Introduction to Hydrolab
1.1 Introduction to the concepts of Hydrophobicity
Hydrophobicity is one of the key mechanisms behind protein folding and drives many chemical processes. Hydrocarbon chains are one of the most hydrophobic molecules. They are virtually insoluble in water and quickly form a separate phase when mixed with water. An everyday example of hydrophobicity is the separation of water and oil.
Hydrophobic molecules are usually non-polar and therefore cannot form strong bonds with water (specifically hydrogen bonds). As a result, water molecules tend to form “cages” of relatively rigid hydrogen-bonded pentagons and hexagons around non-polar molecules. This state is energetically unfavorable. If non-polar molecules in an aqueous environment aggregate with their hydrophobic surfaces facing each other, there is a reduction in the hydrophobic surface area exposed to water. This results in more stable formations.
In this software, you will be able to tune the interaction between water and hydrocarbon chains (modeled by a single particle with an effective potential) and observe the changes in hydrophobicity and aggregation.
Lennard Jones potential, expresses the strength of repulsion and attraction of two particles with varying distances. Below is a sample Lennard Jones potential plot.
- Short range repulsion can be observed in the region where the potential is more than 0 and the intermolecular separation is less than the equilibrium distance.
- Long range weak attraction can be observed in the region where the potential is less than 0 and the intermolecular separation is more than the equilibrium distance.
- Equilibrium position can be observed at the well of the curve, where the potential reaches its minimum.
3.1 Program Inputs Description
- C6 corresponds to and C12
corresponds to of the Lennard-Jones potential, . The default values are shown below.
- The temperature parameter allows the user to input any value
between 0 and 1000 Kelvin. The default temperature is 300 Kelvin.
- The initial configuration parameter has two options. The high
concentration creates a simulation box with a higher concentration of hydrocarbons and the low concentration creates a simulation box with a lower concentration of hydrocarbons. Note that the simulation box size stays constant at 3nm x 3nm x 3nm.
- The time step parameter specifies the number of time steps the
simulation takes. Each time step is 0.001 pico seconds. The number of time steps can vary between 2 and 500000 steps. The default value is 1000 steps.
More time steps increase the simulation time.
- The PDB content has the options of generating the trajectory files
of carbon atoms only, water molecules only or both. We recommend that you save the trajectory file with a “.pdb” extension onto your local machine. You can then view the trajectory using this file with your preferred molecular visualization tool. We recommend VMD or Pymol.
Link to PDB format:
Link to VMD:
Link to Pymol:
4.1 Program Outputs Description
Hydrolab generates several different types of output files such as:
- Lennard-Jones potential plots
- Initial and final configuration images
- Trajectory file in a PDB format
- Log file of the simulation run
These files can be saved either by using the download button next to the scroll down icon or scroll down and click "download".
5.1 Shapes of the Lennard-Jones plots
Follow the steps below to observe the effects of epsilon and sigma values on the shape of the Lennard-Jones plots.
- For C-C interaction, assume sigma=0.337nm and
epsilon=1624kJ. Compute C6 and C12 and observe the minimum point and the x-intercept of the Lennard Jones potential curve.
- Multiply epsilon by 2, compute C6 and C12 again and observe the
- Multiply sigma by 2, compute C 6 and C12 and observe the
- Comment on your observations.
6 Clustering and Dissolution of Hydrocarbons in Water
Now, observe the effects of the strengths of C-C and C-O bonds on the clustering of the hydrocarbons. After mixed with water molecules, hydrocarbons can act in three different ways: clustering into a sphere, clustering into a slab, and dissolution into water.
The number of time steps must be set to 10000 for all the procedures below.
6.1 Spherical Clustering
Spherical clustering occurs when there is a low concentration of hydrocarbons and strong C-C bonds and weak C-O bonds. Observe the spherical clustering of hydrocarbons for low concentration of hydrocarbons.
- Run a simulation with the default bond strengths and observe the
shape of the hydrocarbon clustering. It should be close to a sphere.
- Multiply C6 C-C by 10, run the simulation again and observe the
clustering of the hydrocarbons into a perfect sphere.
- Additional simulation: set the bond strengths back to the default
and divide C6 C-O by 100, run the simulation and observe the clustering of the hydrocarbons into a sphere.
Spherical clustering visualized by VMD
6.2 Slab Clustering
Slab clustering occurs when there is a high concentration of hydrocarbons inside the box. This is due to the periodic boundary conditions imposed on the system.
Hence, repeat the above steps by changing the concentration to high concentration. In each case, you should observe hydrocarbon clustering into a slab.
Slab clustering visualized by VMD
6.3 Dissolution in Water
Dissolution of hydrocarbons into water occurs when C-C bonds are weakened and C-O bonds are strengthened. This situation is similar to polar molecules or ionic molecules in water. Follow the procedures below to observe hydrocarbons dissolving in water.
- Multiply C6 C-O by 400, run the simulation and observe the final
arrangements of hydrocarbons.
- To observe the scattering of hydrocarbons better, download the
trajectory file in a PDB format and save it as a “.pdb” file. Use your preferred molecular visualization program on your local computer to view the scattering of the hydrocarbons.
Dissolution of hydrocarbons in water visualized by VMD
|Contributor Name||nanoHUB login or other contact information|
|Eric Darve||darve Stanford University|
|Artit Wangperawong||artitw Stanford University|
|Kazutora Hayashida||hayaska Stanford University|