Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

Abstract

X-ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host-guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X-ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light-atom-only crystal. Atomic displacement parameters obtained independently from the X-ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Å(2) indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host-guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host-guest interaction (e.g., in protein-drug complexes), at least for polar molecules.

Electron Density Studies in Materials Research

“…This wasc onfirmed in the second study of the hydroquinone with acetonitrile included. [94] The acetonitrile molecules order in the cavities and decreaset he symmetry of the structure, but in all cases, they align along the three-fold symmetry axisw ith the electronegative nitrogen reaching furthest into the positive region of the EP as expected from the unperturbed EP.H owever,i tw as shown that the guest molecule polarizes the host structure,w hich leads to as ignificant change in the EP around the host molecule and an increase in the EF by an order of magnitude in the center of the cavity (Figure 8). These changes couldn ot be attributedt ot he changes in geometry of the host, and therefore it was concluded that the mutual electrostatic interactions perturb the electronic structure of the host.…”

“…In this Review,w eh ave as hown aw ide range of materials problems, where analysis of the ED have gained information beyondt he structure. Important examples that we have described in detail are the analysis of the Zintl concept in thermoelectric materials,w hich is not alwaysv alid as assumed, [31] the ionicity of bondingi ne lemental boron, [39,40] the new emerging class of high pressure electrides, [71][72][73] the mutual electric polarization in host-guest structures, [93][94] andt he magnetic interaction pathways in coordination polymers. [77,79,81,83,84] Thus, there is definitely valuable informationi nt he ED not directly contained in the structure of a material.…”

“…In two publications, Clausen et al studied the empty apohost of the b-hydroquinone organic clathrate [93] and the same clathratew ith acetonitrile as guest molecule. [94] From the ED of the apohost, it wass hown that the EP at the centero ft he cavity was close to zero and increasing on moving towards the host structure. This suggestst hat molecules will align with their electropositive regionsa tt he centero ft he cavity and the electronegative regions along the three-fold inversion axis through the cage.…”

Intermolecular Interaction Energies in Hydroquinone Clathrates at High Pressure

“…Inclusion of the larger acetonitrile guest molecule results in a significant change in the host framework, namely, a shorter aaxis (15. host centering of the HQ/MeCN structure (h − k + l ≠ 3n), 37 while the full structure and space group symmetry, P3, was established almost 60 years later by Clausen et al 38 In the latter crystallographic study, the collection of high quality data at both synchrotron and neutron facilities was used in combination with theoretical calculations to model the guest ordering. 38 The study revealed that in any cavity channel all acetonitrile molecules are oriented in the same direction. However, there are three crystallographically different MeCN molecules, and thus cavity channels in the crystal structure and the orientation of MeCN are reversed in one of these three.…”

Contemporary X-ray electron-density studies using synchrotron radiation

“…Evaluation of the EP was also employed by Clausen et al (2011Clausen et al ( , 2014 in the study of guest-host effects in -hydroquinone frameworks, by the introduction of polar molecules into the cavities of the structure. For the empty framework a feature articles (Left) Experimental electrostatic potential (EP) of C 60 F 18 mapped onto the ED isosurface at = 0.8 e Å À3 .…”