Crossed conformer

The dynamics of polymers may be interpreted by assuming the existence of domains. At high temperature (T Tg), each domain is occupied by a single conformer and the interactions between neighboring segments or conformers are considered to be negligible. Once the potential barrier is crossed, conformers relax independently of their neighbors. Each domain... 

In a detailed study of transannular cyclizations of all the possible isomers of naturally occurring hedy-caryol (86) in the presence of formic or tosic acid, ltd et al. have been able to rationalize the reaction pathways on the basis of the preferred conformations, i.e. crossed conformation (CC, CT) or parallel conformations (TT, TC), of the reacting dienes (Scheme 10). - ... 

In nine-membered rings ( )- and (Z)-olcftns appear, and for the transannular reaction, these double bonds can be arranged into two different relative conformations, namely the crossed conformation [adopted by (E,E)- and ( ,Z)-nonadienes] and the parallel conformation [adopted by ( , )-, (E.Z)- and (Z,Z)-nonadienes]. 

Fluorescence correlation spectroscopy (FCS) is based on exciting a small number of molecules in a femtoliter volume and correlating the fluctuations of the fluorescence intensity. The fluctuations are caused by diffusion, rotation, intersystem crossing, conformational changes, or other random effects. The technique dates back to a work of Magde, Elson and Webb published in 1972 [335]. Theory and applications of FCS are described in [51, 429, 430, 431, 456, 457, 497, 537, 556]. 

Fig. 10. Conformational flooding accelerates conformational transitions and makes them accessible for MD simulations. Top left snapshots of the protein backbone of BPTI during a 500 ps-MD simulation. Bottom left a projection of the conformational coordinates contributing most to the atomic motions shows that, on that MD time scale, the system remains in its initial configuration (CS 1). Top right Conformational flooding forces the system into new conformations after crossing high energy barriers (CS 2, CS 3,. . . ). Bottom right The projection visualizes the new conformations they remain stable, even when the applied flooding potentials (dashed contour lines) is switched off.

A stretch-torsion cross term can be used to model the stretching of a bond that occurs in ai eclipsed conformation. Two possible functional forms are ... 

The consistent force field (CFF) was developed to yield consistent accuracy of results for conformations, vibrational spectra, strain energy, and vibrational enthalpy of proteins. There are several variations on this, such as the Ure-Bradley version (UBCFF), a valence version (CVFF), and Lynghy CFF. The quantum mechanically parameterized force field (QMFF) was parameterized from ah initio results. CFF93 is a rescaling of QMFF to reproduce experimental results. These force fields use five to six valence terms, one of which is an electrostatic term, and four to six cross terms. 

In order to reach a crystalline state, polymers must have sufficient freedom of motion. Polymer crystals nearly always consist of many strands with a parallel packing. Simply putting strands in parallel does not ensure that they will have the freedom of movement necessary to then find the low-energy con-former. The researcher can check this by examining the cross-sectional profile of the polymer (viewed end on). If the profile is roughly circular, it is likely that the chain will be able to change conformation as necessary. 

A cross-linked polymer has a density of 0.94 g cm" at 25°C and a molecular weight between crosslinks of 28,000. The conformation of one bond in the middle of the molecule changes from trans to gauche, and the molecule opens up by 120°. In w-butane, the trans to gauche transformation requires about 3.3 kJ mol". Estimate a value for AH of stretching based on this model, and use the law of cosines to estimate the magnitude of the opening up that results. 

In this section we examine some examples of cross-linked step-growth polymers. The systems we shall describe are thermosetting polymers of considerable industrial importance. The chemistry of these polymerization reactions is more complex than the hypothetical AB reactions of our models. We choose to describe these commercial polymers rather than model systems which might conform better to the theoretical developments of the last section both because of the importance of these materials and because the theoretical concepts provide a framework for understanding more complex systems, even if they are not quantitatively successful. 

The conformational characteristics of PVF are the subject of several studies (53,65). The rotational isomeric state (RIS) model has been used to calculate mean square end-to-end distance, dipole moments, and conformational entropies. C-nmr chemical shifts are in agreement with these predictions (66). The stiffness parameter (5) has been calculated (67) using the relationship between chain stiffness and cross-sectional area (68). In comparison to polyethylene, PVF has greater chain stiffness which decreases melting entropy, ie, (AS ) = 8.58 J/(molK) [2.05 cal/(molK)] versus... 

Dl A. Supercoiling. Supercoiling is a topological property of closed-circular DNA molecules. Circular DNA molecules can exist in various conformations differing in the number of times one strand of the helix crosses the other. These different isomeric conformations are called topoisomers and maybe characterized in terms of the linking number, Ek. A linear DNA molecule having Nbase pairs and h base pairs per turn of the helix, if joined end to end, has the following ... 

The temperature of esterification has a significant influence on isomerization rate, which does not proceed above 50% at reaction temperatures below 150°C. In resins produced rapidly by using propylene oxide and mixed phthaUc and maleic anhydrides at 150°C, the polyester polymers, which can be formed almost exclusively in the maleate conformation, show low cross-linking reaction rates with styrene. 

The most characteristic coupling constant in indazoles is the cross-ring Vs, present both in indazoles and in isoindazoles unsubstituted in positions 3 and 7. 2-Methyl isomers show an additional Vmc.h coupling which can serve to identify an isoindazole unsubstituted in position 3. In 3-azidoindazole, as in 3-azidopyrazole (56), the prototropic exchange is slowed down sufficiently to allow the measurement of a zig-zag /i,4 coupling constant. The deshielding effects observed in A-acetyl derivatives, e.g. 1-acetyl (60) on H-7 and 2-acetyl (61) on H-3, are related to a preferred E conformation (Section 4.04.1.4.3). 

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