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Computers in Chemistry—CHEM 3111 Problem Set 5
Use ChemDraw to draw molecules and perform simple calculations.
In this exercise, you will use ChemDraw and Chem3D to draw some simple and
not so simple molecules, then determine their 3D structure, and setup and
pertorm some simple molecular dynamics calculations. You should submit either
a ChemDraw or MSWord document with the pictures, structures, and
descriptions. These can be emailed to me or simply uploaded to your account on
k2.chem.uh.edu
1. Practice using ChemDraw to make the following molecules:
a.) trans-stilbene
b.) water
c.) an amino acid sequence of 4 amino acids: (e.g)
O
H 2N
CH
H
C
O
N
H
CH
H
C
O
N
H
CH
C
OH
H
d.) caffine
2. Using the "Scripts" menu, determine the 3D structure of each of the molecules
or clusters you just drew. For eacn case, use Chem3D to use MM2 to minimize
the energy of the molecule. (e.g. for the amino acid sequence above, the minimal
energy structure looks like:
3. For the amino acid sequence, add some water molecules about it (using
ChemDraw), then setup and perform a molecular dynamics calculation at
300K. Let the system run for about 10000 steps (I’d suggest using a 1fs
time step.) and discuss the location of the water molecules about the
amino acid chain. (eg. For the chain above, adding 4 waters:
H
H
O
O
O
H
H 2N
O
O
H
CH
H
C
N
H
H
O
H
CH
C
N
H
CH
C
OH
H
H
H
O
H
then running the calculation produces the following configuration.
4. Finally make a block polymer of 3 blocks of different amino acids. Choose
the middle segment to have hydrophobic side chains. For example:
O
O
O
O
H
H
H 2N CHC N CHC N CHC N CHC
H
CH3
CH3 H 3C
CH2
H 2C
CH2
H 2C
NH2
O
N CHC
H
CH2
H 2C
CH2
H 2C
NH2
O
H
N CHC N
CH2 H
H 2C
CH2
H 2C
NH2
O
CH C
H
O
H
N
CH C
O
H
N
H
CH C
H
Place some waters around it and minimize the energy. Run a MD simulation
for about 5000 steps and discuss the structures you observe. For example,
here’s a snap shot of a simulation based on the molecule above with 10
waters. Notice the waters tend to avoid the alkane side chain segments.
Looking at the output data, plot the total energy, potential energy, and
temperature as a function of time. Has the system approached
thermodynamic equilibrium at 300K at the end of your calculation?
OH