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Structure Elucidation of Natural Compounds by X-Ray Crystallography

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Progress in the Chemistry of Organic Natural Products 100

Part of the book series: Progress in the Chemistry of Organic Natural Products ((POGRCHEM,volume 100))

Abstract

This contribution deals with the methodology of X-ray crystallography, which offers the most powerful techniques for the elucidation of the three-dimensional structure of molecules or molecular assemblies at atomic resolution, in particular of natural products. Modern crystallography can roughly be divided into two sub-disciplines, the crystallography of “small molecules” (i.e. of molecules with molecular masses up to few thousand Daltons) and “macromolecular” crystallography (dealing with molecules or molecular assemblies above, say, 5 kDa).

Crystallography of natural compounds—be they of low molecular weight or macromolecular—offers today a wealth of techniques and technologies. Thus, the determination of a crystal structure of a low-molecular natural compound is a routine operation with alomost guaranteed success provided crystals of the substance are available. Macromolecular crystallography is much less of a routine, although even here the wealth of techniques makes it very likely that a three-dimensional structure will sooner or later be obtained provided well-diffracting crystals are at hand. The time required to perform a structure analysis has dropped dramatically during the last decades, thanks to excellent hardware (crystallization robots, synchrotrons with automatic beamlines, etc.) and software.

Virtually all structural data from single-crystal crystallographic experiments have been deposited and are available worldwide from appropriate databases (Cambridge Structural Data Base, Protein Data Bank). The amount of structural information contained in these data bases is indeed breathtaking—it constitutes a major part of the foundations of modern structural chemistry and of the molecular biosciences.

The contribution reviews available crystallographic techniques for structure analysis, describes the databases where the enormous wealth of structural information is stored and from which it can be retrieved, and discusses two more specialized techniques, i.e. time-resolved macromolecular crystallography and neutron crystallography.

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Notes

  1. 1.

    The refractive index for X-rays is very close to 1 for all known materials, and all materials absorb X-rays to some extent. However, X-ray lenses based on multilayer-systems and Fresnel zone plates are in the process of being developed for X-ray microscopy.

  2. 2.

    Such brilliant radiation sources will in fact become available in the future with the advent of free electron lasers, and imaging experiments on single molecules are indeed forseeable.

  3. 3.

    This is equivalent to the well-known Bragg equation nλ = 2d sin ϑ, where λ is the wavelength and ϑ is the angle between incoming wave and the plane of lattice points with spacing d.

  4. 4.

    Friedel’s law only holds when anomalous dispersion effects are negligible. Significant anomalous effects allow to determine the absolute configuration of molecules (36) and form the basis for a powerful set of techniques to determine the phases of macromolecular crystals (see Sect. 4).

  5. 5.

    A frequently cited criterion for atomic resolution requests that 50% of the reflections between 1.2 and 1.1 Å have to be observed above 3σ.

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Acknowledgments

UGW wants to thank Prof. Randy Read for providing his program fftimg and assisting with its implementation, and Judith Kerstner for help with the manuscript. We thank Michael Wulff for providing Fig. 31b.

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  1. Institut für molekulare Biowissenschaften, Karl Franzens Universität Graz, Humboldtstrasse 50, 8010, Graz, Austria

    Ulrike Wagner & Christoph Kratky

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  1. Ulrike Wagner
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  2. Christoph Kratky
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Correspondence to Christoph Kratky .

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  1. College of Pharmacy, The Ohio State University, Columbus, Ohio, USA

    A. D. Kinghorn

  2. Institut für Organische Chemie, Johannes-Keppler-Universität Linz, Linz, Austria

    H. Falk

  3. Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan

    J. Kobayashi

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Wagner, U., Kratky, C. (2015). Structure Elucidation of Natural Compounds by X-Ray Crystallography. In: Kinghorn, A., Falk, H., Kobayashi, J. (eds) Progress in the Chemistry of Organic Natural Products 100. Progress in the Chemistry of Organic Natural Products, vol 100. Springer, Cham. https://doi.org/10.1007/978-3-319-05275-5_1

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