Implicit Hydrogens Section

[rapodaca]

Previously: "Hydrogen Suppression"

Comprehensively describe, modulo selection (aka "aromaticity"), the rules for computing implicit hydrogen count.

• virtual hydrogens
  • described in previous section
  • unambiguous, but verbose
• implicit hydrogens
  • replace attribute with computed value
  • computation without corruption requires a detailed protocol
• target valence
  • the number of hydrogens the free atom can bind to
  • one or more values, depending on atom
• target valence table
  • star (*) always has target = 0
  • defines target valences for atoms supporting implicit hydrogen
  • for example
  • a free carbon atom can bind four hydrogens
  • a free nitrogen atom can bind three or five hydrogens
• atoms with elements not on the table are not eligible
  • they must use virtual or graph hydrogens
• works with graph hydrogens
  • hydrogen acts like any other atom
• example computations
  • simple cases
  • C
  • N
  • CC
  • N(C)(C)(C)(C)
  • *
  • weird/counterintutive cases
• either implicit hydrogens or virtual hydrogens, never both