Modern Polymer Spect..

252 5 Vibvritional Spectroscopji of Polvpeptides
small one in NMA-(HzO)?. (It is not clear why NH ib makes no contribution in
NMA-(FA)z [63].) The position and nature of this mode is variable in polypeptides
[5], since NH ib contributes significantly to a number of normal modes in the 1400-
1200 cn-' region, with tlie mixing being dependent on tlie side-chain structure.
The amide IV mode is a mixture of CO ib and CC s in NMA, although the latter
contribution is often replaced by other coordinates in polypeptide structures [j]. This is
an example of a peptide group mode that is not in general localized and well defined.
The ainide V mode, on the other hand, seems to be a characteristic band of
hydrogen-bonded peptide groups, although an unusual feature seems not to have
been noted previously. This mode, which is generally a combination of CN t and
NH out-of-plane bend (ob), has been assigned to a band near 725 cm-' in neat
NMA [65, 661 and possibly -750 cni-' in aqueous NMA [69]. It is found to have a
counterpart, the amide VII mode, calculated at -200 cm-' [54, 55, 51 and observed
near this frequency [62, 701. However, ah iriitio calculations on an isolated molecule
[57, 591 produce only a single CN t, NH ob mode at -400 cn-', consistent with an
observed Ar-matrix band at 391 cnir' [71]. The increase in the NH ob force constant
of an isolated molecule needed to give a hydrogen-bonded frequency in the
700 cm-' region apparently divides the contributions of these coordinates between
the two frequency regions. Isolated molecules also exclude the contributions from
hydrogen-bond deformation modes (see Table 5-1).
The amide VI mode is predominantly CO ob, with a significant CCH3 outof-plane
rock (or) contribution. This, of course, cannot be represented in a CH3
point-mass model [5]. The nature of this mode is also significantly dependent on
conformation in polypeptide structures [5].
5.3.2 Blocked Dipeptides
Although the analysis of NMA serves to introduce the representative types of
characteristic modes of the peptide group, it does not provide insights into how
these modes might be influenced by varying conforniational interactions between
adjacent groups, such as can occur in polypeptide chains. For this purpose it is
useful to examine the modes of a blocked dipeptide, such as N-acetyl-L-alanine-Ninethylamide,
the Ala dipeptide. This was first done for just the amide I and amide
I11 modes using a fixed empirical force field and no TDC [72], so the conclusions are
necessarily limited. Better insights can be obtained from an ab iriirio study of four
non-hydrogen-bonded conformers of this molecule [33].
In Table 5-2 we show the calculated aniide I, 11, 111, and V frequencies and PEDs
of the four non-hydrogen-bonded conformers of the Ala dipeptide, which differ
mainly in the values of the p(NCa), $(C"C) torsion angles (see Figure 5-1). (The
amide IV and VI modes are no longer distinguishable as relatively pure modes, CO
ib and CO ob contributing significantly and mixing with other coordinates in the
region of -830-515 cm-' [33].) It should be noted that in this calculation the 4-21
ah iizitio force constants were scaled with six general scale factors, so the frequencies
are not necessarily representative of true experimental values. However, the changes
in frequency should be indicative of the effects of changes in conformation.