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.     

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.     

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     

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 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?     

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.     

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.     

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.     

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.     

What can a "quantum black-box" do for the inorganic thermochemist?

Enthalpies of formation of ABO3 (A = Ca, Sr, Ba; B = Ti, Zr, Hf) from the binary constituent oxides have been calculated by ab initio density functional theory. The resulting values compare well with the large number of experimental determinations reported in literature. The trends in the calculated enthalpies of formation correlate with the difference in acidity between the binary constituent oxides. Density functional theory is shown to be a valuable tool that should be used routinely in thermochemical studies of inorganic compounds.     

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

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

What 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.     

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 do we know and when do we know it?

Two essential aspects of virtual screening are considered: experimental design and performance metrics. In the design of any retrospective virtual screen, choices have to be made as to the purpose of the exercise. Is the goal to compare methods? Is the interest in a particular type of target or all targets? Are we simulating a ‘real-world’ setting, or teasing out distinguishing features of a method? What are the confidence limits for the results? What should be reported in a publication? In particular, what criteria should be used to decide between different performance metrics? Comparing the field of molecular modeling to other endeavors, such as medical statistics, criminology, or computer hardware evaluation indicates some clear directions. Taken together these suggest the modeling field has a long way to go to provide effective assessment of its approaches, either to itself or to a broader audience, but that there are no technical reasons why progress cannot be made.     

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 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 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.     

Solid or liquid? Solidification of a nanoconfined liquid under nonequilibrium conditions

There has been a long-standing debate about the physical state and possible phase transformations of confined liquids. In this report, we show that a model-confined liquid can behave both as a Newtonian liquid with very little change in its dynamics and as a pseudosolid, depending solely on the rate of approach of the confining surfaces. Thus, the confined liquid does not exhibit any confinement-induced solidification in thermodynamic equilibrium. Instead, solidification is induced kinetically when the two confining surfaces are approached with a minimum critical rate. This critical rate is surprisingly slow (on the order of 6 A/s), explaining the frequent observation of confinement-induced solidification.