The gas-phase structures of protonated thymidine, [dThd + H]+, and its modified form, protonated 5-methyluridine, [Thd + H]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy combined with electronic structure calculations. IRMPD action spectra are measured over the ranges extending from ~600 to 1900 cm–1 and ~2800 to 3800 cm–1 using the FELIX free electron laser and an optical parametric oscillator/amplifier (OPO/OPA) laser system, respectively. Comparisons between the B3LYP/6-311+G(d,p) linear IR spectra calculated for the stable low-energy conformers and the measured IRMPD spectra are used to determine the most favorable tautomeric conformations of [dThd + H]+ and [Thd + H]+ and to identify those populated in the experiments. Both B3LYP and MP2 levels of theory predict a minor 2,4-dihydroxy tautomer as the ground-state conformer of [dThd + H]+ and [Thd + H]+ indicating that the 2'-hydroxyl substituent of Thd does not exert a significant impact on the structural features. [dThd + H]+ and [Thd + H]+ share parallel IRMPD spectral profiles and yields in both the FELIX and OPO regions. Comparisons between the measured IRMPD and calculated IR spectra suggest that minor 2,4-dihydroxy tautomers and O2 protonated conformers of [dThd + H]+ and [Thd + H]+ are populated in the experiments. Comparison of this work to our previous IRMPD spectroscopy study of protonated 2'-deoxyuridine and uridine suggests that the 5-methyl substituent alters the preferences of O2 versus O4 protonation.
The gas-phase structures of protonated and sodium cationized complexes of triethyl phosphate, [TEP + H]+ and [TEP + Na]+, are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated
by a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer with an electrospray ionization source,
and theoretical electronic structure calculations. Measured IRMPD action spectra are compared to linear IR spectra calculated
at the B3LYP/6-31 G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison,
theoretical studies of neutral TEP are also performed. Sodium cationization and protonation produce changes in the central
phosphate geometry, including an increase in the alkoxy ∠OPO bond angle and shortening of the alkoxy P–O bond. Changes associated
with protonation are more pronounced than those produced by sodium cationization. 相似文献
The gas-phase structures of deprotonated, protonated, and sodium-cationized complexes of diethyl phosphate (DEP) including
[DEP − H]−, [DEP + H]+, [DEP + Na]+, and [DEP − H + 2Na]+ are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated by
a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) with an electrospray ionization
(ESI) source, and theoretical electronic structure calculations. Measured IRMPD spectra are compared to linear IR spectra
calculated at the B3LYP/6-31G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison,
theoretical studies of neutral complexes are also performed. These experiments and calculations suggest that specific geometric
changes occur upon the binding of protons and/or sodium cations, including changes correlating to nucleic acid backbone geometry,
specifically P–O bond lengths and ∠OPO bond angles. Information from these observations may be used to gain insight into the
structures of more complex systems, such as nucleotides and solvated nucleic acids. 相似文献
Infrared multiphoton dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering
RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that
obtained by traditional ion trap-based collision induced dissociation (CID). The single-strand siRNA anions were observed
to dissociate via cleavage of the 5′ P—O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full
sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base
loss ions, accounting for ∼25% to 40% of the product ion current, these ions were eliminated through secondary dissociation
by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With
longer irradiation times, however, internal ions corresponding to cleavage of two 5′ P—O bonds began to populate the product
ion mass spectra as well as higher abundances of [a − Base] and w-type ions. IRMPD of siRNA cations predominantly produced
c- and y-type ions with minimal contributions of [a − Base] and w-type ions to the product ion current; the presence of only
two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD
produced high abundances of protonated nucleobases, [G + H]+, [A + H]+, and [C + H]+, which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps.
CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the dissociation trends
observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary dissociation
to yield informative sequence ions not obtained by CID. 相似文献
Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B2), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600–1850 cm?1) by means of IR multiple‐photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low‐energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1‐protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2‐ and N1‐protonated tautomers. The frequencies and relative intensities of the two C?O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site. 相似文献
The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu]+ and [Ura+Ag]+, were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu]+ and [Ura+Ag]+ that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu]+ and [Ura+Ag]+. B3LYP suggests that Cu+ exhibits a slight preference for O4 binding, whereas Ag+ exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu+ and Ag+ exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag]+ than [Ura+Cu]+. The dissociation behavior and relative stabilities of the [Ura+M]+ complexes, M+ = Cu+, Ag+, H+, and Na+) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu+ and Ag+ are compared with previous and present results for those of H+ and Na+.
The electronic characteristics of mixed‐valence complexes are often inferred from the shape of the inter‐valence charge transfer (IVCT) band, which usually falls in the near infrared (NIR) region, and relationships derived from Marcus‐Hush theory. These analyses typically assume one single, dominant molecular conformation. The NIR spectra of the prototypical delocalised (Class III Robin–Day mixed‐valence) complexes [{Ru(pp)Cp’}2(μ‐C≡C?C≡C)]+ ([ 1 ]+: Cp’=Cp, pp=(PPh3)2; [ 2 ]+: Cp’=Cp, pp=dppe; [ 3 ]+: Cp’=Cp*, pp=dppe) feature a ‘two‐band’ pattern, which complicates band‐shape analysis using these traditional methods. In the past, the appearance of sub‐bands within or near the IVCT transition has been attributed to vibronic effects or localised d‐d transitions. Quantum‐chemical modelling of a series of rotational conformers of [ 1 ]+–[ 3 ]+ reveals the two components that contribute to the NIR absorption band envelope to be a π‐π* transition and an MLCT transition. The MLCT components only gain appreciable intensity when the orientation of the half‐sandwich ruthenium ligand spheres deviates from idealised cis (Ω P?Ru?Ru?P=0°) or trans (Ω P?Ru?Ru?P=180°) conformations. The increased steric demand of the supporting ligands, together with some underlying inter‐phosphine ligand T‐shaped CH???π stacking interactions across the series [ 1 ]+ to [ 2 ]+ to [ 3 ]+ results in local minima biased towards such non‐idealised conformations of the metal‐ligand fragments (Ω P?Ru?Ru?P=33–153°). Experimentally, this is indicated by appearance of multiple bands within the IR (C≡C) band envelopes and increasing intensity of the higher‐energy MLCT transition(s) relative to the π‐π* transition across the series, and the appearance of a pronounced ‘two‐band’ pattern in the experimental NIR absorption envelopes. These conformational effects and the methods of analysis presented here, which combine analysis of IR and NIR spectra with quantum‐chemical calculations on a range of energetically similar conformational minima, are expected to be quite general for mixed‐valence systems. 相似文献
The unimolecular chemistry and structures of self‐assembled complexes containing multiple alkaline‐earth‐metal dications and deprotonated GlyGly ligands are investigated. Singly and doubly charged ions [Mn(GlyGly?H)n‐1]+ (n=2–4), [Mn+1(GlyGly?H)2n]2+ (n=2,4,6), and [M(GlyGly?H)GlyGly]+ were observed. The losses of 132 Da (GlyGly) and 57 Da (determined to be aminoketene) were the major dissociation pathways for singly charged ions. Doubly charged Mg2+ clusters mainly lost GlyGly, whereas those containing Ca2+ or Sr2+ also underwent charge separation. Except for charge separation, no loss of metal cations was observed. Infrared multiple photon dissociation spectra were the most consistent with the computed IR spectra for the lowest energy structures, in which deprotonation occurs at the carboxyl acid groups and all amide and carboxylate oxygen atoms are complexed to the metal cations. The N?H stretch band, observed at 3350 cm?1, is indicative of hydrogen bonding between the amine nitrogen atoms and the amide hydrogen atom. This study represents the first into large self‐assembled multimetallic complexes bound by peptide ligands. 相似文献
Gas-phase interactions between Ba2+ and deprotonated cytosine (C(−H)) were studied in [C(−H)Ba]+ and [C(−H)BaC]+ complexes by IRMPD spectroscopy coupled to tandem mass-spectrometry in combination with DFT calculations. For the [C(−H)BaC]+ complex only one [C(−H)KAN1O−Ba-Canti]+ isomer was found, although the presence of another structure cannot be excluded. This isomer features a central tetracoordinated Ba2+ that simultaneously interacts with keto-amino [C(−H)]− deprotonated on N1 and neutral keto-amino C. Both moieties are in different planes as a consequence of an additional NH…O=C hydrogen bond between C and [C(−H)] − . A sequential IRMPD dynamics is observed in this complex. For the [C(−H)Ba]+ complex produced by electrospray ionization two isomers ([C(−H)KAN1OBa]+ and [C(−H)KAN3OBa]+) were identified, in which Ba2+ interacts simultaneously with the C=O group and the N1 or N3 atom of the keto-amino [C(−H)]−, respectively. A comparison with the related [C(−H)Pb]+ complex (J. Y. Salpin et al., Chem. Phys. Chem. 2014 , 15, 2959–2971) is also presented. 相似文献
Thymidine (dThd) is a fundamental building block of DNA nucleic acids, whereas 5-methyluridine (Thd) is a common modified nucleoside found in tRNA. In order to determine the conformations of the sodium cationized thymine nucleosides [dThd+Na]+ and [Thd+Na]+ produced by electrospray ionization, their infrared multiple photon dissociation (IRMPD) action spectra are measured. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations and frequency analyses are performed at the B3LYP/6-311+G(d,p) level of theory, whereas energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory. As protonation preferentially stabilizes minor tautomers of dThd and Thd, tautomerization facilitated by Na+ binding is also considered. Comparisons of the measured IRMPD and computed IR spectra find that [dThd+Na]+ prefers tridentate (O2,O4',O5') coordination to the canonical 2,4-diketo form of dThd with thymine in a syn orientation. In contrast, [Thd+Na]+ prefers bidentate (O2,O2') coordination to the canonical 2,4-diketo tautomer of Thd with thymine in an anti orientation. Although 2,4-dihydroxy tautomers and O2 protonated thymine nucleosides coexist in the gas phase, no evidence for minor tautomers is observed for the sodium cationized species. Consistent with experimental observations, the computational results confirm that the sodium cationized thymine nucleosides exhibit a strong preference for the canonical form of the thymine nucleobase. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized dThd and Thd follow the order [dThd+H]+ < [Thd+H]+ < [dThd+Na]+ < [Thd+Na]+.
The mass spectra of 30 sulfinamide derivatives (RSONHR', R' alkyl or p-XC6H4) are reported. Most of the spectra had peaks attributable to thermal decomposition products. For some compounds these were identified by pyrolysis under similar conditions to be: RSO2NHR', RSO2SR, RSSR and NH2R' (in all kinds of sulfinyl amides); RSNHR' (in the case of arylsulfinyl arylamides); RSO2C6H4NH2, RSOC6H4NH2 and RSC6H4NH2 (in the case of arylsulfinyl arylamides of the type of X = H) The mass spectra of the three thermally stable compounds showed that there are several kinds of common fragment ions. The mass spectra of the thermally labile compounds had two groups of ions; (i) characteristic fragment ions of the intact molecules and (ii) the molecular ions of the thermal decomposition products. It was concluded that the sulfinamides give the following ions after electron impact: [M]+, [M ? R]+, [M ? R + H]+, [M ? SO]+, [RS]+, [NHR']+, [NHR' + H]+, [RSO]+, [RSO + H]+, [R]+, [R + H]+, [R']+ and [M ? OH]+, and that the thermal decomposition products give the following ions: [RSO2SR]+, [RSSR]+, [M ? O]+, [M + O]+ and [RSOC6H4NH2]+. 相似文献
The [C4H70]+ ions [CH2?CH? C(?OH)CH3]+ (1), [CH3CH?CH? C(?OH)H]+ (2), [CH2?C(CH3)C(?OH)H]+ (3), [Ch3CH2CH2C?O]+ (4) and [(CH3)2CHC?O]+ (5) have been characterized by their collision-induced dissociation (CID) mass spectra and charge stripping mass spectra. The ions 1–3 were prepared by gas phase protonation of the relevant carbonyl compounds while 4 and 5 were prepared by dissociative electron impact ionization of the appropriate carbonyl compounds. Only 2 and 3 give similar spectra and are difficult to distinguish from each other; the remaining ions can be readily characterized by either their CID mass spectra or their charge stripping mass spectra. The 2-pentanone molecular ion fragments by loss of the C(1) methyl and the C(5) methyl in the ratio 60:40 for metastable ions; at higher internal energies loss of the C(1) methyl becomes more favoured. Metastable ion characteristics, CID mass spectra and charge stripping mass spectra all show that loss of the C(1) methyl leads to formation of the acyl ion 4, while loss of the C(5) methyl leads to formation of protonated vinyl methyl ketone (1). These results are in agreement with the previously proposed potential energy diagram for the [C5H10O]+˙ system. 相似文献
The gas-phase ion chemistry of protonated O,O-diethyl O-aryl phosphorothionates was studied with tandem mass spectrometric and ab initio theoretical methods. Collision-activated dissociation (CAD) experiments were performed for the [M+H]+ ions on a triple quadrupole mass spectrometer. Various amounts of internal energy were deposited into the ions upon CAD by variation of the collision energy and collision gas pressure. In addition to isobutane, deuterated isobutane C4D10 also was used as reagent gas in chemical ionization. The daughter ions [M+H?C2H4]+ and [M+H?2C2H4]+ dominate the CAD spectra. These fragments arise via various pathways, each of which involves γ-proton migration. Formation of the terminal ions [M+H?2C2H4?H2O]+, [M+H?2C2H4?H2S]+, [ZPhOH2]+, [ZPhSH2]+, and [ZPhS]+ [Z = substituent(s) on the benzene ring] suggests that (1) the fragmenting [M+H]+ ions of O,O-diethyl O-aryl phosphorothionates have protons attached on the oxygen of an ethoxy group and on the oxygen of the phenoxy group; (2) thiono-thiolo rearrangement by aryl migration to sulfur occurs; (3) the fragmenting rear-ranged [M+H]+ ions have protons attached on the oxygen of an ethoxy group and on the sulfur of the thiophenoxy group. To get additional support for our interpretation of the mass spectrometric results, some characteristics of three protomers of O,O-diethyl O-phenyl phosphorothionate were investigated by carrying out ab initio molecular orbital calculations at the RHF/3–21G* level of theory. 相似文献
Mass spectra of isotope-labeled triptycenes, triphenylmethanes and diphenylmethanes rule out the bulk of postulated decomposition mechanisms and fragment-ion structures. The formation of [M ? H]+ and [M ? 2H]2+ from triptycene, of [M ? H]+, [M ? CH3]+ and [M ? CH4]+ from triphenylmethane, and of [M ? H]2+ and [M ? 2H]2+-as well as the previously reported [M ? H]+ and [M ? CH3]+-from diphenylmethane all seem to be preceded or accompanied by complete loss of position identity of the α and ring hydrogens in the original molecules. A statistical preference for loss of α hydrogens is found in the process leading to [M ? 2H]+ and [M ? H]2+ from triptycene, as in the formation of [M ? H]2+ from toluene. 相似文献