Conformational accessibility

The other important feature of the primary stmcture of RNA is the presence of the 2 -hydroxyl group in ribose. Although this hydroxyl group is never involved in phosphodiester linkages, it does impose restrictions on the heHcal conformations accessible to double-stranded RNA. 

Several other points are worth noticing Well-defined motions lead to well-defined spectra. Thus chain motion can be studied, where the analysis of 2H line shapes yields directly the number of conformations accessible for a given segment. Moreover, even more complicated motions not considered explicitely here lead to spectra, the angular dependence of which can be described by Equation (1 a). The corresponding line shapes can easily be calculated facilitating the analysis of the data. In glassy... 

The number of the constraints to chain mobility shown in Fig. 16 decreases with increasing temperature, reflecting the increase of the free volume. From a comparison of the spectra in Fig. 15 with line shapes calculated for flexible chains on a diamond lattice 23 (one can infer that the average length of the flexible unit increases from 3-5 bonds at room temperyture to about 10-15 bonds at 380 K. Our model thus can quantitatively explain the gradual increase of the number of conformations accessible to the chain motion. The earlier XH wide line data 72 are also in accord with our findings. 

The higher energy features can indeed be associated with transitions of He lCl(K,v" = 0) ground-state complexes with rigid He I—Cl linear geometries. In contrast to the T-shaped band that is associated with transitions to the most strongly bound intermolecular vibrational level in the excited state without intermolecular vibrational excitation, n = 0, the transitions of the linear conformer access numerous excited intermolecular vibrational levels, n > 1. These levels are delocalized in the angular coordinate and resemble hindered rotor levels with the He atom delocalized about the l Cl molecule. 

As we have reviewed here, the linear region is not fully repulsive, and transitions of the ground-state, linear conformer access vibrationally excited intermolecular levels that are delocalized in the angular coordinate. As depicted in Fig. 1, however, the internuclear distance is significantly longer in the excited state at the linear geometry. Consequently, there is favorable Franck-Condon overlap of the linear conformer with the inner-repulsive wall of the excited-state potential. It is therefore possible for the linear Rg XY conformers to be promoted to the continuum of states just above each Rg - - XY B,v ) dissociation limit. 

The changes in structure of denatured nuclease as a function of urea concentration (Fig. 3) suggest that, as hydrophobic interactions are weakened and the backbone becomes more highly solvated, the chain expands gradually. The data presented by Millet et al. in this volume suggest that this expansion does not continue asymptotically as predicted by simple polymer physical chemistry. This is the behavior expected for a polypeptide chain trapped in a small region of conformation space. Most, perhaps all, of the conformations accessible in the expanded denatured state may have a native-like topology. 

Discussion. We can now propose a coarse description of the paraffinic medium in a lamellar lyotropic mesophase (potassium laurate-water). Fast translational diffusion, with D 10"6 at 90 °C, occurs while the chain conformation changes. The characteristic times of the chain deformations are distributed up to 3.10"6 sec at 90 °C. Presence of the soap-water interface and of neighboring molecules limits the number of conformations accessible to the chains. These findings confirm the concept of the paraffinic medium as an anisotropic liquid. One must also compare the frequencies of the slowest deformation mode (106 Hz) and of the local diffusive jump (109 Hz). When one molecule wants to slip by the side of another, the way has to be free. If the swinging motions of the molecules, or their slowest deformation modes, were uncorrelated, the molecules would have to wait about 10"6 sec between two diffusive jumps. The rapid diffusion could then be understood if the slow motions were collective motions in the lamellae. In this respect, the slow motions could depend on the macroscopic structure (lamellar or cylindrical, for example)... 

The flexible helix modeled here is best described by the entire array of conformations it can assume. A comprehensive picture of this array is provided by the three-dimensional spatial probability density function Wn(r) of all possible end-to-end vectors (25, 35). This function is equal to the probability per unit volume in space that the flexible chain terminates at vector position relative to the chain origin 0,as reference. An approximate picture of this distribution function is provided by the three flexible single-stranded B-DNA chains of 128 residues in Figure 5(a). The conformations of these molecules are chosen at random by Monte Carlo methods (35, 36) from the conformations accessible to the duplex model. The three molecules are drawn in a common coordinate system defined by the initial virtual bond of each strand. For clarity, the sugar and base moieties are omitted and the segments are represented by the virtual bonds connecting successive phosphorus atoms. 

Two articles have addressed the variation of the optical rotatory power upon dimerization. In the first one, the different conformation accessible monomers and dimers of chlorofluoroiodoacetic acid (Scheme 3.30) have been theoretically calculated [153]. Using these results, the population weighted rotations for the... 

For symmetric molecules, this result has to be divided by the symmetry factor o, which is the number of equivalent conformations accessible to the molecule when the operation of total rotation is carried out. 

Eight derivatives of the dihydrodiazocine, for example 1, were prepared utilizing the known reaction of 1,2,4,5-tetraazines with the enolate of cyclobutanones with the aim to obtain the isoxazolyl eight-membered diazahetero-cycles with relatively few low-energy conformationally accessible states and, in turn, limited conformational flexibility <2006JOC2480>. 

The explicit modeling approach surrounds a solute molecule with solvent molecules and then examines each molecule in that solvated environment. Quantum chemical methods, both semiempiricaP and ab initio" have been used to do this however, molecular dynamics and Monte Carlo simulations using force fields are used most often.Calculations on ensembles of molecules are more complex than those on individual molecules. Dykstra et al. discuss calculations on ensembles of molecules in a chapter in this book series. Because of the many conformations accessible to both solute and solvent molecules, in addition to the great number of possible solute molecule-solvent molecule orientations, such direct QM calculations are very computer intensive. However, the information resulting from this type of calculation is comprehensive because it provides molecular structures of the solute and solvent, and takes into account the effect of the solvent on the solute. This is the method of choice for assessing specific bonding information. 

In general, the very extensively studied family of steroids (Duax and Norton 1975 Duax et al. 1 %2b) have exhibited a remarkable degree of conformational consistency (Duax etal.l 982a). Quite a few of them do exhibit polymorphism, however (Kuhnert-Brandstatter 1971) and as has been pointed out elsewhere (Duax et al. 1982a), any variety observed in the conformations of these molecules can provide useful information on the range of conformations accessible, and even on the mode of physiological action of a particular molecule or family of molecules. For instance, cortisone acetate 5-V is known to crystallize in at least three unsolvated forms (Kanters et al. 1985)... 

The high degree of specificity in the relationship between the conformations accessible to a particular DNA molecule and its nucleotide sequence is well illustrated by the occurrence of the D and S forms. The A, B and C forms have been observed with all naturally occurring DNAs which have been studied and also with both the alternating copolymers poly d(A-T).poly d(A-T) and poly d(G-C).poly d(G-C). However the D form but not the S form has so far only been observed with poly d(A-T).poly d(A-T) and conversely the S form but not the D form has been observed with poly d(G-C).poly d(G-C) but not with poly d(A-T).poly d(A-T). 

The biosynthesis of the cofactor and its insertion into [FeMo] apparently requires the presence of [Fe] and ATP in A. vinelandii. Whether this involves redox or conformational change in [FeMo] induced by [Fe] is unknown, but the fact that inactive versions of [Fe] are effective would seem to favor the nonredox mechanism. An attractive idea is that [Fe] -MgATP binds to [FeMo], producing a state that is conformationally accessible for cofactor insertion. 

In homo-DNA (h-DNA) and pyranosyl-RNA (p-RNA), the hexitol ring is frozen in a single y-endo- ke eonformation, as opposed to the multiple conformations accessible to the furanose of DNA and RNA. The h-DNA duplexes have a quasi-linear orientation as opposed to the superhelical structure of DNA duplexes, and the distance between the base stacking planes is larger relative to that of DNA. The h-DNA duplexes also have different pairing stability, e.g., the pairing priorities of A-A exceeds that of A-T. In contrast to h-DNA, p-RNA, which is also quasi-linear, does not show altered pairing priorities. 

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