Micellar catalysis by perfluorooctanoic acid

Rates of acidic hydrolysis of hexano-, octano-, and decanohydroxamic acids and of 4-bromophenylaceto- and phenylacetohydroxamic acids have been determined in aqueous perfluorooctanoic acid—a reactive counterion surfactant system. Typical micellar catalysis was observed for the hydrolyses of the n-alkyl hydroxamic acids but not for the arylacetohydroxamic acids. The Arrhenius activation energy for hydrolysis of octano-hydroxamic acid is smaller above the cmc of the surfactant than it is below the cmc.     

Titration of mixtures of acids of nearly equal strengths

Accurate and precise experimental methods that were developed for the purpose of determining stability constants in aqueous solutions are employed in titrations of acids which have nearly equal strengths. A computer program capable of handling five acids simultaneously has been designed to evaluate the titration data. The results show that it is possible to determine two acids which have stability constants differing by only about one logarithmic unit with an accuracy better than 1%. If the conditions are favourable, it is even possible to analyse a mixture of two acids with about 2% accuracy when the constants differ by as little as 0.2 logarithmic units.     

Protein alignment: Exact versus approximate. An illustration

We illustrate solving the protein alignment problem exactly using the algorithm VESPA (very efficient search for protein alignment). We have compared our result with the approximate solution obtained with BLAST (basic local alignment search tool) software, which is currently the most widely used for searching for protein alignment. We have selected human and mouse proteins having around 170 amino acids for comparison. The exact solution has found 78 pairs of amino acids, to which one should add 17 individual amino acid alignments giving a total of 95 aligned amino acids. BLAST has identified 64 aligned amino acids which involve pairs of more than two adjacent amino acids. However, the difference between the two outputs is not as large as it may appear, because a number of amino acids that are adjacent have been reported by BLAST as single amino acids. So if one counts all amino acids, whether isolated (single) or in a group of two and more amino acids, then the count for BLAST is 89 and for VESPA is 95, a difference of only six. © 2015 Wiley Periodicals, Inc.     

氨基苯磺酸和氨基萘磺酸在反相离子对色谱和离子色谱中分离行为的比较

本文考察了氨基苯磺酸和氨基萘磺酸染料中间体在反相离子对色谱和离子色谱中的分离行为，结果表明一些异构体在反相色谱中的保留顺序与离子色谱中的顺序发生颠倒。静电作用力在离子色谱中对保留值的贡献比在反相离子对色谱中对保留值的贡献要大，而疏水作用力在反相离子对色谱中对保留值的贡献却较在离子色谱中对保留值的贡献要大。离子对色谱更有利于有机离子的分离分析。     

Acidimétrie dans les solvants organiques

The relative strengths of acids vary from one solvent to another according to the value of the dielectric constant and the acidic or basic properties of the solvent.Some simple rules explain in a rational manner all the known acidimetric reactions in organic solvents 1. The relative strength of uncharged acids (HF, HNO₂, R.COOH) remains constant, that of acids charged positively (NH₄+), salts of amines and hydrated cations such as Al(H₂O)₃⁴⁺ increases, and that of acids charged negatively (acid salts of diacids, etc.) decreases with decreasing dielectric constant of the solvent.However, for values of this constant below twenty the relative strength of positively charged acids no longer varies, while that of negatively charged acids tends to increase. 2. If the solvent has acidic or basic properties, there cannot exist in solution acids or bases stronger than the solvent itself that is, the range of strengths of the acids is limited as compared with what it is in an inert solvent.These rules allow of prediction of the strength of acids in a given solvent and consequently , of the determinations which can be carried out in it.     

Silver-catalyzed decarboxylative chlorination of aliphatic carboxylic acids

Decarboxylative halogenation of carboxylic acids, the Hunsdiecker reaction, is one of the fundamental functional group transformations in organic chemistry. As the initial method requires the preparations of strictly anhydrous silver carboxylates, several modifications have been developed to simplify the procedures. However, these methods suffer from the use of highly toxic reagents, harsh reaction conditions, or limited scope of application. In addition, none is catalytic for aliphatic carboxylic acids. In this Article, we report the first catalytic Hunsdiecker reaction of aliphatic carboxylic acids. Thus, with the catalysis of Ag(Phen)(2)OTf, the reactions of carboxylic acids with t-butyl hypochlorite afforded the corresponding chlorodecarboxylation products in high yields under mild conditions. This method is not only efficient and general, but also chemoselective. Moreover, it exhibits remarkable functional group compatibility, making it of more practical value in organic synthesis. The mechanism of single electron transfer followed by chlorine atom transfer is proposed for the catalytic chlorodecarboxylation.     

Use of Flow-Injection Conductometry of Strong and Weak Protolytes in Solutions Containing Amino Acids

Based on the results of systematic studies, it was demonstrated that flow-injection conductometry can be used in solutions containing amino acids for the determination of low concentrations of strong and weak acids and bases. For the analysis of aqueous and organic solutions, it was proposed to use protolytic reactions of zwitterionic forms of some amino acids as highly sensitive and universal reagents.     

Recovery Techniques Enabling Circular Chemistry from Wastewater

In an era where it becomes less and less accepted to just send waste to landfills and release wastewater into the environment without treatment, numerous initiatives are pursued to facilitate chemical production from waste. This includes microbial conversions of waste in digesters, and with this type of approach, a variety of chemicals can be produced. Typical for digestion systems is that the products are present only in (very) dilute amounts. For such productions to be technically and economically interesting to pursue, it is of key importance that effective product recovery strategies are being developed. In this review, we focus on the recovery of biologically produced carboxylic acids, including volatile fatty acids (VFAs), medium-chain carboxylic acids (MCCAs), long-chain dicarboxylic acids (LCDAs) being directly produced by microorganisms, and indirectly produced unsaturated short-chain acids (USCA), as well as polymers. Key recovery techniques for carboxylic acids in solution include liquid-liquid extraction, adsorption, and membrane separations. The route toward USCA is discussed, including their production by thermal treatment of intracellular polyhydroxyalkanoates (PHA) polymers and the downstream separations. Polymers included in this review are extracellular polymeric substances (EPS). Strategies for fractionation of the different fractions of EPS are discussed, aiming at the valorization of both polysaccharides and proteins. It is concluded that several separation strategies have the potential to further develop the wastewater valorization chains.     

Ester‐Mediated Amide Bond Formation Driven by Wet–Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth

Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α‐amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α‐hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α‐hydroxy acids and α‐amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long‐standing hypothesis that peptides might have arisen from ester‐based precursors.     

Lysergic acids. II. Isolation and separation of lysergic acids (author's transl)]

During studies on the isolation of both lysergic acids, D-and D-iso-, from hydrolytic mixtures of ergot alkaloids, it became necessary to find a simple chromatographic system for column isolation of lysergic acids. The column with controlled pore glass is highly effective for these purposes. The separation of both isomeric lysergic acids occurs on the column with silica gel. The assay and the composition of lysergic acid are estimated by thin-layer chromatography on precoated plates.     

Chiral capillary electrophoresis-mass spectrometry of amino acids in foods

In this work, the development of a new chiral capillary electrophoresis-mass spectrometry (CE-MS) method to separate D- and L-amino acids is shown. On-line coupling between CE and MS is established through an electrospray-coaxial sheath flow interface. Enantiomer separation is achieved by using a cheap, nonvolatile, chiral selector as beta-cyclodextrin in the background electrolyte (BGE) together with a physically coated capillary that is aimed to prevent contamination of the electrospray. The capillary coating is simple and easy to obtain as it only requires flushing of the capillary with a polymer aqueous solution for 3 min. Optimization of CE parameters (pH of BGE, type and concentration of chiral selector, and capillary inner diameter) and electrospray-MS parameters (nature and flow rate of the sheath liquid, nebulizer pressure) is carried out. Two different derivatization protocols of amino acids using dansyl chloride (DNS) and fluorescein isothiocyanate (FITC) are compared in terms of MS sensitivity and chiral resolution. Under optimum CE-MS conditions it is observed that the MS sensitivity obtained for FITC- and DNS-amino acids is similar (with limit of detection (LOD) in the microM range, corresponding to amounts injected in the fmol range) while chiral resolution is better for FITC-amino acids. The optimized method is demonstrated to provide the simultaneous analysis of 15 selected amino acids (i.e., FITC-D/L-Asp, -Glu, -Ser, -Asn, -Ala, -Pro, -Arg, and FITC-gamma-aminobutyric acid (GABA) in a single chiral CE-MS run, corresponding to the main amino acids that can be found in orange. Moreover, as a result of the high resolution achieved, it is possible to detect down to 2% of D-Asp in the presence of 98% of L-Asp. The good possibilities of chiral CE-MS in food analysis are corroborated through the detection of the main amino acids in a commercial orange juice (i.e., FITC-L-Asp, -Glu, -Ser, -Asn, -Pro, -Arg, and the nonchiral FITC-GABA) as well as the determination of the fraudulent addition of synthetic amino acids (containing D- and L-forms) to a fresh orange juice.     

Thermodynamics and the mechanism of interaction of adenine with amino acids in water

Two groups of amino acids, which react differently with adenine, are distinguished. In the case of nonpolar and aliphatic amino acids, the endothermic effect of dehydration plays a decisive role, while in the case of aromatic, polar, and charged amino acids the exothermic effect of interaction with adenine is dominant. Associates of Ade with Lys. HCl, His, Trp, Asp, and Glu were found. It was demonstrated that the complex-forming ability of purines (Ade and Caf) is higher than that of pyrimidines. Based on the linear enthalpy-entropy compensation effect for complexes of amino acids with adenine, it was suggested that the hydration state of interacting molecules contributes significantly to interactions of Ade with amino acids.     

Decomposition of thiazolidines in acidic and basic solution : Spectroscopic evidence for Schiff base intermediates

Stability of thiazolidine-4-carboxylic acids and chain tautomerism are studied in acidic, basic and neutral solution. In acidic solution aliphatic substituted thiazolidine-4-carboxylic acids are stable, but aromatic substituted thiazolidine-4-carboxylic acids decompose to the mercaptal if there is not steric inhibition. Mercaptal formation establishes the presence of tautomerism because it is the only pathway through which thiol can be provided for in the reaction. It is suggested that this reaction may proceed through a sulfonium ion intermediate. In neutral solution aliphatic substituted thiazolidine-4-carboxylic acids are stable. In strongly basic solution both aromatic and aliphatic substituted thiazolidine-4-carboxylic acids decompose to the aldehyde and the aminothiol. By adjusting the base concentration, the intermediate imine is detected by α-hydrogen exchange for aliphatic systems and by line broadening or direct NMR observation of the ArCH=N proton resonance in aromatic systems.     

Development and validation of a hydrophilic interaction ultra‐high‐performance liquid chromatography with triple quadrupole MS/MS for the absolute and relative quantification of amino acids in Sophora alopecuroides L.†

Amino acids are naturally occurring compounds in many edible or medicinal plants, which possess a variety of pharmacological effects on humans. The aim of this study is to develop and validate a hydrophilic interaction LC coupled with MS/MS method for the absolute and relative quantification of amino acids without derivatization. The application of this method has been proven through 20 naturally occurring amino acids in 21 samples from different parts and phenological growth stage of Sophora alopecuroides. The method was performed on an ultra‐high performance LC separation system coupled with ESI‐MS on a triple quadrupole mass spectrometer. The proposed absolute quantitative method was fully validated in terms of linearity, sensitivity, precision, repeatability as well as recovery. The analysis results showed that S. alopecuroides is rich in free amino acids. In addition, relative quantitative determination of amino acids with several amino acids selected for the best accuracy was investigated. The accuracies of relative quantitative method for amino acids determinations suggest that it is feasible to quantify amino acids by the proposed relative quantitative determination method, which contributes to breaking through the choke point of lack of standards.     

Diaminophosphine oxides as preligands for Ni-catalyzed Suzuki cross-coupling reactions of aryl chlorides with arylboronic acids

The first investigation of air- and moisture-stable diaminophosphine oxides as preligands in the Ni-catalyzed Suzuki cross-coupling reactions of aryl chlorides with arylboronic acids has been reported. The results show that under the optimized reaction conditions, the new catalytic system with a Ni(II) σ-aryl complex as precatalyst and a diaminophosphine oxide as preligand tolerates a variety of functional groups and is efficient for both electron-rich and electron-deficient aryl chlorides, though it shows higher efficiency for activated arylboronic acids than deactivated ones. Steric effects were observed for both aryl chlorides and arylboronic acids.     

N-Methylation and N,N-dimethylation of amino acids. An artifact production in the analysis of organic acids using diazomethane as derivatizing agent

In the fractions of the methyl esters of urinary organic acids seventeen N-methylated or N,N-dimethylated amino acid methyl esters are identified by gas chromatography-mass spectrometry. It is shown for twelve amino acids that their amino group reacts with diazomethane to form these derivatives. Using deuterated reagents, in particular deuterated diazomethane, in the sample preparation procedure during the organic acid analysis, it is shown that the N-methylated and N,N-dimethylated amino acids are artifacts from diazomethane and are not biochemical N-methylation products.     

ESI‐MS/MS analysis of protonated N‐methyl amino acids and their immonium ions

Methylation is one of the important posttranslational modifications of biological systems. At the metabolite level, the methylation process is expected to convert bioactive compounds such as amino acids, fatty acids, lipids, sugars, and other organic acids into their methylated forms. A few of the methylated amino acids are identified and have been proved as potential biomarkers for several metabolic disorders by using mass spectrometry–based metabolomics workstation. As it is possible to encounter all the N‐methyl forms of the proteinogenic amino acids in plant/biological systems, it is essential to have analytical data of all N‐methyl amino acids for their detection and identification. In earlier studies, we have reported the ESI‐MS/MS data of all methylated proteinogenic amino acids, except that of mono‐N‐methyl amino acids. In this study, the N‐methyl amino acids of all the amino acids ( 1 ‐ 21 ; including one isomeric pair) were synthesized and characterized by ESI‐MS/MS, LC/MS/MS, and HRMS. These data could be useful for detection and identification of N‐methyl amino acids in biological systems for future metabolomics studies. The MS/MS spectra of [M + H]⁺ ions of most N‐methyl amino acids showed respective immonium ions by the loss of (H₂O, CO). The other most common product ions detected were [MH‐(NH₂CH₃]⁺, [MH‐(RH)]⁺ (where R = side chain group) ions, and the selective structure indicative product ions due to side chain and N‐methyl group. The isomeric/isobaric N‐methyl amino acids could easily be differentiated by their distinct MS/MS spectra. Further, the MS/MS of immonium ions inferred side chain structure and methyl group on α‐nitrogen of the N‐methyl amino acids.     

Classification of amino acids and oligopeptides with the use of multi-mode chemical images obtained with ion selective electrode array

The analysis of amino acids and oligopeptides as important bioanalytes is a significant task in medical diagnostics and proteomic research and currently it is based on chromatographic and electrophoretic methods. In this paper, an approach based on sensor array coupled with titration is proposed for effective recognition of 5 amino acids and 4 oligopeptides. It is shown, that the increase of information gained during measurements of sensors’ signals in various pH allows for capturing more data on interaction of amino acids and oligopeptides with various polymeric membranes of potentiometric electrodes used in the array, and that leads to the lowering of classification errors in partial least squares analysis.     

First-principle calculation of equilibrium cesium ion-pair acidities in tetrahydrofuran

The ion-pair acidities of organic acids in THF are fundamental to synthetic organic chemistry. Although the ion-pair acidities of a number of carbon acids have been experimentally measured by Streitwieser and co-workers, it is important to develop a theoretical method that can accurately predict these quantities because not all the organic acids (e.g., very weak acids or complex synthetic intermediates with multiple acidic positions) are amenable to experimental characterization. In the present study is reported the first theoretical protocol for predicting the cesium ion-pair acidities in THF whose reliability has been tested against almost all the available experimental data. It is found that the root-mean-square error of the current theoretical model equals 1.2 pK units. With the newly developed theoretical method in hand, the structures of cesium ion pairs of different types of carbon acids are then studied. The cesium ion-pair acidities in THF and absolute ionic acidities in DMSO are also systematically compared, which confirms Streitwieser's previous finding that the two scales of acidities have only minor difference. Significantly, from detailed energy analysis the mechanism for the "fortunate" match of the two scales of acidities is found. That is, the combined process of the Cs binding ("micro"-solvation) and the solvation of the ion pair resembles the one-step solvation of a carbanion in DMSO. Finally, it is found that the cesium ion-pair acidities of nitrogen acids in THF have only minor difference from the absolute ionic acidities in DMSO. Consequently, one can easily estimate the cesium ion-pair acidities of almost all types of organic nitrogen acids in THF on the basis of Bordwell's data.     

Light-Driven Enzymatic Decarboxylation of Dicarboxylic Acids

Photodecarboxylase from Chlorella variabillis (CvFAP) is one of the three known light-activated enzymes that catalyzes the decarboxylation of fatty acids into the corresponding C1-shortened alkanes. Although the substrate scope of CvFAP has been altered by protein engineering and decoy molecules, it is still limited to mono-fatty acids. Our studies demonstrate for the first time that long chain dicarboxylic acids can be converted by CvFAP. Notably, the conversion of dicarboxylic acids to alkanes still represents a chemically very challenging reaction. Herein, the light-driven enzymatic decarboxylation of dicarboxylic acids to the corresponding (C2-shortened) alkanes using CvFAP is described. A series of dicarboxylic acids is decarboxylated into alkanes in good yields by means of this approach, even for the preparative scales. Reaction pathway studies show that mono-fatty acids are formed as the intermediate products before the final release of C2-shortened alkanes. In addition, the thermostability, storage stability, and recyclability of CvFAP for decarboxylation of dicarboxylic acids are well evaluated. These results represent an advancement over the current state-of-the-art.