Lone pair-pi and pi-pi interactions play an important role in proton-coupled electron transfer reactions

Proton-coupled electron transfer (PCET), a class of formal hydrogen atom transfer (HAT) reactions, is of widespread interest because it is implicated in a broad range of chemical and biochemical processes. PCET is typically differentiated from HAT by the fact that it occurs when a proton and electron are transferred between different sets of molecular orbitals. Previous theoretical work predicted that hydrogen bonding between reactants is a necessary but not sufficient condition for H exchanges to take place by PCET. This implies that HAT is the only mechanism for H exchange between two carbon atoms. In this work, we present computational results that show that the H exchange in the tert-butylperoxyl/phenol couple, a prototypical antioxidant exchange reaction, occurs by PCET and that the transfer of the electron can occur via an oxygen lone pair-ring pi overlap. We then show that the H exchange in a model for the tyrosyl/tyrosine couple, which is implicated in ribonucleotide reductase chemistry, occurs via PCET and that one path for the electron transfer is provided by a strong pi-stacking interaction. Finally, we show that a pi-stacking interaction in the benzyl/toluene couple, a system in which there is no H-bonding, can result in this exchange occurring via PCET to some extent. Collectively, these results indicate that PCET reactions are not unique to systems that can engage in H-bonding and that lone pair-pi and pi-pi interactions in these systems may be more important than previously understood.     

Initiating nuclear-chemical transformations in native systems: Phenomenology

A possible mechanism of nuclear transformations in biological systems in vivo is proposed. Reasons why there is no ionizing radiation that could be detrimental to native systems during the corresponding nuclear reactions are given. It is established that the initial stage of these processes is associated with that of ATP hydrolysis, which initiates the action of the inner-shell electron of an atom participating in the reaction on its nucleus according to the mechanism of weak nuclear interaction. This results in the formation of a nucleus in a metastable state with a disturbed nucleon structure and a charge one unit lower than that of the initial nucleus. It is also assumed that the atom participating in the reaction is adsorbed near the mouth of one of the transport ATPases in the cell’s cytoplasmic membrane, and the reason for the initiating impact the electron has on the nucleus is due to the emergence of a local electric field formed during ATP hydrolysis near the ion channel of a donor–acceptor pair of charges that is opposite to the direction of the average membrane field. It is concluded that as a result of the key role of weak nuclear interaction in these processes, the energy of nuclear transformations in biological systems in vivo is released through the emission of neutrino–antineutrino pairs that are harmless to living organisms.     

On chemical reactions in the laser-induced breakdown of a liquid

It is shown experimentally that a laser-induced breakdown of a liquid is accompanied by chemical reactions initiated by radicals and excited species formed in the spark. It is found that, in water, the laser-induced breakdown is accompanied by the dissociation of water and dissolved nitrogen molecules with the formation of HNO₂ and HNO₃, while, in a FeSO₄ aqueous solution, by the Fe²⁺ → Fe³⁺ oxidation reaction. It is assumed that the mechanism of the process is analogous to that of the action of ionizing radiations and the chemical action of ultrasonically induced cavitation (it is proposed that this mechanism of chemical action of a laser-induced spark proposed be termed indirect). Energy yields of these reactions are found to be of the same order of magnitude as for sonochemical redox reactions. It is shown that the laser-induced breakdown of an aqueous solution of maleic acid is accompanied by its stereoisomerization into fumaric acid, a process catalyzed by small amounts of an alkyl bromide. It is established that, for the formation of fumaric acid in a laser-induced spark, the energy yield is about five orders of magnitude higher than that typical of the above-mentioned redox reactions in the laser-induced spark.     

Coulometric sensors,the application of a sensor-actuator system for long-term stability in chemical sensing

We present a new type of chemical transducer, the coulometric sensor. This sensor is in fact an integrated sensor-actuator system that is able to measure the concentration of acids and bases by means of coulometric titration. An ISFET is used as the sensor to monitor the pH changes induced by the actuator, which is a gold electrode that fits closely around the ISFET's gate area. Coulometry is an absolute method and therefore the output of the new sensor is only determined by its dimensions and is not subject to changes in offset and sensitivity of the indicator electrode. It is thus expected that the operation of the sensor will be stable for a long time, so that only a one-time calibration is needed. As a first example of this new class of chemical transducers, a carbon dioxide sensor is presented. It is shown that the stability is some orders of magnitude better than that for a ‘classical” potentiometric sensor.     

Light-induced surface wettability of a tethered DNA base

We show that the DNA base thymine and other uracil derivatives, when alkylated with a hydrocarbon chain and assembled at a gold interface, dimerize when subjected to UV irradiation. The process is robust and reversible and is accompanied by a substantial decrease in wettability as well as a marked decrease in acidity constant when the dimer is formed. There is a concerted molecular reorientation that accompanies photodimerization, with the dimer displaying a marked affinity for the gold surface. The spatial requirements for this reorganization are satisfied during dimerization by the reduction in intermolecular distance that occurs when the cyclobutane ring is formed between adjacent bases. The structural changes observed here for a tethered DNA base provide a direct route for exploring reactions, in two dimensions, that are of central interest in biology.     

Maximum Flux Transition Paths of Conformational Change

Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and more manageable if done for a reduced set of collective variables chosen so that paths cluster in collective variable space. The computational task becomes that of computing the "center" of such a cluster. A good way to define the center employs the concept of a committor, whose value at a point in collective variable space is the probability that a trajectory at that point will reach B before A. The committor "foliates" the transition region into a set of isocommittors. The maximum flux transition path is defined as a path that crosses each isocommittor at a point which (locally) has the highest crossing rate of distinct reactive trajectories. This path is based on the same principle as the minimum resistance path of Berkowitz et al (1983), but it has two advantages: (i) the path is invariant with respect to a change of coordinates in collective variable space and (ii) the differential equations that define the path are simpler. It is argued that such a path is nearer to an ideal path than others that have been proposed with the possible exception of the finite-temperature string method path. To make the calculation tractable, three approximations are introduced, yielding a path that is the solution of a nonsingular two-point boundary-value problem. For such a problem, one can construct a simple and robust algorithm. One such algorithm and its performance is discussed.     

Diffusion model of solute dynamics in a membrane channel: mapping onto the two-site model and optimizing the flux

The steady-state flux through a singly occupied membrane channel is found for both discrete and continuum models of the solute dynamics in the channel. The former describes the dynamics as nearest-neighbor jumps between N sites, while the latter assumes that the molecule diffuses in a one-dimensional potential of mean force. For both models it is shown that the flux is the same as that for a simple two-site model with appropriately chosen rate constants, which contain all the relevant information about the more detailed dynamics. An interesting consequence of single occupancy is that the flux has a maximum as a function of the channel-solute interaction. If this interaction is too attractive, the molecule will never leave the channel, thus blocking it for the passage of other molecules. If it is too repulsive, the solute molecule will never enter the channel. Thus the flux vanishes in the two limits and, hence, has a maximum somewhere in-between. In the framework of the diffusion model, we find the optimal intrachannel potential of mean force that maximizes the flux using the calculus of variations. For a symmetric channel this potential is flat and occupies the entire channel. In the general case of an asymmetric channel, the optimal potential is obtained by tilting the optimal flat potential for the corresponding symmetric channel around the channel center, so that the solute is driven towards the reservoir with the lower solute concentration by a constant force. This implies that the flux is higher when the solute binding near the channel exit is stronger than that near the entrance.     

Global,local and unique decompositions in OnPLS for multiblock data analysis

OnPLS is an extension of O2PLS that decomposes a set of matrices, in either multiblock or path model analysis, such that each matrix consists of two parts: a globally joint part containing variation shared with all other connected matrices, and a part that contains locally joint and unique variation, i.e. variation that is shared with some, but not all, other connected matrices or that is unique in a single matrix.     

Concentration dependence of the structure of aqueous solutions of lutetium nitrate according to X-ray diffraction

Aqueous solutions of lutetium nitrate over a wide range of concentrations are studied by X-ray diffraction under standard temperature and pressure. The low-angle peaks in experimental scattering intensity curves are interpreted. It is shown that the structure of these solutions can be of two types. It is found that a saturated solution and solutions concentrated to a molar ratio of 1: 20 have a quasi-crystalline structure resulting from interionic interactions. It is determined that dilute solutions form a water-like structure characterized by a tetrahedral network of hydrogen bonds between the water molecules. It is found that low-angle peaks also appear in the intensity curves of dilute solutions; this proves that the so-called “long-range” order is preserved in these solutions. It is revealed that in all the studied systems, the contributions to the total scattering pattern that are responsible for the occurrence of pre-peaks are intercationic interactions.     

Phase-space overlap measures. II. Design and implementation of staging methods for free-energy calculations

We consider staged free-energy calculation methods in the context of phase-space overlap relations, and argue that the selection of work-based methods should be guided by consideration of the phase-space overlap of the systems of interest. Stages should always be constructed such that work is performed only into a system that has a phase-space subset relation with the starting system. Thus multiple stages are required if the systems of interest are not such that one forms a phase-space subset with the other. Three two-stage methods are possible, termed umbrella sampling, overlap sampling, and funnel sampling. The last is appropriate for cases in which the subset relation holds, but only in the extreme, meaning that one system's important phase space constitutes a very small portion of the others. Umbrella sampling is most suitable for nonoverlap systems, and overlap sampling is appropriate for systems exhibiting partial phase-space overlap. We review recently introduced metrics that characterize phase-space overlap, showing that the performance of the single- and two-stage methods is consistent with the phase-space picture. We also demonstrate that a recently introduced bias-detection measure is effective in identifying inaccuracy in single- and multistage calculations. The examples used are the chemical-potential calculation for a Lennard-Jones liquid at moderate and at high densities, the same for model water at ambient conditions, and a process of charging a neutral ion in water.     

On the role of dissipation on the Casimir-Polder potential between molecules in dielectric media

An expression for the Casimir-Polder potential between molecules in a homogeneous dispersive and absorptive dielectric medium is derived. The effect of retardation on the interaction energy is discussed by examining the wave-zone and nonretarded limits of the potential. Unlike Lifshitz theory, the interaction energy is not derived from the potential between macroscopic bodies. In this work, a Green function that explicitly accounts for absorption in the medium is obtained. This function leads to possible dissipation effects and presents a near-zone form that vanishes in the limit of nonabsorptive medium. Employing a two-level model, it is shown that the retarded van der Waals dispersion potential in a medium may become repulsive as a consequence of absorption by the medium. It is suggested that the repulsive dispersion force may delay precipitation of nonpolar molecules from a dielectric solvent or even inhibit chemical reaction between them.     

Laplacian of the Hamiltonian Kinetic Energy Density as an Indicator of Binding and Weak Interactions

The kinetic energy is the center of a controversy between two opposite points of view about its role in the formation of a chemical bond. One school states that a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism of covalent bonding. In contrast, the opposite school holds that a chemical bond is formed by a decrease in the potential energy due to a concentration of electron density within the binding region. In this work, a topographic analysis of the Hamiltonian Kinetic Energy Density (KED) and its laplacian is presented to gain more insight into the role of the kinetic energy within chemical interactions. This study is focused on atoms, diatomic and organic molecules, along with their dimers. In addition, it is shown that the laplacian of the Hamiltonian KED exhibits a shell structure in atoms and that their outermost shell merge when a molecule is formed. A covalent bond is characterized by a concentration of kinetic energy, potential energy and electron densities along the internuclear axis, whereas a charge-shift bond is characterized by a fusion of external concentration shells and a depletion in the bonding region. In the case of weak intermolecular interactions, the external shell of the molecules merge into each other resulting in an intermolecular surface comparable to that obtained by the Non-covalent interaction (NCI) analysis.     

Structuring of a disperse system of ethylene-chlorine complexes in a nonequilibrium vitreous film at liquid helium temperatures

A two-component vitreous, structurally nonequilibrium reaction mixture is considered as an open thermodynamic system of a set of molecules in the gas phase at room temperature. The system is subjected to external action via the rapid transfer of gases in a vitreous film below the vitrification temperature. After the first structuring in the film’s formation, a second structuring that consisted of initiating a set of complexes is attained within the released phase of complexes in the process of structural self-organization. It is found that laser photolysis of the solid-phase reaction mixture is a structure-sensitive diagnostic tool for states of nonequilibrium glass. It is concluded that the change from explosive to stationary kinetic behavior during photolysis is due to the second structuring, the accelerated attainment of which is a product of thermal annealing.     

The "Wimple": rippled deformation of a fluid drop caused by hydrodynamic and surface forces during thin film drainage

It is well-known that hydrodynamic pressures in a thin draining liquid film can cause inversion of the curvature of a drop or bubble surface as it approaches another surface, creating a so-called "dimple". Here it is shown that a more complicated rippled shape, dubbed a "wimple", can be formed if a fluid drop that is already close to a solid wall is abruptly pushed further toward it. The wimple includes a central region in which the film remains thin, surrounded by a ring of greater film thickness that is bounded at the outer edge by a barrier rim where the film is thin. This shape later evolves into a conventional dimple bounded by the barrier rim, which then drains in the normal way. During the evolution from wimple to dimple, some of the fluid in the thicker part of the film ring flows toward the central region before eventually draining in the opposite direction. Although the drop is pressed toward the wall, the central part of the drop moves away from the wall before approaching it again. This is observed even when the inward push is too small to create a wimple.     

Bevelled carbon-fiber ultramicroelectrodes

A technique for polishing the surface of carbon-fiber ultramicroelectrodes to a bevelled tip is described which simplifies electrode preparation. The bevelled surface has an active area that is more than twice that of a disk electrode fabricated from the same material. This results in larger faradaic currents. It is found that the chronoamperometric current at these electrodes is equal to that calculated for a disk of equivalent area to the elliptical area of the electrode. While the area is increased, the residual current is not, and thus quantitative applications of these electrodes as in vivo probes as facilitated. Furthermore, the bevelled tip results in an electrode that minimizes tissue damage during insertion into brain tissues.     

Reachability,persistence, and constructive chemical reaction networks (part II): a formalism for species composition in chemical reaction network theory and application to persistence

Chemical Reaction Network Theory uses mathematics to study systems of reactions and infer their properties from their structure. At the onset is an abstract definition of a chemical reaction network which is very general and is pertinent beyond chemistry, e.g. in modeling interactions of microscopic and macroscopic living species. This allows the theory to provide widely applicable theorems. It also results in that the idea of chemical composition is mostly used implicitly in examples to illustrate theorems, not explicitly to establish new properties. In this paper we propose a formalism for species composition in a way that generalizes the idea of atomic composition—for instance, elementary species will extend the idea of atoms. We envision that this formalism could lead to more theorems on classes of networks that are of interest in biochemistry. Toward that prospect, we prove that if there is no isomerism among elementary species, and if a newly formalized and widely applicable reversibility condition holds, then a reaction network is vacuously persistent: no species will tend to extinction if all species are implicitly present at initial time. This paper is the second in a series of three articles. The first paper studies vacuous persistence and the third one probes a class of enzymatic networks.     

The International System of Units��a case for reconsideration

The International System of Units (SI) follows a concept that goes back to Maxwell. At that time, a logic sound foundation of mathematics was not yet available. This has lead to concepts and terms that are contradictory and in conflict with today??s standard mathematical concepts. The inconsistencies that have evolved in metrology due to the lack of appropriate notions are pointed out. This is most important, as the metrology is a field that is internationally well organized under the umbrella of the Meter Convention, an international treaty for acting on all matters relating to units of measurement. Committees and working groups under the Meter Convention have a leading role in the elaboration of important metrological guides, among others the International Vocabulary of Metrology. Therefore, it is highly desirable that their publications use well-founded concepts and terminology. It is consensus that it is desirable to find a system of units on invariant properties of nature and not on human artifacts, e.g., the prototype of the kilogram. However, the current proposals to improve that are in conflict with standard scientific concepts. It is shown in the paper how these inconsistencies can be avoided. The argumentation is based on the interpretation of numbers developed by mathematicians like Cantor, Dedekind, Peano, and others that have led the logic foundation of mathematics with set and number theory. This foundation excludes dogmas that have been forwarded in the last century under the umbrella of the Meter Convention.     

Strictosidine synthase: mechanism of a Pictet-Spengler catalyzing enzyme

The Pictet-Spengler reaction, which yields either a beta-carboline or a tetrahydroquinoline product from an aromatic amine and an aldehyde, is widely utilized in plant alkaloid biosynthesis. Here we deconvolute the role that the biosynthetic enzyme strictosidine synthase plays in catalyzing the stereoselective synthesis of a beta-carboline product. Notably, the rate-controlling step of the enzyme mechanism, as identified by the appearance of a primary kinetic isotope effect (KIE), is the rearomatization of a positively charged intermediate. The KIE of a nonenzymatic Pictet-Spengler reaction indicates that rearomatization is also rate-controlling in solution, suggesting that the enzyme does not significantly change the mechanism of the reaction. Additionally, the pH dependence of the solution and enzymatic reactions provides evidence for a sequence of acid-base catalysis steps that catalyze the Pictet-Spengler reaction. An additional acid-catalyzed step, most likely protonation of a carbinolamine intermediate, is also significantly rate controlling. We propose that this step is efficiently catalyzed by the enzyme. Structural analysis of a bisubstrate inhibitor bound to the enzyme suggests that the active site is exquisitely tuned to correctly orient the iminium intermediate for productive cyclization to form the diastereoselective product. Furthermore, ab initio calculations suggest the structures of possible productive transition states involved in the mechanism. Importantly, these calculations suggest that a spiroindolenine intermediate, often invoked in the Pictet-Spengler mechanism, does not occur. A detailed mechanism for enzymatic catalysis of the beta-carboline product is proposed from these data.     

Electronic structure of Li2Ga and Li9Al4, two solids containing infinite and uniform zigzag chains

The electronic structure of inorganic solids such as Li(2)Ga and Li(9)Al(4) containing infinite zigzag homoatomic chains is discussed. It is shown that Li(2)Ga, a solid for which a Zintl-type electron-counting approach would suggest that a half-filled pi-type band occurs as in trans-polyacetylene, is really a three-dimensional solid with strong covalent interchain connections and small effective charge transfer. The zigzag chains do not play a dominant role as far as the electronic structure near the Fermi level is concerned, and there is no reason for the occurrence of a Peierls distortion despite the possible analogy with trans-polyacetylene. It is suggested that even assuming that a Zintl-type approach is appropriate for electron counting purposes, the infinite zigzag chains in this compound and those in trans-polyacetylene are not isolobal. The bonding in Li(9)Al(4) and Li(2)Ga is very similar, and both phases are predicted to be stable three-dimensional metals.