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).     

Standardized Characterization of Electrocatalytic Electrodes

This paper investigates the utility of ‘cross–lab’ comparative analysis of electrocatalytic electrode performance using standardized modular stack cells and test protocols. Using poly(methylene green)‐modified glassy carbon electrodes as the model system, we characterized electrode fabrication and performance with respect to the catalytic oxidation of NADH at neutral pH and low overpotential. Three sets of experiments were duplicated across four independent laboratories and the experimental results from each set were analyzed and compared in terms of key electroanalytical parameters. Statistical analyses were performed at three distinct levels: 1) the standard deviation among repetitive cycles within an experiment; 2) the standard deviation among repetitive experiments in the same laboratory, and 3) the standard deviation among experiments performed across all four laboratories. Using predefined criteria of ‘reproducibility’ for each level, most parameters were found to be statistically reproducible at most levels. When a particular parameter was found to be irreproducible in a given level, commentary is given on how that information can be used diagnose what chemical/physical aspects of the process were uncontrolled or poorly understood and therefore candidates for future research. This exercise, which is presented as a ‘proof–of‐principle’ step towards the concept of standardizing electrocatalytic evaluation, illustrates the importance of executing electrochemical characterization protocols across several labs and using fixed geometry and dimensions, system configuration, and applied electrochemical conditions. Future work is under way to extend these principles to systems with fluid flow.     

Mechanisms of Autocatalysis

Self‐replication is a fundamental concept. The idea of an entity that can repeatedly create more of itself has captured the imagination of many thinkers from von Neumann to Vonnegut. Beyond the sciences and science fiction, autocatalysis has found currency in economics and language theory, and has raised ethical fears memorably summed up by the “gray goo” trope. Autocatalysis is central to the propagation of life and intrinsic to many other biological processes. This includes the modern conception of evolution, which has radically altered humanity’s image of itself. Organisms can be thought of as imperfect self‐replicators which produce closely‐related species, allowing for selection and evolution. Hence, any consideration of self‐replication raises one of the most profound questions of all: what is life? Minimal self‐replicating systems have been studied with the aim of understanding the principles underlying living systems, allowing us to refine our concepts of biological fitness and chemical stability, self‐organization and emergence, and ultimately to discover how chemistry may become biology.     

The Odor Value Concept in the Formal Analysis of Olfactory Art

In the past 15 years, there has been a tremendous increase in the emergence of olfactory artworks despite the traditional skepticism with respect to scents as subjects of art. This essay submits that this skepticism lacks aesthetic justification; art is what is accepted as such, and olfactory art is in fact already well accepted as an art form by the general public. However, there exists no methodological tool for the formal analysis of olfactory artworks. The essay suggests such a method, based on odor values; this is elaborated using the fragrance ‘Dune’ (Dior, 1991), and is compared with a purely visual approach to the same subject. This new concept allows for the derivation of simple compositional sketches and is then exemplified by the formal analysis of three more recent olfactory artworks: Elodie Pong/Roman Kaiser, ‘White‘ (2016), Martynka Wawrzyniak/Yann Vasnier, ‘Tears (T6)’ (2012), and Christophe Laudamiel, ‘heat’ (2003).     

Multi-functional stimuli-responsive biomimetic flower assembled from CLCE and MOF-based pedals

Simulating the structures and behaviors of living organisms are of great significance to develop novel multi-functional intelligent devices. However, the development of biomimetic devices with complex deformable structures and synergistic properties is still on the way. Herein, we propose a simple and effective approach to create the multi-functional stimuli-responsive biomimetic devices with independently pre-programmable colorful visual patterns, complex geometries and morphable modes. The metal organic framework (MOF)-based composite film acts as a rigidity actuation substrate to support and mechanically guide the spatial configuration of the soft chiral nematic liquid crystal elastomer (CLCE) sheet. We can directly program the structural color of the CLCE sheet by adjusting the thickness distribution without tedious chemical modification. By using this coordination strategy, we fabricate an artificial flower, which exhibits a synergistic effect of both shape transformation and color change like paeonia ‘Coral Sunset’ at different flowering stages, and can even perform different flowering behaviors by bending, twisting and curling petals. The assembled bionic flower is innovatively demonstrated to respond to local stimuli of humidity, heat or ultraviolet irradiation. Therefore, the spatial assembly of CLCE combined with functional MOF materials has a wide range of potential application in multi-functional integrated artificial systems.     

Enantioselective Approach for Expanding the Three-Dimensional Space of Tetrahydroquinoline to Develop BET Bromodomain Inhibitors**

The pharmaceutical industry has a pervasive need for chiral specific molecules with optimal affinity for their biological targets. However, the mass production of such compounds is currently limited by conventional chemical routes, that are costly and have an environmental impact. Here, we propose an easy access to obtain new tetrahydroquinolines, a motif found in many bioactive compounds, that is rapid and cost effective. Starting from simple raw materials, the procedure uses a proline-catalyzed Mannich reaction followed by the addition of BF₃ ⋅ OEt₂, which generates a highly electrophilic aza-ortho-quinone methide intermediate capable of reacting with different nucleophiles to form the diversely functionalized tetrahydroquinoline. Moreover, this enantioselective one-pot process provides access for the first time to tetrahydroquinolines with a cis-2,3 and trans-3,4 configuration. As proof of concept, we demonstrate that a three-step reaction sequence, from simple and inexpensive starting compounds and catalysts, can generate a BD2-selective BET bromodomain inhibitor with anti-inflammatory effect.     

Chemistry and the Origin of Life

The natural genesis of life on Earth is a hypothesis of evolutionary science; it is the task of synthetic organic chemistry to test this hypothesis experimentally. The aim of an experimental aetiological chemistry is not primarily to delineate the pathways along which our (‘natural’) life on Earth could have originated, but to provide decisive experimental evidence, through the realization of model systems (‘artificial chemical life’), that life can arise as a result of the organization of organic matter.     

A Chemist's View of BCS Theory for Low Tc Superconductivity and Its Relationship to Charge Transfer and High Tc Superconductivity

Based on a chemist's understanding of electron transfer, attempts are made to interpret the physicists' BCS theory for low Tc superconductivity in terms of quantum chemical views. To show how to improve and apply some of the principles of the BCS theory for high Tc superconductors, especially those having to do with many-body aspects of correlation, coherence and long-range order, we (1) extend the two-partner, donor-acceptor electron transfer to large periodic systems with cyclic boundary conditions and with double-well potentials beyond Peierls distortion. (2) introduce second-order Jahn-Teller stabilization and introduce vibronic mixing as configuration interaction. To take advantage of existing bonds in high Tc superconductors we propose a linear combination of bonding (two-electron) geminals to form molecular bonding geminals which we call “Vibronic Geminals” after mixing with different running waves of bond structure vibrations. To take advantage of the valence bonds and double-well potentials due to anti-symmetric and other vibrations, we propose a ‘Covalon’ type model for the propagation and tunneling of such bonds which transform as Bosons.     

Emergence in Chemistry: Chemistry as the Embodiment of Emergence

The main aim of the paper is to reinforce the notion that emergence is a basic characteristic of the molecular sciences in general and chemistry in particular. Although this point is well accepted, even in the primary reference on emergence, the keyword emergence is rarely utilized by chemists and molecular biologists and chemistry textbooks for undergraduates. The possible reasons for this situation are discussed. The paper first re-introduces the concept of emergence based on very simple geometrical forms; and considers some simple chemical examples among low and high molecular weight compounds. On the basis of these chemical examples, a few interesting philosophical issues inherent to the field of emergence are discussed – again making the point that such examples, given their clarity and simplicity, permit one to better understand the complex philosophical issues. Thus, the question of predictability is discussed, namely whether and to what extent can emergent properties be predicted on the basis of the component’s properties; or the question of the explicability (a top down process). The relation between reductionism and emergentism is also discussed as well as the notion of downward causality and double causality (macrodeterminism); namely the question whether and to what extent the emergent properties of the higher hierarchic level affect the properties of the lower level components. Finally, the question is analyzed, whether life can be considered as an emergent property. More generally, the final point is made, that the re-introduction of the notion of emergence in chemistry, and in particular in the teaching, may bring about a deeper understanding of the meaning of chemical complexity and may bring chemistry closer to the humanistic areas of philosophy and epistemology. This revised version was published online in July 2006 with corrections to the Cover Date.     

Austere quantum mechanics as a reductive basis for chemistry

This paper analyses Richard Bader’s ‘operational’ view of quantum mechanics and the role it plays in the the explanation of chemistry. I argue that QTAIM can partially be reconstructed as an ‘austere’ form of quantum mechanics, which is in turn committed to an eliminative concept of reduction that stems from Kemeny and Oppenheim. As a reductive theory in this sense, the theory fails. I conclude that QTAIM has both a regulatory and constructive function in the theories of chemistry.     

Connecting the philosophy of chemistry,green chemistry,and moral philosophy

This paper aims to connect philosophy of chemistry, green chemistry, and moral philosophy. We first characterize chemistry by underlining how chemists: (1) co-define chemical bodies, operations, and transformations; (2) always refer to active and context-sensitive bodies to explain the reactions under study; and (3) develop strategies that require and intertwine with a molecular whole, its parts, and the surroundings at the same time within an explanation. We will then point out how green chemists are transforming their current activities in order to act upon the world without jeopardizing life. This part will allow us to highlight that green chemistry follows the three aforementioned characteristics while including the world as a partner, as well as biodegradability and sustainability concerns, into chemical practices. In the third part of this paper, we will show how moral philosophy can help green chemists: (1) identify the consequentialist assumptions that ground their reasoning; and (2) widen the scope of their ethical considerations by integrating the notion of care and that of vulnerability into their arguments. In the fourth part of the paper, we will emphasize how, in return, this investigation could help philosophers querying consequentialism as soon as the consequences of chemical activities over the world are taken into account. Furthermore, we will point out how the philosophy of chemistry provides philosophers with new arguments concerning the key debate about the ‘intrinsic value’ of life, ecosystems and the Earth, in environmental ethics. To conclude, we will highlight how mesology, that is to say the study of ‘milieux’, and the concept of ‘ecumeme’ proposed by the philosopher and geographer Augustin Berque, could become important both for green chemists and moral philosophers in order to investigate our relationships with the Earth.     

Commercialization of Ionic Liquids in Pursuit of Green Chemistry: Must we Each Become an Entrepreneur?

There will be common challenges to scaling-up any ionic liquids separations technologies which require very large volumes of ionic liquid. Some of these challenges are illustrated in this personal account which chronicles the extraction of chitin from shrimp shell from discovery to current commercialization efforts. The road being taken from discovery in an academic laboratory, through attempts to navigate the scaling-up to commercial scale using the vehicle of a faculty startup company is rewarding, but fraught with roadblocks, detours, and unexpected challenges. The differences in ‘technically feasible’ and ‘commercially viable’ are not always evident from the beginning of the journey, however, one wonders what achievements we miss as a Society because it was assumed to not be commercially viable.     

Theoretical Analysis of a Surface Catalytic Mechanism Associated with Reversible Chemical Reaction Under Conditions of Cyclic Staircase Voltammetry

In this work, we present theoretical results in cyclic staircase voltammetry of a surface catalytic mechanism that features reversible chemical step, the so‐called “surface catalytic EC_rev’ mechanism”. We consider specific surface regenerative mechanism, in which both of the electro‐inactive substrates are present in large excess in electrochemical cell from the beginning of the experiment. The chemical reversibility brings at this mechanism more complexity in respect to the features of well‐elaborated surface catalytic EC’ mechanism coupled with chemically irreversible regenerative reaction. As we present plenty of simulated cyclic voltammograms, we also propose methods to get insight to kinetics and thermodynamics parameters relevant to chemical regenerative step. The elaboreted results can be important in analysing the kinetics and thermodynamics of many drug‐drug and drug‐DNA interactions, for example. In addition, with the results elaborated in this work we can access relevant information about the chemistry of important lipophilic enzymes studied in protein‐film voltammetry set up.     

Unsteady state flux response: a method to determine the nature of the solute and gel layer in membrane filtration

The unsteady-state permeate flux response to a step change in transmembrane pressure is shown to result in unique flux–pressure profiles for the three types of solutes common in membrane ultrafiltration (UF): (a) solutes which exert an osmotic pressure but do not form a ‘gel’; (b) solutes which do not exert an osmotic pressure but form a ‘gel’ and (c) solutes which exert an osmotic pressure and also form a ‘gel’. It is also shown that for stirred cell UF, changes in the bulk feed solution properties (concentration, volume) are negligible on the time scale needed to attain a stable permeate flux. Unsteady-state permeate flux measurements could therefore be made at short filtration times so that the results would not be masked by changes in bulk properties.     

The periodic table: revelation by quest rather than by revolution

The concept of major scientific advances occurring as a short-term ‘revolutionary’ change in thinking interspersed by long periods of so-called ‘normal’ science seems to be losing ground to more ecological models, which are more inimical of the twists and turns of life. From this idea it is a short step to charting science’s progress against stages used in fictional storytelling, which after all is life-based. This paper explores the development of the periodic table in terms of the achievement of a fictional ‘quest’, and finds the stages of such a story are well represented. While Mendeleev or perhaps Meyer might be considered by some to be the hero of the quest, its first stage—the call—is represented by the Karlsruhe conference in 1860, with an international cast of ‘companions’ and ‘helpers’ who contributed to the Table’s early development. The ‘journey’ may have been frustrated by lack of appropriate data and understanding of concepts, but the ‘arrival’ phase is clearly marked by the award of the Davy medal jointly to Mendeleev and Meyer in 1882, Throughout these stages there are lesser, although still significant contributions made by “little people” of science to the overall progress of the Table. The end of the journey is not the end of the quest: the discovery of new elements—“new ordeals”—and their incorporation into an increasing range of types and styles of periodic table, which—akin to the “life-renewing goal” of the fictional quest—continue.     

Chiral Crystals,Jack, Conductivity and Magnetism

Recently, the application of magnetic fields to chiral chemical systems has been rewarding. In a forward-looking 1986 paper, ‘Chiral Metals?’, Wallis, Karrer, and Jack D. Dunitz forecast ‘that the limitation to proper symmetry elements in a chiral conductor could be associated with the emergence of new properties, those connected with interactions between applied electric and magnetic fields and their internal counterparts.’ This was a prescient remark, but it has become manifest in ways that would not have been foreseen in its details by the authors. Here are reviewed the development of chiral conductors broadly imagined by Dunitz and coworkers, based on enantiopure tetrathiafulvalene derivatives that restrict space groups to those that have only symmetry operations of the first kind, as well as the new emergent properties associated with the transport of electrons when magnetic fields are applied to chiral crystals among other systems. These include electrical magnetochiral anisotropy (eMChA), inverse electrical magnetochiral anisotropy (ieMChA), helimagnetism and chirality induced spin selectivity (CISS). The conclusion discussing the circumstances under which achiral TTF crystals becomes chiral, only seems to introduce an oxymoron.     

Principles for the organization of gene-sets

A gene-set, an important concept in microarray expression analysis and systems biology, is a collection of genes and/or their products (i.e. proteins) that have some features in common. There are many different ways to construct gene-sets, but a systematic organization of these ways is lacking. Gene-sets are mainly organized ad hoc in current public-domain databases, with group header names often determined by practical reasons (such as the types of technology in obtaining the gene-sets or a balanced number of gene-sets under a header). Here we aim at providing a gene-set organization principle according to the level at which genes are connected: homology, physical map proximity, chemical interaction, biological, and phenotypic-medical levels. We also distinguish two types of connections between genes: actual connection versus sharing of a label. Actual connections denote direct biological interactions, whereas shared label connection denotes shared membership in a group. Some extensions of the framework are also addressed such as overlapping of gene-sets, modules, and the incorporation of other non-protein-coding entities such as microRNAs.     

Cooperative Catalysis for Selective Alcohol Oxidation with Molecular Oxygen

The activation of dioxygen for selective oxidation of organic molecules is a major catalytic challenge. Inspired by the activity of nitrogen‐doped carbons in electrocatalytic oxygen reduction, we combined such a carbon with metal‐oxide catalysts to yield cooperative catalysts. These simple materials boost the catalytic oxidation of several alcohols, using molecular oxygen at atmospheric pressure and low temperature (80 °C). Cobalt and copper oxide demonstrate the highest activities. The high activity and selectivity of these catalysts arises from the cooperative action of their components, as proven by various control experiments and spectroscopic techniques. We propose that the reaction should not be viewed as occurring at an ‘active site’, but rather at an ‘active doughnut’–the volume surrounding the base of a carbon‐supported metal‐oxide particle.