Water clusters made up of various numbers of water molecules have been described.
Are all of these structures theoretical?
What experimental evidence supports any of these structures?

How does the free energy of a particular water cluster (per number of molecules in the cluster) vary from one thermodynamically stable arrangement to another? Is there a general trend, e.g. larger clusters are more stable?

In response to Martin's initial comment:

I am curious about water clusters in the context of receptor-ligand interactions (for example, in protein receptors, enzymes or synthetic host cavities).

In cases where the cavities of these macromolecules is small (for example, a small enzyme active site) what kinds of water clusters are likely to fill this void in the absence of ligand?

Put more broadly, does the structure of the water that is filling the cavity destabilize the receptor in such a way that ligand binding is enhanced?

Considering a hypothetical receptor that is known to bind ligands (whose sizes range between 4 and 20 non-hydrogen atoms) in water, what are likely structures for the encapsulated water cluster that will be displaced by the ligands upon binding?

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    $\begingroup$ What do you mean by 'stable'? Also, many arrangements exist and experiment has been able to identify some of these low energy configurations. $\endgroup$ Jul 24, 2014 at 12:56
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    $\begingroup$ Have a look at this site. There's a large section devoted to water clustering. $\endgroup$ Jul 25, 2014 at 15:14
  • $\begingroup$ @LordStryker I feel thermodynamic stability would be most helpful in answering this question, but info on kinetic stability is also welcome (although I imagine kinetic barriers to cluster rearrangement would be very low). $\endgroup$
    – dollabillz
    Jul 25, 2014 at 19:56
  • $\begingroup$ @NicolauSakerNeto Thanks for the helpful link! Very cool site $\endgroup$
    – dollabillz
    Jul 25, 2014 at 19:57
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    $\begingroup$ If you're interested in water inside enzymes, I know this paper did some simulations about it. I don't understand it, he just works down the hall from me.Whalen, K.L., Spies, M.A. Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations. 2013, J Chem Inf Model. 53(9):2349-59. PubMed PMID: 24111836. $\endgroup$
    – user137
    Jul 27, 2014 at 3:54

1 Answer 1


The Cambridge Cluster Database can give you a start with theoretical binding energies, but only one isomer for each size is shown.


  • $\begingroup$ Could you elaborate a bit more on the answer? I realize there's probably a ton of information there, but one or two examples of what they offer would be helpful. $\endgroup$
    – jonsca
    Sep 18, 2014 at 9:04

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