What is the most significant result of this study?This study showst hat in quantumc rystallography (QCr) an amalgamationb etweent heory and experiment leads to improvedp roperties. These geometrico re lectron-density properties are in better agreement with the measured data and simultaneously with benchmarking high-level theory than alternative methods that model the X-ray diffraction data. In fact, the reason for being in better agreement with the experiment is that more sophisticated theory is used in the modeling. It is important to realizet hat it is not ac ontradiction that more theory leads to better agreement with the experiment, but it is the very nature of the modeling process. Astudy that validates X-ray wavefunction refinement (XWR) as aQ Cr technique for modeling X-ray diffraction data was missingu ntil now.F rom now on it is not only ac laim anymore that QCr methods are a moderna lternative to established multipole or independent atom models of X-ray diffraction data analysis. Did serendipity play apart in this work?In this study,s erendipity did not play any role. The study had been planned over years and was designed to fulfil the purpose of validating X-ray wavefunction refinement. Te st compounds and data sets werer ationally selected to cover ar ange from lower quality to highest quality data to probe the performance of the methods compared. In place of serendipity, perseveranceo ft he first authorD r. Woinska played an important role in finishing the study,w hich generateda ne normousThe front cover artwork is provided by the group of Prof. Krzysztof Woźniak, Dr.P aulina M. Dominiak, and Dr.M agdalena Woiń ska. The image showsX -ray wavefunction refinement as am ethod of electrond ensity reconstruction (symbolized by a jigsaw puzzle), which allows to obtain accurate and precise molecular geometries as wella sp ropertieso fe lectrond ensity, and to perform data quality evaluations. Read the full text of the article at
Correction for ‘Towards accurate and precise positions of hydrogen atoms bonded to heavy metal atoms’ by Magdalena Woińska et al., Chem. Commun., 2021, 57, 3652–3655, DOI: 10.1039/D0CC07661A.
Multipole expansion of electron density distribution is an efficient tool for evaluating the energy of interactions in molecules. In as much as atoms in macromolecules such as peptides are modeled with certain types of atoms derived from small organic molecules, investigating transferability of atomic multipoles for various partitions of molecular electron density is an important issue. In this study, multipole moments up to hexadecapoles for types of atoms present in selected amino acids, as well as di- and tripeptides composed of these amino acids, are computed using three density partitions: Hansen-Coppens aspherical pseudoatoms formalism, Hirshfeld's stockholder partition, and Bader's atoms in molecules theory. Electron density of relevant molecules is derived in a procedure including molecular wave function ab initio calculation for isolated molecules in geometry from X-ray measurements, calculation of theoretical structure factors for molecules put in a pseudocubic cell, and multipole refinement as in crystallographic data processing and computation of multipoles. The results were compared to calculations of multipole moments in AIM and in stockholder density partitions obtained directly from molecular wave functions. The presented comparison does not point unambiguously to any particular influence of multipole refinement on moments obtained from these two partitions. The advantage of stockholder partitioning in terms of transferability of atomic multipoles is affirmed. AIM and pseudoatoms provide slightly less transferable multipoles of lower order. Higher rank of multipole expansion reveals a transferability improvement in the case of AIM and meaningful deterioration for pseudoatoms.
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 transitionmetal-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 standardresolution X-ray data was used, for the highest-quality data, we obtained excellent agreement between the X-ray and the neutronderived 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.
Figure 1. High pressure can alter the dimensionality of the magnetic exchange in Cu-pyz based quantum magnets. Thick lines represent magnetic exchange pathways and different colours indicate H-bonds-, pyz-or X-mediated interactions, (in red, blue and green, respectively).
Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using HartreeFock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints -even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogenatom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å 2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements -an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å .
The application of Hirshfeld atom refinement (HAR) fragmentation method is demonstrated for the refinement of metal-organic framework (MOF) crystal structures. The presented method enables anisotropic refinement of imidazolate hydrogen atoms,...
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