Hydrogen bonding lights up overtones in pyrazoles

The spectral complexity in the NH stretching mode of hydrogen-bonded pyrazoles is traced back to an extensive Fermi resonance system involving combinations and overtones of at least four aromatic ring modes with significant in plane hydride bending character. The couplings are shown to be inherent in the monomer, but hydrogen bonding is required to bring them into resonance with the NH stretching chromophore. A cost-efficient variational "monomers-in-clusters" model is presented and applied to a five-dimensional subspace of pyrazole. Spectra of substituted pyrazoles confirm the robustness of the coupling, which remains dark in strained dimers, but lights up in linearly hydrogen-bonded trimers.     

Bioorthogonal chemical tagging of protein cholesterylation in living cells

We report the first chemical probe for bioorthogonal chemical tagging of post-translationally cholesterylated proteins with an azide in living cells. This enables rapid multiplexed fluorescence detection and affinity labelling of protein cholesterylation, as exemplified by Sonic hedgehog protein, opening up new approaches for the de novo identification of cholesterylated proteins.     

DNA-templated nickel nanostructures and protein assemblies

We report a straightforward method for the fabrication of DNA-templated nickel nanostructures on surfaces. These nickel nanomaterials have potential to be applied as nanowires, as templated catalyst lines, as nanoscale magnetic domains, or in directed protein localization. Indeed, we show here that histidine-tagged phosducin-like protein (His-PhLP) binds with high selectivity to both Ni2+-treated surface DNA and DNA-templated nickel metal to create linear protein assemblies on surfaces. The association of His-PhLP with DNA-templated nickel ions or metal is reversible under appropriate rinsing conditions. Nanoscale DNA-templated protein assemblies might be useful in the construction of high-density protein lines for proteomic analysis, for example. Importantly, these nanofabrication procedures are not limited to linear DNA and can be applied readily to other self-assembled DNA topologies.     

Activation in prochiral reaction assemblies on Pt(111)

Trifluoroacetophenone (TFAP) forms C O...H-C bonded dimers and trimers at room temperature on Pt(111). It is proposed that these systems mimic the prochiral carbonyl-chiral modifier interaction in the enantioselective hydrogenation of TFAP on cinchona-modified Pt catalysts. That is, the activation of TFAP in homomolecular assemblies at racemic sites is expected to be roughly the same as in the diastereomeric complex formed at chiral sites. This interpretation suggests a reason why alpha-phenyl ketones do not display a strong measured rate enhancement effect in the Orito reaction.     

Depletion-flocculation in oil-in-water emulsions using fibrillar protein assemblies

This paper shows that low concentrations of beta-lactoglobulin fibrils can induce depletion-flocculation in beta-lactoglobulin-stabilized oil-in-water emulsions. The minimum required fibril concentration for flocculation was determined experimentally for fibril lengths of about 3 and 0.1 microm. The minimum fibril concentration for flocculation is two orders of magnitude higher for the short fibrils than for the long ones. These experimental results correspond well with a theoretical prediction based on a model of spinodal decomposition. In addition, rheological measurements were performed, verifying that flocculation was induced by a depletion mechanism. The results of this study show that the minimum concentration required for depletion-flocculation can be tuned by varying the length of the fibrils.     

Picking up the chemical thread

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Picking up the chemical thread     

6-Aminoacridizinium bromide: a fluorescence probe which lights up in AT-rich regions of DNA

The title compound exhibits a selective enhancement of its fluorescence intensity in the presence of AT-rich DNA.     

Organized molecular assemblies as receptor centers of solid state chemical sensors

The paper discusses receptor properties of organized molecular assemblies constructed on the basis of the Langmuir-Blodgett films, modified porous SiO₂ films, and metal-oxide systems.Institute of Semiconductor Physics, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 6, pp. 86–89, November–December, 1993.Translated by O. Kharlamova     

Identifiability of chemical reaction networks

We consider the dynamics of chemical reaction networks under the assumption of mass-action kinetics. We show that there exist reaction networks for which the reaction rate constants are not uniquely identifiable, even if we are given complete information on the dynamics of concentrations for all chemical species of . Also, we show that there exist reaction networks such that their dynamics are identical under appropriate choices of reaction rate constants, and present theorems that characterize the properties of , , that make this possible. We use these facts to show how we can determine dynamical properties of some chemical networks by analyzing other chemical networks.     

Electron beam stimulated chemical reaction in solids

Use of electron beams allows to obtain new effects in high temperature chemistry of solid state. A stimulated influence of irradiation at comparable temperature conditions may be a subject of technological interest taking into account that increase of reaction rate can reach significant values.     

Applications of reaction calorimetry in chemical engineering

Reaction calorimetry strongly penetrated process development laboratories in the fine chemicals industry. Applications of calorimetry to different fields of process optimization, chemical reactions and physical unit operations were developed. Applications were first developed in the field of process safety. The thermal data of reaction obtained in the calorimeters allow us to check if a reaction will be controllable at full scale under normal operating conditions and in case of equipment failure. Further, the accurate temperature control and heat flow measurement opened the door to more engineering related data, in the fields of phase equilibria like vapour liquid, solubilities, crystallization and also in the mixing techniques. Some examples of developments in these different fields will be reviewed.     

Atoms of multistationarity in chemical reaction networks

Chemical reaction systems are dynamical systems that arise in chemical engineering and systems biology. In this work, we consider the question of whether the minimal (in a precise sense) multistationary chemical reaction networks, which we propose to call ‘atoms of multistationarity,’ characterize the entire set of multistationary networks. Our main result states that the answer to this question is ‘yes’ in the context of fully open continuous-flow stirred-tank reactors (CFSTRs), which are networks in which all chemical species take part in the inflow and outflow. In order to prove this result, we show that if a subnetwork admits multiple steady states, then these steady states can be lifted to a larger network, provided that the two networks share the same stoichiometric subspace. We also prove an analogous result when a smaller network is obtained from a larger network by ‘removing species.’ Our results provide the mathematical foundation for a technique used by Siegal- Gaskins et al. of establishing bistability by way of ‘network ancestry.’ Additionally, our work provides sufficient conditions for establishing multistationarity by way of atoms and moreover reduces the problem of classifying multistationary CFSTRs to that of cataloging atoms of multistationarity. As an application, we enumerate and classify all 386 bimolecular and reversible two-reaction networks. Of these, exactly 35 admit multiple positive steady states. Moreover, each admits a unique minimal multistationary subnetwork, and these subnetworks form a poset (with respect to the relation of ‘removing species’) which has 11 minimal elements (the atoms of multistationarity).     

Non-meanfield deterministic limits in chemical reaction kinetics

A general mechanism is proposed by which small intrinsic fluctuations in a system far from equilibrium can result in nearly deterministic dynamical behaviors which are markedly distinct from those realized in the meanfield limit. The mechanism is demonstrated for the kinetic Monte Carlo version of the Schnakenberg reaction where we identified a scaling limit in which the global deterministic bifurcation picture is fundamentally altered by fluctuations. Numerical simulations of the model are found to be in quantitative agreement with theoretical predictions.     

Strategies for chemical reaction searching in SciFinder

The bibliographic, chemical structure, and chemical reaction databases produced by Chemical Abstracts Service allow a number of possibilities for chemical reaction searching. While these same databases may be searched through the STN network, many end-users find the intuitive software interface SciFinder simpler, but there still are issues to address. Searching may be performed through keywords, chemical structures, or chemical reactions, and the answers may vary with respect to precision and comprehension. Often combinations of search options may be needed to best solve the problem. Retrosynthetic analyses are easily performed in the chemical reaction database and can give unique insights into synthetic alternatives.     

Regiospecific plasmonic assemblies for in situ Raman spectroscopy in live cells

Multiple properties of plasmonic assemblies are determined by their geometrical organization. While high degree of complexity was achieved for plasmonic superstructures based on nanoparticles (NPs), little is known about the stable and structurally reproducible plasmonic assemblies made up from geometrically diverse plasmonic building blocks. Among other possibilities, they open the door for the preparation of regiospecific isomers of nanoscale assemblies significant both from a fundamental point of view and optical applications. Here, we present a synthetic method for complex assemblies from NPs and nanorods (NRs) based on selective modification of NRs with DNA oligomers. Three types of assemblies denoted as End, Side, and Satellite isomers that display distinct elements of regiospecificity were prepared with the yield exceeding 85%. Multiple experimental methods independently verify various structural features, uniformity, and stability of the prepared assemblies. The presence of interparticle gaps with finely controlled geometrical parameters and inherently small size comparable with those of cellular organelles fomented their study as intracellular probes. Against initial expectations, SERS intensity for End, Side, and Satellite isomers was found to be dependent primarily on the number of the NPs in the superstructures rationalized with the help of electrical field simulations. Incubation of the label-free NP-NR assemblies with HeLa cells indicated sufficient field enhancement to detect structural lipids of mitochondria and potentially small metabolites. This provided the first proof-of-concept data for the possibility of real-time probing of the local organelle environment in live cells. Further studies should include structural optimization of the assemblies for multitarget monitoring of metabolic activity and further increase in complexity for applications in transformative optics.     

Wet chemical needlelike assemblies of single-walled carbon nanotubes on a silicon surface

Single-walled carbon nanotubes (SWCNT) have been organized covalently to form a uniform needlelike structure on a silicon surface using a wet chemical assembly technique. In this work, we successfully combine silanization with the condensation reaction of the carboxylic group with the amino group.     

Biomimetic dual templating of silica by polysaccharide/protein assemblies

The control of silica growth by living organisms such as diatoms is known to involve the templating effect of several biomolecules working concomitantly. However, until now, biomimetic studies involving model molecules have mainly been performed with single templates. We show here that the addition of two biopolymers, gelatin and alginic acid, to silicate solutions allows the formation of complex structures resulting from the combined templating effect of both components at different scales. Gelatin is able to activate silica formation resulting in hybrid aggregates at the nanoscale. Alginic acid does not interfere with silica condensation but is able to control silica morphology through the assembly of these gelatin-silica aggregates at the microscale. For all materials, calcination up to 700 degrees C degrades the polymer component of the hybrid material and opens macroporosity in the silica network. In parallel, the high thermal stability of gelatin allows a good preservation of initial silica nanoparticle size upon heating whereas a coarsening process is observed in the sole presence of alginate. These results correlate well with previous models of biosilicification and suggest that the use of multiple templates is a suitable approach to elaborate more complex silica architectures.     

String model of chemical reaction coordinate

A geometrical model for estimating the effects of external fields upon a reaction path is proposed. The reaction path is defined as the intrinsic reaction coordinate (IRC) which is treated as a string. The IRC frame is introduced in order to uniquely determine the attitude of the string with respect to the reaction medium. The string is thrown in the external fields of the reaction medium, and slides or rotates, and is deformed. The cell structure attached to the string is also deformed. A perturbational approach to the reaction rate formula is presented.