Temperature dependence of Uiso constraints in riding hydrogen treatments

"Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of ""riding"" hydrogen atoms are frequently constrained to values of their ""parent"" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR [1], Invariom refinement [2], time-of-flight Neutron diffraction and the TLS+ONIOM approach [3]. In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations."

On the temperature dependence of H-U_iso in the riding hydrogen model

The temperature dependence of hydrogen U_iso and parent U_eq in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K.

Hirshfeld atom refinement for modelling strong hydrogen bonds

Different X-ray refinement methods for modelling hydrogen bonds in the compound L-phenylalaninium hydrogen maleate are compared. It is found that Hirshfeld atom refinement (HAR) produces bond lengths involving hydrogen atoms in agreement with benchmarking results from neutron diffraction, and it is the only X-ray method to obtain a symmetric hydrogen site in the intramolecular hydrogen bond of this compound. Residual-density distributions in HAR are better than in the multipole-based models.

Supramolecular Stark Effect in Host-Guest Complexes via Charge Density Analysis

The effect of an electric field on the vibrational spectra, the Vibrational Stark Effect (VSE), has been utilized extensively to probe the local electric field in the active sites of enzymes [1, 2]. For this reason, the electric field and consequent polarization effects induced by a supramolecular host system upon its guest molecules attain special interest due to the implications for various biological processes. Although the host-guest chemistry of crown ether complexes and clathrates is of fundamental importance in supramolecular chemistry, many of these multicomponent systems have yet to be explored in detail using modern techniques [3]. In this direction, the electrostatic features associated with the host-guest interactions in the inclusion complexes of halogenated acetonitriles and formamide with 18-crown-6 host molecules have been analyzed in terms of their experimental charge density distribution. The charge density models provide estimates of the molecular dipole moment enhancements which correlate with the simulated values of dipole moments under electric field. The accurate electron density mapping using the multipole formalism also enable the estimation of the electric field experienced by the guest molecules. The electric field vectors thus obtained were utilized to estimate the vibrational stark effect in the nitrile (-C≡N) and carbonyl (C=O) stretching frequencies of the guest molecules via quantum chemical calculations in gas phase. The results of these calculations indicate remarkable elongation of C≡N and C=O bonds due to the electric fields. The electronic polarization in these covalent bonds induced by the field manifests as notable red shifts in their characteristic vibrational frequencies. These results derived from the charge densities are further supported by FT-IR experiments and thus establish the significance of a phenomenon that could be termed as the "supramolecular Stark effect" in crystal environment.

Applications of X-ray Wavefunction Refinement

X-ray wavefunction refinement (XWR) is a way of modeling the total aspherical electron density from an X-ray diffraction experiment on a single crystal of a molecular compound. It is a combination of existing quantum-crystallographical techniques: In the first step, geometry is determined using Hirshfeld atom refinement,[1] which is based on a stockholder partitioning of quantum-mechanical aspherical electron densities. In the second step, the same wavefunction is fitted to the experimental data to reproduce the diffraction pattern and simultaneously minimize the molecular energy.[2] The XWR protocol involves embedding the molecule into a field of point charges and dipoles as well as termination strategies to avoid overfitting.[3] Results from an X-ray wavefunction refinement are not restricted to the analysis of electron density: the full reconstructed density matrix is available. Therefore, chemical problems can be tackled with suitable tools for any given question including, e.g., experimentally derived bond orders, electron-pair localisation information, or energetics. We will present first applications of this protocol for a selection of organic (hydrogen maleate salts, sulfur-containing protease inhibitors) and inorganic (siloxanes, sulfur dioxide) compounds, for which we measured high-resolution low-temperature X-ray diffraction data at various synchrotron facilities. We will show geometry improvements, anisotropic displacement parameters for hydrogens, anharmonic motion parameters for sulfur and chlorine atoms, and improved total electron-density distributions in comparison to results from multipole modeling. Moreover, we will discuss the contribution of the experimental data to the final constrained wavefunction (defect density) and demonstrate how the experimentally derived orbital-based descriptors assist in solving fundamental chemical problems.