Transition dipole, peptides

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. 

Vibrational spectroscopy has been used in the past as an indicator of protein structural motifs. Most of the work utilized IR spectroscopy (see, for example, Refs. 118-128), but Raman spectroscopy has also been demonstrated to be extremely useful (129,130). Amide modes are vibrational eigenmodes localized on the peptide backbone, whose frequencies and intensities are related to the structure of the protein. The protein secondary structures must be the main factors determining the force fields and hence the spectra of the amide bands. In particular the amide I band (1600-1700 cm-1), which mainly involves the C=0-stretching motion of the peptide backbone, is ideal for infrared spectroscopy since it has an large transition dipole moment and is spectrally isolated... 

Figure 18 Models from which the excitonic coupling between pairs of peptide groups were calculated (a) The direction and location of the transition dipole of the amide I mode (118,123) from which the coupling between two peptide groups is calculated according to a dipole-dipole interaction term [Eqaution (28)] (b) The nuclear displacements, partial charges, and charge flow of the amide I normal mode obtained from a DFT calculation on deuterated N -methylacetamide (all experiments were performed in D2O) (42). With this set of transition charges, the multipole interaction is computed, avoiding the limitations of the dipole approximation.

Keiderling TA, Kubelka J, Hilario J (2006) Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures. Vibrational Spectroscopy of Biological and Polymer Materials 253-324... 

Our goal is to evaluate the contribution to Vinter due to the interaction between similar transition dipoles on peptide groups A and B. The potential for the interaction between two dipoles Ha and 1b a distance 7 ab apart is (Jackson, 1975)... 

Figure 2. The peptide moiety showing charge distributions on each of four atoms. The result is a permanent (ground state) dipole moment indicated by the arrow with the head of the arrow pointing in the positive direction. On absorption of a photon, the electron distribution changes. This results in the atoms having a new distribution of charge and the excited state will have a different dipole moment. The difference dipole moment (between the ground and excited states) is called the electric transition dipole moment, /i,., and its magnitude can be calculated from the area of the absorption curve as shown in Figure 3.

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 CD spectrum of mammalian CdyMT to the red of the peptide CD bands at 215 nm (CD bands are also denoted as Cotton effects) has been proposed to arise from the peptide-induced asymmetry of the binding sites and from chirality brought about by interactions of asymmetrically oriented transition dipole moments of similar chromophores (bridging thiolate ligands) within the cluster structure. 

Fig. 3.6. Stereoelectronic control of the cleavage of the tetrahedral intermediate during hydrolysis of a peptide bond by a serine hydrolase. The thin lines represent the reactive groups of the enzyme (serine, imidazole ring of histidine) the thick lines represent the tetrahedral intermediate of the transition state. The full circles are O-atoms open circles are N-atoms. The dotted lines represent H-bonds the thick double arrow indicates an unfavorable dipole-dipole interaction [21]. A (R)-configured N-center B (S)-configured N-center.

The computations of dipole and rotational strengths for the polymers are carried out using Cartesian coordinates of the C and O atoms of the various carbonyl groups on the purine and pyrimidine bases or the peptide linkages. Furthermore, the transition frequency i>0 of an unperturbed carbonyl transition is needed, and its monomeric dipole strength D, which is proportional to n2. For the conversion between rotational (or dipole) strengths (in esu cm)2 and the extinction coefficients (in LmoHcm1) the approximations... 

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. 

We model the amide band as a system of N interacting localized vibrations. For the sake of third-order spectroscopies, we only need to consider the lowest three levels of each peptide group with energies 0, Gm, Gnl(m = 1,..., N). The matrix elements of the dipole operator corresponding to the 0-1 and 1-2 transitions are denoted /j.m and //ra, respectively, and their ratio is Km = To introduce the vibrational Frenkel exciton model,... 

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