Computer Applications in Chemistry

GENERAL OBJECTIVES:

1. Be able to use chemistry drawing packages such as "ChemDraw" or "ISIS Draw".

2. Be able to use molecular modelling packages such as "Chem3D" or similar

3. Be able to use specialist graph plotting and analysis software packages such as "Origin", "Sigmaplot", "Igor" or similar.

Students should be able to:

1. launch the drawing package, create new documents, save documents and open existing documents.

2. use menus to set or select drawing preferences such as bond length, bond angles, line width, page set up, etc.

3. select drawing tools from the menus to draw new bonds, add new bonds, and construct drawings of very simple organic molecules

4. print the drawing.

5. draw double and triple bonds

6. draw rings by using the appropriate ring tool or template from the menus

7. draw fused rings by using the same ring tools as above

8. add atom labels to drawings/repeat atom labels and delete atom labels

9. add captions to drawings

10. Format text

11. use orbital tools to select and draw orbitals

12. use chemical symbol tools to select and draw lone pairs, radicals, and charges.

13. select and use the appropriate tools to draw: reaction arrows, arcs, and other shapes.

14. use the eraser tool to delete individual bonds, charges, arrows, etc.

15. select objects by using the selection tool

16. select objects by using the mouse buttons

17. add to the selection and delete the selection

18. select and move objects

19. select and duplicate objects

20. select and rotate objects

21. select and resize objects

22. select and group objects

23. select and align objects

24. use the crosshair

25. cut and paste within the package

26. cut and paste from the package into other packages such as word processing packages

1. Explain the reasons for modelling molecules and reaction intermediates on computers

2. Understand the general concepts involved in computer molecular modelling

3. Understand the mathematical principles underlying modelling procedures (Newtonian Mechanics [e.g. MM2], semiempirical [e.g. MOPAC] and quantum mechanical methods.

4. Discuss the relative merits of the different methods of modelling given above.

5. launch a modelling programme and create an empty model page or window

6. select a pre-existing model from a template menu

7. use rotation tools to rotate and examine the molecule

8. save the new rotation and print the new view

9. open an existing file

10. import a model created by the same or a different modelling programme

11. build a new molecule by using the tools available in menus

12. build a new model by using a drawing programme and importing the resulting file into the modelling programme

13. change an atom to another element

14. change bonds

15. add fragments

16. delete atoms and bonds

17. set charges

18. change stereochemistry

19. select atoms, bonds or groups of atoms and bonds by using the selection tools from menus

20. select atoms, bonds and features by using the mouse buttons

21. move atoms or models

22. rotate fragments of models

23. change orientations of fragments

24. resize models

25. change the appearance of a model (wire frame, sticks, ball and stick, space filling, dot surfaces, ribbons, etc)

26. change colours

27. change atom and bond sizes

28. change element symbols

29. display stereo views

30. display model data (atoms and serial numbers, bond angles, dihedral angles, distance between two atoms, etc)

31. dock models

32. compare models by overlaying

33. export using different file formats

34. export by using the clipboard

35. use the modelling programme to compute the stability of different conformations of the same simple molecule

36. use the modelling programme to minimise the energy of molecules

37. use the modelling programme to find the lowest energy conformation of simple and more complex molecules e.g. aspirin

38. use the semi-empirical functions [MOPAC] of the programme to determine Δ Hf.

Students should be able to:

1. Explain the relationship between a specialist graph plotting and analysis programme and a spreadsheet programme such as Excel.

2. launch the specialist graph plotting and analysis programme

3. input data directly into the programme's worksheet

4. import data into the worksheet from a spreadsheet package such as Excel

5. use menu commands to plot a graph of the data contained in the worksheet

6. use menu and or mouse commands to edit the resulting graph (change: axes, labels, symbols, text, resizing, etc)

7. save graphs and data files

8. save files in different formats (e.g. "standard formats such as TIF files)

9. export data files and graphs into other programmes such as spreadsheets and word processors

10. use menu commands to analyse data in the worksheet

11. obtain basic statistical from the data in the worksheet (statistics on rows and columns, t-tests, ANOVA, etc)

12. use the curve fitting functions e.g. exponential, linear regression, sigmoidal, hyperbolic, etc.

13. use the hyperbolic functions to analyse Michaelis Menten kinetics and obtain the kinetic parameters for suitable enzyme catalysed reactions