van der waals forces and hydrogen bonds j. israelichvili, „intermolecular and surface forces”,...

Van der Waals forces and hydrogen bonds

J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997

Types of „weak” interactions

Types of „weak” interactions (continued)

Interactions between backbone peptide groups

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Liwo et al., Prot. Sci., 2, 1697 (1993); J. Phys. Chem. B 108, 9421 (2004)

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What are hydrogen bonds?

• X, Y are usualy (99% or so) electronegative atoms• q is usually close to 180o • d(X …Y) < rVDW(X)+rVDW(Y); d(H…Y)<rVDW(H)+rVDW(Y)• d(X-H) is greater than in the free X-H molecule• d+H and d-Y are pronounced wrt non-interacting molecules

HX Yq

d+

d-

rVDW(O)=1.52 ArVDW(H)=1.09 A

Types of hydrogen bonds

• Weak (DH<1 kcal/mol) usually involve non-polar or weakly polar groups.

• Moderately strong (1<DH<20 kcal/mol) involve polar groups.

• Strong (DH>20 kcal/mol) involve ions.

Examples

weak

moderately strong

strong

H-bonds in proteins

• backbone-backbone• backbone-sidechain• sidechain-sidechain• backbone-solvent• sidechain-solvent

Examples

Hydrogen bonding and proton transfer

X H Y

X-H…Y X-…H-Y+

polarity

Symmetric hydrogen bonds

Kojić-Prodić & Molcanov, Acta Chim. Slov., 2008, 55, 692-708

H-bonding energy surfaces are reflected in structural structures

H.B. Burgi, J.D. Dunitz, Acc. Chem. Res., 1983, 16, 153-161

Energy decompositionE=ESX+EPOL+ECT+EDISP

E=EES+EXC+EPOL+ECT

Singh and Kollman, J. Chem. Phys., 1985, 83, 4033-4040

Korochowiec et al., J. Chem. Phys., 2000, 112, 1623-1632