TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

Abstract

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min 0.83 Å ) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

Accurate crystal structures and chemical properties from NoSpherA2

“…Since the format file underlying NoSpherA2 is entirely general, interfacing Olex2 with other flavors of X-ray non-spherical structure refinement is simple and straightforward. First tests have been made for the HAR-ELMO method 39 and the multipole databank software Discamb 29 . Moreover, any of these kinds of non-spherical structure refinement are not restricted to Xradiation.…”

“…Multipole parameters are then transferred from the databank to the compound under investigation, and non-spherical atomic form factors are calculated for use in the refinement on the fly from the transferred multipole populations. Although such refinements produce, e.g., better structural parameters for hydrogen atoms, 29 they are currently restricted to organic and bio-organic compounds, for which the number of atom types is manageable. A simplification to only dipole level for chemical bonds is now also implemented in the ShelXL software.…”

On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model

“…TAAM refinement has also been avalaible for many years now through multipolar model related software programs (Volkov et al, 2004(Volkov et al, , 2006Hü bschle et al, 2007;Jelsch et al, 2005;Petricek et al, 2014). It has recently been implemented in the software library DiSCaMB (Chodkiewicz et al, 2018) and interfaced to OLEX2 (Jha et al, 2020).…”

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

“…For bond types common in organic compounds, mean X-H bond lengths obtained with HAR are underestimated by 0.01-0.02 Å compared to the neutron values, 2 which on average results only in a 0.014 Å difference. 4 HAR also enables refinement of anisotropic displacement parameters (ADPs) of hydrogen atoms, with the proviso that the HAR ADPs are less accurate than the ones derived from neutron diffraction or estimated with other methods. 2,5 Transition metal (TM) bound hydrides pose a challenge for X-ray crystallography.…”