Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

Abstract

Nonspherical cages in inclusion compounds can result in non-uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO(2) molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO(2) guests in terms of a polar angle theta and azimuth angle phi and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO(2) sI clathrate. The experimental (13)C NMR lineshapes of CO(2) guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the (13)C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.

Rotational and translational dynamics of CO2 adsorbed in MOF Zn2(bdc)2(dabco)

“…Details of this method including the corresponding transformation matrices are described by Alavi [34]. Subsequently, the shift tensor was averaged over all molecular orientations using the probability density p(q,4) as obtained from the MD simulations.…”

A molecular dynamics study of ethanol–water hydrogen bonding in binary structure I clathrate hydrate with CO2

“…The 13 C NMR lineshape measurements 26 and molecular dynamics simulations 13 show that CO 2 molecules are oriented preferably in the equatorial plane of the cages as the cages have a large radius in this direction.…”

“…For non-or weakly hydrogen bonding guests in the clathrate hydrate phase, the decay of the M 1 (t) and M 2 (t) functions are described in terms of double exponential decay functions with decay times τ 1 and τ 2 , 13, 27…”

“…2). For linear molecules, the equatorial direction of the cages is found to be the preferred direction of orientation of the molecules 13 and so it is of interest to determine (i) whether hydrogen bonding occurs between the ethanol guests and the cage waters in this compact cage, and (ii) whether the hydrogen bonding occurs with the water molecules of the pentagonal faces in the equatorial plane or the water molecules of the hexagonal faces in the polar direction.…”

Understanding a Host–Guest Model System through 129Xe NMR Spectroscopic Experiments and Theoretical Studies

“…Several simulations of host-guest complexes, including those of cryptophanes, [13][14][15] C 60 , [16][17][18] and clathrates, [19,20] have been performed by quantum chemistry or molecular dynamics. None of them elucidated the nature of the host-guest interaction or the origin of the xenon chemical shift.…”