Cryo-tomography and 3D Electron Diffraction Reveal the Polar Habit and Chiral Structure of the Malaria Pigment Crystal Hemozoin.

Detoxification of heme in Plasmodium depends on its crystallization into hemozoin. This pathway is a major target of antimalarial drugs. The crystalline structure of hemozoin was established by X-ray powder diffraction using a synthetic analog, ß-hematin. Here, we apply emerging methods of in situ cryo-electron tomography and 3D electron diffraction to obtain a definitive structure of hemozoin directly from ruptured parasite cells. Biogenic hemozoin crystals take a striking polar morphology. Like ß-hematin, the unit cell contains a heme dimer, which may form four distinct stereoisomers: two centrosymmetric and two chiral enantiomers. Diffraction analysis, supported by density functional theory analysis, reveals a selective mixture in the hemozoin lattice of one centrosymmetric and one chiral dimer. Absolute configuration has been determined by morphological analysis and confirmed by a novel method of exit-wave reconstruction from a focal series. Atomic disorder appears on specific facets asymmetrically, and the polar morphology can be understood in light of water binding. Structural modeling of the heme detoxification protein suggests a function as a chiral agent to bias the dimer formation in favor of rapid growth of a single crystalline phase. The refined structure of hemozoin should serve as a guide to new drug development.

Quantitative three-dimensional local order analysis of nanomaterials through electron diffraction.

Structure-property relationships in ordered materials have long been a core principle in materials design. However, the introduction of disorder into materials provides structural flexibility and thus access to material properties that are not attainable in conventional, ordered materials. To understand disorder-property relationships, the disorder - i.e., the local ordering principles - must be quantified. Local order can be probed experimentally by diffuse scattering. The analysis is notoriously difficult, especially if only powder samples are available. Here, we combine the advantages of three-dimensional electron diffraction - a method that allows single crystal diffraction measurements on sub-micron sized crystals - and three-dimensional difference pair distribution function analysis (3D-ΔPDF) to address this problem. In this work, we compare the 3D-ΔPDF from electron diffraction data with those obtained from neutron and x-ray experiments of yttria-stabilized zirconia (Zr0.82Y0.18O1.91) and demonstrate the reliability of the proposed approach.

Optimal estimated standard uncertainties of reflection intensities for kinematical refinement from 3D electron diffraction data.

Estimating the error in the merged reflection intensities requires a full understanding of all the possible sources of error arising from the measurements. Most diffraction-spot integration methods focus mainly on errors arising from counting statistics for the estimation of uncertainties associated with the reflection intensities. This treatment may be incomplete and partly inadequate. In an attempt to fully understand and identify all the contributions to these errors, three methods are examined for the correction of estimated errors of reflection intensities in electron diffraction data. For a direct comparison, the three methods are applied to a set of organic and inorganic test cases. It is demonstrated that applying the corrections of a specific model that include terms dependent on the original uncertainty and the largest intensity of the symmetry-related reflections improves the overall structure quality of the given data set and improves the final Rall factor. This error model is implemented in the data reduction software PETS2.

Characterizing modulated structures with first-principles calculations: a unified superspace scheme of ordering in mullite.

The benefit of computational methods applying density functional theory for the description and understanding of modulated crystal structures is investigated. A method is presented which allows one to establish, improve and test superspace models including displacive and occupational modulation functions from first-principles calculations on commensurate structures. The total energies of different configurations allow one to distinguish stable and less stable structure models. The study is based on a series of geometrically optimized superstructures of mullite (Al4+2xSi2-2xO10-x) derived from the superspace group Pbam(α0½)0ss. Despite the disordered and structurally complex nature of mullite, the calculations on ordered superstructures are very useful for determining the ideal Al/Si ordering in mullite, extracting atomic modulation functions as well as understanding the SiO2-Al2O3 phase diagram. The results are compared with experimentally established models which confirm the validity and utility of the presented method.

Exploiting superspace to clarify vacancy and Al/Si ordering in mullite.

Synchrotron single-crystal X-ray diffraction has revealed diffuse scattering alongside sharp satellite reflections for different samples of mullite (Al4+2x Si2-2x O10-x ). Structural models have been developed in (3+1)-dimensional superspace that account for vacancy ordering and Al/Si ordering based on harmonic modulation functions. A constraint scheme is presented which explains the crystal-chemical relationships between the split sites of the average structure. The modulation amplitudes of the refinements differ significantly by a factor of ∼3, which is explained in terms of different degrees of ordering, i.e. vacancies follow the same ordering principle in all samples but to different extents. A new approach is applied for the first time to determine Al/Si ordering by combining density functional theory with the modulated volumes of the tetrahedra. The presence of Si-Si diclusters indicates that the mineral classification of mullite needs to be reviewed. A description of the crystal structure of mullite must consider both the chemical composition and the degree of ordering. This is of particular importance for applications such as advanced ceramics, because the physical properties depend on the intrinsic structure of mullite.