Amides vibrational frequencies

MM2 was, according the web site of the authors, released as MM2 87). The various MM2 flavors are superseded by MM3, with significant improvements in the functional form [10]. It was also extended to handle amides, polypeptides, and proteins [11]. The last release of this series was MM3(%). Further improvements followed by starting the MM4 series, which focuses on hydrocarbons [12], on the description of hyperconjugative effects on carbon-carbon bond lengths [13], and on conjugated hydrocarbons [14] with special emphasis on vibrational frequencies [15]. For applications of MM2 and MM3 in inorganic systems, readers are referred to the literature [16-19]. 

Fig. 6 Amide C = 0 and C-N vibrational frequencies (cm ) and bond lengths (A in parentheses), twist angles (t), average angles at nitrogen computed at HF/6-31G level for ground state and orthogonal conformations of (a) A-formyloxy- /V-mcthoxyformamidc 40, (b) iV-methoxyfomiamidc 41 and (c) formamide 42. Energies (Hartrees) at B3LYP/6-31G // HF/6-31G level.

The situation with 7V-acyloxy-/V-alkoxyureas and carbamates is similar although infrared data were mostly determined by liquid film or condensed phase (KBr/nujol mull).52,131 However, the limited data for V-acyloxy-TV-alkoxyureas (Table 2, entries 69-72) give amide carbonyl frequencies ca. 1730 cm-1 that are raised by some 37-40 cm-1 by acyloxylation. Values for carbamates (Table 2, entries 73-77) are higher (mostly 1780 cm-1) but are raised to a lesser extent (10-20 cm-1) relative to their parent carbamates. Clearly, carbonyl vibrational frequencies will be influenced strongly by the adjacent amino or alkoxyl group in both analogues. 

The amide carbonyl vibrational frequencies of A-acyloxy-Af-alkoxyamides are similar to that observed for the twisted l-aza-2-adamantanone (98, 1731 cm ) . It is apparent from the extensive data available for both A-chlorohydroxamic esters (Table 2, Section in.B.2) and Af-acyloxy-A-alkoxyamides that when an amide nitrogen lone pair loses conjugation with the carbonyl (either through twisting/pyramidalization or, in the case of anomeric amides, pyramidalization alone), the configuration is analogous to an ester rather than a ketone. As with esters, acid halides and anhydrides or diacyl peroxides , the carbonyl stretch frequency is higher than that of ketones and aldehydes... 

Amide carbonyl vibrational frequencies for the series behave similarly while those of the hydroxamic esters in this subset vary between 1678 and 1698 cm , the V-acyloxy-V-alkoxyamide carbonyl frequencies span only six wave numbers. 

Characterization of amide vibrational modes as seen in IR and Raman spectra has developed from a series of theoretical analyses of empirical data. The designation of amide A, B, I, II, etc., modes stem from several early studies of the (V-methyl acetamide (NMA) molecule vibrational spectra which continues to be a target of theoretical analysis. 15 27,34 162 166,2391 Experimental frequencies were originally fitted to a valence force field using standard vibrational analysis techniques and subsequently were compared to ab initio quantum mechanical force field results. 

The correlation of the vibrational frequency distributions of two modes can be determined from 2D-IR experiments and such effects are particularly evident in dual frequency experiments. For example, positive correlations between the amide-A and amide-I frequencies apparent from the spectra of acylalaninemethoxide (AcAlaOMe) in Figure 5, imply that when... 

The VCD features for a number of larger peptide models have been calculated in the course of our efforts to define their solution conformation. These calculations proceeded exactly in the same manner as the ones described for small oligonucleotides. Cartesian coordinates from X-ray experiments, or from the program MacroModel [21), were used, along with a vibrational frequency for an unperturbed, single amide I or amide I vibration. The dipole transition moment for the amide I vibration was taken somewhat lower than that of the nucleotide base carbonyl stretching vibration, in agreement with observed data and literature values. Details of these calculations will also be provided in Section 4. 

Table 4-6 lists observed frequencies and band assignments of structure-sensitive amide vibrations. Here, we discuss only amide I and III bands for which abundant data are available. The general trends shown in the table below were found by correlating x-ray structural data with Raman frequencies. 

The picture of almost harmonic excitonically coupled states is particularly appropriate in the localization or weak coupling limit. This limit will be valid in smaller peptides that do not have the rather strict symmetries of helices or sheets. It is very likely that the vibrational frequencies of each amide unit will be different even in the absence of any coupling. An example of this limit is found in the pentapeptide discussed below. If the frequency separations between the uncoupled modes are large compared with the individual coupling terms, IAj/( i — ej)l < E the coupled states... 

We have presented two types of nonlinear IR spectroscopic techniques sensitive to the structure and dynamics of peptides and proteins. While the 2D-IR spectra described in this section have been interpreted in terms of the static structure of the peptide, the first approach (i.e., the stimulated photon echo experiments of test molecules bound to enzymes) is less direct in that it measures the influence of the fluctuating surroundings (i.e., the peptide) on the vibrational frequency of a test molecule, rather than the fluctuations of the peptide backbone itself. Ultimately, one would like to combine both concepts and measure spectral diffusion processes of the amide I band directly. Since it is the geometry of the peptide groups with respect to each other that is responsible for the formation of the amide I excitation band, its spectral diffusion is directly related to structural fluctuations of the peptide backbone itself. A first step to measuring the structural dynamics of the peptide backbone is to measure stimulated photon echoes experiments on the amide I band (51). 

Amide I vibrations - characteristic amide I frequencies in H20 and 2H20 solvents... 

UV resonance Raman spectroscopy (UVRR), Sec. 6.1, has been used to determine the secondary structure of proteins. The strong conformational frequency and cross section dependence of the amide bands indicate that they are sensitive monitors of protein secondary structure. Excitation of the amide bands below 210 nm makes it possible to selectively study the secondary structure, while excitation between 210 and 240 nm selectively enhances aromatic amino acid bands (investigation of tyrosine and tryptophan environments) (Song and Asher, 1989 Wang et al., 1989, Su et al., 1991). Quantitative analysis of the UVRR spectra of a range of proteins showed a linear relation between the non-helical content and a newly characterized amide vibration referred to as amide S, which is found at 1385 cm (Wang et al., 1991). 

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