What is the best definition of a liquid cluster at the molecular scale?

We investigate the ability of different cluster definitions to serve as a good reaction coordinate in molecular simulations of nucleation. In particular, the most commonly used Stillinger criterion [J. Chem. Phys. 38, 1486 (1963)] is compared with the cluster definition introduced by ten Wolde and Frenkel [J. Chem. Phys. 109, 9901 (1998)]. The accuracy of these two different cluster definitions is tested by using molecular dynamics to study the vapor-liquid nucleation of Lennard-Jones argon as a model system. We are able to compare the size of the critical cluster identified by each cluster definition with a completely model-independent value provided by the nucleation theorem, aided by a recently introduced method that accurately extracts the location of the transition state directly from the kinetics. It is found that the Stillinger definition strongly overestimates the size of small molecular clusters by up to a factor of 2. A simple change of the Stillinger radius is unable to rectify this deficiency. On the contrary, the ten Wolde-Frenkel definition, while being only slightly more elaborate than a simple Stillinger criterion, is remarkably successful in identifying the correct molecular excess of the small clusters if the parameters are chosen adequately. The method described here can also be generalized to identify a proper reaction coordinate in other activated processes.     

What is the mole?

The mole is a difficult concept. Surveys have shown that even many teachers do not have a proper understanding of it. To help to meet this problem, the SI/IUPAC formulation of the mole is carefully presented and explained. New SI proposals are also briefly discussed.     

Oligophenylenaminones as scaffolds for α-helix mimicry

The design and synthesis of small molecule α-helix mimetics has been a productive field over the past decade. These compounds have performed well in a variety of biological systems as functional disruptors of α-helix-mediated protein-protein interactions. In our studies we have continued to develop novel, more biologically compatible scaffolds, which are often easier to assemble and capable of mimicking longer and/or more diverse helices. To this end, we have constructed a new series of i, i+4, i+7 α-helix mimics based on the enaminone scaffold. These molecules represent a step forward in the pursuit of idealized monofacial α-helix mimetics.     

What is the structure of the RecA-DNA filament?

The bacterial RecA protein has been a model system for understanding how a protein can catalyze homologous genetic recombination. RecA-like proteins have now been characterized from many organisms, from bacteriophage to humans. Some of the RecA-like proteins, including human RAD51, appear to function as helical filaments formed on DNA. However, we currently have high resolution structures of inactive forms of the protein, and low resolution structures of the active complexes formed by RecA-like proteins on DNA in the presence of ATP or ATP analogs. Within a crystal of the E. coli RecA protein, a helical polymer exists, and it has been widely assumed that this polymer is quite similar to the active helical filament formed on DNA. Recent developments have suggested that this may not be the case.     

What is an element? What is the periodic table? And what does quantum mechanics contribute to the question?

This article considers two important traditions concerning the chemical elements. The first is the meaning of the term “element” including the distinctions between element as basic substance, as simple substance and as combined simple substance. In addition to briefly tracing the historical development of these distinctions, I make comments on the recent attempts to clarify the fundamental notion of element as basic substance for which I believe the term “element” is best reserved. This discussion has focused on the writings of Fritz Paneth which are here analyzed from a new perspective. The other tradition concerns the reduction of chemistry to quantum mechanics and an understanding of chemical elements through their microscopic components such as protons, neutrons and electrons. I claim that the use of electronic configurations has still not yet settled the question of the placement of several elements and discuss an alternative criterion based on maximizing triads of elements. I also point out another possible limitation to the reductive approach, namely the failure, up to now, to obtain a derivation of the Madelung rule. Mention is made of some recent similarity studies which could be used to clarify the nature of ‘elements’. Although it has been suggested that the notion of element as basic substance should be considered in terms of fundamental particles like protons and electrons, I resist this move and conclude that the quantum mechanical tradition has not had much impact on the question of what is an element which remains an essentially philosophical issue.     

Amyloid formation from an α-helix peptide bundle is seeded by 3(10)-helix aggregates

Transformation of proteins and peptides to fibrillar aggregates rich in β sheets underlies many diseases, but mechanistic details of these structural transitions are poorly understood. To simulate aggregation, four equivalents of a water‐soluble, α‐helical (65 %) amphipathic peptide (AEQLLQEAEQLLQEL) were assembled in parallel on an oxazole‐containing macrocyclic scaffold. The resulting 4α‐helix bundle is monomeric and even more α helical (85 %), but it is also unstable at pH 4 and undergoes concentration‐dependent conversion to β‐sheet aggregates and amyloid fibrils. Fibrils twist and grow with time, remaining flexible like rope (>1 μm long, 5–50 nm wide) with multiple strings (2 nm), before ageing to matted fibers. At pH 7 the fibrils revert back to soluble monomeric 4α‐helix bundles. During α→β folding we were able to detect soluble 3₁₀ helices in solution by using 2D‐NMR, CD and FTIR spectroscopy. This intermediate satisfies the need for peptide elongation, from the compressed α helix to the fully extended β strand/sheet, and is driven here by 3₁₀‐helix aggregation triggered in this case by template‐promoted helical bundling and by hydrogen‐bonding glutamic acid side chains. A mechanism involving α?α₄?(3₁₀)₄?(3₁₀)_n?(β)_n?m(β)_n equilibria is plausible for this peptide and also for peptides lacking hydrogen‐bonding side chains, with unfavourable equilibria slowing the α→β conversion.     

Protein crystal nucleation: is the pair interaction potential the primary determinant of kinetics?

Fundamental understanding of protein crystal nucleation facilitates crystallization of biological macromolecules for structure determination and control of crystal size distribution. In the studies presented here, nucleation kinetics of hen egg-white lysozyme crystals were measured at solution conditions that exhibited equal solubility by adjusting pH, temperature, or sodium chloride concentration. It was observed that solution conditions that lead to equal solubility resulted in equal nucleation rates and hence kinetic parameters. Since the solubility of globular proteins correlates with the osmotic second virial coefficient, B(22), an integral measure of the protein pair interaction potential, this observation indicates that the protein pair interaction plays a key role in determining nucleation kinetic parameters.     

What is the correct form of BET isotherm for modeling liquid phase adsorption?

In this work subtleties of application of BET isotherm for liquid phase adsorption is presented. It has been shown that direct use of the classical BET equation (which was developed for gas phase adsorption) to liquid phase adsorption leads to ambiguous and erroneous results. Some cases of misuse of BET equation for liquid phase adsorption have been revisited. By close examination of the development of the classical equation, the causes of misunderstandings were elucidated and the suitable form of the BET equation for liquid phase adsorption was developed. As case studies, the classical form of the BET equation along with the correct form of the equation for liquid phase have been applied for modeling liquid phase adsorption of methyl tert-butyl ether (MTBE) on perfluorooctyl alumina, phenol on activated carbon and pentachlorophenol on carbonized bark. It has been shown that direct application of the classical BET isotherm to liquid phase adsorption results in poor and erroneous estimation of the equation parameters. For example, in aqueous phase adsorption of MTBE on perfluorooctyl alumina, the monolayer adsorption capacity of the adsorbent was calculated as 9.7 mg/g instead of 3.3 mg/g or the saturation concentration of MTBE in water was calculated as 1212 mg/L instead of 42000 mg/L.     

A sequence-based computational model for the prediction of the solvent accessible surface area for α-helix and β-barrel transmembrane residues

Predicting the solvent accessible surface area (ASA) of transmembrane (TM) residues is of great importance for experimental researchers to elucidate diverse physiological processes. TM residues fall into two major structural classes (α-helix membrane protein and β-barrel membrane protein). The reported solvent ASA prediction models were developed for these two types of TM residues respectively. However, this prevents the general use of these methods because one cannot determine which model is suitable for a given TM residue without information of its type. To conquer this limitation, we developed a new computational model that can be used for predicting the ASA of both TM α-helix and β-barrel residues. The model was developed from 78 α-helix membrane protein chains and 24 β-barrel membrane protein. Its prediction ability was evaluated by cross validation method and its prediction result on an independent test set of 20 membrane protein chains. The results show that our model performs well for both types of TM residues and outperforms other prediction model which was developed for the specific type of TM residues. The prediction results also proved that the random forest model incorporating conservation score is an effective sequence-based computational approach for predicting the solvent ASA of TM residues.     

Supramolecular chemistry: What is the commercialisation plan?

Opportunities for commercialisation along with personal views are provided in this essay.     

What is the mechanism of soap film entrainment?

Classical Frankel's law describes the formation of soap films and their evolution upon pulling, a model situation of film dynamics in foams (formation, rheology, and destabilization). With the purpose of relating film pulling to foam dynamics, we have built a new setup able to give an instantaneous measurement of film thickness, thus allowing us to determine film thickness profile during pulling. We found that only the lower part of the film is of uniform thickness and follows Frankel's law, provided the entrainment velocity is small. We show that this is due to confinement effects: there is not enough surfactant in the bulk to fully cover the newly created surfaces which results in immobile film surfaces. At large velocities, surfaces become mobile and then Frankel's law breaks down, leading to a faster drainage and thus to a nonstationary thickness at the bottom of the film. These findings should help in understanding the large dispersion of previous experimental data reported during the last 40 years and clarifying the pulling phenomenon of thin liquid films.     

What is the acidity of a plutonium solution?

The determination of the pH of a plutonium solution has traditionally depended on an electrode or a titration in the presence of a complexing agent. A new approach uses the equilibrium distribution of the Pu oxidation states to estimate the hydrogen ion concentration. The method is used to estimate the equilibrium constant of the first hydrolysis reaction of tetravalent plutonium.     

What is the enthalpy of formation of acrylonitrile?

Acrylonitrile is a key industrial compound with numerous uses. Despite its importance, its enthalpy of formation is still contentious. There is a 12 kJ mol⁻¹ range of values reported for the gas phase quantity: 173–185 kJ mol⁻¹. Quantum chemical calculations, using current methodologies and defining reactions, suggest values between 185 and 191 kJ mol⁻¹: the recommended value, an average, is 188 ± 7 kJ mol⁻¹.     

What is the unperturbed state in polymer solutions?

We report theoretical results about amphiphilic random copolymers in a quasi‐ideal conformation with an overall size very close to that of the analogue homopolymers. We found that a few states may coexist with about the same free energy and a similar radius of gyration, but with different intramolecular conformations. We also argue that, in most cases, amphiphilic copolymers may never achieve the unperturbed Θ state, defined thermodynamically by a vanishing second virial coefficient. Thus, we suggest that such copolymers usually show neither an unperturbed conformation nor an unperturbed state from the thermodynamic viewpoint. We also briefly discuss star homopolymers, which show a depression of the Θ temperature with respect to linear chains and a significant, though finite, Θ swelling, as well as linear chains in the Θ state and in the melt. The main general conclusion is that interactions between chain segments do not cancel each other and are non‐negligible. Accordingly, we suggest that the word "unperturbed" be used only with reference to solution thermodynamics and not for the chain size or conformation.     

What exactly is uncertainty?

Uncertainty is defined in VIM3 as a ‘parameter’ but that, in my view, is a mistake that detracts from the clarity of the concept. Trying to overcome the resulting difficulties while retaining ‘parameter’ has brought about progressive amendments to the definition, and an increasing list of footnotes that have failed to resolve the issue. Surely the uncertainty of a result is the density function (or mass function) that best describes the probability of possible values of the measurand.     

Cyclophanes or Cyclodextrins: What is the Best Host for Aromatic Volatile Organic Compounds?

The first results of the complexing ability of cyclobis-(paraquat-p-phenylene) as supramolecular host with different aromatic volatile organic compounds are presented. The formation constants of cyclobis(paraquat-p-phenylene) with toluene and halogenobenzenes were determined in aqueous solution by static headspace associated with gas chromatography and compared with the ones obtained by cyclodextrins. The data indicated the formation of 1:1 inclusion compounds in both cases. The results underlined a greater complexation ability for cyclobis(paraquat-p-phenylene) which was confirmed by a theoretical study.     

What is Conservation Science?

‘Conservation science’ or ‘cultural heritage research’ is defined through a discussion of research needs, training and employment patterns world-wide, and trends in published work. Parallels with mainstream polymer science are drawn throughout. Some aspects are discussed in more detail: traditional paint composites; studies in modern, synthetic, paint composites; the relevance of accelerated ageing to a range of polymer types.     

What is dietary fiber?

Dietary fiber consists of the remnants of the edible plant cell, polysaccharides, lignin, and associated substances resistant to digestion (hydrolysis) by human alimentary enzymes. This physiological definition has been translated into a chemical method (AOAC Method 985.29), which has recently been shown to miss substances of 10, 11, and 12 degrees of polymerization. It also fails to precipitate some hydrolysis-resistant oligosaccharides which contain many physiological properties expected in dietary fiber, such as inulin and oligofructose, indigestible dextrin (Fibersol-2), galactooligosaccharides and the synthetic polymer polydextrose. The Executive Board of the American Association of Cereal Chemists has appointed a committee to explore the possibility of expanding the definition or chemical methodology for dietary fiber to accommodate components that are not hydrolyzed by human alimentary enzymes, yet have the physiological attributes normally associated with dietary fiber. However, the present review suggests that the current definition is sufficient, along with new methodology, to detect recently discovered components of the dietary fiber complex.