Gas Phase Reactivity of Isomeric Hydroxylated Polychlorinated Biphenyls

Identification of stereo- and positional isomers detected with high-resolution mass spectrometry (HRMS) is often challenging due to near-identical fragmentation spectra (MS2), similar retention times, and collision cross-section values (CCS). Here we address this challenge on the example of hydroxylated polychlorinated biphenyls (OH-PCBs) with the aim to (1) distinguish between isomers of OH-PCBs using two-dimensional ion mobility spectrometry (2D-IMS) and (2) investigate the structure of the fragments of OH-PCBs and their fragmentation mechanisms by ion mobility spectrometry coupled to high-resolution mass spectrometry (IMS-HRMS). The MS2 spectra as well as CCS values of the deprotonated molecule and fragment ions were measured for 18 OH-PCBs using flow injections coupled to a cyclic IMS-HRMS. The MS2 spectra as well as the CCS values of the parent and fragment ions were similar between parent compound isomers; however, ion mobility separation of the fragment ions is hinting at the formation of isomeric fragments. Different parent compound isomers also yielded different numbers of isomeric fragment mobilogram peaks giving new insights into the fragmentation of these compounds and indicating new possibilities for identification. For spectral interpretation, Gibbs free energies and CCS values for the fragment ions of 4'-OH-CB35, 4'-OH-CB79, 2-OH-CB77 and 4-OH-CB107 were calculated and enabled assignment of structures to the isomeric mobilogram peaks of [M-H-HCl]- fragments. Finally, further fragmentation of the isomeric fragments revealed different fragmentation pathways depending on the isomeric fragment ions.

Chiral Carborane Acids Decorated with Binol-Based Phosphonates: Synthesis, Characterization, and Application

The syntheses of hexabrominated closo-carborates decorated with different chiral Binol-derived phosphonates and their conjugate acids are described. X-ray diffraction analysis reveals a polymeric structure for the sodium salt with the anionic units connected by [B-Br-Na-O═P]+ linkages. For the acid, coordination of the proton to the phosphonate's P═O oxygen atom is assumed. The pKa value was estimated by combining experiments and computations. Application of these Brønsted acids as chiral catalysts in an imino-ene and a Mukaiyama-Mannich reaction was moderately successful.

Multifunctional Organocatalysts - Singly-Linked and Macrocyclic Bisphosphoric Acids for Asymmetric Phase-Transfer and Brønsted-Acid Catalysis

The linking of phosphoric acids via covalent or mechanical bonds has proven to be a successful strategy for the design of novel organocatalysts. Here, we present the first systematic investigation of singly-linked and macrocyclic bisphosphoric acids, including their synthesis and their application in phase-transfer and Brønsted acid catalysis. We found that the novel bisphosphoric acids show dramatically increased enantioselectivities in comparison to their monophosphoric acid analogues. However, the nature, length and number of linkers has a profound influence on the enantioselectivities. In the asymmetric dearomative fluorination via phase-transfer catalysis, bisphosphoric acids with a single, rigid bisalkyne-linker give the best results with moderate to good enantiomeric excesses. In contrast, bisphosphoric acids with flexible linkers give excellent enantioselectivities in the transfer-hydrogenation of quinolines via cooperative Brønsted acid catalysis. In the latter case, sufficiently long linkers are needed for high stereoselectivities, as found experimentally and supported by DFT calculations.

On-off-on Control of Molecular Inversion Symmetry via Multi-stage Protonation: Elucidating Vibronic Laporte Rule

The Laporte rule dictates that one- and two-photon absorption spectra of inversion-symmetric molecules should display alternatively forbidden electronic transitions; however, for organic fluorophores, drawing clear distinction between the symmetric- and non-inversion symmetric two-photon spectra is often obscured due to prevalent vibronic interactions. We take advantage of consecutive single- and double-protonation to break and then reconstitute inversion symmetry in a nominally symmetric diketopyrrolopyrrole, causing large changes in two-photon absorption. By performing detailed one- and two-photon titration experiments, with supporting quantum-chemical model calculations, we explain how certain low-frequency vibrational modes may lead to apparent deviations from the strict Laporte rule. As a result, the system may be indeed considered as an on-off-on inversion symmetry switch, opening new avenues for two-photon sensing applications.

One Hundred Carboxylate Receptors

This work presents a compilation of binding constant (logKass) values in DMSO-d6/H2O (0.5% m/m) for a variety of receptors with 12 carboxylate anions (formate, acetate, lactate, pivalate, sorbate, hexanoate, benzoate, glyphosate, glucuronate, ibuprofen, naproxen, and ketoprofen). A total of 489 logKass values are listed for 100 anion receptor molecules. Most logKass values originate from previously published articles, along with some values for previously unpublished receptor molecules, spanning a workflow of 8 years. The purpose of this study is to serve as a comprehensive information source for selecting suitable receptor candidates to be used in practical carboxylate sensing applications, such as constructing ion-selective electrodes (ISE-s). To support such decision making, all receptors are presented together with lipophilicity (logPo/w) data.

A Chemically Fuelled Molecular Automaton Displaying Programmed Migration of Zn2+ Between Alternative Binding Sites

A molecular system comprising a cationic zinc complex and an amino acid-derived ambident ligand having phosphate and carboxylate binding sites undergoes a series of rearrangements in which the metal cation migrates autonomously from one site to another. The location of the metal is identified by the circular dichroism spectrum of a ligated bis(2-quinolylmethyl)-(2-pyridylmethyl)amine (BQPA) chromophore, which takes a characteristic shape at each binding site. Migration is fuelled by the decomposition of trichloroacetic acid to CO₂ and CHCl₃ , which progressively neutralises the acidity of the system as a function of time, revealing in sequence binding sites of increasing basicity. The migration rate responds to control by variation of the temperature, water content and triethylamine concentration, while an excess of fuel controls the duration of an induction period before the migration event.

Protomer Formation Can Aid the Structural Identification of Caffeine Metabolites

The structural annotation of isomeric metabolites remains a key challenge in untargeted electrospray ionization/high-resolution mass spectrometry (ESI/HRMS) metabolomic analysis. Many metabolites are polyfunctional compounds that may form protomers in electrospray ionization sources and therefore yield multiple peaks in ion mobility spectra. Protomer formation is strongly structure-specific. Here, we explore the possibility of using protomer formation for structural elucidation in metabolomics on the example of caffeine, its eight metabolites, and structurally related compounds. It is observed that two-thirds of the studied compounds formed high- and low-mobility species in high-resolution ion mobility. Structures in which proton hopping was hindered by a methyl group at the purine ring nitrogen (position 3) yielded structure-indicative fragments with collision-induced dissociation (CID) for high- and low-mobility ions. For compounds where such a methyl group was not present, a gas-phase equilibrium could be observed for tautomeric species with two-dimensional ion mobility. We show that the protomer formation and the gas-phase properties of the protomers can be related to the structure of caffeine metabolites and facilitate the identification of the structural isomers.

Sodium adduct formation with graph-based machine learning can aid structural elucidation in non-targeted LC/ESI/HRMS

Non-targeted screening with LC/ESI/HRMS aims to identify the structure of the detected compounds using their retention time, exact mass, and fragmentation pattern. Challenges remain in differentiating between isomeric compounds. One untapped possibility to facilitate identification of isomers relies on different ionic species formed in electrospray. In positive ESI mode, both protonated molecules and adducts can be formed; however, not all isomeric structures form the same ionic species. The complicated mechanism of adduct formation has hindered the use of this molecular characteristic in the structural elucidation in non-targeted screening. Here, we have studied the adduct formation for 94 small molecules with ion mobility spectra and compared collision cross-sections of the respective ions. Based on the results we developed a fast support vector machine classifier with polynomial kernels for accurately predicting the sodium adduct formation in ESI/HRMS. The model is trained on five independent data sets from different laboratories and uses the graph-based connectivity of functional groups and PubChem fingerprints to predict the sodium adduct formation in ESI/HRMS. The validation of the model showed an accuracy of 74.7% (balanced accuracy 70.0%) on a dataset from an independent laboratory, which was not used in the training of the model. Lastly, we applied the classification algorithm to the SusDat database by NORMAN network to evaluate the proportion of isomeric compounds that could be distinguished based on predicted sodium adduct formation. It was observed that sodium adduct formation probability can provide additional selectivity for about one quarter of the exact masses and, therefore, shows practical utility for structural assignment in non-targeted screening.

Inducing a pH-dependent conformational response by competitive binding to Zn2+ of a series of chiral ligands of disparate basicity

Molecules that change shape in response to environmental conditions are central to biological molecular communication devices and their synthetic chemical analogues. Here we report a molecular system in which a series of chiral anionic ligands of differing basicity are selectively protonated according to the pH of the medium. A cationic circular dichroism (CD) reporter complex responds to anion binding by selecting one of two alternative enantiomeric conformations. Exploiting the principle that less basic anions have, in general, weaker electrostatic interactions than more basic anions, a set of three chiral acids with large (>5 unit) pK_a differences and differing configurations were sequentially deprotonated in acetonitrile by addition of base, allowing the most basic anion in the mixture at any time to bind to the reporter complex. A characteristic CD output resulted, which changed in sign as the next-most basic anion was revealed by the next deprotonation in the series. Four cycles of switching between three ligand-bound states were achieved with minimal changes in signal magnitude, by alternating addition of base and acid. The pH-dependent conformational response was used to transduce a signal by appending to the binding site a 2-aminoisobutyric acid (Aib) oligomer, whose M or P helical conformation depended on the chirality of the bound ligand, and was reported by a remote ¹³C-labelled NMR reporter group. The multicomponent system thus converts a pH signal into a programmable conformational response which induces a remote spectroscopic effect.

A chemical system comprising a series of chiral acids of differing pK_a, a metal, and a conformationally labile chromophore responds to pH with a CD spectrum that reports the absolute stereochemistry of the most basic anion in the mixture.

Quantitative electrospray ionization efficiency scale: 10 years after

RATIONALE

The first comprehensive quantitative scale of the efficiency of electrospray ionization (ESI) in the positive mode by monoprotonation, containing 62 compounds, was published in 2010. Several trends were found between the compound structure and ionization efficiency (IE) but, possibly because of the limited diversity of the compounds, some questions remained. This work undertakes to align the new data with the originally published IE scale and carry out statistical analysis of the resulting more extensive and diverse data set to derive more grounded relationships and offer a possibility of predicting logIE values.

METHODS

Recently, several new IE studies with numerous compounds have been conducted. In several of them, more detailed investigations of the influence of compound structure, solvent properties, or instrument settings have been conducted. IE data from these studies and results from this work were combined, and the multilinear regression method was applied to relate IE to various compound parameters.

RESULTS

The most comprehensive IE scale available, containing 334 compounds of highly diverse chemical nature and spanning 6 orders of magnitude of IE, has been compiled. Several useful trends were revealed.

CONCLUSIONS

The ESI ionization efficiency of a compound by protonation is mainly affected by three factors: basicity (expressed by pK_aH in water), molecular size (expressed by molar volume or surface area), and hydrophobicity of the ion (expressed by charge delocalization in the ion or its partition coefficient between a water-acetonitrile mixture and hexane). The presented models can be used for tentative prediction of logIE of new compounds (under the used conditions) from parameters that can be computed using commercially available software. The root mean square error of prediction is in the range of 0.7-0.8 log units.

Acid-Base and Anion Binding Properties of Tetrafluorinated 1,3-Benzodiazole, 1,2,3-Benzotriazole and 2,1,3-Benzoselenadiazole

The influence of fluorination on the acid-base properties and the capacity of structurally related 6-5 bicyclic compounds - 1,3-benzodiazole 1, 1,2,3-benzotriazole 2 and 2,1,3-benzoselenadiazole 3 to σ-hole interactions, i. e. hydrogen (1 and 2) and chalcogen (3) bondings, is studied experimentally and computationally. The tetrafluorination increases the Brønsted acidity of the diazole and triazole scaffolds and the Lewis acidity of selenadiazole scaffold decreases the basicity. Increased Brønsted acidity facilitates anion binding via the formation of hydrogen bonds; particularly, tetrafluorinated derivative of 1 (compound 4) binds Cl^- . Increased Lewis acidity of tetrafluorinated derivative of 3 (compound 10), however, is not enough for binding with Cl^- and F^- via chalcogen bonds in contrast to previously studied Te analog of 10. It is suggested that the maximum positive values of molecular electrostatic potential at the σ-holes, V_S,max , can be a reasonable metric for design and synthesis of new anion receptors with selenadiazole-diazole/triazole hybrids as a special target. Related chlorinated compounds are also discussed.

Synthesis and Physicochemical Properties of 2-SF5-(Aza)Indoles, a New Family of SF5 Heterocycles

Structural diversity in heterocyclic chemistry is key to unlocking new properties and modes of action. In this regard, heterocycles embedding emerging fluorinated substituents hold great promise. Herein is described a strategy to access 2-SF₅-(aza)indoles for the first time. The sequence relies on the radical addition of SF₅Cl to the alkynyl π-system of 2-ethynyl anilines followed by a cyclization reaction. A telescoped sequence is proposed, making this strategy very appealing and reproducible on a gram scale. Downstream functionalizations are also demonstrated, allowing an easy diversification of N- and C3-positions. Ames test, pK _a, log P, and differential scanning calorimetry measurements of several fluorinated 2-Rf-indoles are also disclosed. These studies highlight the strategic advantages that a C2-pentafluorosulfanylated motif impart to a privileged scaffold such as an indole.

Quantitative analysis of the relationship of derivatization reagents and detection sensitivity of electrospray ionization-triple quadrupole tandem mass spectrometry: Hydrazines as prototypes

Chemical derivatization-assisted electrospray ionization-triple quadrupole mass spectrometry (ESI-QqQ-MS) has become an efficient tool for the quantification of low-molecular-weight molecules. Many studies found that the derivatives of the same analytes derivatized by different derivatization reagents with the same reaction group had different detection sensitivity, even under the same conditions of electrospray ionization-mass spectrometry (ESI-MS). This phenomenon was suggested to be caused by the different modifying groups in the derivatization reagents. However, there is still a lack of systematic study on how modifying groups in the derivatization reagents affect the detection sensitivity of their corresponding derivatives of analytes, especially theoretical investigations. In this study, we employed a quantitative structure-activity relationship (QSAR) modeling approach to explore the relationship between modifying group structures and the detection sensitivity of derivatization reagents and their derivatives during ESI-MS detection. A total of 110 derivatization reagents of the hydrazine family and their hexanal derivatives (substituted hydrazones) were selected as the prototypes to construct QSAR models. The established models suggested that several molecular descriptors, related to hydrophobicity, electronegativity, and molecular shape, were related to the detection sensitivity of hexanal derivatives induced by different modifying groups in the derivatization reagents. Besides, we found that the detection sensitivity of compounds detected in selected ion mode (SIM) showed a positive correlation with that obtained in multiple reaction monitoring mode (MRM), and the ionization efficiency was the key factor on the detection sensitivity in both modes.

Experimental and Computational Study of Aminoacridines as MALDI(-)-MS Matrix Materials for the Analysis of Complex Samples

Monoaminoacridines (1-, 2-, 3-, 4-, and 9-aminoacridine) were studied for suitability as matrices in the negative ion mode matrix-assisted laser desorption/ionization mass spectrometry (MALDI(-)-MS) analysis of various samples. This is the first study to examine 1-, 2-, and 4-aminoacridine as potential matrix material candidates for MALDI(-)-MS. In addition, spectral (UV-Vis absorption and fluorescence), proton transfer-related (basicity and autoprotolysis), and crystallization properties of these compounds were characterized experimentally and/or computationally. For testing the capabilities of these aminoacridines as matrix materials, four samples related to cultural heritage materials-stearic acid, colophony resin, dyer's madder dye, and a resinous case-study sample from a shipwreck-were analyzed with MALDI(-)-MS. A novel algorithm (implemented as an executable Python script) for MS data analysis was developed to compare the five matrix materials and to help mass spectrometrists rapidly identify peaks originating from the sample and matrix material. It was determined that all five of the studied aminoacridines can successfully be used as matrix materials in MALDI(-)-MS analysis. As an interesting finding, in several cases, the best mass spectra were obtained by using a relatively small amount of matrix material mixed with an excess amount of sample. 3- and 4-aminoacridine outperformed the other aminoacridines in the ease of obtaining acceptable spectra, average number of ions identified in the mass spectra, and low dependence of the sample-to-matrix mass ratio on experimental results.

LogP determination for highly lipophilic hydrogen-bonding anion receptor molecules

Lipophilicity, usually expressed as octanol-water partition coefficient (logP_o/w), is an important property in biomedical research, drug design and technology. However, high logP_o/w values of complex hydrogen-bonding molecules are not easy to measure or calculate. Exemplary problematic molecules are prospective active components (ionophores) of polymeric sensor membranes - the working elements of ion-selective electrodes. High lipophilicities of the membrane components are crucial for the sensor lifetime. In this work, lipophilicities of a wide range of urea-, carbazole- and indolocarbazole-based anion receptor molecules (some newly synthesized) and two common plasticizers were determined using a chromatography-based approach and/or the COSMO-RS method. Very high logP_o/w values, up to around 20, i.e. far beyond directly experimentally accessible range, were obtained. The agreement between the two approaches ranged from very good to satisfactory. Based on these results, simple fragment-based equations were developed for quick lipophilicity estimation without any specialized software. Membrane-water partition coefficients for the studied compounds were modeled. Limitations and biases of the used methods are discussed.

Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS

Performance of COSMO-RS method as a tool for partition and distribution modeling in 20 solvent pairs-composed of neutral or acidic aqueous solution and organic solvents of different polarity, ranging from alcohols to toluene and hexane-was evaluated. Experimental partition/distribution data of lignin-related and drug-like compounds (neutral, acidic, moderately basic) were used as reference. Several aspects of partition modeling were addressed: accounting for mutual saturation of aqueous and organic phases, variability of systematic prediction errors across solvent pairs, taking solute ionization into account. COSMO-RS was found to predict extraction outcome for both ligneous and drug-like compounds in various solvent pairs fairly well without any additional empirical input. The solvent-specific systematic errors were found to be moderate, despite being statistically significant, and related to the solvent hydrophobicity. Accounting for mutual solubilities of the two liquids was proven crucial in cases where water was considerably soluble in the organic solvent. The root mean square error of a priori logP prediction varied, depending mainly on the solvent pair, from 0.2 to 0.7, overall value being 0.6 log units. The accuracy was higher in case of hydrophilic than hydrophobic solvents. The logD predictions were less accurate, due to pK_a prediction being an additional source of error, and also because of the complexity of modeling the behaviour of ionic species in the two-phase system. A simple correction for partitioning of free ions was found to notably improve logD prediction accuracy in case of the most hydrophilic organic phase (butanol/water).

Systematic Optimization of Liquid-Liquid Extraction for Isolation of Unidentified Components

We present a systematic approach for predicting the best solvents for selective extraction of components with unknown structure from complex mixtures (e.g., natural products)-a tool promising dramatic simplification of extraction process optimization. Its key advantage is that identification of the component(s) is unnecessary-prediction is based on a small set of experimental distribution coefficients (obtained using a combination of shake-flask extraction and chromatographic analysis) rather than structure-based descriptors. The methodology is suitable for the very common situations in practice where the desired compound needs to be separated from unknown impurities (i.e., selectively extracted from the mixture), as well as for large-scale and high-throughput work. The proof-of-concept methodology was developed and evaluated using an extensive set of experimental distribution data of lignin-related compounds obtained in this work.

Method development for the analysis of resinous materials with MALDI-FT-ICR-MS: novel internal standards and a new matrix material for negative ion mode

Matrix-assisted laser desorption/ionization (MALDI) is a mass spectrometry (MS) ionization technique suitable for a wide variety of sample types including highly complex ones such as natural resinous materials. Coupled with Fourier transform ion cyclotron resonance (FT-ICR) mass analyser, which provides mass spectra with high resolution and accuracy, the method gives a wealth of information about the composition of the sample. One of the key aspects in MALDI-MS is the right choice of matrix compound. We have previously demonstrated that 2,5-dihydroxybenzoic acid is suitable for the positive ion mode analysis of resinous samples. However, 2,5-dihydroxybenzoic acid was found to be unsuitable for the analysis of these samples in the negative ion mode. The second problem addressed was the limited choice of calibration standards offering a flexible selection of m/z values under m/z 1000. This study presents a modified MALDI-FT-ICR-MS method for the analysis of resinous materials, which incorporates a novel matrix compound, 2-aminoacridine for the negative ion mode analysis and extends the selection of internal standards with m/z <1000 for both positive (15 different phosphazenium cations) and negative (anions of four fluorine-rich sulpho-compounds) ion mode. The novel internal calibration compounds and matrix material were tested for the analysis of various natural resins and real-life varnish samples taken from cultural heritage objects. Copyright © 2017 John Wiley & Sons, Ltd.

Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions

Biomolecular systems are able to respond to their chemical environment through reversible, selective, noncovalent intermolecular interactions. Typically, these interactions induce conformational changes that initiate a signaling cascade, allowing the regulation of biochemical pathways. In this work, we describe an artificial molecular system that mimics this ability to translate selective noncovalent interactions into reversible conformational changes. An achiral but helical foldamer carrying a basic binding site interacts selectively with the most acidic member of a suite of chiral ligands. As a consequence of this noncovalent interaction, a global absolute screw sense preference, detectable by (13)C NMR, is induced in the foldamer. Addition of base, or acid, to the mixture of ligands competitively modulates their interaction with the binding site, and reversibly switches the foldamer chain between its left and right-handed conformations. As a result, the foldamer-ligand mixture behaves as a biomimetic chemical system with emergent properties, functioning as a "proton-counting" molecular device capable of providing a tunable, pH-dependent conformational response to its environment.