Conformation of the Alkyl Chains

Information on the conformation of the alkyl chains can be obtained only from the infrared spectrum since, according to ECC theory, the Raman spectrum shows only a very few lines originating from the J-dependent skeletal modes which involve n electron delocalisation. 

A more complete analysis of the order/disorder phenomena in polyalkyl thiophenes is reported in ref 154. We limit our discussion here to a few spectroscopic manifestations relevant for this review article. We aim here at the flexibility of the side chains in relation to the flexibility of the chain backbone. 

As mentioned before the existence of the band progressions due to the q O phonons of the alkyl chains is evidence that chains are fully coplanar when liquid-like structures are formed the broad g( ) is mapped in the IR spectra from which localized characteristic defect states can be observed. 

The temperature dependence of the flexibility of the side chain can be followed with the infrared spectrum (fig.23) and is quantitatively measured from the intensities of the defect modes normalized to the intensity of the CH 3 umbrella defomation mode at 1375 cm (fig.19a). From fig.19 it becomes apparent that the thermal evolution 

Fig 22 Infrared spectra in the CH2 rocking range of poly-octylthiophene at T= 180°C (A) and at room temperature (B) compared with the spectra of pheny loctane in solid (T=-178 C) (C) and liquid (D) phase (from ref. 154). 

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Extensive discussions have focused on the conformation of the alkyl chains in the interior ". It has been has demonstrated that the alkyl chains of micellised surfactant are not fully extended. Starting from the headgroup, the first two or three carbon-carbon bonds are usually trans, whereas gauche conformations are likely to be encountered near the centre of tlie chain ". As a result, the methyl termini of the surfactant molecules can be located near the surface of the micelle, and have even been suggested to be able to protrude into the aqueous phase "". They are definitely not all gathered in the centre of tire micelle as is often suggested in pictorial representations. NMR studies have indicated that the hydrocarbon chains in a micelle are highly mobile, comparable to the mobility of a liquid alkane ... 

Independent of the contact geometry, the calculations also demonstrated that the introduction of gauche defects resulted in a decrease of the bridge conductance by a factor of 10, as compared to an all-trans alkanedithiol chain (see Fig. 14b, triangles). Due to variations in the number and positions of gauche defects, as well as various contact geometries, the molecular junctions can exhibit conductance values up to two orders of magnitude below the conductance values of an all-trans conformation of the alkyl chain. 

Comparison of the experimental data with the trends predicted from quantum chemistry ab initio simulations demonstrated that the multiple conductance values of Au-alkanedithiol-Au junctions could be attributed to different Au-sulfur coordination geometries and to different conformations of the alkyl chain. In particular, the medium conductance corresponds to an all-trans conformation of the alkyl chain, with each sulfur atom coordinated in atop position to a single... 

The unterstanding of amphiphile association clearly must include detailed knowledge of the internal structure and dynamics, e.g., what is the conformation of the alkyl chains and what are their flexibility and packing conditions is the interior of micelles exclusively of hydrocarbon nature or is there any water penetration We will here consider the state of the hydrocarbon chains and defer a discussion of water penetration to the section on hydration. 

Conformations based on the few available X-ray structures of phospholipids in the crystalline state, generated from energy minimization or from conformational libraries of phospholipid alkyl chains, have been used as starting structures for the simulation. It has been argued that the latter is preferable in order to save time necessary for equilibration when starting from all-trans conformations of the alkyl chains observed in X-ray structures. To build up the configuration of the system, e.g. the lateral positions of the phospholipids, either crystal structure data or programs... 

Fig. 10. An artist s visualization of a C, reversed phase in the presence of an aqueous mobile phase (I) and in the presence of butanol (H). The polar and nonpolar regions are denoted by the letters A and B, respectively. The possible conformations of the alkyl chain are represented by the sawtooth figures. Adapted from Hancock and Sparrow (198ld).

In the most stable conformation of the alkyl chain all carbon atoms are coplanar this plane is called the carbon zigzag plane. The ideal C—C bond distance is 1.54A,... 

The comparison of the experimental data with the quantum chemical simulations leads to the following conclusions [208] The mid conductance junctions M represent an all-trans conformation of the alkyl chains with the sulfur atoms bound in atop position to a single gold atom. All trans chains with sulfur atoms bound to two gold atoms in bridge position represent the high conductance junctions H, a factor four larger then the former. The low... 

Conformation of the alkyl chain Effect of head group... 

The vibrational spectra of DLPC, DMPC, DPPC and DSPC with the polarization combination of ssp (s polarized SF, s polarized visible, p polarized IR) have been obtained in order to ascertain the conformation of the alkyl chains of the various phospholipids. Representative spectra of DLPC and DSPC in the symmetric stretch region are shown in the inset of Fig. 6. A clear correlation between the adsorption isotherms and the Ir+lh ratio obtained from spectroscopic measurements is observed. The methyl/methylene symmetric stretch ratio data for DLPC when plotted against bulk concentration (Fig. 6) resembles the DLPC pressure-concentration isotherm plotted in Fig. 6. Starting out with a value ratio of... 

All spectra presented in Fig. 1 were calculated assuming an all-trans conformation. In the experimental Raman spectra of both surfactants with hydrocarbon chains possessing more than 10 carbons, the band at 2884 1/cm (asymmetric CH2) is the strongest band of all, followed by the one at 2875 1/cm (symmetric CH2). The intensity ratio between these two bands can be used to study the conformation of the alkyl chain. Snyder et al. [25] have presented a very nice experimental treatment of this issue. To the best knowledge of the authors, up to now only force field calculations have been used to study this issue from a theoretical point of view [26, 27]. In this calculations the force field parameters were fitted to represent the observed frequencies. 

The selective abstraction of y hydrogen is a purely geometric phenomenon, due to the fact that in normal conformations of the alkyl chain it is the y hydrogen that is nearest to the oxygen atom. The overriding importance of geometry in these reactions is exemplified by the fact that variations in the photochemical reactivity in a series of straight-chain and polycyclic alkyl ketones could be attributed almost entirely to variations in AS for the reactions. ... 

A similar study has been conducted using TIR-SFG [81] on the conformational order of sodium dodecyl sulfate (SDS) adsorbed at the D2O/CCI4 interface. A change in conformation of the alkyl chain with increased surface coverage was observed. Polarization studies indicated that the terminal methyl group axis was oriented primarily along the surface normal. 

H NMR was very successful in the investigation of surfactant adsorption, and provides the majority of all surfactant studies. A few 13C spectral studies reveal information about trans conformations of the alkyl chain, and furthermore the dynamics of adsorption can be monitored by IH self-diffusion. Other approaches which will not be further described here involved investigations of the counterions, e.g. 23Na relaxation in latex particles/ ionic surfactant mixtures [20], and 7Li DQF spectra of clay suspensions containing nonionic surfactants [21]. The counterion behaviour is rather complex and direct implications for adsorbed surfactant layers are difficult to obtain. 

The knowledge accumulated on the exchange process in aqueous surfactant solutions has been used to investigate the conformation of the alkyl chain of... 

The closely packed, -anti conformation of the alkyl chains results in many London attractive forces. 

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