Some examples of how to use theoretical crystal structure data in the ICSD
D. Zagorac, J. Zagorac, A. Steudel, S. Rehme
The Inorganic Crystal Structure Database (ICSD) is the world’s largest database of fully evaluated and published crystal structure data, mostly obtained from experimental results. However, the purely experimental approach is no longer the only route to discover new compounds and structures. Numerous computational methods for simulating and predicting structures of inorganic solids have emerged, creating a large amount of theoretical crystal data (1). In the following text, we will show some examples on how to use theoretical data in the ICSD, and for more details about methodology, standardization, and classification, as well as specific applications, we refer the reader to the corresponding reference (1) and the ICSD web page (2).
Maybe one of the most important examples for the experimental ICSD users is the use of the theoretical category: predicted (non-existing) crystal structure. As crystal structure predictions become more and more reliable, this category can be an excellent tool for synthesis planning. In particular, obtaining information on not-synthesized unknown compounds or/and not-synthesized modifications of known compounds could be an important advantage for ICSD users with numerous scientific, technological, and industrial applications. Here, we show that most of the theoretical structures (3860 CIF files) are predicted and waiting to be synthesized (Table 1). Of course, we would like to note that predicted structures have a time restriction since each of the predicted structures is evaluated and categorized within the publication year. On the other hand, many theoretical structures remain non-synthesized many years after publication. Search for new (not-yet synthesized) structures or materials can be more precise if the user combines search with standardized keywords in the ICSD. An example of such a search in the ICSD using keywords for materials with a potential application in the field of batteries is given in the reference (3), narrowing the search to less than a hundred predicted (non-existing) crystal structures.
Table 1: Number of theoretical crystal structures (CIF files) in the ICSD Desktop (2019.2)
Next, we will show some examples of how to use optimized and combined structures from Table 1. Optimized (or existing) crystal structures are theoretically calculated structures of existing experimental crystal structures in the ICSD. In experimental materials science and related sciences, they can be used as an excellent tool for industrial and technological applications where it is very important to fine-tune materials because slight deviations between the calculation and experiment can lead to different properties of the material (1). In computational materials science and related sciences, optimized structures can be used for method development and to generate parameters for future calculations. In the following text, we show one such example.
At the beginning of the search, the user should choose theoretical structures (red circle, Fig. 1). In the next step, the user should choose experimental information (green circle, left) and from the drop-down menu, should choose the Calculation Method (green circle, center). There are in total 16 theoretical categories that can be used in the search (1). Let’s assume that the user is interested to generate parameters for his future PAW calculations, which are quite common. Then the user should select the Projector augmented wave (PAW) method and Optimized (existing) crystal structure and click on the Count Experimental Info Search. This search will result in 1324 theoretical CIF files. The results show that it is a very popular method (1324/2461 CIF files, Table 1), however not easy to extract data from such large data sets. Thus, the user is pointed to the Comment field (green circle), where the user can search for additional computational information used in the calculation of the respective theoretical crystal structures. This computational information provides details about the code, search algorithm, method, basis set information, and technical details of the calculation (e.g. cutoff energy, K-point mesh, etc.), providing information on reproducibility and quality of computations (1, 2). Finally, the user should type the theoretical details of interest, e.g. Cutoff energy 400 eV (Fig. 1), and click on the Count Experimental Info Search. This will result in 182 theoretical structures (black circle) feasible for further analysis and data mining.
Optimized structures are an excellent tool for various applications, and maybe one of the most interesting is the combination of optimized structures with standardized keywords. This searches can involve properties of materials (electronic, magnetic, optical, etc.), or the use of keywords combined with, for example, chemical (elements) or structural (structure types) information easily enables searches for special materials like superconductors or piezoelectric materials or technical applications like solar cells or solid electrolytes (1, 3). In the following examples, we will show how to search the ICSD for nanostructures.
Figure 2: Example of how to search the ICSD for theoretical nanostructures (ICSD Desktop 2019.2) - Part one.
The user should choose theoretical structures at the beginning of the search (red circle, Fig.2). In the next step, the user should choose experimental information (green circle, left) and from the drop-down menu, should choose the Calculation Method (green circle in Fig. 1). Then the user should select the Optimized (existing) crystal structure, and click on the Count Experimental Info Search. This search will result in 2461 theoretical CIF files (green circle, Fig. 2). The user is now directed to the Bibliography section (blue circle on the left, Fig. 2), where the user can search for bibliographic information. In the (standardized) Keyword field (blue circle, middle, Fig. 2) the user should type: Nano, and click on the Count Bibliography Search. This search will result in 625 theoretical CIF files in total (blue circle, right), and 404 theoretical CIF files of a combined keyword search with optimized structures (black circle, Fig.2). Finally, the user should click on the Run Query button and proceed to further analysis in Figure 3.
Figure 3a shows the first ten results of the 404 theoretical CIF files made of combined keyword search (Nano) and optimized structures. At first glance, most of these structures look like experimentally known elemental or binary compounds, with not so much interest in material science or nanotechnology. However, if we take a deeper look, and select one of the structures from the list, we will observe very interesting nanostructures. In the following example, the first structure from the list has been chosen as elemental Mo with known bcc structure (Fig. 3a). As a result, the user will find structural data and other relevant (bibliographic) information. The abstract of the manuscript where the example Mo structure has been published is shown in figure 3b. Lin et al. (4) show predicted structures of Mo nanowires, which do not possess the bcc configuration found in bulk Mo material. In this example, we show the way to find predicted nanostructures via known optimized crystal structures. We would like to note that the complex field of nanotechnologies often uses known optimized bulk structures (like molybdenum), for investigations of not related nanostructures, which can result in storing multiple Mo bulk structures in the ICSD, but with various additional nanostructures in different manuscripts. On the other hand, Schönecker et al. (5) predicted metastable cubic and tetragonal crystal phases of transition metals, and, their first cobalt structure (among others) listed in Fig. 3a has been used as a thin film, where the thickness and composition of the substrate have been varied within the same manuscript.
Figure 3: Example of how to search the ICSD for theoretical nanostructures (ICSD Desktop 2019.2) - Part two. a) the first ten results of the search made combining standardized keyword (nano) and optimized structures; b) the abstract of the manuscript by Lin et al. in RSC Adv. (4), where the example Mo structure has been published. Reproduced from Ref. (4) with permission from The Royal Society of Chemistry.
Search for nanostructures can be even further examined by including experimental nanostructures. This can be performed by using the theoretical category: the combination of theoretical and experimental structure (Table 1). If such data exist in the manuscript they are highly valuable to all materials scientists with a great variety of possible applications, owing to the high precision of the published data. The user should use the same procedure as explained in the example with optimized (existing) theoretical structures (Fig.2), only should choose the combination of theoretical and experimental structure in the field Calculation Method (Fig. 2). This search will result in 1368 theoretical CIF files, while the Bibliography Search will result in the same 625 theoretical CIF files in
Figure 4: Example on how to search the ICSD for combined theoretical and experimental nanostructures (ICSD Desktop 2019.2); a) the first ten results of the search made combining standardized keyword (nano) and theoretical category: the combination of theoretical and experimental structure; b) the abstract of the manuscript by Zhang et al. in RSC Adv. (6), where the example rutile (TiO2) structure has been published. Reproduced from Ref. (6) with permission from The Royal Society of Chemistry.
total. However, now by combining the results, there are 96 crystal structures of experimental and theoretical data with nanostructures. Similarly, the user should click on the Run Query button and proceed to further analysis in Figure 4.
Figure 4a shows the first ten results of the 96 crystal structures of experimental and theoretical data with nanostructures made of combined keyword search (nano) and theoretical category ‘combination of theoretical and experimental structure’. Similarly to the previous example, we need to select one of the structures from the list to observe interesting experimental and theoretical nanostructures. In the following example, the first TiO2 structure has been chosen with a well-known rutile structure (Fig. 4b). The abstract of the manuscript where the example rutile structure has been published is shown in figure 4b. Zhang et al. (6) show density functional theory (DFT) and experimental studies of caffeic acid adsorption on zinc oxide and titanium dioxide nanoparticles. In such a way, we show how to search for experimental and theoretical data on nanoparticles and nanorods using bulk zinc oxide and titanium dioxide data (CIF files) and the ICSD database.
1) Zagorac, D., Müller, H., Ruehl, S., Zagorac, J. & Rehme, S. (2019). Recent developments in the Inorganic Crystal Structure Database: theoretical crystal structure data and related features. J. Appl. Cryst., 52, 918-925, 10.1107/S160057671900997X.
4) Lin, K.-H., Liao, B.-Y., Ju, S.-P., Lin, J.-S. & Hsieh, J.-Y. (2015). Mechanical properties and thermal stability of ultrathin molybdenum nanowires. RSC Adv., 5, 31231-31237, 10.1039/C5RA01359C.
5) Schönecker, S., Li, X., Koepernik, K., Johansson, B., Vitos, L. & Richter, M. (2015). Metastable cubic and tetragonal phases of transition metals predicted by density-functional theory. RSC Adv., 5, 69680-69689, 10.1039/C5RA14875H.
6) Zhang, T., Wojtal, P., Rubel, O. & Zhitomirsky, I. (2015). Density functional theory and experimental studies of caffeic acid adsorption on zinc oxide and titanium dioxide nanoparticles. RSC Adv., 5, 106877-106885, 10.1039/c5ra21511k.
Some examples of how to use theoretical crystal structure data in the ICSD