Oriented single molecules

Oriented Single Molecules with Switchable Mobility in Long Unidimensional Nanochannels... 

Figure Bl.22.11. Near-field scanning optical microscopy fluorescence image of oxazine molecules dispersed on a PMMA film surface. Each protuberance in this three-dimensional plot corresponds to the detection of a single molecule, the different intensities of those features being due to different orientations of the molecules. Sub-diffraction resolution, in this case on the order of a fraction of a micron, can be achieved by the near-field scaiming arrangement. Spectroscopic characterization of each molecule is also possible. (Reprinted with pennission from [82]. Copyright 1996 American Chemical Society.)...

Figure Cl.5.3. Near-field fluorescence image 4.5 p.m square) of single oxazine 720 molecules dispersed on die surface of a PMMA film. Each peak (fwhm 100 nm) is due to a single molecule. The different intensities are due to different molecular orientations and spectra. Reprinted widi pennission from Xie 11221. Copyright 1996 American Chemical Society.

The polarization properties of single-molecule fluorescence excitation spectra have been explored and utilized to detennine botli tlie molecular transition dipole moment orientation and tlie deptli of single pentacene molecules in a /7-teriDhenyl crystal, taking into account tlie rotation of tlie polarization of tlie excitation light by tlie birefringent... 

Figure C 1.5.13. Schematic diagram of an experimental set-up for imaging 3D single-molecule orientations. The excitation laser with either s- or p-polarization is reflected from the polymer/water boundary. Molecular fluorescence is imaged through an aberrating thin water layer, collected with an inverted microscope and imaged onto a CCD array. Aberrated and unaberrated emission patterns are observed for z- and xr-orientated molecules, respectively. Reprinted with pennission from Bartko and Dickson [148]. Copyright 1999 American Chemical Society.

Figure Cl.5.14. Fluorescence images of tliree different single molecules observed under the imaging conditions of figure Cl.5.13. The observed dipole emission patterns (left column) are indicative of the 3D orientation of each molecule. The right-hand column shows the calculated fit to each observed intensity pattern. Molecules 1, 2 and 3 are found to have polar angles of (0,( ))=(4.5°,-24.6°), (-5.3°,51.6°) and (85.4°,-3.9°), respectively. Reprinted with pennission from Bartko and Dickson [148]. Copyright 1999 American Chemical Society.

Figure Cl.5.15. Molecular orientational trajectories of five single molecules. Each step in tire trajectory is separated by 300 ms and is obtained from tire fit to tire dipole emission pattern such as is shown in figure Cl.5.14. The radial component is displayed as sin 0 and tire angular variable as (ji. The lighter dots around tire average orientation represent 1 standard deviation. Reprinted witli pennission from Bartko and Dickson 11481. Copyright 1999 American Chemical Society.

Bartko A P and Dickson R M 1999 Three-dimensional orientations of polymer-bound single molecules J. Chem. Phys. B 103 3053-6... 

Hollars C W and Dunn R C 2000 Probing single molecule orientations in model lipid membranes with near-field scanning optical microscopy J. Phys. Chem 112 7822-30... 

Other orientational correlation coefficients can be calculated in the same way as tf correlation coefficients that we have discussed already. Thus, the reorientational coiTelatio coefficient of a single rigid molecule indicates the degree to which the orientation of molecule at a time t is related to its orientation at time 0. The angular velocity autocorrelatio function is the rotational equivalent of the velocity correlation function ... 

Disk-shaped molecules based on a metal atom possess discotic Hquid crystal phases. An example is octasubstituted metaHophthalocyanine. FiaaHy, metallomesogens which combine both rod-like and disk-like features iato a single molecule adopt the biaxial nematic phase. In addition to there being a preferred direction for orientation of the longest molecular axis as is tme for the nematic phase, perpendicular to this direction is another preferred direction for orientation of the shortest molecular axis (12). NonmetaHomesogens which combine both rod- and disk-like features iato a single molecule also adopt a biaxial nematic phase, but at least ia one case the amount of biaxiaHty is very small (15). 

Any extended part of a linear polymer molecule exhibits a strong anisotropy of many properties since its atoms and atomic groups are oriented and the macromolecule is actually a one-dimensional crystal . The parallel packing of these parts during the formation of a uniaxially oriented polymer substance imparts the anisotropie properties of a single molecule to the whole polymeric material. 

In highly diluted solutions the surfactants are monodispersed and are enriched by hydrophil-hydrophobe-oriented adsorption at the surface. If a certain concentration which is characteristic for each surfactant is exceeded, the surfactant molecules congregate to micelles. The inside of a micelle consists of hydrophobic groups whereas its surface consists of hydrophilic groups. Micelles are dynamic entities that are in equilibrium with their surrounded concentration. If the solution is diluted and remains under the characteristic concentration, micelles dissociate to single molecules. The concentration at which micelle formation starts is called critical micelle concentration (cmc). Its value is characteristic for each surfactant and depends on several parameters [189-191] ... 

For smectic phases the defining characteristic is their layer structure with its one dimensional translational order parallel to the layer normal. At the single molecule level this order is completely defined by the singlet translational distribution function, p(z), which gives the probability of finding a molecule with its centre of mass at a distance, z, from the centre of one of the layers irrespective of its orientation [19]. Just as we have seen for the orientational order it is more convenient to characterise the translational order in terms of translational order parameters t which are the averages of the Chebychev polynomials, T (cos 2nzld)-, for example... 

We have seen that the transition dipole moment occurring upon excitation of a molecule has a distinct orientation with regard to the molecular axis. This orientation can be determined by measuring the absorption of polarized light (oscillating in only one plane) by oriented single crystals,... 

To extract useful results from a molecular electronic device, or just to measure its electronic characteristics, connections must be made to macroscopic probes. That is, metallic electrodes must interface to different ends of the molecule of interest. An experiment may interrogate a single molecule, or may measure a one-molecule-thick layer, i.e., a monolayer, of the molecules of interest, provided all the molecules are oriented in the same direction. In either case, several questions arise. What is the nature of the contact between metal and molecule(s) What metal should be chosen, and what should be the form or shape of this electrode ... 

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