Alchemy III: Builder (Examples)

1 D-Glyceraldehyde

  1. Atoms -> C3 (to aux; free valences (FV) magenta (~), active green (x))
  2. click into main window
  3. click at a [magenta] tip of a FV
    R: (LMB) rotate about a bond
  4. Atoms -> C2 (active: single; evtl. Display->Display Labels)
  5. click at a [magenta] tip of a FV
  6. Atoms -> O2
  7. click at the tip of a "double" FV at C-1
  8. Atoms -> O3
  9. click at the (stereochemical correct) FV at C-2
  10. click at any FV at C-3
  11. Build->Add->Hydrogens
  12. Build->Charge->Compute Charges
  13. Build->Minimize
  14. Build->Chiral->Label Centers (R)
  15. [Save->As Molecule...]

2 Naphthalene

before you begin: Build->Delete->Molecule; click an atom

  1. Build->Add->Fragment...
    [..][frag] benzene.grp
  2. click into main window
  3. Build->Fuse
    click 3 pairs (first in main window, then in aux window: 1. two "overlapping" carbon atoms, 2. two "overlapping" carbon atoms, 3. a carbon atom and an overlapping FV (!))
  4. Done->Ready
  5. Build->Add->Hydrogens

3 Cyclobutane

before you begin: Build->Delete->Molecule; click an atom

  1. Atoms -> C3
  2. click into main window
  3. click at a FV
  4. click at a FV of C-2
  5. click at a FV of C-3 (now you got all four carbon atoms!)
  6. Build->Connect
  7. click at FVs of atoms to connect
  8. Build->Add->Hydrogens
  9. Build->Minimize

4 (NH2)-gly-ala-cys-(OH)

before you begin: Build->Delete->Molecule; click an atom

  1. File->Open...
    [frag] cys.frg (two FVs)
  2. Build->Add->Fragment... [frag] ala.frg (active: CO-x green)
  3. click at amide FV (in main window)
    R: rotate amide bond into trans-coplanar conformation
  4. Build->Add->Fragment... [frag] gly.frg
  5. click at amide FV (in main window)
    R: rotate amide bond into trans-coplanar conformation
  6. Atoms -> O3
  7. click at FV of terminal COOH
  8. Atoms -> H
  9. click at FV of terminal COO
  10. click at FV of terminal NH
  11. Build->Charge->Compute Charges
  12. Build->Minimize
  13. Build->Chiral->Label Centers (R, S)