Hydrogen Bonding II

1
Hydrogen Bonding II

• John Pedersen
• ME 438 Nanoscale Fluid Dynamics
• January 2003

2
Articles

• Hummer, G., Rasaiah, J.C. and J.P. Noworyta.
  Water conduction through the hydrophobic channel
  of a carbon nanotube. Nature. 414 188-190
  (2001).
• Truskett, T.M., Debenedetti, P.G. and S.
  Torquato. Thermodynamic implications of
  confinement for a water like fluid. Journal of
  Chemical Physics. 1142401-2418 (2001).

3
Hummer (Nature) Overview

• Nanotube (13.4 A long, 8.1 A dia) floating free
  in a water bath. 144 carbon atoms
• Water modeled as potential functions (TIP3P)
  1034 of these
• Molecular dynamics simulation 66 ns sim time,
  time step was 2 fs.
• Algorithm is AMBER 6.0

Figure 1c from Hummer et al.
4
Hummer (Nature) Background

• Water molecules entering nanotube lose 2 of 4
  hydrogen bonds filling of tube energetically
  unfavorable
• Hydrogen bonds of molecules inside tube are
  shielded from molecular fluctuations average
  bond lifetime is 5.6 ps vs. 1.0 ps for bulk water
• Water is restricted to bond essentially along
  nanotube axis retains entropy due to ability to
  rotate around bonds

5
Hummer (Nature) Results
Red is normal carbon-water interaction, blue is
modified for weakened van der Waals tube/water
interaction
6
Hummer (Nature) Results (2)

• Flow average was 17 water molecules/nanosecond
  51x10-14 cm3/s measured water flow through
  transmembrane protein aquaporin-1
• Flow occurred in bursts rupturing the hydrogen
  bonds in the water chain is energetically costly
  and thus rare.

7
Truskett (J Chem Phys) Overview

• Water molecules are hard spheres with hydrogen
  bond directions
• Water can interact via van der Waals with wall,
  but cannot bond with wall
• Two confinement effects shown by theory in this
  paper
• Confinement reduces favorable H-bonding/ molecule
  ? liquid-liquid critical point moves to lower T,
  higher r, higher P (also inhibits freezing)
• Confinement introduces density modulations into
  fluid film

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Truskett (J Chem Phys) Pictures
Figures 2 and 3 from Truskett et al.
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Truskett (J Chem Phys) Results
Figures from Truskett et al.
10
Truskett (J Chem Phys) Results (2)
Figures from Truskett et al.