Working Group 2

Deliverable 3. Description of gas adsorption, separation, and storage in MOFs along with Working Group 1 (M24); Optimized encapsulation of different active entities in MOFs along with Working Group 1 (M24). Catalytically active COF materials with pore incorporated catalysts along with Working Group 3 (M36).

3.1. Description of gas adsorption, separation, and storage in MOFs along with Working Group 1 (M24)

Delivered – As scheduled, the work on the first sub-deliverable has been completed in collaborations involving Serbia, France, Tunisia, Estonia, and Germany.

  1. Grubišić, S.; Dahmani, R.; Djordjević, I.; Sentić, M.; Hochlaf, M. Selective Adsorption of Sulphur Dioxide and Hydrogen Sulphide by Metal–Organic Frameworks. Physical Chemistry Chemical Physics, 2023, 25, 954–965. https://doi.org/10.1039/d2cp04295a. Cover feature: https://pubs.rsc.org/cp/article/25/2/882/803589/Inside-front-cover

    COSY-DIN datasets incorporating force field parameters for modeling sulfur gas adsorption inside MOFs have been generated and published.

  2. Rybicki, M.; Sillar, K.; Sauer, J. Dual-Site Model for Ab Initio Calculations of Gibbs Free Energies and Enthalpies of Adsorption: Methane in Zeolite Mobile Five (H-MFI). The Journal of Physical Chemistry Letters, 2022, 13, 11595–11600. https://doi.org/10.1021/acs.jpclett.2c03302.
  3. Nicole, M.; Fabian, B.; Marcin, R.; Sillar, K.; Sauer, J .Atomistic Model for Water Adsorption in Mg-MOF-74: Quantum Chemical Prediction of Structures and Isotherms. Journal of the American Chemical Society, 2026. 148 (11), 12296-12306. DOI: 10.1021/jacs.6c01686.

3.2. Optimized encapsulation of different active entities in MOFs along with Working Group 1 (M24)

Delivered – The work on the second sub-deliverable has been also completed within the framework of a collaboration between Estonia and Germany resulting a paper on ab initio predictions of adsorption selectivity for binary gas mixtures on a heterogeneous metal–organic framework surface.

  1. Sillar, K.; Kundu, A.; Sauer, J. Ab Initio Prediction of Adsorption Selectivities for Binary Gas Mixtures on a Heterogeneous Metal–Organic Framework Surface. The Journal of Physical Chemistry C, 2023, 127, 13317–13326. https://doi.org/10.1021/acs.jpcc.3c02494.

3.3. Catalytically active COF materials with pore incorporated catalysts along with Working Group 3 (M36).

Delivered – As scheduled, the final sub-deliverable has been successfully completed through the collaborative efforts of researchers from Estonia, Serbia, and France. New force field parameters have been developed for modeling CO₂ adsorption in CALF-20, providing a versatile computational methodology applicable to similar porous framework materials, including covalent organic frameworks (COFs), for CO₂ capture and catalytic applications. In addition, the COSY-DIN datasets incorporating these force field parameters have been generated and published (DOI: 10.1002/sstr.202500781).

1. Sillar, K.; Grubisic, S.; Đorđević, S. I. ; Hochlaf, M.Chemically Accurate Prediction of CO2 Adsorption Thermodynamics in Metal–Organic Framework CALF‐20: Complementary Ab Initio Modeling and Grand Canonical Monte Carlo Simulations. Small Structures, 2026, 7:e202500781. https://doi.org/10.1002/sstr.202500781.

Deliverable 4. New protocols to characterize nucleic acids in crowded environments (M36); Quantification of binding specificity between organic compounds and confining environments (M36); Study of metal clusters in biological environments: optical/non-optical properties and charge transfer along with Working Group 3 (M36); Quantum dynamics of molecules under electromagnetic fields (M48).

4.1. New protocols to characterize nucleic acids in crowded environments (M36)

Delivered – In a collaboration between IT, SE, UA and RO research groups, theoretical model has been proposed for the investigation of conformational flexibility of spermidine3+ interacting with DNA double helix

  1. Perepelytsya, S.; Vasiliu, T.; Laaksonen, A.; Engelbrecht, L. D. V.; Brancato, G.; Mocci, F. Conformational Flexibility of Spermidine3+ Interacting with DNA Double Helix. Journal of Molecular Liquids, 2023, 389, 122828. https://doi.org/10.1016/j.molliq.2023.122828.
  2. Perepelytsya, S.; Piatnytskyi, D.; Bubon, T.; Cibotariu, N.; Laaksonen, A.; Mocci, F. Ions as Architects of DNA Nanostructures: Mechanisms, Simulations, and Technological Frontiers, Small Structures, 2026, 7, e202500786. https://doi.org/10.1002/sstr.202500786. Cover feature: https://onlinelibrary.wiley.com/doi/10.1002/sstr.70409

    Paper on the modeling of complex DNA nanostructures has been published by researchers based in Austria.

    3. Jacobi, R.; González, L. Controlling DNA Three-Way Junction Conformations via Base Pairing, Small Structures, 2026, 7, e202500815. https://doi.org/10.1002/sstr.202500815.

4.2. Quantification of binding specificity between organic compounds and confining environments (M36)

Delivered – COSY WG2 members from Serbia and Italy presented several approaches for the optimization of non-polarizable and polarizable force fields and their application to model compounds:

  1. Grubišić, S.; Đorđević, I.; Popović, D. M. Optimization of Non-Polarizable and Polarizable Force Fields and Their Application to Model Compounds. Comprehensive Computational Chemistry, 2024, 964–986. https://doi.org/10.1016/b978-0-12-821978-2.00117-3.
  2. Grubišić, S.; Đorđević, I.; Mocci. F. Biomolecular force fields: Advances in Nonstandard Amino Acid and Nucleic Acid Development, Handbook of Electronic Structure Theory: Methods and Applications, Elsevier, Chapter 036, 2026, 685-701. https://doi.org/10.1016/B978-0-443-26596-9.00013-2

Studies on the interactions of ionizable lipid nanodroplets with biomembranes and the modeling of Nafion polymer for proton exchange membrane fuel cells were conducted through collaborative efforts between the Czech Republic and France, and Serbia and Germany, respectively.

  1. Čechová, P.; Paloncýová, M.; Šrejber, M.; Otyepka, M. Mechanistic Insights into Interactions between Ionizable Lipid Nanodroplets and Biomembranes. Journal of Biomolecular Structure and Dynamics, 2024, 1–11. https://doi.org/10.1080/07391102.2024.2329307.
  2. Čechová, P.; Kührová, P.; Šrejber, M.; Valério, M.; Borbuliak, M.; Souza, P. C. T.; Otyepka, M.; Paloncýová,M. Computational Microscopy of Lipid Confined Systems: Challenges and Opportunities, Small Structures, 2026, 7,e202500697. https://doi.org/10.1002/sstr.202500697.
  3. Jovanović, M.; Bernhard, N.; Baldofski, M.; Rybicki, M.; Dašić,M.; Stanković, I.; Linking Density and Nanoscale Crystallinity to Hydration in Nafion PEMFC Membranes: Insights From Experiment and Molecular Dynamics Simulations. Small Structures 2026, 7, e202500573. https://doi.org/10.1002/sstr.202500573.

Collaborative studies involving researchers from Lithuania, Italy, and Sweden have demonstrated that combining computational methods with NMR experiments is an effective approach for investigating the structure and dynamics of ionic liquid (IL) materials.

  1. Murnikova, Ž.; Klimavicius, V.; Mocci, F.; Laaksonen, A.;Aidas, K. On the mechanism behind the enhanced solubility of glibenclamide in aqueous ionic liquid solution. Journal of Molecular Liquids, 2025, 422. https://doi.org/10.1016/j.molliq.2025.127153.

4.3. Study of metal clusters in biological environments: optical/non-optical properties and charge transfer along with Working Group 3 (M36)

Delivered – Research groups from Spain presented an extended first-principles study of the oxidation of Cu5–Cu5 and circumpyrene-supported Cu5, comparing it with that of unsupported Cu5, and combine dispersion-corrected density-functionals, first principles thermochemistry, and ab initio molecular dynamics (AIMD) simulations within an adiabatic approach:

  1. Garrido-Aldea, J.; de Lara-Castells, M. P. Aggregation and Support Effects in the Oxidation of Fluxional Atomic Metal Clusters. The Paradigmatic Cu5 Case. Physical Chemistry Chemical Physics, 2022, 24, 24810–24822. https://doi.org/10.1039/d2cp02169b.
  2. Molina L. M.; Alonso J. A.; Structural and chemical properties of Pt-rich PtxZry nanoalloys. Physical Chemistry Chemical Physics, 2026, 28, 304–314. https://doi.org/10.1039/d5cp02864g

4.4. Quantum dynamics of molecules under electromagnetic fields (M48)

Delivered – Research group from Switzerland published paper on the family of gaussian wavepacket dynamics methods from the perspective of a nonlinear Schrödinger equation:

  1. J. L. Vaníček, J. Family of Gaussian Wavepacket Dynamics Methods from the Perspective of a Nonlinear Schrödinger Equation. The Journal of Chemical Physics, 2023, 159. https://doi.org/10.1063/5.0146680.

A new far-infrared spectra of (HF)2 has been obtained by high resolution long-path fourier transformInfrared (FTIR) spectroscopy via a collaboration of CH and UK research groups. The accuracy of the published results are discussed in relation to full-dimensional quantum dynamics and predictions based on recent ab initio calculations and empirically refined potential energy hypersurfaces:

2. Hollenstein, H.; Hippler, M.; Seyfang, G.; Quack, M. High-Resolution FTIR Spectroscopy and Analysis of the K a  = 0 ← 1 Subbands of the Fundamentals ν 3 and ν 6 of the Dimer (HF)2. Molecular Physics, 2024, 122. https://doi.org/10.1080/00268976.2024.2341106.

Several other papers have been published in connection with this deliverable:

3. Albert, S.; Chen, Z.; Keppler, K.; Wichmann, G.; Quack, M.; Stohnner, J.; Schurig, V. and Trapp, O. High resolution infrared spectroscopy of monodeutero-oxirane (c-C2H3DO) and analysis two fundamentals between 820 and 950 cm-1. Phys. Chem. Chem. Phys., 2025, 27 (27): 14240–14253. https://doi.org/10.1039/D5CP00880H.

4. Martín Santa Daría, A.; Hernández-Rodríguez, J.; Ibele, L. M.; Gómez, S., Photofragmentation of Cyclobutanone at 200 nm: TDDFT vs CASSCF Electron Diffraction.

The Journal of Chemical Physics, 2024, 160, 114303. https://doi.org/10.1063/5.0197895.

5. Gómez, S.; Vindel-Zandbergen, P.; Farkhutdinova, D.;González, L. Perspective: Vibronic Coupling Potentials for Trajectory-Based Excited-State Dynamics. J Chem Theory Comput. 2025, 21(18):8634-8649. https://doi.org/ 10.1021/acs.jctc.5c01002.
6. Li, X.; Yin X.; Bai, Y-L; Biczysko M. Interpretation and prediction of optical properties: novel fluorescent dyes as a test case. Front. Phys., 2023, 11:1236987. https://doi.org/ 10.3389/fphy.2023.1236987.