Multiple expression of molecular information: enforced generation of different supramolecular inorganic architectures by processing of the same ligand information through specific coordination algorithms

The multisubunit ligand 2 combines two complexation substructures known to undergo, with specific metal ions, distinct self-assembly processes to form a double-helical and a grid-type structure, respectively. The binding information contained in this molecular strand may be expected to generate, in a strictly predetermined and univocal fashion, two different, well-defined output inorganic architectures depending on the set of metal ions, that is, on the coordination algorithm used. Indeed, as predicted, the self-assembly of 2 with eight CuII and four CuI yields the intertwined structure D1. It results from a crossover of the two assembly subprograms and has been fully characterized by crystal structure determination. On the other hand, when the instructions of strand 2 are read out with a set of eight CuI and four MII (M = Fe, Co, Ni, Cu) ions, the architectures C1-C4, resulting from a linear combination of the two subprograms, are obtained, as indicated by the available physico-chemical and spectral data. Redox interconversion of D1 and C4 has been achieved. These results indicate that the same molecular information may yield different output structures depending on how it is processed, that is, depending on the interactional (coordination) algorithm used to read it. They have wide implications for the design and implementation of programmed chemical systems, pointing towards multiprocessing capacity, in a one code/ several outputs scheme, of potential significance for molecular computation processes and possibly even with respect to information processing in biology.     

Super-resolution and Raman chemical imaging: from multiple low resolution images to a high resolution image

Imaging in Raman spectroscopy is a valuable tool for analytical chemistry. Although molecular characterization at micron level is achieved for many applications, it usually fails producing chemical images of micron size samples as expected in chemical, environmental and biological analysis. The aim of the work is to introduce the potential of super-resolution in vibrational spectroscopic imaging. This original chemometrics approach uses several low resolution images of the same sample in order to retrieve a higher resolution chemical image. It is thus possible to overcome in a certain way some physical and instrumentals limitations. To illustrate the methodology, sub-micronic details of a Si/Au sample are retrieved from low resolution images with different super-resolution algorithms. The better results are obtained with Iterative L2/Bilateral Total Variation regularization method. The use of a regularization procedure gives also better results since its first property is to preserve edges during the reconstruction of the super-resolved image. This concept of chemical image data processing should open new analytical opportunities.     

Structures lamellaires: Syntaxie,polytypie et non-stoechiométrie

The paper recalls elementary principles useful for the understanding of some types of nonstoichiometry in the solid state. The structures of layered compounds are mostly characterized by the existence of layered “molecular” entities exhibiting a simple type of bonding; in between are inserted, depending on the case, cations, anions, structural frameworks, or molecules. The layers have a quaternary or a ternary symmetry; in the last case the structures can be polytypic. The phenomenon of syntaxy occurs between polymorphs or between species with different chemical compositions but with structural affinities (identical atomic planes). In some cases an ordered syntaxy between structural blocks yields the chemical compositions of the multiple phases observed for some nonstoichiometric systems, for instance rare earth ones. Ordered syntaxy and polytypism, which can occur simultaneously, give a regular repetition of structural or chemical elements over very long crystalline distances. Those phenomena of order in solids, as yet unexplained, recall ordering phenomena observed in the scope of biological chemistry.     

Molecular path for ligand search

A ligand is a small molecule bind to several residues of a receptor.We adapt the concept of molecular path for effective ligand search with its contacting residues.Additionally,we allow wild type definitions on atoms and bonds of molecular paths for fuzzy algorithms on structural match.We choose hydrogen bond interactions to characterize the binding mode of a ligand by several proper molecular paths and use them to query the deposited ligands in PDBe that interact with their residues in the same way. Expression of molecular path and format of database entries are described with examples.Our molecular path provides a new approach to explore the ligand-receptor interactions and to provide structural framework reference on new ligand design.     

Integration of chemical and biochemical analysis systems into a glass microchip.

This review focuses on the integration of chemical and biochemical analysis systems into glass microchips for general use. By combining multiphase laminar flow driven by pressure and micro unit operations, such as mixing, reaction, extraction and separation, continuous-flow chemical processing systems can be realized in the microchip format, while the application of electrophoresis-based chip technology is limited. The performances of several analysis systems were greatly improved by microchip integration because of some characteristics of microspace, i.e., a large specific interface area, a short molecular diffusion time, a small heat capacity and so on. By applying these concepts, several different analysis systems, i.e., wet analysis of cobalt ion, multi-ion sensor, immunoassay, and cellular analysis, were successfully integrated on a microchip. These microchip technologies are promising for meeting the future demands of high-throughput chemical processing.     

De novo design by pharmacophore-based searches in fragment spaces

De novo ligand design supports the search for novel molecular scaffolds in medicinal chemistry projects. This search can either be based on structural information of the targeted active site (structure-based approach) or on similarity to known binders (ligand-based approach). In the absence of structural information on the target, pharmacophores provide a way to find topologically novel scaffolds. Fragment spaces have proven to be a valuable source for molecular structures in de novo design that are both diverse and synthetically accessible. They also offer a simple way to formulate custom chemical spaces. We have implemented a new method which stochastically constructs new molecules from fragment spaces under consideration of a three dimensional pharmacophore. The program has been tested on several published pharmacophores and is shown to be able to reproduce scaffold hops from the literature, which resulted in new chemical entities.     

The mass-mobility correlation redux: The conformational landscape of anhydrous biomolecules

Structural separations on the basis of gas-phase ion mobility-mass spectrometry are increasingly used for the analysis of complex biological samples. As a tool to elucidate biomolecular structure, ion mobility-mass spectrometry methods are unique in that direct molecular structural information is obtained for all resolved species, largely irrespective of the complexity of the sample. Computational approaches are used to interpret and discern structural details consistent with the empirical results. To a first approximation, correlations of mobility with mass allow for qualitative identification of the molecular class to which a particular species belongs. These correlations allow simultaneous characterization of different classes of biomolecules, which provides a means for combining omics measurements, such as lipidomics, proteomics, glycomics, and metabolomics, in the same analysis. Examination of the correlation of fine structure reveals that specific structural motifs, chemical functionality, chemical connectivity, and composition may also be determined, depending on the specific biomolecular class. Mapping the coarse and fine structure in ion mobility-mass spectrometry conformation space measurements provides an atlas for interpretation and discovery in complicated spectra.     

Signal processing with multicomponent systems based on metal complexes

Molecular-level systems that respond to external stimulation by changing some physical or chemical properties can be viewed as input–output devices and therefore may be useful for processing information. In recent years, several investigations on species capable of mimicking the function of macroscopic wires, switches, connectors, memories, logic gates, and circuits have been reported. The rational basis for this research stems from the fact that in living organisms information is transported, elaborated and stored by molecular or ionic substrates operating in a solution-based environment. Because of their diverse and valuable physico-chemical properties, metal complexes have been extensively used as functional components for the construction of artificial molecular devices capable of processing information. Here we illustrate recent progress, and discuss limitations and perspectives of this research area.     

Neural Networks in Chemistry

The capabilities of the human brain have always fascinated scientists and led them to investigate its inner workings. Over the past 50 years a number of models have been developed which have attempted to replicate the brain's various functions. At the same time the development of computers was taking a totally different direction. As a result, today's computer architectures, operating systems, and programming have very little in common with information processing as performed by the brain. Currently we are experiencing a reevaluation of the brain's abilities, and models of information processing in the brain have been translated into algorithms and made widely available. The basic building-block of these brain models (neural networks) is an information processing unit that is a model of a neuron. An artificial neuron of this kind performs only rather simple mathematical operations; its effectiveness is derived solely from the way in which large numbers of neurons may be connected to form a network. Just as the various neural models replicate different abilities of the brain, they can be used to solve different types of problem: the classification of objects, the modeling of functional relationships, the storage and retrieval of information, and the representation of large amounts of data. This potential suggests many possibilities for the processing of chemical data, and already applications cover a wide area: spectroscopic analysis, prediction of reactions, chemical process control, and the analysis of electrostatic potentials. All these are just a small sample of the great many possibilities.     

Renewal theory for single-molecule systems with multiple reaction channels

Some single-molecule systems share a common feature: the system performs different cycles returning after each cycle to the same state. In such systems we deal with renewal processes. Examples include (1) single-molecule enzymatic reactions, (2) membrane transport through single-occupancy channels, (3) single-molecule fluorescence spectroscopy, and (4) motion of molecular motors. The paper is focused on the analysis of such systems by means of the renewal theory. To be more specific, the theory of renewal processes is used to study multivariate distribution functions of the numbers of different events in a given observation time. Our main results are simple formulas derived for the Laplace transforms of the distribution functions. General results are illustrated by consideration of several examples.     

Identification and characterization of the chemical constituents of Simiao Wan by ultra high performance liquid chromatography with mass spectrometry coupled to an automated multiple data processing method

The chemical constituents of Simiao Wan (SW), a traditional Chinese medicine preparation, are difficult to determine and remain unclear. To more efficiently detect ions, a multiple data processing approach has been used in the characterization of the compounds. In this study, a rapid and sensitive method based on ultra high performance liquid chromatography with mass spectrometry and the multiple data processing approach was established to characterize the chemical constituents of SW. Ultra high performance liquid chromatography with mass spectrometry coupled with the multiple data processing approach could efficiently remove nonrelated ion signals from accurate mass data. We report the application of the multiple data processing approach for comprehensive detection and rapid identification of chemical constituents of SW. Of note, the total analysis time for separation was less than 20 min without losing any resolution. In the variable, importance in projection plot of orthogonal projection to latent structure‐discriminant analysis, a total of 72 ions of interest (37 ions in positive mode, 38 ions in negative mode and three ions in both mode) were extracted or tentatively characterized based on their retention times, exact mass measurement for each molecular ion and subsequent fragment ions. In summary, the methodology proposed in this study could be valuable for the structural characterization and identification of the multiple constituents in the traditional Chinese medicine formula SW.     

Simultaneous measurement of diffusion along multiple directions

This paper introduces the first NMR approach for simultaneously measuring the full diffusion tensor. Using magnetic field gradients of different directions to generate multiple modulations of nuclear spin magnetization, multiple echoes of different modulations are acquired in a single scan to simultaneously measure diffusion along different directions. The experimental demonstrations were conducted in both isotropic and anisotropic systems. Since the diffusion anisotropy holds structural and dynamical information, this approach may be useful for monitoring liquid crystals and electrolytes in metastable states and for studying fluidity in situ in porous networks and in vivo in biological systems.     

From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry

Supramolecular chemistry has developed over the last forty years as chemistry beyond the molecule. Starting with the investigation of the basis of molecular recognition, it has explored the implementation of molecular information in the programming of chemical systems towards self-organisation processes, that may occur either on the basis of design or with selection of their components. Supramolecular entities are by nature constitutionally dynamic by virtue of the lability of non-covalent interactions. Importing such features into molecular chemistry, through the introduction of reversible bonds into molecules, leads to the emergence of a constitutional dynamic chemistry, covering both the molecular and supramolecular levels. It considers chemical objects and systems capable of responding to external solicitations by modification of their constitution through component exchange or reorganisation. It thus opens the way towards an adaptive and evolutive chemistry, a further step towards the chemistry of complex matter.     

Par-delà la synthèse : l’auto-organisation

The evolution of the universe from the particle to the thinking organism has taken place through self-organization. Chemistry has a major role to play in understanding these processes leading to the generation of complex matter. Chemistry has developed a highly powerful molecular synthetic chemistry, mastering the combination and recombination of atoms into increasingly complex molecules through selective chemical reactions. Supramolecular chemistry is harnessing intermolecular forces for the generation of informed supramolecular systems and processes through supramolecular synthetic chemistry implementing molecular information carried by electromagnetic interactions. Supramolecular chemistry has been actively exploring systems undergoing self-organization, i.e., systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, under the control of interactional molecular recognition events, thus behaving as programmed chemical systems. Molecular chemistry may similarly take advantage of the selectivity of covalent reactions to assemble complex molecular architectures through self-organization processes implementing functional molecular recognition. Supramolecular/non-covalent and molecular/covalent SELF-ORGANIZATION may thus be considered as the ULTIMATE SYNTHETIC CHEMISTRY, whereby chemical objects at both levels are generated on the basis of recognition processes involving either interactional or reactional features. Illustrations from the supramolecular domain will serve as illustrations. Supramolecular entities as well as molecules containing reversible bonds are able to undergo a continuous change in constitution by reorganization and exchange of building blocks. This capability defines a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels. CDC introduces a paradigm shift with respect to constitutionally static chemistry. It takes advantage of dynamic constitutional diversity to allow variation and selection and thus leads towards the emergence of adaptive and evolutive chemistry.     

Exploring Caffeine–Phenol Interactions by the Inseparable Duet of Experimental and Theoretical Data

Intermolecular interactions are difficult to model, especially in systems formed by multiple interactions. Such is the case of caffeine–phenol. Structural data has been extracted by using mass-resolved excitation spectroscopy and double resonance techniques. Then the predictions of seven different computational methods have been explored to discover structural and energetic discrepancies between them that may even result in different assignments of the system. The results presented herein highlight the difficulty of constructing functionals to model systems with several competing interactions, and raise awareness of problems with assignments of complex systems with limited experimental information that rely exclusively on energetic data.     

Several hypotheses and regularities in the chemistry of highly organized substances

It was found that level of structural substance organization, amount of embodied information, and consequently, substance properties are determined by the degree of the substance polyatomicity. This substantiates the fact that both covalent and noncovalent supermolecular individuals, which are the matter of the chemistry of highly organized compounds, fulfil the same general chemical but different specific regularities. Among the former there is extended Prust's law, which was re-established by the fact of production and identification of solids with the constant composition. It was also found that formation of any individuals is due to production and realization of a certain amount of information sufficient for their structural organization. Chemical modeling of biosynthesis was chosen as the common approach for developing the processes of production and realization of information. It was shown that well-known processes of chemical buildup (CB) and molecular self-assembling (MSA) are those chemical models. The application of announced regularities has opened up a new perspective to create chemical-information technology (CIT), allowing us to produce material resources making no perturbations in the planet ecosystem.     

Hyphenation and hypernation the practice and prospects of multiple hyphenation

In the past two decades, combining a chromatographic separation system on-line with a spectroscopic detector in order to obtain structural information on the analytes present in a sample has become the most important approach for the identification and/or confirmation of the identity of target and unknown chemical compounds. In most instances, such hyphenation can be accomplished by using commercially available equipment. For most (trace-level) analytical problems encountered today, the combination of column liquid chromatography or capillary gas chromatography with a mass spectrometer (LC–MS and GC–MS, respectively) is the preferred approach. However, it is also true that additional and/or complementary information is, in quite a number of cases, urgently required. This can be provided by, for example, atomic emission, Fourier-transform infrared, diode-array UV–vis absorbance or fluorescence emission, or nuclear magnetic resonance spectrometry. In the present review, the various options are briefly discussed and a few relevant applications are quoted for each combination. Special attention is devoted to systems in which multiple hyphenation, or hypernation, is an integral part of the setup. As regards this topic, the relative merits of various combinations—which turn out to include a mass spectrometer as one of the detectors in essentially all cases—are discussed and the fundamental differences between GC- and LC-based systems are outlined. Finally, the practicability of more extensive hypernation in LC, viz. with up to four spectrometers, is discussed. It is demonstrated that, technically, such multiple hyphenation is possible and that, from a practical point of view, rewarding results can be obtained. In other words, further research in this area is certainly indicated. However, in the foreseeable future, using several separate conventional hyphenated systems will be the commonly implemented solution in most instances.