Stabilization of excess charge in isolated adenosine 5'-triphosphate and adenosine 5'-diphosphate multiply and singly charged anions

Ultrafast Dynamics of the Isolated Adenosine-5'-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging

The excited state dynamics of the doubly deprotonated dianion of adenosine-5'-triphosphate, [ATP-H₂]^2-, has been spectroscopically explored by time-resolved photoelectron spectroscopy following excitation at 4.66 eV. Time-resolved photoelectron spectra show that two competing processes occur for the initially populated ¹ππ* state. The first is rapid electron emission by tunneling through a repulsive Coulomb barrier as the ¹ππ* state is a resonance. The second is nuclear motion on the ¹ππ* state surface leading to an intermediate that no longer tunnels and subsequently decays by internal conversion to the ground electronic state. The spectral signatures of the features are similar to those observed for other adenine-derivatives, suggesting that this nucleobase is quite insensitive to the nearby negative charges localized on the phosphates, except of course for the appearance of the additional electron tunneling channel, which is open in the dianion.

Site-Specific Photo-oxidation of the Isolated Adenosine-5'-triphosphate Dianion Determined by Photoelectron Imaging

Photoelectron imaging of the isolated adenosine-5'-triphosphate dianion excited to the ¹ππ* states reveals that electron emission is predominantly parallel to the polarization axis of the light and arises from subpicosecond electron tunneling through the repulsive Coulomb barrier (RCB). The computed RCB shows that the most probable electron emission site is on the amino group of adenine. This is consistent with the photoelectron imaging: excitation to the ¹ππ* states leads to an aligned ensemble distributed predominantly parallel to the long axis of adenine; the subsequent electron tunneling site is along this axis; and the negatively charged phosphate groups guide the outgoing electron mostly along this axis at long range. Imaging of electron tunneling from polyanions combined with computational chemistry may offer a general route for probing the intrinsic photo-oxidation site and dynamics as well as the overall structure of complex isolated species.

Structural characterization of nucleotide 5'-triphosphates by infrared ion spectroscopy and theoretical studies

The molecular family of nucleotide triphosphates (NTPs), with adenosine 5'-triphosphate (ATP) as its best-known member, is of high biochemical importance as their phosphodiester bonds form Nature's main means to store and transport energy. Here, gas-phase IR spectroscopic studies and supporting theoretical studies have been performed on adenosine 5'-triphosphate, cytosine 5'-triphosphate and guanosine 5'-triphosphate to elucidate the intrinsic structural properties of NTPs, focusing on the influence of the nucleobase and the extent of deprotonation. Mass spectrometric studies involving collision induced dissociation showed similar fragmentation channels for the three studied NTPs within a selected charge state. The doubly charged anions exhibit fragmentation similar to the energy-releasing hydrolysis reaction in nature, while the singly charged anions show different dominant fragmentation channels, suggesting that the charge state plays a significant role in the favorability of the hydrolysis reaction. A combination of infrared ion spectroscopy and quantum-chemical computations indicates that the singly charged anions of all NTPs are preferentially deprotonated at their β-phosphates, while the doubly-charged anions are dominantly αβ-deprotonated. The assigned three-dimensional structure differs for ATP and CTP on the one hand and GTP on the other, in the sense that ATP and CTP show no interaction between nucleobase and phosphate tail, while in GTP they are hydrogen bonded. This can be rationalized by considering the structure and geometry of the NTPs where the final three dimensional structure depends on a subtle balance between hydrogen bond strength, flexibility and steric hindrance.

Gas-Phase Stability of Negatively Charged Organophosphate Metabolites Produced by Electrospray Ionization and Matrix-Assisted Laser Desorption/Ionization

The formation mechanisms of singly and multiply charged organophosphate metabolites by electrospray ionization (ESI) and their gas phase stabilities were investigated. Metabolites containing multiple phosphate groups, such as adenosine 5'-diphosphate (ADP), adenosine 5'-triphosphate (ATP), and D-myo-inositol-1,4,5-triphosphate (IP₃) were observed as doubly deprotonated ions by negative-ion ESI mass spectrometry. Organophosphates with multiple negative charges were found to be unstable and often underwent loss of PO₃^-, although singly deprotonated analytes were stable. The presence of fragments due to the loss of PO₃^- in the negative-ion ESI mass spectra could result in the misinterpretation of analytical results. In contrast to ESI, matrix-assisted laser desorption ionization (MALDI) produced singly charged organophosphate metabolites with no associated fragmentation, since the singly charged anions are stable. The stability of an organophosphate metabolite in the gas phase strongly depends on its charge state. The fragmentations of multiply charged organophosphates were also investigated in detail through density functional theory calculations. Graphical Abstract.

Photoexcitation of Adenosine 5'-Triphosphate Anions in Vacuo: Probing the Influence of Charge State on the UV Photophysics of Adenine

We report the first UV laser photodissociation spectra (4.0-5.8 eV) of gas-phase deprotonated adenosine 5'-triphosphate, diphosphate and monophosphate anions. The photodepletion spectra of these anions display strong absorption bands across the region of 4.6-5.2 eV, consistent with excitation of a primarily adenine-centered π-π* transition. The spectra appear insensitive to the charge of the species (i.e., the spectrum of [ATP-2H]^2- closely resembles that of [ATP-H]^-), while the spectral profile is affected to a greater extent by the variation of the molecular structure, i.e. the [AMP-H]^- and [ADP-H]^- photodepletion spectra display similar profiles while the [ATP-H]^- spectrum is distinctive. The photodepletion cross-section also decreases for the ATP anions compared to both the AMP and ADP anions, reflecting a high intrinsic photostability of ATP versus both AMP and ADP. A range of photofragments are produced across the 4.0-5.8 eV spectral range for all of the ATP analogues studied. These fragments are primarily associated with fragmentation on the ground-state electronic surface, indicative of a statistical decay process where ultrafast decay is followed by ergodic dissociation. However, while the photofragments observed following photoexcitation of the monoanionic species, [AMP-H]^- to [ADP-H]^- to [ATP-H]^- are entirely consistent with statistical decay, an additional group of photofragments are observed for the dianionic species, [ADP-2H]^2- and [ATP-2H]^2-, that we associate with electron detachment, and subsequent fragmentation of the resulting electron-detached photofragment. TDDFT calculations are presented to support the interpretation of the experimental data, and confirm that the electronic structure of the adenine moiety is relatively unperturbed by varying the overall charge.

Performance of M06, M06-2X, and M06-HF density functionals for conformationally flexible anionic clusters: M06 functionals perform better than B3LYP for a model system with dispersion and ionic hydrogen-bonding interactions

We present a comparative assessment of the performance of the M06 suite of density functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calculating the relative energies and geometric structures of the Cl(-)·arginine and Br(-)·arginine halide ion-amino acid clusters. Additional results are presented for the popular B3LYP density functional. The Cl(-)·arginine and Br(-)·arginine complexes are important prototypes for the phenomenon of anion-induced zwitterion formation. Results are presented for the canonical (noncharge separated) and zwitterionic (charge separated) tautomers of the clusters, as well as the numerous conformational isomers of the clusters. We find that all of the M06 functions perform well in terms of predicting the general trends in the conformer relative energies and identifying the global minimum conformer. This is in contrast to the B3LYP functional, which performed significantly less well for the canonical tautomers of the clusters where dispersion interactions contribute more significantly to the conformer energetics. We find that the M06 functional gave the lowest mean unsigned error for the relative energies of the canonical conformers (2.10 and 2.36 kJ/mol for Br(-)·arginine and Cl(-)·arginine), while M06-2X gave the lowest mean unsigned error for the zwitterionic conformers (0.85 and 1.23 kJ/mol for Br(-)·arginine and Cl(-)·arginine), thus providing insight into the types of physical systems where each of these functionals should perform best.

Spectroscopic and theoretical investigations of adenosine 5'-diphosphate and adenosine 5'-triphosphate dianions in the gas phase

Doubly deprotonated adenosine 5'-diphosphate ([ADP-2H](2-)) and adenosine 5'-triphosphate ([ATP-2H](2-)) dianions were investigated using infrared multiple photon dissociation (IR-MPD) and photoelectron spectroscopy. Vibrational spectra acquired in the X-H stretch region (X = C, N, O) and augmented by isotope-labelling were compared to density functional theory (DFT) calculations at the B3LYP/TZVPP level. This suggests that in [ATP-2H](2-) the two phosphate groups adjacent to the ribose ring are preferentially deprotonated. Photoelectron spectra recorded at 4.66 and 6.42 eV photon energies revealed adiabatic detachment energies of 1.35 eV for [ADP-2H](2-) and 3.35 eV for [ATP-2H](2-). Repulsive Coulomb barriers were estimated at ~2.2 eV for [ADP-2H](2-) and ~1.9 eV for [ATP-2H](2-). Time-dependent DFT calculations have been used to simulate the photoelectron spectra. Photodetachment occurs primarily from lone pair orbitals on oxygen atoms within the phosphate chain.

Tandem mass spectrometry for the analysis of self-sorted pseudorotaxanes: the effects of Coulomb interactions

The increasing complexity of self-assembled supramolecules generates the need for analytical techniques that can accurately elucidate their structures. Here, we explore the ability of tandem mass spectrometry to deliver structural information on a series of self-sorted crown ether/ammonium pseudorotaxanes. Of these intertwined molecules, different charge states are accessible and the effects of Coulomb interactions on the fragmentation pattern can be examined. Three different cases can be distinguished: (1) one or more counterions are present in the complex and compete with the crown for binding to the ammonium ion. This destabilizes the supramolecular bond. (2) In multiply charged complexes, charge repulsion significantly alters the fragmentation behavior as compared with singly charged ions. (3) If guest and host are both charged, the supramolecular bond becomes very weak. The different charge states provide different pieces of information about the supramolecules under study. Although singly charged complexes provide data on the building block connectivity, the doubly charged analogs are more reliable with respect to complex stoichiometry. As there are several factors which may cause differences in the gas phase and solution behavior of supramolecules (the presence and absence of solvation, changes in the strength of non-covalent interactions upon ionization), it is important to establish well understood correlations between the complexes' gas-phase behavior and their solution structures. A more detailed understanding will help to characterize the structures of even more complex supramolecular architectures by mass spectrometry.

Analysis of endogenous ATP analogs and mevalonate pathway metabolites in cancer cell cultures using liquid chromatography-electrospray ionization mass spectrometry

Nitrogen-containing bisphosphonates (N-BPs) are shown to inhibit a key enzyme of intracellular mevalonate pathway, FPP synthase, leading to intracellular accumulation of pathway metabolites isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). In our previous studies we have shown that a new type of ATP analog, ApppI (triphosphoric acid 1-adenosin-5'-yl ester 3-(3-methylbut-3-enyl) ester), is also formed in addition to IPP and DMAPP accumulation. ApppI has cytotoxic effects leading to direct apoptosis of various cancer cells. In this study we present a validated method based on ion-pair LC-MS(2) for the analysis of isomeric mevalonate pathway metabolites and ATP analogs in cell culture samples. Limit of quantitation for IPP and DMAPP was 0.030microM (1.35fmol on-column) and for ApppI and ApppD 0.020microM (0.9fmol on-column). Acceptable accuracies and precision were also obtained for quality control samples in low and high concentrations of the calibration curve. In addition, we present a new method for quantitation of each coeluting isomer utilizing the peak intensity ratios of two characteristic fragment ions of each compound. For IPP and DMAPP, fragment ions m/z 177 and m/z 159 in the MS(2) were monitored, whereas for ATP analogs, ApppI and ApppD (triphosphoric acid 1-adenosin-5'-yl ester 3-(3-methylbut-2-enyl) ester), the same fragments in the MS(3) spectra were followed. IPP and DMAPP accumulation as well as ApppI and ApppD formation was demonstrated using MCF-7 breast cancer cells. Cells were treated with 25muM zoledronic acid (an N-BP) for 24h, conditions found to induce significant production of the metabolites. We found that the total amount of IPP and DMAPP was 2.4nmol/mg of protein and amount of ApppI and ApppD was 1.1nmol/mg protein. Relative portions of the isomers were approximately 1:4 IPP:DMAPP and 3:7 ApppI:ApppD. Untreated control samples did not contain IPP, DMAPP, ApppI or ApppD.

Effect of cation complexation on the structure of a conformationally flexible multiply charged anion: stabilization of excess charge in the Na+ x adenosine 5'-triphosphate dianion ion-pair complex

We report a computational study of the conformationally and tautomerically flexible cation-dianion complex of Na(+) with doubly deprotonated adenosine 5'-triphosphate (ATP) using a hierarchical selection method. The method uses molecular dynamics to generate initial conformeric structures, followed by a classification process that groups conformers into five "families" to ensure that a representative sample of structures is retained for further analysis, while very similar conformational structures are eliminated. Hierarchical ab initio calculations (DFT and MP2) of typical conformers of the families are then performed to identify the lowest-energy conformeric structures. The procedure described should provide a useful methodology for conducting higher-level ab initio calculations of medium-sized gas-phase biological molecules for interpreting contemporary laser spectroscopy measurements. For Na(+) x [ATP-2H](2) (considering tautomers where the phosphate chain of ATP is doubly deprotonated), the calculations reveal that the sodium cation interacts directly with the negatively charged phosphates (maximum distance = 2.54 A) in all of the low-energy conformers, while a number of the structures also display close cation-adenine interactions producing compact ball-like structures. These compact structures generally correspond to the lowest-energy conformers. The structural variation between the bare [ATP-2H](2-) molecular ion (Burke et al. J. Phys. Chem. A 2005 , 109 , 9775-9785) and the Na(+) x [ATP-2H](2-) cluster is discussed in detail, including the effect of sodiation on the intramolecular hydrogen-bonding network within ATP in a gas-phase environment.

Gas-Phase Chemistry of Diphosphate Anions as a Tool To Investigate the Intrinsic Requirements of Phosphate Ester Enzymatic Reactions: The [M1M2HP2O7]− Ions

Experimental studies on gaseous inorganic phosphate ions are practically nonexistent, yet they can prove helpful for a better understanding of the mechanisms of phosphate ester enzymatic processes. The present contribution extends our previous investigations on the gas-phase ion chemistry of diphosphate species to the [M(1)M(2)HP(2)O(7)](-) ions where M(1) and M(2) are the same or different and correspond to the Li, Na, K, Cs, and Rb cations. The diphosphate ions are formed by electrospray ionization of 10(-4) M solutions of Na(5)P(3)O(10) in CH(3)CN/H(2)O (1/1) and MOH bases or M salts as a source of M(+) cations. The joint application of mass spectrometric techniques and quantum-mechanical calculations makes it possible to characterize the gaseous [M(1)M(2)HP(2)O(7)](-) ions as a mixed ionic population formed by two isomeric species: linear diphosphate anion coordinated to two M(+) cations (group I) and [PO(3)M(1)M(2)HPO(4)](-) clusters (group II). The relative gas-phase stabilities and activation barriers for the isomerization I-->II, which depend on the nature of the M(+) cations, highlight the electronic susceptibility of P-O-P bond breaking in the active site of enzymes. The previously unexplored gas-phase reactivity of [M(1)M(2)HP(2)O(7)](-) ions towards alcohols of different acidity was investigated by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The reaction proceeds by addition of the alcohol molecule followed by elimination of a water molecule.

Quantitative detection of metabolites using matrix-assisted laser desorption/ionization mass spectrometry with 9-aminoacridine as the matrix

Quantitative detection of metabolites is a highly desirable feature in metabolome analyses. Recently, the successful detection of multiple metabolites using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) in the negative ion mode employing 9-aminoacridine as the organic matrix was reported (Edwards JL, Kennedy RT. Anal. Chem. 2005; 77: 2201-2209). However, there is little information available on quantitative detection of multiple metabolites using MALDI-MS and in particular the influence changes in metabolite levels have on such detections. We investigated this aspect by spiking a synthetic metabolite cocktail (consisting of 39 metabolites including amino acids, organic acids and phospho-metabolites) with five representative metabolites at increasing concentrations, one metabolite at a time, and assessed the signals from replicate determinations. It was possible to detect quantitative changes in the spiked metabolites. Although analyte suppression was observed, it was possible to observe scenarios where the spiked metabolite had little or no influence on the quantitative detection of some metabolites. It appears that the mass spectral response of the metabolite is suppressed only when the spiked chemical species are relatively similar in chemical terms. This suggests that quantitation is possible in scenarios where changes in a specific metabolite or a class of metabolites are monitored following appropriate analyte separation strategies, and that careful interpretations must be made when using the technique for quantitative analysis in unbiased metabolomic approaches.

Probing the intrinsic features and environmental stabilization of multiply charged anions

Multiply charged anions (MCAs) represent exotic, highly energetic species in the gas-phase due to their propensity to undergo unimolecular decay via electron loss or ionic fragmentation. There is considerable fundamental interest in these systems since they display novel potential energy surfaces that are characterized by Coulomb barriers. Over recent years, considerable progress has been made in understanding the factors that affect the stability, decay pathways and reactivity of gas-phase MCAs, mainly as a result of the application of electrospray ionization as a generic technique for transferring solution-phase MCAs into the gas-phase for detailed characterization. We review contemporary work in this field, focusing on the factors that control the intrinsic stability of MCAs, both as isolated gas-phase ions, and on their complexation with solvent molecules and counter-ions. While studies of MCAs are primarily of fundamental interest, several classes of important biological ions are commonly observed as MCAs in the gas-phase (e.g. oligonucleotides, sugars). Recent results for biologically relevant ions are emphasised, since a fundamental understanding of the properties of gas-phase MCAs will be highly valuable for developing further analytical methods to study these important systems.