Innovative 3D Visualization for Molecular Structures

1. Let’s take thought 3DPossibilitiesforVisualisation structure ofOrganic Compounds and systemsFarkas Mariann fm@tomtec.hu

2. What you can find: • Visualisetheplasticatom-systemmodelsof the 20’s centuryusedbeforegraphic computer existance. E.g. • Calotte model -Spacefilling,butno possibilitytoseethestructure of themolecule • Stick and Ball model: bond-sticksarethickerthanbond-linesdonothelpthetransparency of chemicalstructures • Use of trianglesymbolstorepresentbonddirections • UsethenewpossibilitieswhattheInformationtechnologymakespossible

3. Result of hard Informatic work: Marvellous burnishing lines, clouding structures (https://en.wikipedia.org/wiki/Molecular_graphics) Incase of onedimensionbond-lines thebrighteninglinesarebeautiful, Sorryasoureye is notsensitiveenoughtofeelthestereo-structure. Itseems, oureye is more sensitívefortaperingbond-lines

4. Usage of triangles: We can sign the direction of some H or substituent.Traditions are strong, even it is among the IUPAC recommendations.OK, we have to use it, until there is no better solution.

5. UsingtrianglesIt’s time to declare some applicability restraint. The two triangles showhalf-way between the two possible existing structure.axial or equatorial Smaller problem, that the bond of benzene ring and carbonyl group is broken. - Amongoffers of a compound library: http://www.tomtecplastics.com/3dmg/Tapering_Lines.htm Speciallyusefulforsurrounding of chiralcenters http://cominnex.com/project/library_design_and_synthesis/

6. Using any molecular graphic program finallyyougetatomicnumber, bonds and x,y,z koordinataes of atoms.EitheruseTapering Lines” program tobuildupyourmolecule, or import yourdataBond-lines going far from your eyes are tapering proportionately Measure of tapering depends on the distance of the atom and your eyesAll of the actual thickening is calculated and made by the program, not user-dependent.

7. Rotating your molecule the actual thicknesses change – depending what is nearer to you Tapering lines

8. The user can modify the maximal thicknes of bond-lines Estradiol TRH (1981) Youcanseethe propeller structure of thethreerings The red part is planar

9. It helps in the interpretation of your results in stereochemistry(e.g. see possible conformations of Dibenzo dioxazocine)

10. Numerous Data Systems of molecular geometry are available for the users.The program accepts data files with extensions .MAE, .SDF and .MOL2 , but all the data can be imported – containing the x,y,z coordinate and name or atomic number

11. Open or import a datafile: as a first look the picture fills the screen

12. You can rotate the molecule, or change the maximal thickness of lines, or change the font-size. If you want to modify data e.g. you want to change alternating double bonds to aromatic ring, or choose new color for fragments, or change molecular structure (e.g. see another configuration), choose DATA/Modify Data

13. As a first step you have to see the serial number of atoms,than eliminate the double bond in the “Multi bond” column – modifying the value to 0, than turn to the other grid, declare the number of atoms and serial number of member atoms in the ring

14. When it is OK, you can change back the Data/Without serial number and see again the Full screen picture You can save either the Data, or the Picture

15. You can use it for teaching: Represent the meaning of chirality

16. Teach more complex structurese.g. represent different stereoisomers of Sterane skeleton Classic picture Stick and Ball model Show chirality: 5a és 5b configurations Using Tapering lines method Rotate Only the skeleton (without H)

17. Build larger molecules using saved fragments

18. When you managed to choose the liked data, choose OK :

20. And you can step further

21. The program is available: (notfortrading)www.tomtecplastics.com/3Dmg Donotforgettoaskfor licence(Username and password) Farkas Mariann fm@tomtec.hu