Confonner pairs

Figure C2.5.2. Scaling of the number of MBS C(MES) (squares) is shown for the hydrophobic parameter = -0.1 and A = 0.6. Data were obtained for the cubic lattice. The pairs of squares for each represent the quenched averages for different samples of 30 sequences. The number of compact stmctures C(CS) and self-avoiding confonnations C(SAW) are also displayed to underscore the dramatic difference of scaling behaviour of C(MES) and C(CS) (or C(SAW)). It is clear that C(MES) remains practically flat, i.e. it grows no faster than In N.

V (the potential) is identified with the enthalpy, i.e. the number n of base pairings (contacts), and T corresponds to the entropy. At each stage in the folding process, as many as possible new favourable intramolecular interactions are fonned, while minimizing the loss of confonnational freedom (the principle of sequential minimization of entropy loss, SMEL). The entropy loss associated with loop closure is (and the rate of loop closure exp... 

F. M. Pohl and T. M. Jovin. Sait-tmiaced cooperatin confonnational change of a srnthetic D.MA. Eqnilihrhtnt and kinetic studies with pair-idG-dC). in J. Mot. Biol., 1972, 67. 375 396. 

Since the polaron resonance is also observed in dilute methylene dichloride solutions, one may be tempted to assign it to intrachain polaron recombination. Yet this assignment may be incorrect on two counts (i) it is not clear that the polymer chains ate completely separated from each other by the solvent (ii) even if the chains are tnily isolated by the solvent, confonnational defects, typically kinks, may generate interconjugation-segment polaron pairs, which are dynamically similar to interchain pairs [30,49]. Indeed, it should be noted that toluene solutions of P3HT did not yield any ODMR, and in CCI4 solutions the polaron resonance decayed below the noise level after 488 nm photoexcitation at room temperature for a few minutes [23,59.73]. This clearly demonstrates that the polaron resonance is sensitive to the interaction between the polymer and the solvent, and may possibly involve its effect on chain separation and/or formation of kinks in the chains. 

Filled orbitals which cannot physically separate because they are part of the same molecule may have substantially larger overlap than the intennolecular case, and the destabilizing interaction, Asu, may be much larger than the stabilizing interaction, Ael. The net repulsion will lead to confonnational changes so as to minimize the repulsive interactions. If the interaction cannot be avoided by confonnational change, then as the result of the interaction, a pair of electrons is raised in energy. The system has a lower... 

Another application of substituent-based conformational analysis is pharmacophore searching. In the work of Olender and Rosenfeld, confonner hbraries of substituents are created with the attachment point to a central scaffold as the reference. To search the virtual library with minimal enumeration, they first apply a series of filters to eliminate most of the possibiUties. First conformers that clash when attached to the scaffold are removed, followed by substituents that do not contain any of the features speeifled in the pharmacophore queries. The next filter looks at pairs of substituents, to remove rotamers that cannot meet the distance constraints, followed by triples and so on. Using this hierarchy of filters, most rotamers/substituents ean be eliminated quiekly, leaving a small nrnnber to be enumerated and tested explieitly. A library based on five scaffolds with six substituents, each with 143 rotamers (equivalent to 10 entries), was scanned with a six-point pharmaeophore in a few hours. 

Figure 6. Qualitative confonnational analysis of the homo-DNA single strand backbone based on idealized conformations. Three simple criteria predict one single pairing conformation of a nucleotide uniL provided that the phosphodiester groups have a synclinal/ synclinal bond arrangement [2].

Figure 8. The two pairing confonnations of the homo-DNA nu units OMresptmd to rfigonucleotide single strands w heUcal, but linear C n d eir idealized conformation).

Figure 36. Top views of (idealized) pairing confonnations of hexq)yranosyl systems. Arrows indicate sources of severe steric hindrance in die pairing conformation.

Figure 50. Qualitative confonnational analysis (cf. fig. 6,7, and 8 in lecture 1) predicts that the backbone of p-RNA has a single pairing conformation. This conformation belongs to an ensemble of (nine) least strained confcnmations.

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