Formation of complexes between uracil and calcium ions: an ESI/MS/MS study in combination with theoretical calculations

Cationized uracil clusters around calcium metal ions were generated in the gas phase by electrospray ionization (ESI). A previous study showed that with particular experimental conditions, hexamer, octamer, decamer, dodecamer and tetradecamer uracil clusters are present in high quantities. New experiments were carried out to understand the reasons for the particular stability of these complexes. MS/MS experiments suggested that these uracil clusters belong to the same family. Based on ab initio and DFT quantum chemistry calculations, structures in agreement with experimental results are proposed for these clusters. Copyright © 2009 John Wiley & Sons, Ltd.     

Decameric uracil complexes around Li+

Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li⁺ ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U₁₀Li⁺ is formed, which was referred to as an indication for so‐called ‘magic number’ cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas‐phase structure which is compatible with all experimental findings. Copyright © 2010 John Wiley & Sons, Ltd.     

Structures and energetics of electrosprayed uracil(n)Ca2+ clusters (n = 14-4) in the gas phase

Clusters of uracil (U) about a calcium dication, U(n)Ca(2+) (n = 14-4), have been studied in the gas phase by both experimental and theoretical methods. Temperature dependent blackbody infrared radiative dissociation (BIRD) experiments were performed on U(n)Ca(2+) clusters with n = 14-5 and the observed Arrhenius parameters are reported here. Master equation modeling of the BIRD kinetics data was carried out to determine threshold dissociation energies. Initial geometry calculations were performed using the B3LYP density functional and 3-21G(d) basis set. A sample of ten conformations per cluster was obtained through a simulated annealing study. These structures were optimized using B3LYP/6-31G(d) level of theory. Fragment-based hybrid many body interaction (HMBI) MP2/6-311++G(2df,2p)/Amoeba calculations were performed on representative conformations to determine theoretical binding energies. Results were examined in relation to cluster size (n). A significant increase in the energy required to remove uracil from U(6)Ca(2+) when compared to larger clusters supports previous reports that the calcium ion is coordinated by six uracil molecules in the formation of an inner shell. For clusters larger than n = 6, an odd-even alternation in threshold dissociation energies was observed, suggesting that the outer shell uracil molecules bind as dimers to the inner core. Proposed binding schemes are presented. Multiple structures of U(5)Ca(2+) are suggested as being present in the gas phase where the fifth uracil may be either part of the first or second solvation shell.     

Large mixed complexes involving uracil,cytosine, thymine and/or 1‐methyl uracil around Ca2+ ions: an electrospray ionization/MS study

We investigated the possible formation of mixed B_nB′_n′Ca²⁺ complexes where B and B′ are two different nucleobases. Electrospray ionization (ESI) mass spectrometric experiments from solutions containing two different kinds of nucleobases and calcium ions were carried out to investigate the formation of magic number clusters that may be relevant in a biological point of view. The results presented here clearly show that mixed complexes can be formed and are stable in the gas phase. This represents an important step toward more complex solutions in which several nucleobases are present simultaneously and may compete in the formation of cationized clusters. We believe that thorough investigations on such systems may help understanding biological processes that may effect the tridimensional structure of the DNA macromolecule. The formation of mixed hexamers, decamers, dodecamers and tetradecamers are clearly favored from solution containing uracil (Ura), thymine (Thy) and Ca²⁺, whereas mixed octamers are preferred from 1‐methyl uracil (MeU), uracil and Ca²⁺ mixtures. Cytosine (Cyto) can form mixed complexes with either uracil or 1‐methyl uracil or thymine. On the other hand, the main species formed in these latter cases are mixed tetramers. Copyright © 2013 John Wiley & Sons, Ltd.     

Computational studies of the cationic aluminium(chloro) hydroxides by quantum chemical ab initio methods

Cationic aluminium(chloro) hydroxide complexes with two to four aluminium atoms were studied using quantum chemical methods. Complexes were studied in both gas and liquid phase. The liquid environment was modeled by using a conductor-like screening model (COSMO). COSMO calculations were carried out as a single point calculation at the optimized gas phase structures. Water (epsilon = 78.54) was used as the solvent. The minimum energy structures obtained from the gas phase studies were mostly compact cyclic structures. Aluminium preferred to be five-coordinated in oxygen rich clusters. Core oxygen preferred three-fold coordination but in the largest clusters the four-coordinated oxygen was observed. Water reacted dissociatively with hydrogen poor clusters. The COSMO calculations showed that the optimal structures of cationic aluminium(chloro) hydroxides tend to be more open in the liquid than in the gas phase.     

Investigations of the fragmentation pathways of benzylpyridinium ions under ESI/MS conditions

Benzylpyridinium ions are often used as ‘thermometer ions’ in order to evaluate the internal energy distribution of the ions formed in sources of mass spectrometers. However, the detailed fragmentation pathways of these parent ions were not well established. In particular, fragmentation involving a rearrangement (RR) process may be influencing the simulated distribution curves. In a previous study, we suggested that such RR actually occurred under electrospray ionization/mass spectrometry (ESI/MS) and fast atom bombardment/mass spectrometry (FAB/MS) experiments. Here, we present a systematic study of different substituted benzylpyridinium ions. Theoretical calculations showed that RR fragmentation leading to substituted tropylium ions could occur under ‘soft ionization’ conditions, such as ESI or FAB. Experimental results obtained under gas‐phase reactivity conditions showed that some substituted benzylpiridinium compounds actually undergo RR fragmentations under ESI/MS conditions. Mass‐analyzed kinetic experiments were also carried out to gain information on the reaction pathways that actually occur, and these experimental results are in agreement with the reaction pathways theoretically proposed. Copyright © 2009 John Wiley & Sons, Ltd.     

Formation of cyclic acylphosphoramidates in mass spectra of N‐monoalkyloxyphosphoryl amino acids using electrospray ionization tandem mass spectrometry

The fragmentation reactions of N‐monoalkyloxyphosphoryl amino acids (N‐MAP‐AAs) were studied by electrospray ionization tandem mass spectrometry (ESI‐MS). The sodiated cyclic acylphosphoramidates (CAPAs) were formed through a characteristic pentacoordinate phosphate participated rearrangement reaction in the positive‐ion ESI‐MS/MS and HR‐MS/MS of N‐MAP‐AAs, in which the fragmentation patterns were clearly different from those observed in the corresponding ESI‐MS/MS of N‐dialkyloxyphosphoryl amino acids/peptides and N‐phosphono amino acids. The formation of CAPAs depended on the chemical structures of N‐terminal phosphoryl groups, such as alkyloxy group, negative charge and alkali metal ion. A possible integrated rearrangement mechanism for both P‐N to P‐O phosphoryl group migration and formation of CAPAs was proposed. The fragmentation patterns of CAPAs as novel intermediates in gas phase were also investigated. In addition, it was found that the formation of α‐amino acid CAPAs was more favorable than β‐ or γ‐CAPAs in gas phase, which was consistent with previous solution‐phase experiments. Copyright © 2010 John Wiley & Sons, Ltd.     

Size selective spectroscopy of Se microclusters

The electronic structure and photofragmentation in outer and inner valence regions of Se(n) (n ≤ 8) clusters produced by direct vacuum evaporation have been studied with size-selective photoelectron-photoion coincidence technique by using vacuum-ultraviolet synchrotron radiation. The experimental ionization potentials of these clusters were extracted from the partial ion yield measurements. The calculations for the possible geometrical structures of the Se(n) microclusters have been executed. The ionization energies of the clusters have been calculated and compared with the experimental results. In addition, theoretical fragment ion appearance energies were estimated. The dissociation energies of Se(n) clusters were derived from the recurrent relation between the gas phase enthalpies of the formation of corresponding cationic clusters and experimental ionization energies.     

Identification and structural characterization of in vivo metabolites of ketorolac using liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS)

In vivo metabolites of ketorolac (KTC) have been identified and characterized by using liquid chromatography positive ion electrospray ionization high resolution tandem mass spectrometry (LC/ESI‐HR‐MS/MS) in combination with online hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, blood urine and feces samples were collected after oral administration of KTC to Sprague–Dawley rats. The samples were prepared using an optimized sample preparation approach involving protein precipitation and freeze liquid separation followed by solid‐phase extraction and then subjected to LC/HR‐MS/MS analysis. A total of 12 metabolites have been identified in urine samples including hydroxy and glucuronide metabolites, which are also observed in plasma samples. In feces, only O‐sulfate metabolite and unchanged KTC are observed. The structures of metabolites were elucidated using LC‐MS/MS and MSⁿ experiments combined with accurate mass measurements. Online HDX experiments have been used to support the structural characterization of drug metabolites. The main phase I metabolites of KTC are hydroxylated and decarbonylated metabolites, which undergo subsequent phase II glucuronidation pathways. Copyright © 2012 John Wiley & Sons, Ltd.     

Combined use of tandem mass spectrometry and computational chemistry to study 2H‐chromenes from Piper aduncum

Natural 2H‐chromenes were isolated from the crude extract of Piper aduncum (Piperaceae) and analyzed by electrospray ionization tandem mass spectrometry (ESI‐MS/MS) applying collision‐induced dissociation. Density functional theory (DFT) calculations were used to explain the preferred protonation sites of the 2H‐chromenes based on thermochemical parameters, including atomic charges, proton affinity, and gas‐phase basicity. After identifying the nucleophilic sites, the pathways were proposed to justify the formation of the diagnostic ions under ESI‐MS/MS conditions. The calculated relative energy for each pathway was in good agreement with the energy‐resolved plot obtained from ESI‐MS/MS data. Moreover, the 2H‐chromene underwent proton attachment on the prenyl moiety via a six‐membered transition state. This behavior resulted in the formation of a diagnostic ion due to 2‐methylpropene loss. These studies provide novel insights into gas‐phase dissociation for natural benzopyran compounds, indicating how reactivity is correlated to the intrinsic acid‐base equilibrium and structural aspects, including the substitution pattern on the aromatic moiety. Therefore, these results can be applied in the identification of benzopyran derivatives in a variety of biological samples.     

Effect of Sr2+ association on the tautomerization processes of uracil and its dithio- and diseleno-derivatives

The structures and relative stabilities of the complexes formed by uracil and its thio- and seleno-derivatives with the Sr(2+) cation, in the gas phase, have been analyzed by means of G96LYP density functional theory (DFT) calculations. The attachment of the Sr(2+) cation to the heteroatom at position 4 is preferred systematically. Although the enolic forms of uracil and its derivatives should not be observed in the gas phase, the corresponding Sr(2+) complexes are the most stable. The enhanced stability of these tautomers is two-fold, on the one hand Sr(2+) interacts with two basic sites simultaneously, and on the other hand an aromatization of the six-membered ring takes place upon Sr(2+) association. Sr(2+) attachment also has a clear catalytic effect in the tautomerization processes involving uracil and its derivatives. This catalytic effect increases when oxygen is replaced by sulfur or selenium. The Sr(2+) binding energy with uracil and its derivatives is bigger than the tautomerization barriers connecting the dioxo forms with the corresponding enolic tautomers. Consequently, when associated with Sr(2+), all tautomers are energetically accessible and should all be observed in the gas phase.     

Gas phase synthesis, structure and unimolecular reactivity of silver iodide cluster cations, Ag(n)I(m)(+) (n = 2-5, 0 < m < n)

Multistage mass spectrometry (MS(n)) experiments reveal that gas phase silver iodide cluster cations, Ag(n)I(m)(+), are readily built up in a stepwise fashion via ion-molecule reactions between mass selected silver (Ag(3)(+) and Ag(5)(+)) or silver hydride (Ag(2)H(+) and Ag(4)H(+)) cluster cations and allyl iodide, in contrast to their reactions with methyl iodide, which solely result in ligation of the clusters. The stoichiometries of these clusters range from 1 < or = n < or = 5 and 1 < or = m < or = 4, indicating the formation of several new subvalent silver iodide clusters. Collision induced dissociation (CID) experiments were carried out on each of these clusters to shed some light on their possible structures. The products arising from CID of the Ag(n)I(m)(+) clusters are highly dependent on the stoichiometry of the cluster. Thus the odd-electron clusters Ag(4)I(2)(+) and Ag(5)I(+) fragment via loss of a silver atom. In contrast, the even-electron cluster ions all fragment via loss of AgI. In addition, Ag(2)I(2) loss is observed for the Ag(4)I(3)(+) and Ag(5)I(2)(+) clusters, while loss of Ag(3)I(3) occurs for the stoichiometric Ag(5)I(4)(+) cluster. DFT calculations were carried out on these Ag(n)I(m)(+) clusters as well as the neutrals associated with the ion-molecule and CID reactions. A range of different isomeric structures were calculated and their structures are described. A noteworthy aspect is that ligation of these silver clusters by I can have a profound effect on the geometry of the silver cluster. For example, D(3h) Ag(3)(+) becomes C(2v) Ag(3)I(+), which in turn becomes C(2h) Ag(3)I(2)(+). Finally, the DFT predicted thermochemistry supports the different types of reaction channels observed in the ion-molecule reactions and CID experiments.     

Sequential reactions of silicon clusters with SiD4: constrained heterogeneous nucleation of deuterated silicon particles

The sequential clustering reactions of gas phase silicon cluster ions are ideally suited for studying heterogeneous nucleation of silicon particles. Stepwise reactions of silicon cluster ions with silane have been observed which lead to growth of larger deuterated silicon clusters. Extensive information is obtained about their exothermic gas phase reaction rates and product distributions as a function of cluster size and degree of hydrogenation. What is found is that each size of silicon cluster exhibits a unique pattern of growth. Furthermore, nearly all of the silicon clusters encounter chemical constraints to rapid nucleation. These constraints are a consequence of specific electronic and structural requirements in the chemical reactions. The nature of these requirements are deduced using experimental results in concert with ab initio electronic structure theoretical calculations of the energetics and structures of various species.     

Inter- and Intramolecular Aryl–Aryl Interactions in Partially Fluorinated Ethylenedioxy-bridged Bisarenes**

Several ethylenedioxy-bridged bisarenes with a variety of type and number of aryl groups were synthesized to study non-covalent dispersion-driven inter- and intramolecular aryl–aryl interactions in the solid state and gas phase. Intramolecular interactions are preferably found in the gas phase. DFT calculations with and without dispersion correction show larger interacting aromatic groups increase the stabilization energy of folded conformers and decrease the intermolecular centroid–centroid distance. Single-molecule structures generally adopt folded conformations with short intramolecular aryl–aryl contacts. Gas electron diffraction experiments were performed exemplarily for 1-(pentafluorophenoxy)-2-(phenoxy)ethane. A new procedure for structure refinement was developed to deal with the conformational complexity of such molecules. The results are an experimental confirmation of the existence of folded conformations of this molecule with short intramolecular aryl–aryl distances in the gas phase. Solid-state structures are dominated by stretched structures without intramolecular aryl–aryl interactions but interactions with neighboring molecules.     

Microsolvation of uracil and its conjugate bases: a DFT study of the role of solvation on acidity

The effect of microsolvation on the deprotonation energies of uracil was examined using DFT. The structures of uracil and its N(1) and N(3) conjugate bases were optimized with zero to six associated water molecules. Multiple configurations (upward of 93) of these hydrated clusters were located at PBE1PBE/6-311+G(d,p). Trends in these geometries are discussed, with the waters generally forming chains with small numbers of waters (one-three), rings (three-five waters), or cages (five-six waters). The difference in energy between the N1 and N3 conjugate bases is 13 kcal mol(-1) in the gas phase, and it decreases with each added water up to four. At this point the energy difference has been halved, but addition of a fifth or sixth water has little effect on the energy difference. This is understood in terms of the water structures and their ability to stabilize the negatively charged atoms in the conjugate bases.     

Can mass dissociation patterns of transition‐metal complexes be predicted from electrochemical data?

The Cooks kinetic method has been very convenient to correlate the relative dissociation rates obtained by collision-induced fragmentation experiments with the energies of two related bonds in molecules and complexes in the gas phase. Reliable bond energy data are, however, not always available, particularly for polynuclear transition-metal complexes, such as the triruthenium acetate clusters of the general formula [Ru(3) (micro(3)-O)(micro-CH(3)COO)(6)(py)(2)(L)](+), where L = ring substituted N-heterocyclic ligands. Accordingly, their gas-phase collision-induced tandem mass spectrometry (CID MS/MS) dissociation patterns have been analyzed pursuing a relationship with the more easily accessible redox potentials (E(1/2)) and Lever's E(L) parameters. In fact, excellent linear correlations of ln(1/2A(L)/A(py)), where A(py) and A(L) are the abundance of the fragments retaining the pyridine (py) and L ligand, respectively, with E(1/2) and E(L) were found. This result shows that those electrochemical parameters are correlated with bond energies and can be used in the analysis of the dissociation data. Such modified Cooks method can be used, for example, to determine the electronic effects of substituents on the metal-ligand bonds for a series of transition-metal complexes.     

TiP+6, Ti2P+6二元团簇的密度泛函理论研究

利用含有电子相关效应校正的密度泛函理论DFT中的B3LYP方法，选择LANL2DZ双ξ基组，并考虑极化函数，对TiP6^ ,Ti2P6^ 二元团簇各种可能存在的几何构型及电子结构进行了密度泛函理论研究，得到了TimPn^ 二元团簇的最稳定构型，其中TiP6^ 的最稳定构型为具有C3v对称性的半笼状结构，Ti2P6^ 的最稳定构型为具有D6h对称性的六角双锥，所得构型很好地说明了激光光解的实验结果。     

A mass spectrometry study of tirapazamine and its metabolites. insights into the mechanism of metabolic transformations and the characterization of reaction intermediates

Tandem mass spectrometry methods were used to study the sites of protonation and for identification of 3-amino-1,2,4-benzotriazine 1,4-dioxide (1, tirapazamine), and its metabolites (3-amino-1,2,4-benzotriazine 1-oxide (3), 3-amino-1,2,4-benzotriazine 4-oxide (4), 3-amino-1,2,4-benzotriazine (5), and a related isomer 3-amino-1,2,4-benzotriazine 2-oxide (6). Fragmentation pathways of 3 and 5 indicated the 4-N-atom as the most likely site of protonation. Among the N-oxides studied, the 4-oxide (4) showed the highest degree of protonation at the oxygen atom. The differences in collision-induced dissociation of isomeric protonated 1-, 2- and 4-oxides allowed for their identification by LC/MS/MS. Gas phase and liquid phase protonation of tirapazamine occurred exclusively at the oxygen in the 4-position. A loss of OH radical from these ions (2(+)) resulted in ionized 3. Neutralization-reionization mass spectrometry (NR MS) experiments demonstrated the stability of the neutral analogue of protonated tirapazamine in the gas phase in the micro s time-frame. A significant portion of the neutral tirapazamine radicals (2) dissociated by loss of hydroxyl radical during the NR MS event, which indicates that previously proposed mechanisms for redox-activated DNA damage are reasonable. The activation energy for loss of hydroxyl radical from activated tirapazamine (2) was estimated to be approximately 14 kcal mol(-1). Stable neutral analogues of [3 + H](+) and [5 + H](+) ions were also generated in the course of NR MS experiments. Structures of these radicals were assigned to the molecules having an extra hydrogen atom at one of the ring N-atoms. Quantum chemical calculations of protonated 1, 3, 4 and 5 and the corresponding neutrals were performed to assist in the interpretation of experimental results and to help identify their structures.     

The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications

The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have deltaH(acid) values of 331-333 kcal mol(-1); the acidity of the N3 sites fall between 347-352 kcal mol(-1). The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol(-1), and 369 kcal mol(-1) in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol(-1). Calculations conducted at B3LYP/6-31+G* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed.