Conventional refinement strategies used for three-dimensional electron diffraction (3D ED) data disregard the bonding effects between the atoms in a molecule by assuming a pure spherical model called the Independent Atom model (IAM) and may lead to an inaccurate or biased structure. Here we show that it is possible to perform a refinement going beyond the IAM with electron diffraction data. We perform kappa refinement which models charge transfers between atoms while assuming a spherical model. We demonstrate the procedure by analysing five inorganic samples; quartz, natrolite, borane, lutecium aluminium garnet, and caesium lead bromide. Implementation of kappa refinement improved the structure model obtained over conventional IAM refinements and provided information on the ionisation of atoms. The results were validated against periodic DFT calculations. The work presents an extension of the conventional refinement of 3D ED data for a more accurate structure model which enables charge density information to be extracted.

1 Institute for Theoretical Physics Universität Hamburg Hamburg Germany

Biological and Chemical Research Centre University of Warsaw Warsaw Poland

Faculty of Mathematics and Physics Charles University Prague Czech Republic

Institute of Physics of the Czech Academy of Sciences Prague Czech Republic

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Gemmi, M. et al. 3D Electron diffraction: The nanocrystallography revolution. PubMed DOI PMC

Kolb, U., Gorelik, T. & Otten, M. T. Towards automated diffraction tomography. Part II—Cell parameter determination. PubMed DOI

Gemmi, M. & Oleynikov, P. Scanning reciprocal space for solving unknown structures: energy filtered diffraction tomography and rotation diffraction tomography methods.

Boullay, P., Palatinus, L. & Barrier, N. Precession electron diffraction tomography for solving complex modulated structures: the case of Bi5Nb3O15. PubMed DOI

Jones, C. G. et al. The cryoEM method microED as a powerful tool for small molecule structure determination. PubMed DOI PMC

Zhang, D., Oleynikov, P., Hovmöller, S. & Zou, X. Collecting 3D electron diffraction data by the rotation method. DOI

Yuan, S. et al. Ti8Zr2O12(COO)16] Cluster: An ideal inorganic building unit for photoactive metal-organic frameworks. PubMed DOI PMC

Cichocka, M. O., Ångström, J., Wang, B., Zou, X. & Smeets, S. High-throughput continuous rotation electron diffraction data acquisition via software automation. PubMed DOI PMC

Ge, M., Zou, X. & Huang, Z. Three-dimensional electron diffraction for structural analysis of beam-sensitive metal-organic frameworks. PubMed DOI

Yörük, E., Klein, H. & Kodjikian, S. Dose symmetric electron diffraction tomography (DS-EDT): Implementation of a dose-symmetric tomography scheme in 3D electron diffraction. PubMed DOI

Plana-Ruiz, S. et al. Fast-ADT: A fast and automated electron diffraction tomography setup for structure determination and refinement. PubMed DOI

Sheldrick, G. M. Crystal structure refinement with SHELXL. PubMed DOI PMC

Wan, W., Sun, J., Su, J., Hovmöller, S. & Zou, X. Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing. PubMed DOI PMC

Clabbers, M. T. B., Gruene, T., Parkhurst, J. M., Abrahams, J. P. & Waterman, D. G. Electron diffraction data processing with DIALS. PubMed DOI PMC

Burla, M. C. et al. Crystal structure determination and refinement via SIR2014. DOI

Palatinus, L. et al. Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. PubMed DOI

Palatinus, L. & Chapuis, G. SUPERFLIP – a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions. DOI

Petříček, V., Palatinus, L., Plášil, J. & Dušek, M. Jana2020 – a new version of the crystallographic computing system Jana. DOI

Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, Ja. K. & Puschmann, H. OLEX2: a complete structure solution, refinement and analysis program. DOI

Guillot, B., Viry, L., Guillot, R., Lecomte, C. & Jelsch, C. Refinement of proteins at subatomic resolution with MOPRO. DOI

Zou, X. et al.

None

Hammond, C.

Palatinus, L., Petříček, V. & Corrêa, C. A. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. PubMed DOI

Palatinus, L. et al. Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data. PubMed DOI

Klar, P. B. et al. Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data. PubMed DOI PMC

Genoni, A. et al. Quantum crystallography: Current developments and future perspectives. PubMed DOI

Guillot, B., Jelsch, C. & Macchi, P. in

Gruza, B., Chodkiewicz, M. L., Krzeszczakowska, J. & Dominiak, P. M. Refinement of organic crystal structures with multipolar electron scattering factors. PubMed DOI PMC

Hansen, N. K. & Coppens, P. Testing aspherical atom refinements on small-molecule data sets. DOI

Stewart, R. F. Electron population analysis with rigid pseudoatoms. DOI

Kulik, M. & Dominiak, P. M. Electron density is not spherical: the many applications of the transferable aspherical atom model. PubMed DOI PMC

Jha, K. K. et al. Multipolar atom types from theory and statistical clustering (MATTS) data bank: restructurization and extension of UBDB. PubMed DOI PMC

Pichon-Pesme, V., Lecomte, C. & Lachekar, H. On building a data bank of transferable experimental electron density parameters applicable to polypeptides. DOI

Brock, C. P., Dunitz, J. D. & Hirshfeld, F. L. Transferability of deformation densities among related molecules: atomic multipole parameters from perylene for improved estimation of molecular vibrations in naphthalene and anthracene. DOI

Nelyubina, Y. V., Korlyukov, A. A., Lyssenko, K. A. & Fedyanin, I. V. Transferable aspherical atom modeling of electron density in highly symmetric crystals: A case study of alkali-metal nitrates. PubMed DOI

Malinska, M. & Dauter, Z. Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data. PubMed DOI PMC

Jelsch, C., Pichon-Pesme, V., Lecomte, C. & Aubry, A. Transferability of multipole charge-density parameters: Application to very high resolution oligopeptide and protein structures. PubMed DOI

Jelsch, C. et al. Accurate protein crystallography at ultra-high resolution: Valence electron distribution in crambin. PubMed DOI PMC

Olech, B., Brázda, P., Palatinus, L. & Dominiak, P. M. Dynamical refinement with multipolar electron scattering factors. PubMed DOI PMC

Lippmann, T. et al. Charge-density analysis of YBa2Cu3O6.98. Comparison of theoretical and experimental results. PubMed DOI

Koritsánszky, T. et al. Accurate experimental electronic properties of DL-proline monohydrate obtained within 1 Day. PubMed DOI

Schmøkel, M. S. et al. Atomic properties and chemical bonding in the pyrite and marcasite polymorphs of FeS2: a combined experimental and theoretical electron density study. DOI

Avilov, A., Lepeshov, G., Pietsch, U. & Tsirelson, V. Multipole analysis of the electron density and electrostatic potential in germanium by high-resolution electron diffraction. DOI

Wu, J. S. & Spence, J. C. H. Structure and bonding in alpha-copper phthalocyanine by electron diffraction. PubMed DOI

Friis, J., Jiang, B., Spence, J., Marthinsen, K. & Holmestad, R. Extinction-free electron diffraction refinement of bonding in SrTiO3. PubMed DOI

Wu, L., Meng, Q. & Zhu, Y. Mapping valence electron distributions with multipole density formalism using 4D-STEM. PubMed DOI

Coppens, P. et al. Net atomic charges and molecular dipole moments from spherical-atom X-ray refinements, and the relation between atomic charge and shape. DOI

Brázda, P., Klementová, M., Krysiak, Y. & Palatinus, L. Accurate lattice parameters from 3D electron diffraction data. I. Optical distortions. PubMed DOI PMC

Pastero, L., Turci, F., Leinardi, R., Pavan, C. & Monopoli, M. Synthesis of α-Quartz with controlled properties for the investigation of the molecular determinants in silica toxicology. DOI

Simpson, P. G. & Lipscomb, W. N. MOLECULAR STRUCTURE OF B18H22. PubMed DOI PMC

Londesborough, M. G. S. et al. Distinct photophysics of the isomers of B18H22 explained. PubMed DOI

King, R. B. Three-dimensional aromaticity in polyhedral boranes and related molecules. PubMed DOI

Cerdán, L., Braborec, J., Garcia-Moreno, I., Costela, A. & Londesborough, M. G. S. A borane laser. PubMed DOI

Guter, G. A. & Schaeffer, G. W. THE STRONG ACID BEHAVIOR OF DECABORANE. DOI

Heřmánek, S. & Plotová, H. Chemistry of boranes. XXII. The acidity of boranes. DOI

Hamilton, E. J. M. et al. A stacking interaction between a bridging hydrogen atom and aromatic π density in the n-B18H22–benzene system. PubMed DOI

Olsen, F. P., Vasavada, R. C. & Hawthorne, M. F. The chemistry of n-B18H22 and i-B18H22. DOI

Londesborough, M. G. S. et al. Effect of iodination on the photophysics of the laser borane anti-B18H22: generation of efficient photosensitizers of oxygen. PubMed DOI

Møller, C. K. Crystal structure and photoconductivity of Cæsium plumbohalides. DOI

Euler, F. & Bruce, J. A. Oxygen coordinates of compounds with garnet structure. DOI

Kulik, M., Chodkiewicz, M. L. & Dominiak, P. M. Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank. PubMed DOI PMC

Mott., S. N. F. & Massey, S. H. S. W.

Stevens, E. D., DeLucia, M. L. & Coppens, P. Experimental observation of the effect of crystal field splitting on the electron density distribution of iron pyrite. DOI

Coppens, P. X-Ray diffraction and the charge distribution in transition metal complexes. DOI

Farrugia, L. J. & Evans, C. Experimental X-ray charge density studies on the binary carbonyls Cr(CO)6, Fe(CO)5, and Ni(CO)4. PubMed DOI

Farrugia, L. J., Evans, C., Lentz, D. & Roemer, M. The QTAIM approach to chemical bonding between transition metals and carbocyclic rings: A combined experimental and theoretical study of (η5-C5H5)Mn(CO)3, (η6-C6H6)Cr(CO)3, and (E)-{(η5-C5H4)CF═CF(η5-C5H4)}(η5-C5H5)2Fe2. PubMed DOI

Stokkebro Schmøkel, M., Overgaard, J. & Brummerstedt Iversen, B. Experimental electron density studies of inorganic materials. DOI

Zhurov, V. V., Zhurova, E. A. & Pinkerton, A. A. Chemical bonding in cesium uranyl chloride based on the experimental electron density distribution. PubMed DOI

Pant, A. K. & Stevens, E. D. Experimental electron-density-distribution study of potassium iron disulfide, a low-dimensional material. PubMed DOI

Bats, J. W. & Fuess, H. Deformation density in complex anions. III. Potassium perchlorate. DOI

Yeh, S. K., Wu, S. Y., Lee, C. S. & Wang, Y. Electron-density distribution in a crystal of dipotassium tetrafluoronickelate, K2NiF4.

Děcká, K. et al. Scintillation response enhancement in nanocrystalline lead halide perovskite thin films on scintillating wafers. PubMed DOI PMC

Jan Pejchal et al. Luminescence and scintillation properties of Mg-codoped LuAG:Pr single crystals annealed in air. DOI

Brázda, P., Palatinus, L. & Babor, M. Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal. PubMed DOI

Erba, A. et al. CRYSTAL23: A Program for computational solid state physics and chemistry. PubMed DOI PMC

Lee, C., Yang, W. & Parr, R. G. Development of the colle-salvetti correlation-energy formula into a functional of the electron density. PubMed DOI

Becke, A. D. Density‐functional thermochemistry. III. The role of exact exchange. DOI

Vilela Oliveira, D., Laun, J., Peintinger, M. F. & Bredow, T. BSSE-correction scheme for consistent gaussian basis sets of double- and triple-zeta valence with polarization quality for solid-state calculations. PubMed DOI

Blaha, P. et al. WIEN2k: An APW+lo program for calculating the properties of solids. PubMed DOI

Mott, N. F. & Bragg, W. L. The scattering of electrons by atoms.