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. A familiar example is the separation of water and oil.

Hydrophobic molecules are usually non-polar and therefore cannot form hydrogen bonds with water. 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 unfavourable. 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 conformations. In a sense, rather than constituting an attractive force such as hydrogen bonds, the hydrophobic effect results from an avoidance of an unstable state.

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.

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Researchers should cite this work as follows:

• Eric Darve, Artit Wangperawong, Kazutora Hayashida (2015), "Hydrophobicity Lab," https://nanohub.org/resources/hydrolab. (DOI: 10.4231/D3QB9V65Z).

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1. chemistry
2. educational tool
3. GROMACS
4. nano/bio