Blue-phase templated fabrication of three-dimensional nanostructures for photonic applications

A promising approach to the fabrication of materials with nanoscale features is the transfer of liquid-crystalline structure to polymers. However, this has not been achieved in systems with full three-dimensional periodicity. Here we demonstrate the fabrication of self-assembled three-dimensional nanostructures by polymer templating blue phase I, a chiral liquid crystal with cubic symmetry. Blue phase I was photopolymerized and the remaining liquid crystal removed to create a porous free-standing cast, which retains the chiral three-dimensional structure of the blue phase, yet contains no chiral additive molecules. The cast may in turn be used as a hard template for the fabrication of new materials. By refilling the cast with an achiral nematic liquid crystal, we created templated blue phases that have unprecedented thermal stability in the range-125 to 125°C, and that act as both mirrorless lasers and switchable electro-optic devices. Blue-phase templated materials will facilitate advances in device architectures for photonics applications in particular. © 2012 Macmillan Publishers Limited. All rights reserved.

Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain

The ligand binding domain of the human vitamin D receptor (VDR) was modeled based on the crystal structure of the retinoic acid receptor. The ligand binding pocket of our VDR model is spacious at the helix 11 site and confined at the β-turn site. The ligand 1α,25-dihydroxyvitamin D3 was assumed to be anchored in the ligand binding pocket with its side chain heading to helix 11 (site 2) and the A-ring toward the β-turn (site 1). Three residues forming hydrogen bonds with the functionally important 1α- and 25-hydroxyl groups of 1α,25-dihydroxyvitamin D3 were identified and confirmed by mutational analysis: the 1α-hydroxyl group is forming pincer-type hydrogen bonds with S237 and R274 and the 25-hydroxyl group is interacting with H397. Docking potential for various ligands to the VDR model was examined, and the results are in good agreement with our previous three-dimensional structure-function theory.

Three-dimensional image reconstruction of dephosphorylated smooth muscle heavy meromyosin reveals asymmetry in the interaction between myosin heads and placement of subfragment 2

Regulation of the actin-activated ATPase of smooth muscle myosin II is known to involve an interaction between the two heads that is controlled by phosphorylation of the regulatory light chain. However, the three-dimensional structure of this inactivated form has been unknown. We have used a lipid monolayer to obtain two-dimensional crystalline arrays of the unphosphorylated inactive form of smooth muscle heavy meromyosin suitable for structural studies by electron cryomicroscopy of unstained, frozen-hydrated specimens. The three-dimensional structure reveals an asymmetric interaction between the two myosin heads. The ATPase activity of one head is sterically “blocked” because part of its actin-binding interface is positioned onto the converter domain of the second head. ATPase activity of the second head, which can bind actin, appears to be inhibited through stabilization of converter domain movements needed to release phosphate and achieve strong actin binding. When the subfragment 2 domain of heavy meromyosin is oriented as it would be in an actomyosin filament lattice, the position of the heads is very different from that needed to bind actin, suggesting an additional contribution to ATPase inhibition in situ.

An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images

We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-Å resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules.

Hydrate stabilization in the three-dimensional hydrogen-bonded structure of the brucinium compound, bis(2,3-dimethoxy-10-oxostrychnidinium) biphenyl-4,4'-disulfonate hexahydrate

The crystal structure of the 2:1 proton-transfer compound of brucine with biphenyl-4,4’-disulfonate, bis(2,3-dimethoxy-10-oxostrychnidinium) biphenyl-4,4'-disulfonate hexahydrate (1) has been determined at 173 K. Crystals are monoclinic, space group P21 with Z = 2 in a cell with a = 8.0314(2), b = 29.3062(9), c = 12.2625(3) Å, β = 101.331(2)o. The crystallographic asymmetric unit comprises two brucinium cations, a biphenyl-4,4'-disulfonate dianion and six water molecules of solvation. The brucinium cations form a variant of the common undulating and overlapping head-to-tail sheet sub-structure. The sulfonate dianions are also linked head-to-tail by hydrogen bonds into parallel zig-zag chains through clusters of six water molecules of which five are inter-associated, featuring conjoint cyclic eight-membered hydrogen-bonded rings [graph sets R33(8) and R34(8)], comprising four of the water molecules and closed by sulfonate O-acceptors. These chain structures occupy the cavities between the brucinium cation sheets and are linked to them peripherally through both brucine N+-H...Osulfonate and Ocarbonyl…H-Owater to sulfonate O bridging hydrogen bonds, forming an overall three-dimensional framework structure. This structure determination confirms the importance of water in the stabilization of certain brucine compounds which have inherent crystal instability.

Three-dimensional geological modelling and multivariate statistical analysis of water chemistry data to analyse and visualise aquifer structure and groundwater composition in the Wairau Plain, Marlborough District, New Zealand

Concerns regarding groundwater contamination with nitrate and the long-term sustainability of groundwater resources have prompted the development of a multi-layered three dimensional (3D) geological model to characterise the aquifer geometry of the Wairau Plain, Marlborough District, New Zealand. The 3D geological model which consists of eight litho-stratigraphic units has been subsequently used to synthesise hydrogeological and hydrogeochemical data for different aquifers in an approach that aims to demonstrate how integration of water chemistry data within the physical framework of a 3D geological model can help to better understand and conceptualise groundwater systems in complex geological settings. Multivariate statistical techniques(e.g. Principal Component Analysis and Hierarchical Cluster Analysis) were applied to groundwater chemistry data to identify hydrochemical facies which are characteristic of distinct evolutionary pathways and a common hydrologic history of groundwaters. Principal Component Analysis on hydrochemical data demonstrated that natural water-rock interactions, redox potential and human agricultural impact are the key controls of groundwater quality in the Wairau Plain. Hierarchical Cluster Analysis revealed distinct hydrochemical water quality groups in the Wairau Plain groundwater system. Visualisation of the results of the multivariate statistical analyses and distribution of groundwater nitrate concentrations in the context of aquifer lithology highlighted the link between groundwater chemistry and the lithology of host aquifers. The methodology followed in this study can be applied in a variety of hydrogeological settings to synthesise geological, hydrogeological and hydrochemical data and present them in a format readily understood by a wide range of stakeholders. This enables a more efficient communication of the results of scientific studies to the wider community.

Synthesis, structure and magnetic behavior of a new three-dimensional Manganese phosphite-oxalate: [C2N2H10][Mn-2(II)(OH2)(2)(HPO3)(2)(C2O4)]

A novel manganese phosphite-oxalate, [C2N2H10][Mn-2(II)(OH2)(2)(HPO3)(2)(C2O4)] has been hydothermally synthesized and its structure determined by single-crystal X-ray diffraction. The structure consists of neutral manganese phosphite layers, [Mn(HPO3)](infinity), formed by MnO6 octahedra and HPO3 units, cross-linked by the oxalate moieties. The organic cations occupy the middle of the 8-membered one dimensional channels. Magnetic studies indicate weak antiferromagnetic interactions between the Mn2+ ions. (C) 2009 Elsevier Inc. All rights reserved.

Two- and Three-Dimensional Open-Framework Uranium Arsenates: Synthesis, Structure, and Characterization

Hydrothermal reactions between uranium salts and arsenic pentoxide in the presence of two different amines yielded six new uranium arsenate phases exhibiting open-framework structures, ethylenediamine (en): [C2N2H9]-[(UO2)(ASO(4))] I; [C2N2H10][(UO2)F(HASO(4))]2 center dot 4H(2)O, II; [C2N2H9][U2F5(HASO(4))(2)], III; [C2N2H9][UF2(ASO(4))], IV; diethylenetriamine (DETA), [C4N3H16][U2F3(ASO(4))(2)(HAsO4)] V; and [C4N3H16][U2F6(AsO4)(HAsO4)], VI. The structures were determined using single crystal studies, which revealed two- (I, II, V) and three-dimensional (III, IV, VI) structures for the uranium arsenates. The uranium atom, in these compounds, exhibits considerable variations in the coordination (6 to 9) that appears to have some correlation with the synthetic conditions. The water molecules in [C2N2H10][(UO2)F(HAsO4)](2 center dot)4H(2)O, II, could be reversibly removed, and the dehydrated phase, [C2N2H10][(UO2)F(HAsO4)](2), IIa, was also characterized using single crystal studies. The observation of many mineralogical structures in the present compounds suggests that the hydrothermal method could successfully replicate the geothermal conditions. As part of this study, we have observed autunite, Ca[(UO2)(PO4)](2)(H2O)(11), metavauxite, [Fe(H2O)(6)][Al(OH)(H2O)(PO4)](2), finarite, PbCU(SO4)(OH)(2), and tancoite, LiNa2H[Al(PO4)(2)(OH)], structures. The repeated observation of the secondary building unit, SBU-4, in many of the uranium arsenate structures suggests that these are viable building units. Optical studies on the uranium arsenate compound, [C4N3H16][U2F6(AsO4)(HASO(4))), VI, containing uranium in the +4 oxidation state indicates a blue emission through an upconversion process. The compound also exhibits antiferromagnetic behavior.

Synthesis, Structure and Optical Studies of a Family of Three-Dimensional Rare-Earth Aminoisophthalates M(mu(2)-OH)(C8H5NO4)] (M = Y3+, La3+, Pr3+, Nd3+, Sm3+, Eu3+, Gd3+, Dy3+, and Er3+)

A hydrothermal reaction of the acetate salts of the rare-earths, 5-aminoisophthalic acid (H(2)AIP), and NaOH at 150 degrees C for 3 days gave rise to a new family of three-dimensional rare-earth aminoisophthalates, M(mu(2)-OH)(C8H5NO4)] M = Y3+ (I), La3+ (II), Pr3+ (III), Nd3+ (IV), Sm3+ (V), Eu3+ (VI), Gd3+ (VII), Dy3+ (VIII), and Er3+ (IX)]. The structures contain M-O(H)-M chains connected by AIP anions. The AIP ions are connected to five metal centers and each metal center is connected with five AIP anions giving rise to a unique (5,5) net. To the best of our knowledge, this is the first observation of a (5,5) net in metal-organic frameworks that involve rare-earth elements. The doping of Eu3+/(3+) ions in place of Y3+/ La3+ in the parent structures gave rise to characteristic metal-centered emission (red = Eu3+, green = Tb3+). Life-time studies indicated that the excited emission states in the case of Eu3+ (4 mol-% doped) are in the range 0.287-0.490 ms and for Tb3+ (4 mol-% doped) are in the range of 1.265-1.702 ms. The Nd3+-containing compound exhibits up-conversion behavior based on two-photon absorption when excited using lambda = 580 nm.

ChemInform Abstract: Slicing the Perovskite Structure into Layers: Synthesis of Novel Three- Dimensional and Layered Perovskite Oxides, ALaSrNb2M(II)O9 (A: Na, Cs)

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Hydrothermal synthesis and structure of organically templated one-dimensional and three-dimensional iron fluorophosphate

Two new open-framework iron fluorophosphates, [C(4)N(2)H(12)](0.5) [FeF(HPO(4))(H(2)PO(4))] (I) and [C(4)N(2)H(12)][Fe(4)F(2)(H(2)O)(4)(PO(4))(4)]. 0.5H(2)O (II), were synthesized hydrothermally using piperazine as a templating agent. The structures were determined by single-crystal X-ray diffraction. Compound I crystallizes in the orthorhombic space group Pbca, a = 7.2126(2) Angstrom, b = 14.2071(4) Angstrom, c = 17.1338(2) Angstrom, Z = 8. The structure is composed of infinite anionic chains of [FeF(HPO(4))(H(2)PO(4))](n)(-) built by trans-fluorine sharing FeF(2)O(4) octahedra. These chains are similar to those found in tancoite-type minerals. Compound II crystallizes in the monoclinic space group P2(1)/n, a = 9.9045(3) Angstrom, b = 12.3011(3) Angstrom, c = 17.3220(4) Angstrom, beta = 103.7010(10)degrees, Z = 4. The structure of compound II has a three-dimensional (3D) architecture with an eight-membered channel along the b axis, in which protonoted piperazine molecules reside. The complex framework is built from two types of secondary building unit (SBU): one hexamer [Fe(3)F(2)(H(2)O)(2)(PO(4))(3)] (SBU6), and one dimer [FeO(4)(H(2)O)(2)PO(4)] (SBU2). The vertex sharing between these SBUs create the 3D structure.

Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures?

The rapidly growing structure databases enhance the probability of finding identical sequences sharing structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this work, we plan to study the ambiguity between sequence-structure relationships and examine if sequentially identical peptide fragments adopt similar three-dimensional structures. Fragments of varying lengths (five to ten residues) were used to observe the behavior of sequence and its three-dimensional structures. The STAMP program was used to superpose the three-dimensional structures and the two parameters (Sequence Structure Similarity Score (Sc) and Root Mean Square Deviation value) were employed to classify them into three categories: similar, intermediate and dissimilar structures. Furthermore, the same approach was carried out on all the three-dimensional protein structures solved in the two organisms, Mycobacterium tuberculosis and Plasmodium falciparum to validate our results.

A video method for quantifying size distribution, density, and three-dimensional spatial structure of reef fish spawning aggregations

There is a clear need to develop fisheries independent methods to quantify individual sizes, density, and three dimensional characteristics of reef fish spawning aggregations for use in population assessments and to provide critical baseline data on reproductive life history of exploited populations. We designed, constructed, calibrated, and applied an underwater stereo-video system to estimate individual sizes and three dimensional (3D) positions of Nassau grouper (Epinephelus striatus) at a spawning aggregation site located on a reef promontory on the western edge of Little Cayman Island, Cayman Islands, BWI, on 23 January 2003. The system consists of two free-running camcorders mounted on a meter-long bar and supported by a SCUBA diver. Paired video “stills” were captured, and nose and tail of individual fish observed in the field of view of both cameras were digitized using image analysis software. Conversion of these two dimensional screen coordinates to 3D coordinates was achieved through a matrix inversion algorithm and calibration data. Our estimate of mean total length (58.5 cm, n = 29) was in close agreement with estimated lengths from a hydroacoustic survey and from direct measures of fish size using visual census techniques. We discovered a possible bias in length measures using the video method, most likely arising from some fish orientations that were not perpendicular with respect to the optical axis of the camera system. We observed 40 individuals occupying a volume of 33.3 m3, resulting in a concentration of 1.2 individuals m–3 with a mean (SD) nearest neighbor distance of 70.0 (29.7) cm. We promote the use of roving diver stereo-videography as a method to assess the size distribution, density, and 3D spatial structure of fish spawning aggregations.

I. The Superstition Hills, California, earthquakes of 24 November 1987. II. Three-dimensional velocity structure of southern California.

Part 1 of this thesis is about the 24 November, 1987, Superstition Hills earthquakes. The Superstition Hills earthquakes occurred in the western Imperial Valley in southern California. The earthquakes took place on a conjugate fault system consisting of the northwest-striking right-lateral Superstition Hills fault and a previously unknown Elmore Ranch fault, a northeast-striking left-lateral structure defined by surface rupture and a lineation of hypocenters. The earthquake sequence consisted of foreshocks, the M_s 6.2 first main shock, and aftershocks on the Elmore Ranch fault followed by the M_s 6.6 second main shock and aftershocks on the Superstition Hills fault. There was dramatic surface rupture along the Superstition Hills fault in three segments: the northern segment, the southern segment, and the Wienert fault.

In Chapter 2, M_L≥4.0 earthquakes from 1945 to 1971 that have Caltech catalog locations near the 1987 sequence are relocated. It is found that none of the relocated earthquakes occur on the southern segment of the Superstition Hills fault and many occur at the intersection of the Superstition Hills and Elmore Ranch faults. Also, some other northeast-striking faults may have been active during that time.

Chapter 3 discusses the Superstition Hills earthquake sequence using data from the Caltech-U.S.G.S. southern California seismic array. The earthquakes are relocated and their distribution correlated to the type and arrangement of the basement rocks. The larger earthquakes occur only where continental crystalline basement rocks are present. The northern segment of the Superstition Hills fault has more aftershocks than the southern segment.

An inversion of long period teleseismic data of the second mainshock of the 1987 sequence, along the Superstition Hills fault, is done in Chapter 4. Most of the long period seismic energy seen teleseismically is radiated from the southern segment of the Superstition Hills fault. The fault dip is near vertical along the northern segment of the fault and steeply southwest dipping along the southern segment of the fault.

Chapter 5 is a field study of slip and afterslip measurements made along the Superstition Hills fault following the second mainshock. Slip and afterslip measurements were started only two hours after the earthquake. In some locations, afterslip more than doubled the coseismic slip. The northern and southern segments of the Superstition Hills fault differ in the proportion of coseismic and postseismic slip to the total slip.

The northern segment of the Superstition Hills fault had more aftershocks, more historic earthquakes, released less teleseismic energy, and had a smaller proportion of afterslip to total slip than the southern segment. The boundary between the two segments lies at a step in the basement that separates a deeper metasedimentary basement to the south from a shallower crystalline basement to the north.

Part 2 of the thesis deals with the three-dimensional velocity structure of southern California. In Chapter 7, an a priori three-dimensional crustal velocity model is constructed by partitioning southern California into geologic provinces, with each province having a consistent one-dimensional velocity structure. The one-dimensional velocity structures of each region were then assembled into a three-dimensional model. The three-dimension model was calibrated by forward modeling of explosion travel times.

In Chapter 8, the three-dimensional velocity model is used to locate earthquakes. For about 1000 earthquakes relocated in the Los Angeles basin, the three-dimensional model has a variance of the the travel time residuals 47 per cent less than the catalog locations found using a standard one-dimensional velocity model. Other than the 1987 Whittier earthquake sequence, little correspondence is seen between these earthquake locations and elements of a recent structural cross section of the Los Angeles basin. The Whittier sequence involved rupture of a north dipping thrust fault bounded on at least one side by a strike-slip fault. The 1988 Pasadena earthquake was deep left-lateral event on the Raymond fault. The 1989 Montebello earthquake was a thrust event on a structure similar to that on which the Whittier earthquake occurred. The 1989 Malibu earthquake was a thrust or oblique slip event adjacent to the 1979 Malibu earthquake.

At least two of the largest recent thrust earthquakes (San Fernando and Whittier) in the Los Angeles basin have had the extent of their thrust plane ruptures limited by strike-slip faults. This suggests that the buried thrust faults underlying the Los Angeles basin are segmented by strike-slip faults.

Earthquake and explosion travel times are inverted for the three-dimensional velocity structure of southern California in Chapter 9. The inversion reduced the variance of the travel time residuals by 47 per cent compared to the starting model, a reparameterized version of the forward model of Chapter 7. The Los Angeles basin is well resolved, with seismically slow sediments atop a crust of granitic velocities. Moho depth is between 26 and 32 km.