TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules.

3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.

Supramolecular Synthons in Protein-Ligand Frameworks.

Supramolecular synthons, defined as reproducible intermolecular structural units, have greatly aided small molecule crystal engineering. In this paper, we propose that supramolecular synthons guide ligand-mediated protein crystallization. The protein RSL and the macrocycle sulfonato-calix[8]arene cocrystallize in at least four ways. One of these cocrystals is a highly porous cube comprising protein nodes connected by calixarene dimers. We show that mutating an aspartic acid to an asparagine results in two new cubic assemblies that depend also on the crystallization method. One of the new cubic arrangements is mediated by calixarene trimers and has a ∼30% increased cell volume relative to the original crystal with calixarene dimers. Crystals of the sulfonato-calix[8]arene sodium salt were obtained from buffered conditions similar to those used to grow the protein-calix[8]arene cocrystals. X-ray analysis reveals a coordination polymer of the anionic calix[8]arene and sodium cation in which the macrocycle is arranged as staggered stacks of the pleated loop conformation. Remarkably, the calixarene packing arrangement is the same in the simple salt as in the protein cocrystal. With the pleated loop conformation, the calixarene presents an extended surface for binding other calixarenes (oligomerization) as well as binding to a protein patch (biomolecular complexation). Small-angle X-ray scattering data suggest pH-dependent calixarene assembly in solution. Therefore, the calix[8]arene-calix[8]arene structural unit may be regarded as a supramolecular synthon that directs at least two types of protein assembly, suggesting applications in protein crystal engineering.

Cucurbit[7]uril-mediated Histidine Dimerization: Exploring the Structure and Binding Mechanism.

Cucurbit[7,8]urils are known to form inclusion complexes with hydrophobic amino acids such as Trp, Tyr, Phe, and Met, as well as peptides containing these residues at the N-terminus. Despite their widespread use in protein purification, the affinity of histidine (His) for cucurbit[7,8]urils has not been extensively explored. In this study, X-ray diffraction experiments were conducted to investigate the binding of two histidine moieties to the cucurbit[7]uril (CB7) cavity, resulting in a network of π-π and hydrogen bonds. This assembly was found to induce a His pKa shift of ΔpKa=-4. Histidine weakly bound to CB7 or CB8; however, isothermal titration calorimetry revealed micromolar equilibrium dissociation constant values for CB7 and CB8 when bound to dipeptides containing His at the C-terminus. Conversely, dipeptides with His at the N-terminus exhibited millimolar values. Additionally, the His-Gly-Gly tripeptide formed a 2 : 1 complex with CB7. These findings suggest the potential use of histidine and histidine-containing tags in conjunction with CB7 for various biological applications.

Influence of modelling disorder on Hirshfeld atom refinement results of an organo-gold(I) compound.

Details of the validation of disorder modelling with Hirshfeld atom refinement (HAR) for a previously investigated organo-gold(I) compound are presented here. The impact of refining disorder on HAR results is discussed using an analysis of the differences of dynamic structure factors. These dynamic structure factor differences are calculated from thermally smeared quantum mechanical electron densities based on wavefunctions that include or exclude electron correlation and relativistic effects. When disorder is modelled, the electron densities stem from a weighted superposition of two (or more) different conformers. Here this is shown to impact the relative importance of electron correlation and relativistic effect estimates expressed by the structure factor magnitudes. The role of disorder modelling is also compared with the effect of the treatment of hydrogen anisotropic displacement parameter (ADP) values and atomic anharmonicity of the gold atom. The analysis of ADP values of gold and disordered carbon atoms showed that the effect of disorder significantly altered carbon ADP values and did not influence those of the gold atom.

Rotamers in Crystal Structures of Xylitol, D-Arabitol and L-Arabitol.

Rotamers are stereoisomers produced by rotation (twisting) about σ bonds and are often rapidly interconverting at room temperature. Xylitol-massively produced sweetener-(2R,3r,4S)-pentane-1,2,3,4,5-pentol) forms rotamers from the linear conformer by rotation of a xylitol fragment around the C2-C3 bond (rotamer 1) or the C3-C4 bond (rotamer 2). The rotamers form two distinguishable structures. Small differences in geometry of rotamers of the main carbon chain were confirmed by theoretical calculations; however, they were beyond the capabilities of the X-ray powder diffraction technique due to the almost identical unit cell parameters. In the case of rotamers of similar compounds, the rotations occurred mostly within hydroxyl groups likewise rotations in L-arabitol and D-arabitol, which are discussed in this work. Our results, supported by theoretical calculations, showed that energetic differences are slightly higher for rotamers with rotations within hydroxyl groups instead of a carbon chain.

Aurophilic Interactions Studied by Quantum Crystallography.

This is the first use of a wave-function-based crystallographic method to characterize aurophilic interactions from X-ray diffraction data. Theoretical calculations previously suggested the importance of electron correlation and dispersion forces, but no influence of relativistic corrections to the Au...Au interaction energy was found. In this study, we confirm the importance of relativistic corrections in the characterization of aurophilic interactions in addition to electron correlation and dispersion.

First Experimental Quantitative Charge Density Studies of Advanced Intermediate of Vitamin D Analogues.

Vitamins D are a group of fat-soluble secosteroids which play a regulatory role in the functioning of most cells. Rational design of new vitamin D analogs, of increased therapeutic potency and lowered calcemic side effects, requires high-resolution initial structures and a deep understanding of interactions with the molecular targets. In this paper, using quantum crystallography, we present the first determination of the experimental quantitative charge density of an advanced intermediate of vitamin D analogues as well as a reconstruction of the theoretical electron density of final vitamin D analogues. Application of these methods allows for topological and electrostatic interaction energy analysis. We showed that the A-ring chair conformation has a significant influence on the topological properties of vitamin D compounds. Moreover, the interactions between the CD-ring and side-chain additionally stabilize the crystal structure. These results are supported by our theoretical calculations and previous biological studies.

Ruthenium Olefin Metathesis Catalysts Bearing a Macrocyclic N-Heterocyclic Carbene Ligand: Improved Stability and Activity.

Formation of sterically hindered C-C double bonds via catalytic olefin metathesis is considered a very challenging task for Ru catalysts. This limitation led to the development of specialised catalysts bearing sterically reduced N-heterocyclic carbene (NHC) ligands that are very active in such transformations, yet significantly less stable as compared to general purpose catalysts. To decrease the small-size NHC catalysts susceptibility to decomposition, a new NHC ligand was designed, in which two sterically reduced aryl arms were tied together by a C-8 alkyl chain. The installation of this macrocyclic ligand on the ruthenium centre led to the formation of an olefin metathesis catalyst (trans-Ru6). Interestingly, this complex undergoes transformation into an isomer bearing two Cl ligands in the cis-arrangement (cis-Ru6). These two isomeric complexes exhibit similarly high thermodynamic stability, yet different application profiles in catalysis.

Insights into molecular recognition from the crystal structures of p-tert-butyl-calix[6]arene complexed with different solvents.

Calixarenes are host molecules that can form complexes with one or more guest molecules, and molecular recognition in calixarenes can be affected by many factors. With a view to establishing molecular recognition rules, the host p-tert-butyl-calix[6]arene (TBC6) was crystallized with different guest molecules (cyclo-hexane, anisole, heptane, toluene, benzene, methyl acetate, ethyl acetate, di-chloro-methane, tetra-hydro-furan and pyridine) and the obtained structures were characterized by X-ray diffraction. With most solvents, 1:1 and/or 1:3 host-guest complexes were formed, although other stoichiometries were also observed with small guest molecules, and crystallization from ethyl acetate produced the unsolvated form. The calculated fill percentage of the TBC6 cavity was ∼55% for apolar guests and significantly lower for polar solvents, indicating that polar molecules can bind to apolar cavities with significantly lower packing coefficients. The most stable crystals were formed by 1:1 host-guest inclusion complexes. The ratio between the apolar surface area and the volume was used to predict the formation of inclusion versus exclusion complexes, with inclusion complexes observed at ratios <40. These findings allow the binding of potential guest molecules to be predicted and a suitable crystal packing for the designed properties to be obtained.

Further Validation of Quantum Crystallography Approaches.

Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of hydrogen atoms (anisotropic, isotropic, and with the aid of SHADE or NoMoRe), and the type of radiation used (Mo Kα and Cu Kα) on the final results. To achieve this aim, we performed a series of refinements against X-ray diffraction data for three model compounds and compared their final structures, geometries, shapes of ADPs, and charge density distributions. Our results were also supported by theoretical calculations that enabled comparisons of the lattice energies of these structures. It appears that geometrical parameters are better described (closer to the neutron values) when HAR is used; however, bonds to H atoms more closely match neutron values after MM or TAAM refinement. Our analysis shows the superiority of the NoMoRe method in the description of H-atom ADPs. Moreover, the shapes of the ADPs of H atoms, as well as their electron density distributions, were better described with low-resolution Cu Kα data in comparison to low-resolution Mo Kα data.

Relativistic Hirshfeld atom refinement of an organo-gold(I) compound.

The main goal of this study is the validation of relativistic Hirshfeld atom refinement (HAR) as implemented in Tonto for high-resolution X-ray diffraction datasets of an organo-gold(I) compound. The influence of the relativistic effects on statistical parameters, geometries and electron density properties was analyzed and compared with the influence of electron correlation and anharmonic atomic motions. Recent work in this field has indicated the importance of relativistic effects in the static electron density distribution of organo-mercury compounds. This study confirms that differences in electron density due to relativistic effects are also of significant magnitude for organo-gold compounds. Relativistic effects dominate not only the core region of the gold atom, but also influence the electron density in the valence and bonding region, which has measurable consequences for the HAR refinement model parameters. To study the effects of anharmonic motion on the electron density distribution, dynamic electron density difference maps were constructed. Unlike relativistic and electron correlation effects, the effects of anharmonic nuclear motion are mostly observed in the core area of the gold atom.

Experimental and Computational Studies on Structure and Energetic Properties of Halogen Derivatives of 2-Deoxy-D-Glucose.

The results of structural studies on a series of halogen-substituted derivatives of 2-deoxy-D-glucose (2-DG) are reported. 2-DG is an inhibitor of glycolysis, a metabolic pathway crucial for cancer cell proliferation and viral replication in host cells, and interferes with D-glucose and D-mannose metabolism. Thus, 2-DG and its derivatives are considered as potential anticancer and antiviral drugs. X-ray crystallography shows that a halogen atom present at the C2 position in the pyranose ring does not significantly affect its conformation. However, it has a noticeable effect on the crystal structure. Fluorine derivatives exist as a dense 3D framework isostructural with the parent compound, while Cl- and I-derivatives form layered structures. Analysis of the Hirshfeld surface shows formation of hydrogen bonds involving the halogen, yet no indication for the existence of halogen bonds. Density functional theory (DFT) periodic calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings. NMR studies in the solution show that most of the compounds do not display significant differences in their anomeric equilibria, and that pyranose ring puckering is similar to the crystalline state. For 2-deoxy-2-fluoro-D-glucose (2-FG), electrostatic interaction energies between the ligand and protein for several existing structures of pyranose 2-oxidase were also computed. These interactions mostly involve acidic residues of the protein; single amino-acid substitutions have only a minor impact on binding. These studies provide a better understanding of the structural chemistry of halogen-substituted carbohydrates as well as their intermolecular interactions with proteins determining their distinct biological activity.

Charge density analysis of abiraterone acetate.

A high-resolution single-crystal X-ray diffraction study of abiraterone acetate (1) has been carried out. The charge density distribution in the crystal of this anticancer drug is reconstructed from experimental data. The nature and the contributions of various intermolecular interactions to the total crystal energy are studied by means of the quantum theory `Atoms-in-Molecules', a non-covalent interactions method and energy framework plots. In general, dispersion C-H...H-C and C-H...π interactions play the main role in crystal packing of 1. The Voronoi tessellation analysis of 1 confirmed that contribution of hydrophobic and hydrophilic interactions to the molecular surface is close to their contribution to the total crystal energy. Similar analysis of abiraterone complexes with the cytochrome P450 family demonstrated that contribution of the C-H...H-C and C-H...π interactions to the molecular surface of the drug remains unchanged to fit the binding pocket, despite the presence of water and heme molecules, and hydrophilic groups within the pocket.

Interplay between packing, dimer interaction energy and morphology in a series of tricyclic imide crystals.

Crystal morphology is a very important feature in many industrial applications. Tricyclic imides, derivatives of 10-oxa-4-azatricyclo[5.2.1.02,6]dec-8-ene-3,5-dione with differing small hydrophobic groups (Me, Et), were studied and grouped based on Etter's rule. Using experimental X-ray studies, dimer energy calculations, framework analysis and periodic DFT-D calculations, it is shown that knowledge of the hydrogen-bond pattern can be used to determine the final crystal shape. Molecules forming a ring hydrogen-bond motif crystallize as plate crystals with the {100} facet as the slowest growing, whereas those molecules forming an infinite hydrogen-bond motif in the crystal structure crystallize as needles with the {101} facet having the largest surface area.

Structure and Morphology of Indole Analogue Crystals.

Indole and six simple analogues were crystallized in different environments to study the crystal habit changes. All crystal structures were determined by X-ray diffraction experiments. Lattice energies based on DFT-D3 periodic calculations and framework analysis were used to define the most important intermolecular interactions in the crystal structures: N-H···π (-28 kJ/mol), hydrogen bonds (-34 kJ/mol), π···π stacking interactions (-18 kJ/mol), and dipole-dipole (-18 kJ/mol). As morphology is an important feature in many industrial applications, such as photovoltaic cells, electronic devices, and drug discovery, we predicted the crystal morphology of selected crystals using the BFDH and AE models. Facet character depends on the orientation of the molecules at the surface and is therefore sensitive to the variation of crystallization conditions such as solvent, method, and temperature. All indole derivatives tend to form plate crystals with the largest {002} facet. We showed that the morphological importance of the {002} facet increases, whereas the {011} facet decreases with solvent polarity for 5-nitroindole and 4-cyanindole crystals, resulting in a change of crystal habit from needle to plate and from plate to prism, respectively.

The Influence of Various N-Heterocyclic Carbene Ligands on Activity of Nitro-Activated Olefin Metathesis Catalysts.

A set of nitro-activated ruthenium-based Hoveyda-Grubbs type olefin metathesis catalysts bearing sterically modified N-hetero-cyclic carbene (NHC) ligands have been obtained, characterised and studied in a set of model metathesis reactions. It was found that catalysts bearing standard SIMes and SIPr ligands (4a and 4b) gave the best results in metathesis of substrates with more accessible C-C double bonds. At the same time, catalysts bearing engineered naphthyl-substituted NHC ligands (4d-e) exhibited high activity towards formation of tetrasubstituted C-C double bonds, the reaction which was traditionally Achilles' heel of the nitro-activated Hoveyda-Grubbs catalyst.

Relation Between Crystal Structures of Precursors and Final Products: Example of Vitamin D Intermediates.

In this paper, we proved that the solid-state structure of vitamin D analog is well represented by the structures of its structural fragments. This is important in predicting the biological activity of vitamin D analogs that are not available in the solid form. The previously published crystal structure of advanced vitamin D intermediate provided additional insights into vitamin D properties. A similar analysis based on simple vitamin D intermediate analogues showed that precursors crystallized in the space groups typical for vitamins D; geometrical parameters were related to the corresponding parameters in the vitamin D analogues; and crystal structures of the basic intermediates and their final products contained similar intermolecular interactions, essential for the infinite hydrogen bond motif observed in the vitamin D analogues. The energy of these interactions is related as shown by theoretical calculations, that is, energy frameworks analysis. Moreover, analysis of the hydrogen bonds motifs revealed a relation between these motifs and the absolute configuration of basic intermediates as well as the space orientation of the exocyclic methylene group in the final structures.

Charge density view on bicalutamide molecular interactions in the monoclinic polymorph and androgen receptor binding pocket.

High-resolution single-crystal X-ray measurements of the monoclinic polymorph of bicalutamide and the aspherical atom databank approach have served as a basis for a reconstruction of the charge density distribution of the drug and its androgen receptor (AR) and albumin complexes. The contributions of various types of intermolecular interactions to the total crystal energy or ligand:AR energy were estimated. The cyan and amide groups secured the ligand placement in the albumin (Lys-137) and the AR binding pocket (Leu-704, Asn-705, Arg-752), and also determined the packing of the small-molecule crystals. The total electrostatic interaction energy on average was -230 kJ mol-1, comparable with the electrostatic lattice energy of the monoclinic bicalutamide polymorph. This is the result of similar distributions of electropositive and electronegative regions on the experimental and theoretical molecular electrostatic potential maps despite differences in molecular conformations. In general, bicalutamide interacted with the studied proteins with similar electrostatic interaction energies and adjusted its conformation and electrostatic potential to fit the binding pocket in such a way as to enhance the interactions, e.g. hydrogen bonds and π⋯π stacking.

Experimental observation of charge-shift bond in fluorite CaF2.

On the basis of a multipole refinement of single-crystal X-ray diffraction data collected using an Ag source at 90 K to a resolution of 1.63 Å-1, a quantitative experimental charge density distribution has been obtained for fluorite (CaF2). The atoms-in-molecules integrated experimental charges for Ca2+ and F- ions are +1.40 e and -0.70 e, respectively. The derived electron-density distribution, maximum electron-density paths, interaction lines and bond critical points along Ca2+...F- and F-...F- contacts revealed the character of these interactions. The Ca2+...F- interaction is clearly a closed shell and ionic in character. However, the F-...F- interaction has properties associated with the recently recognized type of interaction referred to as `charge-shift' bonding. This conclusion is supported by the topology of the electron localization function and analysis of the quantum theory of atoms in molecules and crystals topological parameters. The Ca2+...F- bonded radii - measured as distances from the centre of the ion to the critical point - are 1.21 Šfor the Ca2+ cation and 1.15 Šfor the F- anion. These values are in a good agreement with the corresponding Shannon ionic radii. The F-...F- bond path and bond critical point is also found in the CaF2 crystal structure. According to the quantum theory of atoms in molecules and crystals, this interaction is attractive in character. This is additionally supported by the topology of non-covalent interactions based on the reduced density gradient.

Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.

In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.