Clustering of nucleosides in the presence of alkali metals: Biologically relevant quartets of guanosine, deoxyguanosine and uridine observed by ESI-MS/MS

Binding of Quercetin Derivatives toward G-Tetrads as Studied by the Survival Yield Method

Recently, much interest has been devoted to finding effective G-quadruplex ligands, both of synthetic or natural origins, which may be of potential use in the field of cancer therapy. Among compounds of natural origin, a common flavonol quercetin has attracted notable attention. Yet, only a modest number of papers have been concerned with a comparison of quercetin conjugates binding to G-quadruplexes. In this study, we applied the survival yield (SY) method in order to compare the stability of G-tetrad complexes with quercetin and its conjugates, namely, 3-O-glycosides and O-methylated conjugates. According to the determined values of Ecomδ50, flavonol glycosides bind most effectively with G-tetrads, whereas, among flavonols, 3-O-methylquercetin makes the most effective bonds. Because the aglycone structure is of crucial importance for biological processes, 3-O-methylquercetin seems to be a suitable candidate for anticancer therapeutics, and the extracts from the plants, which contain high amounts of 3-O-methylquercetin or its glycosides, should be considered as interesting materials for preparation of pharmaceuticals or dietary supplements.

Native mass spectrometry-based metabolomics identifies metal-binding compounds

Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Hydrogen bonding influences collision-induced dissociation of Na+ -bound guanine tetrads

Na+ -bound guanine (G)-tetrads possess square planar structures formed solely by noncovalent interactions including multiple hydrogen bonds. Unlike G-tetrads facilitated by other alkali metal ions, an intriguing behavior in collision-induced dissociation (CID) has been observed in Na+ -bound G-tetrads, which features a preferential, simultaneous loss of two G ligands in the low energy regime. To understand this unique behavior, we investigated the CID of Na+ -bound G-tetrads with mixed ligands of G and 9-methylguanine (9mG), [Na·Gm ·9mGn ]+ (m + n = 4), and [Li·9mG4 ]+ for comparison. In the CID experiments, the simultaneous losses of two ligands were by far more pronounced than the loss of a single ligand for all five Na+ -bound G-tetrads. However, it appeared that the CID of [Li·9mG4 ]+ prefers to lose single ligands sequentially. An analysis of the fragment abundances suggested that the generation of Na+ -bound dimeric fragments might have occurred with two adjacent ligands. This theoretical study predicted for [Li·9mG4 ]+ that the loss of a single ligand is more energetically favorable than the production of neutral hydrogen-bonded fragments by 35.5 kJ/mol (ΔG). This contradicts our previous calculations for [Na·9mG4 ]+ that a neutral loss of hydrogen-bonded dimers provides the lowest energy product state of Na+ -bound dimeric fragments, which is lower than that of Na+ -bound trimeric fragments by 15.6 kJ/mol. From the results, this comparative study suggests that the pronounced generation of Na+ -bound dimeric fragments in CID of the G-tetrads is likely promoted by the dissociation pathway associated with neutral loss of hydrogen-bonded dimers. It thus demonstrates that multiple hydrogen bonding participating in formation of Na+ -bound G-tetrads may also strongly influence the fate of dissociating complexes of G-tetrads.

A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G-C base pairs

The structures and properties of metal cationized complexes of 9-ethylguanine (9eG) and 1-methylcytosine (1mC), (9eG:1mC)M⁺, where M⁺ = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ as well as the protonated complex, (9eG:1mC)H⁺, have been studied using a combination of IRMPD spectroscopy and computational methods. For (9eG:1mC)H⁺, the dominant structure is a Hoogsteen type complex with the proton covalently bound to N3 of 1mC despite this being the third best protonation site of the two bases; based on proton affinities N7 of 9eG should be protonated. However, this structural oddity can be explained considering both the number of hydrogen bonds that can be formed when N3 of 1mC is protonated as well as the strong ion-induced dipole interaction that exists between an N3 protonated 1mC and 9eG due to the higher polarizability of 9eG. The anomalous dissociation of (9eG:1mC)H⁺, forming much more (1mC)H⁺ than would be predicted based on the computed thermochemistry, can be explained as being due to the structural oddity of the protonation site and that the barrier to proton transfer from N3 of 1mC to N7 of 9eG grows dramatically as the base pair begins to dissociate. For the (9eG:1mC)M⁺; M = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ complexes, single unique structures could not be assigned. However, the experimental spectra were consistent with the computed spectra. For (9eG:1mC)Li⁺, the lowest energy structure is one in which Li⁺ is bound to O6 of 9eG and both O2 and N3 of 1mC; there is also an interbase hydrogen bond from the amine of 1mC to N7 of 9eG. For Na⁺, K⁺, and Rb⁺, similar binding of the metal cation to 1mC is calculated but, unlike Li⁺, the lowest energy structure is one in which the metal cation is bound to N7 of 9eG; there is also an interbase hydrogen bond between the amine of 1mC and the carbonyl of 9eG. The lowest energy structure for the Cs complex is the Watson-Crick type base pairing with Cs⁺ binding only to 9eG through O6 and N7 and with three hydrogen bonds between 9eG and 1mC. It also interesting to note that the Watson-Crick base pairing structure gets lower in Gibbs energy relative to the lowest energy complexes as the metal gets larger. This indicates that the smaller, more densely charged cations have a greater propensity to interfere with Watson-Crick base pairing than do the larger, less densely charged metal cations.

The intrinsic stabilities and structures of alkali metal cationized guanine quadruplexes

The structures and stabilities of self-assembled guanine quadruplexes, M(9eG)₈⁺ (M = Na, K, Rb, Cs; 9eG = 9-ethylguanine), have been studied in the gas phase by blackbody infrared radiative dissociation kinetics to determine the effect the metal cations have on the decomposition energies and reactions of the quadruplex.

ESI-MS studies of the non-covalent interactions between biologically important metal ions and N-sulfonylcytosine derivatives

The aim of this report is to present the electrospray ionization mass spectrometry results of the non-covalent interaction of two biologically active ligands, N-1-(p-toluenesulfonyl)cytosine, 1-TsC, 1 and N-1-methanesulfonylcytosine, 1-MsC, 2 and their Cu(II) complexes Cu(1-TsC-N3)₂ Cl₂ , 3 and Cu(1-MsC-N3)₂ Cl₂ and 4 with biologically important cations: Na⁺ , K⁺ , Ca²⁺ , Mg²⁺ and Zn²⁺ . The formation of various complex metal ions was observed. The alkali metals Na⁺ and K⁺ formed clusters because of electrostatic interactions. Ca²⁺ and Mg²⁺ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn²⁺ with 1-4 produced monometal and dimetal Zn²⁺ complexes as a result of the affinity of Zn²⁺ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.

Mechanisms and energetics for N-glycosidic bond cleavage of protonated 2'-deoxyguanosine and guanosine

Experimental and theoretical investigations suggest that hydrolysis of N-glycosidic bonds generally involves a concerted SN2 or a stepwise SN1 mechanism. While theoretical investigations have provided estimates for the intrinsic activation energies associated with N-glycosidic bond cleavage reactions, experimental measurements to validate the theoretical studies remain elusive. Here we report experimental investigations for N-glycosidic bond cleavage of the protonated guanine nucleosides, [dGuo+H](+) and [Guo+H](+), using threshold collision-induced dissociation (TCID) techniques. Two major dissociation pathways involving N-glycosidic bond cleavage, resulting in production of protonated guanine or the elimination of neutral guanine are observed in competition for both [dGuo+H](+) and [Guo+H](+). The detailed mechanistic pathways for the N-glycosidic bond cleavage reactions observed are mapped via electronic structure calculations. Excellent agreement between the measured and B3LYP calculated activation energies and reaction enthalpies for N-glycosidic bond cleavage of [dGuo+H](+) and [Guo+H](+) in the gas phase is found indicating that these dissociation pathways involve stepwise E1 mechanisms in analogy to the SN1 mechanisms that occur in the condensed phase. In contrast, MP2 is found to significantly overestimate the activation energies and slightly overestimate the reaction enthalpies. The 2'-hydroxyl substituent is found to stabilize the N-glycosidic bond such that [Guo+H](+) requires ∼25 kJ mol(-1) more than [dGuo+H](+) to activate the glycosidic bond.

Ion mobility spectrometry: A personal view of its development at UCSB

Ion mobility is not a newly discovered phenomenon. It has roots going back to Langevin at the beginning of the 20th century. Our group initially got involved by accident around 1990 and this paper is a brief account of what has transpired here at UCSB the past 25 years in response to this happy accident. We started small, literally, with transition metal atomic ions and transitioned to carbon clusters, synthetic polymers, most types of biological molecules and eventually peptide and protein oligomeric assembly. Along the way we designed and built several generations of instruments, a process that is still ongoing. And perhaps most importantly we have incorporated theory with experiment from the beginning; a necessary wedding that allows an atomistic face to be put on the otherwise interesting but not fully informative cross section measurements.

Protonated primary amines induced thymine quintets studied by electrospray ionization mass spectrometry and density functional theory calculations

As the novel magic number clusters of nucleobases, the thymine quintets induced by ammonium ion (NH4(+)), and particularly by its derivatives such as protonated alkyl amines and protonated aryl amines, have been studied by electrospray ionization mass spectrometry (ESI-MS) and density functional theory (DFT) calculations. The DFT-optimized geometry of NH4(+) induced thymine quintet ([T5 + NH4](+)) reveals some new features including three additional hydrogen bonds between NH4(+) and its surrounding thymine molecules when compared with that of the alkali metal ions induced thymine quintets. In addition, the fourth hydrogen atom of NH4(+) is sticking out the assembly, and, thus, it might be replaced by an organic group R to form the protonated primary amine induced thymine quintet ([T5 + R - NH3](+)), a hypothesis that has been confirmed by both DFT calculations and ESI-MS experiments. Furthermore, the relative abilities of the different protonated primary amines for inducing the thymine quintets are investigated by ESI-MS competition experiments, and the results have shown a clear trend of stronger ability as the alkyl chain gets longer or as the aryl ring gets larger for the alkyl amines or the aryl amines. Two basic influence factors are consequently identified: one is the ability of the alkyl amine to accept proton, another is the π-π stacking interaction between the aryl ring and the π-surface of the thymine molecule(s), whose explanations are strongly supported by multiple types of thermochemical data, various control experiments and DFT calculations.

Gas-phase fragmentation of metal adducts of alkali-metal oxalate salts

Upon collisional activation, gaseous metal adducts of lithium, sodium and potassium oxalate salts undergo an expulsion of CO2, followed by an ejection of CO to generate a product ion that retains all three metals atoms of the precursor. Spectra recorded even at very low collision energies (2 eV) showed peaks for a 44-Da neutral fragment loss. Density functional theory calculations predicted that the ejection of CO2 requires less energy than an expulsion of a Na(+) and that the [Na3CO2](+) product ion formed in this way bears a planar geometry. Furthermore, spectra of [Na3C2O4](+) and [(39)K3C2O4](+) recorded at higher collision energies showed additional peaks at m/z 90 and m/z 122 for the radical cations [Na2CO2](+•) and [K2CO2](+•), respectively, which represented a loss of an M(•) from the precursor ions. Moreover, [Na3CO2](+), [(39)K3CO2](+) and [Li3CO2](+) ions also undergo a CO loss to form [M3O](+). Furthermore, product-ion spectra for [Na3C2O4](+) and [(39)K3C2O4](+) recorded at low collision energies showed an unexpected peak at m/z 63 for [Na2OH](+) and m/z 95 for [(39)K2OH](+), respectively. An additional peak observed at m/z 65 for [Na2(18)OH](+) in the spectrum recorded for [Na3C2O4](+), after the addition of some H2(18)O to the collision gas, confirmed that the [Na2OH](+) ion is formed by an ion-molecule reaction with residual water in the collision cell.

UV-MALDI mass spectrometric quantitation of uracil based pesticides in fruit soft drinks along with matrix effects evaluation

This study focused on the development of the accurate and precise quantitative method for the determination of pesticides bromacil (1), terbacil (2), lenacil (3), butafenacil (4) and flupropacil (5) in fruit based soft drinks. Three different types of drinks are bought from market; huddled orange fruit drink (100%) (I), red-oranges (II) and multivitamin drink containing strawberry, orange, banana and maracuja (III). Samples were analyzed "with" and "without" pulp utilizing LC-ESI (or APCI) MS/MS, HPLC-ESI-(or APCI)-MS/MS and UV-MALDI-Orbitrap-MS methods. The effect of high complexity of the food matrix on the analysis was discussed. Study focuses on the advantages of the UV-MALDI-Orbitrap-MS method compared to the traditionally involved GC alone or hybrid methods such as GC-MS and LC-MS/MS for quantification of pesticides in water and soft drinks. The developed method included the techniques performed for validation, calibration and standardization. The target pesticides are widely used for the treatment of citrus fruits and pineapples, but for soft drink products, there are still no clear regulations on pesticide residues limits. The matrix effects in the analysis of fruit drinks required implementation of the exact standard reference material corresponds to the variety of food matrices. This paper contributed to the broad analytical implementation of the UV-MALDI-Orbitrap-MS method in the quality control and assessment programs for monitoring of pesticide contamination in fruit based sodas.

Inosine octamer stabilized by alkali earth metal cations - as studied by electrospray ionization mass spectrometry

By using electrospray ionization mass spectrometry, inosine was found to be able to form an octamer stabilized by alkali earth metal cation, namely Ca(2+), Sr(2+) and Ba(2+), of which the most stable is that stabilized by Ca(2+) (ion [I8+Ca](2+)). It was established that 9-methylhypoxanthine (M) did not form an analogical octamer, since ion [M8+Ca](2+) was not detected. On the other hand, 9-methylhypoxanthine can form "mixed" octamers together with inosine (ions [InMm+Ca](2+), n + m = 8, were detected).

Clustering of simple aminosulfonic acids--electrospray ionization mass spectrometric study

RATIONALE

Aminosulfonic acids are structurally related to amino acids as bifunctional compounds. Some of them like taurine and homotaurine play important roles in biology. Although there is a vast literature devoted to the electrospray ionization mass spectrometric (ESI-MS) study of amino acid aggregation, no such study has been performed so far for aminosulfonic acids.

METHODS

A gas-phase clustering study was performed for aminomethanesulfonic acid (AMS), taurine (Tau), homotaurine (HT), and cysteic acid (CA) from water and methanol/water solutions, using a Bruker TOF-Q spectrometer equipped with an ESI source, in the negative-ion mode. For selected anionic clusters the tandem mass (MS/MS) spectra were recorded and the breakdown curves were obtained. The cluster formation abilities (ACS parameter) of the studied molecules were calculated.

RESULTS

Both singly and doubly charged clusters were formed when the acids were electrosprayed from water solutions; they may be described as [(H3N-R-SO3)n-zH](z-), where z = 1 or 2. The largest identified clusters are built of 20, 22, 20 and 4 monomers of AMS, Tau, HT and CA, respectively. The doubly negatively charged clusters were observed for n ≥9, 12, 14 in the case of AMS, Tau and HT. AMS pentamers and Tau, HT tetramers and hexamers show higher stabilities than the other clusters.

CONCLUSIONS

The results indicate that aminosulfonic acids form large stable clusters, similarly to aminocarboxylic acids. The cluster formation ability decreases with an increase in CH2 chain length within the series of the studied compounds. The large singly and doubly charged aggregates are formed under the conditions of the experiment, possibly in the droplets. Taurine dissolved in water seems to be a good calibrant for electrospray instruments in negative ion mode.

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(n)B'(n')Ca(2+) 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 Ca(2+), whereas mixed octamers are preferred from 1-methyl uracil (MeU), uracil and Ca(2+) 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.

Bonding, Structure, and Stability of Clusters: Some Surprising Results from an Experimental and Theoretical Investigation in Gas Phase

Structure and stability of clusters in the ground state were analyzed at the theoretical and experimental levels. Our experimental and theoretical findings showed that the clusters in gas phase tend to form mainly planar rings of four members. The symmetry and the small dipole moment in these specific configurations suggested that their stability could be associated with an alignment of the water molecules, maximizing attractive electrostatic interactions caused by changes in the charge distribution of the clusters.

Structures and physical properties of gaseous metal cationized biological ions

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

Mass spectrometry of G-quadruplex DNA: formation, recognition, property, conversion, and conformation

G-quadruplexes are special secondary structures formed from G-rich sequences of DNA, and have proven to play important roles in a number of biological systems, including the regulation of gene transcription and translation. The highly distinctive nature of G-quadruplex structures and their functions suggest that G-quadruplexes can act as novel targets for drug development. As a highly sensitive analytical tool, mass spectrometry has been widely used for the analysis of G-quadruplex structures. Electrospray-ionization mass spectrometry, in particular, has found captivating applications to probe interactions between small molecules and G-quadruplex DNA. In this review, we will discuss: (1) mass spectrometry probing of the formation, binding affinity, and stoichiometry between G-quadruplexes and small molecules; (2) stabilization and collision-dissociation behavior of G-quadruplex DNA; (3) the exploration of the equilibrium transfer between a G-quadruplex and duplex DNA; and (4) the ESI-MS analysis of the conversion of intramolecular and intermolecular G-quadruplexes. Finally, we will also introduce the application of new techniques in the analysis of G-quadruplex conformation, such as ion-mobility and infrared multiphoton-dissociation mass spectrometry. We believe that, with the new technical developments, mass spectrometry will play an unparalleled role in the analysis of the G-quadruplex structures.

Serine-phosphoric acid cluster ions studied by electrospray ionization and tandem mass spectrometry

More than 310 kinds of cluster ions of S(m) P(n) H(k) (k+) are observed in a single ESI mass spectrum of a mixed solution of serine and phosphoric acid. Some typical cluster ions are selected, activated by collision in a FT ICR cell, and the dissociation pathways were deduced in detail. For large singly protonated ions, the collisions cause the ejection of subunits of serine or phosphoric acid subsequently producing the ions of S(2) P(4) H(1) (1+) , which can be further dissociated by the loss of phosphoric acid molecules in turn and form the protonated serine dimer and monomer. However, for the doubly protonated ions, the dissociation pathways change from the loss of a protonated serine dimer for the ions of S(7) P(9) H(2) (2+) to the neutral loss of H(3) PO(4) for the ions of S(7) P(12) H(2) (2+) or the neutral loss of serine or H(3) PO(4) for the larger clusters, indicating the effect of cluster sizes on the process of dissociation. The structure of S(2) P(4) H(1) (1+) is suggested based on B3LYP/6-31G(d,p) calculations. The diversity and structural orderliness of the hetero-cluster ions are mainly attributed to the network of hydrogen bonds inside the cluster ions and the extraordinary amphotericity of the components.

Intramolecular scrambling of aryl groups in organopalladium complexes [ArPd(PPh3)2]+: from solution to the gas phase, back again, and in-between

Gas-phase experiments are used to probe the intramolecular scrambling of aryl groups between palladium and phosphorus in organopalladium complexes, [ArPd(PPh(3))(2)](+), generated by means of electrospray ionization (ESI). To this aim, ESI mass spectrometry, including tandem mass spectrometric experiments, were carried out on deuterated, non-deuterated, and substituted [ArPd(PPh(3))(2)](+) complexes. The fragment ions obtained from the deuterated parent ions clearly show the occurrence of intramolecular scrambling between the aryl group bound to palladium and the phenyl groups of the phosphine in the gas phase. Fragmentation pathways, supported by a statistical model, are proposed to explain these migrations and the implications for the condensed-phase chemistry are probed experimentally by using ESI mass spectrometry.

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 U(10)Li(+) 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.

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads.

ESI-MS studies of palladium (II) complexes with 1-(p-toluenesulfonyl)cytosine/cytosinato ligands

The mononuclear complex Pd(1-TosC-N3)(2)Cl(2) (2) containing 1-(p-toluenesulfonyl)cytosine (1) as a ligand, as well as dinuclear complexes Pd(2)(1-TosC(-)-N3,N4)(4) (3) and Pd(2)(1-TosC(-)-N3,N4)(2)DMSO(2)Cl(2) (4) containing the ligand anion (1-TosC(-)), was mass analyzed by electrospray ionization ion trap MS/MS and high resolution MS. Complexes 3 and 4 were obtained by recrystallization of 2 from DMF and DMSO, respectively. The behavior of complex 2 in different solutions was monitored by electrospray ionization mass spectrometry (ESI-MS). Under the applied ESI-MS conditions, complex 2 in methanol reorganized itself dominantly as new complex 3 and the solvent did not coordinate the formed species. In H(2)O/DMSO, CH(3)CN/DMSO and CH(3)OH/DMSO solutions, complex 2 formed several new species with solvent molecules involved in their structure, e.g. complex 4 was formed as the major product. The newly formed species were also examined by LC-MS-DAD, confirming the solvent induced reorganization and the solution instability of complex 2.

Generation of gas-phase sodiated arenes such as [(Na3(C6H4)+] from benzene dicarboxylate salts

Upon collision-induced activation, gaseous sodium adducts generated by electrospray ionization of disodium salts of 1,2- 1,3-, and 1,4-benzene dicarboxylic acids (m/z 233) undergo an unprecedented expulsion of CO(2) by a rearrangement process to produce an ion of m/z 189 in which all three sodium atoms are retained. When isolated in a collision cell of a tandem-in-space mass spectrometer, and subjected to collision-induced dissociation (CID), only the m/z 189 ions derived from the meta and para isomers underwent a further CO(2) loss to produce a peak at m/z 145 for a sodiated arene of formula (Na(3)C(6)H(4))(+). This previously unreported m/z 145 ion, which is useful to differentiate meta and para benzene dicarboxylates from their ortho isomer, is in fact the sodium adduct of phenelenedisodium. Moreover, the m/z 189 ion from all three isomers readily expelled a sodium radical to produce a peak at m/z 166 for a radical cation [(*C(6)H(4)CO(2)Na(2))(+)], which then eliminated CO(2) to produce a peak at m/z 122 for the distonic cation (*C(6)H(4)Na(2))(+).

Flavonoid-matrix cluster ions in MALDI mass spectrometry

The behaviour of 2,5-dihydroxybenzoic acid (2,5-DHB) matrix under matrix-assisted laser desorption/ionisation (MALDI) conditions was investigated, and the formation of 2,5-DHB cluster ions, mainly dehydrated 2,5-DHB ions, is reported. Interestingly, in the mass spectra of this compound, besides dimers and trimers, protonated tetramers, pentamers, hexamers and heptamers were also found with significant abundance.The MALDI behaviour of four flavonoids, quercetin, myricetin, luteolin and kaempferol, using 2,5-DHB as matrix, was also investigated. The mass spectra of the flavonoids studied revealed a number of flavonoid-2,5-DHB cluster ions (mainly with the dehydrated 2,5-DHB). The number of clusters formed is dependent on the structure of the analyte. For luteolin and kaempferol, in particular, evidence was found for the formation of cluster ions involving retro Diels Alder fragments and intact flavonoids molecules, as well as the corresponding protonated retro Diels Alder fragments with dehydrated DHB molecules. All ion compositions were attributed taking into account high accuracy mass measurements and tandem mass spectrometry experiments.

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.

Theoretical and experimental studies of cationized uracil complexes in the gas phase

Cationized uracil clusters were generated in the gas phase by electrospray ionization (ESI). Mass spectrometry experiments showed that with particular experimental conditions, decameric uracil clusters are magic number clusters. MS/MS experiments demonstrated that the structure of these decameric uracil clusters depends substantially on the size and the charge of the cation. On the basis of the ab initio and density functional theory (DFT) quantum chemistry calculations, structures for these decameric clusters were proposed. These structures are in agreement with the experimental mass spectra of modified nucleobases. Theoretical calculations showed that complexes experimentally observed using ESI-MS techniques, are not naturally the most stable in the gas phase.

Interactions of nucleosides with CrO(4) (2-) and Cr(3+) as studied by electrospray ionization mass spectrometry

The interactions of CrO(4) (2-) and Cr(3+) with nucleosides studied by electrospray ionization mass spectrometry (ESI-MS) are reported. In water, the nucleosides which do not contain the NH(2) group form the unstable [M+HCrO(4)](-) anion. In the presence of a reducing agent, namely methanol, chromate anion forms stable complexes with nucleosides, [M+CH(3)CrO(4)](-) anions. The fragmentation of [M+CH(3)CrO(4)](-) anions involve elimination of the methanol molecule. Chromium cation-nucleoside complexes were not observed in water. In methanol solutions, adenosine and cytidine form [(M-H)+CrOCH(3)](+) and [(M-H)(2)+Cr](+) ions. Most probably, deprotonated imine tautomers form complexes in which a metal cation is simultaneously coordinated by two nitrogen atoms. Complexes containing chloride anions and a few methanol molecules were observed for other nucleosides. Guanosine and inosine form doubly charged ions of the type [M(2)+CrOCH(3)](2+) that probably contain a bond between the oxygen atom and the chromium cation, (HN(1)--C(6)==O)(2) (....)Cr(3+)).

Gas-Phase Formation of Radical Cations of Monomers and Dimers of Guanosine by Collision-Induced Dissociation of Cu(II)−Guanosine Complexes

An electrosprayed water/methanol solution of guanosine and Cu(NO3)2 was observed to give rise to gas-phase copper complexed ions of [CuLn]*2+, [CuL(MeOH)n]*2+, and [CuG n(NO3)]*+, as well as the ions [L]*+, [L+H]+, [G]*+, and [G+H]+ (L=guanosine, G=guanine). The Collision-Induced Dissociation (CID) of [CuL3]*2+ and [CuL(MeOH)n]*2+ (n=2, 3) generates guanosine radical cations [L]*+, while dimeric guanosine radical cations [L2]*+ are generated in the dissociation of [CuL4]*2+. Protonated guanosine [L+H]+ is one of the main products in the primary dissociation of [CuL2]*2+, while the dissociation of the higher-order [CuG2]*2+ produces the [G]*+ radical cation. The guanosine dimer radical cation, [L2]*+ presumably arises from the interaction of two guanosine molecules via proton and hydrogen bonding and is observed to dissociate into [L+H]+ and [L-H]* at low energies. We propose that the first two ligands bind strongly with Cu(II) through N7 and O6 to form a [CuL2]*2+ complex with a four-coordinated planar structure and that a third ligand binds loosely with copper to form [CuL3]*2+. Additional ligation observed in the formation of [CuLn]*2+ (n<or=6) ions is presumed to occur by hydrogen bonding. The ribose group of guanosine appears to play an important role in the stabilization of the doubly charged Cu-guanosine complex and in intraligand proton transfer upon CID. The molecular radical cations [L]*+ observed in the ESI-MS spectrum at low declustering potentials originate primarily from [CuL(MeOH)2,3]*2+ complexes which can dissociate more easily than [CuL3]*2+.