Molecules, coupling structure

Fig. 8.9 Stereoviews of the NMR structure of a DNA dodeca-mer calculated using residual dipolar couplings, a and b differ in a 90° rotation around the helix axis to highlight the non-cylin drical symmetry of the molecule. These structures differ considerably from solution structures calculated without dipolar couplings. (Reproduced with permission from N. Tjandra, S.-l. Tate, A. Ono, M. Kainosho and A. Bax,...

HIV is a typical member of the retrovirus family, in that it is an enveloped virus that carries RNA as its genetic information. The structure of HIV (Fig. 2) has been determined by electron microscopy. The viral membrane is acquired from the infected cell as the virus buds through the cell membrane. Inserted into the viral membrane are protein molecules coupled to carbohydrates (glycoproteins) which are essential for viral infectivity and probably also play a role in the... 

It is instructive to illustrate the use of Equations 5.19 and 5.29 using a simplistic 3-atom model calculation for water. Even though it is well established that the condensed phase structure of water is complicated and involves the coordinated motions of many molecules coupled through a constantly fluctuating hydrogen bond network, the fundamentals of the VPIE are represented reasonably well by the simplified model. 

The success of these new multi-alignment approaches for the extraction of generalized order parameters from RDCs relies on a couple of fundamental assumptions. The first of these, as described in Section 2, is that the molecule is structured enough that the internal dynamics remain uncorrelated with the overall alignment. This corresponds to the assumption that the separation of averaging in Eq. (21) remains valid. If this does not hold, then overall alignment and internal motion will be convoluted in some nonlinear manner. The second assumption is that the structure and dynamics of the molecule is not influenced by change of medium. Provided that both of these assumptions are permissible, the acquisition of sufficient... 

The MCSCF/CM response method provide procedures for obtaining frequency-dependent molecular properties when investigating a molecule coupled to a structured environment and the basis is achieved by treating the quantum mechanical subsystem on a quantum mechanical level and the structured environment as a classical subsystem described by a molecular mechanics force field. The important interactions between the two subsystems are included directly in the optimized wave function. 

In polyesterification and other polycondensation reactions, polymer molecules condense with one another by the same mechanism by which they add monomer units. There is no immediately apparent explanation, however, for the coupling of two polyarylene ether molecules of structure I. Three possible routes were first outlined by Finkbeiner (13), and each has received some support since. 

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