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Chemically Accurate Dopamine
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Chemically Accurate DopamineTo my knowledge, the presented 3D model is the most accurate representation of dopamine.MethodsModel was generated with a custom Python script with the RDKit module, and the STL file was rendered in OpenSCAD. Atom coordinates, and therefore bond lengths, atom radii and overall shape of the molecule, were calculated with the Merck Molecular Force Field.Force fields are mathematical models used to describe the interactions between atoms and molecules. They are based on empirical parameters that represent the forces and energies associated with different types of atomic interactions, such as bond stretching, angle bending, and non-bonded interactions. These parameters are derived from experimental data and quantum mechanical calculations.NotesI decided to go with the ball-and-stick type, as it is easiest to color, is rigid, and looks awesome.Aromatic bonds are modeled as single stick but 1.5x thicker to represent ~1.5 bond order. I oriented the model for optima
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