Report on the outcomes of a Short-Term Scientific Mission

Action number: CA21101

Applicant name: Heribert Reis

Details of the STSM

Title: Force fields for simulations of bonded complexes of squaraines and (C6F5)nX (n=1,2; X=OH,Hal,Chal) in solvents and membranes

Start and end date: 23/10/2023 to 27/10/2023

Description of the work carried out during the STSM

Any deviations from the initial working plan shall also be described in this section.

The goal of this STSM was to start the development of force fields of halogen- and chalcogen-bonded squaraines with (C6F5)nX (n=1,2; X=OH, Hal, Chal) molecules in the framework of the Amber force field description. The original idea was to do this in the old style, optimising each parameter separately and iterate, but it turned out that there exists already a program in Amber which allows to do the parameter optimization for several parameters at once and for a large number of different structures in a crude ‘machine learning’ fashion, called mdgx and applied in the development of the modern ff15ipq force field1. It has also the possibility to apply mass-less point charges, which is now our favoured way to treat those non-bonded directed interactions, as test calculations showed that the more elaborate force field ffBXB developed by Shing Ho and Rappe2 seems to have problems to work in conjunction with the lipid force fields of Amber. Calculations were set up and started to determine the minimal size of model structures still able to mimic the behaviour of the final target molecules. This is necessary as the final parameter optimization may require up to several thousands ab-initio calculations. In addition, the influence of reducing the standard MP2/cc-pVTZ method used for ff15ipq by a cheaper DFT model is monitored carefully.

During my stay in Torun we had several discussions with Dr. Anna Kaczmarek-Kedziera about her previous calculations of the target systems and the organization of our future work. I also had the opportunity to present our work in a seminar given to the Institute.

1 K. T. Debiec et al. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model, J. Chem. Theory Comput. 12, 3926-47 (2016).

2 M. C. Ford, A. K. Rappe, P. Shing Ho A Reduced Generalized Field for Biological Halogen Bonds, J. Chem. Theory Comput. 17, 5369-78 (20).

Description of the STSM main achievements and planned follow-up activities

A plan for the further proceedings on the road to the final goal of the Torun-Athens collaboration, i.e. the ‘Supramolecular tuning of the photophysical properties of Squaraine dyes with applications to Biomedicine and Materials science’ was discussed and agreed upon. Also, the procedure to follow for the first next steps, the development of force fields for the accurate description of the target structures has been investigated and narrowed down to a specific procedure, for which first calculations have been started. We will later incorporate the basis sets specifically developed by Dr. Dariusz Kedziera for halogen-bonded structures in a previous STSM into the force field optimization procedure. It will also be necessary to develop optimized basis sets for chalcogen-bonded structures, so that both kinds of non-covalent bonding patterns will be treated on the same level of accuracy. Both activities contribute to the general objective of WG2 of developing general strategies for the investigation of molecular motion in confined systems, and to some extent to the goal of creating new open-access codes for macroscopic studies of confinement effects and contribute to the capacity building objective to provide a platform for exchange and collaboration between research groups working on confined molecular systems. In addition, they contribute to Deliverable 5 expected of WG2, namely “Quantification of binding specificity between organic compounds and confining environments”.  Finally, they are in line with the objective of the first grant period in WG2 to test computational methods addressing the dynamics of molecular systems in confined systems.

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