Reference no: EM132343029
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
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