Enhancing hydrogen positions in X-ray structures of transition metal hydride complexes with dynamic quantum crystallography.

Hirshfeld atom refinement (HAR) is a method which enables the user to obtain more accurate positions of hydrogen atoms bonded to light chemical elements using X-ray data. When data quality permits, this method can be extended to hydrogen-bonded transition metals (TMs), as in hydride complexes. However, addressing hydrogen thermal motions with HAR, particularly in TM hydrides, presents a challenge. At the same time, proper description of thermal vibrations can be vital for determining hydrogen positions correctly. In this study, we employ tools such as SHADE3 and Normal Mode Refinement (NoMoRe) to estimate anisotropic displacement parameters (ADPs) for hydrogen atoms during HAR and IAM refinements performed for seven structures of TM (Fe, Ni, Cr, Nb, Rh and Os) and metalloid (Sb) hydride complexes for which both the neutron and the X-ray structures have been determined. A direct comparison between neutron and HAR/SHADE3/NoMoRe ADPs reveals that the similarity between neutron hydrogen ADPs and those estimated with NoMoRe or SHADE3 is significantly higher than when hydrogen ADPs are refined with HAR. Regarding TM-H bond lengths, traditional HAR exhibits a slight advantage over the other methods. However, combining NoMoRe/SHADE3 with HAR results in a minor decrease in agreement with neutron TM-H bond lengths. For the Cr complex, for which high-resolution X-ray data were collected, an investigation of resolution-related effects was possible.

Hirshfeld atom refinement of metal-organic frameworks for accurate positioning of hydrogen atoms and disorder analysis.

The application of Hirshfeld atom refinement (HAR) fragmentation is demonstrated for the refinement of metal-organic framework (MOF) crystal structures. The presented method enables anisotropic refinement of imidazolate hydrogen atoms, as well as complex analysis of solvent disorder within MOF pores. The data used were derived from standard resolution in-house single crystal X-ray diffraction measurements, demonstrating that high quality structural analysis of MOFs no longer requires access to neutron or synchrotron facilities.

Hirshfeld Atom Refinement of Metal-Organic Complexes: Treatment of Hydrogen Atoms Bonded to Transition Metals.

Hydrogen positions in hydrides play a key role in hydrogen storage materials and high-temperature superconductors. Our recently published study of five crystal structures of transition-metal-bound hydride complexes showed that using aspherical atomic scattering factors for Hirshfeld atom refinement (HAR) resulted in a systematic elongation of metal-hydrogen bonds compared to using spherical scattering factors with the Independent Atom Model (IAM). Even though only standard-resolution X-ray data was used, for the highest-quality data, we obtained excellent agreement between the X-ray and the neutron-derived bond lengths. We present an extended version of this study including 10 crystal structures of metal-organic complexes containing hydrogen atoms bonded to transition-metal atoms for which both X-ray and neutron data are available. The neutron structures were used as a benchmark, and the X-ray structures were refined by applying Hirshfeld atom refinement using various basis sets and DFT functionals in order to investigate the influence of the technical aspects on the length of metal-hydrogen bonds. The result of including relativistic effects in the Hamiltonian and using a cluster of multipoles simulating interactions with a crystal environment during wave function calculations was examined. The effect of the data quality on the final result was also evaluated. The study confirms that a high quality of experimental data is the key factor allowing us to obtain significant improvement in transition metal (TM)-hydrogen bond lengths from HAR in comparison with the IAM. Individual adjustments and better choices of the basis set can improve hydrogen positions. Average differences between TM-H bond lengths obtained with various DFT functionals upon including relativistic effects or between double-ζ and triple-ζ basis sets were not statistically significant. However, if all bonds formed by H atoms were considered, significant differences caused by different refinement strategies were observed. Finally, we examined the refinement of atomic thermal motions. Anisotropic refinement of hydrogen thermal motions with HAR was feasible only in some cases, and isotropically refined hydrogen thermal motions were in similar agreement with neutron values whether obtained with HAR or with the IAM.

Accurate crystal structure of ice VI from X-ray diffraction with Hirshfeld atom refinement.

Water is an essential chemical compound for living organisms, and twenty of its different crystal solid forms (ices) are known. Still, there are many fundamental problems with these structures such as establishing the correct positions and thermal motions of hydrogen atoms. The list of ice structures is not yet complete as DFT calculations have suggested the existence of additional and - to date - unknown phases. In many ice structures, neither neutron diffraction nor DFT calculations nor X-ray diffraction methods can easily solve the problem of hydrogen atom disorder or accurately determine their anisotropic displacement parameters (ADPs). Here, accurate crystal structures of H2O, D2O and mixed (50%H2O/50%D2O) ice VI obtained by Hirshfeld atom refinement (HAR) of high-pressure single-crystal synchrotron and laboratory X-ray diffraction data are presented. It was possible to obtain O-H/D bond lengths and ADPs for disordered hydrogen atoms which are in good agreement with the corresponding single-crystal neutron diffraction data. These results show that HAR combined with X-ray diffraction can compete with neutron diffraction in detailed studies of polymorphic forms of ice and crystals of other hydrogen-rich compounds. As neutron diffraction is relatively expensive, requires larger crystals which can be difficult to obtain and access to neutron facilities is restricted, cheaper and more accessible X-ray measurements combined with HAR can facilitate the verification of the existing ice polymorphs and the quest for new ones.

Towards accurate and precise positions of hydrogen atoms bonded to heavy metal atoms.

A comparison of five X-ray structures of transition-metal-bound hydride complexes, successfully refined using Hirshfeld Atom Refinement (HAR) against low resolution X-ray diffraction data (including the positions and ADPs of all hydrogen atoms), with neutron structures shows that using aspherical atomic scattering factors instead of spherical ones results in systematic elongation of metal-hydrogen bonds, which in the case of the highest-quality data leads to excellent agreement of the X-ray and the neutron-derived bond lengths.

Correction: Towards accurate and precise positions of hydrogen atoms bonded to heavy metal atoms.

Correction for 'Towards accurate and precise positions of hydrogen atoms bonded to heavy metal atoms' by Magdalena Woinska et al., Chem. Commun., 2021, 57, 3652-3655, DOI: 10.1039/D0CC07661A.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB, 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

Bond energy, aromatic stabilization energy and strain in IPR fullerenes.

Various models applied to DFT structures and energies of 2-D and 3-D aromatic molecules shed new light on the effects of strain and aromaticity in these systems. The cyclic pi electron delocalisation does not stabilize the fullerene C60 formation; and 5-6 and 6-6 CC bonds have near-identical bond stretch potentials.