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Fig. 4 | BMC Bioinformatics

Fig. 4

From: Sculpting molecules in text-3D space: a flexible substructure aware framework for text-oriented molecular optimization

Fig. 4

Exemplary optimizations involving spatial information in the polarity-related prompts. Above are the 2D graphs of molecules and below are their corresponding 3D conformations. a Under the prompt “This molecule has low polarity”, a hydroxyl group is added to the molecule, which neutralizes the dipole of the neighboring hydroxyl group due to the opposite alignment, as illustrated by the arrows. Consequently, the dipole moment of the molecule is reduced from 1.898 Debye to 0.914 Debye. b Under the prompt “This molecule has high polarity”, the output molecule discards two C-F bonds which counteract the dipole of the pyridine ring and hence do not contribute much to the polarity. The removal of C-F bonds and the introduction of an aligned hydroxyl group raise the dipole moment of the molecule from 0.467 Debye to 0.905 Debye

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