Accurate Bond Lengths to Hydrogen Atoms from Single‐Crystal X‐ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

Abstract

Amino acid structures are an ideal test set for method‐development studies in crystallography. High‐resolution X‐ray diffraction data for eight previously studied genetically encoding amino acids are provided, complemented by a non‐standard amino acid. Structures were re‐investigated to study a widely applicable treatment that permits accurate X−H bond lengths to hydrogen atoms to be obtained: this treatment combines refinement of positional hydrogen‐atom parameters with aspherical scattering factors with constrained “TLS+INV” estimated hydrogen anisotropic displacement parameters (H‐ADPs). Tabulated invariom scattering factors allow rapid modeling without further computations, and unconstrained Hirshfeld atom refinement provides a computationally demanding alternative when database entries are missing. Both should incorporate estimated H‐ADPs, as free refinement frequently leads to over‐parameterization and non‐positive definite H‐ADPs irrespective of the aspherical scattering model used. Using estimated H‐ADPs, both methods yield accurate and precise X−H distances in best quantitative agreement with neutron diffraction data (available for five of the test‐set molecules). This work thus solves the last remaining problem to obtain such results more frequently. Density functional theoretical QM/MM computations are able to play the role of an alternative benchmark to neutron diffraction.

The robust, readily available cobalt(iii) trication [Co(NH2CHPhCHPhNH2)3]3+ is a progenitor of broadly applicable chirality and prochirality sensing agents

“…5 . The I···HN and I···N distances (2.725–2.835 Å (avg 2.767 Å) 63 – 65 and 3.612–3.712 Å (avg 3.648 Å)) are in typical ranges. 66 The closest contacts for the third iodide anion (see Fig.…”

Quantum Crystallography: Current Developments and Future Perspectives

“…[53,54] In its current implementation, molecular electron densities are theoretically calculated and afterwards partitioned using Hirshfeld's stockholder partitioning method. [108,109,134] Af uture challenge forH AR is the need of extending its applicability to large molecules (e.g.,p roteins)a nd to heavy-metals ystems (e.g.,c oordination compounds). These contain all the information from the parent wavefunction( or electron density) from which they have been partitioned.…”

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

“…In TAAM, instead of refining the parameters of atomic electron density, they are simply constrained to values typical for the corresponding atom type. The use of TAAM instead of IAM in the crystal structure refinement procedure with the standard diffraction [d min 0.83 Å , sin / = 0.6 Å À1 recommended in the crystallographic journals (Spek, 2003(Spek, , 2020] has largely improved the X-H bond lengths which became comparable to corresponding averaged neutron lengths (Dittrich et al, 2005Bendeif & Jelsch, 2007;Domagała et al, 2011;Dadda et al, 2012;Ahmed et al, 2011;Bąk et al, 2011;Dittrich et al, 2017). Other refinement parameters, such as reliability factor (R f ) and residual densities, are also improved Volkov et al, 2004;Pichon-Pesme et al, 2004;Bąk et al, 2011).…”