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.     

What can be Learned from Silage Breeding Programs?

Improving the quality of cellulosic ethanol feedstocks through breeding and genetic manipulation could significantly impact the economics of this industry. Attaining this will require comprehensive and rapid characterization of large numbers of samples. There are many similarities between improving corn silage quality for dairy production and improving feedstock quality for cellulosic ethanol. It was our objective to provide insight into what is needed for genetic improvement of cellulosic feedstocks by reviewing the development and operation of a corn silage breeding program. We discuss the evolving definition of silage quality and relate what we have learned about silage quality to what is needed for measuring and improving feedstock quality. In addition, repeatability estimates of corn stover traits are reported for a set of hybrids. Repeatability of theoretical ethanol potential measured by near-infrared spectroscopy is high, suggesting that this trait may be easily improved through breeding. Just as cell wall digestibility has been factored into the latest measurements of silage quality, conversion efficiency should be standardized and included in indices of feedstock quality to maximize overall, economical energy availability.     

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.     

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.     

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.     

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.     

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 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?     

Enzyme accessibility and solid supports: which molecular weight enzymes can be used on solid supports? An investigation using confocal Raman microscopy

The accessibility of various solid supports (TentaGel, PEGA 1900, and beaded controlled pore glasses (CPGs)) to a range of enzymes was investigated. The different beaded materials were loaded with the peptide 4-cyanobenzamide-Gly-Pro-Leu-Gly-Leu-Phe-Ala-Arg-OH and incubated with the enzymes MMP-12 (22 kDa), thermolysin (35 kDa), MMP-13 (42.5 kDa), clostridium collagenase (68 kDa), and NEP (90 kDa). The absence/presence of the cyano stretching frequency was measured by means of confocal Raman microscopy. It was found that none of the investigated enzymes could enter the polymer matrices of TentaGel. PEGA 1900 was compatible only with the two smallest enzymes, while beaded CPG was successful even with NEP (90 kDa), proving its superiority over other materials in terms of bio-compatibility.     

Sensing or no sensing: can the anomeric effect be probed by a sensing molecule?

The anomeric effect plays a central role in carbohydrate chemistry, but its origin is controversial, and both the hyperconjugation model and the electrostatic model have been proposed to explain this phenomenon. Recently, Cocinero et al. designed a peptide sensor, which can bind to a sugar molecule methyl D-galactose, and claimed that the anomeric effect can be sensed by the spectral changes from the β- to the α-complex, which are ultimately attributed to the lone pair electron density change on the endocyclic oxygen atom [Nature 2011, 469, 76; J. Am. Chem. Soc. 2011, 133, 4548]. Here, we provide strong computational evidence showing that the observed spectral changes simply come from the conformational differences between the α- and β-anomers, as the replacement of the endocyclic oxygen atom with a methylene group, which disables both the endo- and the exo-anomeric effects in methyl D-galactose, leads to similar spectral shifts. In other words, the "sensor" cannot probe the anomeric effect as claimed. We further conducted detailed energetic and structural analyses to support our arguments.     

What is an atom in a molecule?

The derivation of the Hirshfeld atoms in molecules from information theory is clarified. The importance for chemistry of the concept of atoms in molecules (AIM) is stressed, and it is argued that this concept, while highly useful, constitutes a noumenon in the sense of Kant.     

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     

Not any new functional polymer can be for medicine: what about artificial biopolymers?

Man-made artificial organic polymers are among the more recent sources of materials used by humans. In medicine, they contribute to applications in surgery, dentistry and pharmacology. Nowadays, innovations in the field of therapeutic polymers rely on novel polymers for specific applications such as guided tissue regeneration, tissue engineering, drug delivery systems, gene transfection, etc. Introducing reactive chemical functions within or along polymer backbones is an attractive route to generate functional polymers for medicine. However, any candidate to effective application must fulfil a number of requirements, grouped under the terms biocompatibility and biofunctionality, to be of real interest and have a future for effective application. Whenever the application requires a therapeutic aid for a limited period of time to help natural healing, bioresorbability is to be taken into account on top of biocompatibility and biofunctionality. This contribution presents the case of "artificial biopolymers" and discusses the potential of some members of the family with respect to temporary therapeutic applications that require functional polymers.     

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.     

Polymers coalesced from their cyclodextrin inclusion complexes: What can they tell us about the morphology of melt‐crystallized polymers?

Cyclodextrins (CDs) are cyclic polysaccharides with nano‐size, largely hydrophobic cavities, and exteriors covered with hydrophilic hydroxyl groups, making them water soluble. Threading and filling their cavities with polymer chains produces noncovalently bonded crystalline inclusion compounds (ICs). In this study, we formed fully covered, stoichiometric ICs between guest poly(L ‐lactic acid), poly(ε‐caprolactone), and nylon‐6 chains and host α‐CD. Coalesced samples of all three polymers were obtained after appropriately removing the stacked α‐CD host channels from their ICs. Distinct differential scanning calorimetriy (DSC) thermograms were observed for as‐received and coalesced samples, with the coalesced samples crystallizing faster at higher temperatures from their melts, and this distinction was maintained even after extensive, long‐time melt‐annealing (hours, days, and weeks). We believe this is due to the largely unentangled chains with extended conformations that are more densely packed in the initially coalesced samples. When small amounts (～2 wt %) of the coalesced polymers are used as self‐nucleating agents for their as‐received samples, the resulting self‐nucleated samples show DSC thermograms similar to those of the neat coalesced polymers, including their long‐time stability to melt‐annealing. Coalesced polymers, whether neat or in samples they self‐nucleate, may conserve their organization in the melt (largely extended and unentangled chains) for long periods, because the process of entangling the many chains influenced by a single initially extended unentangled coalesced chain, after it randomly coils, is extremely sluggish. By contrast, in melt‐crystallized or solution‐cast samples, polymer chains generally become fully randomly coiled, interpenetrate, and entangle after being heated and held in their melts for comparatively much shorter times. For example, we have recently observed (DSC) that ultra high molecular weight, gel‐spun spectra polyethylene (PE) fibers^® did not conserve or retain any memory of their as‐spun and highly drawn semicrystalline morphology even after spending as little as 2 min in the melt. As a consequence of the comparison to the behavior of coalesced polymer melts, we believe that polyethylene chains in Spectra fibers^® must be at least intimately dispersed within their crystalline regions, and likely partially coiled and entangled in their noncrystalline regions, thereby facilitating their rapid transformation into a full entanglement network of randomly coiling chains in the melt. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

What does an ionic liquid surface really look like? Unprecedented details from molecular simulations

We present the first intrinsic analysis of the surface of the [bmim][PF(6)] room-temperature ionic liquid. Our detailed analysis reveals unprecedented details about the structure of the interface by providing the relative prevalence of different molecular orientations. These results suggest that experimental data should be reinterpreted considering a distribution of molecular arrangements.     

What can you learn from a molecular probe? New insights on the behavior of C343 in homogeneous solutions and AOT reverse micelles

The behavior of C343, a common molecular probe utilized in solvation dynamics experiments, was studied in homogeneous media and in aqueous and nonaqueous reverse micelles (RMs). In homogeneous media, the Kamlet and Taft solvatochromic comparison method quantified solute-solvent interactions from the absorption and emission bands showing that the solvatochromic behavior of the dye depends not only on the polarity of the medium but also on the hydrogen-bonding properties of the solvent. Specifically, in the ground state the molecule displays a bathochromic shift with the polarity polarizability (pi) and the H-bond acceptor (beta) ability of the solvents and a hypsochromic shift with the hydrogen donor ability (alpha) of the media. The carboxylic acid group causes C343 to display greater sensitivity to the beta than to the pi polarity parameter; this sensitivity increases in the excited state, while the dependence on alpha vanishes. This demonstrates that C343 forms a stable H-bond complex with solvents with high H-bond acceptor ability (high beta) and low H-bond donor character (low alpha). Spectroscopy in nonpolar solvents reveals J-aggregate formation. With information from the Kamlet-Taft analysis, C343 was used to explore RMs composed of water or polar solvents/sodium 1,4-bis-2-ethylhexylsulfosuccinate (AOT)/isooctane using absorption, emission, and time-resolved spectroscopies. Sequestered polar solvents included ethylene glycol (EG), formamide (FA), N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA). Dissolved in the AOT RM systems at low concentration, C343 exists as a monomer, and when introduced to the RM samples in its protonated form, C343 remains protonated driving it to reside in the interface rather than the water pool. The solvathochromic behavior of the dye depends the specific polar solvent encapsulated in the RMs, revealing different types of interactions between the solvents and the surfactant. EG and water H-bond with the AOT sulfonate group destroying their bulk H-bonded structures. While water remains well segregated from the nonpolar regions, EG appears to penetrate into the oil side of the interface. In aqueous AOT RMs, C343 interacts with neither the sulfonate group nor the water, perhaps because of intramolecular H-bonding in the dye. DMF and DMA interact primarily through dipole-dipole forces, and the strong interactions with AOT sodium counterions destroy their bulk structure. FA also interacts with the Na+ counterions but retains its H-bond network present in bulk solvent. Surprisingly, FA appears to be the only polar solvent other than water forming a "polar-solvent pool" with macroscopic properties similar to the bulk.