SOFTWARE -Molecular Design Studio "ONYX" (MDS)

The program is a perfect tool for teaching and studying many parts of general and organic chemistry in universities and colleges, and may be useful for professionals in the field of chemistry.

The program is supposed to be used in PC having operating system Windows 98/NT/2000/ME.

Moreover the animations previously done were fixed in their camera angle and their execution. MDS animations can be viewed from the three main axis while running and smoothly rotated when paused at any frame. Additionally the animation files that are being played in the viewer can be reopened for modification in MDS.

In previous animation work of chemical reactions for supplemental material for an organic chemistry textbook it took a skilled animator two days to set up and run the animations. With MDS it takes about fifteen minutes or less once one learns the basic commands. Additionally the animations took 3 to 20 Mbytes of space depending on length. The control files that represent the animations are 5 to 25 Kb.

An interesting feature of the binary builder is the spread sheet that shows of the atoms that will be combined to make a molecule. The bonding of electrons to make the molecule can be either automatic or manual. In manual mode the number of electrons in the shells of each atom is shown in the spread sheet. Electrons can be promoted within an atom and electrons can be dragged from one atom and dropped on another atom creating a bond. The result of this action on the spreadsheet shows immediately in the graphical view window and this action illustrates Lewiss rule.

The main elements of MDS are the graphical view window, the animation tools and the various chemical editors. The geometrical builder creates geometrical molecules and crystals. The organic builder creates organic structures. The binary builder creates simple molecules and ions. The chemical editor allows these basic structures to be combined and edited.

MDS and the chemistry animation player or viewer are in roughly their final form. There is still work being done on the help files so please understand that these help files are still a work in progress. As the help file is a separate program custom versions can easily be developed or the existing one modified with standard help editors.

MDS consists of the main program, which is the rules based simulation of chemical reactions, and a Player which will play the animations and also display molecules. It is intended that the Player be distributed free and the MDS program be sold.

Ground states of valence orbitals, van der Waals radii, and electro negativities of chemical elements are in the database of the program.
While writing the name of the atom, this program shows atomic orbital diagrams of the main state of an atom It also can change the atom to the excited state to get hybridization of orbitals and build a covalent bonds with other atoms.
The program constructs covalent binary molecules automatically from the written formula. This also can be done manually. Larger molecules are then manually created by connecting molecules and ions by moving and joining valence electrons in the main window of the program. The program builds the main types of organic compounds including organic chains and cycles automatically.
The program automatically calculates and builds 3-dimension structures of molecules by every change on the valence orbital. It calculates and builds the changed hybridization state of an atom in the process of moving valence electrons. It calculates values of standard angles of covalent bonds of different types of hybridization. It calculates and shows charges and formal charges in the picture of the atom. It calculates and shows an oxidation state of atoms in the process of modeling molecules and ions and in the process of chemical reaction animation.
The program builds geometrical 3-dimensional structure models of crystals and complex compounds.

MDS is created for: