SHADE3server: a streamlined approach to estimate H-atom anisotropic displacement parameters using periodicab initiocalculations or experimental information

Abstract

A major update of the http://shade.ki.ku.dk (http://shade.ki.ku.dk) is presented. In addition to all of the previous options for estimating H‐atom anisotropic displacement parameters (ADPs) that were offered by SHADE2, the newest version offers two new methods. The first method combines the original translation–libration–screw analysis with input from periodic ab initio calculations. The second method allows the user to input experimental information from spectroscopic measurements or from neutron diffraction experiments on related structures and utilize this information to evaluate ADPs of H atoms. Tools are provided to set up the ab initio calculations and to derive the internal motion from the calculations. The new server was tested on a range of compounds where neutron diffraction data were available. In most cases, the results are significantly better than previous estimates, and for strong hydrogen bonds in proton sponges, the ab initio calculations become crucial.

Experimental evidence of a 3-centre, 2-electron covalent bond character of the central O–H–O fragment on the Zundel cation in crystals of Zundel nitranilate tetrahydrate

“…The lenghts of the O-H bonds in water and Zundel molecules were restrained to 0.983(2) Å. The thermal motion of the hydrogen atoms were modelled as anisotropic, their ADPs being constrained to values calculated by the SHADE3 server 25 .…”

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

“…There are various tools available for estimation of hydrogen ADPs. These are, for example, the segmented-body translation libration screw (TLS) refinement method along with Invariom approach used in the ADP-toolkit program (Lü bben et al, 2015), or the SHADE method using ADPs from neutron experiments to approximate hydrogen ADPs and available from the SHADE web server (Madsen et al, 2003;Madsen & Hoser, 2014). It was also shown that for sub-atomic resolution X-ray data of exceptional quality, the multipolar model with polarized hydrogen atoms and additional bond-directed dipoles also lead to hydrogen ADPs close to the neutron values (Zhurov et al, 2011).…”

A method to estimate statistical errors of properties derived from charge-density modelling

“…The MoPro program has numerous functionalities with respect to constraints, restraints and similarity applying to the stereochemistry and charge density. For the H atoms, the values of anisotropic U ij parameters were fixed to those obtained from the SHADE3 server (Madsen & Hoser, 2014). The H-X distances of H atoms were restrained to the values obtained from neutron diffraction studies (Allen & Bruno, 2010) with a restraint sigma rest of 0.01 Å .…”