Transition moments amide

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. 

IRRAS was also employed to determine the orientation of the peptide at the interface [69]. Spectra were acquired with p-polarized light at various angles of incidence (Fig. 7). /1-Sheets split into two components the transition dipole moment at 1627 cm 1 is oriented along the plane of the interchain hydrogen bonds, perpendicular to the peptide chain, and the one at 1690 cm-1 is oriented along the peptide chain [70]. The transition moment of amide II band is oriented along the peptide chain. 

The structure and tilt angle of the molecules relative to the surface normal were determined by their FTIR spectra. In helical peptides, the transition moment of amide-I band lies nearly parallel to the helix axis and that of amide-II perpendicular. Since transition moments, which lie parallel to the gold surface, cannot be detected in grazing angle FTIR, the ratio between the intensities of the amide-I band (1,665 cm-1) and amide-II band (1,550 cm-1) indicates to what extend the molecules in the monolayer are oriented perpendicular to the gold surface. Based on the FTIR spectra it was possible to calculate the tilt angle, namely the angle between the molecular axis and the surface normal. The frequencies of amide-I and amide-II vibrations indicate that the monolayer is indeed in an a helix form (Fig. 2a). 

Figure 3.3. The arrows within the tape show the direction of the transition moment in each amide chromophore (a-helix illustrative only). Coupling of transition moments between regularly arranged chromophores enhances the CD intensity.

Since multiple modes occur for a helix, it can be difficult to determine which frequencies should be seen in the spectra. This problem can be resolved for IR-active modes for which the transition moment direction is known, such as amide 1 It is only necessary to sum the transition moments in a translational repeat of the helix, taking account of the appropriate phase relationships between motions in adjacent l,d units. The intensity is proportional to the square of this summed transition moment. 

Transition dipole moment interactions between peptide groups can influence higher frequency modes, as was shown by their effects on the splittings of amide I and amide II modes of a-helix and 5-sheet polypeptides [15, 16]. Such transition dipole coupling (TDC) arises from the potential energy of interaction, between transition moments, Ap, in different peptide groups, and is given by [17]... 

The need for caution in the interpretation of polarisation studies is indicated by the recent work of Fraser and Price [59]. They point out that the transition moment of the carbonyl stretching mode responsible for the amide I absorption will be displaced from the CO direction due to interaction with the C—N vibration, and to an orbital following effect. They have calculated the dichroism of an oriented polypeptide in which the chains have the configuration of Pauling and Corey [60] with a 3.7 residue helix, and have shown that if allowance is made for a displacement of the CO transition moment by 20° towards the NO, the dichroic value obtained is very close to that observed experimentally [54]. The objection to the 3.7 helix based on polarisation studies [61] cannot therefore be maintained. 

The most successful for prediction of the CD due to the amide backbone of large proteins is the matrix method. Charge distributions, and the electric dipole, and magnetic dipole transitions moments of four electronic states, are derived by CNDO/S calculations on the model amide. 

In an a-helix, the coupling of the 7t Tt transition moments in each amide chromophore results in a component at about 208 nm which contributes to the characteristic a-helix CD spectrum. For UV-visi-ble spectroscopy, however, the far-UV spectroscopy is usually of little use either for concentration determination or structural analysis as the accessible region (above 200 nm) is almost a linear plot of increasing intensity with decreasing wavelength. 

The CD of the plant hormone abscisic acid exhibits a positive couplet arising from the enone- dienoic acid coupling (directions of electric transition moments are shown by thick lines). The positive twist between these two moieties shovm in Figure 4 directly indicates that the absolute configuration of the tert-OH is pointing dovm, or a. Similarly, the negative couplet of dendryphleUin F shows the dienoate side-chain to be p whereas that of manumycin shows the triene amide chain to be a. In the case of lithospermic... 

The elimination of peaks at 3347 cm and 1680 cm in equal dichroic ratios indicates their belonging to v h and Amide 1 modes. In parallel, a peak at 607 cm is also eliminated, which could be assigned to S nfindole) due to the colinearity of its transition moment and Amide 1. 

The simultaneous disappearance of the bands at 3314 cm and 3195 cm- showing that the maxima correspond to V nh2 and v nh2 modes. In parallel the reduction provokes an elimination of the peak at 1625 cm , which is assigned to 8 02 (Amide II) due to the coliuear orieutatiou of v nh2 and 8nh2 transition moments in the plane of the NH2 group. The wave number value is of the latter vibration typical for the Amide II mode of primary amides, usually observed in the range of 1615 25 cm. ... 

In IR-spectrum of L-leucinamide esteramide ester amide of squaric acid diethyl ester (Figure 4.35), elimination of the peak at 1583 cm provokes a disappearance of a 3122 cm maximum, thereby establishing their character as 8nh2 as far as within an individual NHj group, the corresponding transition moments are colinearly oriented. The simultaneous elimination of Ynh and Yc=o(Sq) with the Amide 1 peak in the compound is explained by the fact that within the framework of the unit cell, the neighboring molecules of L-leucinamide esteramide ester amide of squaric acid diethyl ester are mutually oriented at an angle of 53.1(6)°. This results... 

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