Evolutionary expansion of a regulatory network by counter-silencing.

Horizontal gene transfer plays a major role in bacterial evolution. Successful acquisition of new genes requires their incorporation into existing regulatory networks. This study compares the regulation of conserved genes in the PhoPQ regulon of Salmonella enterica serovar Typhimurium with that of PhoPQ-regulated horizontally acquired genes, which are silenced by the histone-like protein H-NS. We demonstrate that PhoP upregulates conserved and horizontally acquired genes by distinct mechanisms. Conserved genes are regulated by classical PhoP-mediated activation and are invariant in promoter architecture, whereas horizontally acquired genes exhibit variable promoter architecture and are regulated by PhoP-mediated counter-silencing. Biochemical analyses show that a horizontally acquired promoter adopts different structures in the silenced and counter-silenced states, implicating the remodelling of the H-NS nucleoprotein filament and the subsequent restoration of open-complex formation as the central mechanism of counter-silencing. Our results indicate that counter-silencing is favoured in the regulatory integration of newly acquired genes because it is able to accommodate multiple promoter architectures.

Dielectric dependence of the first molecular hyperpolarizability for electro-optic chromophores.

Experimental and computational studies of the solvent dependence of the first molecular hyperpolarizability (ß) for two donor-bridge-acceptor chromophores (CLD-1 and YLD156) are presented. Hyper-Rayleigh scattering (HRS) measurements are performed with 1907 nm excitation in a series of solvents with dielectric constants ranging from ~2 (toluene) to ~36 (acetonitrile). For both chromophores an approximately 2-fold increase in ß is observed by HRS over this range of dielectric constants. Computational studies employing a polarized continuum model to represent the solvent are capable of reproducing this experimental result. The experimental and computational results are compared to the predictions of the widely employed two-state model (TSM) for ß. Surprisingly, for the chromophores studied here the TSM predicts that ß should decrease with increasing dielectric constant over the range investigated. The results presented here demonstrate that the TSM provides neither a quantitative nor qualitative description of the solvent dependence of ß for CLD-1 and YLD156. The enhancement of ß with increased dielectric constant suggests that modification of the dielectric surrounding the chromophore is one path by which the performance of nonlinear optical devices employing these chromophores may be significantly enhanced.

Reduced dimensionality in organic electro-optic materials: theory and defined order.

Identification of electronic intermolecular electrostatic interactions that can significantly enhance poling-induced order is important to the advancement of the field of organic electro-optics. Here, we demonstrate an example of such improvement achieved through exploitation of the interaction of coumarin pendant groups in chromophore-containing macromolecules. Acentric order enhancement is explained in terms of lattice-symmetry effects, where constraint of orientational degrees of freedom alters the relationship between centrosymmetric and acentric order. We demonstrate both experimentally and theoretically that lattice dimensionality can be defined using the relationship between centrosymmetric order and acentric order. Experimentally: Acentric order is determined by attenuated total reflection measurement of electro-optic activity coupled with hyper-Rayleigh scattering measurement of molecular first hyperpolarizability, and centrosymmetric order is determined by the variable angle polarization referenced absorption spectroscopy method. Theoretically: Order is determined from statistical mechanical models that predict the properties of soft condensed matter.

Modeling the optical behavior of complex organic media: from molecules to materials.

For the past three decades, a full understanding of the electro-optic (EO) effect in amorphous organic media has remained elusive. Calculating a bulk material property from fundamental molecular properties, intermolecular electrostatic forces, and field-induced net acentric dipolar order has proven to be very challenging. Moreover, there has been a gap between ab initio quantum-mechanical (QM) predictions of molecular properties and their experimental verification at the level of bulk materials and devices. This report unifies QM-based estimates of molecular properties with the statistical mechanical interpretation of the order in solid phases of electric-field-poled, amorphous, organic dipolar chromophore-containing materials. By combining interdependent statistical and quantum mechanical methods, bulk material EO properties are predicted. Dipolar order in bulk, amorphous phases of EO materials can be understood in terms of simple coarse-grained force field models when the dielectric properties of the media are taken into account. Parameters used in the statistical mechanical modeling are not adjusted from the QM-based values, yet the agreement with the experimentally determined electro-optic coefficient is excellent.

Rational enhancement of second-order nonlinearity: bis-(4-methoxyphenyl)hetero-aryl-amino donor-based chromophores: design, synthesis, and electrooptic activity.

Two new highly hyperpolarizable chromophores, based on N,N- bis-(4-methoxyphenyl) aryl-amino donors and phenyl-trifluoromethyl-tricyanofuran (CF3-Ph-TCF) acceptor linked together via pi-conjugation through 2,5-divinylenethienyl moieties as the bridge, have been designed and synthesized successfully for the first time. The aryl moieties on the donor side of the chromophore molecules were varied as to be thiophene and 1-n-hexylpyrrole. The linear and nonlinear optical (NLO) properties of all compounds were evaluated in addition to recording relevant thermal and electrochemical data. The properties of the two new molecules were comparatively studied. These results are critically analyzed along with two other compounds, reported earlier from our laboratories and our collaborator's, that contain (i) aliphatic chain-bearing aniline and (ii) dianisylaniline as donors, keeping the bridge (2,5-divinylenethienyl-), and the acceptor (CF3-Ph-TCF), constant. Trends in theoretically (density functional theory, DFT) predicted, zero-frequency gas-phase hyperpolarizability [beta(0;0,0)] values are shown to be consistent with the trends in beta HRS(-2omega;omega,omega), as measured by Hyper-Rayleigh Scattering (HRS), when corrected to zero-frequency using the two-level model (TLM) approximation. Similarly, trends in poling efficiency data (r33/E(p)) and wavelength dispersion measured by reflection ellipsometry (using a Teng-Man apparatus) and attenuated total reflection (ATR) are found to fit the TLM and DFT predictions. A 3-fold enhancement in bulk nonlinearity (r33) is realized as the donor subunits are changed from alkylaniline to dianisylaminopyrrole donors. The results of these studies provide insight into the complicated effects on molecular hyperpolarizability of substituting heteroaromatic subunits into the donor group structures. These studies also demonstrate that, when frequency dependence and electric-field-induced ordering behavior are correctly accounted for, ab initio DFT generated beta(0;0,0) is effective as a predictor of changes in r33 behavior based on chromophore structure modification. Thus DFT can provide valuable insight into the electronic structure origin of complex optical phenomena in organic media.