Electron Microscopy of Ammonium Urate Crystallization under Tautomerism

The molecular structure of Amonium Urate crystals is here identified with transmission electron microscopy. This material shows an extremely high sensitivity to the beam and special adjustments are required regarding the electron dose. A complete electron microscopy characterization is achieved together with image analysis by using a rather low dose mode and in an aberration corrected electron microscope so as to achieve atomic resolution and a good spatial resolution. Synthesis of the samples is related to crystallization of tautomeric molecules [1]. The use of foreign species as modifiers in natural, biological, and synthetic crystallization is a common regulatory mechanism for tailoring the growth of diverse materials. The structure and/or composition of a modifier differ from a solute molecule but often contains similar functional motifs that facilitate molecular recognition for modifier binding to crystal surfaces. One class of modifiers that has yet to be realized is tautomers, or structural isomers where the dynamic interconversion between solute and its corresponding tautomer(s) produces native modifiers that self-inhibit crystal growth. Crystallization of tautomeric molecules plays a central role in the development of pharmaceutical and biological drugs and materials with diverse optical, magnetic, electrical, and chemical properties. Tautomerism is a ubiquitous phenomenon in nature widely presented in many small organics and bio-macromolecules such as peptides, nucleic acids, and proteins. These naturally forming structural isomers undergo interconversions via intramolecular relocation of atoms, most commonly hydrogens (i.e. prototropic tautomerism). Unlike constitutional isomers or stereoisomers, tautomer interconversion in solution is less rapid than conformers, but faster than that of functional, skeletal, cis-/trans-, enantiomer, or position isomers. NH4HU crystals have been prepared as a reference condition at a pH of 11 in order to determine structure [1]. High-resolution TEM has been performed at the TEAM 1.0 electron microscope from the Molecular Foundry at 80 keV and in low dose conditions of 10 e-/Å2s. Image series are used at a definite focus (near Scherzer defocus). The stability of the sample can be preserved only for 10 images and an exposure time of 1 s. A total dose (∼ 100 Å-2) can be accumulated before any detectable structure changes take place by using a low dose rate together with a resolution of 1.4 Å. All images are aligned and processed using the MacTempass software package. The image alignment is performed with sub-pixel accuracy. Straight and bent crystals or nanorods have been investigated. Fig. 1 shows images of straight crystals at different magnifications. Fig. 1a shows a panoramic view of the nanorods. Fig. 1b shows the image with visible contrast after overlapping of 10 experimental images taken in low dose conditions. The contrast is sufficient to follow the crystalline arrangement of the urate nanorod that has not been modified by the e-beam interaction. Fig. 1c gives an Inverse Fourier Transform (IFFT) image. The IFFT image shows discontinuities that can be interpreted as linear defects or dislocations, similar to inorganic crystals. Fig. 1d shows a direct image after the image treatment procedure of overlapping 10 experimental images. The circle marks a site in the sample with several linear discontinuities in the crystalline structure i.e., dislocations. Fig. 2 shows details of a bent urate crystal. Bent crystals are rather common features in this material. The interference that give rise to the high resolution images is related to molecular arrangements involving different atoms of C, H, N and they form a crystalline structure with linear defects or dislocations as shown in Fig. 2a shows a relatively lower magnification image after overlapping 10 images at the same defocus value. The imaged area is relatively large but still some features of the ordered crystalline arrangement can be seen. Fig. 2b shows a smaller area with the crystalline structure of the nanorods, the image is rather clear with respect to the molecular ordering and the different types of linear defects that can be observed. In Figs. 2c and 2d two different areas are shown with a clearer view of the crystalline distribution of molecules in the material. In these two cases, the IFFTs are presented. They are produced by using masks on the corresponding FFTs. They show lattice distortions off the molecular arrangements in addition to the dislocations [2]. (a) Overview of a straight crystal. (b) Image of the straight crystal after overlapping 10 experimental images in low dose, the contrast is sufficient to fallow the crystalline arrangement of molecules in the nanorod. (c) IFFT image of (b), the crystalline arrangement shows discontinuities or linear defects similar to dislocations in materials. (d) Section of a nanorod with dislocations, the circle marks sites of linear defects in the crystalline structure in this direct HREM image. Curved urate nanorods. (a) Relatively large area of a curved nanorod with different types of defects. (b) Section of (a) showing the crystalline arrangement in the selected nanorod. (c) Inverse Fourier transform (IFFT) of (b) showing more clearly the different types of molecular arrangements and defects in this rod. (d) IFFT of a neighboring area showing additional molecular arrangements.