What does polycondensation mean?

This contribution has the function of an introduction to the entire volume. It deals with several fundamental definitions and classifications related to the chemistry of polycondensation processes, and it includes modifications of the classical theory of step-growth polymerizations.     

How do aminoadamantanes block the influenza M2 channel, and how does resistance develop?

The interactions between channels and their cognate blockers are at the heart of numerous biomedical phenomena. Herein, we unravel one particularly important example bearing direct pharmaceutical relevance: the blockage mechanism of the influenza M2 channel by the anti-flu amino-adamantyls (amantadine and rimantadine) and how the channel and, consequently, the virus develop resistance against them. Using both computational analyses and experimental verification, we find that amino-adamantyls inhibit M2's H(+) channel activity by electrostatic hindrance due to their positively charged amino group. In contrast, the hydrophobic adamantyl moiety on its own does not impact conductivity. Additionally, we were able to uncover how mutations in M2 are capable of retaining drug binding on the one hand yet rendering the protein and the mutated virus resistant to amino-adamantyls on the other hand. We show that the mutated, drug-resistant protein has a larger binding pocket for the drug. Hence, despite binding the channel, the drug remains sufficiently mobile so as not to exert a H(+)-blocking positive electrostatic hindrance. Such insight into the blocking mechanism of amino-adamantyls, and resistance thereof, may aid in the design of next-generation anti-flu agents.     

When does gold behave as a halogen? Predicted uranium tetraauride and other MAu4 tetrahedral species, (M = Ti,Zr, Hf,Th)

Quantum chemical calculations suggest that a series of molecules with the general formula MAu4 are stable, where M = U, Th, and a group-4 atom. They correspond to Au in the formal valence state -1 and indicate that gold can act as a ligand similar to the halogen series. Of the MAu4 species studied, UAu4, the first predicted mixed gold uranium compound, has a short M-Au bond distance, 2.71 A, which would locate Au between Br and I from the bond length point of view in the U-tetrahalide series. Energetically, the U-Au bond is weaker than the corresponding U-Br and U-I bonds.     

How much does the SI,namely the proposed “New SI”, conform to principles of the Metre Treaty?

The International System of Units (SI) was first adopted in 1960, as the more recent implementation of the Metre Treaty signed in 1875. Basic features of the original SI are that (a) seven units are chosen as “base units”, all the others being “derived units”, and (b) the definitions of the base units should not create interdependence. This way, the SI conforms to the basic principle of the Metre Treaty that each signatory country can realise its choice of primary national standards of the very definitions of the units without needing to resort to calibrations obtained from another country, and without obligation to have them realised for all the units. A mismatch already occurs to some extent with respect to the above features in the present definitions of SI base units. This contribution, strictly based on metrological considerations, illustrates how the present proposal concerning new definitions for the base units, called “New SI”, would extend the mismatch. In this frame, also the meaning is discussed of the concepts of hierarchy and traceability in metrology. By outlining some of the consequences, a discussion is stimulated related to the status of base unit, to the meaning of calibration at the level of the standards of the unit definitions, and to the interdependence of countries’ standards.     

What does shape a topological atom?

In this pedagogical communication after demonstrating the legitimacy for using the quantum theory of atoms in molecules (QTAIM) to non-Coulombic systems, Hookean H₂ ⁺/H₃ ²⁺ species are used for AIM analysis. In these systems, in contrast to their Coulombic counterparts, electron density is atom-like and instead of expected two/three topological atoms, just a single topological atom emerges. This observation is used to demonstrate that what is really “seen” by the topological analysis of electron densities is the clustering of electrons. The very trait of monotonic decay of electron density around the “centers” of clustering guarantees the appearance of topological atoms as basin of attraction of the gradient vector field of the electron density. Although observations with Hookean molecules may seem disappointing at first glance, a careful reasoning points to the fact that the QTAIM methodology is extendable to novel domains, by a knowledge of the morphology of underlying densities, beyond the typical Coulombic systems.     

Terpene bioconversion--how does its future look?

The usage of essential oils as such or of volatile fractions thereof is widespread in the flavor and fragrance industry to aromatize perfumery and cosmetic products, foodstuffs, and many household and pharmaceutical products. The increased market share of convenience food together with consumers' request for constant high quality and natural products have established a lasting increase in the demand for natural flavorings that cannot be satisfied by the traditional plant materials. This review summarizes selected work on terpene bioconversion/transformation and focuses on recently published papers dealing with novel strains and products, high product yields, intriguing genetic engineering approaches, and integrated bioprocesses. The future perspectives of an industrial realization of a biotechnological production of terpene-derived natural flavors are critically evaluated.     

How does organic matter constrain the nature, size and availability of Fe nanoparticles for biological reduction?

Few studies have so far examined the kinetics and extent of the formation of Fe-colloids in the presence of natural organic ligands. The present study used an experimental approach to investigate the rate and amount of colloidal Fe formed in presence of humic substances, by gradually oxidizing Fe(II) at pH 6.5 with or without humic substances (HS) (in this case, humic acid--HA and fulvic acid--FA). Without HS, micronic aggregates (0.1-1 μm diameter) of nano-lepidocrocite is obtained, whereas, in a humic-rich medium (HA and FA suspensions at 60 and 55 ppm of DOC respectively), nanometer-sized Fe particles are formed trapped in an organic matrix. A proportion of iron is not found to contribute to the formation of nanoparticles since iron is complexed to HS as Fe(II) or Fe(III). Humic substances tend to (i) decrease the Fe oxidation and hydrolysis, and (ii) promote nanometer-sized Fe oxide formation by both inhibiting the development of hydroxide nuclei and reducing the aggregation of Fe nanoparticles. Bioreduction experiments demonstrate that bacteria (Shewanella putrefaciens CIP 80.40 T) are able to use Fe nanoparticles associated with organic matter about eight times faster than in the case of nano-lepidocrocite. This increase in bioreduction rate appears to be related to the presence of humic acids that (i) indirectly control the size, shape and density of oxyhydroxides and (ii) directly enhance biological reduction of nanoparticles by electron shuttling and Fe complexation. These results suggest that, in wetlands but also elsewhere where mixed organic matter-Fe colloids occur, Fe nanoparticles closely associated with organic matter represent a bioavailable Fe source much more accessible for microfauna than do crystallized Fe oxyhydroxides.     

How does a thin volatile film move?

When a water film evaporates from a mica substrate, an interface similar to a solidification front develops, separating two films of different thicknesses. We show experimentally that the evolution dynamics is controlled mainly by material diffusion through the vapor phase rather than by hydrodynamic flow through the film. Our results illustrate the role of different contributions to pattern formation of volatile liquid films.     

Do theories of the glass transition, in which the structural relaxation time does not define the dispersion of the structural relaxation, need revision?

Upon decreasing temperature or increasing pressure, a noncrystallizing liquid will vitrify; that is, the structural relaxation time, taualpha, becomes so long that the system cannot attain an equilibrium configuration in the available time. Theories, including the well-known free volume and configurational entropy models, explain the glass transition by invoking a single quantity that governs the structural relaxation time. The dispersion of the structural relaxation (i.e., the structural relaxation function) is either not addressed or is derived as a parallel consequence (or afterthought) and thus is independent of taualpha. In these models the time dependence of the relaxation bears no fundamental relationship to the value of taualpha or other dynamic properties. Such approaches appear to be incompatible with a general experimental fact recently discovered in glass-formers: for a given material at a fixed value of taualpha, the dispersion is constant, independent of thermodynamic conditions (T and P); that is, the shape of the alpha-relaxation function depends only on the relaxation time. If derived independently of taualpha, it is an unlikely result that the dispersion of the structural relaxation would be uniquely defined by taualpha.     

Fluorine in the Earth and the solar system,where does it come from and can it be found?

This review (1) presents a summary of the distribution of fluorine in different fluid (surficial, subterranean, metamorphic, and magmatic–hydrothermal–geothermal) and solid (oceanic and continental crust, mantle, and core) domains of the Earth, and various extraterrestrial materials and bodies (meteorites, planets and moons, and the Sun); (2) it provides an estimate of the total fluorine abundance for the Earth and in its dominant reservoirs contributing to the Earth's fluorine endowment; and (3) it discusses key observations that could further improve our understanding of fluorine abundances and geochemical systematics.     

Thermochemical kinetics: does it still give insights?

This tutorial review revisits the subject of the seminal book written by Sidney Benson in 1968. A short summary of the nature of the subject is presented, including its place in the wider world of quantitative chemistry. A number of themes are selected to illustrate its previous and continuing usefulness in evaluating numerical values of important quantities, and probing ideas of reaction mechanism. These include strain enthalpies for biradical combination, chain reactions, why some reactions don't occur and the involvement of carbenes in hydrocarbon rearrangements.     

Why does uranium oxide phosphate contract on heating?

(U₂O)(PO₄)₂ is related to ultra-low expansion β-(Zr₂O)(PO₄)₂ ceramics, but shows a continuous thermal contraction. High-temperature neutron diffraction has allowed to follow accurately the thermal variations of its cell edges and to give a structural explanation to the phenomenon: like in β-(Zr₂O)(PO₄)₂, the dilatometric anomaly arises simultaneously from a contractive push-pull effect due to Coulombic repulsions and from a libration of the PO₄ and UO₇ polyhedra, but in the present case, the second mechanism predominates. The size of the tetravalent cation appears as a key parameter in monitoring the thermal expansion of ceramics of this family.     

How does a hydrocarbon staple affect peptide hydrophobicity?

Water is essential for the proper folding of proteins and the assembly of protein–protein/ligand complexes. How water regulates complex formation depends on the chemical and topological details of the interface. The dynamics of water in the interdomain region between an E3 ubiquitin ligase (MDM2) and three different peptides derived from the tumor suppressor protein p53 are studied using molecular dynamics. The peptides show bimodal distributions of interdomain water densities across a range of distances. The addition of a hydrocarbon chain to rigidify the peptides (in a process known as stapling) results in an increase in average hydrophobicity of the peptide–protein interface. Additionally, the hydrophobic staple shields a network of water molecules, kinetically stabilizing a water chain hydrogen‐bonded between the peptide and MDM2. These properties could result in a decrease in the energy barrier associated with dehydrating the peptide–protein interface, thereby regulating the kinetics of peptide binding. © 2015 Wiley Periodicals, Inc.     

How does vanadium nitrogenase reduce CO to hydrocarbons?

Nitrogenase enzymes containing molybdenum normally reduce N(2) to NH(3), and are severely inhibited by CO, but vanadium-nitrogenase reduces CO to hydrocarbons C(2)H(4), C(2)H(6) and C(3)H(8). Aspects of the mechanism of this unexpected and unprecedented reaction have been investigated by density functional simulations of the iron-vanadium cofactor FeV-co [NFe(7)VS(9)(homocitrate)] protein-bound by cysteine and histidine. It is found that the intramolecular hydrogenating machinery previously proposed for N(2) reduction (including H-atom tunneling) can also effect reduction of CO. There are feasible steps for all of the requisite components of the overall reaction, namely (i) the binding of CO, (ii) the initial hydrogenation of CO to HCO, (iii) continued hydrogenations of CO at both C and O to HCOH and H(2)COH, (iv) eliminations of O as H(2)O, and (v) the C-C bond formation steps. Intermediate organic fragments can migrate around the active face of FeV-co, and hydrogen bonding between COH functions and S or SH components of FeV-co can occur and contribute to the stabilisation and orientation of intermediates. It is suggested that the difference between Mo-nitrogenase and V-nitrogenase occurs in the immediately surrounding protein, which facilitates (possibly via water associated with homocitrate bound to V) the exogenous protonation and dehydration of -COH intermediates.     

How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP,TP2 and ONEG?

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) ¹H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

A protocol for simulating intrinsically disordered peptides in aqueous and hydrophobic solvents is proposed. Results from four force fields are compared with experiment. CHARMM36m performs the best for the simulated IDPs in all environments.     

Radical clock substrates, their C-H hydroxylation mechanism by cytochrome P450, and other reactivity patterns: what does theory reveal about the clocks' behavior?

There is an ongoing and tantalizing controversy regarding the mechanism of a key process in nature, C-H hydroxylation, by the enzyme cytochrome P450 (Auclaire, K.; Hu, Z.; Little, D. M.; Ortiz de Montellano, P. R.; Groves, J. T. J. Am. Chem. Soc. 2002, 124, 6020-6027. Newcomb, M.; Aebisher, D.; Shen, R.; Esala, R.; Chandrasena, P.; Hollenberg, P. F.; Coon, M. J. J. Am. Chem. Soc. 2003, 125, 6064-6065). To definitely resolve this controversy, theory must first address the actual systems that have been used by experiment, and that generated the controversy. This is done in the present paper, which constitutes the first extensive theoretical study of such two experimental systems, trans-2-phenylmethyl-cyclopropane (1) and trans-2-phenyl-iso-propylcyclopropane (4). The theoretical study of these substrates reveals that the only low energy pathway for C-H hydroxylation is the two-state rebound mechanism described originally for methane hydroxylation (Ogliaro, F.; Harris, N.; Cohen, S.; Filatov, M.; de Visser, S. P.; Shaik, S. J. Am. Chem. Soc. 2000, 122, 8977-8989). The paper shows that the scenario of a two-state rebound mechanism accommodates much of the experimental data. The computational results provide a good match to experimental results concerning the very different extents of rearrangement for 1 (20-30%) vs 4 (virtually none), lead to product isotope effect for the reaction of 1, in the direction of the experimental result, and predict as well the observed metabolic switching from methyl to phenyl hydroxylation, which occurs upon deuteration of the methyl group. Furthermore, the study reveals that an intimate ion pair species involving an alkyl carbocation derived from 4 gives no rearranged products, again in accord with experiment. This coherent match between theory and experiment cannot be merely accidental; it comes close to being aproof that the actual mechanism of C-H hydroxylation involves the two-state reactivity revealed by theory. Analysis of the rearrangement modes of the carbocations derived from 1 and 4 excludes the participation of free carbocations during the hydroxylation of these substrates. Finally, the mechanistic significance of product isotope effect (different isotope effects for the rearranged and unrearranged alcohol products) is analyzed. It is shown to be a sensitive probe of two-state reactivity; the size of the intrinsic product isotope effect and its direction reveal the structural differences of the hydrogen abstraction transition states in the low-spin vs high-spin reaction manifolds.     

Why does the Cassie–Baxter equation apply?

Application of the Cassie–Baxter equation to the calculation of apparent contact angles is discussed. It is demonstrated that taking into account the precursor film surrounding the drop justifies the application of the Cassie–Baxter equation. Consideration of the precursor film is important for design of self-cleaning superhydrophobic surfaces.     

When does the Michaelis-Menten equation hold for fluctuating enzymes?

Enzymes are dynamic entities: both their conformation and catalytic activity fluctuate over time. When such fluctuations are relatively fast, it is not surprising that the classical Michaelis-Menten (MM) relationship between the steady-state enzymatic velocity and the substrate concentration still holds. However, recent single-molecule experiments have shown that this is the case even for an enzyme whose catalytic activity fluctuates on the 10(-4)-10 s range. The purpose of this paper is to examine various scenarios in which slowly fluctuating enzymes would still obey the MM relationship. Specifically, we consider (1) the quasi-static condition (e.g., the conformational fluctuation of the enzyme-substrate complex is much slower than binding, catalysis, and the conformational fluctuations of the free enzyme), (2) the quasi-equilibrium condition (when the substrate dissociation is much faster than catalysis, irrespective of the time scales or amplitudes of conformational fluctuations), and (3) the conformational-equilibrium condition (when the dissociation and catalytic rates depend on the conformational coordinate in the same way). For each of these scenarios, the physical meaning of the apparent Michaelis constant and catalytic rate constant is provided. Finally, as an example, the theoretical analysis of a recent single-molecule enzyme assay is considered in light of the perspectives presented in this paper.     

Accreditation of RM producers: what does it mean?

A comparative study of different papers published in this special edition of ACQUAL "Accreditaton of RM producers" (see Editorial) is presented. The main question is: Is accreditation the key to guaranteeing the quality of RMs or is it certification? The arguments and different options of the authors are compared and evaluated against existing rules and present practice. In the conclusion options are given which depend on the type of RM producer (namely, laboratory or product certification body), and which could be acceptable to the community of analysts and metrologists, as well as to the market.