Mechanism of C-3 Acyl Neighboring Group Participation in Mannuronic Acid Glycosyl Donors.

One of the main challenges in oligosaccharide synthesis is the stereoselective introduction of the glycosidic bond. In order to understand and control glycosylation reactions, thorough mechanistic studies are required. Reaction intermediates found by NMR spectroscopy often cannot explain the glycosylation's stereochemical outcome.

Unravelling the Structure of One-Electron Oxidation Products of Model Peptide Backbones Containing Methionine by IRMPD Spectroscopy: the Effect of the Neighbouring Groups.

A series of Methionine (Met) derivatives, where either the amino group and/or the carboxylic acid group is blocked by acetyl and/or methyl ester functionalities, has been investigated by Collision Induced Dissociation-tandem mass spectrometry (CID-MS) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. The CID-MS experiments were performed using a Fourier-transform ion-cyclotron-resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization (ESI) source. The IRMPD spectra were recorded employing a Paul type ion-trap coupled with the free-electron laser (FEL) FELIX in the fingerprint region from 600 to 2000 cm.

IR spectra of cationic 1,5,9-triazacoronene and two of its cationic derivatives.

Infrared emission features are observed towards diverse astronomical objects in the interstellar medium (ISM). Generally, the consensus is that these IR features originate from polycyclic aromatic hydrocarbons (PAHs) and are hence named aromatic infrared bands (AIBs). More recently, it has been suggested that nitrogen substituted PAHs (PANHs) contribute to the AIBs as well and it has even been shown that nitrogen inclusion in PAHs can improve the match with the AIBs, specifically around the 6.

Structure Determination of Zinc and Cadmium Dication Complexes with Intact and Deprotonated Histidyl Glycine and Glycyl Histidine Dipeptides.

Metalated intact and deprotonated histidyl glycine and glycyl histidine dipeptides were investigated in the gas phase by using infrared multiple photon dissociation (IRMPD) spectroscopy with light from a free-electron laser (FEL). The dipeptides M(GlyHis), M(HisGly), [M(GlyHis-H)], and [M(HisGly-H)], where M = Zn and Cd, were probed to elucidate how the His position along the peptide chain and ligand charge state might influence the structures observed in the gas phase. Simulated annealing calculations were performed to determine energetically low-lying conformers and isomers of these structures.

Rearrangement of Proline Complexes with Zn: An Infrared Multiple Photon Dissociation and Theoretical Investigation.

Complexes of proline (Pro) cationized with Zn and Cd were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. Complexes of intact Pro with CdCl, CdCl(Pro), a complex of (Zn+Pro-H) where a proton has been lost, as well as Zn(Pro-H)(Pro) were formed by electrospray ionization. In order to identify the structures formed experimentally, the IRMPD spectra were compared to those calculated from optimized structures at the B3LYP/6-311+G(d,p) level for zinc complexes and B3LYP/def2-TZVP level with an effective core potential on cadmium for the CdCl(Pro) system.

Investigation of Neighboring Group Participation in 3,4-Diacetylated Glycosyl Donors in the Gas Phase.

A key challenge in oligosaccharide synthesis is the stereoselective installation of glycosidic bonds. Each glycosidic linkage has one of two possible stereo-chemical geometries, α/β or 1,2-cis/trans. An established approach to install 1,2-trans glycosidic bonds is neighboring group participation (NGP), mediated by a 2-O-acyl group.

Structure and fragmentation chemistry of the peptide radical cations of glycylphenylalanylglycine (GFG).

Herein, we explore the generation and characterization of the radical cations of glycylphenylalanylglycine, or [GFG]•+, formed via dissociative electron-transfer reaction from the tripeptide to copper(II) within a ternary complex. A comprehensive investigation employing isotopic labeling, infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations elucidated the details and energetics in formation of the peptide radical cations as well as their dissociation products. Unlike conventional aromatic-containing peptide radical cations that primarily form canonical π-radicals, our findings reveal that 75% of the population of the experimentally produced [GFG]•+ precursors are [GFα•G]+, where the radical resides on the middle α-carbon of the phenylalanyl residue.

Laboratory infrared spectra and fragmentation chemistry of sulfur allotropes.

Sulfur is one of six life-essential elements, but its path from interstellar clouds to planets and their atmospheres is not well known. Astronomical observations in dense clouds have so far been able to trace only 1 percent of cosmic sulfur, in the form of gas phase molecules and volatile ices, with the missing sulfur expected to be locked in a currently unidentified form. The high sulfur abundances inferred in icy and rocky solar system bodies indicate that an efficient pathway must exist from volatile atomic sulfur in the diffuse interstellar medium to some form of refractory sulfur.

Exploring the Scaling Factors for Infrared Modes of PANHs - A Case Study on Cationic 3-Azafluoranthene⋅ and Protonated 3-Azafluoranthene.

Infrared (IR) emission bands by interstellar polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocycles (PANHs) are observed towards a large variety of interstellar objects and offer detailed insights into the chemistry and physics of the interstellar medium. The analysis of the emission bands, and thus the interpretation of the molecular characteristics of the carriers, heavily relies on the use of density functional theory (DFT) calculated IR spectra. However, there are significant challenges in accurately predicting the experimental IR band positions, particularly for PANH emission vibrational modes around 6 μm.

Characterization of elusive rhamnosyl dioxanium ions and their application in complex oligosaccharide synthesis.

Attaining complete anomeric control is still one of the biggest challenges in carbohydrate chemistry. Glycosyl cations such as oxocarbenium and dioxanium ions are key intermediates of glycosylation reactions. Characterizing these highly-reactive intermediates and understanding their glycosylation mechanisms are essential to the stereoselective synthesis of complex carbohydrates.

Vibrational signatures of dynamic excess proton storage between primary amine and carboxylic acid groups.

Ammonium and carboxylic moieties play a central role in proton-mediated processes of molecular recognition, charge transfer or chemical change in (bio)materials. Whereas both chemical groups constitute acid-base pairs in organic salt-bridge structures, they may as well host excess protons in acidic environments. The binding of excess protons often precedes proton transfer reactions and it is therefore of fundamental interest, though challenging from a quantum chemical perspective.

Anomeric Triflates versus Dioxanium Ions: Different Product-Forming Intermediates from 3-Acyl Benzylidene Mannosyl and Glucosyl Donors.

Minimal structural differences in the structure of glycosyl donors can have a tremendous impact on their reactivity and the stereochemical outcome of their glycosylation reactions. Here, we used a combination of systematic glycosylation reactions, the characterization of potential reactive intermediates, and in-depth computational studies to study the disparate behavior of glycosylation systems involving benzylidene glucosyl and mannosyl donors. While these systems have been studied extensively, no satisfactory explanations are available for the differences observed between the 3--benzyl/benzoyl mannose and glucose donor systems.

Structural Elucidation of Agrochemical Metabolic Transformation Products Based on Infrared Ion Spectroscopy to Improve In Silico Toxicity Assessment.

Toxicological assessments of newly developed agrochemical agents consider chemical modifications and their metabolic and biotransformation products. To carry out an in silico hazard assessment, understanding the type of chemical modification and its location on the original compound can greatly enhance the reliability of the evaluation. Here, we present and apply a method based on liquid chromatography-mass spectrometry (LC-MS) enhanced with infrared ion spectroscopy (IRIS) to better delineate the molecular structures of transformation products before in silico toxicology evaluation.

An expeditive and green chemo-enzymatic route to diester sinapoyl-l-malate analogues: sustainable bioinspired and biosourced UV filters and molecular heaters.

Sinapoyl malate, naturally present in plants, has proved to be an exceptional UV filter and molecular heater for plants. Although there are nowadays industrially relevant sustainable synthetic routes to sinapoyl malate, its incorporation into certain cosmetic formulations, as well as its adsorption on plant leaves, is limited by its hydrophilicity. To overcome these obstacles, it is important to find a way to effectively control the hydrophilic-lipophilic balance of sinapoyl malate to make it readily compatible with the cosmetic formulations and stick on the waxy cuticle of leaves.

Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid.

Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics.

Amino Acids as Chelating Ligands for Platinum: Enhanced Stability in an Aqueous Environment Promoted by Biocompatible Molecules.

Platinum-based chemotherapeutics are a cornerstone in the treatment of many malignancies. However, their dose-limiting side effects have rooted efforts to develop new drug candidates with higher selectivity for tumor tissues and less problematic side effects. Here, we developed a cytotoxic platinum(II) complex based on Zeise's salt, containing the nonsteroidal anti-inflammatory drug acetylsalicylic acid and alanine as ligands ().

OH Radical-Induced Oxidation in Nucleosides and Nucleotides Unraveled by Tandem Mass Spectrometry and Infrared Multiple Photon Dissociation Spectroscopy.

OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry (CID-MS ) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. CID-MS results have shown that the addition of one oxygen atom occurs on the nucleobase moiety. The gas-phase geometries of +16 mass increment products of 2'-deoxyadenosine (dA(O)H ), 2'-deoxyadenosine 5'-monophosphate (dAMP(O)H ), 2'-deoxycytidine (dC(O)H ), and 2'-deoxycytidine 5'-monophosphate (dCMP(O)H ) are extensively investigated by IRMPD spectroscopy and quantum-chemical calculations.

Identification of organic micro-pollutants in surface water using MS-based infrared ion spectroscopy.

Comprehensive monitoring of organic micro-pollutants (OMPs) in drinking water sources relies on non-target screening (NTS) using liquid-chromatography and high-resolution mass spectrometry (LC-HRMS). Identification of OMPs is typically based on accurate mass and tandem mass spectrometry (MS/MS) data by matching against entries in compound databases and MS/MS spectral libraries. MS/MS spectra are, however, not always diagnostic for the full molecular structure and, moreover, emerging OMPs or OMP transformation products may not be present in libraries.

Infrared Ion Spectroscopic Characterization of the Gaseous [Co(15-crown-5)(HO)] Complex.

We report fingerprint infrared multiple-photon dissociation spectra of the gaseous monohydrated coordination complex of cobalt(II) and the macrocycle 1,4,7,10,13-pentaoxacyclopentadecane (or 15-crown-5), [Co(15-crown-5)(HO)]. The metal-ligand complexes are generated using electrospray ionization, and their IR action spectra are recorded in a quadrupole ion trap mass spectrometer using the free-electron laser FELIX. The electronic structure and chelation motif are derived from spectral comparison with computed vibrational spectra obtained at the density functional theory level.

Unusual Actinyl Complexes with a Redox-Active N,S-Donor Ligand.

Understanding the fundamental chemistry of soft N,S-donor ligands with actinides across the series is critical for separation science toward sustainable nuclear energy. This task is particularly challenging when the ligands are redox active. We herein report a series of actinyl complexes with a N,S-donor redox-active ligand that stabilizes different oxidation states across the actinide series.

Distinguishing Oligosaccharide Isomers Using Far-Infrared Ion Spectroscopy: Identification of Biomarkers for Inborn Errors of Metabolism.

Distinguishing isomeric saccharides poses a major challenge for analytical workflows based on (liquid chromatography) mass spectrometry (LC-MS). In recent years, many studies have proposed infrared ion spectroscopy as a possible solution as the orthogonal, spectroscopic characterization of mass-selected ions can often distinguish isomeric species that remain unresolved using conventional MS. However, the high conformational flexibility and extensive hydrogen bonding in saccharides cause their room-temperature fingerprint infrared spectra to have broad features that often lack diagnostic value.

An Infrared Spectral Library of Molecular Ions for Metabolite Identification.

Infrared ion spectroscopy (IRIS) continues to see increasing use as an analytical tool for small-molecule identification in conjunction with mass spectrometry (MS). The IR spectrum of an / selected population of ions constitutes a unique fingerprint that is specific to the molecular structure. However, direct translation of an IR spectrum to a molecular structure remains challenging, as reference libraries of IR spectra of molecular ions largely do not exist.

Hydrogen Bonding Shuts Down Tunneling in Hydroxycarbenes: A Gas-Phase Study by Tandem-Mass Spectrometry, Infrared Ion Spectroscopy, and Theory.

Hydroxycarbenes can be generated and structurally characterized in the gas phase by collision-induced decarboxylation of α-keto carboxylic acids, followed by infrared ion spectroscopy. Using this approach, we have shown earlier that quantum-mechanical hydrogen tunneling (QMHT) accounts for the isomerization of a charge-tagged phenylhydroxycarbene to the corresponding aldehyde in the gas phase and above room temperature. Herein, we report the results of our current study on aliphatic trialkylammonio-tagged systems.