A review of advances in two-dimensional thin-layer chromatography

Although there are many simple thin-layer chromatography (TLC) separations, many more are complex and involve more than a few components, that means having to use special high-performance TLC (HPTLC) plates or microspotting or banding devices to increase its resolving power if developing in only one direction. However, adding a second development to perform two-dimensional TLC (2D TLC) allows even better resolution of complex samples. This is because different modes of chromatography are being invoked by the use of one stationary phase with two mobile phases, bilayer plates, graft TLC, or multidimensional TLC. This paper is a review of recent applications that have benefitted from using 2D TLC in its various forms. They were chosen for their variety of sample types as well as the unique choices of plates and/or mobile phases made by the researchers to yield improved separations.     

Linear compartmental systems. I. kinetic analysis and derivation of their optimized symbolic equations

The study of many biological systems requires the application of a compartmental analysis, together with the use of isotopic tracers, parameter identification and methods to evaluate the mean parameters. For all this, the kinetic equations of the compartmental system as a function of its parameters are needed. In this paper, we present some considerations on the diagrams of connectivity of linear compartmental systems and obtain new properties from the matrix corresponding to the ordinary first-order linear differential equation systems which describe their kinetic behaviour. Using these properties, symbolic equations are obtained in a simplified form. These equations provide the instantaneous amount of substance in any compartment of the system when zero input is injected into one or more of the system compartments, solely as a function of those parameters of compartmental systems which really have an influence on the sought expression. This is unlike what happens in the other symbolic equations obtained in a previous contribution that included all the fractional transfer coefficients involved in the compartmental system, regardless of whether or not they had an influence on the instantaneous amount of substance.     

[2+2] Photodimerization of Stilbazoles Promoted by Oxalic Acid in Suspension

In this study, a very simple technique to perform efficiently photodimerization of some vinylpyridines is reported. By irradiating a stirred mixture of several stilbazoles with solid oxalic acid dihydrate dispersed in a nonpolar (i.e., cyclohexane) or moderately polar (benzene, dichloromethane, dioxane) solvent, the corresponding dimeric cyclobutane adducts were obtained in high yields and excellent regio- and stereoselectivities. The strategy could also be applied successfully to oily, waxy, or even insoluble stilbazoles. Moreover, the oxalic acid loading could be lowered to substoichiometric amounts. When further optimizations were needed, our strategy was found to be highly flexible to identify other oligocarboxylic acids as alternative additives to improve, or even overturn, the regioselectivity. Oxalic acid and other oligocarboxylic acids were found to be capable of orienting more than 50 stilbazoles toward photodimerization under these conditions.     

Classification of byzantine glass samples by the use of different chemical component features

Summary An attempt is made to perform a classification of a small data set (nine unique Byzantine glass samples) by the use of different chemical component features (all components, major components, minor metallic components and colouring components). The strategy applied was cluster analysis (average and single linkage, centroid linkage). The classification using different variables has indicated that some samples have a more special position in the sample set than required by the traditional approaches of determination of similarities or dissimilarities between samples.

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Klassifizierung von byzantinischen Glasproben mit Hilfe verschiedenartiger chemischer Komponenten

     

DNA Repair by the Radical SAM Enzyme Spore Photoproduct Lyase: From Biochemistry to Structural Investigations

Radical S‐adenosyl‐L‐methionine (SAM) enzymes have emerged as one of the last superfamilies of enzymes discovered to date. Arguably, it is the most versatile group of enzymes involved in at least 85 biochemical transformations. One of the founding members of this enzyme superfamily is the spore photoproduct (SP) lyase, a DNA repair enzyme catalyzing the direct reversal repair of a unique DNA lesion, the so‐called spore photoproduct, back into two thymidine residues. Discovered more than 20 years ago in the bacterium Bacillus subtilis, SP lyase has been shown to be widespread in the endospore‐forming Firmicutes from the Bacilli and Clostridia classes and to use radical‐based chemistry to perform C‐C bond breakage, a chemically challenging reaction. This review describes how the work on SP lyase has illuminated a unique strategy for DNA repair and provided major advances in our understanding of the emerging radical SAM superfamily of enzymes, from a biochemical and structural perspective.     

Computerized evaluation of mean residence times in multicompartmental linear system and pharmacokinetics

Deriving mean residence times (MRTs) is an important task both in pharmacokinetics and in multicompartmental linear systems. Taking as starting point the analysis of MRTs in open or closed (Garcia-Meseguer et al., Bull Math Biol 2003, 65, 279) multicompartmental linear systems, we implement a versatile software, using the Visual Basic 6.0 language for MS-Windows, that is easy to use and with a user-friendly format for the input of data and the output of results. For any multicompartmental linear system of up to 512 compartments, whether closed or open, with traps or without traps and with zero input in one or more of the compartments, this software allows the user to obtain the symbolic expressions, in the most simplified form, and/or the numerical values of the MRTs in any of its compartments, in the entire system or in a part of the system. As far as we known from the literature, such a software has not been implemented before. The advantage of the present software is that it reduces on the work time needed and minimizes the human errors that are frequent in compartmental systems even those that are relatively staightforward. The software bioCelTer, along with instructions, can be downloaded from http://oretano.iele-ab.uclm.es/~fgarcia/bioCelTer/.     

Electrochromic smart windows: energy efficiency and device aspects

This paper covers three aspects of electrochromic smart windows. Their energy efficiency is discussed, and it is argued that a control strategy considering whether a room is in use or not can lead to large savings of the energy needed for space cooling. With regard to durability, it is shown that chemical compatibility between the electrolyte and electrochromic films of tungsten oxide and nickel oxide can be achieved without loss of optical transparency. Finally, we consider device manufacturability and present data on precharging of electrochromic nickel oxide films by ozone treatment. Electronic Publication     

Inosine in Neurodegenerative Diseases: From the Bench to the Bedside

Neurodegenerative diseases, such as Alzheimer′s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS), currently represent major unmet medical needs. Therefore, novel therapeutic strategies are needed in order to improve patients’ quality of life and prognosis. Since oxidative stress can be strongly involved in neurodegenerative diseases, the potential use of inosine, known for its antioxidant properties, in this context deserves particular attention. The protective action of inosine treatment could be mediated by its metabolite urate. Here, we review the current preclinical and clinical studies investigating the use of inosine in AD, PD, ALS, and MS. The most important properties of inosine seem to be its antioxidant action and its ability to raise urate levels and to increase energetic resources by improving ATP availability. Inosine appears to be generally safe and well tolerated; however, the possible formation of kidney stones should be monitored, and data on its effectiveness should be further explored since, so far, they have been controversial. Overall, inosine could be a promising potential strategy in the management of neurodegenerative diseases, and additional studies are needed in order to further investigate its safety and efficacy and its use as a complementary therapy along with other approved drugs.     

Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.     

A first approach using micellar electrokinetic capillary chromatography for the determination of fipronil and fipronil-sulfone in eggs

Fipronil is an insecticide that is not approved in the European Union in food. In 2017, fipronil was involved in a European health alert due to its presence in fresh hen eggs because of an illicit use in poultry farms, so reliable methods are needed to determine fipronil and its main metabolites in these matrixes. In this work, we report the first approach to the study of fipronil and two metabolites, fipronil-sulfone and fipronil-sulfide by CE. MEKC mode was employed using a solution of 50 mM ammonium perfluorooctanoate pH 9.0 with 10% (v/v) methanol as background electrolyte. The proposed method was combined with a simple sample treatment based on salting-out assisted LLE (SALLE) using acetonitrile as extraction solvent and ammonium sulfate as salt. The SALLE–MEKC–UV method allowed the simultaneous quantification of fipronil and fipronil-sulfone. Validation parameters yielded satisfactory results, with precision, expressed as relative SD, below 14% and recoveries higher than 83%. Limits of detection were 90 µg/kg for fipronil and 150 µg/kg for fipronil-sulfone, so in terms of sensitivity further studies of sample treatments allowing extra preconcentration or the use of more sensitive detection, such as MS, would be needed.     

Improving the visualization of the Pareto-optimal front for the multi-response optimization of chromatographic determinations

The paper shows tools to visualize and more easily interpret the effect that some experimental factors may exert on analytical responses of interest when optimization of several responses is needed.It is based on an adaptation of the parallel coordinate plot, a tool for graphical representation of points in multidimensional spaces that, theoretically and contrary to the usual Cartesian plots, does not have limits in the dimension of the points being depicted.The joint use of the Pareto-optimal solutions and their visualization allows a deeper knowledge about the problem at hand as well as the wise selection of the conditions of experimental factors for achieving specific goals about the responses.Although the methodology is for a general use, the procedure, its interpretation and usefulness is shown with several analytical cases in chromatography. The first one refers to the experimental conditions to obtain simultaneously the maximum allowable area for both the peak of the malachite green and its metabolite leucomalachite green in fish by liquid chromatography with tandem mass spectrometry detection (LC–MS/MS). The second one is about the simultaneous determination of steroid hormones estrone and 17-α-ethinylestradiol by gas chromatography–mass spectrometry (GC/MS). In the last case, the chromatographic separation by GC/MS of the diastereoisomers, α- and β-estradiol is needed taking into account that these hormones have the same mass fragments.     

基于侧向磁泳的微流控芯片对两种磁性纳米球的同时分选

基于磁性纳米球在微流控芯片上的侧向磁泳,利用微流控芯片分选了不同磁响应性的磁球.提出了包含磁性纳米球聚集与偏移的理论模型,用于分析磁球在芯片上的侧向位移.在理论分析的基础上设计了芯片系统,使不同磁响应性的磁纳米球可以在芯片系统上依次被分选.实验结果表明,2种磁性纳米球的分选效率均可接受,且实验操作简单;磁响应性强的磁球可被完全分离,这对于珍贵分析样品的分选很有价值.该分选系统被成功用于同时分选样品中乙型肝炎病毒的DNA与丙型肝炎病毒的反转录DNA,在生化分析中具有广阔的应用前景.     

Molecular Dynamics Simulations in Designing DARPins as Phosphorylation-Specific Protein Binders of ERK2

Extracellular signal-regulated kinases 1 and 2 (ERK1/2) play key roles in promoting cell survival and proliferation through the phosphorylation of various substrates. Remarkable antitumour activity is found in many inhibitors that act upstream of the ERK pathway. However, drug-resistant tumour cells invariably emerge after their use due to the reactivation of ERK1/2 signalling. ERK1/2 inhibitors have shown clinical efficacy as a therapeutic strategy for the treatment of tumours with mitogen-activated protein kinase (MAPK) upstream target mutations. These inhibitors may be used as a possible strategy to overcome acquired resistance to MAPK inhibitors. Here, we report a class of repeat proteins—designed ankyrin repeat protein (DARPin) macromolecules targeting ERK2 as inhibitors. The structural basis of ERK2–DARPin interactions based on molecular dynamics (MD) simulations was studied. The information was then used to predict stabilizing mutations employing a web-based algorithm, MAESTRO. To evaluate whether these design strategies were successfully deployed, we performed all-atom, explicit-solvent molecular dynamics (MD) simulations. Two mutations, Ala → Asp and Ser → Leu, were found to perform better than the original sequence (DARPin E40) based on the associated energy and key residues involved in protein-protein interaction. MD simulations and analysis of the data obtained on these mutations supported our predictions.     

SynCar: an approach to automated synthesis

The automation of all aspects of manual solution-phase synthesis into one integrated, efficient, and reliable system could be regarded as something of an unmet challenge in organic chemistry. The requirements for modern solution-phase libraries in mainstream drug discovery is typically 50-250 high-purity compounds on a 10-100-mg scale, whether for target class libraries or lead optimization, and short cycle time in combination with high capacity is critical. To achieve these goals, in a codevelopment between Aventis and Accelab GmbH, Kusterdingen, Germany, we designed a completely novel system of independent workstations connected by a shuttle transfer system produced by Montech, Derendingen, Switzerland. Seven modular workstations process four reactions on each shuttle in parallel, with the ability to perform synthesis (temperature control and liquid reagent handling), filtration, liquid-liquid extraction, evaporation, weighing, solid-phase extraction, and HPLC/MS analysis. The modular design enables the continuous loading of shuttles at any time, and each shuttle can have its own workflow. The design also allows easy expansion for future needs. The result is a combination of high flexibility and high throughput.     

Photolithography-free fabrication of photoresist-mold for rapid prototyping of microfluidic PDMS devices

Traditional soft lithography based PDMS device fabrication requires complex procedures carried out in a clean room. Herein, we report a photolithography-free method that rapidly produces PDMS devices in 30 min. By using a laser cutter to ablate a tape, a male photoresist mold can be obtained within 5 min by a simple heating-step, which offers significant superiority over currently used photolithographybased method. Since it requires minimal energy to cut the tape, our fabrication strategy shows ...     

Imidazotetrazines as Weighable Diazomethane Surrogates for Esterifications and Cyclopropanations

Diazomethane is one of the most versatile reagents in organic synthesis, but its utility is limited by its hazardous nature. Although alternative methods exist to perform the unique chemistry of diazomethane, these suffer from diminished reactivity and/or correspondingly harsher conditions. Herein, we describe the repurposing of imidazotetrazines (such as temozolomide, TMZ, the standard of care for glioblastoma) for use as synthetic precursors of alkyl diazonium reagents. TMZ was employed to conduct esterifications and metal‐catalyzed cyclopropanations, and results show that methyl ester formation from a wide variety of substrates is especially efficient and operationally simple. TMZ is a commercially available solid that is non‐explosive and non‐toxic, and should find broad utility as a replacement for diazomethane.     

Analysis of lipid peroxidation kinetics. 1. Role of recombination of alkyl and peroxyl radicals

The kinetics of the lipid peroxidation reaction is only partly understood. Although the set of reactions constituting the overall reaction are believed to be known, it has not been possible to predict how the reaction will respond to a change of one or more of the parameters, e.g., initial concentrations of reactants or different ways of initiating the reaction, nor has it been possible to predict the time dependence of the products. The reason for these problems is the complicated structure of the kinetic scheme, which includes a chain reaction. In this work we perform an in-depth analysis of the importance of the individual reaction steps, and we introduce a new quasi-stationary concentration method based on the assumption that one or more concentrations vary much slower than the others. We show that it is justified to use a quasi-stationary concentration approximation for the alkyl radical L (*), but not for the peroxyl radicals LO 2 (*) as assumed in previous works. The method allows us to derive manageable analytical expressions. On the basis of literature values of the rate constants, we are able to introduce specific simplifications that allow us to obtain simple analytical expressions for the time dependence of all concentrations involved in the process.     

Induced in-source fragmentation for the selective detection of organic bound iodine by liquid chromatography/electrospray mass spectrometry

The detection of unknown organic compounds, e.g., transformation products of known trace pollutants in environmental samples, is a difficult task which can be simplified if the compounds of interest are characterized by a functional group or a heteroatom which can selectively be detected. For the detection of iodinated benzene derivatives, used as X-ray contrast media, we have studied whether such compounds can be selectively detected by negative ion (NI) electrospray ionization via iodide as a product ion of in-source fragmentation, generated by applying a high cone voltage. It was found that selective detection of iodinated benzene derivatives is possible by liquid chromatography/negative ion electrospray ionization (LC/NI-ESI) if the compounds are destroyed before entering the mass spectrometer. To our knowledge this is the first report of the use of NI in-source fragmentation MS for analyses traditionally performed with inductively coupled plasma (ICP)-MS. The novel application of NI in-source fragmentation MS is a tool for those who do not possess the facilities to perform ICP-MS. Furthermore, NI-ESI at varying cone voltages provides both structural information and elemental detection, whereas ICP-MS can only provide elemental detection.     

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black‐box method that is easily applied, but requires careful set‐up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work‐protocols developed in our groups for running successful QM/MM calculations.