A comparison of the static SIMS and G‐SIMS spectra of biodegradable homo‐polyesters

Static SIMS (SSIMS) is a surface analytical technique capable of providing molecular chemical information from solids. A major barrier to the wider take‐up of the technique is the complexity associated with the interpretation of SSIMS spectra. Quality of the interpretation depends on the expertise of analysts and making references to the limited mass spectral libraries. For many materials, there are no SSIMS library spectra. A new library‐independent method, G‐SIMS, is capable of facilitating the interpretation of SSIMS data. G‐SIMS spectra contain parent fragments, which are formed without substantial degradation or rearrangements, and highlight molecular fragments, which are directly related to the surface. In our study, G‐SIMS has been tested on medically relevant biodegradable polyester series, including poly (glycolic acid) (PGA), poly‐l‐(lactic acid) (PLA), poly‐β‐(hydroxybutyrate) (PHB) and poly‐ε‐(caprolactone) (PCL). The polyester series chosen here have closely related structures, which allow us to explore the capabilities of G‐SIMS. The G‐SIMS spectra have facilitated the identification of different polyesters by exhibiting mainly characteristic ions, representative of the polymers' molecular structures. The results also indicated that for the chosen polyester series, the larger the repeating monomer structures, the smaller the maximum number of repeat units were seen in the G‐SIMS spectra. The G‐SIMS spectra for the homologous polyester series have provided an insight into the fragmentation mechanisms as a function of repeating monomer molecular weights and structures. Copyright © 2008 John Wiley & Sons, Ltd.     

Study of the end‐group contribution to ToF‐SIMS and G‐SIMS spectra of poly (lactic acid) using deuterium labelling

In this study, polymeric (MW 50 000) and oligomeric (MW 2000) poly (lactic acid) (PLA), both with and without end‐group deuterium exchange, were analysed using static secondary ion mass spectrometry (SSIMS) to investigate the contribution of end‐group‐derived secondary ions to the SSIMS spectra. By monitoring the SSIMS intensities between the non‐deuterated and deuterated PLA, it is evident that the only significant end‐group‐derived secondary ions are [nM + H]⁺ (n > 1) and C₄H₉O₂⁺. The gentle‐SIMS (G‐SIMS) methodology was employed to establish that deuterated fragments were produced through low energy processes and were not the result of substantial rearrangements. It was noted that end‐group‐derived secondary ions had higher G‐SIMS intensities for oligomeric PLA than polymeric PLA, showing that these secondary ions are simple fragment products that are not the result of rearrangement or degraded product ions. Copyright © 2007 John Wiley & Sons, Ltd.     

Static TOF‐SIMS. A VAMAS interlaboratory study. Part II — accuracy of the mass scale and G‐SIMS compatibility

An interlaboratory study involving 32 time‐of‐flight static SIMS instruments from 13 countries has been conducted. In Part I of the analysis of data, we showed that 84% of instruments have excellent repeatabilities of better than 1.9% and that a relative instrument spectral response (RISR) can be used to evaluate variations between different generic types of instrument. Use of the RISR improves comparability between instruments by a factor of 33. Here, in Part II, we study the accuracy of the mass scale calibration in TOF‐SIMS and evaluate instrument compatibility with G‐SIMS. We show that the accuracy of calibration of the mass scale is much poorer than generally expected (?60 ppm for peaks <200 u and ?150 ppm for a large molecular peak at 647 u). This is a major issue for analysts. Elsewhere, we have developed a detailed study of the factors affecting the mass calibration and have developed a generic protocol that improves accuracy by a factor of 5. Here, this framework of understanding is used to interpret the results presented. Furthermore, we show that eight out of the ten participants submitting data for G‐SIMS could use operating conditions that generated G‐SIMS spectra of the PC reference material. This demonstrates that G‐SIMS may be conducted with a wide variety of instrument designs. © Crown Copyright 2007. Reproduced by permission of the Controller of HMSO. Published by John Wiley & Sons, Ltd.     

Reduction of matrix effects in TOF‐SIMS analysis by metal‐assisted SIMS (MetA‐SIMS)

We investigated reduction of the matrix effect in time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) analysis by the deposition of a small amount of metal on the sample surfaces (metal‐assisted SIMS or MetA‐SIMS). The metal used was silver, and the substrates used were silicon wafers as electroconductive substrates and polypropylene (PP) plates as nonelectroconductive substrates. Irganox 1010 and silicone oil on these substrates were analyzed by TOF‐SIMS before and after silver deposition. Before silver deposition, the secondary ion yields from the substances on the silicon wafer and PP plate were quite different due to the matrix effect from each substrate. After silver deposition, however, both ion yields were enhanced, particularly the sample on the PP plate, and little difference was seen between the two substrates. It was therefore found that the deposition of a small amount of metal on the sample surface is useful for reduction of the matrix effect. By reducing the matrix effect using this technique, it is possible to evaluate from the ion intensities the order of magnitude of the quantities of organic materials on different substrates. In addition, this reduction technique has clear utility for the imaging of organic materials on nonuniform substrates such as metals and polymers. MetA‐SIMS is thus a useful analysis tool for solving problems with real‐world samples. Copyright © 2005 John Wiley & Sons, Ltd.     

Investigation of ionic liquids under Bi‐ion and Bi‐cluster ions bombardment by ToF‐SIMS

A systematic study of five different imidazolium‐based room temperature ionic liquids, 1‐butyl‐3‐methylimidazolium acetate, 1‐butyl‐3‐methylimidazolium nitrate, 1‐butyl‐3‐methylimidazolium iodide, 1‐butyl‐3‐methylimidazolium hexafluorophosphate and 1‐butyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide were carried out by means of time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) in positive and negative ion mode. The compounds were measured under Bi‐ion and Bi‐cluster ions (Bi_2–7⁺, Bi_{3, 5}²⁺) bombardment, and spectral information and general rules for the fragmentation pattern are presented. Evidence for hydrogen bonding, due to high molecular secondary cluster ions, could be found. Hydrogen bonding strength could be estimated by ToF‐SIMS via correlation of the anionic yield enhancement with solvent parameters. Copyright © 2010 John Wiley & Sons, Ltd.     

Base‐Pairing Directed Folding of a Bimolecular G‐Quadruplex: New Insights into G‐Quadruplex‐Based DNAzymes

Base pairs, magic hands : An additional base‐pairing duplex is utilized to control the folding topologies of a bimolecular G‐quadruplex formed by two G‐rich single‐stranded DNAs (see picture), which is dependent on the position of base pairs. This study clearly reveals an important intrinsic role of additional base pairs in the G‐quadruplex structure, and also provides a clue to the formation mechanism of the G‐quadruplex‐based DNAzyme.

     

Elucidating Noncovalent Reaction Mechanisms: G‐Quartet as an Intermediate in G‐Quadruplex Assembly

In analogy to covalent reactions, the understanding of noncovalent association pathways is fundamental to influence and control any supramolecular process. Following an approach that is reminiscent of covalent methodologies, we study here, for the first time, the mechanism of G‐quadruplex formation in organic solvents. Our results support a reaction pathway in which the cation shifts the equilibrium towards a G‐quartet transient intermediate, which then acts as a template in the formation of the G‐quadruplex product.     

Click Chemistry for the Identification of G‐Quadruplex Structures: Discovery of a DNA–RNA G‐Quadruplex

A trap that closes with a “click” : The copper‐catalyzed azide–alkyne cycloaddition can occur in different G‐quadruplex structures (see scheme). The species trapped by the click reaction can then be separated and analyzed. By using this approach, a DNA–RNA hybrid‐type G‐quadruplex structure formed by human telomeric DNA and RNA sequences was detected.

     

Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

We present the direct and single‐molecule visualization of the in‐pathway intermediates of the G‐quadruplex folding that have been inaccessible by any experimental method employed to date. Using DNA origami as a novel tool for the structural control and high‐speed atomic force microscopy (HS‐AFM) for direct visualization, we captured images of the unprecedented solution‐state structures of a tetramolecular antiparallel and (3+1)‐type G‐quadruplex intermediates, such as G‐hairpin and G‐triplex, with nanometer precision. No such structural information was reported previously with any direct or indirect technique, solution or solid‐state, single‐molecule or bulk studies, and at any resolution. Based on our results, we proposed a folding mechanism of these G‐quadruplexes.     

Extraction of hidden information of ToF‐SIMS data using different multivariate analyses

Time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) is a powerful tool for determining surface information of complex systems such as polymers and biological materials. However, the interpretation of ToF‐SIMS raw data is often difficult. Multivariate analysis has become effective methods for the interpretation of ToF‐SIMS data. Some of multivariate analysis methods such as principal component analysis and multivariate curve resolution are useful for simplifying ToF‐SIMS data consisting of many components to that explained by a smaller number of components. In this study, the ToF‐SIMS data of four layers of three polymers was analyzed using these analysis methods. The information acquired by using each method was compared in terms of the spatial distribution of the polymers and identification. Moreover, in order to investigate the influence of surface contamination, the ToF‐SIMS data before and after Ar cluster ion beam sputtering was compared. As a result, materials in the sample of multiple components, including unknown contaminants, were distinguished. Copyright © 2014 John Wiley & Sons, Ltd.     

TOF‐SIMS studies of yttria‐stabilised zirconia

The surface of an as‐polished and an as‐sintered yttria‐stabilised zirconia pellet was analysed with XPS and TOF‐SIMS (depth profiling and imaging) in order to study the distribution of impurities. The polished sample was slightly contaminated with Na, K, Mg and Ca. The sintered sample showed a thin surface film of segregated species, especially Na, Si and Al. Below the surface film, it was found that the grain boundaries were filled with impurities. The chemical compositions of the as‐polished and as‐sintered surfaces are very different and the surface state should be considered when performing electrochemical measurements. Copyright © 2006 John Wiley & Sons, Ltd.     

Inverting the G‐Tetrad Polarity of a G‐Quadruplex by Using Xanthine and 8‐Oxoguanine

G‐quadruplexes are four‐stranded nucleic acid structures that are built from consecutively stacked guanine tetrad (G‐tetrad) assemblies. The simultaneous incorporation of two guanine base lesions, xanthine (X) and 8‐oxoguanine (O), within a single G‐tetrad of a G‐quadruplex was recently shown to lead to the formation of a stable G?G?X?O tetrad. Herein, a judicious introduction of X and O into a human telomeric G‐quadruplex‐forming sequence is shown to reverse the hydrogen‐bond polarity of the modified G‐tetrad while preserving the original folding topology. The control exerted over G‐tetrad polarity by joint X?O modification will be valuable for the design and programming of G‐quadruplex structures and their properties.     

Ketene dithioacetals‐source for different heterocycles

Some pyrazoline, isoxazoline and pyrimidine derivatives were synthesized from ketene dithioacetals using appropriate nucleophiles.