Molecular scale anisotropy

More recently, simulation studies focused on surface melting [198] and on the molecular-scale growth kinetics and its anisotropy at ice-water interfaces [199-204]. Essmann and Geiger [202] compared the simulated structure of vapor-deposited amorphous ice with neutron scattering data and found that the simulated structure is between the structures of high and low density amorphous ice. Nada and Furukawa [204] observed different growth mechanisms for different surfaces, namely layer-by-layer growth kinetics for the basal face and what the authors call a collected-molecule process for the prismatic system. 

One of the most popular applications of molecular rotors is the quantitative determination of solvent viscosity (for some examples, see references [18, 23-27] and Sect. 5). Viscosity refers to a bulk property, but molecular rotors change their behavior under the influence of the solvent on the molecular scale. Most commonly, the diffusivity of a fluorophore is related to bulk viscosity through the Debye-Stokes-Einstein relationship where the diffusion constant D is inversely proportional to bulk viscosity rj. Established techniques such as fluorescent recovery after photobleaching (FRAP) and fluorescence anisotropy build on the diffusivity of a fluorophore. However, the relationship between diffusivity on a molecular scale and bulk viscosity is always an approximation, because it does not consider molecular-scale effects such as size differences between fluorophore and solvent, electrostatic interactions, hydrogen bond formation, or a possible anisotropy of the environment. Nonetheless, approaches exist to resolve this conflict between bulk viscosity and apparent microviscosity at the molecular scale. Forster and Hoffmann examined some triphenylamine dyes with TICT characteristics. These dyes are characterized by radiationless relaxation from the TICT state. Forster and Hoffmann found a power-law relationship between quantum yield and solvent viscosity both analytically and experimentally [28]. For a quantitative derivation of the power-law relationship, Forster and Hoffmann define the solvent s microfriction k by applying the Debye-Stokes-Einstein diffusion model (2)... 

As we explained in the previous section, fluorescence decays do not bring any direct evidence about energy transfer among DNA bases within a helix. In contrast, fluorescence anisotropy decays can provide this type of information. Such a possibility is based on the correlation of macroscopic observables to molecular parameters. On the molecular scale, r is related to the angle 6 formed between the transition dipoles associated to photon absorption and photon emission ... 

In the case of crystals, one usually encounters structures that are anisotropic on a molecular scale, due to anisotropic interactions between the molecules. Clusters formed by colloidal-scale particles often do not exhibit anisotropy due to the isotropic character of the interactions on that colloidal scale. One may introduce anisotropy in that case by applying an external field, for example, a flow field or electric-magenetic field, and subsequently freezing the morphology by, for example, gelation. 

Molecular-scale imaging in FFM [46, 81], PFM-AFM [82], noncontact atomic force microscopy (nc-AFM) [83-88] and anisotropy in friction and molecular stick-shp motion [89] have been discussed. Other important issues in CFM are chiral discrimination [90-92] and calibration of AFM cantilever spring constants [67,93, 94] and tip radii [39, 95]. 

When the disorder is weaker (pr 3), the weak localization contribution dominates to lower temperatures (T < K). Thus, the anisotropy in both conductivity and MC is related to the extent of misaligned chains (anisotropy on the molecular scale) and to the anisotropy in the diffusion coefficient. 

Nada, H. and Fumkawa, Y. (1997) Anisotropy in molecular-scaled growth kinetics at ice-water interfaces. J. Phys. Chem. B, 101, 6163-6166. 

Theoretical calculations for ultrafast neat water spectroscopy are difficult to perform and difficult to interpret (because of the near-resonant OH stretch coupling). One classical calculation of the 2DIR spectrum even preceded the experiments [163] Torii has calculated the anisotropy decay [97], finding reasonable agreement with the experimental time scale. Mixed quantum/ classical calculations of nonlinear spectroscopy for many coupled chromo-phores is a daunting task. We developed the TAA for linear spectroscopy, and Jansen has very recently extended it to nonlinear spectroscopy [164]. We hope that this will allow for mixed quantum/classical calculations of the 2DIR spectrum for neat water and that this will provide the context for a molecular-level interpretation of these complex but fascinating experiments. 

The major reasons for using intrinsic fluorescence and phosphorescence to study conformation are that these spectroscopies are extremely sensitive, they provide many specific parameters to correlate with physical structure, and they cover a wide time range, from picoseconds to seconds, which allows the study of a variety of different processes. The time scale of tyrosine fluorescence extends from picoseconds to a few nanoseconds, which is a good time window to obtain information about rotational diffusion, intermolecular association reactions, and conformational relaxation in the presence and absence of cofactors and substrates. Moreover, the time dependence of the fluorescence intensity and anisotropy decay can be used to test predictions from molecular dynamics.(167) In using tyrosine to study the dynamics of protein structure, it is particularly important that we begin to understand the basis for the anisotropy decay of tyrosine in terms of the potential motions of the phenol ring.(221) For example, the frequency of flips about the C -C bond of tyrosine appears to cover a time range from milliseconds to nanoseconds.(222)... 

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