This data set contains the results of CRYSTAL23 calculations of normal mode frequencies for crystal structures of four MOFs or coordination polymers (REFCODEs: CAMTET, CAMTET01, CUGLYM08; CCDC 2447246 - called here SZ3150 K) and four minerals (alum-K, amarantite, kroehnkite, langite).
Research context:
X-ray crystallography is a powerful tool for characterizing the structure and electron density of crystalline compounds. In recent years, it has undergone rapid development in both experimental techniques and the theoretical and computational methods used for data extraction. While electron density description techniques are highly advanced, progress in modeling thermal motion has been slower. For over a decade, the most advanced tools for estimating hydrogen anisotropic displacement parameters (H ADPs), such as SHADE3 or Normal Mode Refinement (NoMoRe) [1], have been based on the spherical atom model, which is overly simplified. Recently, these methods have been enhanced to incorporate the aspherical atom model derived from Hirshfeld Atom Refinement (HAR) [2] and the Transferable Aspherical Atom Model (TAAM) [3]. Specifically, the aspherical NoMoRe method has been shown to yield H ADPs comparable to neutron diffraction data for several small-molecule crystals, as well as heat capacities in agreement with calorimetric data [4]. Since neither the spherical nor the spherical NoMoRe method have been tested for network crystals, in this study we decided to perform such a test using X-ray structures of four coordination polymers (including MOFs) and four minerals.
[1] A. A. Hoser, A. Ø. Madsen, Acta Cryst., 2016, A72, 206–214; A. A. Hoser, A. Ø. Madsen, Acta Cryst., 2017, A73, 102–114.
[2] (a) Jayatilaka, D. & Dittrich, B. (2008). Acta Cryst. A64, 383–393. ; (b) Capelli, S. C., Buergi, H.-B., Dittrich, B., Grabowsky, S. & Jayatilaka, D. (2014). Hirshfeld atom refinement. IUCrJ, 1, 361-379.
[3] Jha, K. K., Gruza, B., Kumar, P., Chodkiewicz, M. L. & Dominiak, P. M. (2020). Acta Cryst. B76, 296–306.
[4] Butkiewicz, H., Chodkiewicz, M., Madsen, A. O. & Hoser, A. A. (2025). IUCrJ, 12, 123-136.
Methodology:
In this study, the aspherical and spherical NoMoRe method is further tested on network crystal structures, including seven metal-organic frameworks (MOFs) from the CCDC, a copper coordination polymer measured in-house (SZ3150K), and several minerals (amarantite, kroehnkite, langite and alum-K) for which neutron structures are established at 100 K. These compounds are computationally demanding due to the presence of transition metal atoms and crystal lattices that lack easily distinguishable molecular units, aside from solvent molecules.
The NoMoRe procedure requires calculations of normal mode frequencies at the Gamma point for the preoptimized geometry. This was performed for each of the structures using CRYSTAL 23 software (https://www.crystal.unito.it/) and the DFT method with the B3LYP functional. The basis sed used varioed according to the structure:
- Coordination polymers and amarantite: 6-31G(d,p) + def2-SVP for Cu/Fe
- alum-K, kroehnkite, langite: POB-TZVP-rev2
The calculated frequencies of normal modes are subsequently used in the NoMoRe procedure in which the low-energy normal modes are refined against X-ray data and the high-energy modes are fixed at the calculated values.
Structure of the data set:
The data set contains the results of normal mode frequency calculations in CRYSTAL23 for the 8 specified compounds. For each compound the data is placed in a separate folder. Each folder contains (1) a file called "skrypt" which is the script used to run calculations on a computer cluster, (2) the .d12 file which is the input for CRYSTAL23, (3) the .out file which is the main output of CRYSTAL23 and (4) other CRYSTAL23 output files. For the detailed description of the structure of each of the files refer to the CRYSTAL webpage (https://www.crystal.unito.it/).
Information on the software which can be used to open the files:
The files can be opened with a text file editor. In the case of some of the files there is dedicated software which can be used to visualize the results (see https://www.crystal.unito.it/). E.g. the normal modes and the crystal geometry saved in the .out file can be visualized using Jmol (https://jmol.sourceforge.net/).
