What can be learned about molecular reorientation from single molecule polarization microscopy?

We have developed a general approach for the calculation of the single molecule polarization correlation function C(t), which delivers a correlation of the emission dichroisms at time 0 and t. The approach is model independent and valid for general asymmetric top molecules. The key dynamic quantities of our analysis are the even-rank orientational correlation functions, the weighted sum of which yields C(t). We have demonstrated that the use of nonorthogonal schemes for the detection of the single molecule polarization responses makes it possible to manipulate the weighting coefficients in the expansion of C(t). Thus valuable information about the orientational correlation functions of the rank higher than the second can be extracted from C(t).     

The reactivity of endohedral fullerenes. What can be learnt from computational studies?

The last two decades have witnessed major advances in the synthesis and characterization of endohedral fullerenes. These species have interesting physicochemical properties with many potential interesting applications in the fields of magnetism, superconductivity, nonlinear optical properties, radioimmunotherapy, and magnetic resonance imaging contrast agents, among others. In addition to the synthesis and characterization, the chemical functionalization of these species has been a main focus of research for at least four reasons: first, to help characterize endohedral fullerenes that could not be well described structurally otherwise; second, to generate materials with fine-tuned properties leading to enhanced functionality in one of their multiple potential applications; third, to produce water-soluble endohedral fullerenes needed for their use in medicinal sciences; and fourth, to generate electron donor-acceptor conjugates that can be used in solar energy conversion/storage. The functionalization of these species has been achieved through different types of reactions, the most common being the Diels-Alder reactions, 1,3-dipolar cycloadditions, Bingel-Hirsch reactions, and free-radical reactions. It has been found that the performance of these reactions in endohedral fullerenes may be quite different from that of the empty fullerenes. Indeed, encapsulated species have a large influence on the thermodynamics, kinetics, and regiochemistry of these reactions. A detailed understanding of the changes in chemical reactivity due to incarceration of atoms or clusters of atoms is essential to assist the synthesis of new functionalized endohedral fullerenes with specific properties. This Perspective seeks to highlight the key role played by computational chemistry in the analysis of the chemical reactivity of these systems. It is shown that the information obtained through calculations is highly valuable in the process of designing new materials based on endohedral fullerenes.     

What can we learn from single molecule trajectories?

Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion.     

Designer haem proteins: What can we learn from protein engineering?

Iron protoporphyrin(IX) is one of the most versatile and widespread pieces of catalytic machinery known in biology and is a key component of a multitude of proteins and enzymes. One of most challenging questions in this area has been to identify and understand the relationships that exist between different classes of haem proteins and to use protein engineering methods to rationalize the mechanisms by which the protein structure controls the specific chemical reactivity of the haem group. The application of this approach to the haem enzyme ascorbate peroxidase and the haem protein leghaemoglobin is discussed. © 2002 Wiley Periodicals, Inc. Heteroatom Chem 13:501–505, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10094     

How can enzymes be so efficient?

Dudley Williams and his colleagues discuss how ligands can gain binding energy to their receptors, and substrate transition states to their enzymes, by tightening the protein structures, with a decrease in their dynamic behaviour.     

Plant wastes and sustainable refineries: What can we learn from fungi?

The valorization of plant wastes allows access to renewable carbon feedstocks without increasing the demand for plant biomass production. Plant wastes are the non-edible residues and waste streams from agriculture, agroindustry and forestry. The chemical diversity and recalcitrance to degradation of such wastes challenge our ability to transform and valorize these resources into value-added compounds. Fungi that thrive on plant tissues have gained a huge diversity of enzymatic toolkits for the finely-tuned degradation of glycan and lignin polymers. Our knowledge on the enzymatic systems developed by fungi now guides innovations for plant waste bioprocessing. Here, we provide an overview of the most recent findings in the hydrolytic and oxidative systems used by fungi for the degradation of recalcitrant plant polymers. We present recent promising success in applying fungal enzymes or fungal fermentations on plant wastes, and discuss the forthcoming developments that could reinforce fungal biotechnology entering a variety of industrial applications.     

What can we learn from the adiabatic connection formalism about local hybrid functionals?

Local hybrid functionals with position-dependent exact-exchange admixture are a promising new generation of exchange-correlation functionals for a large variety of applications. So far, the local mixing functions (LMFs) determining the position dependence have been largely constructed in an ad hoc manner, albeit based on physical reasoning. Here the basic formalism of the adiabatic connection is employed to investigate the formal basis of local hybrids and to construct a priori LMFs. Both a local spin density approximation to the LMF (AC-LSDA LMF) and generalized gradient approximation approximations (AC-PW91 LMF and AC-PBE LMF) turn out to provide inferior performance when used in local hybrids to compute atomization energies and reaction barriers compared to previous semiempirical LMFs. This is rationalized by limited flexibility of these first-principles LMFs and some basic limitations of the adiabatic connection formalism in this context. Graphical analyses and formal considerations provide nevertheless important new insight into the physical background of local hybrid functionals.     

What can positronium tell us about adsorption?

The condensation and evaporation of n-heptane at 298 K in mesopores of silica material obtained by the polymer templating method have been studied by PALS measurements. It is demonstrated that the ortho-positronium lifetimes and intensities provide valuable information on pore filling and emptying which are not accessible from a conventional adsorption experiment. The results confirm the specific adsorption mechanism of n-heptane in pores with narrow openings (ink-bottle shape) which is different from that known for other pore geometries. The results from PALS experiment are compared to those derived from the conventional n-heptane and nitrogen adsorption data.     

To what extent can aromaticity be defined uniquely?

Statistical analyses of quantitative definitions of aromaticity, ASE (aromatic stabilization energies), RE (resonance energies), Lambda (magnetic susceptibility exaltation), NICS, HOMA, I5, and A(J), evaluated for a set of 75 five-membered pi-electron systems: aza and phospha derivatives of furan, thiophene, pyrrole, and phosphole (aromatic systems), and a set of 30 ring-monosubstituted compounds (aromatic, nonaromatic, and antiaromatic systems) revealed statistically significant correlations among the various aromaticity criteria, provided the whole set of compounds is involved. Hence, broadly considered, the various manifestations of aromaticity are related and aromaticity can be regarded statistically as a one-dimensional phenomenon. In contrast, when comparisons are restricted to some regions or groups of compounds, e.g., aromatic compounds with ASE > 5 kcal/mol or polyhetero-five-membered rings, the quality of the correlations can deteriorate or even vanish. In practical applications, energetic, geometric, and magnetic desriptors of aromaticity do not speak with the same voice. Thus, in this sense, the phenomenon of aromaticity is regarded as being statistically multidimensional.     

What can nano-chemistry offer to the paint industry?

Iron surface was modified by organic, self assembled nano-layer of 1,7-diphosphono heptane. The self-assembling film formation and the self-healing process of the injured layers was monitored by electrochemical methods. The morphological changes of paint and lacquer layers which was due to different pre-treatments were monitored by surface analyzing techniques.     

What can we learn about the mechanisms of thermal decompositions of solids from kinetic measurements?

Aspects of the theories that are conventionally and widely used for the kinetic analyses of thermal decompositions of solids, crystolysis reactions, are discussed critically. Particular emphasis is placed on shortcomings which arise because reaction models, originally developed for simple homogeneous reactions, have been extended, without adequate justification, to represent heterogeneous breakdowns of crystalline reactants. A further difficulty in the mechanistic interpretation of kinetic data obtained for solid-state reactions is that these rate measurements are often influenced by secondary controls. These include: (i) variations of reactant properties (particle sizes, reactant imperfections, nucleation and growth steps, etc.), (ii) the effects of reaction reversibility, of self-cooling, etc. and (iii) complex reaction mechanisms (concurrent and/or consecutive reactions, melting, etc.). A consequence of the contributions from these secondary rate controls is that the magnitudes of many reported kinetic parameters are empirical and results of chemical significance are not necessarily obtained by the most frequently used methods of rate data interpretation. Insights into the chemistry, controls and mechanisms of solid-state decompositions, in general, require more detailed and more extensive kinetic observations than are usually made. The value of complementary investigations, including microscopy, diffraction, etc., in interpreting measured rate data is also emphasized. Three different approaches to the formulation of theory generally applicable to crystolysis reactions are distinguished in the literature. These are: (i) acceptance that the concepts of homogeneous reaction kinetics are (approximately) applicable (assumed by many researchers), (ii) detailed examination of all experimentally accessible aspects of reaction chemistry, but with reduced emphasis on reaction kinetics (Boldyrev) and (iii) identification of rate control with a reactant vaporization step (L’vov). From the literature it appears that, while the foundations of the widely used model (i) remain unsatisfactory, the alternatives, (ii) and (iii), have not yet found favour. Currently, there appears to be no interest in, or discernible effort being directed towards, resolving this unsustainable situation in which three alternative theories remain available to account for the same phenomena. Surely, this is an unacceptable and unsustainable situation in a scientific discipline and requires urgent resolution?     

What can we learn by squeezing a liquid?

Relaxation times tau(T,upsilon) for different temperatures, T, and specific volumes, upsilon, collapse to a master curve vs Tupsilon(gamma), with gamma a material constant. The isochoric fragility, mV, is also a material constant, inversely correlated with gamma. From these experimental facts, we obtain a three-parameter function that accurately fits tau(T,upsilon) data for several glass-formers over the supercooled regime, without any divergence of tau below Tg. Although the values of the three parameters depend on the material, only gamma significantly varies; thus, by normalizing material-specific quantities related to gamma, a universal power law for the dynamics is obtained.     

What can electrochemistry tell us about individual enzymes?

We provide here a critical analysis of electrochemistry's potential and limitations in investigating single-enzyme catalysis, highlighting papers of interest from the past 2–3 years with an emphasis on nano-impact electrochemistry (NIE) and electrochemical scanning tunneling microscopy. NIE can report single-enzyme activity; however, its future broad applicability for studying freely diffusing individual enzymes is questionable. Electrochemical scanning tunneling microscopy, an alternative to NIE, measures single enzyme's electronic conductivity when suspended between two electrodes. Recent discoveries indicate that enzyme conductance depends directly on biophysical parameters such as substrate binding, oxidation state of the catalytic center, and structural fluctuations. We conclude with a short perspective on additional electrochemical routes and combinations of existing techniques that may be useful for studying single-enzyme characteristics.     

Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data?

Phosphate monoester hydrolysis reactions in enzymes and solution are often discussed in terms of whether the reaction pathway is associative or dissociative. Although experimental results for solution reactions have usually been considered as evidence for the second alternative, a closer thermodynamic analysis of observed linear free energy relationships shows that experimental information is consistent with the associative, concerted and dissociative alternatives.     

Solvation in pure liquids: what can be learned from the use of pairs of indicators?

The solvation of six solvatochromic probes in a large number of solvents (33-68) was examined at 25 degrees C. The probes employed were the following: 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl) phenolate (RB); 4-[(E)2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePM; 1-methylquinolinium-8-olate, QB; 2-bromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr, 2,6-dichloro-4-(2,4,6-triphenyl pyridinium-1-yl) phenolate (WB); and 2,6-dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr(2), respectively. Of these, MePMBr is a novel compound. They can be grouped in three pairs, each with similar pK(a) in water but with different molecular properties, for example, lipophilicity and dipole moment. These pairs are formed by RB and MePM; QB and MePMBr; WB and MePMBr(2), respectively. Theoretical calculations were carried out in order to calculate their physicochemical properties including bond lengths, dihedral angles, dipole moments, and wavelength of absorption of the intramolecular charge-transfer band in four solvents, water, methanol, acetone, and DMSO, respectively. The data calculated were in excellent agreement with available experimental data, for example, bond length and dihedral angles. This gives credence to the use of the calculated properties in explaining the solvatochromic behaviors observed. The dependence of an empirical solvent polarity scale E(T)(probe) in kcal/mol on the physicochemical properties of the solvent (acidity, basicity, and dipolarity/polarizability) and those of the probes (pK(a), and dipole moment) was analyzed by using known multiparameter solvation equations. For each pair of probes, values of E(T)(probe) (for example, E(T)(MePM) versus E(T)(RB)) were found to be linearly correlated with correlation coefficients, r, between 0.9548 and 0.9860. For the mercyanine series, the values of E(T)(probe) also correlated linearly, with (r) of 0.9772 (MePMBr versus MePM) and 0.9919 (MePMBr(2) versus MePM). The response of each pair of probes (of similar pK(a)) to solvent acidity is the same, provided that solute-solvent hydrogen-bonding is not seriously affected by steric crowding (as in case of RB). We show, for the first time, that the response to solvent dipolarity/polarizability is linearly correlated to the dipole moment of the probes. The successive introduction of bromine atoms in MePM (to give MePMBr, then MePMBr(2)) leads to the following linear decrease: pK(a) in water, length of the phenolate oxygen-carbon bond, length of the central ethylenic bond, susceptibility to solvent acidity, and susceptibility to solvent dipolarity/polarizability. Thus studying the solvation of probes whose molecular structures are varied systematically produces a wealth of information on the effect of solute structure on its solvation. The results of solvation of the present probes were employed in order to test the goodness of fit of two independent sets of solvent solvatochromic parameters.     

What chemistry should be taught in modern schools?

The goals of school education and the role of lessons in natural sciences, particularly chemistry, in intellectual development of school children are analyzed. The reasons for the negative attitude to chemistry from the young people and the society are determined. The problems arising from the forthcoming reform of school education are discussed. The structure of the chemistry course for modern general schools is presented.     

What can we learn from N2O isotope data? – Analytics,processes and modelling

The isotopic composition of nitrous oxide (N₂O) provides useful information for evaluating N₂O sources and budgets. Due to the co-occurrence of multiple N₂O transformation pathways, it is, however, challenging to use isotopic information to quantify the contribution of distinct processes across variable spatiotemporal scales. Here, we present an overview of recent progress in N₂O isotopic studies and provide suggestions for future research, mainly focusing on: analytical techniques; production and consumption processes; and interpretation and modelling approaches. Comparing isotope-ratio mass spectrometry (IRMS) with laser absorption spectroscopy (LAS), we conclude that IRMS is a precise technique for laboratory analysis of N₂O isotopes, while LAS is more suitable for in situ/inline studies and offers advantages for site-specific analyses. When reviewing the link between the N₂O isotopic composition and underlying mechanisms/processes, we find that, at the molecular scale, the specific enzymes and mechanisms involved determine isotopic fractionation effects. In contrast, at plot-to-global scales, mixing of N₂O derived from different processes and their isotopic variability must be considered. We also find that dual isotope plots are effective for semi-quantitative attribution of co-occurring N₂O production and reduction processes. More recently, process-based N₂O isotopic models have been developed for natural abundance and ¹⁵N-tracing studies, and have been shown to be effective, particularly for data with adequate temporal resolution. Despite the significant progress made over the last decade, there is still great need and potential for future work, including development of analytical techniques, reference materials and inter-laboratory comparisons, further exploration of N₂O formation and destruction mechanisms, more observations across scales, and design and validation of interpretation and modelling approaches. Synthesizing all these efforts, we are confident that the N₂O isotope community will continue to advance our understanding of N₂O transformation processes in all spheres of the Earth, and in turn to gain improved constraints on regional and global budgets.     

Interfaces between coexisting phases in polymer mixtures: What can we learn from Monte Carlo simulations?

Symmetric binary polymer mixtures are studied by Monte Carlo simulation of the bond fluctuation model, considering both interfaces between coexisting bulk phases and interfaces confined in thin films. It is found that the critical behavior of interfacial tension and width is compatible with that of the Ising model, as expected from the universality principle. In the strong segregation limit, only qualitative but not quantitative agreement with the self-consistent field (SCF) theory is found. It is argued that the SCF theory requires but for the short chains studied (N = 32 effective monomer units per chain), the limit is only reached for close to unity. Also, the effective χ-parameter decreases in the interface. It is shown that the interfacial width w does not increase by the adsorption of block copolymers as long as their areal density is still dilute (“mushroom” regime). But a broadening of interfaces does occur for thin films confined between walls at distance D, due to fluctuations that lead to for short-range forces, in agreement with experiment.     

AFM of biological complexes: What can we learn?

The term “biological complexes” broadly encompasses particles as diverse as multisubunit enzymes, viral capsids, transport cages, molecular nets, ribosomes, nucleosomes, biological membrane components and amyloids. The complexes represent a broad range of stability and composition. Atomic force microscopy offers a wealth of structural and functional data about such assemblies. For this review, we choose to comment on the significance of AFM to study various aspects of biology of selected non-membrane protein assemblies. Such particles are large enough to reveal many structural details under the AFM probe. Importantly, the specific advantages of the method allow for gathering dynamic information about their formation, stability or allosteric structural changes critical for their function. Some of them have already found their way to nanomedical or nanotechnological applications. Here we present examples of studies where the AFM provided pioneering information about the biology of complexes, and examples of studies where the simplicity of the method is used toward the development of potential diagnostic applications.