Crystalline Urea Research Articles

Determination of the electron localization function from electron density

Approximate determination of electron localization function (ELF) from electron density and its first and second derivatives is described. It is demonstrated that the second-order gradient expansion of the kinetic energy density yields the modified ELF, which exhibits all the features characterizing electron pairing. Calculations based on the accurate electron densities derived from X-ray diffraction data carried out for crystalline magnesium oxide, chlorine and urea: they demonstrate that the ELF reveals important peculiarities of crystal architecture.

Polar Assembly of 2,6-Diethynylpyridine through C(sp2)–H···N, C(sp)–H···π and π–π Stacking Interactions: Crystal Structure and Nonlinear Optical Properties

Abstract The crystallization of 2,6-diethynylpyridine 1 leads to C(sp2)–H···N hydrogen bonded head-to-tail tapes which are held together by C(sp)–H···π hydrogen bridges to form 2D polar sheets; further assembly through π–π stacking interaction results in 3D polar crystals which show intense powder SHG response, 5-fold stronger than crystalline urea.

Hydrogen bonding in urea

The hydrogen bond consisting of a hydrogen atom positioned asymmetrically between a nitrogen and an oxygen atom $(\mathrm{N}---\mathrm{H}\ensuremath{\cdot}\ensuremath{\cdot}\ensuremath{\cdot}\mathrm{O})$ plays a central role in the structure and functionality of proteins and amino acids. The urea crystal is a simple system in which such a hydrogen bond exists. We have measured Compton profile anisotropies in crystalline urea which reveal subtle modulations linked to this chemical bond. The data presented here have sufficient statistical accuracy to isolate features arising from intermolecular interaction which is weak in urea and consequently difficult to detect experimentally.

Oriented n-Alkanes in urea-d4 Inclusion Complexes for Inelastic Neutron Scattering Vibrational Studies

Crystalline urea inclusion complexes (UIC) formed with urea-d4 and hexadecane are used to orient the n-alkane relative to a neutron beam for inelastic neutron scattering studies. Deuteration of the host lattice makes it nearly transparent for neutron studies. Comparison of the results for UIC orientation parallel and perpendicular to the neutron beam permits separation of the low frequency vibrational spectrum into those vibrations that are parallel to the alkane long axis and those perpendicular to the long axis.

Crystal engineering using very short and linear C(sp)–H⋯N hydrogen bonds: formation of head-to-tail straight tapes and their assembly into nonlinear optical polar crystals

The crystallization of 4-ethynylpyridine (1) and 4-(4-ethynylphenyl)ethynylpyridine (2) leads to C(sp)-H⋯N hydrogen bonded straight tapes that further assemble into polar crystals, in the case of 2, and show intense powder SHG response, 8 times more efficient than crystalline urea.

Electron correlation in large molecular systems using the atomic orbital formalism. The case of intermolecular interactions in crystalline urea as an example

Electron correlation in large molecular systems using the atomic orbital formalism. The case of intermolecular interactions in crystalline urea as an example

A Combined Experimental and Theoretical 17O NMR Study of Crystalline Urea: An Example of Large Hydrogen-bonding Effects

We report the first experimental determination of the carbonyl 17O electric-field-gradient (EFG) tensor and chemical-shift (CS) tensor of a urea-type functional group, R1NHC(O)NHR2. Analysis of magic-angle spinning (MAS) and stationary 17O NMR spectra of crystalline [17O]urea yields not only the principal components of the carbonyl 17O EFG and CS tensors, but also their relative orientations. The carbonyl 17O quadrupole coupling constant (QCC) and the asymmetry parameter (η) in crystalline urea were found to be 7.24 ± 0.01 MHz and 0.92, respectively. The principal components of the 17O CS tensor were determined: δ11 = 300 ± 5, δ22 = 280 ± 5 and δ33 = 20 ± 5 ppm. The direction with the least shielding, δ11, is perpendicular to the CO bond and the principal component corresponding to the largest shielding, δ33, is perpendicular to the NC(O)N plane. The observed 17O CS tensor suggests that, in crystalline urea, the 17O paramagnetic shielding contributions from the σ → π* and π → σ* mixing are greater than t...

Electron correlation in large molecular systems using the atomic orbital formalism. The case of intermolecular interactions in crystalline urea as an example

Electron correlation in large molecular systems using the atomic orbital formalism. The case of intermolecular interactions in crystalline urea as an example

Density functional calculations of the structure of crystalline urea under high pressure

The geometry of the urea crystal is optimized for several different pressures using a pseudopotential density functional (DFT) approach with a plane-wave basis set and the Ceperley–Alder local density correlation potential. All the optimized intra- and intermolecular geometrical parameters, as well as the lattice vectors, are found to be in good agreement with experiment. Under high pressures, the crystal changes anisotropically; the lattice constants a and b reduce by almost 10 times more with the pressure than the constant c. Changes of the geometrical parameters within the molecule as a function of the external pressure are found to be in good agreement with the donor–acceptor theory.

Electron-density-based calculations of intermolecular energy: case of urea.

The intermolecular interaction energy in crystalline urea has been calculated both from diffraction data and from the Hartree-Fock crystalline electron-density distribution, using a modified atom-atom approximation scheme. The electrostatic part of this energy has been calculated from the atomic multipole moments, obtained by adjustment of the multipole model to experimental X-ray and to theoretical Hartree-Fock structure amplitudes. To obtain the induction energy, multipole moments were calculated from structure amplitudes for the crystalline electron density and from those that refer to the electron density of a superposition of isolated molecules. This worked well for the calculation of the interaction energy from Hartree-Fock data (6% difference from the sublimation-energy value), but not for the interaction energy from experimental data, where the moments of the superposition have to come from Hartree-Fock calculations: the two sets of multipole moments are far too different. The uncertainty of the phases of the structure amplitudes, combined with systematic errors in the theoretical data and noise in the experimental values, may account for the discrepancies. The nature of the different contributions to intermol-ecular interactions for urea is examined.

The design of a molecularly selective capillary based on an incommensurate intergrowth structure

A general design strategy for a molecularly selective capillary is proposed, based on the properties of incommensurate intergrowth materials. The strategy is illustrated for urea inclusion compounds, in which guest molecules are contained within one-dimensional tunnels in a crystalline urea host structure. It is shown that net transport of guest molecules in one direction along the tunnel can be achieved by inserting new guest molecules at one end of the crystal (by dipping it into the liquid phase of another potential guest), with the original guest molecules expelled from the other end. Such phenomena have considerable potential as the basis of highly selective micro-scale separation techniques, based on discrimination of molecular size, shape and chirality.

Vibrational Analysis of Urea

Although a lot of work has been done on the vibrational analysis of urea, there still remain some contradictions and uncertainties, mainly due to interpretation of the vibrational spectrum of crystalline urea based on force field calculations on isolated urea instead of on urea in its crystal phase. We have shown that this approach is not allowed in the case of urea. The vibrational spectrum of urea was interpreted by measuring the solid state infrared spectra of eight isotopomers of urea at room temperature and at −196 °C, and Raman spectra at room temperature and at −120 °C, and of a urea−water solution. Force field calculations from our recently published article on isolated urea and on urea in its crystal structure, at the Hartree−Fock level with a 6-31++G** basis set, were also used. We have also shown that high-pressure measurements using a “diamond anvil cell” are not useful by performing a vibrational analysis.

Treatment with crystalline ultra-pure urea reduces the aggregation of integral membrane proteins without inhibiting N-terminal sequencing.

We have demonstrated that N-terminal sequencing can be performed successfully despite boiling protein samples in the presence of urea under precise conditions, before loading them onto SDS-PAGE and transfer to polyvinylidene difluoride membrane. Using myoglobin as a test protein, we found that its ability to undergo N-terminal sequencing was not affected by the presence of urea provided "ultra-pure" urea was used. Consistent with this result, we verified that urea did not carbamylate myoglobin since its molecular mass was measured by mass spectrometry after electroelution of the protein band from the gel. These observations are useful for the study of integral membrane proteins, in particular to study their topology from proteolysis experiments, since heating in the presence of urea before SDS-PAGE reduces membrane protein aggregation [Soulié, S., Mo/ller, J.V., Falson, P., and le Maire, M. (1996) Anal. Biochem. 236, 363-364]. We show that the sequencing yield of a hydrophobic peptide from reticulum Ca2+-ATPase was more than doubled in the presence of urea in accord with the quantification of the Coomassie Blue staining of the gel and of the amount present on the polyvinylidene difluoride membrane. For three peptides of the gastric H+K+-ATPase, the sequencing yield after urea treatment increased almost threefold.

Computational investigation of surface structural relaxation in crystalline urea

The effects of surface structural relaxation on the energetic and morphological properties of crystalline urea have been investigated. Specifically, the {001}, {110}, {200}, {101}, {111} and {[graphic ommitted]} surfaces have been considered. Upon relaxation of the cleaved surfaces, significant perturbations in the positions and internal geometries of the molecules (compared with the corresponding positions in the bulk crystal structure) are observed. Interestingly, the {[graphic ommitted]} surface has a lower surface energy than the {111} surface, and thus a polar morphology is predicted. The predicted crystal shape is compared with that observed experimentally (for crystals grown by deposition from the vapour phase), and reasons for discrepancies between the calculated and experimental morphologies are discussed.

Crystal field effects on the topological properties of the electron density in molecular crystals: The case of urea

The Quantum Theory of Atoms in Molecules, due to Bader, is applied to periodic systems. Results for molecular and crystalline urea are presented. Changes in both bond critical points and atomic properties due to changes of chemical environment are described. A rationale for the different lengths of the in-plane and out-of-plane hydrogen bonds and for the lengthening of the CO bond in bulk urea is provided in terms of the properties of the Laplacian of the oxygen atom electron density distribution. An evaluation of molecular and atomic volume changes indicates that the decrease of molecular volume upon change of phase from gas to solid originates primarily from a contraction of the atomic basins directly involved in hydrogen bonds. Other atoms show a small expansion. The considerable decrease of oxygen and hydrogen atomic volumes is related to the mutual penetration of their van der Waals envelopes following hydrogen bond formation. The results confirm that urea is more polar in the solid phase.

Adsorption ofn-Paraffin Wax from Isooctane Solution on Crystalline Urea

ABSTRACT Equilibrium isotherms and kinetics of adsorption of n-paraffin wax from isooctane solution on crystalline urea were obtained at 50 and 70°C and at 50, 70, and 90°C, respectively. The equilibrium data were correlated according to the Polanyi potential theory, which provided a single characteristic curve of the experimental data at two temperatures. The batch kinetic data suggest that the adsorption of n-paraffin wax on crystalline urea is diffusion controlled. Effective diffusion coefficients derived from fractional uptake versus time were in the order of 10−14 to 10−13 cm2/s. The apparent activation energies of diffusion decreased with increasing uptake, as expected.

Interfaces between a Saturated Aqueous Urea Solution and Crystalline Urea: A Molecular Dynamics Study

Interfaces between a saturated urea solution and crystalline urea surfaces have been studied by means of molecular dynamics simulations. Mean densities of solute urea and water at both (001) and (110) interfaces show an enhanced adsorption probability for solute urea compared to water. Orientation distributions and positions in the horizontal plane have been calculated for urea molecules in the first adsorption layer. These indicate a preorganization for growth of a new crystal layer at the (001) interface. The adsorbed urea molecules at the (110) interface, on the other hand, are much more randomly distributed and oriented than at the (001) interface and even show a slight preference for wrong positions above the crystal surface. This indicates an increased interfacial entropy which may stabilize the (110) crystal surface.

The adsorption of long-chain n-paraffin from isooctane solution on crystalline urea

The adsorption of long-chain n-paraffin from isooctane solution on crystalline urea

Production of high-quality liquid fertilizers from wet-process acid via urea phosphate

A pilot-plant process is described that purifies wet-process phosphoric acid for the production of a high-quality urea-ammonium polyphosphate base solution. An intermediate product, crystalline urea phosphate, is produced from urea and merchant-grade (54% P2O5) wet-process phosphoric acid. The urea phosphate crystals contain only about 15 to 20% of the objectionable impurities (iron, aluminum, and magnesium) originally contained in the feed wet-process acid. The urea phosphate crystals are pyrolyzed, converting orthophosphate to polyphosphate with very little energy consumption. The resulting melt is dissolved and neutralized with ammonia to produce 14-29-0 liquid product of high polyphosphate content.

Large local-field effects in the second-harmonic susceptibility of crystalline urea.

The linear-optical response and the nonlinear susceptibility for second-harmonic generation are calculated for crystalline urea within band theory using the Kohn-Sham local-density approximation, implemented with pseudopotentials and plane waves. In the low-frequency limit, the static dielectric constants are found to be 2.03 (ordinary) and 2.14 (extraordinary), vs 2.17 and 2.49, respectively, for the experimental values. For second-harmonic generation, Kleinmann symmetry is invoked to consider a single independent tensor component, ${\mathit{d}}_{14}$=${\mathit{d}}_{36}$. The calculated value is 1.1 pm/V, compared to an experimental value of 1.2\ifmmode\pm\else\textpm\fi{}0.1 pm/V for ${\mathit{d}}_{36}$. Without local-field corrections, d would have been 2.1 pm/V. Hence, nonlinear local-field corrections are a key element of this calculation.