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 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?     

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     

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.     

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.     

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.     

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.     

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 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).     

Oligonucleotide separation techniques for purification and analysis: What can we learn for today's tasks?

Nucleic acids are the blueprint of life. They are not only the construction plan of the single cell or higher associations of them, but also necessary for function, communication and regulation. Due to the pandemic, the attention shifted in particular to their therapeutic potential as a vaccine. As pharmaceutical oligonucleotides are unique in terms of their stability and application, special delivery systems were also considered. Oligonucleotide production systems can vary and depend on the feasibility, availability, price and intended application. To achieve good purity, reliable results and match the strict specifications in the pharmaceutical industry, the separation of oligonucleotides is always essential. Besides the separation required for production, additional and specifically different separation techniques are needed for analysis to determine if the product complies with the designated specifications. After a short introduction to ribonucleic acids (RNAs), messenger RNA vaccines, and their production and delivery systems, an overview regarding separation techniques will be provided. This not only emphasises electrophoretic separations but also includes spin columns, extractions, precipitations, magnetic nanoparticles and several chromatographic separation principles, such as ion exchange chromatography, ion-pair reversed-phase, size exclusion and affinity.     

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.     

Resonance raman spectroscopy of conjugated polymers what can we learn?

This paper gives a review on the use of resonance Raman spectroscopy to analyse electronic and molecular structures of π-conjugated and σ-conjugated polymers. It starts with a short introduction into the present state of research in the field of conducting polymers and with a very short introduction into the principles of resonance Raman spectroscopy. Then the potentialities of the technique are demonstrated for the examples of the analysis of conjugation length in polyacetylene, for studying the thermochromic phase transition in polysilanes and in polyalkylthiophenes, for a sudy of the doping processes in polyaniline and finally for an analysis of the ground state in the narrow gap system polyisothianaphthene. Advantages and pitfalls for such analyses are outlined.     

Direct and indirect DIET and DIMET from semiconductor and metal surfaces: what can we learn from 'toy models'?

Desorption induced by electronic transitions (DIET) and its variant DIMET (M = 'Multiple'), are among the simplest possible "reactions" of ad-species involving ultra-short lived electronically excited states at surfaces. The non-adiabatic bond-cleavage can be enforced, for example, with laser irradiation or with electrons or holes emitted from the tip of a scanning tunnelling microscope (STM). The transient creation of excited intermediates can proceed directly (localised to the adsorbate-substrate complex), or indirectly (i.e., through the substrate). To understand the basic processes, simple one-mode two-state "toy models" such as the Menzel-Gomer-Redhead (MGR) or the Antoniewicz scenarios have proven very useful in the past. We adopt and extend MGR- and Antoniewicz-type models together with numerically exact open-system density matrix theory to address a few actual problems/experiments in DI(M)ET: (1) Direct, laser-induced desorption of H(D) from Si(100) surfaces which has been realised in the continuous-wave DIET regime only recently [T. Vondrak and X.-Y. Zhu, Phys. Rev. Lett., 1999, 82, 1967], is studied and compared to so-far hypothetical femtosecond laser desorption. The possibility of controlling the reaction by shaping the laser pulses is addressed. (2) For the same system, temperature effects are studied for electron- or hole-stimulated desorption with an STM [T. C. Shen, C. Wang, G. C. Abeln, T. R. Tucker, J. W. Lyding, Ph. Avouris and R. E. Walkup, Science, 1995, 268, 1590; C. Thirstrup, M. Sakurai, T. Nakayama and K. Stokbro, Surf. Sci., 1999, 424, L329]. A modified version of Gadzuk's "sudden transition and averaging" approach is adopted which accounts for temperature dependent excited state lifetimes. (3) For photodesorption of NO from Pt(111), based on quantum dynamical simulations possible experimental tests involving static electric fields are suggested to address the relevance of the recently challenged [F. M. Zimmermann, Surf. Sci., 1997. 390, 174], "negative ion resonance" model of the Antoniewicz type.     

What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations

Potential of mean force (PMF) simulations with a hybrid QM/MM potential function were used to analyze the catalytic mechanism of human cyclophilin A (CypA). PMF calculations were performed for proline isomerization of peptides in solution, the wild-type CypA, and several CypA mutants. With an approximate density functional theory, the self-consistent-charge density functional tight binding (SCC-DFTB) as the QM level, and CHARMM 22 force field as MM, satisfactory energetics compared to available experiments were obtained. Calculations for the Arg55Ala and zero-charge-Arg55 mutants clearly indicated that Arg 55 significantly stabilizes the isomerization transition state through electrostatic interactions. However, the decrease in the average distance (thus the increase in interaction) between Arg 55 and the substrate amide N in going from the stable states to the transition state is mainly due to the pyramidalization of the amide N rather than motions associated with Arg 55. Although the nanosecond simulations cannot exclude the existence of sub-millisecond collective motions proposed on the basis of recent elegant NMR relaxation and line-shape analyses, the energetics obtained for the various enzyme systems here indicate that the contribution from motions of active site residues to catalysis is expected to be small. Instead, the present simulations support that the structural stability rather than mobility of the preorganized active site is more important. Through hydrogen-bonding interactions among the substrate, Arg 55, Gln 63, and Asn 102, the active site of the wild-type enzyme is structurally very stable and puts Arg 55 in a favorable position to perform its catalytic role in the transition state. This is further illustrated with the somewhat unexpected prediction that Arg55Lys is largely catalytically inactive, because Lys does not have the unique bifurcating construct of the guanidino group in Arg and thus the active site of Arg55Lys cannot accommodate Lys in a position capable of providing electrostatic stabilization of the isomerization transition state. Among all the enzyme systems studied, the wild-type CypA is the only one that selects the syn/exo transition state, while the syn/endo conformation is also present in the mutants, which is another reason for their higher barriers. Finally, the present analysis indicated that the population of near-attack-conformations (NAC) is not relevant to catalysis in CypA.     

Weighing synthetic polymers of ultra‐high molar mass and polymeric nanomaterials: What can we learn from charge detection mass spectrometry?

Advances in soft ionization techniques for mass spectrometry (MS) of polymeric materials make it possible to determine the masses of intact molecular ions exceeding megadaltons. Interfacing MS with separation and fragmentation methods has additionally led to impressive advances in the ability to structurally characterize polymers. Even if the gap to the megadalton range has been bridged by MS for polymers standards, the MS‐based analysis for more complex polymeric materials is still challenging. Charge detection mass spectrometry (CDMS) is a single‐molecule method where the mass and the charge of each ion are directly determined from individual measurements. The entire molecular mass distribution of a polymer sample can be thus accurately measured. Described in this perspective paper is how molecular weight distribution as well as charge distribution can provide new insights into the structural and compositional studies of synthetic polymers and polymeric nanomaterials in the megadalton to gigadalton range of molecular weight. The recent multidimensional CDMS studies involving couplings with separation and dissociation techniques will be presented. And, finally, an outlook for the future avenues of the CDMS technique in the field of synthetic polymers of ultra‐high molar mass and polymeric nanomaterials will be provided.     

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.