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Text File | 1994-02-04 | 11.4 KB | 280 lines

CHEMICAL Ver 3.1 Oct 28, 1988 CHEMICAL is a molecular modeling Program to aid in the formation of three dimensional pictures of chemicals. Atoms are selected from a Periodic Table (using the A command) and electron orbital information retrieved. The Atoms are then bonded (using the B command). The chemical is displayed as it is being constructed. The chemical can be viewed from different directions by using the up and down cursor keys and the V command. If desired the Hybrid and Ionize commands can be used to alter the orbitals before bonding. Atoms can be bonded into groups, then the groups bonded to other groups to make large chemicals. CHEMVIEW is a companion program that shows 3-dimensional animation of the models generated with CHEMICAL. CHEMVIEW requires an EGA board and monitor. CHEMVIEW is written in Turbo PROLOG with the graphics routines written in Turbo C. To use CHEMVIEW simply start the program and select the file desired. CRYSTAL is companion program that places atoms on a lattice framework to form crystal structures. The structure is defined by a text file. A text editor is built into the program. The text file is converted to a image that is shown rotating in three dimensions. An EGA or VGA monitor is required. CHEMICAL requires 640K bytes of RAM and a CGA or EGA display. You may need to eliminate RAM resident programs in order to run CHEMICAL. CHEMICAL is started by entering CHEM at the DOS prompt. The CHEM.DOC, CHEM.TUT, and *.BGI files should all be on the same directory. Select the graphic mode desired, then push the Enter key. The program GRAFTABL should be run prior to running CHEMICAL with a CGA monitor. The graphic display format is different for the various modes for a particular monitor. Try each mode to determine your preference. Commands are selected by depressing the first letter of the command or by depressing (cr) if the command has already been selected. The following commands are available: The commands for version 3.1 of chemical are: A - (Atom) This command displays a periodic table. Elements are selected by moving the cursor to the desired Element, then depressing the CR key. The esc key is used to exit this command. B - (Bond) This command is used to bond two atoms. A list of all atoms selected is displayed, along with its electron orbital configuration. The size of the atom is determined the first time it is bonded. A choice of three bond types: Anti, Dative, and Shared, is provided to determine which atom in a bond will supply the two electrons needed for a molecular orbital. A shared bond takes two electron from each atom. A Dative bond takes both electons from one atom. An anti bond allows three or four electrons to be used in the bond. C - (Clear) This command clears the screen and the buffer for all Atoms and Bonds selected so far. A Yes/No menu is used to reduce the change of accidently clearing the buffer. FA - (Animate) This command executes program CHEMVIEW which shows molecules in 3 dimensional rotation (on EGA monitors only). The cursor keys are used to change the direction of rotation, the + and - keys change the size, the End key stops rotation, the space bar returns to the CHEMVIEW window and the Ctrl Break key returns to CHEMCIAL. CHENVIEW.EXE must be on the default disk. FB - (View Buffer) This command stores the buffer under the file name TEMP.DAT, then allows the file to be viewed. FH - Show help file FM - Minimize Chemical File size by deleting unused orbitals. Do not use this command until you are completely done, since no additional bonds can be made to a minimized file. FR - Read a Chemical File FS - Goto Operating System FT - Show Tutorial File FV - View a file from disk FW - Write a Chemical File G - (Group) This command is used to attach groups of atoms that were made using the Bond command. One atom from the group selected is attached to an atom of a group previously selected. The new group can be rotated around the X,Y, or Z axis before it is attached. H - (Hybrid) This command is used to combine electron orbitals into hybrids. A list of possible Hybrids is displayed. A _5 or _6 ending indicates that the bonding angles have been adjusted to make a 5 or 6 bond flat ring. I - (Ionize) This command is used to ionize an atom. A list of the possible ionizations is displayed. MA - (Move) This command is used to manually move an Atom or Group. MC - Change color of atom. The color for all atoms of the type selected are changed. MD - Deletes a selected atom from the current buffer. This command is most useful for modifing an existing file into a similar chemical. All atoms following the one selected are re-numbered. This command may require several seconds on large files. MR - (Re-center) All atoms are re-centered on the screen. This command is used when reading files generated by older versions of CHEMICAL. MS - Rotate around Sigma Bond - Atoms are free to move around sigma bonds, and will generally do so to minimize the energy of the system. This command will rotate an atom and other attached atoms. MX - Rotate atoms around X axis. Do not use any of the rotate commands until the molecule is complete. The angle for bonds made after rotation may not be correct. MY - Rotate atoms around Y axis MZ - Rotate atoms around Z axis R - (Not on Menu) Read to buffer from TEMP.DAT SB - Toggles Bond lines on/off. Bond lines are only available in graphic mode with 16 colors. SC - Toggles electronegativity scale on/off. When on, a color scale is shown at the bottom of the display window (EGA mode only). The atom colors are changed to correspond to the electronegtivity of the atom. When off no scale is shown and the colors are changed to have more contast. SE - Toggles expanded view on/off. SG - Toggles grid on/off. SN - Toggles atom numbering on/off. V - (View) This command will show the view of the chemical that has been selected by the up/down cursor keys. The horizonal axis and vertical axis are shown in the upper right hand corner of the screen. Lines are shown to indicate bonds. The upper right hand corner of the screen shows which axis (X, Y, or Z) is aligned with the vertical and horizontal view shown. Atoms are listed on the left. In 16 color modes, the color is used to designate the atoms. In 2 and 4 color modes, the atoms are labeled. W - (Not on Menu) The Write command write the buffer to the file TEMP.DAT. The Write and the Read commands can be used to recover from an error during construction of a chemical. Contruction of Ring Structures Ring structures are difficult to make because of the large number of possible bonds. Also the angles need adjustment to make a closed ring. Special hybrids ending in _5 or _6 are provided in CHEMICAL for constructing 5 and 6 flat ring structures. The ' and ` bonds should be selected to form rings. CHEMICAL defaults (high- lights) to this choice to simplify ring formation. The formation of combined six and five ring structures such as Purine requires adjustment of the angles for the atoms to meet correctly. CHEMICAL will make this adjustment if the six atom ring (using _6 hybrids) is made first (don't forget to bond the 1st and 6th atoms before added the 7th). Then three _5 hybrids should be selected. The default bonds should then form the correct double ring structure. The first ring is generated clockwise and the second ring is generated counter-clockwise. The angles in the sp3 hybrid do not allow a flat ring. A twisted ring can be made by selecting the default bond selection sequence. Example 1: Make Water Molecule 1) Use the A command to show periodic table 2) Select O,H, and H using the cursor keys and Enter Key 3) use esc to exit A command 4) Select the Bond Command 5) Select O and H 6) Select shared (default) bond 7) Select one of the O-H bonds 8) Use the Bond Command to make the other O-H bond (Two atoms always need to be selected to make a bond) Note: The angle between the Hydrogen atoms can be made closer to the actual angle by selecting the sp3 hybrid for Oxygen. Example 2: Benzene C6H6 1) Clear previous entries with (C)lear 2) Enter 6 Carbon Atoms using (A)tom 3) Select the sp2 hybrid for each Carbon Atom using (H)ybrid 4) Use the Up/Down cursor key to set view to TOP 5) Bond Atoms 1-2, 2-3, 3-4, 4-5, 5-6, 1-6 (selecting highlighted bond) 6) Make a pi bond between atoms 1-2, 3-4, and 5-6 using (B)ond 7) Enter 6 Hydrogen Atoms using (A)tom 8) Bond each hydrogen atom to a carbon atom Example 3) [Co(NH3)6]3+ Coordination Compound 1) Select Co and six N atoms 2) Select the +3 ionization and d2sp3 Hybridization of Co using the Ionize and the Hybrid commands 3) Select the sp3 Hybrization of N using the Hybrid command 4) Bond the six d2sp3 orbitals on Co with the six N atoms using the dative bond 5) Select 18 hydrogen atoms 6) bond the hydrogen atoms to the six nitrogen atoms CHEMICAL, CHEMVIEW, and CRYSTAL are placed in the Public Domain and may be freely copied and distributed. The latest version of including source code can be obtained from the author for $20. Updates are $10 for registered users. The source code is not for public distibution and is only available from the author. PLANETS is an astronomy program that is also available. This program shows motion of the planets, moons, and sun. Version 4.0 is now available. Larry Puhl 6 Plum Court Sleepy Hollow, Ill. 60118 ORDER FORM: CHEMICAL/CHEMVIEW/CRYSTAL $20 ____ CHEMICAL/CHEMVIEW/CRTSTAL (registered users) $10 ____ PLANETS $10 ____ PLANETS (for registered users) $5 ____ Shipping outside of USA $5 ____ 3 1/2 inch disks $2 ____ TOTAL ____ send to: ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ Comments: