Application of computational quantum chemistry to chemical processes involved in mass spectrometry

The field of application of mass spectrometry (MS) has increased considerably due to the development of ionization techniques. Other factors that have stimulated the use of MS are the tandem mass spectrometry (MS/MS) and sequential mass spectrometry (MSn) techniques. However, the interpretation of the MS/MS and MSn data may lead to speculative conclusions. Thus, various quantum chemical methods have been applied for obtaining high quality thermochemical data in gas phase. In this review, we show some applications of computational quantum chemistry to understand the formation and fragmentation of gaseous ions of organic compounds in a MS analysis.Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)FAPESPCNP

A Fragmentation study of di-acidic mycosporine-like amino acids in electrospray and nanospray mass spectrometry

Two mycosporine (MAAs), containing an extra acid function, were analyzed by nanospray and electrospray ionization tandem mass spectrometry. In contrast to the previous studies it is demonstrated that no significant characteristic methyl radical loss occurred in positive mode. The fragmentation pathway in negative mode was also proposed in this work, along with theoretical calculations to characterize the site of protonation.No presente estudo, duas micosporinas (MAAs) contendo um segundo ácido carboxílico foram submetidas à fragmentação em eletrospray e nanospray em diferentes equipamentos. Em contraste com resultados anteriores, a eliminação de radical metila no modo positivo de análise foi um processo minoritário de fragmentação. Neste trabalho apresentamos também a via de fragmentação destas substâncias em modo negativo e cálculos teóricos para caracterizar os sítios de protonação.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Fragmentation study of di-acidic mycosporine-like amino acids in electrospray and nanospray mass spectrometry

No presente estudo, duas micosporinas (MAAs) contendo um segundo ácido carboxílico foram submetidas à fragmentação em eletrospray e nanospray em diferentes equipamentos. Em contraste com resultados anteriores, a eliminação de radical metila no modo positivo de análise foi um processo minoritário de fragmentação. Neste trabalho apresentamos também a via de fragmentação destas substâncias em modo negativo e cálculos teóricos para caracterizar os sítios de protonação. Two mycosporine (MAAs), containing an extra acid function, were analyzed by nanospray and electrospray ionization tandem mass spectrometry. In contrast to the previous studies it is demonstrated that no significant characteristic methyl radical loss occurred in positive mode. The fragmentation pathway in negative mode was also proposed in this work, along with theoretical calculations to characterize the site of protonation. Keywords: mycosporine, nanoESI-MS/MS, ESI-MS/MS, natural products, algae Introduction Mycosporine-like amino acids (MAAs) are a group of chemically related, water soluble compounds responsible for UV photoprotection in a diverse range of organisms including invertebrates, fish, bacteria, cyanobacteria, micro-and macroalgae. 1-3 These compounds are chemically characterised by the presence of either a cyclohexenone or cyclohexenimine chromophore conjugated with a substituent nitrogen of an amino acid, amino alcohol or amino group 1 MAAs normally show a strong UV absorption between 310 and 360 nm with high molar extinction coefficients. These characteristics indicate a possible photoprotective role that has been demonstrated in a number of studies 11-13 17 In the last few years, nanospray ionisation (nanoESI) is beginning to increase in importance, especially with the development of automated systems using 'chips' (arrays of uniform nanospray needles that are used only once to avoid contamination). 21 NanoESI offers the possibility of improved sensitivity and lower sample consumption over conventional ESI for the analysis of natural products. 22 This is especially important for the study of extracts from biological and medicinal sources when often only a very small amount of material is available. In 'chip based' nanoESI, the analyte solution is sprayed from a conducting pipette tip pressed against the rear of a chip using a small gas pressure and much lower voltages to create the spray. Recently, analysis of some natural antioxidants (retinoids Experimental Chemicals All solvents used were HPLC grade (Tedia, J. Baker and Fisher). Water was purified using a Milli-Q system (Millipore, Bedford, MA, USA). Trifluoroacetic acid (99.9%) was purchased from Aldrich. Galena Química e Farmacêutica Ltda/Brazil kindly supplied the standards of shinorine and porphyra-334 (product Helioguard ® 365-Porphyra umbilicalis extracts) Instrumentation Nanospray ionisation analyses were performed on two quadrupole-time of flight hybrid instruments: (a) an UltrOTOF-Q (Bruker Daltonics, Billerica, MA) using Tip™ Emittek (glass tip capillaries working with 500 V) or (b) a QStar-XL (Applied Biosystems, Warrington, UK) using a Nanomate HD automatic 'chip based' nanospray system (Advion Biosciences, Norwich, UK). The Nanomate was set for 5 µL of solution to be aspirated and sprayed through a Nanomate 400 chip at 1.45 kV, with a nitrogen back pressure of 0.4 psi. On both instruments, the ion source gas and curtain gas were nitrogen. Electrospray ionisation analyses were performed on five instruments: (a) an Apex 4 7.0 Tesla Fouriertransform ion-cyclotron resonance mass spectrometer (Bruker Daltonics, Billerica, MA, USA). Samples were directly infused into the Apollo electrospray source from a syringe pump at 100 µL h -1 . Analyses were performed at a capillary voltage, of 4600V and capillary exit potential of 200 V (except were indicated otherwise). The N 2 drying gas temperature was 200 °C. A mixture of PEG grades was used as an external calibrant for accurate-mass ESI analysis; (b) on a quadrupole-time of flight instrument (UltrOTOF-Q, Bruker Daltonics, Billerica, MA). The analyses were performed in positive ion ESI mode at a capillary voltage of 3400 V and N 2 drying gas temperature of 180 °C. NaTFA 10 mmol L -1 was used as a standard for internal and external calibration; (c) on a QStar-XL quadrupole-time-of-flight instrument (Applied Biosystems, Warrington, UK); (d) on a Quattro-LC triple quadrupole mass spectrometer (Micromass, Manchester, UK); (e) on an Esquire HCT ion trap instrument (Bruker Daltonics, Billerica, MA, USA) using a syringe pump (Cole-Parmer, Vernon Hills, IL, USA). Ion trap analyses were performed using nitrogen as the nebulising and drying gas and helium as the bath gas (4×10 -6 mbar). Theoretical calculations All calculations were performed in Gaussian 03 27 suite of programs using the B3LYP/6-31+G(d,p) model. 28,29 The geometries of neutral and protonated species were optimised and the potential energy surface minima were indicated by analysis of vibrational frequencies. The gasphase basicity and proton affinity were calculated via a protonation reaction, using Gibbs energies and enthalpies, respectively. 30 Cardozo et al. 1627 Vol. 20, No. 9, 2009 Results and Discussion Mycosporine-like amino acids with one acidic function were previously analysed by positive mode ESI sequential mass spectrometry (at high-resolution and accurate-mass). The loss of a methyl radical by the homolytic cleavage of the O-C bond was observed to be the preferred fragmentation pathway. As expected, analysis in negative ion mode Conclusions These results indicate that the presence of a second carboxylic acid function significantly reduces the intensity of the observed product ions from the radical methyl cleavage in positive mode MS/MS. As expected, in the negative ion mode, the radical fragmentation pathway does not occur. Taken together, these results confirm the importance of careful selection of the product ions used for analytical protocols for the analysis of crude extracts containing MAAs where the presence of the second acid function may change the fragmentation behavior and the classical analysis of loss of methyl radical may lead to the wrong conclusions during screening for MAAs

Qual o sítio de reação? Um experimento computacional

A computational quantum chemistry experiment is described on the determination of the most reactive atom in a molecule for a reaction. The reaction studied was the S N2 of 4-(dimethylamino)pyridine and methyl iodide. Several indexes (HOMO coefficent, (c), charges, (q), nucleophilic softness, (s+), and Fukui index, (f+)) were employed to verify which correctly describe what nitrogen will react. The calculations were made by AM1 and HF/STO-3G methods. The correct reactivity order is only reproduced by s+ and f+. The lack of agreement of FMO based indexes was discussed

Ozone and Other 1,3-Dipoles: Toward a Quantitative Measure of Diradical Character

International audienceOzone and its sulfur-substituted isomers are studied by means of the Breathing Orbital Valence Bond ab initio method, with the objective of estimating their controversial diradical characters. The calculated weights of the various VB structures and their individual diabatic energies are found to be consistent with each other. All 1,3-dipoles can be described in terms of three major VB structures, one diradical and two zwitterionic ones, out of the six structures, forming a complete basis. Ozone has a rather large diradical character, estimated to 44%–49%. SOO and SOS are even more diradicalar, whereas SSO and especially OSO are better described as closed-shell zwitterions. Moreover, the description of 1,3-dipoles, in terms of the three major structures, yields VB weights in full agreement with simple chemical wisdom, i.e., a diradical weight of 33% when the three structures are quasi-degenerate, and a smaller (larger) value when the diradical structure is higher (lower) in energy than the zwitterionic ones. Therefore, the VB-calculated weight of the diradical structure of a molecule qualifies itself as a quantitative measure of diradical character, and not only as an indicator of tendencies. Other definitions of the diradical character, based on molecular orbital/configuration interaction methods, are discussed

Efeitos de substituintes na ligação de hidrogênio do 3-hidroxipropenal

The effect of substituents on the energies and geometries of 3-hydroxypropenal was studied using the B3LYP/6-311++G(d,p) model. The hydrogen bond energies indicate that the strongest donors and the weakest acceptors present the highest and the weakest hydrogen bonds, respectively, indicating the validity of the Madsen RAHB model. Geometric parameters indicate that the intensity of the hydrogen bond is proportional to the resonance, as suggested by the RHAB model. The effect of substituents diverges from the model proposed by Gilli et al. Sometimes the results indicate that the donor or acceptor effect is more important than the point of substitution

An electronic and vibrational study of the cyclopropenyl ion and its fluoroderivatives

This article presents the results of ab initio SCF-MO calculations on both the electronic structure and vibrational spectra of the cyclopropenyl cation (C3H3+) and its fluoroderivatives, C3H2F+, C3HF2+ and C3F3+. A very simple and unambiguous criterion for choosing the combination of diffuse and polarization functions which, together with the 6311G basis set, best describes the electron distribution in these ions is presented. The electronic structures of the cations are analysed in detail; particular emphasis is given to the analysis of the electronic effects due to successive hydrogen-by-fluorine replacements. The results of vibrational normal mode analysis carried out for all hydrogen-deuterium isotopomers of the studied ions are presented and compared with the available experimental data. The theoretical results are used both to review some band assignments previously proposed for the fluorosubstituted molecules and to give a stronger theoretical foundation to the general interpretation of the vibrational spectra of these compound