Go to and Go to My Account from Top Menu Bar

Go to http://chemistry.ncssm.edu/ and go to my account from top menu bar

Part I. Select New Job, Create new job, Build Molecule, click open Editor, Select Tools, then Build, then pick the atoms of your choice in order to build methanol, ethanol, acetaldehyde and C2H6O. Draw these molecules on the table at the end of this document. Under Build, you can add a fragment of your choice, either a functional group. Careful if you select new under file all your work will go away.

Under build is other and up pops the PT, select element with each click a new one appears in the screen, then select from the menu bar on the side the bond tool- click on the inside of the atom and drag to other atom, repeat until all bonds formed, repeat form multiple bonds

View Zoom, move mouse from rt to lt or lt to rt to change size.

The current tool is always displayed on the editor's status bar. In addition, information such as bond distances, angles, etc. may also be displayed on the status bar, depending on the current editor tool.

When happy, close under the file menu and your molecule appears on the original page. Put at least 2 molecules per page.

The Build Molecule page allows you to draw the 3-D chemical structure for which you wish to

perform calculations. Initially the display in the page will be blank, indicating that no molecule

has been drawn. A navigation bar at the bottom of the page describes your progress in building

the molecule, choosing a computational engine, setting job options, and submitting your job.

Click Open Editor to invoke the 3-D molecular editor and build a molecule.

Click on Clean-Up and select one or more of the following options. When built correctly let me see your molecules please.

· Add hydrogens
This menu item will fill the unfilled valencies of all the atoms in the molecule with hydrogen atoms.
Hybridization: This menu item will attempt to assign the correct hybridization to every atom in the molecule.

· Geometry: The menu item will use the assigned hybridization in an attempt to generate a starting geometry for the molecule that is somewhat close to the optimized geometry.

· Comprehensive: This menu item will attempt to fill empty valencies with hydrogens, assign the correct hybridization, and then optimize the starting geometry in a single step. This option is also accessible from the tool bar .

· Selection Only: Activating this menu item will cause future clean-up operations to be restricted to the currently selected atoms. All other portions of the molecule will be left unaffected.

Help Menu

· Index

· This menu item brings up the help file you are reading now.

· http://chemistry.ncssm.edu/book/index.html

· Chapter 10 Molecular Modeling

Part II. To use this you do not need to login: Government made molecules: http://srdata.nist.gov/cccbdb/

Using the CCCBDB

The CCCBDB is set up to allow you to get experimental data, calculated data and comparisons between experimental and calculated data. The general design is to allow you to specify what you want in the following order:

1) choose a property (such as calculated vibrational frequencies)

2) choose a molecule (or molecules)

1. Specifying a moleculeWhen asked for a formula the CCCBDB can recognize entries such as CH3OH or (CH2)3O
Index of properties in the CCCBDB

2. Check out the list of different molecules;

3. Pick geometry from side bar XII Geometries, then pick E. Compare bonds and angles for specific molecules

4. Enter a molecule i.e. CH3OH, select 2 atoms by clicking in the box and submit query for bond length, then select 3 atoms by clicking in the box for 3 different atoms then submit query.

5. Record for the atoms in methanol, ethanol, acetaldehyde

6. Compare bond lengths and angles for the following compounds by filling in the table, we will discuss the similarities and dissimilarities of each pair

o C6H12 C6H6

o CCl4 CH4

o SO3 N2O4

o CH2CCH2 C3H8

o N(CH3)3 NH3

o CH3OCH3 HOH

o CH3OOH H2O2

name / Structural formula / bond lengths (list atoms) / bond lengths / Bond angles
(list atoms)
methanol
ethanol
acetaldhyde
PCl5 / P-Cl / Cl-P-Cl
PF5