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Hydrogen bond

A hydrogen bond of X–H \(\cdots\) Y–Z, where X is the donor and Y is the acceptor atom, can be classified based on distances and angles. One characteristic recommended by IUPAC is that the H \(\cdots\) Y distance is less than the sum of H and Y van der Waals radii. Hydrogen (1.10 Å) and oxygen (1.52 Å) 1 would have a cutoff of 2.62 Å. Others recommend a cutoff of 2.50 Å 2 based on structural analysis 3 and quantum chemical calculations 4. Since the difference between a 2.5 and 2.62 Å cutoff is likely a substantially weak hydrogen bond, we will use a H \(\cdots\) Y cutoff of 2.5 Å.

  1. Mantina, M., Chamberlin, A. C., Valero, R., Cramer, C. J., & Truhlar, D. G. (2009). Consistent van der Waals radii for the whole main group. Journal of Physical Chemistry A, 113(19), 5806-5812. ↩

  2. Hubbard, R. E., & Haider, M. K. (2010). Hydrogen bonds in proteins: role and strength. Encyclopedia of life sciences, 1, 1-6. ↩

  3. McDonald, I. K., & Thornton, J. M. (1994). Satisfying hydrogen bonding potential in proteins. Journal of molecular biology, 238(5), 777-793. ↩

  4. Liu, Z., Wang, G., Li, Z., & Wang, R. (2008). Geometrical Preferences of the Hydrogen Bonds on Protein− Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations. Journal of Chemical Theory and Computation, 4(11), 1959-1973. ↩