Note: This text currently offers only some basic information relating specifically to Alchemy III for MS Windows. See also the description of Alchemy II (German only).
Alchemy III is a molecular modeling program for PCs running MS Windows from Tripos, Inc.. It allows e.g. the construction of molecular models on screen similarly to a molecule construction set, rotations of wire-frame models, different types of representations (ball-and-stick or space filling models, cylinder model) as well as the optimization of geometries by means of force-field calculations ("Minimize").
Program start in Windows NT: Start 
Programme Chemistry
Alchemy. By default, four windows are opened, besides the
main window, which serves for the representation and manipulation of the molecules,
an auxiliary window (Aux) for molecular fragments, a control box (Gadgets)
and a window for messages (Messages).
Open, Save (As Molecule, Fragment), Sybyl, MM2, Open PDB File, Crystal, Print Main Window, HPGL Setup, Create HPGL File, Quit
Undo, Cut, Copy Main, Paste, Clear
Display Labels, Label Types (Atom Type, ID, Formal Charges, Point Charges), View (Stereo, Ortho, Mono), Color (-> Select color from menu), Spacefill, Ball and Stick, Cylinders, Depth Cueing, Perspective, Show Gadget Box, Show Message Area, Relaxed, Crossed, Reset Global, Reset Relative, Reset Scale, Configure System
Add (Hydrogens, Unfilled Valences, Fragment ...), Delete (Atom, Molecule, Hydrogens), Connect, Disconnect, Center (Atom, Molecule), Duplicate, Move [Molecule], Measure (Length, Angle, Torsion), Alter (Length, Angle, Torsion), Twist, Chiral, Fit, Fuse, Charge (Calculate Formal Charges, Enter Formal Charges, Compute Charges, Clear All Charges), Minimize
In the main window, molecules can be rotated, resized or shifted by means of the mouse.
with depressed left mouse button
rotate
resize
shift
can be found at ("File Open") below:
c:\progra~1\molmod\a3win\mol
c:\progra~1\molmod\a3win\frag
with the Alchemy geometry optimizer MINIMIZE. The potential energy of the molecule is being minimized:
E = Estr + Eang + Etor + Evdw + Eoop + Eel
(str: bond stretch, ang: deformation of bond angles, tor: deformation of torsional angles, vdw: van-der-Waals interactions, oop: out-of-plane bending, el: electrostatic interactions)
1. stretch: Estr = (sum)i {1/2} kid (di - di0)2
(di: bond length in Å, di0: equilibrium bond length in Å, kid: force constant in kcal/Å2·mol; see file MINBND.TAB)
2. angular deformation:
Eang = (sum)i {1/2} ki
(i - i0)2
(i: bond angle in degrees, i0:
equilibrium bond angle in degrees, ki:
force constant in kcal/degree2·mol; see file MINANG.TAB)
3. torsion: Etor = (sum)i {1/2} ki(1 + sign(peri) × cos(|peri|× wi))
(wi: torsional angle in degrees, ki: force constant in kcal/mol, peri: periodicity; see file MINTOR.TAB)
4. van der Waals (Lennard-Jones potential): Evdw = (sum)i (sum)j Eij(1/aij12 - 2/aij6)
(summation is over 1-4 and more remote interactions; Eij: van-der-Waals constant in kcal/mol, aij = rij/(Ri + Rj): relative distance, Ri: van-der-Waals radius in Å; see file MINVDW.TAB)
5. out-of-plane:
Eoop = (sum)i {1/2} ki
di2
(ki: out-of-plane bending constant in
kcal/Å2·mol; for trigonal atoms, e.g. aromatic C,
di is the height of the central atom above the plane of its
substituents in Å; s. MINOOP.TAB)
6. electrostatic interaction (Coulomb): Eel = (sum)i (sum)j {qiqj/D · rij}
| C3 | carbon-sp3 | S3 | sulfur sp3 (sulfide) |
| O3 | oxygen-sp3 | S2 | sulfur sp2 |
| N3 | nitrogen-sp3 | SO | sulfur sulfoxide |
| H | hydrogen | SO2 | sulfur sulfone |
| CAR | carbon aromat. | F | fluorine |
| C2 | carbon-sp2 | CL | chlorine |
| C1 | carbon-sp | BR | bromine |
| O2 | oxygen-sp2 | I | iodine |
| N2 | nitrogen-sp2 | K | potassium |
| N1 | nitrogen-sp | NA | sodium |
| NAR | nitrogen aromat. | FE | iron |
| NPL3 | nitrogen trigonal planar | LI | lithium |
| NAM | nitrogen amide | AL | aluminum |
| N3+ | nitrogen sp3 positively charged | SI | silicon |
| DU | dummy atom | CA | calcium |
| P3 | phosphorous tetravalent | LP | lone pair |
| P4 | phosphorous pentavalent | ~ | system atom type |
| * | system atom type | ||