Hydrogen bonding in amides

Boal AK, Rotello VM (2000) Intra- and intermonolayer hydrogen bonding in amide-functionalized alkanethiol self-assembled monolayers on gold nanoparticles. Langmuir 16 9527-9532... 

Kearley, G. J., Fillaux, F., Baron, M.-Fl., Bennington, S., andTomkinson, J.,A new look at proton transfer dynamics along the hydrogen bonds in amides and peptides. Science 264, 1285-1289 (1994). 

Intermolecular hydrogen bonding in amides, along with the planar geometry of the amide functional group, are the two most important factors governing the conformation of protein chains. WeTl learn more about this in Chapter 25. 

P. Ottiger, C. Pfaffen, R. Leist, S. Leutwyler, R.A. Bachorz. and W. Klopper, Strong N-H...7T hydrogen bonding in amide-benzene interactions,... 

In the traditional model of an amide, resonance is the key concept. As shown below, one can write a reasonable resonance structure for an am ide that places a double bond between the C and the N (structure B). This "doublebond character" leads to a planar structure, and hindered rotation about the C-N bond. To the extent that electrostatic interactions control hydrogen bond strengths (see Chapter 3), the charges implied by resonance structure B suggest strong hydrogen bonding in amides, as is observed. 

Based on isotopic substitution, a low-frequency band with a maximum around 100 cm" in liquid amides and proteins is assigned to a mode involving motions of atoms in the hydrogen bonds. This motion can drive the making or breaking of hydrogen bonds in amides and proteins and this mode is an example of how a fast dynamical mode can drive a conformational change of a biomolecule. 

This is a strong directing effect that can exert stereochemical control even when steric effects are opposed. Entries 4 and 5 in Scheme 12.11 illustrate the hydroxy-directing effect. Other substituents capable of hydrogen bonding, in particular amides, also can exert a. vyn-directing effect.79... 

Hydroperoxides formed due to the oxidation of amides are decomposed into free radicals and accelerate oxidation. Hydroperoxides form hydrogen bonds with amides. The enthalpies, entropies, and equilibrium constants of hydrogen bonding are presented in Table 9.7. 

From a structural point of view the OPLS results for liquids have also shown to be in accord with available experimental data, including vibrational spectroscopy and diffraction data on, for Instance, formamide, dimethylformamide, methanol, ethanol, 1-propanol, 2-methyl-2-propanol, methane, ethane and neopentane. The hydrogen bonding in alcohols, thiols and amides is well represented by the OPLS potential functions. The average root-mean-square deviation from the X-ray structures of the crystals for four cyclic hexapeptides and a cyclic pentapeptide optimized with the OPLS/AMBER model, was only 0.17 A for the atomic positions and 3% for the unit cell volumes. 

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