Molecular surface conformational mobility

Using conformational searching/quench dynamics and 7) relaxation measurements, each back-folded isomer was determined to be smaller than its extended counterpart. Thus, the effective distance of electron transfer was not reflected in the hydrodynamic radius of the molecule. Rather, the back-folded isomers were argued to be less mobile with the iron-sulfur core buried more deeply within them. The extended isomers were more mobile with the iron-sulfur core more able to come closer to the molecular surface. By this reasoning, the back-folded isomers had a larger effective electron transfer distance than the extended isomers. 

As discussed earlier, SAMs of alkanethiols on gold surfaces offer access to highly ordered, surface-confined molecular structures. The use of these assemblies as stable, well-defined spacers for studies of electron transfer between the gold electrode and redox eenters attached to the film surface [50, 73-83] or in solution [44, 46, 84] is depicted in Figure 5. The densely packed monolayer maintains a precise separation between a gold electrode surface and the pendant or dissolved redox center, and effectively eliminates conformational mobility that can complicate electron-transfer rate studies [73]. An advantage of using electrode-confined spacers is that... 

Color-coded molecular surfaces can provide qualitative or quantitative displays of hydrophobic and hydrophilic regions, neutral and charged amino acid side chains, electrostatic potential, and conformational mobility of side chains (based on the temperature factors from X-ray crystallographic refinement or moelcular dynamics simulation). Color-coding by hydro-... 

The extent of adhesion at the polymer/flller interface may be related to various parameters of adsorption and vetting. Factors related to the adsorption of the polymer onto the filler are types of interfacial forces (secondary, primary bonds), molecular orientation/conformation at the interface, and polymer mobility. Contact angle, surface tension, and substrate critical surface tension are among factors related to wetting. 

When the number of atoms in a certain complex molecule or molecular system increases, the number of local minima of the potential energy surface (PES) quickly becomes so large that a systematic search is impossible. The study of stable geometries of large molecular systems characterized hy a high conformational mobility, has to locate possible good candidates... 

Equation 2.16 contains contributions from the translational entropy of the mobile species, the conformational entropy of polymer chains, the free energy associated with the different chemical equilibria in the system, the polymer-polymer and polymer-surface van der Waals (vdW) interaction energies, the electrostatic interaction energies and the repulsive interactions between all the different molecular species. The expressions for each of these terms are shown in Table 2.2, while the definition of the symbols is given in Appendix. Note that in Table 2.2, the densities. 

---