Generation of a plastic crystal including methane rotator within metal-organic cavity by forcible gas adsorption

The structural determination of saturated adsorbed methane inside a metal-organic cavity by the forcible pressure swing adsorption method (ca. 13 MPa) through a gas-adsorption equilibrium state gives a methane inclusion crystal even at 298 K. The adsorbed methane molecules regularly locate in the pocket-like narrow corners of the necks of the 1-D channel without disorder. The thermal motion of the pseudo-spherical methane molecules seems to be effectively suppressed in its translation mode but allowed rotation. In cooling to 90 K, the crystal structure remained essentially unchanged while the thermal motion decreased, indicating that a lower temperature reduces the rotation of the adsorbed pseudo-spherical methane. The observed crystal structure could also be influenced by a reduction of the vibrational magnitude, and a phase transition from a static disordered structure to an ordered state might occur. The observed crystal state at a higher temperature should have a plastic crystal nature in terms of the randomness of the orientation of incorporated guests. The single-crystal adsorbent is effective for crystallographic observation of the thermal activated guest forced into regular alignment in the crystal lattice, which can be used as a model of the supercritical fluid.     

Polymorphism and phase transformation in the dimethyl sulfoxide solvate of 2,3,5,6‐tetrafluoro‐1,4‐diiodobenzene

A new polymorph (form II) is reported for the 1:1 dimethyl sulfoxide solvate of 2,3,5,6‐tetrafluoro‐1,4‐diiodobenzene (TFDIB·DMSO or C₆F₄I₂·C₂H₆SO). The structure is similar to that of a previously reported polymorph (form I) [Britton (2003). Acta Cryst. E 59 , o1332–o1333], containing layers of TFDIB molecules with DMSO molecules between, accepting I…O halogen bonds from two TFDIB molecules. Re‐examination of form I over the temperature range 300–120 K shows that it undergoes a phase transformation around 220 K, where the DMSO molecules undergo re‐orientation and become ordered. The unit cell expands by ca 0.5 Å along the c axis and contracts by ca 1.0 Å along the a axis, and the space‐group symmetry is reduced from Pnma to P2₁2₁2₁. Refinement of form I against data collected at 220 K captures the (average) structure of the crystal prior to the phase transformation, with the DMSO molecules showing four distinct disorder components, corresponding to an overlay of the 297 and 120 K structures. Assessment of the intermolecular interaction energies using the PIXEL method indicates that the various orientations of the DMSO molecules have very similar total interaction energies with the molecules of the TFDIB framework. The phase transformation is driven by interactions between DMSO molecules, whereby re‐orientation at lower temperature yields significantly closer and more stabilizing interactions between neighbouring DMSO molecules, which lock in an ordered arrangement along the shortened a axis.     

A solid-state NMR, X-ray diffraction, and ab initio computational study of hydrogen-bond structure and dynamics of pyrazole-4-carboxylic acid chains

Using high-resolution solid-state (15)N CMAS NMR, X-ray crystallography, and ab initio calculations, we have studied the structure of solid pyrazole-4-carboxylic acid (1). The crystal structure was determined at 295 and 150 K. Molecules of 1 are located on a two-fold axis, implying proton disorder of the NH and OH groups; no phase transition was observed between these two temperatures. The compound forms quasi-linear ribbons in which the molecules are linked by cyclic hydrogen bonds between pyrazole and carboxylic acid groups with disordered hydrogen-bonded protons. Crystallography is unable to decide whether the disorder is dynamic or static. NMR shows that this disorder is dynamic, that is, consisting of very fast degenerate double proton transfers between two rapidly interconverting O-H.N and O.H-N hydrogen bridges. However, at low temperature, NMR shows a proton disorder-order transition where the protons are preferentially localized on given nitrogen and oxygen atoms. An amorphous phase exhibiting proton order is observed when the compound is precipitated rapidly. In this case, the defects are annealed by moderate heating. Ab initio calculations performed on oligomers of 1 show that the O-H.N hydrogen bridge is about 0.064 A shorter and less bent ( approximately 171 degrees ) than the O.H-N hydrogen bridge ( approximately 150 degrees ). For an isolated ribbon, this result leads to structures with localized protons, either to a cycle with about 200 molecules, or to a quasi-linear ribbon involving an undulated structure, or to a combination of both motifs. Only the undulated structure is compatible with the linear ribbon observed by X-ray crystallography, where the fast proton transfer in the high-temperature phase is assisted by the motions of the undulated chain. A disordered structure is assigned to the amorphous phase, which exhibits the combination of the curved and the undulated motifs.     

Geometry and electronic structure of the dimethyl sulfoxide dimer. Calculation by the MNDO method

The geometric and electronic structure of the complex formed by dipole-dipole interaction between two molecules of DMSO in the "head-to-tail" orientation were calculated by the MNDO quantum-chemical method. The minimum total energy corresponds to a distance of 5.5 Å between the sulfur atoms, and the angle between the axis of the molecular dipoles is 16.4°. This agrees with calculations for liquid DMSO by molecular dynamics. The large equilibrium distance between the DMSO molecules explains its low density in the liquid phase and the high intensity of microwave absorption due to free volume sufficient for rotation of one molecule in the complex in relation to the dipole axis of the other.N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 117334 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 6, pp. 1340–1344, June, 1992.     

Adsorption of Carbamazepine in All-Silica Zeolites Studied with Density Functional Theory Calculations**

The anticonvulsant drug carbamazepine (−) is an emerging contaminant of considerable concern due to its hazard potential and environmental persistence. Previous experimental studies proposed hydrophobic zeolites as promising adsorbents for the removal of carbamazepine from water, but only a few framework types were considered in those investigations. In the present work, electronic structure calculations based on dispersion-corrected density functional theory (DFT) were used to study the adsorption of CBZ in eleven all-silica zeolites having different pore sizes and connectivities of the pore system (AFI, ATS, BEA, CFI, DON, FAU, IFR, ISV, MOR, SFH, SSF framework types). It was found that some zeolites with one-dimensional channels formed by twelve-membered rings (IFR, AFI) exhibit the highest affinity towards CBZ. A “good fit” of CBZ into the zeolite pores that maximizes dispersion interactions was identified as the dominant factor determining the interaction strength. Further calculations addressed the role of temperature (for selected systems) and of guest-guest interactions between coadsorbed CBZ molecules. In addition to predicting zeolite frameworks of particular interest as materials for selective CBZ removal, the calculations presented here also contribute to the atomic-level understanding of the interaction of functional organic molecules with all-silica zeolites.     

Conformational dimorphism of 1,1,3,3,5,5-hexachloro-1,3,5-trigermacyclohexane: solvent-induced crystallization of a metastable polymorph containing boat-shaped molecules

Two crystalline modifications of 1,1,3,3,5,5-hexachloro-1,3,5-trigermacyclohexane have been experimentally obtained as phase pure products and studied by single-crystal X-ray diffraction. The six-membered heterocycles adopt a chair conformation in the alpha-phase; this polymorph is accessible by crystallisation from solution and from the melt. In contrast, the beta-form is built up from boat-shaped molecules; it can exclusively be crystallised from n-hexane. At the molecular level, formation energies of the 1,1,3,3,5,5-hexachloro-1,3,5-trigermacyclohexane conformers have been compared by using molecular mechanics, semiempirical and ab-initio quantum mechanical calculations. Possible reasons for the selective formation of the alpha- or beta-phase in specific solvents have been considered. Formation of the metastable phase is suggested to occur via a hypothetical intermediate of composition [(GeCl2CH2)3].0.5C6H14. For such an in-silico solvate, a crystal structure of favourable lattice energy, closely related to the experimentally observed beta-modification, has been found through global energy minimisation. Elimination of the n-hexane molecules from this computer-generated solid and subsequent simulated annealing resulted in a crystal structure that corresponds to the experimentally observed beta-phase within the limits of the force field calculations. This scenario implies solvent directed crystallisation of a metastable polymorphic molecular crystal.     

Molecular recognition in cyclodextrin complexes of amino acid derivatives: the effects of kinetic energy on the molecular recognition of a pseudopeptide in a nonconstraining host environment as revealed by a temperature-dependent crystallographic study

The crystal structure of a triclinic 2:2 inclusion complex of beta-cyclodextrin with N-acetyl-L-phenylalanine methyl ester has been determined at several temperatures between 298 and 20 K to further study molecular recognition using solid-state supramolecular beta-cyclodextrin complexes. The study reveals kinetic energy dependent changes in guest molecule conformations, orientations, and positions in the binding pocket presented by the crystal lattice. Accompanying these changes are observable differences in guest-guest interactions and hydrogen-bonding interactions in the binding pocket that involve guest molecules, water of hydration molecules, and beta-cyclodextrin molecules. On the basis of the differences observed in the crystal structures, we present a solid-state example of a system that displays the properties of both classical and quantum chemical models. At higher temperatures, the structure conforms to a classical mechanical model with dynamic disorder. At lower temperatures, the observations conform to examples in which there is static disorder representative of models in which quantum states differing in conformation, position, and orientation of components in the crystal structure are occupied. Ab initio theoretical calculations on the different guest molecule conformations have been carried out. Superpositions of theoretical electrostatic surface potential diagrams on the observed molecular positions in the complexes provide confidence that the deconvolution of the guest molecule disorder is acceptable. Temperature-dependent solid-state magic angle spinning deuteron NMR measurements provide evidence for large-amplitude, diffusive motion on a microsecond time scale in the complex.     

Tryptammonium (2S,3S)-hydrogentartrate monohydrate [Struct Chem (2008) 19:147–154]: redetermination at 110 K and re-refinement against room temperature data

The crystal structure of the title compound was incorrectly reported as a methanol solvate [Koleva et al. in Struct Chem 19:147–154, 2008] on the basis of room temperature X-ray diffraction data. We have now established the presence of a disordered water molecule rather than the methanol molecule using a low temperature data set collected at 110 K.     

Water assisted growth of C₆₀ rods and tubes by liquid-liquid interfacial precipitation method

C?? nanorods with hexagonal cross sections are grown using a static liquid-liquid interfacial precipitation method in a system of C??/m-dichlorobenzene solution and ethanol. Adding water to the ethanol phase leads instead to C?? tubes where both length and diameter of the C?? tubes can be controlled by the water content in the ethanol. Based on our observations we find that the diameter of the rods/tubes strongly depends on the nucleation step. We propose a liquid-liquid interface growth model of C?? rods and tubes based on the diffusion rate of the good C?? containing solvent into the poor solvent as well as on the size of the crystal seeds formed at the interface between the two solvents. The grown rods and tubes exhibit a hexagonal solvate crystal structure with m-dichlorobenzene solvent molecules incorporated into the crystal structure, independent of the water content. An annealing step at 200 °C at a pressure < 1 kPa transforms the grown structures into a solvent-free face centered cubic structure. Both the hexagonal and the face centered cubic structures are very stable and neither morphology nor structure shows any signs of degradation after three months of storage.     

Spectral Diffusion of Single Dibenzoterrylene Molecules in 2,3‐Dimethylanthracene

We study single dibenzoterrylene molecules embedded in the dipolar disordered crystal 2,3‐dimethylanthracene at 1.25 K. Broad linewidths (about 1 GHz, ～30 times broader than in the anthracene crystal), high saturation excitation intensities (～1000 times larger than in anthracene), as well as strong spectral diffusions are observed. Additionally, spectral jumping is studied by varying the excitation intensity and the temperature. We propose that the spectral diffusion and dynamic disorder in this system arise from the combination of a static disorder with slight reorientations of the methyl groups of the host molecules.     

Partial ordering of tripivaloylmethane at 110 K

Tripivaloylmethane [systematic name: 4‐(2,2‐dimethylpropanoyl)‐2,2,6,6‐tetramethylheptane‐3,5‐dione], C₁₆H₂₈O₃, is known to crystallize at room temperature in the space group R3m with three molecules in the unit cell. The molecules are conformationally chiral and pack so that each molecular site is occupied with equal probability by the two enantiomers. Upon cooling to 110 K, the structure partially orders; two molecules in the unit cell order into two different conformations of opposite chirality, while the third remains disordered. The symmetry of the resulting crystal is P3, with each of the molecules lying about a different threefold rotation axis. This paper describes an unusual case of order–disorder phase transition in which the structure partially orders by changes of molecular conformation in the single crystals. Such behaviour is of interest in the study of phase transitions and molecular motion in the solid state.     

Can proteins and crystals self-catalyze methyl rotations?

The chi (C(alpha)-C(beta)) torsional barrier in the dipeptide alanine (N-methyl-l-alanyl-N-methylamide) crystal was investigated using ab initio calculations at various levels of theory, molecular mechanics, and molecular dynamics. For one of the two molecules in the asymmetric unit the calculations suggest that rotation around the chi dihedral angle is catalyzed by the crystal environment, reducing by up to approximately 2kT the torsional barrier in the crystal with respect to that in the gas phase. This catalytic effect is present at both low and room temperature and originates from a van der Waals destabilization of the minima in the methyl dihedral potential coming from the nonbonded environment of the side chain. Screening of a subset of the Protein Data Bank with a pharmacophore model reproducing the crystal environment around this side chain methyl identified a protein containing an alanine residue with an environment similar to that in the crystal. Calculations indicate that this chi torsional barrier is also reduced in the protein at low temperature but not at room temperature. This suggests that environment-catalyzed rotation of methyl groups can occur both in the solid phase and in native biological structures, though this effect might be temperature-dependent. The relevance of this catalytic effect is discussed in terms of its natural occurrence and its possible contribution to the low-frequency vibrational modes of molecules.     

Variable temperature neutron diffraction and X-ray charge density studies of tetraacetylethane

Single crystal neutron diffraction data have been collected on a sample of enolized 3,4-diacetyl-2,5-hexanedione (tetraacetylethane, TAE) at five temperatures between 20 and 298 K to characterize the temperature-dependent behavior of the short, strong, intramolecular hydrogen bond. Upon decreasing the temperature from 298 K to 20 K, the O2-H1 distance decreases from 1.171(11) to 1.081(2) A and the O1...H1 distance increases from 1.327(10) to 1.416(6) A. The convergence of the C-O bond lengths from inequivalent distances at low temperature to identical values (1.285(4) A) at 298 K is consistent with a resonance-assisted hydrogen bond. However, a rigid bond analysis indicates that the structure at 298 K is disordered. The disorder vanishes at lower temperatures. Short intermolecular C-H...O contacts may be responsible for the ordering at low temperature. The intramolecular O...O distance (2.432 +/- 0.006 A) does not change with temperature. X-ray data at 20 K were measured to analyze the charge density and to gain additional insight into the nature of the strong hydrogen bond. Quantum mechanical calculations demonstrate that periodic boundary conditions provide significant enhancement over gas phase models in that superior agreement with the experimental structure is achieved when applying periodicity. One-dimensional potential energy calculations followed by quantum treatment of the proton reproduce the location of the proton nearer to the O2 site reasonably well, although they overestimate the O-H distance at low temperatures. The choice of the single-point energy calculation strategy for the proton potential is justified by the fact that the proton is preferably located nearer to O2 rather than being equally distant to O1 and O2 or evenly distributed (disordered) between them.     

Complex orientational ordering of C60 molecules on Au(111)

The orientation and adsorption site for C(60) molecules on Au(111) has been studied using low temperature scanning tunneling microscopy. A complex orientational ordering has been observed for molecules inside the "in-phase" (R0°) domain. A 7-molecule cluster consisting a central molecule sitting atop of a gold atom and 6 tilted surrounding molecules is identified as the structural motif. The 2√3 × 2√3-R30° phase consists of molecules bonding to a gold atomic vacancies with a preferred azimuthal orientation. The quasi-periodic R14° phase is composed of groups of similarly oriented molecules with the groups organized into a 4√3 × 4√3-R30° like super-lattice unit cell.     

Polymorphism and solvatomorphism of bicalutamide

Single crystals of the crystallosolvate [bicalutamide + DMSO] with 1:1 stoichiometry were grown, and their structures were solved by X-ray diffraction methods. Polymorphic modifications I and II, the amorphous state, and the DMSO crystallosolvate of bicalutamide were prepared and thermochemistry of fusion processes was studied by DSC technique. The temperature dependence of the saturated vapor pressure of polymorphic form I was obtained and the thermodynamic characteristics of the sublimation process including the crystal lattice energy were calculated. The solution enthalpies of the forms under consideration and the crystallosolvate were acquired by the solution calorimetry procedure. The phase transition enthalpies estimated for form I, form II, and the amorphous state followed the rank order: form I— > form II, form I— > amorphous state, and form II— > amorphous state. The crystal lattice energy of polymorphic form II was determined using the results of sublimation and solution calorimetric experiments. The difference between the crystal lattice energy of the crystallosolvate and unsolvated phases was observed. The dissolution kinetics of forms I, II, the amorphous state, and DMSO solvate in water were investigated.     

Crystallization of carbamazepine pseudopolymorphs from nonionic microemulsions

Crystallization of carbamazepine (CBZ), an antiepileptic drug, precipitated from confined spaces of nonionic microemulsions was investigated. The study was aimed to correlate the structure of the microemulsion [water-in-oil (W/O), bicontinuous, and oil-in-water (O/W)] with the crystalline structure and morphology of solid CBZ. The precipitated CBZ was studied by DSC, TGA, powder XRD, single-crystal XRD, SEM, and optical microscopy. The results suggest that the microstructure of the microemulsions influences the crystallization process and allows crystallizing polymorphs that exhibit different crystal structure and habits. W/O nanodroplets orient the crystallizing CBZ molecules to form a prismlike anhydrous polymorphic form with monoclinic unit cell and P21/n space group. Bicontinuous structures lead to platelike dihydrate crystals with orthorhombic unit cell and Cmca space group. The O/W nanodroplets cause the formation of needlelike dihydrate crystals with monoclinic unit cell and P21/c space group. The morphological features of solid CBZ remain predetermined by the basic symmetry and parameters of its unit cell. Precipitation of CBZ pseudopolymorphs from supersaturated microemulsion is discussed in terms of oriented attachment that provides perfect packing of numerous separately nucleated ordered nuclei of CBZ into microscale platelets and then into macroscopic crystals. Crystallization from microemulsion media enabling one to obtain the drug (CBZ) with predicted structure and morphology should be of great significance for pharmaceutical applications.     

Characterization of non-stoichiometric hydration and the dehydration behavior of sitafloxacin hydrate

Sitafloxacin (STFX) hydrate is a non-stoichiometric hydrate. The hydration state of STFX hydrate varies non-stoichiometrically depending on the relative humidity and temperature, though X-ray powder diffraction (XRPD) of STFX hydrate was not affected by storing at low and high relative humidities. The detailed properties of crystalline water of STFX hydrate were estimated in terms of hygroscopicity, thermal analysis combined with X-ray powder diffractometry, crystallography and density functional theory (DFT) calculation. STFX hydrate changed the water contents continuously and reversibly from an equivalent amount of dihydrate through that of sesquihydrate depending on the relative humidity at 25°C. Thermal analysis and X-ray powder diffraction (XRPD) simultaneous measurement also revealed that STFX hydrate dehydrated into a hydrated state equivalent to monohydrate by heating up to 100°C, whereas XRPD patterns were slightly affected. This indicated that the crystal structure of STFX hydrate was retained at the dehydration level of monohydrate. Single-crystal X-ray structural analysis showed that two STFX molecules and four water molecule sites were contained in an asymmetric unit. STFX molecules formed a channel structure where water molecules were included. At the partially dehydrated state, at least two of four water molecules were considered to be disordered in occupancy and/or coordinates. Insight into the crystal structure of STFX hydrate stored at low and high relative humidities and geometry of the hydrogen bond were helpful to estimate the origin of non-stoichiometric hydration of STFX hydrate.     

First principles molecular dynamics study of filled ice hydrogen hydrate

We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C(2) by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and∕or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and∕or low temperatures.     

Employing a cylindrical single crystal in gas-surface dynamics

We describe the use of a polished, hollow cylindrical nickel single crystal to study effects of step edges on adsorption and desorption of gas phase molecules. The crystal is held in an ultra-high vacuum apparatus by a crystal holder that provides axial rotation about a [100] direction, and a crystal temperature range of 89 to 1100 K. A microchannel plate-based low energy electron diffraction/retarding field Auger electron spectrometer (AES) apparatus identifies surface structures present on the outer surface of the cylinder, while a separate double pass cylindrical mirror analyzer AES verifies surface cleanliness. A supersonic molecular beam, skimmed by a rectangular slot, impinges molecules on a narrow longitudinal strip of the surface. Here, we use the King and Wells technique to demonstrate how surface structure influences the dissociation probability of deuterium at various kinetic energies. Finally, we introduce spatially-resolved temperature programmed desorption from areas exposed to the supersonic molecular beam to show how surface structures influence desorption features.