Calculated vertical ionization energies of the common α-amino acids in the gas phase and in solution

The vertical ionization energies of the low-lying conformers of the α-amino acids found in proteins have been calculated. Geometry optimizations were first performed at the B3LYP/6-311G(d,p) level of theory, and then reoptimized at the MP2/6-311G(d,p) level of theory. Vertical ionization energies were then computed by three methods, electron propagator in the partial third-order (P3) approximation, Outer-Valence-Green's Functions, and by evaluating the difference in the total energy between the cation radical and the neutral amino acid in the geometry of the neutral species. When available, the results are compared to the experimental vertical ionization energies. The vertical ionization energies calculated using the MP2/P3 method gave the best overall agreement with the experimental results. Next, the ionization energies in solution are calculated for the zwitterionic forms of the α-amino acids by using IEFPCM methods. To obtain the vertical ionization energy in solution, it is necessary to use the nonequilibrium polarizable continuum model (NEPCM), the results of which are reported here for the α-amino acids.     

Comparison of the effects of ionization mechanism, analyte concentration, and ion “cool-times” on the internal energies of peptide ions produced by electrospray and atmospheric pressure matrix-assisted laser desorption ionization

The propensities of a series of peptide ions produced by both electrospray and atmospheric pressure matrix assisted laser desorption ionization (AP-MALDI) to fragment in an ion trap mass spectrometer under various conditions were studied in detail by measuring the extent of fragmentation of precursor ions by collision induced dissociation (CID) as a function of applied resonance excitation RF voltage. For the most basic peptides, the energy required to fragment MH+ ions generated by electrospray exceeded that required to fragment equivalent AP-MALDI ions under identical instrumental conditions; the reverse was observed for a peptide incorporating no basic residues, while peptides of intermediate basicity showed little difference between the ionization methods. This correlation between peptide basicity and the difference in the energy required to induce fragmentation of MH+ ions generated by AP-MALDI and electrospray is attributed primarily to a trend in the internal energies of the ions generated by AP-MALDI (the greater the difference in gas-phase basicities between the matrix and the analyte the greater the internal energy of the analyte ions produced). Furthermore the internal energies of ions produced by AP-MALDI, but not the equivalent ions formed by electrospray, were observed to decrease with decreasing analyte concentration. We attribute this finding to the cooling effect of endothermic dissociation of analyte ion/matrix molecule clusters following the matrix assisted laser desorption step. Time-resolved analyses (measurement of extent of fragmentation of precursor ions by CID as a function of pre-CID "cool times") revealed that cooling periods in excess of 250 ms were required to achieve internal energy equilibrium through cooling collisions with the helium buffer gas. Furthermore, these analyses demonstrated that, even after these extended cooling times, equivalent ions formed by the two ionization techniques showed different propensities to fragment. We conclude that the two different ionization techniques produce ion populations that may differ in their three-dimensional structure.     

Analysis of ancient Greco–Roman cosmetic materials using laser desorption ionization and electrospray ionization mass spectrometry

Microsamples of pink cosmetic powders from the Greco–Roman period were analyzed using two complementary analytical approaches for identification of the colouring agents (lake pigments originally manufactured from madder plants with an inert binder, usually a metallic salt) present in the samples. The first technique was a methanolic acidic extraction of the archaeological samples with an additional ethyl acetate extraction of the anthraquinone-type colouring agents which were identified using high performance liquid chromatography coupled to electrospray ionization with high resolution mass spectrometry (LC–ESI–HRMS), and the second was direct analysis of a microsample by laser desorption ionization–mass spectrometry (LDI–MS). The latter technique is well suited when the quantity of samples is very low. This soft ionization technique enables the detection of very small quantities of compounds using the combination of positive and negative-ion modes. It was also successfully applied for the direct analysis of some laboratory-made reference compounds. However, the presence of lead in one of these ancient samples induced a spectral suppression phenomenon. In this case and conditional on a sufficient quantity of available sample, the former method is better adapted for the characterization of these anthraquinone-type molecules. This study also confirmed that purpurin, munjistin, and pseudopurpurin are the principal colouring agents present in these ancient cosmetic powders constituted from madder plants. Presented at the Annual French National Symposium on Mass Spectrometry, Electrophoresis and Proteomics, 20–23 September 2007 in Pau, France.     

What do matrix‐assisted laser desorption/ionization mass spectra reveal about ionization mechanisms?

We present ion mass spectra obtained by matrix-assisted laser desorption/ionization for analytes of approximately 1000 Da across the largest range of wavelengths and pulse durations to date. The matrix used in all cases was 2,5-dihydroxybenzoic acid. Based on the data and fundamentals of laser-material interactions, we evaluated the plausibility of discriminating among such ion formation mechanisms as multiphoton ionization and excited-state ionization from mass spectra alone. Some previously proposed mechanisms appear unlikely for the matrix-analyte systems that we studied, casting doubt on their general applicability. Moreover, although analysis of mass spectra can apparently exclude certain mechanisms, it cannot establish which of several competing mechanisms is actually operative. This is particularly true with respect to variations in pulse duration and wavelength.     

O−• chemical ionization of carbonyl compounds

The negative ion chemical ionization mass spectra of twentyeight C₄ to C₇ carbonyl compounds were recorded using the oxide radical anion O^?? as reagent ion. As noted earlier, the reactions occurring include H⁺ abstraction, H ₂ ^+? abstraction, H? atom displacement, and alkyl radical displacement. In addition, the [M?2H]^? ions fragment further by alkyl radical elimination. The relative importance of these reactions depends strongly on molecular structure, with the result that isomer distinction frequently is possible. Where this is not possible, as for isomeric aldehydes, the collisional charge inversion mass spectra of common product ions provides isomer distinction. The H ₂ ^+? abstraction reaction is shown to involve abstraction not only of two hydrogens from the same α-carbon but also, in part, abstraction of one hydrogen from each α-carbon.     

Electron ionization mass spectrometry: Quo vadis?

Mass spectrometry (MS) is a fundamental technique to identify compounds by their mass-to-charge ratio. It is known that MS can only detect target compounds when they are converted to ions in the gas phase. The ionization procedure is considered one of the most critical steps, and there are distinct techniques for it. One of them is electron ionization (EI), a widely used hard-ionization technique capable of generating several ions due to the excess energy employed. The existence of distinct ionization mechanisms turns EI capable of producing a fingerprint-like spectrum for each molecule. So, it is an essential technique for obtaining structural information. EI is often combined with chromatography to obtain a practical introduction of pretreated samples despite its excellent performance. EI–MS has been applied coupled with gas chromatography (GC) since the 1960s as both are very compatible. Currently, analytes of interest are more suitable for liquid chromatography (LC) analysis, so there are researchers dedicated to developing suitable interfaces for coupling LC and EI–MS. EI excels, as a reliable technique to fill the gap between GC and LC, possibly allowing them to coexist in a single instrument. In this work, the authors will present the fundamentals of EI–MS, emphasizing the development over the years, coupling with gas and LC, and future trends.     

Comparison of negative chemical ionization and electron impact ionization in gas chromatography–mass spectrometry of endocrine disrupting pesticides

The study of pesticide residues belonging to endocrine disrupting chemicals (EDCs) (23 analytes of different chemical classes – organochlorines, organophosphates, pyrethroids, dicarboximides, phtalamides, dinitroanilines, pyrazole, triazinone) in apple matrix with conventional capillary GC–NCI-MS (with methane as reagent gas) in comparison to EI ionization is presented. For sample preparation QuEChERS method was applied. The lowest calibration levels (LCLs) for all pesticides were determined in both modes. Calibration in the NCI mode was performed at the concentration levels from 0.1 to 500 μg kg⁻¹ (R² > 0.999) and for EI in the range from 5 to 500 μg kg⁻¹ (R² > 0.99). From LCLs the instrumental limits of detection (LODs) and quantification (LOQs) were calculated. Chemometric study of pesticide signals in two MS modes was performed. Repeatability of all measurements, expressed by the relative standard deviations of absolute peak areas was better than 10% for the majority of compounds. Significantly lower values were obtained for the NCI mode.     

Do charge-remote fragmentations occur under matrix-assisted laser desorption ionization post-source decompositions and matrix-assisted laser desorption ionization collisionally activated decompositions?

The precursor ions of tetraphenylporphyrins that are substituted with fatty acids can be introduced into the gas phase by matrix-assisted laser desorption ionization (MALDI) and undergo post-source and collisionally activated decompositions (CAD) in a time-of-flight mass spectrometer. The goal of the research is to obtain a better understanding of post-source decompositions (PSD); specifically, we asked the question of whether ions undergoing PSD have sufficient energy to give charge-remote fragmentations along an alkyl chain. We chose the porphyrin macrocycle because we expected it to act as an inert "support," allowing the molecule to be desorbed by MALDI and to be amenable to charge-remote fragmentation. MALDI-PSD and MALDI-CAD spectra are similar to high-energy CAD spectra and considerably more informative than low-energy CAD spectra, showing that charge-remote fragmentations of the fatty acid moieties do occur upon MALDI-PSD and MALDI-CAD.     

How accurate are DFT treatments of organic energies?

Increasing awareness that popular functionals fail to describe many energies accurately has ended expectations of black-box DFT usage. The performance of nine density functionals, compared by computing the bond separation energies of 72 illustrative hydrocarbons with available experimental data, reveals that only Zhao and Truhlar's recently proposed M05-2X functional, with a 2.13 kcal/mol average deviation from experiment, performs satisfactorily. B3LYP and other functionals show larger deviations.     

On the accuracy of numerical Hartree–Fock energies

It is demonstrated that numerical Hartree–Fock (HF) energies reported in the literature in some cases have errors in the milliHartree range. The main cause of these errors is due to the use of too small a value for the practical infinity parameter in the finite difference method for generating the results. By systematically investigating the convergence with respect to the computational parameters, HF energies accurate to at least 1 microHartree are generated for 42 diatomic systems containing first and second row elements, encompassing both cationic, neutral and anionic systems.     

Does electrospray ionization produce gas-phase or liquid-phase structures?

Electrospray ionization of tyrosine from a 3:1 (v:v) CH3OH/H2O solution is found to afford an M - H ion which is a 70:30 mixture of phenoxide and carboxylate ions. This corresponds to the gas-phase equilibrium composition and not the liquid-phase proportions. In contrast, the carboxylate is produced as the dominant ion (approximately 95%) from anhydrous CH3CN and CH3CN/H2O mixtures. The addition of small amounts of CH3OH to the solvent, however, convert the M - H ion back into the gas-phase isomeric ratio. The isomeric structure therefore depends on the solvent system from which an ion is sprayed.     

Generation of multiple charged ions: Photoemission electron impact ionization

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Nanoelectrospray—More than just a minimized-flow electrospray ionization source

The comparison between electrospray ionization (ESI) mass spectra from NaCl solutions with and without analyte obtained under ionspray and nanospray conditions reveals different mass spectral behavior of the two ESI techniques. This can be attributed to the different initial droplet sizes which are in the microns range for ionspray, while in nanospray they are believed to be about one order of magnitude smaller. In the context of the widely accepted uneven-fission model, nanospray would then enter one fission generation later; in addition, a higher initial droplet surface charge density in nanospray results in early fissions without extensive evaporation and thus increase in sample and salt concentration. This rationalizes that ionspray spectra closely resemble nanospray spectra from solutions with about one order of magnitude higher salt concentrations, showing a higher tolerance of nanospray towards salt contamination. When the analyte is a peptide (in a solution containing a high molar surplus of salt), molecule ion formation effectively competes with salt cluster ion formation; when the analyte is a sugar, it is detectable beside a high salt concentration only with nanospray, indicating the supporting effect of surface activity on ion release in the case of peptides. A model is presented which explains the different mass spectral behaviour of ionspray and nanospray by suggesting different "predominant fission pathways" depending on the size of the initial droplets.     

Dissociation energies of O–H bonds in 3-pyridinols

The O?H bond dissociation energy (D _O?H) has been estimated for 20 substituted 3-pyridinols and a substituted 3-pyrimidinol from experimental kinetic data by the intersecting parabolas method using α-tocopherol and 4-methoxyphenol as reference compounds. The following D _O?H values (kJ/mol) have been obtained: 363.7 for 3-pyridinol, 365.3 for 2-alkyl-3-pyridinols (five compounds), 358.8 for 2-alkyl-6-methyl-3-pyridinols (six compounds), 378.1 for 5-benzyl-3-pyridinol, 353.2 for 2,4,6-trimethyl-3-pyridinol, 340.9 for 2-benzyl-6-methoxy-3-pyridinol, 345.8 for 2,6-dimethoxy-5-benzyl-3-pyridinol, 381.7 for 2-ethyl-4-nitro-6-methyl-3-pyridinol, 376.8 for 2-isopropyl-4-nitro-6-methyl-3-pyridinol, 318.3 for 2,4-dimethyl-6-dimethylamino-3-pyridinol, 357.3 for mexidol, and 322.2 for 2,4-dimethyl-6-dimethylamino-3-pyrimidinol. The substituent effect on the O?H bond dissociation energy in 3-pyridinols is considered. The stabilization energies of pyridinoxyl and phenoxyl radicals are compared. The activation energies and rate constants have been calculated for a series of reactions of various radicals with 3-pyridinols.     

Are solvation free energies of homogeneous helical peptides additive?

We investigated the additivity of the solvation free energy of amino acids in homogeneous helices of different length in water and in chloroform. Solvation free energies were computed by multiconfiguration thermodynamic integration involving extended molecular dynamics simulations and by applying the generalized-born surface area solvation model to static helix geometries. The investigation focused on homogeneous peptides composed of uncharged amino acids, where the backbone atoms are kept fixed in an ideal helical conformation. We found nonlinearity especially for short peptides, which does not allow a simple treatment of the interaction of amino acids with their surroundings. For homogeneous peptides longer than five residues, the results from both methods are in quite good agreement and solvation energies are to a good extent additive.     

When does the non-variational nature of second-order Møller-Plesset energies manifest itself? All-electron correlation energies for open-shell atoms from K to Br

All-electron correlation energies E(c) are not very well known for open-shell atoms with more than 18 electrons. The complete basis-set (CBS) limits of second-order M?ller-Plesset (MP2) perturbation theory energies are obtained for open-shell atoms by computations in large basis sets combined with a knowledge of the MP2/CBS limit for the next larger closed-shell atom with the same valence shell structure. Then higher-order correlation corrections are found by coupled-cluster calculations using basis sets that are not quite as large. The method is validated for the open-shell atoms from Al to Cl for which E(c) is reasonably well established. Then, the method is used to obtain non-relativistic E(c) values, probably accurate to 3%, for the open-shell atoms of the fourth period: K, Sc-Cu, and Ga-Br. These energies are compared with the predictions of 19 density functionals and may be useful for the parameterization of new ones. The results show that MP2 overestimates |E(c)| for atoms heavier than Fe.     

Quantifying labile protein—Ligand interactions using electrospray ionization mass spectrometry

A new electrospray ionization mass spectrometry (ES-MS) approach for quantifying protein—ligand complexes that are prone to in-source (gas-phase) dissociation is described. The method, referred to here as the reference ligand ES-MS method, is based on the direct ES-MS assay and competitive ligand binding. A reference ligand (L_ref), which binds specifically to the protein (P), at the same binding site as the ligand (L) of interest, with known affinity and forms a stable protein—ligand complex in the gas phase, is added to the solution. The fraction of P bound to L_ref, which is determined directly from the ES mass spectrum, is sensitive to the fraction of P bound to L in solution and enables the affinity of P for L to be determined. A mathematical framework for the implementation of the method in cases where P has one or two specific ligand binding sites is given. Affinities of two carbohydrate-binding proteins, a single chain fragment of a monoclonal antibody and the lectin concanavalin A, for monosaccharide ligands are reported and the results are shown to agree with values obtained using isothermal titration calorimetry.     

Dispersion dominated halogen-π interactions: energies and locations of minima

The interactions of halogen atoms with aromatic π-systems can be crucial for structural stability and ligand binding. However, many aspects of the nature and energetics of these interactions remain elusive. Therefore, we designed model systems mimicking the T-shaped complex of chloro- and bromobenzene with tyrosine as found, e.g., in serine protease-inhibitor complexes. Three dimensional potential energy surfaces (3D-PES) were calculated at a high level of theory, up to CCSD(T). On these 3D-PES the exact location of the minima and, even more important, the shape of favorable interaction regions were determined. We show that the height of the halogen atom above the tyrosine-ring is decisive, while the lateral position is of minor influence. Finally, a truncated harmonic potential is developed to modify the Amber/GAFF force field to shift the locations of the minima to the correct regions.     

Electrospray ionization suppression,a physical or a chemical phenomenon?

Mass spectrometry is a powerful qualitative and quantitative analytical technique that has been introduced in many bioanalytical and research laboratories in the last 10 years. The combination of HPLC with tandem MS yields a particularly powerful tool and it is now the method of choice for the analysis drugs, metabolites, biomarkers and proteins. However, HPLC-MS methods are not completely without problems that can compromise the quality of the results. An important phenomenon that can affect the quantitative performance of a mass detector is ion suppression. In this study, we measured the influence of the observed current (I) vs signal intensity and the variation of the observed current (I) when analyzing biological samples. Our experiment suggests that, despite the fact that it is possible for other chemicals to compete for protons in the droplets, the increase in the observed current (I) during the signal suppression is important and indicates that the conductivity of the liquid increases significantly. The salts and the charged species influence the conductivity and the surface tension of the droplets and modify the equilibrium between the two main forces involved during the electrospray process, resulting in an erratic spray behavior.