Conformational Changes from Molecular Dynamics Simulations

Nonpolar and dipolar altitudinal rotors (compounds 2 and 3 in Fig. 17.3) have been synthesized. 19F NMR spectroscopy showed that the barrier to rotation in 3 was extremely low in solution. Both systems have then been immobilized on Au(l 11) surfaces and studied with a variety of techniques.57 The results obtained indicated that for a fraction of molecules the static electric field from the scanning tunneling microscopy (STM) tip could induce an orientation change in the dipolar rotor but not in the nonpolar analog (for a recent example of an azimuthal molecular rotor controlled by the STM tip, see Reference 58). Compound 3 can exist as three pairs of helical enantiomers because of the propeller-like conformation of the tetra-arylcyclobutadienes. For at least one out of the three diastereomers, an asymmetric potential energy surface can be predicted by molecular dynamics simulations on application of an alternating electric field.55... 

Wallis and Thompson [61] developed a potential energy surface using these spectroscopic and theoretical data and used it in molecular dynamics simulations to study the chair-to-boat conformational inversion. They followed up this study with simulations of the RDX conformational changes in dense xenon gas as a function of concentration. Since then a great deal more has been learned about the details of the potential from quantum chemistry calculations and could be used to improve the Wallis-Thompson model. 

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