Infrared photodissociation analyses are supported by theoretical calculations that allow a trustworthy interpretation of experimental spectra of gaseous ions. B3LYP calculations are the most prominent method used to model IR spectra, as detailed in our bibliographic survey. However, this and other commonly used methods are known to provide inaccurate energy values and geometries, especially when it comes to long-range interactions, such as intramolecular H-bonds, which show increased anharmonicity. Therefore, we evaluated some of the most commonly used density functional theory methods (B3LYP, CAM-B3LYP, and M06-2X) and basis sets (6-31+G(d,p), 6-311++G(d,p), 6-311++G(3df,2pd), aug-cc-pVDZ, and aug-cc-pVTZ), including anharmonicity and dispersion corrections. The results were compared to MP2 calculations and to experimental high-frequency (2000–4000 cm –1 ) IR multiphotonic dissociation (IRMPD) spectra of two protonated model molecules containing intramolecular hydrogen bonds: biotin and tryptophan. M06-2X/6-31+G(d,p) was shown to be the most cost-effective level of theory, whereas CAM-B3LYP was the most efficient method to describe the van der Waals interactions. The use of the dispersion correction D3, proposed by Grimme, improved the description of O–H vibrations involved in H-bonding but worsened the description of N–H stretches. Anharmonic calculations were shown to be extremely expensive when compared to other approaches. The efficiencies of well-established scaling factors (SFs) in opposition to sample-dependent SFs were also discussed and the use of fitted SFs were shown to be the most cost-effective approach to predict IRMPD spectra. M06-2X/6-31+G(d,p) and CAM-B3LYP/aug-cc-pVDZ were also tested against the fingerprint region. Our results suggest that these methods can also be used for analysis in this lower frequency range and should be regarded as the methods of choice for cost-effective IRMPD simulations rather than the ubiquitous B3LYP method, especially when further molecular properties are needed.

Rationale Methods for isomer discrimination by mass spectroscopy are of increasing interest. Here we describe the development of a three‐dimensional ion trap for infrared multiple photon dissociation (IRMPD) spectroscopy that enables the acquisition of the infrared spectrum of selected ions in the gas phase. This system is suitable for the study of a myriad of chemical systems, including isomer mixtures. Methods A modified three‐dimensional ion trap was coupled to a CO2 laser and an optical parametric oscillator/optical parametric amplifier (OPO/OPA) system operating in the range 2300 to 4000 cm−1. Density functional theory vibrational frequency calculations were carried out to support spectral assignments. Results Detailed descriptions of the interface between the laser and the mass spectrometer, the hardware to control the laser systems, the automated system for IRMPD spectrum acquisition and data management are presented. The optimization of the crystal position of the OPO/OPA system to maximize the spectroscopic response under low‐power laser radiation is also discussed. Conclusions OPO/OPA and CO2 laser‐assisted dissociation of gas‐phase ions was successfully achieved. The system was validated by acquiring the IRMPD spectra of model species and comparing with literature data. Two isomeric alkaloids of high economic importance were characterized to demonstrate the potential of this technique, which is now available as an open IRMPD spectroscopy facility in Brazil.

Benzoxazine formation is a fundamental step in the preparation of polybenzoxazine resins, and a detailed description of the mechanism governing the formation of benzoxazine and side products is vital for improving the properties and performance of these resins. Determination of the nature and properties of reaction intermediates is not trivial. Therefore, a Mannich-type condensation of aniline, formaldehyde, and phenol was evaluated as a potential method to form benzoxazine. Coupling positive mode electrospray ionization mass spectrometry (ESI­(+)-MS) with infrared multiple photon dissociation (IRMPD) spectroscopy allowed unambiguous determination of an iminium-based mechanism and the direct observation of iminium intermediates. The benzoxazine formation mechanism was indirectly confirmed by the observation of side products that are relevant to the polymerization step, and directly confirmed by the identification of four distinct reaction intermediates that were completely characterized by IRMPD spectroscopy. The benzoxazine monomer was also shown to undergo isomerization under standard ESI-MS analysis conditions, suggesting the presence of a mixture of three isomers during their usual ESI-MS analysis.

The diagnosis of multiple sclerosis (MS) has changed over the last decade, but remains a composite of clinical assessment and magnetic resonance imaging to prove dissemination of lesions in time and space. The intrathecal synthesis of immunoglobulin may be a nonspecific marker and there are no plasma biomarkers that are useful in the diagnosis of MS, presenting additional challenges to their early detection. Methods We performed a preliminary untargeted qualitative lipidomics mass spectrometry analysis, comparing cerebrospinal fluid (CSF) and plasma samples from patients with MS, other inflammatory neurological diseases and idiopathic intracranial hypertension. Results Lipid identification revealed that fatty acids and sphingolipids were the most abundant classes of lipids in the CSF and that glycerolipids and fatty acids were the main class of lipids in the plasma of patients with MS. The area under the curve was 0.995 (0.912–1) and 0.78 (0.583–0.917), respectively. The permutation test indicated that this ion combination was useful for distinguishing MS from other inflammatory diseases (p < 0.001 and 0.055, respectively). Conclusion This study concluded that the CSF and plasma from patients with MS bear a unique lipid signature that can be useful as a diagnostic biomarker.