Spontaneous ferroelectric order in a bent-core smectic liquid crystal of fluid orthorhombic layers

Macroscopic polarization density, characteristic of ferroelectric phases, is stabilized by dipolar intermolecular interactions. These are weakened as materials become more fluid and of higher symmetry, limiting ferroelectricity to crystals and to smectic liquid crystal stackings of fluid layers. We report the SmAP(F), the smectic of fluid polar orthorhombic layers that order into a three-dimensional ferroelectric state, the highest-symmetry layered ferroelectric possible and the highest-symmetry ferroelectric material found to date. Its bent-core molecular design employs a single flexible tail that stabilizes layers with untilted molecules and in-plane polar ordering, evident in monolayer-thick freely suspended films. Electro-optic response reveals the three-dimensional orthorhombic ferroelectric structure, stabilized by silane molecular terminations that promote parallel alignment of the molecular dipoles in adjacent layers.     

Two-dimensional nematic colloidal crystals self-assembled by topological defects

The ability to generate regular spatial arrangements of particles is an important technological and fundamental aspect of colloidal science. We showed that colloidal particles confined to a few-micrometer-thick layer of a nematic liquid crystal form two-dimensional crystal structures that are bound by topological defects. Two basic crystalline structures were observed, depending on the ordering of the liquid crystal around the particle. Colloids inducing quadrupolar order crystallize into weakly bound two-dimensional ordered structure, where the particle interaction is mediated by the sharing of localized topological defects. Colloids inducing dipolar order are strongly bound into antiferroelectric-like two-dimensional crystallites of dipolar colloidal chains. Self-assembly by topological defects could be applied to other systems with similar symmetry.     

Ordered liquid aluminum at the interface with sapphire

Understanding the nature of solid-liquid interfaces is important for many processes of technological interest, such as solidification, liquid-phase epitaxial growth, wetting, liquid-phase joining, crystal growth, and lubrication. Recent studies have reported on indirect evidence of density fluctuations at solid-liquid interfaces on the basis of x-ray scattering methods that have been complemented by atomistic simulations. We provide evidence for ordering of liquid atoms adjacent to an interface with a crystal, based on real-time high-temperature observations of alumina-aluminum solid-liquid interfaces at the atomic-length scale. In addition, crystal growth of alumina into liquid aluminum, facilitated by interfacial transport of oxygen from the microscope column, was observed in situ with the use of high-resolution transmission electron microscopy.     

Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide

A polyamide nucleic acid (PNA) was designed by detaching the deoxyribose phosphate backbone of DNA in a computer model and replacing it with an achiral polyamide backbone. On the basis of this model, oligomers consisting of thymine-linked aminoethylglycyl units were prepared. These oligomers recognize their complementary target in double-stranded DNA by strand displacement. The displacement is made possible by the extraordinarily high stability of the PNA-DNA hybrids. The results show that the backbone of DNA can be replaced by a polyamide, with the resulting oligomer retaining base-specific hybridization.     

Predictive self-assembly of polyhedra into complex structures

Predicting structure from the attributes of a material's building blocks remains a challenge and central goal for materials science. Isolating the role of building block shape for self-assembly provides insight into the ordering of molecules and the crystallization of colloids, nanoparticles, proteins, and viruses. We investigated 145 convex polyhedra whose assembly arises solely from their anisotropic shape. Our results demonstrate a remarkably high propensity for thermodynamic self-assembly and structural diversity. We show that from simple measures of particle shape and local order in the fluid, the assembly of a given shape into a liquid crystal, plastic crystal, or crystal can be predicted.     

Biomolecular interactions at phospholipid-decorated surfaces of liquid crystals

The spontaneous assembly of phospholipids at planar interfaces between thermotropic liquid crystals and aqueous phases gives rise to patterned orientations of the liquid crystals that reflect the spatial and temporal organization of the phospholipids. Strong and weak specific-binding events involving proteins at these interfaces drive the reorganization of the phospholipids and trigger orientational transitions in the liquid crystals. Because these interfaces are fluid, processes involving the lateral organization of proteins (such as the formation of protein- and phospholipid-rich domains) are also readily imaged by the orientational response of the liquid crystal, as are stereospecific enzymatic events. These results provide principles for label-free monitoring of aqueous streams for molecular and biomolecular species without the need for complex instrumentation.     

Single-molecule cut-and-paste surface assembly

We introduce a method for the bottom-up assembly of biomolecular structures that combines the precision of the atomic force microscope (AFM) with the selectivity of DNA hybridization. Functional units coupled to DNA oligomers were picked up from a depot area by means of a complementary DNA strand bound to an AFM tip. These units were transferred to and deposited on a target area to create basic geometrical structures, assembled from units with different functions. Each of these cut-and-paste events was characterized by single-molecule force spectroscopy and single-molecule fluorescence microscopy. Transport and deposition of more than 5000 units were achieved, with less than 10% loss in transfer efficiency.     

Liquid crystalline networks composed of pentagonal, square, and triangular cylinders

T-shaped molecules are designed in such a way that they self-organize into nanoscale liquid crystalline honeycombs based on polygons with any chosen number of sides. One of the phases reported here is a periodic organization of identical pentagonal cylinders; the other one is a structure composed of square-shaped and triangular cylinders in the ratio 2:1. These two different packing motifs represent duals of the same topological class. The generalization of the concept applied here allows the prediction of a whole range of unusual complex liquid crystalline phases.     

Polarization-modulated smectic liquid crystal phases

Any polar-ordered material with a spatially uniform polarization field is internally frustrated: The symmetry-required local preference for polarization is to be nonuniform, i.e., to be locally bouquet-like or "splayed." However, it is impossible to achieve splay of a preferred sign everywhere in space unless appropriate defects are introduced into the field. Typically, in materials like ferroelectric crystals or liquid crystals, such defects are not thermally stable, so that the local preference is globally frustrated and the polarization field remains uniform. Here, we report a class of fluid polar smectic liquid crystals in which local splay prevails in the form of periodic supermolecular-scale polarization modulation stripes coupled to layer undulation waves. The polar domains are locally chiral, and organized into patterns of alternating handedness and polarity. The fluid-layer undulations enable an extraordinary menagerie of filament and planar structures that identify such phases.     

Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair

DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees and comprises a synthetic CPD lesion. This CPD lesion is flipped into the active site and split there into two thymines by synchrotron radiation at 100 K. Although photolyases catalyze blue light-driven CPD cleavage only above 200 K, this structure apparently mimics a structural substate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place.     

Structure of membrane surfactant and liquid crystalline smectic lamellar phases under flow

Synchrotron x-ray scattering studies were performed to probe the nonequilibrium structures of two layered systems at high shear rates: the smectic-A phase of the thermotropic liquid crystal 4-cyano-4'-octylbiphenyl (8CB) and the lamellar L(alpha) phases of surfactant membranes composed of sodium dodecyl sulfate and pentanol. Whereas the lamellar surfactant phases oriented primarily with their layers parallel to the shearing plates, as expected intuitively, in the corresponding high shear regime, the smectic-A liquid crystalline material oriented with the layers perpendicular to the shearing plates. A careful numerical study revealed that this surprising layer orientation results from nonlinear dynamics of the liquid crystal director and is caused by the flow distortion of thermal fluctuations.     

An orientational transition of bent-core molecules in an anisotropic matrix

We report the discovery of an orientational transition of bent-core molecules in a background anisotropic medium, in this case a smectic liquid crystal made of rod-like molecules. The resulting director is apolar in nature, and the medium can be described as an orthogonal biaxial smectic. The detailed phase diagram of mixtures of the two types of compounds revealed the induction of two liquid crystalline phases that are specific to compounds with bent-core molecules. The chemical nature of the bounding surface had a marked influence on the observed textures.     

Synthesis of two-dimensional polymers

A synthetic pathway is described to construct "in bulk" two-dimensional (2D) polymers shaped as molecular sheets. A chiral oligomeric precursor is used that contains two reactive sites, a polymerizable group at one terminus and a reactive stereogenic center near the middle of the molecule. The bulk reaction yields bilayer 2D polymers of molecular weight in the order of millions and a monodisperse thickness of 50.2 angstroms. The 2D molecular objects form through molecular recognition by the oligomers, which self-organize into layers that place the reactive groups within specific planes. The oligomers become catenated by two different stitching reactions involving the reactive sites. At room temperature, stacks of these molecular objects can organize as single crystals and at higher temperatures melt into smectic liquid crystals. Nonlinear optical experiments reveal that solid films containing the 2D polymers form structures that are thermally and temporally more stable than those containing analogous 1D polymers. This observation suggests that the transformation of common polymers from a 1D to a 2D architecture may produce generations of organic materials with improved properties.     

Pressure-induced Amorphization of R-Al5Li3Cu: A Structural Relation Among Amorphous Metals, Quasi-Crystals, and Curved Space

A central question in the study of amorphous materials is the extent to which they are ordered. When the crystalline intermetallic R-Al(5)Li(3)Cu is compressed to 23.2 gigapascals at ambient temperature, an amorphous phase is produced whose order can be described as defects in a curved-space crystal. This result supports a structural relation between quasi-crystals and amorphous metals based on icosahedral ordering. This result also shows that a metallic crystal can be made amorphous by compression.     

Endotoxin-induced structural transformations in liquid crystalline droplets

The ordering of liquid crystals (LCs) is known to be influenced by surfaces and contaminants. Here, we report that picogram per milliliter concentrations of endotoxin in water trigger ordering transitions in micrometer-size LC droplets. The ordering transitions, which occur at surface concentrations of endotoxin that are less than 10(-5) Langmuir, are not due to adsorbate-induced changes in the interfacial energy of the LC. The sensitivity of the LC to endotoxin was measured to change by six orders of magnitude with the geometry of the LC (droplet versus slab), supporting the hypothesis that interactions of endotoxin with topological defects in the LC mediate the response of the droplets. The LC ordering transitions depend strongly on glycophospholipid structure and provide new designs for responsive soft matter.     

DNA-functionalized nanotube membranes with single-base mismatch selectivity

We describe synthetic membranes in which the molecular recognition chemistry used to accomplish selective permeation is DNA hybridization. These membranes contain template-synthesized gold nanotubes with inside diameters of 12 nanometers, and a "transporter" DNA-hairpin molecule is attached to the inside walls of these nanotubes. These DNA-functionalized nanotube membranes selectively recognize and transport the DNA strand that is complementary to the transporter strand, relative to DNA strands that are not complementary to the transporter. Under optimal conditions, single-base mismatch transport selectivity can be obtained.     

Molecular cloning of complementary DNA for the alpha subunit of the G protein that stimulates adenylate cyclase

A complementary DNA clone encoding the alpha subunit of the adenylate cyclase stimulatory G protein (Gs) was isolated and identified. A bovine brain complementary DNA library was screened with an oligonucleotide probe derived from amino acid sequence common to known G proteins. The only clone that was obtained with this probe has a complementary DNA insert of approximately 1670 base pairs. An antibody to a peptide synthesized according to deduced amino acid sequence reacts specifically with the alpha subunit of Gs. In addition, RNA that hybridizes with probes made from the clone is detected in wild-type S49 cells; however, cyc- S49 cells, which are deficient in Gs alpha activity, are devoid of this messenger RNA.     

Parallel stranded DNA

A series of four hairpin deoxyoligonucleotides was synthesized with a four-nucleotide central loop (either C or G) flanked by the complementary sequences d(T)10 and d(A)10. Two of the molecules contain either a 3'-p-3' or 5'-p-5' linkage in the loop, so that the strands in the stem have the same, that is, parallel (ps) polarity. The pair of reference oligonucleotides have normal phosphodiester linkages throughout and antiparallel (aps) stem regions. All the molecules adopt a duplex helical structure in that (i) the electrophoretic mobilities in polyacrylamide gels of the ps and aps oligomers are similar. (ii) The ps hairpins are substrates for T4 polynucleotide kinase, T4 DNA ligase, and Escherichia coli exonuclease III. (iii) Salt-dependent thermal transitions are observed for all hairpins, but the ps molecules denature 10 degrees C lower than the corresponding aps oligomers. (iv) The ultraviolet absorption and circular dichroism spectra are indicative of a base-paired duplex in the stems of the ps hairpins but differ systematically from those of the aps counterparts. (v) The bis-benzimidazole drug Hoechst-33258, which binds in the minor groove of B-DNA, exhibits very little fluorescence in the presence of the ps hairpins but a normal, enhanced emission with the aps oligonucleotides. In contrast, the intercalator ethidium bromide forms a strongly fluorescent complex with all hairpins, the intensity of which is even higher for the ps species. (vi) The pattern of chemical methylation is the same for both the ps and aps hairpins. The combined results are consistent with the prediction from force field analysis of a parallel stranded right-handed helical form of d(A)n.d(T)n with a secondary structure involving reverse Watson-Crick base pairs and a stability not significantly different from that of the B-DNA double helix. Models of the various hairpins optimized with force field calculations are described.     

Molecular layering of fluorinated ionic liquids at a charged sapphire (0001) surface

Room-temperature ionic liquids (RTILs) are promising candidates for a broad range of "green" applications, for which their interaction with solid surfaces plays a crucial role. In this high-energy x-ray reflectivity study, the temperature-dependent structures of three ionic liquids with the tris(pentafluoroethyl)trifluorophosphate anion in contact with a charged sapphire substrate were investigated with submolecular resolution. All three RTILs show strong interfacial layering, starting with a cation layer at the substrate and decaying exponentially into the bulk liquid. The observed decay length and layering period point to an interfacial ordering mechanism, akin to the charge inversion effect, which is suggested to originate from strong correlations between the unscreened ions. The observed layering is expected to be a generic feature of RTILs at charged interfaces.