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1. Alchemy III for MS Windows

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 .rarr. Programme .rarr. Chemistry .rarr. 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).

1.1 "Pull-Down-" Menus

File

Open, Save (As Molecule, Fragment), Sybyl, MM2, Open PDB File, Crystal, Print Main Window, HPGL Setup, Create HPGL File, Quit

Edit

Undo, Cut, Copy Main, Paste, Clear

Display

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

Build

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

Atoms
Help

1.2 Hints for using the mouse

In the main window, molecules can be rotated, resized or shifted by means of the mouse.

LMB:

with depressed left mouse button

LMB:

rotate

shift-key+LMB:

resize

ctrl(Strg)-key+LMB:

shift

1.3 Molecule and fragment libraries

can be found at ("File .rarr. Open") below:
c:\progra~1\molmod\a3win\mol
c:\progra~1\molmod\a3win\frag

1.4 Force-field calculations

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.theta.(.theta.i - .theta.i0)2

(.theta.i: bond angle in degrees, .theta.i0: equilibrium bond angle in degrees, ki.theta.: 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.delta. di2

(ki.delta.: 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}

1.5 atom types:

C3 carbon-sp3S3 sulfur sp3 (sulfide)
O3 oxygen-sp3S2 sulfur sp2
N3 nitrogen-sp3SO sulfur sulfoxide
H hydrogenSO2 sulfur sulfone
CAR carbon aromat.F fluorine
C2 carbon-sp2CL chlorine
C1 carbon-spBR bromine
O2 oxygen-sp2I iodine
N2 nitrogen-sp2K potassium
N1 nitrogen-spNA sodium
NAR nitrogen aromat.FE iron
NPL3 nitrogen trigonal planarLI lithium
NAM nitrogen amideAL aluminum
N3+ nitrogen sp3 positively chargedSI silicon
DU dummy atomCA calcium
P3 phosphorous tetravalentLP lone pair
P4 phosphorous pentavalent~ system atom type
* system atom type


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