Urea Inclusion Research Articles

An Efficient Method for Calculating Powder Patterns

A novel approach to the calculation of powder lineshapes is presented. Lineshapes from asymmetric second-rank tensor interactions are produced by summing lineshapes from symmetric tensors. This approach significantly reduces the calculation time, greatly facilitating iterative nonlinear least-squares fitting of experimental spectra. Results are reported for anisotropic 13C NMR lineshapes of glycine, benzoic acid, and octanoic acid in a urea inclusion compound. Lineshapes from nonuniform distributions of crystallite orientations can also be calculated by using distributions of the Euler angles that define the orientation of the principal-axis system of the chemical-shielding tensor with respect to the magnetic field.

A Computational Investigation of the Dynamics of Urea Molecules in Solids

Abstract A computational investigation of the dynamic properties of urea molecules in the pure crystalline phase of urea and in the urea tunnel structure (which is found in the conventional urea inclusion compounds) is reported. Both of these crystalline solids are extensively hydrogen bonded structures, and in both cases it has been shown experimentally that the urea molecules undergo 180° jumps about their C=O bonds at sufficiently high temperature. The computational investigations reported here have probed aspects of the potential energy barriers for this reorientational motion, and the possibility of correlations between the motions of different urea molecules. Various structural models representing clusters of urea molecules in these solids were considered, with two different potential energy parameterizations used to compute the energies of these clusters. The energetic and structural properties of the clusters were investigated as a function of rotation of a reference urea molecule, leading to new insights concerning the degree of correlation between the rotational motions of different urea molecules. A critical assessment is presented of the extent to which the results from these computational investigations can be compared with experimental results on the dynamic properties of the urea molecules.

Erratum: Superstructure Control in the Crystal Growth and Ordering of Urea Inclusion Compounds

In figure 3 (p. 1356) of the Research Article "Superstructure control in the crystal growth and ordering of urea inclusion compounds" by M. D. Hollingsworth et al. (6 Sept., p. 1355), the commensurate relation for 2,12-tridecanedione/urea (C 13 ) should have read, "3c g' = 5c h '," not "13c g ' = 5c h '."

Superstructure Control in the Crystal Growth and Ordering of Urea Inclusion Compounds

A template-directed mechanism of crystal growth is demonstrated for urea inclusion compounds (UICs). For UICs containing n -alkanone or α+1,ω−1-alkanedione guests, x-ray diffraction revealed superstructure relations between host and guest repeats along the channel axis for guests containing 8 to 14 carbons. For a favorable structural match between host and guest, UICs typically grow as flat hexagonal plates, and atomic force microscopy of {001} surfaces revealed molecularly smooth terraces differing in height by multiples of the guest repeat. If the match is poor, protrusion of guests from the {001} surfaces nucleates growth along the channel axis to form hexagonal needles.

Diffuse X-ray scattering and phase transitions of urea inclusion compounds

Diffuse X-ray scattering and phase transitions of urea inclusion compounds

Diffuse X-ray Scattering and Monte-Carlo Study of Guest–Host Interactions in Urea Inclusion Compounds

Detailed diffuse X-ray scattering patterns have been recorded at ambient temperatures (295 K) and at low temperatures (~130–150 K) for two urea inclusion compounds, n-hexadecane-urea and 1,10-dibromo-n-decane-urea. The strong diffuse scattering that occurs in the Bragg layers normal to c for these compounds has been investigated using Monte Carlo simulation of a model system. Although the model is only two dimensional, the work convincingly demonstrates that the scattering is due to the orientational disorder of the alkanes within the channels of the urea framework, together with accompanying relaxations of the framework itself. The model shows that at temperatures just above the phase transition there are quite large domains of the herringbone superstructure that had previously been postulated as the low-temperature phase. At room temperature, the alkanes are much less ordered but show a significant amount of the same kind of order. There is also evidence in the observed diffraction patterns that the anisotropic shape of the molecule causes the urea framework to flex, expanding the framework in directions parallel to the plane of the alkane backbone and contracting it in the perpendicular direction.

Eicosapentaenoic acid (20∶5n‐3) from the marine microalgaPhaeodactylum tricornutum

AbstractEicosapentaenoic acid (EPA, 20∶5n‐3) was obtained from the marine microalgaePhaeodactylum tricornutum by a three‐step process: fatty acid extraction by direct saponification of biomass, polyunsaturated fatty acid (PUFA) concentration by formation of urea inclusion compounds, and EPA isolation by semipreparative high‐performance liquid chromatography (HPLC). Alternatively, EPA was obtained by a similar two‐step process without the PUFA concentration step by the urea method. Direct saponification of biomass was carried out with two solvents that contained KOH for lipid saponification. An increase in yield was obtained because the problems associated with emulsion formation were avoided by separating the biomass from the soap solution before adding hexane for extraction of insaponifiables. The most efficient solvent, ethanol (96%) at 60°C for 1 h, extracted 98.3% of EPA. PUFA were concentrated by the urea method with a urea/fatty acid ratio of 4∶1 at a crystallization temperature of 28°C and by using methanol and ethanol as urea solvents. An EPA concentration ratio of 1.73 (55.2∶31.9) and a recover yield of 78.6% were obtained with methanol as the urea solvent. This PUFA concentrate was used to obtain 93.4% pure EPA by semipreparative HPLC with a reverse‐phase, C18, 10 mm i.d.×25‐cm column and methanol/water (1% acetic acid), 80∶20 w/w, as the mobile phase. Eighty‐five percent of EPA loaded was recovered, and 65.7% of EPA present inP. tricornutum biomass was recovered in highly pure form by this three‐step downstream process. Alternatively, 93.6% pure EPA was isolated from the fatty acid extract (without the PUFA concentration step) with 100% EPA recovery yield. This two‐step process increases the overall EPA yield to 98.3%, but it is only possible to obtain 20% as much EPA as that obtained by three‐step downstream processing.

Molecular dynamics of guest molecules in the channels of urea inclusion compounds investigated by means of IQNS spectroscopy

We present a brief discussion of the models describing the reorientational and translational motions of the guest molecules in the channels of urea inclusion compounds in their hexagonal phase. We discuss in particular the methodology employed to analyse the incoherent quasi-elastic neutron scattering profiles. Preliminary new results on the dynamics of n-nonanoic acid guest molecules in urea are presented and compared to the results so far obtained on n-alkane/urea and α,ω-dibromoalkane/urea inclusion compounds. These results suggest that the two types of motions of n-nonanoic acid, translations and reorientations, are not correlated at the temperatures investigated.

Molecular dynamics simulation of n-nonadecane in urea inclusion compound. I. Comparison with quasielastic neutron scattering experiment

The diffusive dynamics of n-nonadecane molecules in urea inclusion compound at 180 K are examined using molecular dynamics simulations. Incoherent quasielastic neutron scattering profiles are calculated from the simulation trajectories and compared with experiment. The effect on the calculated scattering functions of varying the model system in the simulation is examined. Interactions between alkane chains within the channels are found to strongly influence their rotational and translational dynamics and associated scattering spectra. The diffusive alkane dynamics is well described in terms of the molecules moving as rigid bodies. Analytical models of restricted translational and rotational rigid-molecule diffusion of the alkanes are fitted to the simulation-derived scattering functions in the time and energy domains. The effects of the experimental instrumental energy resolution function on the scattering functions and on the dynamical parameters obtained by fitting to the analytical models are examined. The calculations indicate that whereas the translational dynamics are converged on the time scales accessible to the experiment and the simulation, rotational motions exist that are too slow to be detected experimentally.

Molecular dynamics simulation of n-nonadecane in urea inclusion compound. II. Rotational distribution and elastic incoherent structure factor

The rotational distribution of n-nonadecane molecules around the channel axis in urea inclusion compound at 180 K is examined using molecular dynamics simulation and compared with data derived from incoherent neutron scattering experiment. The potential surface for rotation and translation of a single guest n-nonadecane molecule in a urea channel contains helical valleys. However, it is found that the incommensurate packing of the n-alkane molecules in the inclusion compound prevents their executing helical motion. The calculated rotational potential of mean force exhibits a barrier of ∼0.3 kcal/mol for transitions of the molecules between equivalent sixfold minima. The motion of the urea host molecules is coupled to that of the guest molecules which undergo jump rotational diffusion when the urea substructure is fixed in the simulation and continuous diffusion when the urea molecules are allowed to move. The elastic incoherent structure factor (EISF), which is determined by the rotational distribution of the alkane chains, is computed from the simulations and compared with experiment. When derived using the same approximations, the experimental and simulation-derived EISFs are in agreement. However, the EISF has not converged to its long-time limit in the experiment. A converged EISF is obtained from the simulation by applying appropriate averaging. The origins of the differences between the converged and experimental EISFs are discussed.

Gram-scale purification of eicosapentaenoic acid (EPA, 20:5n-3) from wetPhaeodactylum tricornutum UTEX 640 biomass

Eicosapentaenoic acid (EPA, 20:5n-3) was obtained from the microalgaPhaeodactylum tricornutum following a three-step process: fatty acid extraction by direct saponification of wet biomass, polyunsaturated fatty acid (PUFA) concentration by formation of urea inclusion compounds and EPA isolation by preparative HPLC. Direct saponification of wet biomass was carried out with KOH-ethanol (96% v:v) (1 h, 60 °C), extracting 91% of the EPA. PUFAs were concentrated by the urea method with an urea/fatty acid ratio of 4:1 at a crystallization temperature of 28 °C using methanol as the urea solvent. An EPA concentration ratio of 1.5 (55.2/36.3) and recovery of 79% were obtained. This PUFA concentrate was used to obtain 95.8% pure EPA by preparative HPLC, using a reverse-phase column (C18, 4.7 cm i.d. × 30 cm) and methanol-water (1% AcH) 80:20 w/w as the mobile phase. Ninety-seven per cent of EPA loaded was recovered and 70% EPA present in theP. tricornutum biomass was recovered in a highly pure form by means of this three-step downstream processing. In each of the HPLC preparative runs, 635 mg PUFA concentrate were loaded, obtaining 326 mg of a highly concentrated EPA fraction (2.46 g d−1). Finally, a preliminary cost statement has been calculated.

Diffuse and satellite scattering in urea inclusion compounds with various alkane molecules

Abstract X-ray diffuse scattering phenomena and satellite reflections in urea inclusion compounds with guest molecules of varying lengths (tridecane, tetradecane, pentadecane, heptadecane and a mixture of pentadecane and hexadecane) were investigated between room temperature and 30 K. It was found that diffuse s-layers, which are due to weak lateral correlations of the guest molecules, are not sharp parallel c* at room temperature as assumed previously, but show a broadening of their widths with increasing order. With decreasing temperature the widths of the s-layers decrease and become sharp within the resolution limit at very low temperature, i.e. there is an ordering of the guest molecules along the urea host tunnels. The modulations of the s-layers point towards a lateral correlation of the guest molecules at room temperature which can be described by a box-shaped distribution function. A model is described which explains the existence of (numerous) satellite reflections and satellite s-layers at low temperatures. Some of the satellites are also observable at room temperature in inclusion compounds with guest molecules longer than tetradecane. They can be assigned to a non-negligible interaction between host and guest. Possible commensurations of these satellite reflections with main (guest-) reflections have been a source of misinterpretations in the literature.

Synchrotron White Beam X-Ray Topography Characterization of Defect Structures in 2,10-Undecanedione/Urea Inclusion Compounds

Abstract The defect structure of a crystal of the urea inclusion compound (UIC) of 2,10-undecanedione was investigated using Synchrotron White Beam X-ray Topography. X-ray transmission topographs recorded from different regions show that the crystal is divided into several twin domains. Each region in the crystal is revealed on the topographs by orientation contrast arising from the mutual misorientation of adjacent regions. Using a combination of pinhole Laue pattern analysis and topographic orientation contrast analysis, the twin operation was determined to be consistent with an approximately 60° rotation about the orthorhombic c-axis. Possible twin boundary structures are also presented. Other defects such as dislocations and inclusions are also characterized.

The collected papers of albert einstein, volume 5. The swiss years: Correspondence, 1902–1914

Nervonic acid is the world's first and only potent substance that can repair damaged nerve fibers and promote nerve cell regeneration with high nutritional value. The wide variety of fatty acids in plant oils and fats with similar structures makes the large-scale separation and purification of high-purity nervonic acid very difficult. A new combined process of molecular distillation, urea inclusion and solvent crystallization was established to prepare high-purity nervonic acid with the mixed fatty acids obtained after saponification and acidification of Acer truncatum Bunge oil as raw materials. First, according to the difference in the mean free path of fatty acids, molecular distillation was used to separate and remove C16 saturated fatty acid of palmitic acid and four C18–C20 fatty acids of stearic, oleic, linoleic, and linolenic acids. The content of C16–C20 fatty acids decreased from 72.92% to 19.22% after two-stage molecular distillation processes, in which the contents of saturated fatty acid of palmitic acid decreased to about 0.5%. Then, according to the difference in carbon chain length and saturation of fatty acid, the contents of C22–C24 saturated fatty acids of tetracosanoic and docosanoic acids decreased to 0.21% and 0.07% by urea inclusion with urea/free fatty acid preparation by saponification (SPOMFs) ratio as 0.6. In addition, all saturated fatty acids were basically separated. Finally, according to the difference in the solubility of fatty acids in solvents, the C18–C20 unsaturated fatty acids of oleic, linoleic, and linolenic acids and C22 unsaturated fatty acid of erucic acid were removed by solvent crystallization. The content of C18–C20 unsaturated fatty acids decreased to less than 5% with pentanol as the solvent after the first stage solvent crystallization. The content of erucic acid decreased to 3.47% with anhydrous ethanol as the solvent after the second to fifth stage solvent crystallization. The combined process of molecular distillation, urea inclusion and low temperature crystallization innovatively adopted an efficient, simple and easy-to-industrial solvent crystallization method to separate erucic and nervonic acids, obtaining nervonic acid with purity of 96.53% and final yield of 47.99%.

Structural and dynamic properties of urea and thiourea inclusion compounds

There is currently considerable interest in the chemistry and physics of solid inclusion compounds as a consequence of the wide range of important physico-chemical properties associated with them. In part, scientific interest in these materials is motivated by the desire to compare the structural, dynamic, and chemical properties of organic “guest” molecules embedded within different crystalline environments, and to investigate how the properties of the guest molecule may be influenced by the structural characteristics of its environment. This paper is focused upon urea and thiourea inclusion compounds containing a variety of different types of organic guest molecule. Aspects of the structural and dynamic properties of these inclusion compounds have been probed using solid-state NMR spectroscopy, X-ray diffraction, EXAFS spectroscopy, incoherent quasielastic neutron scattering, Raman spectroscopy, computer simulation and mathematical modelling. On the basis of the results from these investigations, the current level of understanding of the structural and dynamic properties of these materials is assessed.

Structural and dynamic properties of urea and thiourea inclusion compounds

There is currently considerable interest in the chemistry and physics of solid inclusion compounds as a consequence of the wide range of important physico-chemical properties associated with them. In part, scientific interest in these materials is motivated by the desire to compare the structural, dynamic, and chemical properties of organic “guest” molecules embedded within different crystalline environments, and to investigate how the properties of the guest molecule may be influenced by the structural characteristics of its environment. This paper is focused upon urea and thiourea inclusion compounds containing a variety of different types of organic guest molecule. Aspects of the structural and dynamic properties of these inclusion compounds have been probed using solid-state NMR spectroscopy, X-ray diffraction, EXAFS spectroscopy, incoherent quasielastic neutron scattering, Raman spectroscopy, computer simulation and mathematical modelling. On the basis of the results from these investigations, the current level of understanding of the structural and dynamic properties of these materials is assessed.

Structure, Conformation, and Motions of Poly(ethylene oxide) and Poly(ethylene glycol) in Their Urea Inclusion Compounds

X-ray diffraction and FTIR and 13C NMR spectroscopies have been utilized to observe the inclusion compounds (ICs) formed by poly(ethylene oxide) (PEO) and low molecular weight poly(ethylene glycol) (PEG) oligomer with urea (U). We have confirmed that PEO-U-IC formed from solution has a trigonal crystal structure, while recrystallization from the melt produces a hexagonal PEO-U-IC. PEG-U-IC apparently adopts a crystal structure different from the trigonal and hexagonal forms of PEO-U-IC, and single crystals of PEG-U-IC are currently under investigation by X-ray diffraction. The conformations of PEO and PEG chains in their U-ICs appear similar to the TGT bulk crystalline conformation, while the all-trans conformer does not appear to be consistent with either the FTIR or the 13C NMR observations. For solution-formed PEO-U-IC in the trigonal crystal structure, where one-third of the urea molecules are hydrogen-bonded to the PEO chains and reside in the channels, the mobility of the included PEO chains is simi...

Structural and dynamic properties of the 1,10-dibromodecane/urea inclusion compound, investigated by variable-temperature powder X-ray diffraction, solid-state2H NMR lineshape analysis and solid-state2H NMR spin–lattice relaxation time measurements

Powder X-ray diffraction and solid-state 2H NMR lineshape analysis and spin–lattice relaxation time measurements have been used to investigate structural and dynamic properties of the 1,10-dibromodecane/urea inclusion compound. This solid has the characteristic urea ‘host’ tunnel structure of conventional urea inclusion compounds and the 1,10-dibromodecane ‘guest’ molecules are located within these tunnels.Variable-temperarture powder X-ray diffraction studies have demonstrated that a phase transition (at ca. 140–146 K) in 1,10-dibromodecane is associated with a change in the (average) symmetry of the urea tunnel structure from hexagonal (high-temperature phase) to orthorhombic (low-temperature phase) and is associated with only a minor structural distortion. From 2H NMR spectroscopy of [2H20]1,10-dibromodecane/urea, the dynamic properties of the guest molecules are best described as rotational diffusion in a six-fold cosine potential, and there is no significant discontinuity in this dynamic process at the phase-transition temperature. The results suggest that the dynamic properties of all CD2 groups in the guest molecule are indistinguishable (on the timescale of the 2H NMR technique). 2H NMR spectroscopy of 1,10-dibromodecane/[2H4]urea indicates that, at sufficiently high temperature, the urea molecules undergo 180° jumps about their CO bonds. Activation parameters have been determined for the reorientational motions of the 1,10-dibromodecane and urea molecules.The structural and dynamic properties of the 1,10-dibromodecane/urea inclusion compound, determined in this work, are compared in detail with the corresponding properties determined previously for alkane/urea inclusion compounds.

Chain End Dynamical and Conformational Properties of n-Nonadecane Molecules in Urea Inclusion Compounds: A Study by Deuterium NMR Spectroscopy

The 2H NMR spectra of selectively deuterated n-nonadecane guest molecules CD3CD2(CH2)15CD2CD3 included within the channels of urea, CO(NH2)2, have been measured between 120 K and room temperature for two orientations of the applied magnetic field with respect to the single-crystal main axis (channel axis). The spectra reveal clearly the existence of a slow reorientational process (on the 2H NMR time scale) of the whole chain in the low-temperature phase of the sample, while the chain ends perform fast torsional vibrations. On crossing the phase transition, the slow reorientational process transforms into fast uniaxial reorientations of the whole chains while a new fast dynamical process involving transitions between the tt, gt, and tg conformations is evidenced. Assuming that the amplitude of the fast torsional vibrations do not change abruptly on crossing the transition, we find an amount of gt conformers on the order of 5%, in excellent agreement with that obtained from other techniques. We also discuss and summarize the dynamical behavior of the guest n-nonadecane molecules in both the low-temperature and high-temperature phases of the urea inclusion compound, on the basis of the time windows probed by different spectroscopic techniques.

Characterization of gauche end-groups in α,ω-dibromoalkanes: vibrational properties of the 1,6-dibromohexane/urea inclusion compound

The vibrational properties of the 1,6-dibromohexane/urea inclusion compound have been investigated by Raman spectroscopy (between 90 K and room temperature) and IR spectroscopy (at room temperature). The internal vibrational modes for the urea molecules in the 1,6-dibromohexane/urea inclusion compound are similar to those for other urea inclusion compounds, consistent with the similar local structural properties of the urea molecules in these structures. However, significant structural and conformational differences are observed between the 1,6-dibromohexane/urea inclusion compound and other urea inclusion compounds. In particular, the wavenumbers of the lattice modes reflect the different crystallographic properties of these materials. In addition, the 1,6-dibromohexane molecule has two gauche end-groups in its urea inclusion compound while α,ω-CnH2nBr2 molecules in the urea inclusion compound with n > 6 are essentially ‘trans’. This material is therefore a model system for characterization of the vibrational properties of α,ω-dibromoalkane molecules in this conformation. Normal-mode calculations and force-field refinement are reported for the 1,6-dibromohexane molecule with both end-groups gauche(point group Ci).