Structural and computational chemistry | Faculty of Chemistry at the Gdańsk University of Technology

Our research in structural chemistry focuses on the field of crystal engineering, where the main goal is to understand the processes of crystal formation and to study the role of intermolecular interactions in the crystal structure.

Our research activities cover a wide range of topics, starting with the study of intermolecular interactions such as hydrogen, halogen, chalcogen bonding, and layered associations. We aim to synthesize systems with specific topology and symmetry, which allows us to obtain materials with unique physicochemical properties, including the ability to induce chirality.

This research focuses mainly on complex compounds of p- and d-block metals with S-, P-, N-, and O-donor ligands. In our laboratories, we synthesize most of these ligands and then characterize the obtained products using X-ray structural analysis, IR, NMR, UV-Vis spectroscopy, and other techniques available in the Structural Research Laboratory and in collaborating facilities.

The research combines experiment with computation. We use modern computational methods to analyze and predict experimental results:

• predicting the properties of crystalline solids such as: energy gap, band structure, IR, and NMR spectra in solids (Gaussian, ADF, BIOVIA Materials Studio)
• aspherical refinement of crystal structures using Hirshfeld electron density partitioning (Hirshfeld Atom Refinement), which allows better fitting of the X-ray model to experimental results, placing hydrogen atoms in positions closer to reality (neutron studies), and in the case of high-resolution studies, determining thermal vibration ellipsoids of hydrogen atoms, which is not achievable in standard procedures (NoSpherA2, Olex2, Orca).
• electron density analysis (Charge Density Studies), enabling insights into intra- and intermolecular interactions, compound properties, reactivity, and much more (MultiWFN, Gaussian, Orca, NBO, Tonto, CrystalExplorer)

For X-ray structural analysis, we use single crystals with an edge length of 50-200 μm. Measurements are performed at temperatures from 120 K to room temperature. Our STOE diffractometer is equipped with molybdenum (λ_MoKα ≈ 0.17 Å) and copper (λ_CuKα ≈ 1.54 Å) radiation source and an IPDS detector.

We conduct calculations on both PC computers and supercomputers of Gdańsk University of Technology and the nationwide PLGrid infrastructure.

Example Results

Our research has led, among other things, to the development of a new geometrical index τ₄′, which more accurately reflects the deviation of the geometry of coordination compound centers from the ideal tetrahedron [1, 2].

Fig. 1. Illustration of changes in the values of parameters τ₄ and τ₄′ as a function of the geometry of the coordination center [1, 2].

Using electron density analysis (CDS, dual descriptor), we experimentally predicted the reactivity of Schiff bases, which are products of the addition of aniline derivatives to cinnamaldehyde towards nucleophilic agents [3].

Fig. 2. Dual descriptor index values (Δf, e) of the C=N bond for selected imines. Compounds for which the parameter value was highest were found to be the most reactive towards nucleophilic agents (addition to the C=N bond) [3].

We also obtain materials with interesting physicochemical properties (molecular wires, meso-, micro-, and nanoporous materials of the MOF type) or catalytic properties (related to modifiable metallic centers in multimetallic complexes).

Fig. 3. Copper(I) chloride molecular wires (molecular wires) with cuprophilic (Cu···Cu) bonds coordinated by thiourea ligands [4].

Fig. 4. Copper(I) iodide ribbons (ribbons) with cuprophilic (Cu···Cu) bonds coordinated by thiourea ligands: (I) S-donor and (II) N-donor ligands, compared to the structure of copper(I) iodide – phase V [5].

Contact

If you are interested in collaboration in structural research, please contact:

• Prof. Jarosław Chojnacki, Ph.D., D.Sc., Eng.
• Prof. Anna Dołęga, Ph.D., D.Sc., Eng.
• Katarzyna Kazimierczuk, Ph.D., D.Sc.
• Łukasz Ponikiewski, Ph.D., D.Sc., Eng.

If you are interested in the described computational methods, please contact:

• Andrzej Okuniewski, Ph.D., Eng.

References

1. A. Okuniewski, D. Rosiak, J. Chojnacki, B. Becker: Coordination polymers and molecular structures among complexes of mercury(II) halides with selected 1-benzoylthioureas. Polyhedron 90 (2015) 47-57, doi:10.1016/j.poly.2015.01.035.
2. D. Rosiak, A. Okuniewski, J. Chojnacki: Novel complexes possessing Hg‒(Cl, Br, I)···O=C halogen bonding and unusual HgS(Br/I) kernel. The usefulness of τ₄′ structural parameter. Polyhedron 146 (2018) 35-41, doi:10.1016/j.poly.2018.02.016.
3. M. Siedzielnik, A. Okuniewski, K. Kaniewska-Laskowska, M. Erdanowski, A. Dołęga: Reactive imines: Addition of 2-aminopyrimidine to the imine bond and isolation of the aminal from the equilibrium mixture aminal/imine. J. Mol. Struct. 1289 (2023) 135847, doi:10.1016/j.molstruc.2023.135847.
4. D. Rosiak, A. Okuniewski, J. Chojnacki: Copper molecular wires formed out of
   benzoylthiourea complexes. 59 Konwersatorium Krystalograficzne, poster A48 (2017) 115.
5. D. Rosiak, A. Okuniewski, J. Chojnacki: Copper(I) iodide ribbons coordinated with thiourea derivatives. Acta Cryst. C 74 (2018) 1650-1655, doi:10.1107/S2053229618015620.