A Study on configurations of carbon dioxide and nitrogen containing heterocyclic molecules
P. D. Varuna S. Pathirage
Department of Chemistry, University of Tennessee
The distorted spherical structure formed by pyridine engulfing CO2 molecules of a pyridine-CO2 system is visualized below. The conformers used in this study were from a quantum chemical study done by Vogiatzis et al.1 The initial optimized geometries for pyridine and water molecules were obtained from Automated Topology Builder website 2.
This is a study to investigate the configurations of carbon dioxide and nitrogen containing heterocyclic molecules. Three systems were simulated. They are pyridine-CO2 system, pyrazine-CO2 system and imidazo[1,2-a]pyridine-CO2 system. A system consists of 13 -CO2 molecules and 13 of the respective N-containing heterocyclic molecules. Length of a side of the simulation box was 30 Angstrom. Step size for the simulations were 2 fs and the simulation time was 50 ns. GROMOS 54A7 forcefield was used for the simulations. Coordinates of each atom was collected at each 100th step and machine learning was used to determine the distribution of different orientations for pyridine-CO2 system. This study shows that CO2 preferred to stay parallel to the ring plane of pyridine ring. This study can be further developed by using more advanced forcefields for CO2 molecules. Further a grid search can be performed to optimize the hyperparameters used in machine learning algorithms.
Interactive Structures
Color Legend:
- red = Oxygen
- blue = Nitrogen
- gray = Carbon
- white = Hydrogen
References
1. Vogiatzis, K. D.; Mavrandonakis, A.; Klopper, W.; Froudakis, G. E. Ab Initio Study of the Interactions between CO2 and N-Containing Organic Heterocycles. ChemPhysChem 2009, 10 (2), 374-383., doi: 10.1002/cphc.200800583
2. Stroet, M.; Caron, B.; Visscher, K. M.; Geerke, D. P.; Malde, A. K.; Mark, A. E. Automated topology builder version 3.0: Prediction of solvation free enthalpies in water and hexane. Journal of chemical theory and computation 2018, 14(11), 5834-5845.,doi: 10.1021/acs.jctc.8b00768
posted: May 2022.
updated: May 2022.