On the temperature dependence of H-<i>U</i><sub>iso</sub>in the riding hydrogen model

Lübben, Jens; Volkmann, Christian; Grabowsky, Simon; Edwards, Alison J.; Morgenroth, Wolfgang; Fabbiani, Francesca P. A.; Sheldrick, George M.; Dittrich, Birger

doi:10.1107/s2053273314010626

Cited by 44 publications

(22 citation statements)

References 42 publications

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“…Temperature dependence of U H iso =U X eq ratios obtained with the TLS+INV approach. The results are in very good agreement with those from our earlier study (Lü bben et al, 2014) reporting neutron and TLS+ONIOM results. Note: H atoms with the invariom name H1c[1c1h1h] are disordered and therefore appear larger when compared with the TLS+INV model.…”

Section: Figuresupporting

confidence: 91%

Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program

Lübben¹,

Bourhis

Dittrich

2015

J Appl Cryst

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Invariom partitioning and notation are used to estimate anisotropic hydrogen displacements for incorporation in crystallographic refinement models. Optimized structures of the generalized invariom database and their frequency computations provide the information required: frequencies are converted to internal atomic displacements and combined with the results of a TLS (translation-libration-screw) fit of experimental non-hydrogen anisotropic displacement parameters to estimate those of H atoms. Comparison with TLS+ONIOM and neutron diffraction results for four example structures where high-resolution X-ray and neutron data are available show that electron density transferability rules established in the invariom approach are also suitable for streamlining the transfer of atomic vibrations. A new segmented-body TLS analysis program called APD-Toolkit has been coded to overcome technical limitations of the established program THMA. The influence of incorporating hydrogen anisotropic displacement parameters on conventional refinement is assessed.

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Section: Figuresupporting

confidence: 91%

Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program

Lübben¹,

Bourhis

Dittrich

2015

J Appl Cryst

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“…This information was not stored in the CSD and the quality of the available information strongly depends on quality of experimental data (Capelli, Bü rgi, Dittrich et al, 2014). Therefore here we decided to focus on selected data sets (23,24,49,80,81), for which analogous structures from neutron diffraction data that were measured at the same temperatures were available (Capelli, Bü rgi, Dittrich et al, 2014;Capelli, Bü rgi, Mason & Jayatilaka, 2014;Lü bben et al, 2014;Swaminathan et al, 1984;Madsen et al, 2003).…”

Section: Research Papersmentioning

confidence: 99%

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

Jha

Gruza

Kumar

et al. 2020

Acta Crystallogr Sect B

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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.

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“…Most recent work by the same authors can also rely on frequencies from lattice dynamics computations (adjusted to the X‐ray data) as a source of H‐ADPs . Correct temperature‐dependent behavior combined with automated segmented‐body TLS refinement is possible with the TLS+INV approach and the program APD‐ toolkit , and this was the route followed herein.…”

Section: Introductionmentioning

confidence: 99%

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

Dittrich

Lübben

Mebs

et al. 2017

Chemistry A European J

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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.

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On the temperature dependence of H-U_isoin the riding hydrogen model

Cited by 44 publications

References 42 publications

Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program

Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program

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

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

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On the temperature dependence of H-Uisoin the riding hydrogen model

Cited by 44 publications

References 42 publications

Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program

Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program

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

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

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On the temperature dependence of H-U_isoin the riding hydrogen model