Polymorph Identification and Crystal Structure Determination by a Combined Crystal Structure Prediction and Transmission Electron Microscopy Approach

Electron diffraction offers advantages over X‐ray based methods for crystal structure determination because it can be applied to sub‐micron sized crystallites, and picogram quantities of material. For molecular organic species, however, crystal structure determination with electron diffraction is hindered by rapid crystal deterioration in the electron beam, limiting the amount of diffraction data that can be collected, and by the effect of dynamical scattering on reflection intensities. Automated electron diffraction tomography provides one possible solution. We demonstrate here, however, an alternative approach in which a set of putative crystal structures of the compound of interest is generated by crystal structure prediction methods and electron diffraction is used to determine which of these putative structures is experimentally observed. This approach enables the advantages of electron diffraction to be exploited, while avoiding the need to obtain large amounts of diffraction data or accurate reflection intensities. We demonstrate the application of the methodology to the pharmaceutical compounds paracetamol, scyllo‐inositol and theophylline.     

Concomitant Polymorphism in an Organic Solid: Molecular and Crystal Structure and Intra- and Intermolecular Potential Contributions to tert-Butyl and Methyl Group Rotation

We investigate the relationship between structure (crystal and molecular) and tert-butyl and methyl group dynamics in 2-(tert-butyl)-9-(4-(tert-butyl)phenyl)anthracene. Powder and single-crystal X-ray diffraction, taken together, show that different polycrystalline samples recrystallized from different solvents have different amounts of at least four polymorphs (crystallites having different crystal structures), of which we have identified three by single crystal X-ray diffraction. The molecules in the asymmetric units of the different crystal structures differ by the dihedral angle the tert-butylphenyl group makes with the anthracene moiety. Ab initio electronic structure calculations on the isolated molecule show that very little intramolecular energy is required to change this angle over a range of about 60° which is probably the origin of the concomitant polymorphism (crystals of more than one polymorph in a polycrystalline sample). Solid state ¹H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments support the powder and single-crystal X-ray results and provide average NMR activation energies (closely related to rotational barriers) for the rotation of the tert-butyl groups and their constituent methyl groups. These barriers have both an intramolecular and an intermolecular component. The latter is sensitive to the crystal structure. The intramolecular components of the rotational barriers of the two tert-butyl groups in the isolated molecule are investigated with ab initio electronic structure calculations.     

Structures of Trichloromethyl Thiocyanate,CCl3SCN,in Gaseous and Crystalline State

Trichloromethyl thiocyanate, CCl₃SCN, was structurally studied in both the gas and crystal phases by means of gas electron diffraction (GED) and single‐crystal X‐ray diffraction (XRD), respectively. Both experimental studies and quantum chemical calculations indicate a staggered orientation of the CCl₃ group relative to the SCN group. This conclusion is supported by the similarity of the C?SCN bond length to that of the anti‐structure of CH₂ClSCN (Berrueta Martínez et al. Phys. Chem. Chem. Phys. 2015, 17, 15805–15812). 1 Bond lengths and angles are similar for gas and crystal CCl₃SCN structures; however, the crystal structure presents different intermolecular interactions. These include halogen and chalcogen type interactions, the geometry of which was studied. Characteristic C‐Y???N angles (Y=Cl or S) close to 180° provide evidence for typical σ‐hole interactions along the halogen/chalcogen?carbon bond in N???Cl and N???S, intermolecular units.     

Determination of the Crystal Structure of a New Polymorph of Theophylline

A new approach to crystal structure determination, combining crystal structure prediction and transmission electron microscopy, was used to identify a potential new crystal phase of the pharmaceutical compound theophylline. The crystal structure was determined despite the new polymorph occurring as a minor component in a mixture with Form II of theophylline, at a concentration below the limits of detection of analytical methods routinely used for pharmaceutical characterisation. Detection and characterisation of crystallites of this new form were achieved with transmission electron microscopy, exploiting the combination of high magnification imaging and electron diffraction measurements. A plausible crystal structure was identified by indexing experimental electron‐diffraction patterns from a single crystallite of the new polymorph against a reference set of putative crystal structures of theophylline generated by global lattice energy minimisation calculations.     

Structure and morphology of nylon 46 lamellar crystals: Electron microscopy and energy calculations

A detailed electron microscopy study of the structure and morphology of lamellar crystals of nylon 46 obtained by crystallization from solution has been carried out. Electron diffraction of crystals supported by X‐ray diffraction of their sediments revealed that they consist of a twinned crystal lattice made of hydrogen‐bonded sheets separated 0.376 nm and shifted along the a‐axis (H‐bond direction) with a shearing angle of 65°. The interchain distance within the sheets is 0.482 nm. These parameters are similar to those previously described for nylon 46 lamellar crystals grown at lower temperatures. A combined energy calculation and modeling simulation analysis of all possible arrangements for the crystal‐packing of nylon 46 chains, in fully extended conformation, was performed. Molecular mechanics calculations showed very small energy differences between α (alternating intersheet shearing) and β (progressive intersheet shearing) structures with energy minima for successive sheets sheared at approximately 1/6 c and 1/3 c. A mixed lattice composed of a statistical array of α and β structures with such sheet displacements was found to be fully compatible with experimental data and most appropriate to describe nylon 46 lamellar crystals. Annealing of the crystals at temperatures closely below the Brill transition induced enrichment in β structure and increased chain‐folding order. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 41–52, 2000     

Spectroscopic Properties,Conformation and Structure of Difluorothiophosphoryl Isocyanate in the Gaseous and Solid Phase

Difluorothiophosphoryl isocyanate, F₂P(S)NCO was characterized with UV/vis, NMR, IR (gas and Ar-matrix), and Raman (liquid) spectroscopy. Its molecular structure was also established by means of gas electron diffraction (GED) and single crystal X-ray diffraction (XRD) in the gas phase and solid state, respectively. The analysis of the spectroscopic data and molecular structures is complemented by extensive quantum-chemical calculations. Theoretically, the C_s symmetric syn-conformer is predicted to be the most stable conformation. Rotation about the P−N bond requires about 9 kJ mol⁻¹ and the predicted existence of an anti-conformer is dependent on the quantum-chemical method used. This syn-orientation of the isocyanate group is the only one found in the gas phase and contained likewise in the crystal. The overall molecular structure is very similar in gas and solid, despite in the solid state the molecules arrange through intramolecular O⋅⋅⋅F contacts into layers, which are further interconnected by S⋅⋅⋅N, S⋅⋅⋅C and C⋅⋅⋅F contacts. Additionally, the photodecomposition of F₂P(S)NCO to form CO, F₂P(S)N, and F₂PNCO is observed in the solid Ar-matrix.     

Structural Dynamics upon Photoexcitation in a Spin Crossover Crystal Probed with Femtosecond Electron Diffraction

Photoexcitation of spin crossover (SCO) complexes can trigger extensive electronic spin transitions and transformation of molecular structure. However, the precise nature of the associated ultrafast structural dynamics remains elusive, especially in the solid state. Here, we studied a single‐crystal SCO material with femtosecond electron diffraction (FED). The unique capability of FED allows us to directly probe atomic motions and to track ultrafast structural changes within a crystal lattice. By monitoring the time‐dependent changes of the Bragg reflections, we observed the formation of a photoinduced structure similar to the thermally induced high‐spin state. The data and refinement calculations indicate the global structural reorganization within 2.3 ps, as the metal–ligand bond distribution narrows during intramolecular vibrational energy redistribution (IVR) driving the intermolecular rearrangement. Three independent dynamical group are identified to model the structural dynamics upon photoinduced SCO.     

Molecular structures of free quinuclidine and its adducts with metal trihydrides, MH3 (M=B, Al or Ga), studied by gas-phase electron diffraction, X-ray diffraction and quantum chemical calculations

The structure of quinuclidine, HC(CH(2)CH(2))(3)N, has been re-investigated by quantum chemical calculations and by gas-phase electron diffraction (GED). The GED data, together with published rotational constants, have been analysed using the SARACEN method to determine the most reliable structure (r(h1)) for the gaseous molecule. The structures of two adducts of quinuclidine with group 13 trihydride molecules, MH(3) (M=B, Al), have also been determined by GED and quantum chemical calculations. The effect of the coordination of these hydrides to the quinuclidine nitrogen atom has been investigated, and the structural changes and energetics of adduct formation are discussed. We also present the crystal structure of quinuclidine borane.     

Structure and vibrational spectra of the enol form of hexafluoro-acetylacetone. A density functional theoretical study

Molecular and vibrational structure of 1,1,1,6,6,6-hexafluoropentane-2,4-dione (hexafluoro-acetylacetone) have been investigated by means of density functional theory (DFT) calculations and have been compared with those of acetylacetone, the parent molecule. According to the theoretical calculations HFAA has an asymmetric structure with hydrogen bond strength of about 12 kcal mol(-1), about 6 kcal mol(-1) less than that of acetylacetone. This weakening of hydrogen bond is consistent with frequency shifts for OH/OD stretching, OH/OD out of plane bending and O...O stretching modes upon substitution of methyl hydrogen atoms with fluorine atoms. The symmetric structure based on electron diffraction data is interpreted as superposition of two asymmetric structures.     

Investigation of structure and dynamics in a photochromic molecular crystal by NMR crystallography

A photochromic anil, N-(3,5-di-t-butylsalicylidene)-4-amino-pyridine, has been studied by single-crystal X-ray diffraction, multinuclear magic-angle spinning NMR, and first-principles density functional theory (DFT) calculations. Interpretation of the solid-state NMR data on the basis of calculated chemical shifts confirms the structure is primarily composed of molecules in the ground-state enol tautomer, whereas thermally activated cis-keto and photoisomerised trans-keto states exist as low-level defects with populations that are too low to detect experimentally. Variable temperature ¹³C NMR data reveal evidence for solid-state dynamics, which is found to be associated with fast rotational motion of t-butyl groups and 180° flips of the pyridine ring, contrasting the time-averaged structure obtained by X-ray diffraction. Comparison of calculated chemical shifts for the full crystal structure and an isolated molecule also reveals evidence for an intermolecular hydrogen bond involving the pyridine ring and an adjacent imine carbon, which facilitates the flipping motion. The DFT calculations also reveal that the molecular conformation in the crystal structure is very close to the energetic minimum for an isolated molecule, indicating that the ring dynamics arise as a result of considerable steric freedom of the pyridine ring and which also allows the molecule to adopt a favourable conformation for photochromism.     

Iron dihalides: structures and thermodynamic properties from computation and an electron diffraction study of iron diiodide

The molecular structures, vibrational frequencies, and thermodynamic properties of all four monomeric and dimeric iron dihalide molecules, FeF₂, FeCl₂, FeBr₂, and FeI₂, were determined by quantum chemical calculations and the structure of iron diiodide also by gas-phase electron diffraction (ED). The earlier ED study of iron dibromide was also repeated. All iron dihalides are stable molecules in contrast to the iron trihalides, for which FeBr₃ and FeI₃ are unstable and easily decompose to the corresponding dihalides. The structures of the trimers and tetramers of FeCl₂ were also calculated and compared to the crystal structure.     

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

X‐ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host–guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X‐ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light‐atom‐only crystal. Atomic displacement parameters obtained independently from the X‐ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Ų indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host–guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host–guest interaction (e.g., in protein–drug complexes), at least for polar molecules.     

(Dimethylaminomethyl)trifluorosilane, Me2NCH2SiF3--a model for the alpha-effect in aminomethylsilanes

F3SiCH2NMe2 was prepared as a model for the investigation of the nature of the alpha-effect in alpha-aminosilanes, by fluorination of Cl3SiCH2NMe2 with SbF3. Under less mild conditions Si--C bond cleavage was also observed, leading to the double adduct F4Si(Me2NCH2SiF3)2, which was characterised by a crystal structure analysis showing that the central SiF4 unit is connected to Me2NCH2SiF3 via SiN dative bonds and FSi contacts. F3SiCH2NMe2 was characterised by multinuclear NMR spectroscopy (1H, 13C, 15N, 19F and 29Si), gas-phase IR spectroscopy and mass spectrometry. It is a dimer in the crystal (X-ray diffraction, crystal grown in situ), held together by two Si--N dative bonds. In solution and in the gas phase the compound is monomeric. The structure of the free molecule, determined by gas-phase electron diffraction, showed that, in contrast to former postulates, there are no attractive SiN interactions. Ab initio calculations have been carried out to explain the nature of the bonding. F3SiCH2NMe2 has an extremely flat bending potential for the Si-C-N angle; the high degree of charge transfer from the Si to the N atoms which occurs upon closing the Si-C-N angle is in the opposite direction to that expected for a dative bond. The topology of the electron density of F3SiCH2NMe2 was analysed. Solvent simulation calculations have shown virtually no structural dependence on the medium surrounding the molecule. The earlier postulate of Si-->N dative bonds in SiCN systems is discussed critically in light of the new results.     

Quantitative analyses of precession diffraction data for a large cell oxide.

Kinematical and two-beam calculations have been conducted and are compared to experimental precession data for the large unit cell crystal La4Cu3MoO12. Precession electron diffraction intensities are found to exhibit approximate two-beam behavior and demonstrate clear advantages over conventional SADP intensities for use in structure solution.     

The application of molecular mechanics to the structures of carbohydrates

A study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2-methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI-CARB, a version of MMI with changes in some of the equilibrium C? O bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the C? C? O? H torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for C? C and C? O bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.     

On the Solvent‐free Structure of a Jäger‐type Cobalt(II) N2O2‐Chelate Complex

A combined synchrotron X‐ray and density functional theory (DFT) study on the structure of a Jäger‐type N₂O₂ chelate complex was carried out. The ethoxy‐substituted bis(3‐oxo‐enaminato)cobalt(II) complex ( 1 ) was an original sample from the laboratory of the late Professor Ernst‐G. Jäger (University of Jena, Germany). Single‐crystal X‐ray analysis revealed essentially flat molecules of 1 , which are unsolvated and coordinatively unsaturated. The DFT calculations on the isolated molecule predict a planar structure for the non‐hydrogen atoms, which is a local minimum on the energy surface. The crystal packing is achieved through off‐set stacking (staircase arrangement), resulting in a herringbone pattern in the space group P2₁2₁2₁. The structure of 1 is compared to known structures of related bis(3‐oxo‐enaminato)cobalt(II) complexes ( 2 – 4 ). Original bulk material of 1 was investigated by scanning electron microscopy (SEM), powder X‐ray diffraction (PXRD), melting point determination, and infrared (IR) spectroscopy.     

EPR analysis and DFT computations of a series of polynitroxides

Polynitroxides with varying numbers of nitroxide groups (one to four) derived from different aromatic core structures show intramolecular electron spin-spin coupling. The scope of this study is to establish an easy methodology for extracting structural, dynamical, and thermodynamical information from the EPR spectra of these polynitroxides which might find use as spin probes in complex systems, such as biological and host/guest systems, and as polarizing agents in dynamic nuclear polarization (DNP) applications. Density functional theory (DFT) calculations at the B3LYP/6-31G(d) level provided information on the structural details such as bond lengths and angles in the gas phase, which were compared with the single crystal X-ray diffraction data in the solid state. Polarizable continuum model (PCM) calculations were performed to account for solvent influences. The electron paramagnetic resonance (EPR) spectra of the polynitroxides in chloroform were analyzed in detail to extract information such as the percentages of different conformers, hyperfine coupling constants a, and rotational correlation times τ(c). The temperature dependence on the line shape of the EPR spectra gave thermodynamic parameters ΔH and ΔS for the conformational transitions. These parameters were found to depend on the number and relative positions of the nitroxide and other polar groups.     

3D Electron Diffraction Structure Determination of Terrylene,a Promising Candidate for Intermolecular Singlet Fission

Herein we demonstrate the prowess of the 3D electron diffraction approach by unveiling the structure of terrylene, the third member in the series of peri-condensed naphthalene analogues, which has eluded structure determination for 65 years. The structure was determined by direct methods using electron diffraction data and corroborated by dispersion-inclusive density functional theory optimizations. Terrylene crystalizes in the monoclinic space group P2₁/a, arranging in a sandwich-herringbone packing motif, similar to analogous compounds. Having solved the crystal structure, we use many-body perturbation theory to evaluate the excited-state properties of terrylene in the solid-state. We find that terrylene is a promising candidate for intermolecular singlet fission, comparable to tetracene and rubrene.     

Structural analysis of Gd6FeBi2 from single‐crystal X‐ray diffraction methods and electronic structure calculations

The crystal structure of the gadolinium iron bismuthide Gd₆FeBi₂ has been characterized by single‐crystal X‐ray diffraction data and analyzed in detail using first‐principles calculations. The structure is isotypic with the Zr₆CoAl₂ structure, which is a variant of the ZrNiAl structure and its binary prototype Fe₂P (Pearson code hP9, Wyckoff sequence g f d a). As such, the structure is best viewed as an array of tricapped trigonal prisms of Gd atoms centered alternately by Fe and Bi. The magnetic‐ordering temperature of this compound (ca 350 K) is much higher than that of other rare‐earth metal‐rich phases with the same or related structures. It is also higher than the ordering temperature of many other Gd‐rich ternary phases, where the magnetic exchange is typically governed by Ruderman–Kittel–Kasuya–Yosida (RKKY) interactions. First‐principles calculations reveal a larger than expected Gd magnetic moment, with the additional contribution arising from the Gd 5d electrons. The electronic structure analysis suggests strong Gd 5d–Fe 3d hybridization to be the cause of this effect, rather than weak interactions between Gd and Bi. These details are of importance for understanding the magnetic response and explaining the high ordering temperature in this material.     

Poly(hexamethylene terephthalate)—II. The crystal structure of forms I and II,from electron and x-ray diffraction,and packing analyses

Form I of poly(hexamethylene terephthalate), poly(6GT), has been shown, through electron diffraction of micro-single crystals, and fibre X-ray diffraction to belong to the triclinic system. The unit cell containing only one chain has dimensions $\text{a = 5.217(8), b = 5.284(12), c = 15.738(16)}\text{A}\text{?}\text{(}\text{fibre axis}\text{), α = 129.4(2), β = 97.6(2)}\text{and}\text{γ = 95.6(2)°}$. The space group is PT. The crystal structure of poly(6GT) form I has been established by the model compound approach and confirmed using 19 independent electron diffraction intensities. Upon refinement of the scale and temperature factors, the agreement index R reaches 0.172, with an overall isotropic temperature factor $\text{B = 3.0}\text{A}\text{?}{}_2$. Calculation of dynamical amplitudes, and also of structure amplitudes which allow for crystal bending, confirms that the electron diffraction data are suitable for a conventional structure analysis. The chain of the polyester has the same fully extended conformation as its related model compound hexamethylene glycol dibenzoate. The planar chain in the single cell is at 35° to the α-axis. The unit-cell dimensions of poly(6GT) form II differ from those of form I by the doubling of the b-dimension. The two chains in the double unit-cell are at 31 and 39° respectively from the a-axis. The agreement index R is 0.161 for the 19 reflections of the single cell and R = 0.196 when the 10 reflections causing the doubling of b are included.