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We present a strategy for self-assembly of the smallest yet reported DNA nanostructures that are also addressable in terms of their DNA-base code. Using linear as well as novel branched three-way DNA oligonucleotide building-blocks we demonstrate the formation of a nano-network's fundamental cell, a DNA pseudo-hexagon of side 4 nm. The network's inherent addressability will allow functionalization with sub-nanometer precision yielding unprecedented richness in information density, important in the context of Moore's Law and nano-chip technology. © 2007.

Enthalpy-entropy compensation (EEC) has a definite physical sense. Here, we review EEC from a new standpoint, using the notion of correlation. The latter has two basic meanings: (a) 'A' is correlated to 'B' means 'A' results from 'B' or vice versa; (b) this same means there is some real, but hidden 'C' in connection to both 'A' and 'B'). In accordance with the interpretation (b), we try rationalizing EEC in terms of hidden, but physically real factors.

Circular dichroism (CD) of enantiomers of [Ru(phen)(2)dppz](2+) oriented in a octanoate-decanol-water lamellar liquid crystal has been measured parallel to the orientation axis. where the sample does not exhibit linear dichroism (LD). At an inclined incidence, the emerging LD shows that the chromophores have an along-chain orientation in the liquid crystal. The changes in the CD spectrum compared to an isotropic sample, in conjunction with CD calculations, allow us to assess the absolute configuration of the enantiomers and assign the CD bands to specific electronic transitions.

From linear dichroism data a distinct structure of the strongest complex between the methyl green (MG) dication and the B-form DNA is concluded. MG is not intercalated but binds (probably to hydrophobic surfaces in the major groove) with its x and z axes at an angle to the local helix axis of 48° and 90°, respectively. At higher occupation density, exciton coupling between transition dipoles of adjacent molecules is visualized in the linear and circular dichroism spectra. The final spectra may be understood in terms of a right-handed (MG)N helix in the major groove of the double helix.

The determination of circular dichroism (CD) of an oriented system requires meticulous consideration of the optics of sample and instrumentation unless the system is uniaxial and the light propagating parallel to the optical axis. A main error is due to the combination of a generally unavoidable stray birefringence of the modulator, or other instrumental elements preceding the sample, and a linear dichroism of the sample. A way of analysing and correcting for this effect is presented. The fact that the LD is usually several orders of magnitude greater than the CD in many cases obstructs a sufficiently accurate determination of the apparent CD correction. It was thus found impossible, with two different modern commercial CD spectrometers, to obtain even the sign of the difference between the isotropic CD and the perpendicular element of the CD tensor of DNA.

Many molecules (adducts) bound to DNA are postulated to intercalate between successive DNA base pairs. Linear dichroism (LD) has been used to yield information about the angular orientation of the adduct relative to the helix axis, but cannot probe the orientation within the plane perpendicular to this axis. A model is presented in this paper which predicts that the degree of alignment relative to a DNA fixed axis in this plane may be directly probed through the sign of the circular dichroism (CD) induced in an adduct transition of known polarization. Comparison with experimental data suggests that the method can complement LD studies in giving detailed information about the binding geometry.

Transition moment directions for the double-bond region vibrations of uracil, thymine and cytosine are calculated using the fixed partial charge model approximation. The coupling between the two carbonyl bonds and the carbon—carbon double bond in uracil and thymine is sensitive to the choice of the corresponding stretching force constants. The transition moment directions are correspondingly changed, thus, in principle, enabling the quantitative determination of coupling between the vibrations from linear dichroism measurements.

An experimental technique for detecting magnetic dipole allowed transitions by their dispersion-induced circular dichroism (DICD) is discussed. The DICD spectra of three nitrogen heterocycles (pyridine, pyrazine and tetraphenylporphyrin) are shown to be dominated by the n — π* transitions, as distinct from the normal absorption spectra which are dominated by the electric dipole allowed π — π* bands.

A high-sensitivity linear dichroism (LD) technique has been employed in studying the indirect orientation of benzene by solubilization in rod-shaped micelles in a system of cetyltrimethylammoniumbromide (CTAB): water, oriented by flow in a couvette device. The dependence of the LD signal due to the π-π* transitions in the benzene plane on the temperature, on the shear gradient and on the benzene concentration, has been investigated. The net positive LD, observed from the benzene chromophore, derives from benzene orientation at the surface of the rod-shaped micelles. The orientation of the micelle rods is very high and the system is suggested for use as a standard matrix for studying solubilized molecules in polarized spectroscopy.

Polarized absorption spectra have been measured on acridine, acridone and the 9-aminoacridinium and 9-amino-10-methylacridinium cations in stretched poly(vinyl alcohol) films, in the absorption region 220–500 nm, and corresponding transition moment directions were determined. The acridine derivatives should be suitable as bio-structural probes, as they provide transitions which are polarized exactly parallel to the two symmetry axes in the molecular plane.

Linear dichroism (LD) spectra of tetraphenyl porphin in oriented polyethylene, polypropylene and polyvinylchloride matrices were studied. A negative LD component at 400 nm is suggested to be due to an out-of-plane polarised transition. From evidence of changed polarisations within the (0,0) visible bands it is suggested further that the matrix may play an active role in perturbing the electronic spectrum by stimulating vibronic transitions with differing polarisations.

Linear dichroism (LD) spectra are presented for naphthalene oriented in stretched polyethylene and polypropylene matrices at 77 K and 296 K. From the calculated spectrum LD(λ)/ A (λ), where A (λ) is the corrected absorbance spectrum of the sample by unpolarized light, orientational parameters are calculated and component spectra, 235–315 nm, are resolved corresponding to polarization parallel to the long (B 3u = x ) and the short (B 2u = y ) axes in the molecular plane (D 2h ). The orientational parameters indicate different orientational mechanisms in polyethylene and polypropylene, but the resolving procedure yields mainly identical component spectra. It is suggested that the polarization (B 3u ) predominating in the 245–275 nm region isdue to a B 1g vibronic perturbation of the 1 B 2u state.

The posibilities of drawing conclusions about angular distribution functions F (ω) from measured moments [cos l ω] = ∫ cos l ω F (ω)d(ω) are discussed. F (ω) is expanded as a sum of Legendre polynomials with the moments in the coefficients. In practice only the first few moments are experimentally available. The limited use of a truncated series is demonstrated for distributions in polymers, electric fields and liquid crystals.

The existence of two transitions with opposite MCD in the 38000–45000 cm−1 absorption of thiophene is demonstrated. The B-term for the lowest transition is negative, while it is positive for the higher one. Quantum mechanical calculations in the π-electron approximation resulted in energies, oscillator strengths and MCD terms in good agreement with the observed spectra.

Optically active 1,2-dithiane has been produced in a hydrocarbon g ass at 77 K by photolysis with circularly polarised light. Its CD spectrum (above 270 nm) consists of a single symmetric component coinciding with the position of the low energy absorption band. The possibility of using the method to study any per se chiral but at room temperature statistically optically inactive molecule is stressed. A relation yielding Δϵ is presented.

Studies of linear dichroism, using a differential technique, on pyridine and pyrazine, quasi-oriented in stretched polymer matrices, give evidence for the energy positions of the n-π * transitions. These molecules are mainly oriented in the same way as benzene, i.e., the orientation axes in the molecular plane are almost degenerate, and the out-of-plane polarized transitions appear as negative linear dichroism components.

A new transition recently suggested at 265 nm in dialkyl anilines is confirmed by linear dichroism in an oriented matrix.