Original scientific paper

https://doi.org/10.5562/cca3348

Structure Determination by Joint Effort of X-ray Powder Diffraction and Quantum Calculations: Crystal Structure and Short Hydrogen Bonding in Pentadecafluorooctanoic Acid Hydrate

Jernej Stare ; Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
Anton Meden ; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
Dušan Hadži ; Theory Department, National Institute of Chemistry, Ljubljana, Slovenia

Abstract

A precise X-ray crystal structure determination of systems that exist in a polycrystalline form often poses a challenge due to several factors that limit the resolution of the diffraction measurement. The location of atoms is usually determined at significantly lower precision than the unit cell parameters, rendering the complete characterization of the structure difficult. This is particularly pronounced when precise location of hydrogen atoms is required, for instance in ionizable biomolecules or in hydrogen bonds. In such cases periodic quantum (DFT) calculations may crucially assist structure determination, because they can reliably predict the location of atoms, provided that the unit cell parameters, the space group and tentative atomic positions are known. In this work we present DFT-assisted structure determination of pentadecafluorooctanoic acid hydrate, a benchmark system featuring short hydrogen bonds (RO...O ≈ 2.5 Å) between acid and water molecules. While Rietveld refinement based solely on powder diffraction data cannot reliably resolve the location of crystal water molecules and even less so the position of hydrogen atoms in the network of hydrogen bonds, periodic DFT optimization yields several minimum energy structures suitable for further refinement. Due to the low experimental resolution and similarity, comparison between model and experimental powder diffraction pattern can barely distinguish between certain structure candidates provided by DFT calculations, but it can rule out those featuring larger misfits. The proposed structure solution is delivered from a tandem application of structure determination from powder diffraction data and DFT optimization, the former providing the unit cell parameters and estimated atomic positions that are finely tuned by DFT. The present strategy can in principle be generalized to other examples of structure determination at relatively low resolution, such as is often the case with biological macromolecules.

This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords

powder diffraction; structure determination; periodic DFT calculations; hydrogen bonding

Hrčak ID:

202770

URI

https://hrcak.srce.hr/202770

Publication date:

4.6.2018.

Visits: 1.536 *