Peptide dipole moment

Walden, Paul, 360 Walden inversion. 359-360 Wang resin, solid-phase peptide synthesis and. 1037 Water, acid-base behavior of, 50 dipole moment of, 39 electrostatic potential map of. 53 nucleophilic addition reactions of, 705-706 pKaof, 51-52... 

Here k is the Boltzmann constant, T is the absolute temperature, C is the number of peptide residues per cubic centimeter of solution, / and s are the helical fraction and the Zimm-Bragg parameter for the polypeptide molecule in the absence of external field, and ft is a parameter which represents the average correlation between the helix unit at the end of a helical sequence and the random-coil unit next to it. Though a detailed account of this parameter is left for Ref. (124), we note here that / = 0 corresponds to the complete absence of correlation between these two units, while ft — 1 corresponds to the case in which the dipole moment of a random coil unit points in the same direction as the axis of the preceding helix unit. 

Methods are presented for calculating mean-square dipole moments, , of polypeptide chains, averaged over all configurations of the chain skeleton. They are applicable to chains of any number (x+ U of residues, the residues being In any specified sequence. Dipole moments of glycine peptides are calculated and compared with experimental determinations. The effects of stereosequence on the dipole moment are well reproduced by the calculations. Ip is taken to be 380 pm. 

This study is the first where semiquantitative use of relaxation data was made for conformational questions. A similar computer program was written and applied to the Tl data of several small peptides and cyclic amino acids (Somorjai and Deslauriers, 1976). The results, however, are questionable since in all these calculations it is generally assumed that the principal axis of the rotation diffusion tensor coincides with the principal axis of the moment of inertia tensor. Only very restricted types of molecules can be expected to obey this assumption. There should be no large dipole moments nor large or polar substituents present. Furthermore, the molecule should have a rather rigid backbone, and only relaxation times of backbone carbon atoms can be used in this type of calculation. 

Figure 8.9 DPV of phenylethanethiolate protected Au MPCs (black), and mixed protected Au MPCs with phenylethanethiolate and Aib peptides modified by ligand exchange (gray) showing significant shift in redox potentials due to Aib peptide induced shift in particle dipole moment.42 (Reprinted with permission from A. H. Holm et al., Langmuir 2006, 22, 10584-10589. Copyright 2006 American Chemical Society.)...

Fig. 2. Electronic dipolar nature of the peptide unit. The numbers adjacent to each atom give the approximate fractional electronic charge attributed to each atom (in units of fundamental electronic charge). The magnitude of the dipole moment is 0.72 ek = 3.46 D.

As an example, the charged phosphate group on phosphatidylethanol-amine, for example, can interact with the hydrocarbon (CH2) chain of an amino acid—for example, valine—in a peptide. A similar situation would hold in the example to the right for interaction of the hydrocarbon unit in a peptide chain. In both instances the groups with permanent dipole moments can induce a temporary dipole moment in an adjacent molecule. These interactions, however, are very weak and act only at very short distances thus the polarization energies may be of the order of 0.002-0.004 kcal/mol at a distance of 5 A. 

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... 

The two-exciton manifold consists of two types of doubly excited vibrational states. The first are overtones (local), where a single bond is doubly excited. The other are collective (nonlocal), where two bonds are simultaneously excited (43,50). We denote the former OTE (overtone two-excitation) and the latter CTE (collective two-excitation). A pentapeptide has 5 OTE and 10 CTE. The two-exciton energies are determined by the parameters gn in the Hamiltonian [Equation (17)], which in turn depend on the peptide group energies G , the anharmonicity An, and dipole moment ratio Kn, n = l,...,5. We set them equal for all CO units... 

A new and very promising application of the calculation of electrostatic potential from experimental electron density is its modeling by point charges and dipole moments [43b,53,54]. When the potential calculated from a k refinement [11 a] is fitted by point charges at the atomic sites, the resulting charges are not dependent of the molecular conformation [56] and the fit is excellent outside the van der Waals envelope of the molecule. Figure 21 shows the potential calculated in the peptide plane from the K refinement of AcPhe (Eqs. 24,25) and its fitted potential. 

When the potential is calculated from Eq. 22 (i.e., includes aspherical terms of electron density) the potential is reasonably well reproduced at the van der Waals surface by point charges, as shown in Figure 22 which gives the comparison between the total potential in a peptide plane of tbuCOprohisNHme and the point charges fitted potential. The rms deviation is = 0.03 elk, and it could be important to include dipolar terms on hydrogen atoms [43b,53]. At the present time, it then seems possible to build a data bank of experimental atomic charges and dipole moments which could be used to parametrize the force fields in the molecular modeling codes. 

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