Monophosphate Anions Research Articles

Marcus Cross-Relationship Probed by Time-Resolved CIDNP.

The time-resolved CIDNP method can provide information about degenerate exchange reactions (DEEs) involving short-lived radicals. In the temperature range from 8 to 65 °C, the DEE reactions of the guanosine-5'-monophosphate anion GMP(-H)- with the neutral radical GMP(-H)•, of the N-acetyl tyrosine anion N-AcTyrO- with a neutral radical N-AcTyrO•, and of the tyrosine anion TyrO- with a neutral radical TyrO• were studied. In all the studied cases, the radicals were formed in the reaction of quenching triplet 2,2'-dipyridyl. The reorganization energies were obtained from Arrhenius plots. The rate constant of the reductive electron transfer reaction in the pair GMP(-H)•/TyrO- was determined at T = 25 °C. Rate constants of the GMP(-H)• radical reduction reactions with TyrO- and N-AcTyrO- anions calculated by the Marcus cross-relation differ from the experimental ones by two orders of magnitude. The rate constants of several other electron transfer reactions involving GMP(-H)-/GMP(-H)•, N-AcTyrO-/N-AcTyrO•, and TyrO-/TyrO• pairs calculated by cross-relation agree well with the experimental values. The rate of nuclear paramagnetic relaxation was found for the 3,5 and β-protons of TyrO• and N-AcTyrO•, the 8-proton of GMP(-H)•, and the 3,4-protons of DPH• at each temperature. In all cases, the dependences of the rate of nuclear paramagnetic relaxation on temperature are described by the Arrhenius dependence.

Excess-electron attachment and ionization of aqueous uridine monophosphate anion

We applied quantum mechanics/classical mechanics simulations to study excess-electron attachment and ionization of uridine monophosphate anion (dUMP−) in explicit aqueous solutions. We calculated vertical electron affinities (VEAs), adiabatic electron affinities (AEAs), vertical detachment energies (VDEs), vertical ionization energies (VIEs), and adiabatic ionization energies (AIEs) of the 40 structures obtained from molecular dynamic trajectory. The excess-electron and hole distributions were analyzed in electron attachment and ionization of aqueous dUMP−. The converged mean VEA (−0.31 eV) and AEA (2.13 eV) suggest that excess-electron can easily attach to dUMP−. The mean vertical (−0.50 e) and adiabatic (−0.62 e) excess-electron on uracil reveal that main excess-electrons are localized on nucleobases at the most snapshots. The distributions at several special snapshots demonstrate the excess-electron delocalization over nucleobases/ribose or ribose/phosphate group after the structural relaxations of dUMP2− dianion. The VDE value (2.78 eV) indicates that dUMP2− dianion could be very stable. Moreover, the mean VIE is 8.13 eV which is in agreement with the previous calculation using solvation model. The hole distributions on uracil suggest that the nucleobases are easily ionized after the irradiation of high-energy rays. In vertical ionizations, the holes would be delocalized over uracil and ribose at several snapshots. Observing the adiabatic hole distributions, it can be found that electrons on phosphate group and holes on nucleobases can be transferred to ribose at the special snapshots in the structural relaxation of neutral species.

Synthesis of condensed cobalt (II)-zinc phosphate with the concrete anionic composition

Сondensed cobalt(II)-zinc phosphates with the concrete anionic composition (with а linear structure of anion with = 2–8 of the general formula (Co1-хZnх)(n+2)2PnO3n+1, 0<х<1.00, and a cyclic with = 4 – (Со1-xZnx)2P4O12, 0<x<1.0) were synthesized by heat treatment in the isothermal conditions of crystallohydrates of composition Со1-хZnх(H2PO4)2·2H2O (0<x<1.00).
 The heat treatment of Со1-хZnх(H2PO4)2·2H2O (0<x<1.00) was carried out in the air in the range of 100–350 °C (± 5 °). The sample was maintained at a predetermined temperature for 0.5, 1.5, 3.0, 5.0 and 7.0 hours. Heat treatment products were identified using a set of analytical methods: chemical, X-ray, IR spectroscopy, quantitative chromatography on paper.
 It has been determined that the formation of condensed phosphates in products of heat treatment Со1-хZnх(H2PO4)2·2H2O (0<x<1.00) at 100 °C for 0.5–3.0 h does not occur. The processes of anionic condensation begin under the heat treatment for 5.0–7.0 h at 100 °C and deepen for further temperature rise.
 With the increase in the duration of heat treatment at 150 °C to 3.0–7.0 h, the formation of condensed phosphates with a linear structure of anion with a degree of polycondensation = 2–5 of the general formula (Со1-хZnх)(n+2)2PnO3n+1. is recorded. The degree of conversion of monophosphate anion to polyphosphate is 61-73%, respectively. Similar changes in the composition of heat treatment products are realized with the destruction of the structure and complete amorphization of the solid phase. The formation of a new crystalline lattice is recorded at 225 °C.
 The sample, which lasts 0.5 h, is a crystalline phase identified as Со1-хZnхH2P2О7 with an admixture of Со1-хZnхP2О7. The maximum amount of diphosphate (52.9 % of the total content of P2O5) is formed during the firing of Со1-хZnх(H2PO4)2·2H2O for 1.5 h at 225 °C. The amount of diphosphate is reduced by almost 2 times during heat treatment for 7.0 hours. Similar changes in the composition of linear condensed phosphates are observed at 275 °C: with the increase in the duration of heat treatment the number of low-molecular phosphates with = 2–4 decreases, the high-molecular with = 5–8 of the general formula (Со1-хZnх)(n+2)2PnO3n+1 increases . Fosted condensed phosphate with a cyclic structure of the anion with = 4 – cyclotetraphosphate of the composition (Со1-хZnх)2Р4O12 . It increases the temperature to 350 °C and becomes the only heat treatment product.
 Quantitative dependences of the content of condensed phosphates with different anion structure and phosphate acids, which released as intermediate products, on the temperature regime and roasting duration were established.
 The influence of cation nature on the conditions of synthesis and quantitative composition of the condensed phosphates of cobalt(II)-zinc with concrete anionic composition (with а linear structure of anion with = 2–8 of the general formula (Co1-хZnх)(n+2)2PnO3n+1, 0<х<1.00, and a cyclic with = 4 – (Со1-xZnx)2P4O12, 0<x<1.0) is shown.

The structure and properties of xZnO–(67-x)SnO–33P2O5 glasses: (II) Diffraction, NMR, and chromatographic studies

Glasses with nominal molar compositions xZnO–(67-x)SnO–33P2O5 were prepared and their structures were determined by 31P MAS-NMR spectroscopy, HPLC, and by X-ray and neutron diffraction. Compositional dependent changes in the thermal and optical properties described in Part I of this study are attributed to changes in the coordination environments of Sn2+- and Zn2+-ions and their effects on the phosphate anionic network. The 31P MAS-NMR and HPLC data reveal broader distributions of P-tetrahedra in glasses with greater ZnO-contents, due to disproportionation reactions of diphosphate anions in the glass melts to form isolated monophosphate anions and larger triphosphate anions, and due to the loss of some phosphate during glass preparation. The diffraction experiments reveal that Zn2+ prefers tetrahedral coordination, whereas Sn2+ is initially incorporated in isolated, three-coordinated sites that convert to four-coordinated sites with greater ZnO contents. These four-coordinated sites must share corners when incorporated into the glass structure and the transition from glasses dominated by isolated SnO3 pyramids to those with subnetworks of (Sn, Zn)O4 polyhedra occurs near x = 20, and is reflected by breaks in the composition-property trends. The second break in properties occurs near x = 40, and reflects both the dominance of the ZnO4 units in the metal subnetwork, as well an increase in the relative numbers of monophosphate anions in the glass structure.

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.

Adenosine monophosphate recognition by zinc–salophen complexes: IRMPD spectroscopy and quantum modeling study

Zn-salophen complexes are a promising class of fluorescent chemosensors for nucleotides and nucleic acids. We have investigated, by means of IRMPD spectroscopy experiments and quantum chemical calculations, the structure of the host-guest complexes formed by two efficient Zn-salophen receptors and dihydrogen phosphate or adenosine 5′-monophosphate (AMP) anions. In the host-guest complexes the phosphate group is bound with a ZnO(phosphate) bond. In addition, a hydrogen bond can be formed between the POH group and one of the oxygen atoms of the salophen structure. The complexes with AMP anions are endowed with a hydrogen bonded coordination motif together with a weaker π⋯π interaction. It is thus confirmed that the marked changes of the spectroscopic emission properties of Zn-salophen when complexed with AMP can be associated with the existence of π⋯π stacking interactions between the salophen aromatic rings and those of the adenosine nucleobase.

Free energy barrier for dissociation of the guanosine monophosphate anion in water

We report free energy barriers for the ground-state dissociation of the guanosine nucleotide anion in solution, employing implicit and explicit solvation models. The latter was based on the Free Energy Perturbation technique and Monte Carlo simulations. For the lowest-energy structure, both solvation models indicate a solvent-induced transition from a dipole-bound state in the gas phase to a π∗ valence state in solution. The free barrier estimates obtained from explicit and implicit solvation are in fair agreement with each other, although significantly overestimated in comparison to a previously reported explicit solvation model based on ab initio molecular dynamics simulations. Accounting for corrections related to the different DFT functionals used in the present and previous studies significantly improves the agreement.

Intramolecular Base Stacking of Dinucleoside Monophosphate Anions in Aqueous Solution

Time-dependent motions of 32 deoxyribodinucleoside and ribodinucleoside monophosphate anions in aqueous solution at 310 K were monitored during 40 ns using classical molecular dynamics (MD). In all studied molecules, spontaneous stacking/unstacking transitions occurred on a time-scale of 10 ns. To facilitate the structural analysis of the sampled configurations we defined a reaction coordinate for the nucleobase stacking that considers both the angle between the planes of the two nucleobases and the distance between their mass-centers. Additionally, we proposed a physically meaningful transient point on this coordinate that separates the stacked and unstacked states. We applied this definition to calculate free energies for stacking of all pairwise combinations of adenine, thymine (uracil), cytosine and guanine moieties embedded in studied dinucleosides monophosphate anions. The stacking equilibrium constants decreased in the order 5'-AG-3' > GA ~ GG ~ AA > GT ~ TG ~ AT ~ GC ~ AC > CG ~ TA > CA ~ TC ~ TT ~ CT ~ CC. The stacked conformations of AG occurred 10 times more frequently than its unstacked conformations. On the other hand, the last five base combinations showed a greater preference for the unstacked than the stacked state. The presence of an additional 2'-OH group in the RNA-based dinucleoside monophosphates increased the fraction of stacked complexes but decreased the compactness of the stacked state. The calculated MD trajectories were also used to reveal prevailing mutual orientation of the nucleobase dipoles in the stacked state.

Exploring the Binding Ability of Polyammonium Hosts for Anionic Substrates: Selective Size-Dependent Recognition of Different Phosphate Anions by Bis-macrocyclic Receptors

Binding of mono-, di-, and triphosphate, adenosine diphosphate (ADP), and adenosine triphosphatase (ATP) with receptors L1-L3, composed of two [9]aneN(3) units separated by a 2,9-dimethylene-1,10-phenanthroline (L1), a 2,6-dimethylenepyridine (L2), or a 2,3-dimethylenequinoxaline (L3) spacer, has been studied by means of potentiometric titrations, (1)H and (31)P NMR measurements in aqueous solutions, and molecular modeling calculations. In the case of inorganic phosphates, the binding properties of the receptors appear to be determined by their geometrical features, in particular the distance between the two [9]aneN(3) units imposed by the spacer separating the two macrocyclic units. While L1 is able to selectively bind triphosphate over di- and monophosphate, L3 selectively coordinates the smaller monophosphate anion. Finally, L2 shows preferential binding of diphosphate. (1)H and (31)P NMR measurements show that the complexes are essentially stabilized by charge-charge and hydrogen-bonding interactions between the anion and the protonated amine groups of the macrocyclic subunits of the receptors. Molecular dynamics simulations suggest that the larger distance between the two macrocyclic units of L1 allows this receptor to form a larger number of hydrogen-bonding contacts with triphosphate, justifying its selectivity toward this anion. Conversely, in the case of L3, the two facing [9]aneN3 units give rise to a cleft of appropriate dimensions where the small monophosphate anion can be conveniently hosted. Considering nucleotide coordination, L1 is a better receptor for ATP and ADP than L2, thanks to the higher ability of phenanthroline to establish stabilizing π stacking and hydrophobic interactions with the adenine units of the guests.

Quantum chemistry study of interaction of Cu 2+ cation and aqua–copper [Cu(H 2O) 1–4] 2+ complexes with resveratrol stereoisomers, phospholipid and deoxythymidine 5′-monophosphate

The accurate quantum-chemical computations based on DFT, Hartree–Fock and second-order Møller–Plesset (MP2) methods have been performed for the first time to study the interaction of the Cu 2+ ion and [Cu(H 2O) 1–4] 2+ complexes with trans-resveratrol, its cis-stereoisomer, phospholipid and deoxythymidine 5′-monophosphate in vacuum and water medium. On the basis of the interaction energies we have demonstrated that O3 and O5 oxygen atoms of the stereoisomers of resveratrol form the most stable chelate complexes with Cu 2+. It has been shown that the capacity of trans-resveratrol to chelate Cu 2+ is higher than that of cis-resveratrol. The trans-resveratrol–Cu 2+–phospholipid [ trans-resveratrol–Cu(H 2O) 4–phospholipid] 2+, trans-resveratrol–Cu 2+–deoxythymidine 5′-monophosphate and [ trans-resveratrol–Cu(H 2O) 4–deoxythymidine 5′-monophosphate] 2+ systems in which Cu 2+ and [Cu(H 2O) 4] 2+ aqua complex coordinate to the negatively charged oxygen atoms of 5′-monophosphate group of deoxythymidine 5′-monophosphate and phospholipid are characterised by the lowest interaction energy. We have proved that the hydration of the Cu(II) ion by four water molecules contributes to the dramatic reduction of the energetical stability of all the complexes studied. It was pointed out that in aqueous medium the stability of all complexes is significantly higher than in vacuum. The result suggests that trans-resveratrol–Cu(II) and [ trans-resveratrol–Cu(H 2O) 4] 2+ complexes can bind with negatively charged oxygen atoms of 5′-monophosphate anion of phospholipids which form a polar shell surrounding LDL particles. Furthermore, it has been found that trans-resveratrol–3-O–Cu(II) and trans-resveratrol–5-O–Cu(II) complexes are capable of forming the most stable complexes with deoxythymidine 5′-monophosphate and phospholipid. The findings obtained satisfactorily explain the experimental data and give insight into understanding of therapeutical and biological activity of trans-resveratrol–Cu 2+ complexes.

Collisions with biomolecules embedded in small water clusters

We have studied fragmentation of water embedded adenosine 5'-monophosphate (AMP) anions after collisions with neutral sodium atoms. At a collision energy of 50 keV, loss of water molecules from the collisionally excited cluster ions is the dominant process and fragmentation of the AMP itself is almost completely prohibited if the number of attached water molecules is larger than 13. However, regardless of the initial number of water molecules attached to the ion, capture of an electron, i.e. formation of a dianion, always leads to loss of a single hydrogen atom accompanied by evaporation of water molecules. This damaging effect becomes more important as the size of the water cluster increases, which is just the opposite to the protective behavior observed for collision induced dissociation (CID) without electron transfer. For both cases, the loss of water molecules within the experimental time frame is qualitatively well described by means of a common model of an evaporative ensemble. These simulations, however, indicate that characteristically different distributions of internal energy are involved in CID and electron capture induced dissociation.

Determination of the Electron-Detachment Energies of 2′-Deoxyguanosine 5′-Monophosphate Anion: Influence of the Conformation

The vertical electron-detachment energies (VDEs) of the singly charged 2'-deoxyguanosine 5'-monophosphate anion (dGMP-) are determined by using the multiconfigurational second-order perturbation CASPT2 method at the MP2 ground-state equilibrium geometry of relevant conformers. The origin of the unique low-energy band in the gas phase photoelectron spectrum of dGMP-, with maximum at around 5.05 eV, is unambiguously assigned to electron detachment from the highest occupied molecular orbital of pi-character belonging to guanine fragment of a syn conformation. The presence of a short H-bond linking the 2-amino and phosphate groups, the guanine moiety acting as proton donor, is precisely responsible for the pronounced decrease of the computed VDE with respect to that obtained in other conformations. As a whole, the present research supports the nucleobase as the site with the lowest ionization potential in negatively charged (deprotonated) nucleotides at the most stable conformations as well as for B-DNA-like type arrangements, in agreement with experimental evidence.

DFT Study of B-like Conformations of Deoxydinucleoside Monophosphates Containing Gua and/or Cyt and their Complexes with Na+ Cation

B-like minimum energy conformations of deoxydinucleoside monophosphate anions (dD-MPs) containing Gua and/or Cyt and their Na+ complexes have been studied by the DFT PW91PW91/DZVP method. The optimized geometry of the dDMPs is in close agreement with experimental observations and the obtained minimum energy conformations are consistent with purine-purine, purine-pyrimidine, and pyrimidine-purine arrangements in crystals of B-DNA duplexes. All the studied systems are characterized by pyramidalization of the amino groups, which participate in the formation of unusual hydrogen bond between the carbonyl oxygen of the second base in the dGpdC, dCpdG dDMPs, and their Na+ complexes. In all the obtained structures the bases assume a nearly parallel disposition to each other and this effect is independent on the degree of their spatial superposition. From this it is concluded that the parallel disposition of the bases in the B-like single-stranded conformations is dictated by the sugar-phosphate backbone. Correspondingly, the base-base interactions attain a secondary role in the formation of these spatial structures. The formation of a weak C6-H6…O5′ hydrogen bond between cytosine and the phosphate oxygen is reported, in agreement with experimental observations.

Infrared spectroscopy of isolated nucleotides. 1. The cyclic 3′,5′-adenosine monophosphate anion

The intracellular second messenger deprotonated adenosine 3′,5′-cyclic monophosphate anion (cAMP-H) −, generated as gaseous species by electrospray ionization (ESI) and stored in a Paul ion-trap mass spectrometer, has been investigated by mass-resolved infrared multiple photon dissociation (IRMPD) spectroscopy in the 900–1800 cm −1 fingerprint wavenumber range, exploiting the powerful and continuously tunable radiation from a free electron laser (FEL) at the Centre Laser Infrarouge d’Orsay (CLIO). The IRMPD features are interpreted by comparison with the IR spectra obtained by quantum chemical calculations for different low-lying conformers, allowing an assignment for the observed IRMPD bands. It is to be noted that the calculated IR spectra for the most stable conformers look all rather similar and do not allow an unambiguous structural assignment, based exclusively on the IRMPD spectrum. However, the positions and intensities of the IRMPD features of isolated (cAMP-H) − ions are consistent with a species deprotonated at the phosphate group and compatible with the main equilibrium structures lying within 18 kJ mol −1 from the lowest lying conformation, the anti-chair form with a C3′- endo sugar twist.

Determination of the Lowest-Energy Oxidation Site in Nucleotides: 2‘-Deoxythymidine 5‘-Monophosphate Anion

High level ab initio computations anticipate nucleobases as the most favorable sites for oxidation in nucleotides. At the CASPT2 level, the lowest ionization channel for the 2'-deoxythymidine 5'-monophosphate anion is related to a pi-orbital of the thymine base. The present findings lead to revision of the recent assignments of the photodetachment photoelectron spectra of mononucleotide anions in the gas phase and support the classical view of the nucleobase being the main actor in the oxidation process of both nucleosides and nucleotides.

Modifying the bitterness of selected oral pharmaceuticals with cation and anion series of salts.

NaCl has proven to be an effective bitterness inhibitor, but the reason remains unclear. The purpose of this study was to examine the influence of a variety of cations and anions on the bitterness of selected oral pharmaceuticals and bitter taste stimuli: pseudoephedrine, ranitidine, acetaminophen, quinine, and urea. Human psychophysical taste evaluation using a whole mouth exposure procedure was used. The cations (all associated with the acetate anion) inhibited bitterness when mixed with pharmaceutical solutions to varying degrees. The sodium cation significantly (P < 0.003) inhibited bitterness of the pharmaceuticals more than the other cations. The anions (all associated with the sodium cation) also inhibited bitterness to varying degrees. With the exception of salicylate, the glutamate and adenosine monophosphate anions significantly (P < 0.001) inhibited bitterness of the pharmaceuticals more than the other anions. Also, there were several specific inhibitory interactions between ammonium, sodium and salicylate and certain pharmaceuticals. We conclude that sodium was the most successful cation and glutamate and AMP were the most successful anions at inhibiting bitterness. Structure forming and breaking properties of ions, as predicted by the Hofmeister series. and other physical-chemical ion properties failed to significantly predict bitterness inhibition.

Cation Effects on Anion Distributions in Aluminophosphate Glasses

Alkali aluminophosphate glasses, including those in the system xAl2O3·(1−x)CsPO3 (0 ≤x≤ 0.25), were examined by high‐performance liquid chromatography (HPLC), infrared (IR), and 27Al magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopies. Phosphate anions become progressively shorter with the addition of alumina to a metaphosphate glass. Al3+ ions are initially incorporated into the structure in octahedral sites, but the average Al coordination number (CN) decreases with increasing alumina content and tetrahedral species are the preferred moiety when [O]/[P] &gt; 3.5. Al[4] sites appear to be associated with monophosphate (Q0) anions. The role of modifier size on aluminophosphate structure is investigated. At low alumina content (&lt;15 mol%), the disproportionation of pyrophosphate anions into triphosphate and orthophosphate anions is responsible for the lower average Al CN of cesium aluminophosphate glasses compared with sodium aluminophosphate glasses.

The structure characterization of dinucleoside and nucleoside glucopyranosides lipophilic phosphotriesters by fast-atom bombardment tandem mass spectrometry

Rules for the gas-phase fragmentation mechanism of the negative ions of lipophilic phosphotriester molecules of biological interest have been established by fast-atom bombardment mass spectrometry/mass spectrometry. The mass-analyzed ion kinetic energy spectra of the [M − H] − of dinucleoside ( 1–4) and nucleoside glucopyranoside ( 5–9) phosphotriesters show that in the absence of charges on the phosphate bridge, the availability of acidic protons on the 5′-end nucleobase drives a preferred reaction path which leads to 5′- O-nucleotide or 6- O-glucopyranoside monophosphate anions.

Gas-Phase RNA and DNA Ions. 1. H/D Exchange of the [M − H]- Anions of Nucleoside 5‘-Monophosphates (GMP, dGMP, AMP, dAMP, CMP, dCMP, UMP, dTMP), Ribose 5-Monophosphate, and 2-Deoxyribose 5-Monophosphate with D2O and D2S

H/D exchange from D2O and D2S to electrosprayed [M − H]- nucleoside 5‘-monophosphate anions (GMP, dGMP, AMP, dAMP, CMP, dCMP, UMP, TMP) is examined by Fourier transform ion cyclotron resonance mass spectrometry at 9.4 T, along with sugar phosphate controls (ribose 5-monophosphate (R5P) and 2-deoxyribose 5-monophosphate (dR5P)). The relative exchange rates of the nucleotides with D2O were dR5P > dCMP > R5P > CMP > dAMP > UMP > AMP > dTMP ≫ dGMP ≫ GMP, and with D2S were CMP > UMP ≈ dTMP > dCMP > dAMP > AMP > R5P > dR5P ≫ dGMP ≫ GMP. All exchange rates increase dramatically on changing from D2O to D2S, due to the smaller gas-phase acidity difference between exchange reagent and the nucleotide: Δ(ΔHacid) > 60 kcal mol-1 for D2O vs Δ(ΔHacid) > 20 kcal mol-1 for D2S. Ab initio calculations on model compounds at the MP2/6-31+G*//HF/6-31+G* level yield the following order of calculated acidities for each of the exchangeable hydrogens: R2O3PO-H > R2N-H > (R2O-H on ribose) > RN-H2 > (R2O-H on 2-deoxyribose). The ...

Ion trap collisional activation of the deprotonated deoxymononucleoside and deoxydinucleoside monophosphates

Deoxymononucleoside and deoxydinucleoside monophosphate anions formed by electrospray have been subjected to ion trap collisional activation. The threshold for decomposition via loss of base is significantly lower for the deoxymononucleoside 3'-monophosphates than for the corresponding 5'-monophosphates, which indicates that the presence of a charged 3' phosphate group facilitates base loss. The behavior of the bases among each class of isomers shows slight variation in threshold and tandem mass spectrometry efficiency with tile notable exception of 2'-deoxyguanosine 5'-monophosphate. This ion is exceptionally stable toward decomposition via base loss, which reflects a strong hydrogen bonding interaction between the base and the phosphate group. All dinucleotides fragment via similar mechanisms, but the propensity for neutral base loss relative to loss of a charged base is highly dependent on the identities of both the 5' and 3' bases. The behavior of the dinucleotides under collisional activation conditions supports the proposal that base loss proceeds via a proton-bound dimer intermediate in which loss of the charged base directly competes with loss of the neutral base. Application of the kinetic method allows for quantitative predictions of the differences of the gas-phase acidities of the dimer components.