Dynamic structures in solution

FIG. 1 Geometries of electrolyte interfaces, (a) A planar electrode immersed in a solution with ions, and with the ion distrihution in the double layer, (b) Particles with permanent charges or adsorbed surface charges, (c) A porous electrode or membrane with internal structures, (d) A polyelectrolyte with flexible and dynamic structure in solution, (e) Organized amphophilic molecules, e.g., Langmuir-Blodgett film and microemulsion, (f) Organized polyelectrolytes with internal structures, e.g., membranes and vesicles. 

To which degree a transfer of these results of differential geometry , only exactly valid for solid-state conditions, is possible for dynamic structures in solution, remains uncertain at the present time [100]. 

The H NMR spectra of 4.201 and 4.202 are consistent with dynamic structures in solution, which, on time average, are planar and highly symmetric. By contrast, a single crystal X-ray structural analysis of 4.202 showed that, in the solid state, the molecule is not planar and that one of the furan rings is twisted significantly out of the mean molecular plane (Figure 4.6.2). 

Solar energy conversion functions often depend on dynamic structures in solution or on a supporting matrix where a transiently appearing dynamic structure could evolve into a precursor for catalytic intermediates. Such dynamic structures are implicitly depicted by the Debye-Weller factor in the conventional XAS data analysis in Equation (12.1), without specific description of the structural origin. In many homogeneous photochemical reactions, metal complexes interact with solvent molecules to form transient dynamic solvated structures, such as dynamic bonding between the catalyst molecule and the solvent or substrate molecules. These dynamic structures may well be the precursor or transition states in catalytic reactions, but were unfortunately obscured in the conventional data analysis. 

The analogy drawn between -stacked solids and duplex DNA has provided a useful starting point for experiments to probe and understand DNA-medi-ated CT. As with the -stacked solids, the DNA base pair array can provide an effective medium for long range CT. Mechanistically, however, the differences between DNA and these solid state materials may be even more important to consider. Duplex DNA, as a molecular -stacked structure, undergoes dynamical motion in solution. The time-dependent and sequence-dependent structures that arise serve to modulate and gate CT. Indeed in probing DNA CT as a function of sequence and sequence-dependent structure, we may better understand mechanistically how CT proceeds and how DNA CT may be utilized. 

It is emphasized that revealing the dynamics as well as the structure (or conformation) based on several types of spin-relaxation times is undoubtedly a unique and indispensable means, only available from NMR techniques at ambient temperature of physiological significance. Usually, the structure data themselves are available also from X-ray diffraction studies in a more refined manner. Indeed, better structural data can be obtained at lower temperature by preventing the unnecessary molecular fluctuations, which are major subjects in this chapter, since structural data can be seriously deteriorated for domains where dynamics are predominant even in the 2D or 3D crystalline state or proteoliposome at ambient temperature. It should be also taken into account that the solubilization of membrane proteins in detergents is an alternative means to study structure in solution NMR. However, it is not always able faithfully to mimick the biomembrane environment, because the interface structure is not always the same between the bilayer and detergent system. This typically occurs in the case of PLC-81(1-140) described in Section 4.2.4 and other types of peptide systems. 

Effect of enzyme dynamics on catalytic activity, 41, 317 Effective charge and transition-state structure in solution, 27, 1 Effective molarities of intramolecular reactions, 17, 183 Electrical conduction in organic solids, 16, 159 Electrochemical methods, study of reactive intermediates by, 19, 131 Electrochemical recognition of charged and neutral guest species by redox-active receptor molecules, 31, 1... 

Molecular dynamics (MD) simulations fill a significant niche in the study of chemical structure. While nuclear magnetic resonance (NMR) yields the structure of a molecule in atomic detail, this structure is the time-averaged composite of several conformations. Electronic and vibrational circular dichroism spectroscopy and more general ultraviolet/visible and infrared (IR) spectroscopy yield the secondary structure of the molecule, but at low resolution. MD simulations, on the other hand, yield a large set of individual structures in high detail and can describe the dynamic properties of these structures in solution. Movement and energy details of individual atoms can then be easily obtained from these studies. 

Few methods are available for the direct determination of coordination geometry, bond lengths, and bond angles for complexes in solution, although such information is important, for example, for the interpretation of thermodynamic and dynamic data. Complexes, which can be found also in crystals where their structures can be easily determined by diffraction methods, are usually assumed to have the same structure in solution, although the different environment can be expected to influence bond lengths and coordination geometry. But many complexes, which are stable in solution, do not occur in the solid state, where structures with infinite rather than discrete complexes may be preferred. Direct determinations of structures in solution are, therefore, needed and methods that can provide such information are all based on diffraction. 

The crystal and molecular structures of two spiroarsoranes of type XXI (R = Ph, R = R" = CH3 and R = OH, R = R" = H) have been determined by single-crystal X-ray diffraction analyses (68, 69). The crystal data for these compounds are summarized in Table V. Both compounds have a geometry at the arsenic atom that lies on the Berry coordinate between rectangular-pyramidal and trigonal-pyramidal. These structures show close parallels between the structures of related arsenic and phosphorus systems. It has been concluded that, since the solid-state structures of these compounds lie close to the Berry coordinate, the dynamic process in solution is distortion along that coordinate (68, 69). 

Dynamic behavior in solution is revealed by variable temperature NMR measurements and is primarily due to inversion at sulfur. The trans-anti and trans-syn isomers are the major species in the solution of the nickel complex. In solutions of Pd and Pt complexes, the cis-anti isomers are also detectable. The cis-anti isomer of the Pt complex has been isolated and is more stable than that of the Pd analogue (64). Hypothetically, a fourth isomer, the cis-syn isomer, may also exist. However, this species may not be stable even at temperatures as low as —50 °C. Inspection of the crystal structure of the trans-anti isomer... 

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