Structural Determination of Biogenic Crystals Using 3D Electron Diffraction
Fig. 1: Experimental diffraction data obtained with the ELDICO ED-1 show excellent agreement with the simulated data
Biogenic crystals are naturally occurring crystalline materials formed by living organisms. Examples include calcium oxalate crystals in plants, magnetite crystals in bacteria and animals, and various biominerals in the human body. Because of their important biological functions, they are a major focus of scientific research. However, their complexity and sensitivity make them difficult to analyze.
Determining the structures of biogenic molecular crystals is particularly challenging. The crystals can easily be damaged during extraction and are generally available only in small quantities, with sizes ranging from just a few nanometers to several micrometers. Conventional techniques such as single-crystal X-ray diffraction (SC-XRD) and powder X-ray diffraction (PXRD) therefore often reach their limits.
| Sample | Fish | Spider | Scallop |
| Resolution [Å] | 0.67 | 0.67 | 0.80 |
| Reflections | 5155 | 6019 | 2289 |
| Completeness [%] | 87.4 | 97.7 | 80.2 |
| R1(all refl.) | 0.195 | 0.278 | 0.446 |
| R1[I>2δ(I)] | 0.177 | 0.241 | 0.374 |
| wR2 (all refl.) | 0.537 | 0.540 | 0.735 |
| Goodness of fit | 2.43 | 2.03 | 3.01 |
Refinement details for the β-polymorph of guanine
Electron Diffraction
Three-dimensional electron diffraction (3D ED), also known as microcrystal electron diffraction (MicroED), has advanced rapidly in recent years.
Unlike X-ray diffraction, 3D ED uses electrons, which interact much more strongly with matter. This makes it possible to analyze crystals with volumes up to 106 times smaller than those required for X-ray diffraction—even within mixtures of different crystals. As a result, samples previously regarded simply as powders can be analyzed as individual single crystals.
ELDICO ED-1
The ELDICO ED-1—the world’s first dedicated electron diffractometer—was developed to analyze nanometer-sized crystallites under ambient or cryogenic conditions. With minimal electron exposure of less than 0.01 e- Å-² s-¹ and selective illumination of the region of interest, the system is particularly well suited for beam-sensitive materials such as organic crystals.
Case Study: Guanine Crystals in Spider Integument, Fish Scales, and Scallop Eyes
In collaboration with scientists from Ben-Gurion University of the Negev, Cardiff University, and the applications team at ELDICO Scientific AG, biogenic guanine crystals isolated from fish scales, spider integument, and scallop eyes were investigated [1]. The results are presented in the table and were taken from the paper by Hirsch et al. [2].
The 3D ED data enabled the direct localization of hydrogen atoms and the refinement of the β-guanine crystal structure beyond the previously published model.
These findings provide important insights into biogenic crystals and their potential use in sustainable, biocompatible optical applications. Key advantages of the ELDICO ED-1 include:
- Straightforward data acquisition
- Ab initio structure solution
- Unconstrained structure refinement
- No need for a pure compound; data can be collected directly from the raw material
- Precise electrostatic potential maps enabling the direct localization of hydrogen atoms
[1] Wagner, A.; Merkelbach, J.; Samperisi, L.; Pinsk, N.; Kariuki, B. M.; Hughes, C. E.; Harris, K. D. M.; Palmer, B. A. Cryst. Growth Des. 2024, 24, 899–905. doi.org/10.1021/acs.cgd.3c01290.[2] Hirsch, A.; Gur, D.; Polishchuk, I.; Levy, D.; Pokroy, B.; Cruz-Cabeza, A. J.; Addadi, L.; Kronik, L.; Leiserowitz, L. “Guanigma”: The Revised Structure of Biogenic Anhydrous Guanine. Chem. Mater. 2015, 27, 8289–8297.
