Challenge Questions for Students (opens in a new window, so you can keep working on the model while you think of the answers)
The model (molecular coordinates file in pdb format) was prepared by Eric Martz:
10 water molecules were arranged arbitrarily in two approximately straight rows of 5, a bit farther apart than van der Waals radii. This initial arrangement could be thought of as a gas-like conformation (lacking entropy!).
Energy minimization was then applied, causing the molecules to collapse into a small droplet with ample hydrogen bonding. Energy minimization involved van der Waals interactions and electrostatics, and was done with MDL Sculpt. There is no thermal energy in this simulation.
24 frames of atomic coordinates were saved from the minimization process, which can be played as an animation.
For the first 11 frames, only van der Waals energies were applied. Starting with the 12th frame, both van der Waals and electrostatic interactions were utilized. This was done in order to produce a single droplet. When electrostatics were invoked from the outset, two droplets were formed. In the animations, the transition at the 12th frame produces a momentary reversal of the general trend towards compaction.
In this page, the model and the animation are shown using Jmol capabilities. Covalent bonds are automatically determined by Jmol, while hydrogen bonds are generated between those oxygen and hydrogen atoms that are not covalently bonded and are separated by a distance below the value specified above.