Accurate crystal structures and chemical properties from NoSpherA2

Abstract

The relationship between the structure and the properties of a drug or material is a key concept of chemistry. Knowledge of the three-dimensional structure is considered to be of such...

Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules

“…The data resolution was limited to d =0.45 Å after radiation‐damage problems were observed, which was corrected by using a scaling procedure in the software RapidAuto [44] (see more details in the Supporting Information). The crystal structure of 1 K ⋅ H 2 O was solved using ShelxT [45] and refined using olex2.refine and Tonto [46] within the NoSpherA2 framework [47] . HAR was performed on a level of theory of B3LYP/def2‐TZVP using a radius of cluster charges and dipoles of 20 Å. Anisotropic displacement parameters of hydrogen atoms of 1 were determined using the SHADE2.1 webservice, [31] and then iteratively updated in Shade in‐between HAR cycles, whereas the hydrogen atoms of the water molecule were refined with isotropic displacement parameters.…”

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

“…A few attempts of using HAR to tackle X-ray structures containing heavy metals, including relativistic effects, have been made. 10 Nevertheless, to date, only 5 structures of complexes with TM-H bonds have been successfully refined with HAR, 2,13 for only two of which a complementary neutron data set is available. Refinement of such structures demands a flexible HAR procedure, which initiated integration of HAR with Olex2, 11 such as HARt, 12 NoSPherA2 (Non-Spherical Atoms in Olex2) 13 -implementing relativistic effects and anharmonicity refinement, and DiSCaMB (Densities in Structural Chemistry and Molecular Biology) -introducing a choice of electron density partitions and also enabling relativistic effects.…”

“…10 Nevertheless, to date, only 5 structures of complexes with TM-H bonds have been successfully refined with HAR, 2,13 for only two of which a complementary neutron data set is available. Refinement of such structures demands a flexible HAR procedure, which initiated integration of HAR with Olex2, 11 such as HARt, 12 NoSPherA2 (Non-Spherical Atoms in Olex2) 13 -implementing relativistic effects and anharmonicity refinement, and DiSCaMB (Densities in Structural Chemistry and Molecular Biology) -introducing a choice of electron density partitions and also enabling relativistic effects. 14 In this study, the DiSCaMB version of HAR developed in our group (further called DiSCaMB-HAR) is challenged to refine positions and thermal motions of hydrogen atoms in 5 X-ray data sets collected for TM bound hydride complexes (CCDC refcodes: QOSZON, MIGKIY, NOBBOX, SITKUB, XAXMEP), for which also neutron data sets are available.…”

lamaGOET: an interface for quantum crystallography

“…The images were generated with the software VMD (Humphrey et al, 1996). developments in Olex2 (Fugel et al, 2018) and from connections between the tsc format of nonspherical atomic form factors (Midgley et al, 2019) and HAR inside NoSpherA2 (Kleemiss, Dolomanov et al, 2021). These NoSpherA2-related developments make quantum-crystallographic refinements as simple and user friendly as possible and aim at a broad chemical audience, whereas lamaGOET remains a quantumcrystallographic tool centred around Tonto.…”