Distance measures molecular modeling

Structural drawings (molecular models too) can be deceiving For example the chlonne atoms in 1 2 dichlorocyclohexane seem much closer to each other in a drawing of the trans stereoisomer than in the cis Make a molecular model of each and measure the distance between the chlorines What do you find" ... 

Further, a molecular model for the anti-parallel (3-sheet conformation of PG and PLV have been calculated using the X-PLOR 3.1 program, and we have measured carbon-proton distances from the modeled structure. 

In order to clarify the relationship between cross peaks and carbon proton inter-atomic distances, molecular model for the anti-parallel p-sheet conformation of PG and PLV have been calculated using reference data (Wiithrich, et al.)117 by the X-PLOR 3.1 program, and we measured the carbon-proton distances from the modeled structure (Table 14). The distances between the carbons and their directly bonded protons are ca. 1.1 A and their signals can be observed in the FSLG C H HETCOR spectrum with contact time of 0.2 ms. Further, in the FSLG C H HETCOR spectrum with a contact time of 0.5 ms the signals corresponding... 

If the molecular tumbling rate is slow enough that larger electron-electron dipolar couplings are not motionally averaged, Fourier deconvolution can be used to analyze dipolar interactions in fluid solution.18 Distances in doubly spin-labelled rhodopsin were measured by Fourier deconvolution of CW line-shape changes in room temperature solution.78 The broadening function was modelled as the sum of Pake patterns from a distribution of distances. As a reference point for the distance measurements one label was attached at the cytoplasmic termination of transmembrane helix 1. The second label was attached near the cytoplasmic termination of transmembrane helix 7 or in the short helix 8. The distances and conformational flexibility in the dark state are... 

Pulse measurements. A self-complementary RNA with 12 base pairs was spin labelled at uridine near the middle of the strand.83 Three-pulse PELDOR gave an interspin distance of 35 2 A, which is in good agreement with molecular modelling. For a shorter self-complementary RNA, dipolar modulation was not observed, which was attributed to aggregation or weak duplex formation. 

Figure 12. Difference of chemical conformations of ephedrine (5) and pseudoephedrine ( ) and distance between hydrogen and nitrogen measured by molecular modeling (Sybyl 6.5, Tripos).

NMR is the experimental tool of choice to explore conformational properties, especially of flexible small molecules in solution [55-57], Interpretation of NMR-derived structural parameters in combination with molecular modeling usually offers a view of the accessible conformations to ligands. The most relevant structural parameters derived from NMR are interproton distances obtained from NOE or ROE experiments, dihedral angle restraints from 3J scalar coupling measurements and, recently, residual dipolar couplings (RDCs) [58],... 

Problem 4.1 Build a molecular model of ethane, and look at the interconversion of staggered and eclipsed forms. Measure the H-H distances in each case, and see if you can detect a difference. 

The distance between the chromophores Is approximately 21 8 as measured on molecular models and no ground state Interaction could be observed. In dioxane, the singlet energy transfer occurs by a Forster-type mechanism. On the basis of this mechanism, the distance can be calculated from the transfer efficiency. For [16a] a value of 21.211.6 X was found, while for [I6b] one obtained a value of 16.7 1.4 X. This latter discrepancy was explained on the basis of preferential orientation of the chromophores. That this phenomenon Indeed plays an Important role, was proved by Leermakers (59,60) In a series of indole alkaloids. The same author (59) also Illustrated the absence of triplet-triplet transfer at low temperature in compound [16b]. 

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