Repulsive interaction can be a key design element of molecular rotary motors

Low-barrier molecular rotary motors having rotaxane architecture can be constructed using a cucurbituril host and a polyyne guest serving as stator and rotator, respectively. The repulsive interaction between these components is supported by molecular mechanics calculations with model systems and experimentally verified by X-ray crystallography with several synthetic host-guest complexes, all suggesting that the diyne rod floats at the center of the macrocyclic host with no apparent van der Waals contacts between them. Further support for these interactions is suggested by microcalorimetry measurements.     

Three-dimensional nanofabrication with elastomeric phase masks

This Feature Article reviews recent work on an optical technique for fabricating, in a single exposure step, three-dimensional (3D) nanostructures with diverse structural layouts. The approach, which we refer to as proximity field nanopatterning, uses conformable, elastomeric phase masks to pattern thick layers of transparent, photosensitive materials in a conformal contact mode geometry. Aspects of the optics, the materials, and the physical chemistry associated with this method are outlined. A range of 3D structures illustrate its capabilities, and several application examples demonstrate possible areas of use in technologies ranging from microfluidics to photonic materials to density gradient structures for chemical release and high-energy density science.     

Evolutionary algorithms in the optimization of dynamic molecular alignment

We numerically study the optimization of dynamic molecular alignment by shaped femtosecond pulses. It is found that an accurate synchronization of the applied field to the molecular response is needed to obtain maximum alignment. Simple approaches based on low-dimensional parametrizations of the electric field are shown to be clearly inferior, especially in the strongly nonperturbative regime.     

Control of nitromethane photoionization efficiency with shaped femtosecond pulses

The applicability of adaptive femtosecond pulse shaping is studied for achieving selectivity in the photoionization of low-density polyatomic targets. In particular, optimal dynamic discrimination (ODD) techniques exploit intermediate molecular electronic resonances that allow a significant increase in the photoionization efficiency of nitromethane with shaped near-infrared femtosecond pulses. The intensity bias typical of high-photon number, nonresonant ionization is accounted for by reference to a strictly intensity-dependent process. Closed-loop adaptive learning is then able to discover a pulse form that increases the ionization efficiency of nitromethane by ～150%. The optimally induced molecular dynamics result from entry into a region of parameter space inaccessible with intensity-only control. Finally, the discovered pulse shape is demonstrated to interact with the molecular system in a coherent fashion as assessed from the asymmetry between the response to the optimal field and its time-reversed counterpart.     

Pyrolyze this paper: Can biomass become a source for precise carbon electrodes?

To advance science and technology, we must stand on the shoulders of others; they do not have to be giants, but they must be steady. Carbon electrodes made by dry pyrolysis of biomass are ubiquitous thanks to the enormous abundance and variety of biomass. However, making precise and reproducible carbons from highly varied precursors is challenging. One approach is to erase differences by intense etching or heating. Other strategies harness the richness of biomass by investigating biomass–carbon–electrochemistry correlations systematically and by developing chemical and thermal treatments for gentle homogenization. Comparing ～120 articles on ～80 biomass sources demonstrates that full reporting of the biomass origin, organ, age, and other parameters is essential for further development of precise and reproducible carbon electrode materials.     

Integrating proteomics with electrochemistry for identifying kinase biomarkers

We present an integrated approach for highly sensitive identification and validation of substrate-specific kinases as cancer biomarkers. Our approach combines phosphoproteomics for high throughput cancer-related biomarker discovery from patient tissues and an impedimetric kinase activity biosensor for sensitive validation. Using non-small-cell lung cancer (NSCLC) as a proof-of-concept study, label-free quantitative phosphoproteomic analysis of a pair of cancerous and its adjacent normal tissues revealed 198 phosphoproteins that are over-phosphorylated in NSCLC. Among the differentially regulated phosphorylation sites, the most significant alteration was in residue S165 in the Hepatoma Derived Growth Factor (HDGF) protein. Hence, HDGF was selected as a model system for the electrochemical studies. Further motif-based analysis of this altered phosphorylation site revealed that extracellular-signal-regulated kinase 1/2 (ERK1/2) are most likely to be the corresponding kinases. For validation of the kinase–substrate pair, densely packed peptide monolayers corresponding to the HDGF phosphorylation site were coupled to a gold electrode. Phosphorylation of the monolayer by ERK2 and dephosphorylation by alkaline phosphatase (AP) were detected by electrochemical impedance spectroscopy (EIS) and surface roughness analysis. Compared to other methods for quantification of kinase concentration, this label-free electrochemical assay offers the advantages of ultra-sensitivity as well as higher specificity for the detection of cancer-related kinase–substrate pair. With implementation of multiple kinase–substrate biomarker pairs, we expect this integrated approach to become a high throughput platform for discovery and validation of phosphorylation-mediated biomarkers.     

In situ observation of the internal structure and composition of biomineralized Emiliania huxleyi calcite by solid-state NMR Spectroscopy

Biomineralization, particularly the formation of calcium carbonate structures by organisms under ambient conditions, is of vast fundamental and applied interest. Organisms finely control all aspects of the formation of the biomaterials: composition, polymorph, morphology, and macroscopic properties. While in situ molecular-level characterization of the resulting biominerals is a formidable task, solid-state magic angle spinning NMR is one of the most powerful analytical techniques for this purpose. It is employed in this study to elucidate the structure and composition of biogenic calcite formed by Emiliania huxleyi, a unicellular alga distinguished by its exquisitely sculptured calcite cell coverings known as coccoliths. Strain 371 (CCMP) was grown and harvested from (15)N- and (13)C-enriched growth medium, with biosynthetic labeling to enhance the sensitivity of the NMR measurements. Crystalline and interfacial calcite environments were selectively probed using direct and indirect (cross-polarized) (13)C excitation, respectively. Different crystalline environments, in particular structural defect sites at concentrations of up to 1.4% with P and N moieties incorporated, were identified using (13)C rotational-echo double-resonance (REDOR) NMR. REDOR-derived geometrical constraints show that the P and N atoms at the defect sites are 3.2 and 2.3 (+/-0.2) A apart from a crystalline carbon carbonate. The phosphorus and nitrogen moieties within the biogenic calcite are identified as small, non-protonated moieties, attributed to inorganic ions such as PO4(3-) and NO3(-). The carbonates adjacent to these defects are chemically indistinguishable from bulk crystalline carbonates, yet their immediate environments experience reduced rigidity, as reflected by substantial T1((13)CO3(2-)) shortening. Interfacial carbonates, on the other hand, reside in structurally/chemically perturbed environments, as reflected by heterogeneous line broadening. This study is the first to directly unravel evidence on the incorporation of P/N moieties as structural defects within E. huxleyi biogenic calcite, and on the state of the adjacent crystalline carbonates.