Deuteron NMR studies of guest motion in alkanoic acid urea inclusion compounds

Protein dynamics in the solid-state from 2H NMR lineshape analysis. III. MOMD in the presence of Magic Angle Spinning

We report on a new approach to the analysis of dynamic NMR lineshapes from polycrystalline (i.e., macroscopically disordered) samples in the presence of Magic Angle Spinning (MAS). This is an application of the Stochastic Liouville Equation developed by Freed and co-workers for treating restricted (i.e., microscopically ordered) motions. The ²H nucleus in an internally-mobile C-CD₃ moiety serves as a prototype probe. The acronym is ²H/MOMD/MAS, where MOMD stands for "microscopic-order-macroscopic-disorder." The key elements describing internal motions - their type, the local spatial restrictions, and related features of local geometry - are treated in MOMD generally, within their rigorous three-dimensional tensorial requirements. Based on this representation a single physically well-defined model of local motion has the capability of reproducing experimental spectra. There exist other methods for analyzing dynamic ²H/MAS spectra which advocate simple motional modes. Yet, to reproduce satisfactorily the experimental lineshapes, one has either to use unusual parameter values, or combine several simple motional modes. The multi-simple-mode reasoning assumes independence of the constituent modes, features ambiguity as different simple modes may be used, renders inter-system comparison difficult as the overall models differ, and makes possible model-improvement only by adding yet another simple mode, i.e., changing the overall model. ²H/MOMD/MAS is free of such limitations and inherently provides a clear physical interpretation. These features are illustrated. The advantage of ²H/MOMD/MAS in dealing with sensitive but hardly investigated slow-motional lineshapes is demonstrated by applying it to actual experimental data. The results differ from those obtained previously with a two-site exchange scheme that yielded unusual parameters.

Diffusional behavior and guest conformational analysis of hexadecane-1,16-diol and hexadecane in urea crystal model via molecular dynamics simulation approach

Diffusion at the atomic or molecular level is a source of many physical, chemical, and biological processes taking place in plentiful materials. This work is an endeavor toward investigating the diffusional behavior of two different type of guests, hexadecane-1,16-diol and hexadecane enclathration in urea tunnel architecture, whereby the correlation of the diffusion mechanism with the guest's structural and conformational properties is explored. To carry out this study, molecular dynamics simulation approach is adopted. It is found that hexadecane-1,16-diol exhibit slower diffusion with an average diffusion coefficient value [Formula: see text], where hexadecane diffuse more rapidly with an average diffusion coefficient value [Formula: see text]. It is also observed that the structural properties influence the guest's travel distance and torsion angle distribution of the trans and gauche conformational proportion. Furthermore, the observed high energy barrier accounted for hexadecane-1,16-diol and low energy barrier for hexadecane along urea tunnel systems was analyzed. The comparison of our obtained results are in close agreement with the available experimental measurements, i.e., gauche proportion properties between two different guest molecules correlate well with Raman spectroscopy investigation on α,ω-dihalogenoalkane/urea inclusion compounds. Our calculations also successfully endorse the structure-property relation between the two systems.

Behavioral pattern exploration of single guest, hexadecane-1,16-diol and hexadecane in urea inclusion compounds via molecular dynamics simulation

The urea inclusion compounds, a unique polar organic crystalline complex, are considered as a potential candidate for a molecular separator of long chain alkane molecule. A well-defined structure of the crystalline channel systems constructed from hydrogen bonding arrangement of the urea molecules, can be used to understand the fundamental aspects of the processes involving ions or molecules transportation. To do so, in our work, molecular dynamics approach is implemented to understand the behavioral pattern of the hexadecane-1,16-diol and hexadecane guests’ related to translational and rotational orientation along the urea tunnel. Our obtained results reveal that high interaction of hexadecane-1,16-diol with urea host molecules offers a restricted environment inside urea tunnel, resulting in slowing down the guest movement. Hexadecane guest system, on the contrary, exhibits lower interaction whereby the translational and rotational movement is faster. Moreover, as the distance increases (along [Formula: see text]-axis) in the urea tunnel, both guest systems favor a clockwise rotational orientation. Preference of the respected orientation indicates the influence of chiral urea tunnel on achiral guests that is clathrate inside the tunnel structure.

In-plane pyridinium cation reorientation in bis-thiourea chloride, bromide and iodide: quasielastic neutron scattering combined with molecular dynamics simulations

We have studied the dynamics of bis-thiourea pyridinium chloride and bromide by means of quasielastic neutron scattering (QENS). The QENS data allow describing the geometry of the in-plane motion of the pyridinium cation and reveal that it is similar to the motion previously observed in bis-thiourea pyridinium iodide. Molecular dynamics (MD) simulations have been performed to investigate the cation dynamics on the high temperature phase of the full series of compounds: bis-thiourea pyridinium chloride, bromide and iodide. Three different models of intermolecular potential have been tested and the agreement between the simulated and experimental elastic incoherent structure factors (EISFs) is used to select the more realistic one. The detailed analysis of the MD results indicates that Coulombic interactions together with the formation of hydrogen bonds between the pyridinium cation and the host sublattice influence strongly the geometry of the in-plane cation reorientation.

Molecular dynamics simulation of cation dynamics in bis-thiourea pyridinium nitrate inclusion compound

Molecular dynamics simulations have been performed on the high temperature phase of the bis-thiourea pyridinium nitrate inclusion compound. Three different potential models have been tested. In the three cases, the analysis of the centre of mass motion of pyridium cations indicates that they do not diffuse along the channels. However, only the potential including a specific hydrogen bonding interaction provides a description of the in-plane cation reorientation in reasonable agreement with the experimental results deduced from quasielastic neutron scattering (QENS) measurements. This model shows that the pyridinium cation reorients among three non-equivalent positions and gives reorientational correlation times comparable to those extracted from the QENS data. We conclude that the particular geometry of this reorientation is due to the formation of hydrogen bonds of different strength between the pyridinium cation of the guest sublattice and the host sublattice.

The structural and dynamic properties of 1-bromodecane in urea inclusion compounds investigated by solid-state (1)H, (13)C and (2)H NMR spectroscopy

For asymmetric guest molecules in urea, the end-groups of two adjacent guest molecules may arrange in three different ways: head-head, head-tail and tail-tail. Solid-state (1)H and (13)C NMR spectroscopy is used to study the structural properties of 1-bromodecane in urea. It is found that the end groups of the guest molecules are randomly arranged. The dynamic characteristics of 1-bromodecane in urea inclusion compounds are probed by variable-temperature solid-state (2)H NMR spectroscopy (line shapes, spin-spin relaxation: T2 , spin-lattice relaxation: T1Z and T1Q) between 120 K and room temperature. The comparison between the simulation and experimental data shows that the dynamic properties of the guest molecules can be described in a quantitative way using a non-degenerate three-site jump process in the low-temperature phase and a degenerate three-site jump in the high-temperature phase, in combination with the small-angle wobbling motion. The kinetic parameters can be derived from the simulation.

Investigation of multiaxis molecular motion by off-magic angle spinning deuteron NMR

The relatively new deuteron NMR method of off-axis-magic angle spinning (OMAS) has been extended and used to investigate multiaxis rotational jump motion. Floquet theory is developed for simulating deuteron OMAS spectra with multisite jumps at different rates about noncoincident axes, and efficient procedures are presented for computing the sideband line shapes. It is demonstrated experimentally that reproducible adjustment of the angle between the rotor axis and the static magnetic field is feasible with precision approaching +/- 0.01 degrees. This leads to the reintroduction of a scaled, first-order quadrupole coupling that defines a new kinetic window and makes deuteron OMAS much more sensitive than ordinary magic angle spinning to motion on the kilohertz time scale. Temperature-dependent deuteron OMAS line shapes of octanoic acid/urea-d4 inclusion compound have been recorded and fitted, using least-squares procedures, to provide rates of rotation about both CN and CO bonds. The Arrhenius activation parameters for rotation about CN bonds, Ea = 60.4+/-2.4 kJ/mol and ln(A) = 24.9+/-0.3, agree well with previous values determined by selective inversion experiments. However, OMAS yields Ea = 26.3+/-0.4 kJ/mole and ln(A) = 24.9+/-0.3 for whole-body rotation about the CO bond axis in contrast to previous analysis of static quadrupole echo (QE) line shapes which gave Ea = 22.3+/-0.3 kJ/mole and ln(A) = 24.8+/-0.6 for the same sample. The underlying homogeneous linewidths of OMAS spectra are much smaller than those of QE spectra, and this provides higher precision and less systematic error in the determination of rates.