Application of near-infrared spectra on temperature-controlled protein crystallization

Large, high-quality protein crystals are required for the structural determination of proteins via X-ray diffraction. In this article, we propose a technique to facilitate the production of such crystals and validate its feasibility through simulations. An analytical method for protein aqueous solution based on a Fourier transform infrared (FTIR) spectroscopy is combined with a temperature control strategy to manipulate the extent of supersaturation during crystal growth, thus impacting crystal quality. The technique requires minimal knowledge about the growth kinetics a priori. The simulations show that, under ideal conditions, the design can be as effective as predesigned temperature programs for crystallization based on known growth kinetics. Two kinds of errors might be encountered with this design. Error in the estimated number of seed crystals can result in a growth rate deviating from the desired one. Nevertheless, the deviation is usually tolerable and system instability is unlikely to occur. Based on the standard error of our FTIR method, errors in concentration measurement are simulated. Measurement error can result in system instability and impair the control algorithm. Such errors may be compensated by limiting the temperature change taken by the control action, or by improving the measurement precision through the use of regressed concentrations. Through simulations, it is shown that the proposed design is practical and represents a significant improvement over the commonly used isothermal crystallization technique.     

Tuning the size,concaveness, and aspect ratio of concave cubic gold nanoparticles produced with high reproducibility

Reproducible fabrication of concave cubic gold nanoparticles with precise control over size, concaveness, and aspect ratio is important because the nanoscale structural characteristics can influence their plasmonic and catalytic properties. However, this is particularly challenging because the number of synthetic parameters involved in the fabrication strategy adds complexity to the reaction mechanism. Here, we introduce a simplified seed-mediated method and uncover the unknown conceptual insights on how the different halides and their concentration influence the surface structure and stability of underpotential silver monolayer deposited on the high energy facets of nanoparticles. The results reveal that adding Br^? and I^? ions to growth solution offers a predominant way to control the reaction kinetics and engineering nanoparticles with a predefined size, morphology, concaveness, aspect ratio, and plasmonic properties. Using spectroscopy and microscopy techniques, we shed new light on the reaction kinetics of concave cubic gold nanoparticles using the combined influence of silver underpotential deposition and halides. The strategy developed here can be expanded to fabricate gold nanoparticles of complex geometries. The results from our electromagnetic calculations suggest that the self-assembled superstructure of concave cubic gold nanoparticles can be more appealing for developing an ultra-sensitive sensing platform than to self-assembled superstructures of truncated cubic gold nanoparticles.     

Visualizing energy landscapes with metric disconnectivity graphs

The visualization of multidimensional energy landscapes is important, providing insight into the kinetics and thermodynamics of a system, as well the range of structures a system can adopt. It is, however, highly nontrivial, with the number of dimensions required for a faithful reproduction of the landscape far higher than can be represented in two or three dimensions. Metric disconnectivity graphs provide a possible solution, incorporating the landscape connectivity information present in disconnectivity graphs with structural information in the form of a metric. In this study, we present a new software package, PyConnect, which is capable of producing both disconnectivity graphs and metric disconnectivity graphs in two or three dimensions. We present as a test case the analysis of the 69‐bead BLN coarse‐grained model protein and show that, by choosing appropriate order parameters, metric disconnectivity graphs can resolve correlations between structural features on the energy landscape with the landscapes energetic and kinetic properties. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Development of a methodology to predict material properties from environmental exposure. I. Kinetic treatment

This study focuses on bisphenol A polycarbonate and tracks changes in the properties of this material as a function of the degree of degradation, τ, induced by a hostile environment. Among many possible environmental effects, we have limited this investigation to those associated with elevated temperature, although the methodology is general. This τ parameter is a product of the kinetic rate constant, k, found from isothermal kinetics, and the time of degradation, t. The elucidation of τ has been linked to the measurement of the molecular weight distribution, which, in turn, can be related to various properties to yield valuable predictive relationships. Only the thermal history of the polymer and its initial properties are required for the model. This technique is not limited to a specific polymer or even to thermal degradation. As long as the kinetics of the process can be mathematically modeled, this approach should apply to a host of other situations, providing property prediction simply from knowledge of the material history. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 794–801, 2002     

Kinetics of Photoinduced Reactions at the Single-Molecule Level: The KACB Method

The kinetics of photoinduced reactions can be approached by laser flash photolysis techniques. Although such techniques allow for a detailed understanding of the important photophysics of molecules, they normally require a substantial amount of sample for measurements (>1 nmol), and thus, they are difficult to apply to analytical and diagnostic applications. The photophysics of a fluorescent molecule can be accessed by monitoring the kinetics of the fluctuation of fluorescence, which is called blinking. Blinking is a phenomenon that can be monitored only if molecules are observed at the single-molecule level. In bulk solution, blinking kinetics can be measured by using fluorescence correlation spectroscopy (FCS), which normally requires more than 10⁵ times less sample than that required for laser flash photolysis. Blinking is controlled to extract fruitful microenvironmental information around a fluorescent molecule, by using a method named kinetic analysis based on the control of fluorescence blinking (KACB). This Concept highlights the adaption of the KACB method to investigate the local conformation of DNA with less than 1 pmol of DNA sample.     

Binomial leap methods for simulating stochastic chemical kinetics

This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the tau-leap and midpoint tau-leap methods of Gillespie [D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001)], binomial random variables are used in these leap methods rather than Poisson random variables. The motivation for this approach is to improve the efficiency of the Poisson leap methods by using larger stepsizes. Unlike Poisson random variables whose range of sample values is from zero to infinity, binomial random variables have a finite range of sample values. This probabilistic property has been used to restrict possible reaction numbers and to avoid negative molecular numbers in stochastic simulations when larger stepsize is used. In this approach a binomial random variable is defined for a single reaction channel in order to keep the reaction number of this channel below the numbers of molecules that undergo this reaction channel. A sampling technique is also designed for the total reaction number of a reactant species that undergoes two or more reaction channels. Samples for the total reaction number are not greater than the molecular number of this species. In addition, probability properties of the binomial random variables provide stepsize conditions for restricting reaction numbers in a chosen time interval. These stepsize conditions are important properties of robust leap control strategies. Numerical results indicate that the proposed binomial leap methods can be applied to a wide range of chemical reaction systems with very good accuracy and significant improvement on efficiency over existing approaches.     

Slow adsorption reaction between arsenic species and goethite (alpha-FeOOH): diffusion or heterogeneous surface reaction control

The slow stage of phosphate or arsenate adsorption on hydrous metal oxides frequently follows an Elovich equation. The equation can be derived by assuming kinetic control by either a diffusion process (either interparticle or intraparticle) or a heterogeneous surface reaction. The aim of this study is to determine whether the slow stage of arsenic adsorption on goethite is more consistent with diffusion or heterogeneous surface reaction control. Adsorption kinetics of arsenate and dimethylarsinate (DMA) on goethite (alpha-FeOOH) were investigated at different pH values and inert electrolyte concentrations. Their adsorption kinetics was described and compared using Elovich (Gamma vs ln time) plots. Desorption of arsenate and DMA was studied by increasing the pH of the suspension from pH 4.0 to pH 10.0 or 12.0. The effective particle sizes and zeta-potential of goethite were also determined. Effective particle size increased rapidly as the pH approached pH(IEP), both in the absence and presence of arsenic. Inert electrolyte concentrations and pH had no effect on the slow stage of arsenate adsorption on goethite, while the kinetics of DMA adsorption on goethite was influenced by both parameters. The slow stage of arsenate adsorption on goethite follows an Elovich equation. Since effective particle size changes with both pH and inert electrolyte concentrations, and effective particle size influences interparticle diffusion, the arsenate adsorption kinetics indicate that the slow adsorption step is not due to interparticle diffusion. DMA also has complex adsorption kinetics with a slow adsorption stage. DMA desorbed completely and rapidly when the pH was raised, in contrast to the slow adsorption kinetics, indicating that the slow adsorption step is not due to intraparticle diffusion. The slow adsorption is not the result of diffusion, but rather is due either to the heterogeneity of the surface site bonding energy or to other reactions controlling arsenic removal from solution.     

Global study of myoglobin-surfactant interactions

Surfactants interact with proteins in multifarious ways which depend on surfactant concentration and structure. To obtain a global overview of this process, we have analyzed the interaction of horse myoglobin (Mb) with an anionic (SDS) and cationic (CTAC) surfactant, using both equilibrium titration techniques and stopped-flow kinetics. Binding and kinetics of conformational changes can be divided into a number of different regions (five below the cmc and one above) with very distinct features (broadly similar between the two surfactants, despite their difference in head group and chain length), which nuance the classical view of biphasic binding prior to micellization. In stage A, fairly weak interactions lead to a linear decrease in thermal stability. This gives way to a more cooperative process in stage B, where aggregates (presumably hemimicelles) start to form on the protein surface, leading to global denaturation (loss of a thermal transition) and biphasic unfolding kinetics. This is consolidated in stage C with titratable surfactant adsorption. Adsorption of this surfactant species leads to significant changes in kinetics, namely, inhibition of unfolding kinetics in CTAC and altered unfolding amplitudes in SDS, though the process is still biphasic in both surfactants. Stage D commences the reduction in exothermic binding signals, leading to further uptake of 5 (SDS) or 31 (CTAC) surfactant molecules without any major changes in protein conformation. In stage E many more surfactant molecules (46 SDS and 39 CTAC) are bound, presumably as quasi-micellar structures, and we observe a very slow unfolding phase in SDS, which disappears as we reach the cmc. Above the cmc, the unfolding rates remain essentially constant in SDS, but increase significantly in CTAC, possibly because binding of bulk micelles removes the inhibition by hemimicellar aggregates. Our work highlights the fascinating richness of conformational changes that proteins can undergo in the presence of molecules with self-assembling properties.     

Thermodynamic and electron-transfer properties of copper(II/I) polyaminothiaether complexes

In electron-transfer reactions, the change in the oxidation states of the reactants is generally accompanied by structural changes, which influence the electron-transfer kinetics. Previous studies on the systems of Cu(II)/(I) complexes involving cyclic tetrathiaether ligands indicated that inversion of coordinated donor atoms is a major geometric change during the overall electron-transfer process. Complex formation and isomerization studies on complexes with the 1,4,8,11-tetraazacyclotetradecane ligand have demonstrated that a necessary condition for conformational change is deprotonation followed by inversion of coordinated N atoms. When one or more nitrogen donor atoms in a ligand are replaced with sulfur, there is a choice of N or S inversion. It has been hypothesized that donor atom inversion (N or S donors) is a major factor that can lead to conformationally limited electron-transfer kinetics of copper systems. In the current study, the thermodynamic properties, electron-transfer kinetics and conformational changes in copper(II)[1,4,8-trithia-11-azacyclotetradecane], copper(II)[1,8-dithia-4,11-diazacyclotetradecane] and copper(II)[1,11,-dithia-4,8-diazacyclotetradecane] were determined in order to determine the effect of inversion of coordinated N atoms on electron-transfer rates as a function of low concentrations of water in an aprotic solvent (acetonitrile). By using controlled amounts of water as a hydrogen ion acceptor, deprotonation of amine nitrogen and nitrogen donor inversion was followed by comparing self-exchange rate constants for reduction and oxidation of the copper complexes. Data on thermodynamic properties and electron-transfer kinetics are presented. Possible conformational changes and kinetic pathways for complexes with ligands having mixed N and S donor sets are presented.     

Exploring the complexity of aerosol particle properties and processes using single particle techniques

The complex interplay of processes that govern the size, composition, phase and morphology of aerosol particles in the atmosphere is challenging to understand and model. Measurements on single aerosol particles (2 to 100 μm in diameter) held in electrodynamic, optical and acoustic traps or deposited on a surface can allow the individual processes to be studied in isolation under controlled laboratory conditions. In particular, measurements can now be made of particle size with unprecedented accuracy (sub-nanometre) and over a wide range of timescales (spanning from milliseconds to many days). The physical state of a particle can be unambiguously identified and its composition and phase can be resolved with a high degree of spatial resolution. In this review, we describe the advances made in our understanding of aerosol properties and processes from measurements made of phase behaviour, hygroscopic growth, morphology, vapour pressure and the kinetics of water transport for single particles. We also show that studies of the oxidative aging of single particles, although limited in number, can allow the interplay of these properties to be investigated. We conclude by considering the contributions that single particle measurements can continue to make to our understanding of the properties and processes occurring in atmospheric aerosol.     

Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping

We demonstrate the feasibility of a single-molecule microfluidic approach to both sequence detection and obtaining kinetic information for restriction endonucleases on dsDNA. In this method, a microfluidic stagnation point flow is designed to trap, hold, and linearize double-stranded (ds) genomic DNA to which a restriction endonuclease has been pre-bound sequence-specifically. By introducing the cofactor magnesium, we determine the binding location of the enzyme by the cleavage process of dsDNA as in optical restriction mapping, however here the DNA need not be immobilized on a surface. We note that no special labeling of the enzyme is required, which makes it simpler than our previous scheme using stagnation point flows for sequence detection. Our accuracy in determining the location of the recognition site is comparable to or better than other single molecule techniques due to the fidelity with which we can control the linearization of the DNA molecules. In addition, since the cleavage process can be followed in real time, information about the cleavage kinetics, and subtle differences in binding and cleavage frequencies among the recognition sites, may also be obtained. Data for the five recognition sites for the type II restriction endonuclease EcoRI on λ-DNA are presented as a model system. While the roles of the varying fluid velocity and tension along the chain backbone on the measured kinetics remain to be determined, we believe this new method holds promise for a broad range of studies of DNA-protein interactions, including the kinetics of other DNA cleavage processes, the dissociation of a restriction enzyme from the cleaved substrate, and other macromolecular cleavage processes.     

Effects of pretreatments and modifiers on electrochemical properties of carbon paste electrodes

The electrochemical properties of carbon paste electrodes (CPEs), including unmodified and modified with protein and polycations, were investigated by impedance spectroscopy (IS) using ferricyanide and ferrocene monocarboxylic acid (FcMA) as redox probes. Various electrochemical pretreatments were applied to the unmodified CPE. The heterogeneous charge transfer rate constant of ferro/ferricyanide couple is enhanced by 2 to 10 times compared with that obtained at untreated electrodes. It was found that for ferricyanide the more suitable pretreatments are successive cyclic voltammetric scans, cathodization and a square wave-like stepping rather than high-potential anodization. However, the pretreatment only exhibits a slight effect on the kinetics of FcMA. At the CPEs containing modifier, the electron transfer rate of the redox couple depends more on the pH of electrolyte solution if ferro/ferricyanide is used. The results can be explained by the differently charged states of the CPEs that were caused by the protonation or deprotonation of the modifiers in various pH solutions and demonstrate the importance of the electrostatic interaction on the kinetics of the highly polar species such as ferricyanide. The different adsorptive behavior of ferricyanide and FcMA is also discussed.     

Representation of terpolymer kinetics on triangular coordinates

The ideal steady-state kinetics of polymer formation from two or more monomeric species can be derived from basic rate equations by using the theory of discrete parameter Markov chains. Advantages are: (1) steady-state assumptions are not required; and (2) a particularly lucid graphical visulization is possible for the case where there are three monomeric species.     

Design of Multi-Metallic-Based Electrocatalysts for Enhanced Water Oxidation

Electrochemical water splitting by renewable energy resources is an efficient and green approach for hydrogen gas production. However, the anodic oxygen evolution reaction (OER) largely impedes the industrial application due to its sluggish four-electron-transition kinetics. Although various materials have been developed to accelerate the OER rate, still some issues should be addressed to meet the industrial demand: (i) considerable 200–300 mV overpotential as extra onset energy input, (ii) limited survival and performance in acidic electrolyte for the majority of oxide/hydroxide composite materials, (iii) unsatisfying long-term durability and (iv) the need for facile and scalable preparation methods. Here, we emphasize on multi-metallic composites with enhanced OER activity based on both precious and nonprecious elements that outperform the unary and binary composites. The regulation effect from multi-metal incorporation is also summarized systematically: (i) introducing foreign metal atoms to the host material boosts the physical properties such as conductivity, surface area, defect density, morphology, wettability, etc., (ii) metal doping can synergistically regulate the electronic features of the host material, e. g. oxygen vacancy, e_g orbit filling, coordinative number and covalence state, which can optimize the absorption/desorption energy of the M−O intermediate, (iii) chaotic impact from the added atoms twists the catalyst lattice into a more aggressive and higher energy state, which is more feasible to transform to an active intermediate with lower required energy supply. This review aims to provide a practical approach to further improve the OER performance via multi-metallic-based catalysts.     

Analysis of the nonisothermal crystallization kinetics in three linear aromatic polyester systems

Melt or cold crystallization kinetics has a strong bearing on morphology and the extent of crystallization, which significantly affects the physical properties of polymeric materials. Nonisothermal crystallization kinetics are often analyzed by the classical Johnson–Mehl–Avrami–Kolmogorov (JMAK) model or one of its variants, even though they are based on an isothermal assumption. As a result, during the nonisothermal (e.g. constant heating or cooling rate) crystallization of polymeric material, different sets of model parameters are required to describe crystallization at different rates, thereby increasing the total number of model parameters. In addition, due to the uncorrelated nature of these model parameters with the cooling or heating rate, accurate modeling at any intermediate condition is not possible. In the present work, these two limitations of the conventional approach have been eliminated by exhibiting the existence of a functional relationship between cooling or heating rate and effective activation energy during nonisothermal melt or cold crystallization in three linear aromatic polyesters. Furthermore, it has been shown that when the JMAK model is used in conjunction with this functional relationship, it is possible to precisely predict the experimental nonisothermal melt or cold crystallization kinetics at any linear cooling or heating rate with a single set of model parameters.     

Low-temperature synthesis of soluble and processable organic-capped anatase TiO2 nanorods

We demonstrate the controlled growth of high aspect ratio anatase TiO2 nanorods by hydrolysis of titanium tetraisopropoxide (TTIP) in oleic acid (OLEA) as surfactant at a temperature as low as 80 degrees C. Chemical modification of TTIP by OLEA is proven to be a rational strategy to tune the reactivity of the precursor toward water. The most influential factors in shape control of the nanoparticles are investigated by simply manipulating their growth kinetics. The presence of tertiary amines or quaternary ammonium hydroxides as catalysts is essential to promote fast crystallization under mild conditions. The novelty of the present approach relies on the large-scale production of organic-capped TiO2 nanocrystals to which standard processing of colloidal nanocrystals, such as surface ligand exchange, can be applied for the first time. Concentrated colloidal titania dispersions can be prepared for a number of fundamental studies in homogeneous solutions and represent a new source of easily processable oxide material for many technological applications.     

Activated ion electron capture dissociation (AI ECD) of proteins: Synchronization of infrared and electron irradiation with ion magnetron motion

Here, we show that to perform activated ion electron capture dissociation (AI-ECD) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a CO₂ laser, it is necessary to synchronize both infrared irradiation and electron capture dissociation with ion magnetron motion. This requirement is essential for instruments in which the infrared laser is angled off-axis, such as the Thermo Finnigan LTQ FT. Generally, the electron irradiation time required for proteins is much shorter (ms) than that required for peptides (tens of ms), and the modulation of ECD, AI ECD, and infrared multiphoton dissociation (IRMPD) with ion magnetron motion is more pronounced. We have optimized AI ECD for ubiquitin, cytochrome c, and myoglobin; however the results can be extended to other proteins. We demonstrate that pre-ECD and post-ECD activation are physically different and display different kinetics. We also demonstrate how, by use of appropriate AI ECD time sequences and normalization, the kinetics of protein gas-phase refolding can be deconvoluted from the diffusion of the ion cloud and measured on the time scale longer than the period of ion magnetron motion.     

Hydride-Based Separation Materials for High Performance Liquid Chromatography and Open Tubular Capillary Electrochromatography

 Silica hydride is a recent development in chromatographic support materials for high performance liquid chromatography (HPLC) where hydride groups replace 95% of the silanols on the surface. This conversion changes many of the fundamental properties of the material as well as the bonded stationary phases that are the result of further chemical modification of the hydride surface. Some unique chromatographic properties of hydride-based phases are described as well as some general application areas where these bonded materials may be used in preference to or have advantages not available from typical stationary phases. The fabrication, properties and applications of etched chemically modified capillaries for electrophoretic analysis are also reviewed. It is shown that the etching process creates a surface that is fundamentally different than a bare fused silica capillary. The new surface matrix produces unique electroosmotic flow properties and is more compatible with basic and biological compounds. After chemical modification of the surface, the bonded organic moiety (stationary phase) contributes to the control of migration of solutes in the capillary. Both electrophoretic and chromatographic processes take place in the etched chemically modified capillaries leading to a variety of experimental variables that can be used to optimize separations. A number of examples of separations on these capillaries are described.     

Gas-phase ion-molecule reactions of transition metal complexes: the effect of different coordination spheres on complex reactivity

Using a modified quadrupole ion trap mass spectrometer, a series of metal complex ions have been reacted with acetonitrile in the gas phase. Careful control of the coordination number and the type of coordinating functionality in diethylenetriamine-substituted ligands enable the effects of the coordination sphere on metal complex reactivity to be examined. The association reaction kinetics of acetonitrile with these pentacoordinate complexes are followed in order to obtain information about the starting complexes and the reaction dynamics. The kinetics and thermodynamics of acetonitrile addition to the metal complex ions are strongly affected by the chemical environment around the metal center such that significant differences in reactivity are observed for Co(II) and Cu(II) complexes with various coordination spheres. When thiophene, furan, or benzene moieties are present in the coordination sphere of the complex, addition of two acetonitrile molecules is readily observed. In contrast, ligands with better sigma donors react mainly to add one acetonitrile molecule. Among the ligands with good sigma donors, a clear trend in reactivity is observed in which complexes with nitrogen-containing ligands are the least reactive, sulfur-containing complexes are more reactive, and oxygen-containing complexes are the most reactive. In general, equilibrium and reaction rate constants seem to be consistent with the hard and soft acid and base (HSAB) principle. Interestingly, the presence of certain groups (e.g., pyridine and imidazole) in the coordination sphere clearly can change the acid character of the metal as seen by their effect on the binding properties of other functional groups in the same ligand. Finally, we conclude that because complexes with different coordination spheres react to noticeably different extents, ion-molecule (I-M) reactions may be potentially useful for obtaining coordination structure information for transition metal complexes.     

Understanding dynamic disorder fluctuations in single-molecule enzymatic reactions

Single-molecule studies of enzymatic reactions reveal fluctuations in the reaction rate, which cannot be explained by classic Markovian dynamics. This dynamic disorder is attributed to slow transitions in enzyme conformations that take place over timescales longer than reaction cycle times. In this review we summarize current theoretical models for reaction kinetics in fluctuating, single enzyme systems. Also examined are some of the implications of single-molecule fluctuations for reaction rates in systems such as cells or biosensors that contain a moderate number of molecular copies. We conclude that the dynamic disorder in single-molecule enzyme systems is well-described by available models. However, more work is required to study the effect of single-molecule fluctuations on finite systems over limited periods of time.