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.     

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.     

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.     

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.     

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 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?     

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.     

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.     

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.     

Understanding functional diversity and substrate specificity in haem peroxidases: what can we learn from ascorbate peroxidase?

This review summarizes the most recent advances in our understanding of the haem enzyme ascorbate peroxidase. The aim is to show how the combined applications of protein engineering, mechanistic and structural studies can be used to provide an overall picture of enzyme catalysis, and how this information can be used to provide new insight into other, more well-characterized peroxidases (in particular cytochrome c peroxidase). It contains 212 references and covers literature up to March 2003.     

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.     

Does cation dehydration drive the binding of metal ions to polyelectrolytes in water? What we can learn from the behaviour of aluminium(III) and chromium(III)

Much stronger binding is seen in aqueous solutions between the anionic polyelectrolyte potassium poly(vinyl sulfate) and the substitution labile aluminium(III) than with the kinetically inert chromium(III). This strongly supports the idea that entropy driven water loss from the hydration sphere of the metal ion plays a major role in driving binding of the trivalent metal ion to the polyelectrolyte.     

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.     

The kinetic and thermodynamic study of KNiPO4·H2O from DSC and TG data

The DSC and TG data showed the dehydration process occurring over the range of 160?C300?°C. The XRD patterns of the synthesized KNiPO₄·H₂O and the calcined product at 350?°C with exposing in the air over 8?h are indexed as the KNiPO₄·H₂O structure, whereas at 600?°C is indexed as KNiPO₄ structure. Hence, these data confirmed that the water molecule was eliminated from the structure at 300?°C, after that the spontaneously reversible hydration?Crehydration process was observed. The activation energy and pre-exponential factor were calculated by Kissinger, Ozawa, and KAS equations. According to the DSC curves, the enthalpy change (??H) of dehydration process can be calculated and was found to be 100.12?kJ?mol^?1. Besides, we suggested another new method to determine the isokinetic temperature value using spectroscopic data. The surface area of synthesized hydrate and its calcined product at 350?°C with exposing in the air at over 8?h were found to be 21.48 and 134.3?m²?g^?1, respectively. The reversible hydration?Crehydration process was observed, and the surface area of final product at 350?°C (aging time over 8?h) is higher than that of the synthesized compound. This behavior is important to develop alternative desiccant materials or other process based on the rehydration mechanism with increasing the surface area.