Optical control of ultrafast structural dynamics in a fluorescent protein.

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Delivery of stable ultra-thin liquid sheets in vacuum for biochemical spectroscopy.

The development of ultra-thin flat liquid sheets capable of running in vacuum has provided an exciting new target for X-ray absorption spectroscopy in the liquid and solution phases. Several methods have become available for delivering in-vacuum sheet jets using different nozzle designs. We compare the sheets produced by two different types of nozzle; a commercially available borosillicate glass chip using microfluidic channels to deliver colliding jets, and an in-house fabricated fan spray nozzle which compresses the liquid on an axis out of a slit to achieve collision conditions. We find in our tests that both nozzles are suitable for use in X-ray absorption spectroscopy with the fan spray nozzle producing thicker but more stable jets than the commercial nozzle. We also provide practical details of how to run these nozzles in vacuum.

Interaction of an intense few-cycle infrared laser pulse with an ultrathin transparent liquid sheet.

We experimentally study the interaction between intense infrared few-cycle laser pulses and an ultrathin (∼2 µm) flat liquid sheet of isopropanol running in vacuum. We observe a rapid decline in transmission above a critical peak intensity of 50 TW/cm2 of the initially transparent liquid sheet, and the emission of a plume of material. We find both events are due to the creation of a surface plasma and are similar to processes observed in dielectric solids. After calculating the electron density for different laser peak intensities, we find an electron scattering rate of 0.3 fs-1 in liquid isopropanol to be consistent with our data. We study the dynamics of the plasma plume to find the expansion velocity of the plume front.

Attosecond coherent electron motion in Auger-Meitner decay.

In quantum systems, coherent superpositions of electronic states evolve on ultrafast time scales (few femtoseconds to attoseconds; 1 attosecond = 0.001 femtoseconds = 10-18 seconds), leading to a time-dependent charge density. Here we performed time-resolved measurements using attosecond soft x-ray pulses produced by a free-electron laser, to track the evolution of a coherent core-hole excitation in nitric oxide. Using an additional circularly polarized infrared laser pulse, we created a clock to time-resolve the electron dynamics and demonstrated control of the coherent electron motion by tuning the photon energy of the x-ray pulse. Core-excited states offer a fundamental test bed for studying coherent electron dynamics in highly excited and strongly correlated matter.

Electronic Population Transfer via Impulsive Stimulated X-Ray Raman Scattering with Attosecond Soft-X-Ray Pulses.

Free-electron lasers provide a source of x-ray pulses short enough and intense enough to drive nonlinearities in molecular systems. Impulsive interactions driven by these x-ray pulses provide a way to create and probe valence electron motions with high temporal and spatial resolution. Observing these electronic motions is crucial to understand the role of electronic coherence in chemical processes. A simple nonlinear technique for probing electronic motion, impulsive stimulated x-ray Raman scattering (ISXRS), involves a single impulsive interaction to produce a coherent superposition of electronic states. We demonstrate electronic population transfer via ISXRS using broad bandwidth (5.5 eV full width at half maximum) attosecond x-ray pulses produced by the Linac Coherent Light Source. The impulsive excitation is resonantly enhanced by the oxygen 1s→2π^{*} resonance of nitric oxide (NO), and excited state neutral molecules are probed with a time-delayed UV laser pulse.

Radial spreading of turbulent bubble plumes.

Weak bubble plumes carry liquid from the environment upwards and release it at multiple intermediate levels in the form of radial intrusive currents. In this study, laboratory experiments are performed to explore the spreading of turbulent axisymmetric bubble plumes in a liquid with linear density stratification. The thickness, volumetric flowrate and spreading rates of multiple radial intrusions of plume fluid were measured by tracking the movement of dye injected at the source of bubbles. The experimental results are compared with scaling predictions. Our findings suggest that the presence of multiple intrusions reduces their spreading rate, compared to that of a single intrusion. This work is of relevance to the spreading of methane plumes issuing from the seabed in the Arctic Ocean, above methane-hydrate deposits. The slower, multiple spreading favours the presence of methane-rich seawater close to the plume, which may reduce the dissolution of methane in the bubbles, and thus promote the direct transport of methane to the atmosphere. This article is part of the theme issue 'Stokes at 200 (part 2)'.

Micrometer-thickness liquid sheet jets flowing in vacuum.

Thin liquid sheet jet flows in vacuum provide a new platform for performing experiments in the liquid phase, for example X-ray spectroscopy. Micrometer thickness, high stability, and optical flatness are the key characteristics required for successful exploitation of these targets. A novel strategy for generating sheet jets in vacuum is presented in this article. Precision nozzles were designed and fabricated using high resolution (0.2 µm) 2-photon 3D printing and generated 1.49 ± 0.04 µm thickness, stable, and <λ/20-flat jets in isopropanol under normal atmosphere and under vacuum at 5 × 10-1 mbar. The thin sheet technology also holds great promise for advancing the fields of high harmonic generation in liquids, laser acceleration of ions as well as other fields requiring precision and high repetition rate targets.

Functional conductive nanomaterials via polymerisation in nano-channels: PEDOT in a MOF.

Reactions inside the pores of metal-organic frameworks (MOFs) offer potential for controlling polymer structures with regularity to sub-nanometre scales. We report a wet-chemistry route to poly-3,4-ethylenedioxythiophene (PEDOT)-MOF composites. After a two-step removal of the MOF template we obtain unique and stable macroscale structures of this conductive polymer with some nanoscale regularity.

High-resolution scanning precession electron diffraction: Alignment and spatial resolution.

Methods are presented for aligning the pivot point of a precessing electron probe in the scanning transmission electron microscope (STEM) and for assessing the spatial resolution in scanning precession electron diffraction (SPED) experiments. The alignment procedure is performed entirely in diffraction mode, minimising probe wander within the bright-field (BF) convergent beam electron diffraction (CBED) disk and is used to obtain high spatial resolution SPED maps. Through analysis of the power spectra of virtual bright-field images extracted from the SPED data, the precession-induced blur was measured as a function of precession angle. At low precession angles, SPED spatial resolution was limited by electronic noise in the scan coils; whereas at high precession angles SPED spatial resolution was limited by tilt-induced two-fold astigmatism caused by the positive spherical aberration of the probe-forming lens.

Ring expansion reactions of anti-aromatic boroles: a promising synthetic avenue to unsaturated boracycles.

Conjugated boron heterocycles have emerged as attractive synthetic targets due to their potential in medicinal chemistry and as electronic materials. However, the development of unsaturated boracycles has been hampered by difficulties in their preparation. Recently, a new synthetic avenue to access these species has been developed that takes advantage of the high reactivity of boroles. These five-membered anti-aromatic heterocycles can react with substrates to furnish ring expansion products via the insertion of one, two, or three atoms into the boracyclic ring. The ring expansion can occur via two pathways, the first exploits the activated diene moiety of the heterocycle in Diels-Alder chemistry with the resulting bicyclic species undergoing further rearrangements. The second reaction pathway is initiated by the coordination of the Lewis basic site of a substrate to the highly Lewis acidic boron center rendering the endocyclic B-C bond of the borole nucleophilic, inducing the formation of larger boracycles via attack at the electrophilic site of the substrate. This review summarizes the current state of this chemistry and details the mechanisms leading to the products. The methodologies described herein could very well be extended to other substrates, as well as applied to other anti-aromatic heterocycles.

1,2-Phosphaborines: hybrid inorganic/organic P-B analogues of benzene.

Photolysis of the cyclic phosphine oligomer [PPh]5 in the presence of pentaarylboroles leads to the formation of 1,2-phosphaborines by the formal insertion of a phenylphosphinidene fragment into the endocyclic CB bond. The solid-state structure features a virtually planar central ring with bond lengths indicating significant delocalization. Appreciable ring current in the 1,2-phosphaborine core, detected in nuclear independent chemical shift (NICS) calculations, are consistent with aromatic character. These products are the first reported 1,2-BPC4 conjugated heterocycles and open a new avenue for BP as a valence isoelectronic substitute for CC in arene systems.

Threading plasmonic nanoparticle strings with light.

Nanomaterials find increasing application in communications, renewable energies, electronics and sensing. Because of its unsurpassed speed and highly tuneable interaction with matter, using light to guide the self-assembly of nanomaterials can open up novel technological frontiers. However, large-scale light-induced assembly remains challenging. Here we demonstrate an efficient route to nano-assembly through plasmon-induced laser threading of gold nanoparticle strings, producing conducting threads 12±2 nm wide. This precision is achieved because the nanoparticles are first chemically assembled into chains with rigidly controlled separations of 0.9 nm primed for re-sculpting. Laser-induced threading occurs on a large scale in water, tracked via a new optical resonance in the near-infrared corresponding to a hybrid chain/rod-like charge transfer plasmon. The nano-thread width depends on the chain mode resonances, the nanoparticle size, the chain length and the peak laser power, enabling nanometre-scale tuning of the optical and conducting properties of such nanomaterials.

Microstructural analysis of Au/TiO2-SBA-15 nanocomposite.

Properties of gold nanoparticles (AuNPs) are very different from bulk gold, in particular, highly dispersed AuNPs exhibit high catalytic activities on metal oxide supports. Catalytic activities of AuNPs are strongly dependent on: (i) size and morphology; (ii) synthesis methods; (iii) nature of the support; (iv) interaction between AuNPs and the support; and (v) oxidation state of AuNPs in the synthesized catalysts. A goal is to maintain the size and to prohibit aggregation of AuNPs, since aggregations deteriorate catalytic activities. Some strong interactions are therefore required between AuNPs and their supports to prevent the movement of AuNPs. SBA-15 is a promising material for the support of AuNPs since it has ordered two-dimensional hexagonal pore channels, uniform pore size ranging from 5 to 30 nm, narrow pore size distribution, thick amorphous walls ranging from 3 to 6 nm, and high surface area. In this study, SBA-15, TiO2-SBA-15 and TiO2-SBA-15-AuNP nanocomposites were synthesized by the sol-gel method and microstructural characterizations were carried out by both X-ray diffraction analysis and electron microscopy.

Robust cyclometallated Ir(III) catalysts for the homogeneous hydrogenation of N-heterocycles under mild conditions.

Cyclometallated Cp*Ir(N^C)Cl complexes derived from N-aryl ketimines are highly active catalysts for the reduction of N-heterocycles under ambient conditions and 1 atm H2 pressure. The reaction tolerates a broad range of other potentially reducible functionalities and does not require the use of specialised equipment, additives or purified solvent.

Interfacial structure and chemistry of GaN on Ge(111).

The interface of GaN grown on Ge(111) by plasma-assisted molecular beam epitaxy is resolved by aberration corrected scanning transmission electron microscopy. A novel interfacial structure with a 5∶4 closely spaced atomic bilayer is observed that explains why the interface is flat, crystalline, and free of GeN(x). Density functional theory based total energy calculations show that the interface bilayer contains Ge and Ga atoms, with no N atoms. The 5∶4 bilayer at the interface has a lower energy than a direct stacking of GaN on Ge(111) and enables the 5∶4 lattice-matching growth of GaN.

Synthetic retinoids: structure-activity relationships.

Retinoid signalling pathways are involved in numerous processes in cells, particularly those mediating differentiation and apoptosis. The endogenous ligands that bind to the retinoid receptors, namely all-trans-retinoic acid (ATRA) and 9-cis-retinoic acid, are prone to double-bond isomerisation and to oxidation by metabolic enzymes, which can have significant and deleterious effects on their activities and selectivities. Many of these problems can be overcome through the use of synthetic retinoids, which are often much more stable, as well as being more active. Modification of their molecular structures can result in retinoids that act as antagonists, rather than agonists, or exhibit a large degree of selectivity for particular retinoid-receptor isotypes. Several such selective retinoids are likely to be of value as pharmaceutical agents with reduced toxicities, particularly in cancer therapy, as reagents for controlling cell differentiation, and as tools for elucidating the precise roles that specific retinoid signalling pathways play within cells.

Proteomic profiling of the stem cell response to retinoic acid and synthetic retinoid analogues: identification of major retinoid-inducible proteins.

The natural retinoid, all-trans retinoic acid (ATRA), is widely used to direct the in vitro differentiation of stem cells. However, substantial degradation and isomerisation of ATRA in response to UV-vis light has serious implications with regard to experimental reproducibility and standardisation. We present the novel application of proteomic biomarker profiling technology to stem cell lysates to rapidly compare the differentiation effects of ATRA with those of two stable synthetic retinoid analogues, EC19 and EC23, which have both been shown to induce differentiation in the embryonal carcinoma cell line TERA2.cl.SP12. MALDI-TOF MS (matrix-assisted laser desorption ionisation time-of-flight mass spectrometry) protein profiles support previous findings into the functional relationships between these compounds in the TERA2.cl.SP12 line. Subsequent analysis of protein peak data enabled the semi-quantitative comparison of individual retinoid-responsive proteins. We have used ion exchange chromatographic protein separation to enrich for retinoid-inducible proteins, thereby facilitating their identification from SDS-PAGE gels. The cellular retinoid-responsive proteins CRABP-I, CRABP-II, and CRBP-I were up-regulated in response to ATRA and EC23, indicating a bona fide retinoid pathway response to the synthetic compound. In addition, the actin filament regulatory protein profilin-1 and the microtubule regulator stathmin were also elevated following treatment with both ATRA and EC23. The up-regulation of profilin-1 and stathmin associated with retinoid-induced neural differentiation correlates with their known roles in cytoskeletal reorganisation during axonal development. Immunological analysis via western blotting confirmed the identification of CRABP-I, profilin-1 and stathmin, and supported their observed regulation in response to the retinoid treatments.

Organization of nanoparticles in polymer brushes.

We have demonstrated a facile infiltration process, in which gold nanoparticles are assembled into block copolymer brushes. After solvent annealing, the polymer-covered nanoparticles are either sequestered into the corresponding block copolymer domain or expulsed from the brush, depending on the shell density of the nanoparticles.