Z-contrast imaging and ab initio study on 'd' superstructure in sedimentary dolomite

📝 Abstract

Nano-precipitates with tripled periodicity along the c-axis are observed in a Ca-rich dolomite sample from Proterozoic carbonate rocks with “molar tooth” structure. This observation is consistent with previous description of d reflections. High-angle annular dark-field STEM imaging (or Z-contrast imaging) that avoids dynamic diffraction as seen in electron diffraction and high-resolution TEM imaging modes, confirms that d reflections correspond to nanoscale precipitates aligned parallel to (001) of the host dolomite. The lamellae precipitates have a cation ordering sequence of Ca-Ca-Mg-Ca-Ca- Mg along the c direction resulting in a chemical composition of Ca0.67Mg0.33CO3. This superstructure is attributed to the extra or d reflections, thus is referred to as the d superstructure in this study. The structure can be simply described as interstratified calcite/dolomite. The crystal structure of the d superstructure calculated from density functional theory (DFT) has a space group of P31c and has a and c unit-cell parameters of 4.879 and 16.260 {\AA}, respectively, values between those of dolomite and calcite. The detailed structural characteristics and parameters obtained from ab initio calculations are also reported in this paper. The method of combining Z-contrast imaging and ab initio calculations can be used for solving structures of other nano-precipitates and nano-phases.

💡 Analysis

Nano-precipitates with tripled periodicity along the c-axis are observed in a Ca-rich dolomite sample from Proterozoic carbonate rocks with “molar tooth” structure. This observation is consistent with previous description of d reflections. High-angle annular dark-field STEM imaging (or Z-contrast imaging) that avoids dynamic diffraction as seen in electron diffraction and high-resolution TEM imaging modes, confirms that d reflections correspond to nanoscale precipitates aligned parallel to (001) of the host dolomite. The lamellae precipitates have a cation ordering sequence of Ca-Ca-Mg-Ca-Ca- Mg along the c direction resulting in a chemical composition of Ca0.67Mg0.33CO3. This superstructure is attributed to the extra or d reflections, thus is referred to as the d superstructure in this study. The structure can be simply described as interstratified calcite/dolomite. The crystal structure of the d superstructure calculated from density functional theory (DFT) has a space group of P31c and has a and c unit-cell parameters of 4.879 and 16.260 {\AA}, respectively, values between those of dolomite and calcite. The detailed structural characteristics and parameters obtained from ab initio calculations are also reported in this paper. The method of combining Z-contrast imaging and ab initio calculations can be used for solving structures of other nano-precipitates and nano-phases.

📄 Content

Z-contrast imaging and ab initio study on “d” superstructure in sedimentary dolomite
Zhizhang Shen1, Hiromi Konishi1, Izabela Szlufarska2, Philip E. Brown1, and Huifang Xu1*

1 NASA Astrobiology Institute, Department of Geoscience,
University of Wisconsin - Madison
Madison, Wisconsin 53706 2 Department of Materials Science and Engineering,
University of Wisconsin-Madison,
Madison, Wisconsin 53706

• Corresponding author: Dr. Huifang Xu Department of Geoscience, University of Wisconsin-Madison 1215 West Dayton Street, A352 Weeks Hall Madison, Wisconsin 53706 Tel: 1-608-265-5887 Fax: 1-608-262-0693 Email: hfxu@geology.wisc.edu

ABSTRACT Nano-precipitates with tripled periodicity along the c-axis are observed in a Ca-rich dolomite sample from Proterozoic carbonate rocks with “molar tooth” structure. This observation is consistent with previous description of d reflections. High-angle annular dark-field STEM imaging (or Z-contrast imaging) that avoids dynamic diffraction as seen in electron diffraction and high-resolution TEM imaging modes, confirms that d reflections correspond to nanoscale precipitates aligned parallel to (001) of the host dolomite. The lamellae precipitates have a cation ordering sequence of Ca-Ca-Mg-Ca-Ca-Mg along the c direction resulting in a chemical composition of Ca0.67Mg0.33CO3. This superstructure is attributed to the extra or d reflections, thus is referred to as the d superstructure in this study. The structure can be simply described as interstratified calcite/dolomite. The crystal structure of the d superstructure calculated from density functional theory (DFT) has a space group of P31c and has a and c unit cell parameters of 4.879 Å and 16.260 Å, respectively, values between those of dolomite and calcite. The detailed structural characteristics and parameters obtained from ab initio calculations are also reported in this paper. The method of combining Z-contrast imaging and ab initio calculation can be used for solving structures of other nano-precipitates and nano-phases.

INTRODUCTION The dolomite(R3c) structure has alternating Ca2+ and Mg2+ cation layers along the c-axis with the triangular CO3 2- anion layers lying between two cation layers. Since the size of Mg2+ ions is smaller than that of Ca2+, the CO3 2- layers are closer to Mg2+ layers. The lack of c glides in the dolomite structure due to the cation ordering causes the occurrence of extra reflections (b reflections, hℎ0l, l= odd) in dolomite diffraction patterns compared to that of calcite (a reflections only) (Reeder, 1992). Two additional reflections (c and d reflections) have been observed in natural sedimentary dolomite. Previously reported c reflections were interpreted as being a result of cation ordering within dolomite basal planes (Van Tendeloo et al., 1985). Our recent STEM work confirmed that the “c”-reflections could result from multiple diffraction between the host dolomite and twinned Mg-calcite nano-lamellae under TEM imaging and diffraction modes (Shen et al., 2013). The d reflection was first observed in Devonian dolomite samples by Wenk and Zenger (1983) and have been also found in ankerite samples (Rekesten, 1990). The d reflections occur as satellites around a and b reflections with diffraction vector ~1/3 (000l)* and are usually streaking along c* direction (Wenk and Zenger,1983; Wenk and Zhang, 1985; Van Tendeloo et al., 1985).

Dynamical diffraction in transmission electron microscopy (TEM) mode has been a major problem for structure determination as shown in previous work of analyzing “c” superstructures (Shen et al., 2013). The scanning transmission electron microscopy (STEM) method uses the high-angle annular dark-field (HAADF) detector to give the most highly localized 1s Bloch state imaging, which eliminates most of the obvious effects of dynamical diffraction (Pennycook, 2002). With the advantage of a spherical aberration corrector, the resolution of HAADF STEM or Z-contrast images is only limited by the size of the 1s Bloch state that is ~0.6-0.8 Å (Pennycook et al., 2000). The intensity of Z-contrast images is dependent on the atomic number of atoms through the ~ Z2 dependence of the Rutherford scattering cross-section, which thus provides chemical information for the material (Kirkland, 1998; Pennycook et al., 2000). A study of microstructures in natural dolomite samples using Z-contrast images may help find answers to previous observations of superstructures and explore new microstructures in dolomite.

In addition to experimental studies in mineralogy, the application of ab initio calculations of crystal structure, phase stability, and physical properties of minerals at given pressure and temperature has increased in the past few years (Ogonov et al., 2006; Barnard and Xu, 2008; Chatterjee and Saha-Dasgupta, 2010; Stackhouse et al., 2010). Density functional theory (DFT) uses the functional of electro

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