Hydrocarbon chain conformation

There is a long history of controversy in the literature regarding the mode of action of general anesthetics. Experimental results derived from model systems of lipids alone or lipid-cholesterol are somewhat controversial. To mention just a few, using Raman spectroscopy it was found that, at clinical concentrations, halothane had no influence on the hydrocarbon chain conformations, and it was concluded that the interaction between halothane and the lipid bilayer occurs in the head group region [57]. This idea was also supported by 19F-NMR studies. The chemical shifts of halothane in a lipid suspension were similar to those in water and differed from those in hydrocarbons. In contrast, from 2H-NMR experiments, it was concluded that halothane is situated in the hydrocarbon region of the membrane (see also chapter 3.3). 

No influence of halothane on the lipid hydrocarbon chain conformations was found although the overall geometry changed slightly as a consequence of a small lateral expansion, accompanied by a small contraction of the bilayer thickness. Very... 

Winnik, M. A. (1977). Photochemical process of hydrocarbon chain conformation in solution, Acc. Chem. Res., 9 34. 

Casal HL, McElhaney RN (1990) Quantitative determination of hydrocarbon chain conformational order in bilayers of saturated phosphatidylcholines of various chain lengths by fourier-transform infrared spectroscopy. Biochemistry 29 5423... 

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 ... 

Table 2 Conformational Defects m the Hydrocarbon Chains in Fluid Phase Lipid Bilayers...

This effect is also observed with some polymers. The trans form of a hydrocarbon chain requires an energy about 0.8 kcal/mole less than the gauche. The trans form leads to an extended molecule and in hydrocarbons this becomes more favoured as the temperature is lowered. Linear polyethylenes take up this conformation in the crystalline state. 

In a class of reahstic lattice models, hydrocarbon chains are placed on a diamond lattice in order to imitate the zigzag structure of the carbon backbones and the trans and gauche bonds. Such models have been used early on to study micelle structures [104], monolayers [105], and bilayers [106]. Levine and coworkers have introduced an even more sophisticated model, which allows one to consider unsaturated C=C bonds and stiffer molecules such as cholesterol a monomer occupies several lattice sites on a cubic lattice, the saturated bonds between monomers are taken from a given set of allowed bonds with length /5, and torsional potentials are introduced to distinguish between trans and "gauche conformations [107,108]. 

A modification of the united-atom approach, called the anisotropic united-atom (AUA) model was the focus of extensive work by Karabomi et al. [362-365]. As in the other models of hydrocarbon chains described so far, the AUA approach to monolayers was preceded by work on alkanes [367]. hi the AUA model the interaction site is located at the geometrical mean of the valence electrons of the atoms it represents, while the pseudoatom itself is located at the carbon atom position. The movement of each interaction center depends on the conformation of the molecule as a whole. 

A unique feature of such DNA-directed self-assemblies is their site-selective immobilization, which makes it possible to construct well-defined nanostructures. On the other hand, the possibility of the introduction of a vast number of substitutes (like peptidic sequences, nucleoproteins, of hydrophobic hydrocarbon chains) to an adamantane core (adamantyl) makes such a process capable of designing steric colloidal and supramolecular conformations by setting hydrophobic/hydrophilic and other interactions. In addition, the rigidity of the adamantane structure can provide strength and rigidity to such self-assemblies [150]. 

Studies of the effect of permeant s size on the translational diffusion in membranes suggest that a free-volume model is appropriate for the description of diffusion processes in the bilayers [93]. The dynamic motion of the chains of the membrane lipids and proteins may result in the formation of transient pockets of free volume or cavities into which a permeant molecule can enter. Diffusion occurs when a permeant jumps from a donor to an acceptor cavity. Results from recent molecular dynamics simulations suggest that the free volume transport mechanism is more likely to be operative in the core of the bilayer [84]. In the more ordered region of the bilayer, a kink shift diffusion mechanism is more likely to occur [84,94]. Kinks may be pictured as dynamic structural defects representing small, mobile free volumes in the hydrocarbon phase of the membrane, i.e., conformational kink g tg ) isomers of the hydrocarbon chains resulting from thermal motion [52] (Fig. 8). Small molecules can enter the small free volumes of the kinks and migrate across the membrane together with the kinks. 

The model proposed by Menger et al. (Fig. 2) shows two extreme conformations, one in which the hydrocarbon chains are fully extended and another in which they are folded [18, 19], The surface of Menger s micelle is less defined than in the classical model and the surfactants that form the micelle are randomly orientated. The water can penetrate and enter in contact with the hydrophobic part of the surfactants. This model, apart from being more acceptable from an esteric point of view, gives a better explanation than the classical model of a series of experimental results such as viscosity, polarity, or kinetics. 

In the last two decades, there has been a large accumulation of experimental evidence as well as of theoretical interpretations of intramolecular reactions. One notes, however, that attention has been focused on the phenomena of immediate interest to the various specialists. As a consequence of the fact that specialisation implies intensification of knowledge on the one hand but limitation on the other, there has still been insufficient communication and cross-fertilisation between the different schools. This situation is well exemplified by the two most extensive reviews on intramolecular phenomena, namely, that of Kirby (1980), entitled Effective Molarities for Intramolecular Reactions , and that of Winnik (1981a), entitled Cyclisation and the Conformation of Hydrocarbon Chains , which present different approaches and apparently unrelated facts and theories. 

In the same year in which Stoll et al. (1934) defined the cyclisation constant C, Kuhn (1934) laid the foundations of the theoretical approaches to the conformational statistics of hydrocarbon chains and considered the cyclisation probability of the chain as a fundamental, chain length dependent phenomenon related to chain shape. He proposed to view the specific rate kintra of an intramolecular reaction between a pair of reactive groups attached to the ends of a chain molecule as the product of the effective concentration Ceff of... 

The quenching of benzophenone phosphorescence has been used by Mar and Winnik (1981) as a photochemical probe of hydrocarbon chains in solution. The bimolecular reaction for quenching the triplet state of 4-methoxy-carbonylbenzophenone [24] by 1-pentene occurs at rates which are below the diffusion limit by two to three orders of magnitude. Consequently, the intramolecular quenching reactions of to-alkenyl esters of benzophenone-4-carbo-xylic acid [25] occurs under conformational control. In [25] the point of... 

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