Derivatization in mass spectrometry--8. Soft ionization mass spectrometry of small molecules

This is the first of two reviews devoted to derivatization approaches for "soft" ionization mass spectrometry (FAB, MALDI, ESI, APCI) and deals, in particular, with small molecules. The principles of the main "soft" ionization mass spectrometric methods as well as the reasons for derivatizing small molecules are briefly described. Derivatization methods for modification of amines, carboxylic acids, amino acids, alcohols, carbonyl compounds, monosaccharides, thiols, unsaturated and aromatic compounds etc. to improve their ionizability and to enhance structure information content are discussed. The use of "fixed"-charge bearing derivatization reagents is especially emphasized. Chemical aspects of derivatization and "soft" ionization mass spectrometric properties of derivatives are considered.     

Direct Borylation of Primary CH Bonds in Functionalized Molecules by Palladium Catalysis

Organoborane compounds are among the most commonly employed intermediates in organic synthesis and serve as crucial precursors to alcohols, amines, and various functionalized molecules. A simple palladium‐based system catalyzes the conversion of primary C(sp³)? H bonds in functionalized complex organic molecules into alkyl boronate esters. Amino acids, amino alcohols, alkyl amines, and a series of bioactive molecules can be functionalized with the use of readily available and removable directing groups in the presence of commercially available additives, simple ligands, and oxygen (O₂) as the terminal oxidant. This approach represents an economic and environmentally friendly method that could find broad applications.     

Application of CE in hydrodynamically closed systems for analysis of bioactive compounds in food

CE is a family of electrokinetic separation techniques that separate compounds based upon differences in electrophoretic mobilities, phase partitioning, pI, molecular size, or a combination of one or several of these properties. CE has been used in several modes to analyze and characterize a wide variety of analytes from simple inorganic ions, small organic molecules, peptides, proteins, nucleic acids to virus, microbes and particles. Food consists of a complex mixture of a variety of components, many of which are biologically active. Components classified as "nutrients" are essential for growth, maintenance, and repair of the body. Other food constituents, typically occurring in small quantities, are classified as "biologically active substances" and they have beneficial or harmful effects on human health. There are two types of biologically active substances in food - naturally occurring and food additives. The bioactive compounds of food that will be mentioned in this review are inorganic and organic acids, amino acids, vitamins, phenolic compounds, biogenic amines, antinutrients, toxins, etc. This review is focused on the application of CE with hydrodynamically closed system (suppression of EOF) for the analysis of the above-mentioned compounds. CE can be an alternative method to HPLC or other methods for analysis of bioactive compounds in food. The main advantages of CE are low running cost (at least ten times than HPLC) and consideration to environment (hundreds of microliters of diluted water based electrolyte per analysis).     

Direct Borylation of Primary C?H Bonds in Functionalized Molecules by Palladium Catalysis

Organoborane compounds are among the most commonly employed intermediates in organic synthesis and serve as crucial precursors to alcohols, amines, and various functionalized molecules. A simple palladium‐based system catalyzes the conversion of primary C(sp³) H bonds in functionalized complex organic molecules into alkyl boronate esters. Amino acids, amino alcohols, alkyl amines, and a series of bioactive molecules can be functionalized with the use of readily available and removable directing groups in the presence of commercially available additives, simple ligands, and oxygen (O₂) as the terminal oxidant. This approach represents an economic and environmentally friendly method that could find broad applications.     

Semifluorinated alcohols in Langmuir monolayers--a comparative study

A series of semifluorinated alcohols differing in the proportion of the perfluorinated to hydrogenated chains length was synthesized and investigated in Langmuir monolayers using surface pressure and surface potential measurements. All the investigated semifluorinated alcohols were found to be capable of stable floating monolayer formation. The stability of monolayers was found to be higher upon increasing the length of the perfluorinated segment. A lower stability of the monolayers from alcohols having shorter perfluorinated fragment was attributed to the aggregation process, which was visualized with Brewster angle microscopy (BAM). Most condensed monolayers were formed by compounds with longer perfluorinated moiety, whereas monolayers composed by molecules with an iso-branched perfluorinated segment were found to be more expanded. The change of electric surface potential was negative along the whole compression. The maximum absolute values of DeltaV varies, depending on the number of CF(2) groups, from ca. -400 mV for F6H10OH to ca. -700 mV for F10H10OH. The dipole moments of free molecules were calculated with Hyperchem, and the obtained values were approximately the same (within the experimental error), i.e., 2.8D for all the investigated molecules, independently on the perfluorinated fragment length. The dipole moment vector was found to be virtually aligned to the main molecular axis for the studied compounds. Therefore, the observed differences in the measured values of DeltaV can result from a different dielectric permittivity of a particular monolayer.     

分子阵列研究进展

小分子化合物可以调节生物学过程,是研究活性生物大分子（特别是蛋白质）以及药物的重要工具,而高通量筛选是发现活性分子的重要方法。分子阵列是近年来新出现的一种高通量筛选技术,上面含有成千上万种组合合成的化合物以及天然产物,可以用于发现新的先导化合物,以及筛选已有的先导化合物。现在分子阵列已经成功应用于蛋白分析、先导化合物的发现等许多领域。本文综述了近年来分子阵列的构建过程,原位合成、非原位合成等各种固定化策略以及荧光免疫检测,表面等离子体共振成像技术等检测手段,并介绍了化学分子印刷阵列方法,最后总结了分子阵列的应用,并对分子阵列在我国中药发展等有方面将起到的潜在作用作了展望。     

Adsorption of organic molecules on rutile TiO2 and anatase TiO2 single crystal surfaces

The interaction of organic molecules with titanium dioxide surfaces has been the subject of many studies over the last few decades. Numerous surface science techniques have been utilised to understand the often complex nature of these systems. The reasons for studying these systems are hugely diverse given that titanium dioxide has many technological and medical applications. Although surface science experiments investigating the adsorption of organic molecules on titanium dioxide surfaces is not a new area of research, the field continues to change and evolve as new potential applications are discovered and new techniques to study the systems are developed. This tutorial review aims to update previous reviews on the subject. It describes experimental and theoretical work on the adsorption of carboxylic acids, dye molecules, amino acids, alcohols, catechols and nitrogen containing compounds on single crystal TiO(2) surfaces.     

Incorporation of Non‐canonical Amino Acids into 2,5‐Diketopiperazines by Cyclodipeptide Synthases

The manipulation of natural product biosynthetic pathways is a powerful means of expanding the chemical diversity of bioactive molecules. 2,5‐diketopiperazines (2,5‐DKPs) have been widely developed by medicinal chemists, but their biological production is yet to be exploited. We introduce an in vivo method for incorporating non‐canonical amino acids (ncAAs) into 2,5‐DKPs using cyclodipeptide synthases (CDPSs), the enzymes responsible for scaffold assembly in many 2,5‐DKP biosynthetic pathways. CDPSs use aminoacyl‐tRNAs as substrates. We exploited the natural ability of aminoacyl‐tRNA synthetases to load ncAAs onto tRNAs. We found 26 ncAAs to be usable as substrates by CDPSs, leading to the enzymatic production of approximately 200 non‐canonical cyclodipeptides. CDPSs constitute an efficient enzymatic tool for the synthesis of highly diverse 2,5‐DKPs. Such diversity could be further expanded, for example, by using various cyclodipeptide‐tailoring enzymes found in 2,5‐DKP biosynthetic pathways.     

Pathway development and pilot library realization in diversity-oriented synthesis: exploring Ferrier and Pauson-Khand reactions on a glycal template

Through a correlation of the ability of small molecules to bind biological macromolecules and their ability to modulate cellular and organismal processes, chemistry can inform biology and vice versa. Diversity-oriented organic synthesis (DOS), which aims to provide structurally complex and diverse small molecules efficiently, can play a key role in such chemical genetic studies. Here we illustrate the trial-and-error experimentation that can refine an initial pathway-planning exercise and result eventually in an effective diversity pathway. By exploring Ferrier and Pauson-Khand reactions on a glycal template, we have developed efficient and stereoselective syntheses of tricyclic compounds. In this pathway, diversity results from the substituents and their spatial relationships about the tricyclic rings. A pilot split-pool library synthesis of 2500 tricyclic compounds highlights the use of planning considerations in DOS and a "one-bead, one-stock solution" technology platform. Additionally, it illustrates a promising synthetic pathway for future chemical genetic studies.     

Gel permeation chromatography. III. Molecular shape versus elution

Rules were evolved to predict elution of linear, branched, and polar compounds in GPC, based on testing of 130 compounds. With these rules and in tetrahydrofuran solvent, data for all but a few compounds correlated onto a single calibration line. With small molecules, elution often changed, due to hydrogen bonding to the solvent; this occurred with alcohols, acids, and some chlorinated compounds, but not with mercaptans. Branched and linear isomers usually eluted at about the same point. One may conclude that structural elements were additive in their effect on elution volume in this study.     

Rapid probe and isolation of bioactive compounds from Dioscorea panthaica using human serum albumin functionalized magnetic nano-particles (HSA-MNPs)-based ligand fishing coupled with electrospray ionization mass spectrometry

The chemical diversity of secondary metabolites in medicinal plant makes it a huge challenge to isolate the bioactive compounds from herbal extracts, so quick recognition of the bioactive ones is of vital importance for improving the efficiency of isolation. In this study, a ligand fishing experiment based on human serum albumin functionalized magnetic nano-particles (HSA-MNPs) was performed to probe the bioactive components in a traditional Chinese medicinal plant, Dioscorea panthaica. The minor compounds fished out by HSA-MNPs were identified by electrospray ionization mass spectrometry (ESI-MS), and then separated from the extract of the whole plant by one or two steps of column chromatography under the guidance of ESI-MS. Four biologically active compounds, progenin II, progenin III, dioscin and gracillin, were isolated much faster than in the normal lengthy phytochemical procedure. The present study demonstrates that biological macromolecule (protein, enzyme, receptor, et al.) functionalized MNPs may serve as baits to recognize bioactive small molecules in complex herbal extracts. It is expected that a macromolecule functionalized MNPs-based ligand fishing experiment coupled with ESI-MS may accelerate the process of identification and isolation of bioactive components from medicinal plants, and thus benefit the speed of drug discovery.     

An efficient and practical system for the catalytic oxidation of alcohols, aldehydes, and alpha,beta-unsaturated carboxylic acids

Upon exposure to commercial bleach (approximately 5% aqueous sodium hypochlorite), nickel(II) chloride or nickel(II) acetate is transformed quantitatively into an insoluble nickel species, nickel oxide hydroxide. This material consists of high surface area nanoparticles (ca. 4 nm) and is a useful heterogeneous catalyst for the oxidation of many organic compounds. The oxidation of primary alcohols to carboxylic acids, secondary alcohols to ketones, aldehydes to carboxylic acids, and alpha, beta-unsaturated carboxylic acids to epoxy acids is demonstrated using 2.5 mol % of nickel catalyst and commercial bleach as the terminal oxidant. We demonstrate the controlled and selective oxidation of several organic substrates using this system affording 70-95% isolated yields and 90-100% purity. In most cases, the oxidations can be performed without an organic solvent, making this approach attractive as a "greener" alternative to conventional oxidations.     

Practical calculation of molecular acidity with the aid of a reference molecule

A set of linear free energy models are presented for determining the pK(a) values of amines, alcohols, and carboxylic acids. Models are determined from a series of pK(a) predictors, taken both from traditional natural atomic orbital analysis (NAO) and from a novel approach introduced here of using a reference molecule: an ammonium ion for amines and a hydrogen sulfide molecule for alcohols and carboxylic acids. Using these reference molecules, we calculate the barrier to proton transfer and show that a number of properties associated with the transition state are correlated with the pK(a). By considering 38 predictors, we obtain a four-variable model for amines and a three-variable model for oxygen-containing compounds. The model for amines is based on 145 compounds and has a root mean squared error (RMSE) of 0.45 and R(2) = 0.98. The oxygen set has 48 molecules: RMSE = 0.26, and R(2) = 0.993. Similar, linear, and multilinear models are constructed after separating the sets into chemically similar categories: alcohols, carboxylic acids, and primary, secondary, tertiary, and aromatic amines. This separation gives simpler models with relatively low RMSE values, where the most important predictor of the pK(a) is the difference in energy between transferring the proton from the reference molecular base to the conjugate acid from the data set.     

Mechanism of the grafting of organosilanes on mineral surfaces

The grafting of organosilyl groups in the interlamellar space of certain crystalline silicic acids, such as H-magadiite, occurs when the interlayer spaces have been expanded previously by intercalation of some polar organic substances. The interlamellar Si-OH groups are then accessible to silylating reagents and Si-O-Si bridges form between the silicic acid surface and the organic groups.The grafting reaction is controlled by a diffusion mechanism: desorption of the polar organic guest molecules has to occur simultaneously with the diffusion of the reacting molecules into the interlayer space.The resulting materials are organosilicic compounds which retain the lamellar structure of the starting crystalline silicic acids. Their surface properties are determined by the grafted groups.Part I: This Journal 256:135 (1978); Part II: This Journal 257:178 (1979).     

Conformational energy penalties of protein-bound ligands

The conformational energies required for ligands to adopt their bioactive conformations were calculated for 33 ligand–protein complexes including 28 different ligands. In order to monitor the force field dependence of the results, two force fields, MM3 and AMBER, were employed for the calculations. Conformational analyses were performed in vacuo and in aqueous solution by using the generalized Born/solvent accessible surface (GB/SA) solvation model. The protein-bound conformations were relaxed by using flat-bottomed Cartesian constraints. For about 70% of the ligand–protein complexes studied, the conformational energies of the bioactive conformations were calculated to be 3 kcal/mol. It is demonstrated that the aqueous conformational ensemble for the unbound ligand must be used as a reference state in this type of calculations. The calculations for the ligand–protein complexes with conformational energy penalties of the ligand calculated to be larger than 3 kcal/mol suffer from uncertainties in the interpretation of the experimental data or limitations of the computational methods. For example, in the case of long-chain flexible ligands (e.g. fatty acids), it is demonstrated that several conformations may be found which are very similar to the conformation determined by X-ray crystallography and which display significantly lower conformational energy penalties for binding than obtained by using the experimental conformation. For strongly polar molecules, e.g. amino acids, the results indicate that further developments of the force fields and of the dielectric continuum solvation model are required for reliable calculations on the conformational properties of this type of compounds.     

Sodium borohydride-iodine mediated reduction of γ-lactam carboxylic acids followed by DDQ mediated oxidative aromatisation: a simple approach towards N-aryl-formylpyrroles and 1,3-diaryl-formylpyrroles

A simple methodology for the conversion of substituted N-aryl-γ-lactam 2/3-carboxylic acids to substituted N-aryl-2/3-formyl-pyrroles has been developed. Several N-aryl-γ-lactam 2/3-carboxylic acids were reduced to substituted (N-aryl-pyrroliden-2/3-yl)-methanols in good yields by using the NaBH₄-I₂ system. Aromatisation and in situ oxidation of these alcohols using DDQ produced N-aryl-2/3-formyl-pyrroles, which act as key starting material and intermediates in the synthesis of several bioactive compounds.     

A chip-based miniaturized format for protein-expression profiling: the exploitation of comprehensively produced antibodies

Numerous antibodies have been developed and validated in recent years, and show promise for use in novel functional protein assays. Such assays would be an alternative to pre-existing comprehensive assays, such as DNA microarrays. Antibody microarrays are thought to represent those functional protein assays. While a variety of attempts have been made to apply DNA microarray technology to antibody microarrays, a fully optimized protocol has not been established. We have been conducting a project to comprehensively produce antibodies against mouse KIAA ("KI" stands for "Kazusa DNA Research Institute" and "AA" are reference characters) proteins. Using our library of antibodies, we established a novel antibody microarray format that utilizes surface plasmon resonance (SPR) technology. A label-free real-time measurement of protein expression in crude cell lysates was achieved by direct readout of the bindings using SPR. Further refinement of the antibody microarray format enabled us to detect a smaller quantity of target proteins in the lysate without the bulk effect. In this review, we first summarize available antibody array formats and then describe the above-mentioned format utilizing updated SPR technology.     

Last ten years (2008–2018) of chiral ligand‐exchange chromatography in HPLC: An updated review

Chiral ligand‐exchange chromatography is one of the elective strategies for the direct enantioresolution of small chelating compounds: amino acids, diamines, amino alcohols, diols, small peptides, etc. Unlike other methods, the interaction between chiral selector and analyte enantiomers is mediated by a cation, thus producing diastereomeric ternary complexes. Two main approaches are conventionally applied in chiral ligand‐exchange chromatography. The first relies upon chiral stationary phases where the chiral selector is either covalently immobilized or physically adsorbed onto suitable packing materials (coated phases). In the second approach, chiral molecules are added to the eluent, thus generating chiral eluent systems. Among the advantages of chiral ligand‐exchange chromatography, the generation of UV/vis‐active metal complexes, and the use of commercially available or easy‐to‐synthesize chiral selectors, in combination to rather inexpensive achiral columns for coated phases and chiral eluents, are noteworthy. Besides amino acids and amino alcohols, other species have proven suitable for chiral ligand‐exchange chromatography applications. Recently, the use of either chiral ionic liquids or micellar liquid chromatography systems as well as the successful off‐column formation of diastereomeric complexes have expanded the selectivity profiles and application fields. All of these issues are touched in the review, shedding light to the contributions appeared in the last decade.     

Mass spectroscopic approach to amino acids formation processes by UV irradiation to simple organic molecules in aqueous solution.

We have studied amino acid formation by UV (193 nm) irradiation to organic molecules (amines, alcohols and amides) in aqueous solution. Among several types of detected amino acids, small aliphatic amino acids (Gly and alpha-, beta-Ala and alpha-, beta-, gamma-ABA) were quantitatively identified. Among these small aliphatic amino acids, certain amino acids were formed in its free form, even before hydrolysis, contrary to the results of UV irradiation to a gas mixture of CO, NH3, and H2O, where amino acids were hardly detected before hydrolysis. The species distribution of identified amino acids showed a dependence on the starting organic molecules, and also on the presence of ammonia. The formation processes of the identified small aliphatic amino acids were investigated with the aid of electrospray ionization (ESI) MS and MS/MS measurements of photoproducts. Possible formation processes of these amino acid precursors from each starting molecules are proposed. By identifying the amino acid precursor, which has a chiral carbon atom, a new possibility is suggested for asymmetric photosynthesis of amino acid from achiral organic molecules.