Nanokemi (NKEC18)

Kemi, IFM, LiU

Lab instructions:

Computational-chemistry studies
of molecules and nanoparticles

The HYPERCHEM program

The molecular-modelling program HYPERCHEM can be used for molecular mechanics (MM)
calculations, molecular dynamics (MD) and Monte Carlo (MC) simulations as well as quantumchemical (QM) ab initio Hartree-Fock and semiempirical computations for small and mid-sized
molecules on an ordinary MS Windows-equipped PC.
Starting the program
Start the program from Windows XP:s start menu down in the left corner: choose Start All
Programs HyperChem Standard HyperChem Standard 5.1.
Five permanent licenses are available on the student-lab computers. (In addition there are fully
functional but time-limited licenses that can be downloaded from http://www.hyper.com.)
Building molecules
One can start by drawing a skeleton of the molecule where all the atomic nuclei except the
) and then L-click-dragging with the
hydrogens are drawn by first pressing the drawing tool (
mouse. Default is to use carbon when drawing the skeleton, but this can be changed under the
Build pull-down menu by selecting Default Element, Then the Add H and Model Build
command is selected from the Build pull-down menu, which adds hydrogens in typical
positions under the assumption that all carbon atoms with four single bonds have tetrahedral
geometry etc. Alternatively various molecular fragments can be downloaded from the
Databases pull-down menu or read in under File Open. Thereafter a more refined
geometry-optimization can be performed using molecular mechanics, semiempirical or ab initio
quantum-chemical methods.
To perform a calculation, the type of calculation is first selected from the Setup pull-down
menu, where also various computational parameters are specified in the dialogue boxes. Then the
calculation is started by selecting the desired task under the Compute pull-down menu.
The molecule can be rotated in the plane of the picture by pressing the rotation tool (
around two rotation axes in the picture plane by pressing the second rotation tool ( ).

) or

Atoms can be selected using the selection tool (

). Multiple atoms can also be selected by a
square box that can be obtained by simultaneous LR-click-dragging (make sure that Select
Sphere is NOT marked under the Select pull-down menu).
Save your results in a log file by choosing File Start Log. Keep track on where you save your
log files.
Below are some suggestions for exercises. Suggestions and individual initiatives are welcome.

Exercise 1: A capping molecule

Create a hydrocarbon polymer chain. Delete one of the hydrogens at the end of the chain and
replace it with an OH group. (Before you start, make sure that under Build Default Element C is
marked, and under that Build Explicit Hydrogens is NOT marked. To create the OH group, set
Default Element to O and then L-click-drag from a carbon atom followed by Build Add H &
Model Build.) Modify the hydrocarbon chain to create for example a polyethylene-glucol chain.
Energy-minimize this structure using the molecular mechanics method. Select Setup Molecular
Mechanics OPLS. Then start the calculation Compute Geometry Optimization - OK. Note
your final energy, which is shown in the lower bar of the window or in the log file.
(The unit is here kcal/mol. In the MM method the energy is parameterised in such a way that it
corresponds to the enthalpy of formation).
Run an MD simulation for this molecule. Choose Compute Molecular Dynamics and set the
temperature to 2000 K and a run time of around 1 ps, then press OK. Repeat this for a few lower
temperatures, down to 300K. Then perform a geometry optimization for the final MD geometry.
Note the optimized energy. Is it higher or lower than the one obtained above?
Repeat the MD simulation using different simulation lengths and cooling rates, followed by a
geometry optimization. Try to find the structure with the lowest possible energy, the so-called
global minimum. (The method that you just have used is termed Simulated Annealing.)
Once you have obtained a low-energy structure that you like, perform a semiempirical quantumchemical geometry optimization for this structure. Choose Setup Semiempirical PM3 and
under Options make sure that RHF is marked, the total charge is set to 0 (= sum of nuclear
charges number of electrons), the spin is 1 (singlet, so all electrons are paired), and press
Configuration Interaction and make sure that None is selected. Then press OK, OK, OK. To start
the calculation, choose Compute Geometry Optimization as before. Note the energy.
(The energy is given in kcal/mol in the results bar or in kcal/mol and in atomic units in the log
file. The energy obtained is the E from the Schrdinger equation, that is the sum of the potential
and kinetic energies of the electrons and the potential energy of the nuclei. This corresponds to
the thermodynamic function named internal energy, U, at zero Kelvin.)
Compute a single point energy (the energy for this particular set of nuclear coordinates) Compute
Single Point, then study the orbitals by selecting Compute Orbitals and click on the HOMO
(the uppermost green line) and the LUMO energy levels (lowest violet line). Plot the orbitals by
pressing Plot (make sure that Orbital squared is not marked). Note the energies of HOMO and
LUMO and calculate the energy difference.
Also plot the total electron density with the electrostatic potential mapped on the surface:
Compute Plot Molecular Graphs and under Molecular Properties select Electrostatic potential
and 3D Mapped Isosurface, under Isosurface Rendering select Flat surface and contour value
0.05, and under Isosurface Grid select Medium. Can you see which part of the molecule that is
the most electronegative?
Save your molecular structure as a *.hin-file before ending this exercise!

Exercise 2: ZnO nanocrystals

Read in the file ZnOchunk.hin, which contains a big slab from the ZnO wurtzite crystal. The
file can be downloaded from http://www.ifm.liu.se/physchem/courses/NKEC18/, in your web
browser L-click on the file and choose Save target as). Delete ions from this slab (using the
selection tool and LR-click-drag, see the introduction) to create for example small nanorods,
nanodisks or nanospheres. Make sure that they contain as many Zn ions as O ions, and try cut the
crystal in such a way as to get as few dangling bonds as possible. Geometry-optimize these
nanoparticles using the semiempirical PM3 method and record the resulting energies. Save your
structures.
For a systematic increase of the cluster size, plot the energy per ZnO unit versus number of ZnO
units. Also plot the HOMO and LUMO energies as well as the band gap (the difference in energy
between LUMO and HOMO) versus the number of ZnO units.
If you have constructed different shapes, then compare the energies for the different clusters for a
given size to determine which shape is the most favourable for a ZnO nanoparticle.
Exercise 3: Capping the nanocrystal (if time permits)
Select one of the nanocrystals from above and import the capping molecule from Exercise 1 (use
the File Merge command). Try to rearrange the molecule so that it comes fairly close to the
nanoparticle with a realistic geometry (by selecting one molecule and R-clicking you can rotate
that molecule while the other remains fixed). Delete the H from the -OH group and instead add
the H to one of the oxygens (at a distance of about 0.96 ) on the nanoparticle surface.
Geometry-optimize the structure using PM3 and note the energy. Calculate the adsorption energy
(in kcal/mol):
E = [E(molecule) + E(nanoparticle)] E(molecule+nanoparticle)
Perform the same task but exchange the -OH group by -SH, -NH2 or -COOH and investigate how
the adsorption energy changes.
Try to cover the nanoparticle with a monolayer of molecules to study the structure of the capping
layer.
Report
Discuss your results with your fellow participants and finally with your lab instructor before
leaving the lab.