sf9 insect cells is reported. The crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 89.28, c = 174.9 Å, and contained one monomer per asymmetric unit. The hAQP1 biological tetramer is generated via the crystallographic fourfold axis. This work extends previous electron crystallographic studies that used material extracted from human red blood cells, in which the resolution was limited to approximately 3.8 Å. It will inform efforts to improve lattice contacts and the diffraction limit for the future structure-based discovery of specific hAQP1 inhibitors.

Crystal structure of zwitterionic 4-(ammonio-methyl)-benzoate: a simple mol-ecule giving rise to a complex supra-molecular structure

The asymmetric unit of the title compound, C8H9NO2·H2O consists of an isolated 4-(ammonio-meth-yl)benzoate zwitterion derived from 4-amino-methyl-benzoic acid through the migration of the acidic proton, together with a water molecule of crystallization that is disordered over three sites with occupancy ratios (0.50:0.35:0.15). In the crystal structure, N-H⋯O hydrogen bonds together with π-π stacking of the benzene rings [centroid-centroid distance = 3.8602 (18) Å] result in a strongly linked, compact three-dimensional structure.