Infrared Multiple Photon Dissociation (IRMPD) - American Chemical

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Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy of the Proton-Bound Dimer of 1-Methylcytosine in the Gas Phase )

Jos Oomens,†,‡ Aaron R. Moehlig,§ and Thomas Hellman Morton*,§, †

FOM Institute for Plasmaphysics, Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands, van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands, § Department of Chemistry, University of California, Riverside, California 92521-0403, and Laboratoire de Pharmacognosie-UMR8076 BIOCIS, Universit e Paris-Sud XI, 92296 Ch^ atenay-Malabry, France

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ABSTRACT The vibrational spectrum of a hemiprotonated pair of the nucleobase cytosine has been recorded in the 300-1810 cm-1 domain using action spectroscopy on electrosprayed positive ions with a free-electron laser. The singly charged, gaseous cation has the same structure as that reported from crystallography, inferred from a strong absorption seen at 1761 cm-1, identified as the carbonyl stretch of the protonated ring mixed with in-plane bending of the bridging Hþ based on a 29 cm-1 shift to lower frequency when all five of the exchangeable hydrogens are replaced by deuterium. IRMPD expels the neutral from the protonbound dimer, leaving behind a protonated monomer. Whereas the bridging Hþ in the dimer ion lies between the nitrogens of the two rings, IRMPD of the protonated monomer ion resulting from the dimer shows its Hþ preferably situated on the carbonyl oxygen, indicating that the proton moves from one basic atom to another when the dimer ion dissociates. SECTION Dynamics, Clusters, Excited States

proton-bound dimer of free cytosine (also known as the hemiprotonated C pair) or 1-methylcytosine.22-31 Figure 1B illustrates the pattern consistently observed: a strong hydrogen bond between two ring nitrogens sharing one proton flanked on either side by weaker hydrogen bonds between carbonyl oxygen and primary amino groups. However, no definitive crystal structure yet exists exhibiting the i-motif. Whereas additional interactions beyond the strong hydrogen bond between cytosines stabilize the i-motif,32 the infrared multiple photon dissociation (IRMPD) spectrum of the protonbound dimer of the nucleobase in the gas phase, reported here, furnishes data that can assist further characterization. The published infrared absorption spectrum of a crystalline salt of the proton-bound dimer of the nucleoside cytidine exhibits four bands in the 1600-1800 cm-1 domain, which implies that the two nucleobases do not share the bridging proton equally in the equilibrium geometry.33 Theoretical calculations support this conclusion, predicting unequal NH 3 3 3 O lengths for the hydrogen bonds that flank the bridging proton (with one N-O distance ∼10% shorter than the other). However, the computed results indicate a low barrier to Hþ-transit from one base to the other, which renders the two NH 3 3 3 O hydrogen bonds effectively equivalent.34

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atson-Crick binding between complementary nucleobases provides one of the most compelling examples of molecular recognition. The discovery that alternative motifs can emerge when antiparallel strands of DNA pair up reveals the diversity of ways hydrogen bonding can take place. Self-association of G to form quadruplexes creates telomeres from the overhang of one strand relative to the other.1-3 Recent evidence supports the occurrence of G-quadruplexes within double-stranded regions as well,4-9 with the corresponding tract of the complementary strand composed of proton-bound dimers of C intercalated with one another via strand reversal to form an i-motif.7-17 Figure 1A illustrates a short segment of the i-motif schematically, in which a strand doubles back on itself three times. Proton-bound dimers of cytosine, represented by ellipses, connect alternating, parallel tracts of a single strand. Figure 1B depicts a molecular picture of what each ellipse stands for. Structural studies long ago documented the self-association of cytosine-5-acetic acid via strong hydrogen bonding between a zwitterionic and a neutral molecule18 as well as the association between C-rich strands of nucleic acids at low pH.19,20 Lately, circular dichroism experiments attest to the stacking of cytosine proton-bound dimers when short DNA strands containing as few as 6 C units aggregate at slightly acidic or neutral pH.21 In the intervening decades, many X-ray structures have provided atomic resolution for salts of the

r 2010 American Chemical Society

Received Date: August 3, 2010 Accepted Date: September 10, 2010 Published on Web Date: September 16, 2010

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DOI: 10.1021/jz101080x |J. Phys. Chem. Lett. 2010, 1, 2891–2897

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Figure 1. (A) Schematic representation of three proton-bound dimers of cytosine intercalated within a single strand in an i-motif. (B) Formation of an individual proton-bound dimer (which the ellipses stand for) from two C-nucleobases attached in parallel orientation to the same DNA strand. Note that the two NH 3 3 3 O distances are unequal in the equilibrium geometry.

Figure 2 reproduces the IRMPD spectra of 1 (m/z 251, panel A) and its deuterated analogue 2 (m/z 256, panel C), along with appropriately scaled, harmonic IR absorption profiles predicted by DFT (panels B and D, respectively). The observed bands and DFT-calculated peak positions for 1 and 2 are tabulated in the Supporting Information. Monitoring the dissociation of dimer 1 to the protonated monomer displays 10 well-defined bands between 1300 and 1800 cm-1 in the experimental spectrum, of which 9 match theory. The power level of the free-electron laser used for this experiment causes extensive decomposition of 1 at resonant frequencies, as the y-axis indicates, with a fractional dissociation >50% for the most intense band.

Chart 1. N-Protonated Conjugate Acid Ions of 1-Methylcytosine

Previous workers have used action spectroscopy to look at IR signatures of G-quadruplexes formed by short DNA strands in the gas phase.35 Unlike quadruplexes, which require cooperativity among several nucleotides, proton-bound dimers between nucleobases form readily under electrospray conditions.36 The present report describes the gas-phase vibrational spectra of the proton-bound dimer of 1-methylcytosine, 1, and of the protonated monomer formed from its dissociation, recorded using IRMPD spectroscopy in an FT-ICR mass spectrometer.37-41

Animation of the calculated normal modes shows that the highest-frequency band in Figure 2A, 1761 cm-1, combines the carbonyl stretch of the more highly charged ring with an in-plane NH bend of the bridging proton. Consistent with the 30 cm-1 red shift predicted by DFT, this band moves to 1732 cm-1 when the exchangeable hydrogens are replaced by deuterium in dimer 2. Other consequences of deuteration include decoupling the carbonyl stretch of the unprotonated ring from NH bends, which converts the pair of bands at 1600 and 1665 cm-1 for the unlabeled dimer to a pure CdO stretch at 1663 cm-1 in the deuterated dimer plus a much lower frequency band at 1215 cm-1. Alternative dimer structures besides 1 include those in which the bridging proton resides on a carbonyl oxygen. Whereas 1 enjoys three hydrogen bonds, dimer 8 contains only two. DFT calculations show that the bridging proton moves without a barrier from oxygen to nitrogen, preferring to situate the bridging proton on the nitrogen of the left-hand ring (8) rather than on the carbonyl oxygen of the right-hand ring, as eq 2 illustrates, and that 8 is approximately 35 kJ mol-1 less stable than 1. In terms of its possible occurrence within duplex DNA, however, 8 does have the advantage that it could be incorporated between two antiparallel strands without reversal. DFT predicts a (scaled) 1798 cm-1 CdO stretch for the protonated ring in 8, which

As Equation 1 summarizes, the experiments demonstrate that the proton bridges between two nitrogens in the gaseous ion, just as seen in crystalline samples, but that the monomeric cation, 3, formed by IR-induced dissociation, prefers to have the proton attached to oxygen rather than to nitrogen (as it is in structures 5-7 drawn in Chart 1).


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should shift only 11 cm-1 to the red (as compared with the 30 cm-1 shift both predicted and observed for 1) upon deuteration of the five exchangeable positions. The major unassigned band in Figure 2 occurs at 1567 cm-1. None of the alternative dimer structures provide a fit for this intense peak (Figure 4 in the Supporting Information), and it may correspond to transit of the bridging proton from one ring to the other (for which a harmonic calculation predicts an unscaled frequency of 2679 cm-1). Consistent with that notion, this band disappears upon replacement of the five exchangeable hydrogens with deuterium, but assignment of this band requires further exploration.

O-protonation delocalizes charge between oxygen and nitrogen. The hydrogen attached to oxygen can be either syn or anti to the N-methyl on the same ring. In the syn orientation, stable structure 9 to the left in eq 3 encounters a barrier to moving the hydrogen to the anti position. A 180° twist about the HOCN dihedral angle (surmounting the barrier) moves the hydrogen anti to the methyl, The relative orientation of the rings in 9 no longer corresponds to a stable geometry, and (according to DFT calculations) the rings rotate in the plane of the dimer into the orientation shown as structure 10 drawn in eq 3. Both of those O-protonated dimers lie higher in energy than 8 (which, as noted above, lies considerably higher than 1). The predicted IR absorption profiles of 8-10 do not fit the observed IRMPD (or the observed isotopic shift) as well as does that of 1. (See the Supporting Information.) The proton-bound dimer has an IR absorption at 987 cm-1, not far from the main emission line of a CO2 laser. Irradiation with a CO2 laser dissociates it to the protonated 1-methylcytosine monomer quantitatively. The top panel of Figure 3 compares the IRMPD spectrum of the protonated monomer formed in this fashion with that of the 1-methylcytosine conjugate acid from electrospray ionization. The remaining panels of Figure 3 depict IR absorption profiles calculated for four isomers using appropriately scaled DFTcalculations. Computations at this level are known to overestimate CdO stretches by a factor greater than that for other stretching frequencies. For these, the DFT result can be corrected by comparing the calculation for N-protonated 1-methylcytosine, 5, with that of N-protonated cytosine, 1872 versus 1902 cm-1 (unscaled), respectively. Salpin et al. have studied the IRMPD spectrum of the protonated cytosine monomer produced by electrospray ionization from aqueous solution.42 Their published theoretical IR absorption profiles for the two most stable tautomeric cations qualitatively resemble those predicted for a superposition of 3 and 5 in Figure 3. Comparison of Salpin et al.'s experimental spectrum

Figure 2. Experimental IRMPD spectra of the proton-bound dimer of 1-methylcytosine (panel A) electrosprayed from H 2O/CH3OH and of its d5 analogue (panel C) electrosprayed from D2O/CH3OD compared with normal modes calculated at B3LYP/6-31G** (panels B and D with 20 cm-1 Gaussian broadening) for ion structures 1 and 2, in which frequencies >850 cm -1 have been scaled by 0.97. Shaded areas of panels B and D depict the silhouettes of the respective experimental IRMPD spectra.


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to 1-methylcytosine (whose gas-phase basicity is only 8-10 kJ mol-1 higher than that of cytosine43) implies that the IRMPD in the present work yields predominantly 3 as the thermodynamically favored tautomer. The relative intensities of Salpin et al.'s IRMPD bands agree qualitatively with the 94:6 O-protonated/N-protonated equilibrium proportions predicted by theory at 300 K,44 which implies, in turn, that those two protonated cytosines have comparable dissociation efficiencies under IRMPD conditions. In other words, the most stable tautomers of protonated cytosine (and, by extension, 3 and 5) dissociate to nearly equal extents under IRMPD conditions. Other candidates for the minor tautomer of protonated 1-methylcytosine seem less plausible. Considerable discussion has focused on the imino form of cytosine,45,46 whose conjugate acid ion (protonated on the ring nitrogen, which, in the case of the N-methyl homologue 6, has a calculated 0 K heat of formation 125 kJ mol-1 higher than that of 3), if it were present, should exhibit a band around 1723 cm-1 (scaled). According to DFT, this vibration corresponds to in-phase stretching of the CdC and exocyclic CdN bonds and ought to shift by no more than 1 cm-1 upon N-methylation, contrary to the 25 cm-1 shift seen in going from protonated cytosine to protonated 1-methylcytosine. The present experiments do not completely rule out the alternative possibility that the minor tautomer comes from protonation on the exocyclic amino group (e.g., structure 7, whose carbonyl stretch should shift ∼30 cm-1 to the red of its unmethylated homologue), but 7 has a calculated 0 K heat of formation 136 kJ mol-1 higher than that of 3. Ammonia loss constitutes the major pathway for collisionally activated dissociation (CAD) of the protonated monomer of 1-methylcytosine and represents the principal decomposition observed in recording its IRMPD spectrum (with expulsion of the elements of HOCN contributing the next most prominent dissociation, consistently about one-third the intensity of NH3 loss over the domain of Figure 3; the experimental traces in the top panel sum both pathways). Published CAD experiments used isotopic labeling to demonstrate that NH3 loss proceeds via intermediacy of the NH2-protonated isomer 7,47 which should be equally accessible to 3 or 5 when they have sufficient internal energy. There is no evidence to suggest a lower sensitivity of 5 with respect to IRMPD. How might the proton transpose from nitrogen to oxygen in the course of dissociation? Plausible explanations for the observation of 3 as the predominant ion from IRMPD of 1 include the following two interpretations. One hypothesis supposes kinetic control: the vibrationally excited dimer passes through a sequence of hydrogen bonded structures in the course of decomposition, and the resulting monomer ion tends to retain memory of the last structure (e.g., 10) that intervenes prior to final dissociation. An alternative interpretation supposes thermodynamic control: the dissociation initially forms an ion-neutral complex, in which a proton passes back and forth between the partners, sampling all of the accessible possibilities. Such noncovalent complexes have many precedents in unimolecular ion decompositions,48-54 and uncharged analogues have recently been inferred in homolyses of gaseous neutrals via “roaming radicals”.55,56 Assuming that the partners in the complex partition vibrational energy statistically in the course

Figure 3. Experimental IRMPD spectrum of the protonated monomer of 1-methylcytosine (m/z 126) (top panel: black trace from dissociation of the proton-bound dimer by CO2 laser photolysis; red trace from electrospray ionization) compared with normal modes calculated at B3LYP/6-31G** (for which frequencies >850 cm-1 have been scaled by 0.97, with 20 cm-1 Gaussian broadening) for the four possible tautomers 3 and 5-7.

with theory shows that O-protonated cytosine predominates under electrospray conditions, contributing the most intense band at 1641 cm-1, although they observe a weak band at 1804 cm-1, suggesting the presence of a small amount of N-protonated cytosine. The most intense band from protonated 1-methylcytosine occurs at 1648 cm-1 and corresponds to in-phase stretching of the CdC and both CdN bonds of ion 3. If the 1804 cm-1 band from electrosprayed cytosine42 does come from a minor N-protonated tautomer, then (as noted above) the corresponding carbonyl stretch for 5 should occur about 30 cm-1 lower in frequency than in the unmethylated case. This would account for the small band seen in the top panel of Figure 3 at 1779 cm-1. DFT calculations used to match the spectra show two protonation sites of 1-methylcytosine, O-protonation to yield 3 and N-protonation to yield 5, having comparable basicity, consistent with results of previous investigations.43 Geometry optimizations on protonated cytosines (without the attached methyl) at a similar level give the same outcome, but computations at higher levels (e.g., CCSD(T)/aug-cc-pVTZ) predict that the oxygen ought to be more basic by roughly 6 kJ mol-1.44 Extending that finding


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of reversible proton transfer, this picture implies that the products reflect equilibrium at a temperature corresponding to the internal energy shared by the monomeric products. The intensity of the 1779 cm-1 band (from 5) relative to the 1648 cm-1 band (from 3) is nearly the same for both the red and the black traces in the top panel of Figure 3, which implies that the effective temperature of dissociating dimers does not differ greatly from the temperature of the ions produced by an electrospray source. The experimental binding enthalpy of the proton-bound dimer of cytosine is reported as ΔH = -160 kJ mol-1 at 650K.57,58 If the same energetics are assumed for the protonbound dimer of 1-methylcytosine and if IRMPD of 1 at room temperature was to yield monomers at 0 K, then harmonic DFT calculations predict that the above value corresponds to a 300 K dissociation threshold for 1 close to ΔH = 100 kJ mol-1, slightly below the energy of nine photons from the CO2 laser. Room temperature corresponds to the energy of approximately two additional photons above that thermodynamic barrier. Inferring that the protonated monomer resulting from IRMPD represents a mixture of 3 and 5 implies that dissociation under the experimental conditions does not give fragments having internal energies much greater than the ambient medium.

NSF grant CHE0848517 and is part of the research program of FOM, supported by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO).

REFERENCES (1)

(2) (3)

(4)

(5)

(6)

(7)

COMPUTATION AND EXPERIMENTAL SECTION DFT geometry optimizations were performed on positively charged ions derived from cytosine and 1-methylcytosine using the 6-31G(d,p) basis set, including four stable tautomers of the protonated monomer (3, 5-7) and four for the protonbound dimer (1, 8-10) of the title compound. ICR techniques for IRMPD of proton-bound dimers of biological molecules have been previously described elsewhere.59 In the present study, 1-methylcytosine was prepared by standard methods,60 recrystallized from methanol, dissolved in 50:50 methanol/ water (CH3OD/D2O for deuterium-exchanged samples) at a concentration of 1 mM containing a small amount of acetic acid, and electrosprayed into the external source of the ICR.40 IRMPD was accomplished by fifteen 5 μs macropulses (full power of 35 mJ each for the protonated monomers and at halfpower for the proton-bound dimers) at every wavelength over a period of 3 s. Each macropulse consists of a 1 GHz train of picosecond micropulses, each micropulse having a duration of ∼100 optical cycles.

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SUPPORTING INFORMATION AVAILABLE Comparison of experimental IRMPD with scaled spectra calculated for dimer structures 8-10, DFT electronic energies for proton-bound dimers and full Gaussian03 reference, and tabulated assignments of bands observed for 1 and 2. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

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Corresponding Author: *To whom correspondence should be addressed. E-mail: morton@ citrus.ucr.edu.

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ACKNOWLEDGMENT We thank the FELIX staff, in particular, Drs. Britta Redlich and Lex van der Meer. This work was supported by


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Blackburn, E. H. The Telomere and Telomerase: Nucleic Acid-Protein Complexes Acting in a Telomere Homeostasis System. A Review. Biochemistry 1997, 62, 1196–1201. Gottschling, D. E.; Stoddard., B. Telomeres: Structure of a Chromosome's Aglet. Curr. Biol. 1999, R164–R167. Burge, S.; Parkinson, G. N.; Hazel, P.; Todd, A. K.; Neidle, S. Quadruplex DNA: Sequence, Topology, and Structure. Nucleic Acids Res. 2006, 34, 5402–5415. Simonsson, T.; Pecinka, P.; Kubista, M. DNATetraplex Formation in the Control Region of c-myc. Nucleic Acids Res. 1998, 26, 1167–1172. Siddiqui-Jain, A.; Grand, C. L.; Bearss, D. J.; Hurley, L. H. Direct Evidence for a G-Quadruplex in a Promoter Region and its Targeting with a Small Molecule to Repress c-MYC Transcription. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11593–11598. Sun, D.; Hurley, L. H. Biochemical Techniques for the Characterization of G-Quadruplex Structures: EMSA, DMS Footprinting, and DNA Polymerase Stop Assay. Methods Mol. Biol. 2010, 608, 65–79. Guo, K.; Pourpak, A.; Beetz-Rogers, K.; Gokhale, V.; Sun, D.; Hurley, L. H. Formation of Pseudosymmetrical G-Quadruplex and i-Motif Structures in the Proximal Promoter Region of the RET Oncogene. J. Am. Chem. Soc. 2007, 129, 10220– 10228. Sun, D.; Hurley, L. H. The Importance of Negative Superhelicity in Inducing the Formation of G-Quadruplex and i-Motif Structures in the c-Myc Promoter: Implications for Drug Targeting and Control of Gene Expression. J. Med. Chem. 2009, 52, 2863–2874. Dai, J.; Ambrus, A.; Hurley, L. H.; Yang, D. A Direct and Nondestructive Approach To Determine the Folding Structure of the I-Motif DNA Secondary Structure by NMR. J. Am. Chem. Soc. 2009, 131, 6102–6104. Gehring, K.; Leroy, J.-L.; Gu eron, M. A Tetrameric DNA Structure with Protonated Cytosine 3 Cytosine Base Pairs. Nature 1993, 363, 561–565. Leroy, J.-L.; Gehring, K.; Kettani, K. A.; Gu eron, M. Acid Multimers of Oligodeoxycytidine Strands: Stoichiometry, Base-Pair Characterization, and Proton Exchange Properties. Biochemistry 1993, 32, 6019–6031. Leroy, J.-L.; Gu eron, M.; Mergny, J.-L.; H el ene, C. Intramolecular Folding of a Fragment of the Cytosine-Rich Strand of Telomeric DNA into an i-Motif. Nucleic Acids Res. 1994, 22, 1600–1606. Leroy, J.-L. Cytidine Protonation and Base-Pair Intercalation in Nucleic Acid Structures: The i-Motif. Nucleic Acids Res. 2002, 7–8. Esmaili, N.; Leroy, J.-L. i-Motif Solution Structure and Dynamics of the d(AACCCC) and d(CCCCAA) Tetrahymena Telomeric Repeats. Nucleic Acids Res. 2005, 33, 213–224. A. Phan, A.; Mergny, J.-L. Human Telomeric DNA: G-Quadruplex, i-Motif and Watson-Crick Double Helix. Nucleic Acids Res. 2002, 30, 4618–4625. Leroy, J.-L. The Formation Pathway of i-Motif Tetramers. Nucleic Acids Res. 2009, 37, 4127–4134. Laisn e, A.; Pompon, D.; Leroy, J.-L. [C7GC4]4 Association into Supra Molecular i-Motif Structures. Nucleic Acids Res. 2010, 38, 3817–3826.


pubs.acs.org/JPCL

(18)

(19) (20)

(21)

(22)

(23)

(24)

(25)

(26)

(27)

(28)

(29)

(30)

(31)

(32)

Marsh, R. E.; Bierstedt, R.; Eichhorn, E. L. The Crystal Structure of Cytosine-5-acetic Acid. Acta Crystallogr. 1962, 15, 310–316. Langridge, R.; Rich, A. Molecular Structures of Helical Polycytidylic Acid. Nature 1963, 198, 725–728. Guschlbauer, W. Protonated Polynucleotide Structures, I. The Thermal Denaturation of Polycyticylic Acid in Acid Solution. Proc. Natl. Acad. Sci. U.S.A. 1967, 57, 1441–1448. Holm, A. I. S.; Nielsen, L. M.; Kohler, B.; Vrønning Hoffmann, S.; Brøndsted Nielsen, S. Electronic Coupling between Cytosine Bases in DNA Single Strands and i-Motifs Revealed from Synchrotron Radiation Circular Dichroism Experiments. Phys. Chem. Chem. Phys. 2010, 12, 3426–3420. Kistenmacher, T. J.; Rossi, M.; Marzilli, L. G. A Model for the Interrelationship Between Asymmetric Interbase Hydrogen Bonding and Base-Base Stacking in Hemiprotonated Polyribocytidylic Acid: Crystal Structure of 1-Methylcytosine Hemihydroiodide Hemihydrate. Biopolymers 1978, 17, 2581–2585. Kistenmacher, T. J.; Rossi, M; Caradonna, J. P.; Marzilli, L. G. Solution and Solid State Studies on the Interactions of Protonated Cytosine Salts. III. Interpyrimidine Base Stacking and Asymmetric Interbase Hydrogen Bonding in the Structure of 1-Methylcytosine Hemihydroiodide Hemihydrate. Adv. Mol. Relax. Interact. Processes 1979, 15, 119–133. Fujinami, F.; Ogawa, K.; Arakawa, Y.; Shirotake, S.; Fujii, S.; Tomita, K.-I. The Structure of the Complex Cytosinium Hemitetrachlorozincate-Cytosine. Acta Crystallogr., Sect. B 1979, 35, 968–970. Schimanski, A.; Freisinger, E.; Erxleben, A.; Lippert, B. Interactions between [AuX4]- (X = Cl, CN) and Cytosine and Guanine Model Nucleobases: Salt Formation with (Hemi-) Protonated Bases, Coordination, and Oxidative Degradation of Guanine. Inorg. Chim. Acta 1998, 283, 223–232. Armentano, D.; De Munno, G.; Di Donna, L.; Sindona, G.; Giorgi, G.; Salvini, L. Self-Assembling of Cytosine Nucleoside into Triply-Bound Dimers in Acid Media. A Comprehensive Evaluation of Proton-Bound Pyrimidine Nucleosides by Electrospray Tandem Mass Spectrometry, X-ray Diffractometry, and Theoretical Calculations. J. Am. Soc. Mass Spectrom. 2004, 15, 268–279. Kr€ uger, T.; Bruhn, C.; Steinborn, D. Synthesis of [(MeCyt)2H]IStructure and Stability of a Dimeric Threefold Hydrogen-Bonded 1-Methylcytosinium 1-Methylcytosine Cation. Org. Biomol. Chem. 2004, 2, 2513–2516. M€ uller, J.; Freisinger, E. [(1-Methylcytosine)2H] I, an Asymmetric Base Pair. Acta Crystallogr., Sect. E 2005, E61, o320– o322. Murata, T.; Saito, G. Properties of Reaction Products between Cytosine and F4TCNQ in MeOH: Two Hemiprotonated Cytosine Salts with F4TCNQ Radical Anion and Methoxy Adduct Anion. Chem. Lett. 2006, 35, 1342–1343. Murata, T.; Enomoto, Y.; Saito, G. Exploration of ChargeTransfer Complexes of a Nucleobase: Crystal Structure and Properties of Cytosine-Et2TCNQ Salt. Solid State Sci. 2008, 10, 1364–1368. Bosnjakovic-Pavlovic, N; Spasojevic-de Bir e, A.; Tomaz, I.; Bouhmaida, N.; Avecilla, F.; Mioc, U. B.; Pessoa, J. C.; Ghermani, N. E. Electronic Properties of a Cytosine Decavanadate: Toward a Better Understanding of Chemical and Biological Properties of Decavanadates. Inorg. Chem. 2009, 48, 9742–9753. Sponer, J.; Leszczynski, J.; Vetterl, V.; Hobza, P. J. Base Stacking and Hydrogen Bonding in Protonated Cytosine


(33)

(34)

(35)

(36)

(37)

(38)

(39) (40)

(41)

(42)

(43)

(44)

(45)

(46)

(47)

(48) (49) (50)

(51) (52)

2896

Dimer: The Role of Molecular Ion-Dipole and Inductive Interactions. J. Biomol. Struct. Dyn. 1996, 13, 695–706. Borah, B.; Wood, J. L. The Cytidine-Cytidinium Complex: Infrared and Raman Spectroscopic Studies. J. Mol. Struct. 1976, 30, 13–30. Han, S. Y.; Oh, H. B. Theoretical Study of the Ionic Hydrogen Bond in the Isolated Proton-Bound Dimer of Cytosine. Chem. Phys. Lett. 2006, 432, 269–274. Gabelica, V.; Rosu, F.; De Pauw, E.; Lemaire, J.; Gillet, J.-C.; Poully, J.-C.; Lecomte, F.; Gr egoire, G.; Schermann, J.; Desfranc-ois, C. Infrared Signatures of DNA G-Quadruplexes in the Gas Phase. J. Am. Chem. Soc. 2008, 130, 1810–1811. Rajabi, K.; Theel, K.; Gillis, E. A.; Beran, G.; Fridgen, T. D. The Structure of the Protonated Adenine Dimer by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations. J. Phys. Chem. A 2009, 113, 8099–8107. Oepts, D.; van der Meer, A. F. G.; van Amersfoort, P. W. The Free-Electron Laser Facility FELIX. Infrared Phys. Technol. 1995, 36, 297–308. Polfer, N. C.; Oomens, J. Reaction Products in Mass Spectrometry Elucidated with Infrared Spectroscopy. Phys. Chem. Chem. Phys. 2007, 9, 3804–2817. Oomens, J.; Morton, T. H. The Cationic CdFþ Stretching Frequency. Angew. Chem., Int. Ed. 2008, 47, 2106–2108. Steill, J. D.; Oomens, J. Action Spectroscopy of Gas-Phase Carboxylate Anions by Multiple Photon IR Electron Detachment/Attachment. J. Phys. Chem. A 2009, 113, 4941–4946. Oomens, J.; Morton, T. H. Structures of Products from Positive Ion-Molecule Reactions by Means of Vibrational Spectroscopy. Eur. J. Mass Spectrom. 2010, 16, 313–319. Salpin, J.-Y.; Guillaumont, S.; Tortajada, J.; MacAleese, L.; Lemaire, J.; Maître, P. Infrared Spectra of Protonated Uracil, Thymine and Cytosine. Chem. Phys. Chem. 2007, 8, 2235–2244. Liu, M.; Li, T.; Cardoso, D. S.; Fu, Y.; Lee, J. K. Gas Phase Thermochemical Properties of Pyrimidine Nucleobases. J. Org. Chem. 2008, 73, 9283–9291. Yao, C.; Turecek, F.; Polce, M. J.; Wesdemiotis, C. Proton and Hydrogen Atom Adducts to Cytosine. An Experimental and Computational Study. Int. J. Mass Spectrom. 2007, 265, 106–123. Purrello, R.; Molina, M.; Wang, Y.; Smulevich, G.; Fresco, J. R.; Spiro, T. G.; Fossella, J. Keto-Iminol Tautomerism of Protonated Cytidine Monophosphate Characterized by Ultraviolet Resonance Raman Spectroscopy: Implications of Cþ Iminol Tautomer for Base Mispairing. J. Am. Chem. Soc. 1993, 115, 760–767. Szczesniak, M.; Leszczynski, J.; Person, W. B. Identification of the Imino-Oxo Form of 1-Methylcytosine. J. Am. Chem. Soc. 1992, 114, 2731–2733. Yao, C.; Cuadrado-Peinado, M. L.; Pol asek, M.; Tureck, F. GasPhase Tautomers of Protonated 1-Methylcytosine. Preparation, Energetics, and Dissociation Mechanisms. J. Mass Spectrom. 2005, 40, 1417–1428. Bowen, R. D. Ion-Neutral Complexes. Acc. Chem. Res. 1991, 24, 364–371. Morton, T. H. The Reorientation Criterion and Positive IonNeutral Complexes. Org. Mass Spectrom. 1992, 27, 353–368. Longevialle, P. Ion-Neutral Complexes in the Unimolecular Reactivity of Organic Cations in the Gas Phase. Mass Spectrom. Rev. 1992, 11, 157–192. McAdoo, D. J.; Morton, T. H. Gas Phase Analogues of Cage Effects. Acc. Chem. Res. 1993, 26, 295–302. Morton, T. H. Collisional Activation and Dissociation: Decomposition via Ion-Neutral Complexes; The Encyclopedia of Mass Spectrometry; Armentrout, P. B., Ed.; Elsevier: London, 2003; Vol. 1, pp 467-479.


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(53)

(54)

(55)

(56)

(57)

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Morton, T. H. Theoretical Models for Ion-Neutral Complexes in Unimolecular Ion Decompositions. The Encyclopedia of Mass Spectrometry; Nibbering, N. M. M., Ed.; Elsevier: London, 2004; Vol. 4, pp 165-173. Julian, R. R.; Ly, T.; Finaldi, A. M.; Morton, T. H. Dissociation of a Protonated Secondary Amine in the Gas Phase via an IonNeutral Complex. Int. J. Mass Spectrom. 2007, 265, 302–307. Sivaramakrishnan, R.; Michael, J. V.; Klippenstein, S. J. Direct Observation of Roaming Radicals in the Thermal Decomposition of Acetaldehyde. J. Phys. Chem. A 2010, 114, 755– 765. Harding, L. B.; Georgievskii, Y.; Klippenstein, S. J. Roaming Radical Kinetics in the Decomposition of Acetaldehyde. J. Phys. Chem. A 2010, 114, 765–777. Mautner (Meot-Ner), M. Ion Thermochemistry of Low-Volatility Compounds in the Gas Phase. 2. Intrinsic Basicities and Hydrogen-Bonded Dimers of Nitrogen Heterocyclics and Nucleic Bases. J. Am. Chem. Soc. 1979, 101, 2396–2403. Mautner (Meot-Ner), M. The Ionic Hydrogen Bond. Chem. Rev. 2005, 105, 213–284. Oh, H.-B.; Lin, C.; Hwang, H.; Zabrouskov, V.; Zhai, H.; Carpenter, B.; McLafferty, F. W. Infrared Photodissociation of Electrosprayed Ions in a Fourier Transform Mass Spectrometer. J. Am. Chem. Soc. 2005, 127, 4076–4083. Helfer, D.L., II; Ramachandra, S. H.; Leonard, N. J. Selective Alkylation and Aralkylation of Cytosine at the 1-Position. J. Org. Chem. 1981, 46, 4803–4804.


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Infrared Multiple Photon Dissociation (IRMPD) - American Chemical

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