KCH/SWMOS – tasks

All tasks will be done in the HyperChem software. All results (pictures, values) add to this document.

1.  Set rendering of the C60 molecule to the following displays. (C:/hyper80/samples/aromatic/c60.hin)

Insert screenshots including window of HyperChem to this file.

2.  Make model of 2-(aminomethyl)phenol and display it in the following ways (including H-bond).

3.  Determine following parameters of oxalic acid:

a.  C-C bond length.

b.  Distance of the hydrogen atoms.

c.  Angle of the O-C-O bond.

4.  Make model of hexyacyanoferrate anion.

5.  Make model of some protein and nucleic acid according to instructions on the pages 91-98.

6.  Make model of polyehtylene molecule containing 20 units.

7.  Make model of fluoroethane, sign according to picture below and try following setups for polymers:

a. 

b. 

c. 

d. 

8.  Compare energies of the cyclodecane conformers (procedure according manual, pages 129 – 145).

9.  Compare geometry of the alanine molecule in the vacuum and in the aquatic environment.

10.  Make 3D model of ammonia molecule (NH3). Measure angles of bond H-N-H (all should be 109,471°). Perform geometry optimization (AMBER, amber2) and measure angles again. Add free electron pair on the nitrogen atom (Lone pair) and refresh 3D model. Measure the angles of H-N-H again. Perform the geometry optimization (AMBER, amber2). How does the optimization change the angles? Find out how the angles will change in the case of ammonia in the water (both without and with the lone pair).

11.  Molecular dynamics

Perform “simulated heating” (pages 168 - 177). Setup the MM+ method in the molecular mechanics. Create the 3D model of decane molecule and save it with the name “C10build”. Switch on saving of the results to the log file. Compute energy of the molecule (Single point). Perform geometry optimization (Polak-Ribiere) and save model as “C10opt”. Compare both structures (display them in one picture and superimpose 3 carbon atoms on the one side of the molecule. Measure distance of the two terminal carbon atoms (on the opposite side of the molecule). Reload file “C10opt”. Perform heating of the decane molecule at the temperature 300 K by using the molecular dynamics (heat time 0, run time 0,5, cool time 0, step size 0,001, in the vacuum) and after this perform geometry optimization. Compare result with original molecule (before heating).Perform the same computation for the temperature 1000 K and compare again. Switch of the saving of the results to the log file and obtain energies of particular conformations from the log file. Explain differences.

12.  Conformational search

Load file “C10opt”. Select C3 to C6 and a name the selection „cc“. Deselect all. Start Conformational search tool „Compute – Conformational search…“. Choose „Options – Choose torsion” in the tool. Click at “cc” in the next window and move it via “Add” to the list in the right pane and then click at “OK”. Choose „Run – Start“ and let it run for a while (3 rows will appear in the table Conformations found). Click on the first row and choose „Edit – Put molecule“. Save it as „C10a“. Repeat the procedure for second and third found conformation (C10b a C10c). All 3 conformations display on the one image in the superposition of the C3 – C6 carbons (distinguished by different colors).

13.  Compute partial charges on the atoms in the ions H3O+ a OH- (semiempirical – CNDO).

14.  Display surface with density of charge equal to 1 for the water molecule.

15.  Display unoccupied molecular orbitals of the oxygen molecule (semiempirical – CNDO).

16.  Display uccupied molecular orbitals of the ethene molecule.

17.  Create water molecule, compute charges on the atoms (CNDO) and save model to the file. Load the model 4 times and move each molecule so molecules are close to each other. Optimize geometry for the system of 4 molecules (molecular mechanics, AMBER, amber3). Choose “Display – Show dipole moment”. Add the Fe(III) cation among the water molecules and optimize geometry (only for the selection of water molecules) Describe the shape which is formed by water molecules around the Fe(III) cation. Try whole procedure for 5, 6 and 8 molecules of water molecules around the metal ion. Describe polyhedrons.

18.  Compute protonization energy for water, ammonia, methane and hydroxide anion (without MP2).

19.  Compute vibrational spectrum of the naphthalene molecule.