Conformational distribution

We close these introductory remarks with a few comments on the methods which are actually used to study these models. They will for the most part be mentioned only very briefly. In the rest of this chapter, we shall focus mainly on computer simulations. Even those will not be explained in detail, for the simple reason that the models are too different and the simulation methods too many. Rather, we refer the reader to the available textbooks on simulation methods, e.g.. Ref. 32-35, and discuss only a few technical aspects here. In the case of atomistically realistic models, simulations are indeed the only possible way to approach these systems. Idealized microscopic models have usually been explored extensively by mean field methods. Even those can become quite involved for complex models, especially for chain models. One particularly popular and successful method to deal with chain molecules has been the self-consistent field theory. In a nutshell, it treats chains as random walks in a position-dependent chemical potential, which depends in turn on the conformational distributions of the chains in... 

Shinkai [15] concluded that p-zert-butyl calix[n]ar-ene tetra esters form stable monolayers at the air-water interface and the metal responds, therein, quite differently from that in solution. They reported that examination of the metal template effect on the conformer distribution established that when the metal cation present in the base used serves as a template, the cone conformer results are predominant [16]. Hence, Na in... 

NaH should serve as an efficient template ion to yield cone conformers. Conformer distribution for the reaction of p-tert-h Wy calix[4]arene and ethyl bromoacetate is given in Table I. 

Table 1 Conformer Distribution for the Reaction of p-Zerz-Butyl Calix[4]arene and Ethyl Bromoacetate [16]...

Dendrimers with a polyphenyl core around a central biphenyl unit decorated at the rim with peryleneimide chromophores have been investigated both in bulk and at the single-molecule level in order to understand their time and space-resolved behavior [28]. The results obtained have shown that the conformational distribution plays an important role in the dynamics of the photophysical processes. Energy transfer in a series of shape-persistent polyphenylene dendrimers substituted with peryleneimide and terryleneimide chro-mophoric units (4-7) has been investigated in toluene solution [29]. 

The extent of ion binding depends on a number of characteristics of the polyion degree of dissodation, acid strength, conformation, distribution of ionizable groups and cooperative action between these groups (Wilson Crisp, 1977 Oosawa, 1971 Harris Rice, 1954, 1957). The hydration state of the macromolecule, which is in turn dependent on conformation, also affects ion binding (Begala, 1971). 

The CD spectra of nine proteins in 6 M Gdm-HCl were studied by Cortijo etal. (1973). Those proteins with disulfide bridges were reduced and carboxymethylated. The spectra of individual proteins were not reported, but the range of values at wavelengths from 240 to 210 nm was given. The [0]222 values ranged from —800 to —2400 deg cm2/dmol. From this substantial variation, Cortijo etal. (1973) concluded that the proteins studied are not true random coils in 6 M Gdm-HCl, because random coils should have CD spectra essentially independent of amino acid composition and sequence. The observed variation was attributed to differences in the conformational distribution between allowed regions of the Ramachandran map or to residual interactions between different parts of the chain that are resistant to Gdm-HCl denaturation. 

Fig. 6. Ramachandran plots for simulated Ac-Ala-Xaa-Ala-Ala-NMe peptides with Xaa = glutamine or asparagine, with a constrained side chain-to-backbone hydrogen bond. Conformational distribution for glutamine i (A) and for the residue i +1 to which the glutamine is hydrogen-bonded (B). Conformational distribution for asparagine i (C) and for the residue i +1 to which it is hydrogen-bonded (D).

Fig. 2. Illustration of the definitions of conformational coordinate 7Zn, e.g., 7Zn = ri, r2,. .., rn. The conformational distribution s (7U1) is sampled for the single molecule in the absence of interactions with solvent by suitable simulation procedures using coordinates appropriate for those procedures. The normalization adopted in this development is/sf (7Zn) dn1Z = V, the volume of the system. Thus, the conformational average that corresponds to adding the second brackets in going from Eq. (4) to Eq. (3) is evaluated with the distribution function sf (7Zn) = V.

Early conformational studies by HOESY experiments are illustrated by the work of Batta and Kover54 who were able to access oligosaccharide sequencing and conformational distribution around the glycosidic bond in model compounds. These determinations make use of relayed proton-proton-carbon cross-relaxation. 

This chapter considers the distribution of spin Hamiltonian parameters and their relation to conformational distribution of biomolecular structure. Distribution of a g-value or g-strain leads to an inhomogeneous broadening of the resonance line. Just like the g-value, also the linewidth, W, in general, turns out to be anisotropic, and this has important consequences for powder patterns, that is, for the shape of EPR spectra from randomly oriented molecules. A statistical theory of g-strain is developed, and it is subsequently found that a special case of this theory (the case of full correlation between strain parameters) turns out to properly describe broadening in bioEPR. The possible cause and nature of strain in paramagnetic proteins is discussed. 

The conformational behaviour in solution of a dermatan-derived tetra-saccharide has been explored by means of NMR spectroscopy, especially by NOE-based conformational analysis. RDCs were also measured for the tetrasaccharide in a phage solution and interpreted in combination with restrained MD simulations. The RDC-derived data substantially confirmed the validity of the conformer distribution resulting from the NOE-derived simulations, but allowed an improved definition of the conformational behaviour of the oligosaccharides in solution, which show a moderate flexibility at the central glycosidic linkage. Differences in the shapes of the different species with the IdoA in skew and in chair conformations and in the distribution of the sulphate groups were also highlighted.28... 

With acyclic dienes, the quantum yield for cyclobutene formation (4>cb) rarely exceeds ca 0.1, the expected result of the fact that the planar s-trans conformer normally comprises the bulk (96-99%) of the conformer distribution at room temperature. However, 4>cb is often significantly larger than the mole fraction of s-cis form estimated to be present in solution. For example, 1,3-butadiene, whose near-planar (dihedral angle 10-15°105 106) s-cis conformer comprises ca 1% of the mixture at 25 °C, yields cyclobutene with < >cb = 0.04140, along with very small amounts of bicyclo[1.1.0]butane141. A second well-known example is that of 2,3-dimethyl-l,3-butadiene (23 ca 4% gauche s-cis at 25 °C107), which yields 1,2-dimethylcyclobutene (25) with < >cb = 0-12 (equation 16)111. Most likely, these apparent anomalies can be explained as due to selective excitation of the s-cis conformed under the experimental conditions employed, since it is well established that s /raw.v... 

Angyal and co-workers (8) concluded that the conformational distribution of xylitol pentaacetate in CDCl is between two sickle conformations with the extended zig-zag conformation being unimportant. The 3 3 4 average value of 5.2 Hz is from a large coupling from AntipArallel (or H2-H2) and a small... 

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