Gas-Phase Conformations and N-Glycosidic Bond Stabilities of

Subscriber access provided by University of Newcastle, Australia

Article

Gas-Phase Conformations and N-Glycosidic Bond Stabilities of Sodium Cationized 2#-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue Yanlong Zhu, Lucas A. Hamlow, Chenchen He, Justin K. Lee, Juehan Gao, Giel Berden, Jos Oomens, and Mary T. Rodgers J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.7b02906 • Publication Date (Web): 29 Mar 2017 Downloaded from http://pubs.acs.org on April 8, 2017

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

The Journal of Physical Chemistry B is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry

submit to J. Phys. Chem. B

Gas-Phase Conformations and N-Glycosidic Bond Stabilities of Sodium Cationized 2′-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue Y. Zhu†, L. A. Hamlow†, C. C. He†, J. K. Lee†, J. Gao‡, G. Berden‡, J. Oomens‡, and M. T. Rodgers†, * † ‡

Department of Chemistry, Wayne State University, Detroit, MI, 48202

Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands

ABSTRACT 2′-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental building blocks of DNA and RNA nucleic acids. In order to understand the effects of sodium cationization on the gas-phase conformations and stabilities of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ are compared to calculated IR spectra predicted for the stable low-energy structures computed for these species to determine the most favorable sodium cation binding sites, identify the structures populated in the experiments, and elucidate the influence of the 2′-hydroxyl substituent on the structures and IRMPD spectral features. These results are compared with those from a previous IRMPD study of the protonated guanine nucleosides to elucidate the differences between sodium cationization and protonation on structure. Energy-resolved collision-induced dissociation (ER-CID) experiments and survival yield analyses of protonated and sodium cationized dGuo and Guo are performed to compare the effects of these cations toward activating the N-glycosidic bonds of these nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, the gas-phase structures populated in the experiments are found to involve bidentate binding of the sodium cation to the O6 and N7 atoms of guanine, forming a 5-membered chelation ring, with guanine found in both anti and syn orientations and C2′-endo (2T3 or 2T1) puckering of the sugar. The ER-CID results, IRMPD yields and the computed C1′−N9 bond lengths indicate that sodium cationization activates the Nglycosidic bond less effectively than protonation for both dGuo and Guo. The 2′-hydroxyl substituent of Guo is found to impact the preferred structures very little except that it enables a 2'OH···3'OH hydrogen bond to be formed, and stabilizes the N-glycosidic bond relative to that of dGuo in both the sodium cationized and protonated complexes. Corresponding author: M. T. Rodgers, [email protected], Tel. (313)577-2431

ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 2 of 40

2

INTRODUCTION 2′-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental build blocks of DNA and RNA nucleic acids. Figure 1 shows the canonical chemical structures of dGuo and Guo. In the most common B-form of double-stranded (ds) DNA, the nucleobases take on an anti orientation and the 2′-deoxyribose sugar moieties exhibit C2′-endo puckering. Changes of the sugar puckering from C2′-endo to C3′-endo, while preserving the anti orientation of the nucleobases, results in the A-form of ds DNA, with deep and narrow major grooves and wide and shallow minor grooves.1 In contrast to that found for DNA, the A-form is most common in RNA. Changes of the orientation of only the guanine residues from anti to syn of A-form DNA, coiling from right-handed to left-handed, as well as the C3′-endo puckering of the sugar moieties produces the less common Z-form of DNA.2 Intramolecular hydrogen bonding of the 2-amino substituent of guanine to the phosphate backbone stabilizes the syn orientation of guanine.3-7 Structural factors such as nucleobase orientation and sugar puckering, exert a strong influence on the structures of nucleic acids with guanine exhibiting unique behavior vs. the other nucleobases as found for Z-form DNA. Thus, understanding the effects of the local environment on these structural factors of DNA and RNA nucleosides are fundamentally important. In addition to the important roles that dGuo and Guo play as constituents of DNA and RNA, they also serve as important targets for anti-cancer drugs.8-9 The N7 atom of guanine has been found to be the major binding site of cisplatin and its derivatives,10-14 whereas the O6 atom is a minor binding site for platinum.15-16 The interactions between multi-nuclear platinum complexes and guanine in DNA have been found to induce irreversible conformational changes from B-form to A- or Z-form DNA.17-19 Synthetic analogues of dGuo and Guo are used as therapeutic and antiviral agents.20-21 The structures of nucleic acids are also influenced by the local environment, i.e., pH and ionic strength (i.e., the presence of metal cations). DNA triplex structures are stabilized by a low pH environment,22-24 or the presence of the Mg2+.25 A unique ability of guanine is the formation of G-quartets, a square planar structure involving four guanine nucleobases hydrogen bonded via


Page 3 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


3

Hoogsteen base paring; two or more G-quartets can form a G-quadruplex structure by stacking on top of each other.26-28 Sodium and potassium cations have been found to stabilize Gquadruplex structures.29-32 Without hydration, G-quadruplexes exhibit a preference for binding of Na+ over K+.33-34 Previous studies have found that protonation stabilizes a variety of nucleobase mismatches, Hoogsteen C+•G base pairing,35-40 and i-motif DNA structures.41-43 The local environment of nucleic acids may also influence the stabilities of the N-glycosidic bonds that connect the nucleobases to the 2′-deoxyribose or ribose sugar moieties.44 N-glycosidic bond cleavage is commonly involved in nucleobase salvage,45-47 and nucleobase excision repair.48-49 In previous studies, both theoretical calculations and experiments have suggested that the oxo-amino (keto) and hydroxyl-amino (enol) tautomers of guanine and its derivatives are important in the gas phase.50-52 In particular, both density functional theory (DFT) calculations and infrared and ultraviolet spectroscopy studies of 9-methylguanine (m9Gua), as a model for the guanine nucleosides, have demonstrated that oxo-amino and hydroxyl-amino tautomers of m9Gua coexist in the experiments.50, 53-55 Previous DFT calculations have also examined sodium cation binding to the canonical guanine nucleosides at the B3LYP/6-311++G(d,p) level of theory and found that the sodium cation preferentially binds to guanine nucleobase.56-57 In the most stable structures computed in that work, [dGuo+Na]+ exhibits an anti orientation of guanine and C2′-endo (2T3) sugar puckering,56 whereas [Guo+Na]+ exhibits a syn orientation and C2′-endo (2T1) sugar puckering.57 However, the possibility of tautomerization of the DNA and RNA guanine nucleosides was not examined into their calculations, such that further calculations that examine tautomerization as well as experimental data are needed to confirm the conclusions of these theoretical calculations. In order to better understand the influence of sodium cationization on the gas-phase conformations of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy investigations of [dGuo+Na]+ and [Guo+Na]+ are performed using a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) coupled to the freeelectron laser for infrared experiments (FELIX) free-electron laser (FEL) or an OPO laser system.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 4 of 40

4

The stable low-energy conformations and linear IR spectra of these complexes are determined from synergistic complementary electronic structure calculations. Comparison between the measured IRMPD and theoretical IR spectra enable the low-energy conformers populated in the experiments to be determined. This approach has proven effective for the structural characterization of a wide variety of biologically relevant species, including deprotonated, protonated and metal cationized nucleobases,58-65 nucleosides,66-73 and nucleotides.6-7,

74-80

Energy-resolved collision-induced dissociation (ER-CID) experiments of protonated and sodium cationized dGuo and Guo are also performed using a Bruker amaZon ETD quadrupole ion trap mass spectrometer (QIT MS). The relative stabilities of these species, and in particular the Nglycosidic bond stabilities, are examined via survival yield analyses. The effects of sodium cationization vs protonation on the gas-phase conformations and N-glycosidic bond stabilities of dGuo and Guo are elucidated by comparing the IRMPD, ER-CID, and computational results for these systems.

EXPERIMENTAL AND COMPUTATIONAL SECTION FT-ICR MS and Photodissociation. IRMPD action spectra of sodium cationized 2′deoxyguanosine, [dGuo+Na]+, and its RNA counterpart, sodium cationized guanosine, [Guo+Na]+, were measured using a 4.7 T Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) that has been described previously.81-83 Photodissociation is achieved using the widely tunable FELIX free-electron laser84 over the infrared (IR) fingerprint region and an OPO/OPA laser system over the hydrogen-stretching region. 2′-Deoxyguanosine and guanosine were purchased from Sigma-Aldrich (St. Louis, MO, USA) and shipped from Wayne State University to the FELIX laboratory. All other reagents were purchased from Sigma-Aldrich, Zwijndrecht, The Netherlands. The analyte solutions were made by dissolving 1 mM dGuo or Guo and 1 mM NaCl in a 50%:50% (v/v) methanol:water mixture. The ions were generated using a Micromass “Z-spray” electrospray ionization (ESI) source at a flow rate in the range between 2 and 5 µL/min. Ions from the ESI source were accumulated in an rf hexapole ion trap


Page 5 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


5

for several seconds, pulse extracted through a quadrupole bender, and transferred into the ICR cell via a 1 m long rf octopole ion guide. Ion capturing was facilitated by electrostatic switching of the dc bias of the octopole, which also avoids collisional heating of the ions.81 The ions were stored in the ICR cell to cool to room temperature by radiative emission. The [dGuo+Na]+ or [Guo+Na]+ complex was mass isolated using stored waveform inverse Fourier transform (SWIFT) techniques, and then irradiated by the FEL or OPO laser to induce IR photodissociation. The FEL typically produces high-energy macropulses, such that efficient IRMPD can be achieved in 3 s, whereas the reduced output of the OPO laser requires 8.5 s of irradiation to achieve a similar dissociation efficiency. The IRMPD spectra were measured over the frequency ranges extending from ~550 to 1850 cm-1 (in the FELIX, fingerprint region) and between ~3300 and 3800 cm-1 (in the OPO, hydrogen-stretching region). QIT MS and ER-CID. ER-CID experiments were performed using a Bruker amaZon ETD quadrupole ion trap mass spectrometer (Bruker Daltonics, Bremen, Germany) for the [dGuo+H]+, [Guo+H]+, [dGuo+Na]+ and [Guo+Na]+ systems. Samples of dGuo and Guo were dissolved in a 50%:50% (v/v) methanol:water mixture resulting in a final concentration of 10 µM. Acetic acid (purchased from Mallinckrodt Chemicals, St. Louis, MO, USA) was added at 1% (v/v) to facilitate formation of [dGuo+H]+ and [Guo+H]+, whereas NaCl was added at 10 µM to induce formation of [dGuo+Na]+ and [Guo+Na]+. The flow rate of the Apollo ESI source was set to 3 µL/min. Helium was used as the collision gas at a stagnation pressure of ~1 mTorr in the ion trap. The number of trapped ions was kept constant (20,000) using the ion charge control (ICC) in all experiments. The low mass cut-off for the ER-CID experiments was set to 27%, corresponding to a qz value of 0.25. The rf excitation amplitude was varied from 0 V to the amplitude required to produce complete fragmentation of the precursor ion at a step size of 0.01 V. Each experiment was repeated three times to assess reproducibility. Data analysis was performed using Compass Data Analysis 4.0 software (Bruker Daltonics, Bremen, Germany). Survival Yield Analyses. Survival yield analyses, when judiciously applied, can be used to study the relative stabilities of various ions.85-88 The protonated and sodium cationized guanine



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 6 of 40

6

nucleosides represent a nearly ideal case for such studies due to the very similar sizes, structures, and CID pathways these systems undergo. Because N-glycosidic bond cleavage is the only fragmentation pathway observed in the ER-CID experiments, the survival yield analyses provide information directly related to the relative N-glycosidic bond stabilities of the protonated and sodium cationized guanine nucleosides. The survival yields are calculated using eq 1,89 Survival Yield = [ ] ⁄([ ] + [ ] )

(1)

where Nuo = dGuo or Guo, and Cation = H or Na. The survival yield of each precursor ion was measured three times, where the error bars represent the standard deviation for these three measurements. The survival yield of the precursor ion was computed and plotted as a function of the rf excitation amplitude. The rf excitation amplitude required to produce 50% dissociation of the precursor ion, CID50%, is then determined from least-squares fitting of the survival yield using a 4-parameter logistic function as defined in eq 2,89 !"#$!%&

Survival Yield = min + '(() *+/-./

345565789 01% )

(2)

where max and min are the maximum (1) and minimum (0) values of the survival yield, rf EA is the rf excitation amplitude applied in the CID experiment, and Hillslope is the slope of the declining region of the survival yield curve. Comparison of the CID50% values measured for the protonated and sodium cationized guanine nucleosides thus provides the relative N-glycosidic bond stabilities of these cationized nucleosides. Data analysis was performed using SigmaPlot 10.0 (Systat Software, Inc., San Jose, CA, USA). Survival yields were calculated using custom software developed in our laboratory. Computational Details. Figure 1 shows the canonical chemical structures of neutral dGuo and Guo. The nitrogen and oxygen atoms of these nucleosides are the potential binding sites for the sodium cation. Simulated annealing was performed using HyperChem90 with the Amber 3 force field to generate candidate structures for higher level optimization. The initial structures used for simulated annealing examined N3, O6 and N7 as potential Na+ binding sites to the canonical form of the guanine residue, whereas O2', O3', O4' and O5' were examined as


Page 7 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


7

potential binding sites to the sugar moiety. In order to determine the importance of minor tautomers of these guanine nucleosides, we also examined binding of Na+ to nine tautomeric forms of these nucleosides such that initial structures used for simulated annealing include the same potential Na+ binding sites (N3, O6, N7, O2', O3', O4' and O5') as well as N1 and the NH imino substituent for tautomers where the N1 and/or an amino substituent are associated with the change in tautomeric form of the guanine residue. Each initial structure was subjected to 300 cycles of annealing. Each cycle involved three steps, thermal heating for 0.3 ps from 0 to 1000 K, sampling of conformational space for 0.2 ps at 1000 K, and thermal cooling for 0.3 ps from 1000 to 0 K. The resulting structure was then optimized to a local minimum using the Amber 3 force field. A molecular mechanics calculation was performed every 1 fs in each cycle, and a snapshot of the lowest energy structure at the end of each cycle was saved and used to initiate the subsequent cycle. Approximately 100 candidate structures for both [dGuo+Na]+ or [Guo+Na]+ were chosen for high level quantum chemical calculations based on the relative stabilities predicted by the simulated annealing process. Geometry optimization and harmonic vibrational frequency calculations were performed at the B3LYP/6-311+G(d,p) level of theory using the Gaussian 09 suite of programs.91 Single point energies were calculated at the B3LYP/6311+G(2d,2p) level of theory to determine the relative stabilities of the stable low-energy conformers of [dGuo+Na]+ and [Guo+Na]+. The vibrational frequencies in the fingerprint region were scaled by 0.980, whereas vibrational frequencies in the hydrogen-stretching region were scaled by 0.954. In order to better reproduce experimental broadening in the measured IRMPD spectra, the vibrational frequencies were convoluted with a 20 cm-1 fwhm Gaussian line shape over the fingerprint region, whereas a 15 cm-1 fwhm Gaussian line shape was used over the hydrogen-stretching region.

RESULTS IRMPD Action Spectroscopy. The only photodissociation pathway observed for [dGuo+Na]+ and [Guo+Na]+ in both the IR fingerprint and hydrogen-stretching regions involves



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 8 of 40

8

N-glycosidic bond cleavage with the sodium cation retained by guanine as summarized in reaction 3. [Nuo+Na]+ + n hv → [Gua+Na]+ + (Nuo−Gua)

(3)

The photodissociation behavior of [dGuo+Na]+ and [Guo+Na]+ is consistent with the collisioninduced dissociation behavior observed in the ER-CID studies (discussed below). The IRMPD yield was calculated as the ratio of the intensity of sodium cationized guanine product, I[Gua+Na]+, divided by the total ion intensity, as summarized in eq 4. IRMPD yield = ([] )⁄([] + [] )

(4)

The IRMPD yields of [dGuo+Na]+ and [Guo+Na]+ were plotted as a function of vibrational frequency from ~550 to 1850 cm-1 and from ~3300 to 3800 cm-1 to generate the experimental IRMPD spectra. Linear normalization with the FEL or OPO laser power was used to correct for variations in the laser power as a function of wavelength. The measured IRMPD spectra of sodium cationized dGuo and Guo are compared with those reported for the protonated forms of dGuo and Guo in Figure 2.66 The IRMPD yield of [dGuo+Na]+ in the fingerprint region is roughly three times greater than that of [Guo+Na]+, whereas the IRMPD yield of [dGuo+Na]+ only exceeds that of [Guo+Na]+ by ~40% in the hydrogen-stretching region. This result suggests that the 2′-hydroxyl substituent of Guo stabilizes the N-glycosidic bond thereby reducing its photodissociation efficiency, consistent with previous threshold CID studies of the protonated guanine nucleosides,92 and the energy-resolved CID studies performed here and discussed below. Parallel behavior is also found in the IRMPD studies of sodium cationized adenine nucleosides,73 and in analogous threshold collision-induced dissociation (TCID) studies of the protonated adenine, cytosine, and uracil nucleosides.93-95 Taken together, these studies indicate that the N-glycosidic bonds of the protonated and sodium cationized RNA nucleosides are generally more stable than those of the analogous DNA nucleosides. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ in both the fingerprint and hydrogen-stretching regions are highly parallel, except for the weak IR absorptions at ~650 and 938 cm-1 for [dGuo+Na]+ and the weak IR absorption at 3577 cm-1


Page 9 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


9

observed in the measured IRMPD spectrum of [Guo+Na]+. Energy-Resolved Collision-Induced Dissociation. Figure 3 shows the ER-CID mass spectra of [dGuo+H]+, [Guo+H]+, [dGuo+Na]+ and [Guo+Na]+ at rf excitation amplitudes that produce slightly less than 50% dissociation. In all cases, the CID mass spectra are very simple exhibiting only a single fragmentation pathway corresponding to N-glycosidic bond cleavage with the proton or sodium cation retained by the guanine nucleobase. Thus activation by multiple low-energy collisions results in the same unimolecular decomposition pathway as activation by absorption of multiple IR photons. Theoretical Results. The designations employed to describe the orientation of guanine and sugar puckering are depicted in Figure S1. The anti orientation is used to describe conformations where the ∠C4N9C1′O4′ dihedral angle is between 90° to 270°, whereas the syn orientation is used when the ∠C4N9C1′O4′ dihedral angle is between −90° to 90°. Two related designations for the sugar puckering are used. The first designation assumes that the ring is more envelope like such that endo (puckering toward the 5'-substituent) and exo (puckering away from 5'-substituent) are used to designate which atom is puckered out of the plane of the sugar ring, whereas envelope (E) and twist (T) designations are more general and detailed as many stable conformations take on partially twisted structures. The pseudorotation angle, P, of the sugar moiety is calculated using eq (5).96 tan < =

(=> =? )$(=@ =1 ) A×=C ×DE%& FG°E%& HA°I

(5)

The variables, v0, v1, v2, v3 and v4, represent the ∠ C4′O4′C1′C2′, ∠O4′C1′C2′C3′, ∠C1′C2′C3′C4′, ∠C2′C3′C4′O4′ and ∠C3′C4′O4′C1′ dihedral angles, respectively. In the pseudorotation angle diagram (Figure S1), v2 is positive in the upper section of the diagram, and negative in the lower section of the diagram. The E and T designations of sugar puckering can be identified by comparing P and v2 of each nucleoside. In this nomenclature, superscripts designate endo, whereas subscripts designate exo configurations. Numbers precede or follow the letters E and T, based on major or minor puckering of the atoms, respectively.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 10 of 40

10

The ground-state structures of [dGuo+Na]+ and [Guo+Na]+ optimized at the B3LYP/6311+G(d,p) level of theory are shown in Figure 1. As can be seen in the figure, these ground structures are very similar, Na+ binds to the O6 and N7 atoms of the guanine nucleobase, forming a 5-membered chelation ring. The nucleobase orientation in both ground conformers is anti, while the sugar puckering is C2′-endo (2T3). Table 1 compares geometric details of these ground structures. The C1′−N9 glycosidic bond length of [dGuo+Na]+ is 1.469 Å, which contracts slightly to 1.463 Å in [Guo+Na]+, suggesting that the N-glycosidic bond of [Guo+Na]+ is slightly stronger than that of [dGuo+Na]+, consistent with the ER-CID results. A weak noncanonical hydrogen-bonding interaction between the H8 and O5′ atoms is found to provide additional stability to both structures, whereas an additional hydrogen-bonding interaction between the 2′- and 3′-hydroxyls is found and only possible for [Guo+Na]+. Tables S1 and S2 list all calculated stable low-energy conformers of the canonical forms of [dGuo+Na]+ and [Guo+Na]+, respectively, whereas Table S3 lists only the most stable conformers calculated for each of the tautomeric forms of these complexes, except that two lowenergy binding modes are include for the hydroxyl-amino tautomer (t6), with the relative enthalpies at 0 and 298 K, Gibbs free energies at 298 K, pseudorotation angles, guanine orientations, and sugar puckerings. Table 2 summarizes the same information for select stable low-energy conformers of the canonical forms of [dGuo+Na]+ and [Guo+Na]+, where the structures chosen for exhibition are based on comprehensively examining the Na+ binding mode, guanine orientation, sugar puckering, and hydrogen-bonding interactions. Figures S2 and S3 show all stable low-energy structures of the canonical forms of [dGuo+Na]+ and [Guo+Na]+ computed, whereas Figures S4 and S5 show only the most stable conformations for each of the tautomeric forms of these complexes except for the t6 tautomer where two of the low-energy binding modes are again included, respectively, along with their sodium cation binding mode, guanine orientation, sugar puckering, and relative Gibbs free energy at 298 K. Each conformer is designated using an uppercase letter that indicates the number of chelation interactions between the sodium cation and guanine nucleoside, T for tridentate, B for bidentate, and M for


Page 11 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


11

monodentate. Conformers involving the same mode of Na+ binding are differentiated using a number that indicates their order of relative Gibbs free energies at 298 K. Complexes involving a minor tautomer of guanine are additionally appending with a lowercase letter “t” followed by a single number when tautomerization involves transfer of the N1 proton to the atom indicated, and by two numbers when tautomerization involves transfer of the N1 and one of the amino protons to the atoms indicated. Sodium Cation Binding to O6 and N7. Bidentate binding to the O6 and N7 atoms of guanine is the most favorable mode of sodium cation binding to [dGuo+Na]+ and [Guo+Na]+. Both anti and syn orientations of the nucleobase are represented among these B(O6N7) binding conformers, with the anti orientation slightly more favorable than syn, and C2'-endo puckering favored over C3'-endo. For [dGuo+Na]+, syn orientated B(O6N7) binding conformers are at least 6.4 kJ/mol less stable than the ground conformer, whereas for [Guo+Na]+, syn orientated B(O6N7) binding conformers are more competitive such that the most stable B(O6N7) syn conformer is only 0.5 kJ/mol less stable than the ground conformer. Similarly, anti oriented C3′endo conformers of [dGuo+Na]+ and [Guo+Na]+ are at least 2.6 and 3.3 kJ/mol less favorable than the corresponding ground conformers, respectively. Conformers B10(O6N7) of [dGuo+Na]+ and B6(O6N7) of [Guo+Na]+ exactly parallel the ground conformers except that they lack the H8•••O5′ noncanonical hydrogen-bonding interaction, and are 6.5 kJ/mol and 7.0 kJ/mol less stable than the corresponding ground conformer, respectively, indicating that the noncanonical hydrogen-bonding interaction does slightly increase the stability of the complex. Sodium Cation Binding to N3. For both [dGuo+Na]+ and [Guo+Na]+, the N3 atom of guanine is found to be a much less favorable binding site for Na+ such that the most stable N3 binding conformers are > 56.9 kJ/mol less stable than the B1(O6N7) ground conformers. Both anti and syn orientations are found with the syn conformers favored over anti. The syn oriented N3 binding conformers of [dGuo+Na]+ and [Guo+Na]+ exhibit tridentate structures that are similar to the ground conformers found for [dAdo+Na]+ and [Ado+Na]+,73 where Na+ chelates with the N3, O4' and O5' atoms to form 5- and 6-membered chelation rings. N3 cationized anti



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 12 of 40

12

oriented conformers of [dGuo+Na]+ and [Guo+Na]+ are much less stable, by > 130 kJ/mol for dGuo and > 80 kJ/mol for Guo. Thus, chelation between Na+ and the 2′-hydroxyl substituent stabilizes the N3 cationized anti oriented conformers significantly, but is not sufficient to make this mode of binding competitive for Guo. Sodium Cation Binding to the Sugar Moiety. Conformers that bind solely to the sugar moiety of both [dGuo+Na]+ and [Guo+Na]+ are much less favorable than the corresponding ground conformers. The relative Gibbs free energies of sugar binding conformers are at least 106 kJ/mol less stable than corresponding B1(O6N7) ground conformers. Thus, the oxygen atoms of the sugar are not important binding sites for Na+ in [dGuo+Na]+ and [Guo+Na]+. Sodium Cation Binding to Tautomeric Guanine Nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, ]+, complexes involving minor tautomers of the guanine residue are found to be much less stable (by at least 32.2 and 34.2 kJ/mol) than the canonical B1(O6N7) ground conformers, respectively. The relative Gibbs free energies of the sodium cationized tautomeric guanine nucleosides follow the order: B1(O6N7)t3 < B1(N1O6)t7 < (N3O4′O5′)t6 for both [dGuo+Na]+ and [Guo+Na]+. The impact of tautomerization on the stability is even more significant for all minor tautomers that also involve tautomerization of the amino substituent, as these conformations are at least 53.8 and 57.5 kJ/mol less stable than the corresponding ground conformers of [dGuo+Na]+ and [Guo+Na]+, respectively. The relative Gibbs free energies of these sodium cationized tautomeric guanine nucleosides exhibit differing orders of stability, but again the most stable among these tautomers again involve B1(O6N7) binding of Na+. Thus, sodium cation binding to the guanine nucleosides involving minor tautomers also prefer bidentate binding to the guanine residue. Sugar Puckering. A variety of sugar puckerings are found among the stable conformers of [dGuo+Na]+ and [Guo+Na]+ including C1′-exo, C2′-endo, C2′-exo, C3′-endo, C3′-exo, C4′exo and O4′-endo. C2'-endo (2T3) puckering is the most favorable for both guanine nucleosides followed by C3′-endo (3T2). The relative stabilities of the other modes of puckering are influenced by the 2′-hydroxyl substituent. Overall, the influence of the sugar puckering on


Page 13 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


13

stability is found to be much less significant than the Na+ binding mode and guanine orientation.

DISCUSSION Conformers of [dGuo+Na]+ Populated by ESI. The measured IRMPD spectrum and calculated IR spectra of the most stable B(O6N7) binding conformers of [dGuo+Na]+ that show good agreement with the measured IRMPD spectra are compared in Figure 4. Figure S6 shows comparisons of select guanine binding conformers of [dGuo+Na]+ that exhibit spectral mismatches (shaded in red) vs. the calculated IR spectra. Analogous comparisons to sugar binding conformers, which exhibit significant spectral misalignments (shaded in red), are shown in Figure S7. Similarly, comparisons involving complexes that involve minor tautomers of the guanine residue, which all exhibit even more obvious spectral misalignments (shaded in red) are shown in Figure S8. Here only the most stable modes of Na+ binding to each of the minor tautomers are shown, except that the B1(O6N7)t6 conformer is also included as this mode of binding is the most favorable for the isolated t6 tautomer of guanine. However, we note that all stable complexes computed involving the minor tautomers exhibit gross spectral mismatches as the spectral signatures are most sensitive to the tautomeric state of the guanine residue. The calculated IR spectrum of the ground conformer, B1(O6N7) exhibits very good agreement with the measured IRMPD spectrum. However, the intensities of the IR features predicted at 3413 and 3436 cm-1 are inverted compared with the corresponding features in the measured IRMPD spectrum. The calculated IR spectra of other low-energy B(O6N7) conformers (not shown), i.e., B2−B5, are highly parallel, and therefore, these conformers may also be populated in the experiments. The IR feature at 3670 cm-1 predicted for anti oriented B(O6N7) conformers with C3'-endo sugar puckering exhibits a slight blue shift compared with the measured IRMPD spectrum, which indicates that these conformers, i.e., B6−B8 and B11(O6N7), may be populated in the experiments but with lower abundance than the more stable B1−B5(O6N7) conformers. The IR feature associated with O5'H stretching predicted for B9(O6N7) blue shifts by 9 cm-1 to 3444 cm-1 vs B1(O6N7), but is still reasonably well aligned



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 14 of 40

14

with the measured IRMPD spectrum. Slight blue shifts of the IR features at 1536, 1591, 1642 and 3655 cm-1 for B9(O6N7) vs. those of B1(O6N7) and the observed features in the measure IRMPD spectrum suggest that B9(O6N7) may also be present, but if present is in very low abundance. The calculated IR spectrum of B15(O6N7) shows good agreement with the experimental IRMPD spectrum, which indicates B(O6N7) conformers with C3'-exo sugar puckering may be accessed in the experiments with low populations. The predicted IR spectra of the B17, B19, B21, B25, and B26 B(O6N7) conformers are nearly identical to the calculated IR spectrum of B15(O6N7), which indicates that these conformers with C3'-exo sugar puckering may also be populated. Changes in the sugar puckering do not significantly impact the calculated IR spectra, only a minor blue shift of the IR feature at 3673 cm-1 by ~10 cm-1 is found. However, the relative Gibbs free energies of these conformers suggest that the conformers with sugar puckerings that differ from C2'-endo do not have large populations in the experiments. Lack of the noncanonical hydrogen bond between the C8 and O5' atoms splits the IR feature at 3655 cm-1, indicating that this intramolecular hydrogen bond stabilizes these conformers. Thus, the B10, B14, B16, B18, B20, B22−B24, B28 and B29 B(O6N7) conformers are not present in measurable abundance. The IR features predicted above 1500 cm-1 in the fingerprint region as well as those calculated in the hydrogen-stretching region for the syn and anti oriented N3 binding conformers (Figure S4) are sufficiently different from the measured IRMPD spectrum, that T1(N3O4'O5'), T2(N3O4'O5'), T3(N3O4'O5') and B1(N3O3') do not have measurable populations in the experiments. Similar to the N3 binding conformers, sugar binding conformers, e.g., B1(O4'O5'), with high relative Gibbs free energy and significant misalignments between the experimental IRMPD and calculated IR spectra are not populated. Likewise, the high relative Gibbs free energy and very significant spectral misalignments between the measured IRMPD and predicted IR spectra for complexes that involve minor tautomers of the guanine residue, e.g., B1(O6N7)t3, indicate that none of these conformers are populated in the experiments. In summary, the sodium cation prefers bidentate binding to the O6 and N7 atoms of guanine via a 5-membered chelation ring with anti and syn orientations of the nucleobase


Page 15 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


15

observed. The syn orientation is slightly less favorable than anti, based on the computed relative Gibbs free energies and minor shifts in the calculated IR spectrum. C2'-endo puckering is preferred over other sugar puckerings. Therefore, O6N7 bidentate binding conformers with C2'endo puckering of [dGuo+Na]+ are the dominant species present in the experiments. The significant shifts predicted in the fingerprint and hydrogen-stretching regions indicate that N3 and sugar binding conformers, as well as all complexes that involve minor tautomers of the guanine residue do not have measurable populations in the experiments. Conformers of [Guo+Na]+ Populated by ESI. The measured IRMPD spectrum and calculated IR spectra of the most stable B(O6N7) conformers of [Guo+Na]+ that exhibit good spectral alignment with the measured spectrum are compared in Figure 5. Figure S9 shows the comparisons of select guanine binding conformers of [dGuo+Na]+ with spectral misalignments (shaded in red) in the calculated IR spectra. Analogous comparisons to sugar binding conformers that exhibit significant spectral misalignments (shaded in red) are shown in Figure S10. Similarly, comparisons involving complexes that involve minor tautomers of the guanine residue, which all exhibit even more obvious spectral misalignments (shaded in red) are shown in Figure S11. Again, only the most stable modes of Na+ binding to each of the minor tautomers are shown, except that the B1(O6N7)t6 conformer is also again included. Again, we note that all stable complexes computed involving minor tautomers exhibit gross spectral mismatches. Similar to [dGuo+Na]+, the calculated IR spectrum of both anti and syn orientated B(O6N7) binding conformers exhibit good agreement with the measured IRMPD spectrum. Nearly identical IR spectra of similar conformers also exhibit good agreement with measured IRMPD spectrum, such that B1, B2, B9, and B10 B(O6N7) conformers may be populated in the experiments. Both C2'-endo and C3'-endo puckerings are represented among these conformers, with a preference for C2'-endo puckering, thus, B3 and B5 may be present in lower populations. Conformers that lack an intramolecular hydrogen bond are less stable, and also exhibit mismatches vs. the measured IRMPD spectrum in the hydrogen-stretching region, indicating that B4, B6−B8, B12−B19, and B21−B26 of B(O6N7) conformers are not populated in measurable



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 16 of 40

16

abundance in the experiments. The predicted IR spectra of B11(O6N7) and B27(O6N7) with syn orientations of guanine and C4'-exo or C2'-endo (2T3) puckerings show significant spectral misalignments with the measured IRMPD spectrum, which suggests that syn oriented B(O6N7) conformers with high relative Gibbs free energies do not have measurable populations in the experiments. The split in the features at ~3660 cm-1 in the IR spectrum of B20(O6N7) indicates that C3'-exo is less favorable than C2'-endo for [Guo+Na]+, and that this conformer is likely not present in the experiments. Large shifts of the spectral features in the calculated IR spectra of T1(N3O4′O5′) and B1(N3O2′) indicate that neither syn nor anti orientated N3 binding conformers have measurable populations in the experiments. Similar to N3 binding conformers, sugar binding conformers, e.g., B1(O2'O3') and B1(O3'O4'), are much less favorable, and are not populated in the experiments. Again, the high relative Gibbs free energy and very significant spectral misalignments between the measured IRMPD and predicted IR spectra for complexes that involve minor tautomers of the guanine residue, e.g., B1(O6N7)t3, indicate that these species are not populated in the experiments. In summary, anti and syn orientated B(O6N7) binding conformers with a preference for C2'-endo puckering are the dominant conformers populated in the experiments. The syn orientated B(O6N7) binding conformers likely have lower populations, due to the relative Gibbs free energy and minor shifts in the calculated IR spectrum. Because of the obvious mismatches between the measured and calculated IR spectra, N3 and sugar binding conformers are much less favorable than B(O6N7) conformers such that N3 and sugar binding conformers are not present in measurable abundance in the experiments. The significant shifts predicted in the fingerprint and hydrogen-stretching regions indicate that N3 and sugar binding conformers, as well as all complexes that involve minor tautomers of the guanine residue do not have measurable populations in the experiments. Vibrational Assignments for [dGuo+Na]+ and [Guo+Na]+. Vibrational assignments based on the ground B1(O6N7) conformers of [dGuo+Na]+ and [Guo+Na]+ are listed in Table 3. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ exhibit high similarity with shifts


Page 17 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


17

of O6 > N3. For the sodium cationized guanine nucleosides, N3 is also a less favorable binding site for Na+ than B(O6N7), with the relative Gibbs free energies of N3 binding conformers at least 56 kJ/mol less favorable than the ground conformers, i.e., the binding affinities follow the order: O6N7 > N3. For both protonated guanine nucleosides, guanine exhibits a preference for the anti orientation, whereas the sugar prefers C3′-endo (3T2) puckering. The sodium cationized guanine nucleosides exhibit structural factors similar to protonated guanine nucleosides, except for the sugar puckering, where the C2′endo (2T3) configuration for [dGuo+Na]+ and [Guo+Na]+ is preferred. However, the guanine orientation and sugar puckering do not significantly change the calculated IR spectra of the sodium cationized guanine nucleosides. Therefore, B(O6N7) binding conformers of [dGuo+Na]+ and [Guo+Na]+ with both anti and syn orientations and a variety of sugar puckerings coexist in the experiments. The glycosidic bonds of the sodium cationized guanine nucleosides are shorter than those of the protonated species (1.469 Å in [dGuo+Na]+ and 1.463 Å in [Guo+Na]+ vs. 1.508 Å in [dGuo+H]+ and 1.498 Å in [Guo+H]+), indicating that sodium cationization is less effective at activating the glycosidic bond than protonation. A noncanonical hydrogen-bonding interaction between H8 and O5′ is observed in the ground conformers of all of the species. Relative N-Glycosidic Bond Stabilities of Protonated and Sodium Cationized dGuo and Guo. Figure 6 compares the results of survival yield analyses for the protonated and sodium cationized guanine nucleosides. The only fragmentation pathway observed for these species involves N-glycosidic bond cleavage, therefore, trends in the CID50% values are directly correlated with the relative stabilities of the N-glycosidic bonds in these systems. The CID50% of [Guo+H]+ is greater than that of [dGuo+H]+, indicating that the 2′-hydroxyl substituent of Guo stabilizes the N-glycosidic bond. This result is consistent with previous TCID results for


Page 19 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


19

[dGuo+H]+ and [Guo+H]+.92 The same behavior has also been found in previous TCID studies of the protonated adenine, cytosine and uracil nucleosides,93-95 and the ER-CID results for the protonated and sodium cationized adenine nucleosides.73 The same conclusion can be drawn via comparison of the CID50% values of [dGuo+Na]+ and [Guo+Na]+. Among all of our published and ongoing work, the N-glycosidic bonds of the RNA nucleosides are found to be more stable than those of the analogous DNA nucleosides.66-70, 73, 92-95 These results are also consistent with the bond lengths from DFT calculations discussed in the previous section, where the Nglycosidic bond lengths of the RNA nucleosides are slightly shorter than those of the analogous DNA nucleosides. Overall, the N-glycosidic bonds of sodium cationized guanine nucleosides are more stable than those of the analogous protonated guanine nucleosides, clearly indicating that sodium cationization activates the N-glycosidic bond, but less effectively than protonation. Comparison of the Low-Energy Conformers of Sodium Cationized Adenine and Guanine Nucleosides. IRMPD action spectroscopy, ER-CID experiments and theoretical study of the gas-phase conformations and energetics of [dAdo+Na]+ and [Ado+Na]+ has been previously reported by our group.73 Both adenine and guanine are purine nucleobases, however, the preferred Na+ binding mode to adenine nucleosides involves tridentate binding to the N3, O4′ and O5′ atoms. In contrast, the N3 atom is a much less favorable Na+ binding site for the guanine nucleosides. Adenine strongly prefers a syn orientation in [dAdo+Na]+ and [Ado+Na]+, due to the multiple chelation interactions between Na+ and the N3, O4′ and O5′ atoms, whereas guanine shows a preference for the anti orientation as additional chelation interactions with the sugar moiety are not possible for the B(O6N7) conformers, but syn oriented conformers are competitive. The sugar puckerings of [dAdo+Na]+ and [Ado+Na]+ prefer C1′-exo (12T) and C1′exo (1TO), respectively, whereas C2′-endo (2T3) is the preferred sugar puckering observed for both [dGuo+Na]+ and [Guo+Na]+.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 20 of 40

20

CONCLUSIONS Comparisons between the measured IRMPD and calculated linear IR spectra indicate that only B(O6N7) binding conformers of the canonical forms of both [dGuo+Na]+ and [Guo+Na]+ are populated in the experiments. Such bidentate binding leads to the formation of a 5-membered chelation ring with guanine in an anti orientation and C2′-endo sugar puckering. Unlike sodium cationized adenine nucleosides, both high relative Gibbs free energies and spectral misalignments between the calculated IR and measured IRMPD spectra suggest that the N3 atom is not a very favorable binding mode for Na+. Thus, N3 binding conformers of the canonical forms of [dGuo+Na]+ and [Guo+Na]+ do not have measurable populations in the experiments. Likewise, high relative Gibbs free energies and spectral misalignments indicate that none of the sugar binding conformers or minor tautomeric forms of these sodium cationized guanine nucleoside complexes have measurable populations in the experiments. Compared with protonation, sodium cationization activates the N-glycosidic bonds of the guanine nucleosides less effectively. The 2′-hydroxyl substituent of guanosine enables for motion of a 2'OH···3'OH hydrogen bond and stabilizes the N-glycosidic bond compared with 2′-deoxyguanosine. Current results exhibit good agreement with previous TCID studies of protonated guanine nucleosides,92 and are also consistent with the N-glycosidic bond lengths from DFT calculations.

SUPPORTING INFORMATION Complete citation for reference 91. Figures summarizing the B3LYP/6-311+G(d,p) optimized structures of all low-energy canonical and tautomeric conformers of [dGuo+Na]+ and [Guo+Na]+ found along with the sodium cation binding mode, nucleobase orientation, sugar puckering, and relative Gibbs free energy computed at the B3LYP/6-311+G(2d,2p) level of theory at 298 K for each conformer. Figures comparing the experimental IRMPD action spectra of [dGuo+Na]+ and [Guo+Na]+ with the B3LYP/6-311+G(d,p) optimized structures and calculated linear IR spectra for both canonical and minor tautomeric forms of these complexes that exhibit obvious spectral mismatches and thus are not measurably populated in the


Page 21 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


21

experiments. The B3LYP/6-311+G(2d,2p) relative Gibbs free energies at 298 K, guanine orientation, and sugar puckering are also shown.

ACKNOWLEDGMENTS This work was financially supported by the National Science Foundation, Grants OISE0730072 and OISE-1357787 (for the IRMPD measurements), DBI-0922819 (for the Bruker amaZon ETD QITMS employed in this work), and CHE-1409420 (for other research costs). Y.Z., L.A.H. and C.C.H. gratefully acknowledge support from Wayne State University Thomas C. Rumble Graduate Fellowships. J.K.L. acknowledges support as an REU of the MS-PIRE program. We also thank Wayne State University C&IT for computational resources and support. This work is part of the research program of FOM, which is financially supported by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO). The skillful assistance of the FELIX staff is gratefully acknowledged.

REFERENCES 1. van Dam, L.; Ouwerkerk, N.; Brinkmann, A.; Raap, J.; Levitt, M. H., Solid-State NMR Determination of Sugar Ring Pucker in C-13-Labeled 2'-Deoxynucleosides. Biophys. J. 2002, 83, 2835-2844. 2. Rich, A.; Nordheim, A.; Wang, A. H. J., The Chemistry and Biology of Left-Handed Z-DNA. Annu. Rev. Biochem. 1984, 53, 791-846. 3. Rodgers, M. T.; Campbell, S.; Marzluff, E. M.; Beauchamp, J. L., Low-Energy CollisionInduced Dissociation of Deprotonated Dinucleotides-Determination of the Energetically Favored Dissociation Pathways and the Relative Acidities of the Nucleic-Acid Bases. Int. J. Mass Spectrom. Ion Processes 1994, 137, 121-149. 4. Rodgers, M. T.; Campbell, S.; Marzluff, E. M.; Beauchamp, J. L., Site-Specific Protonation Directs Low-Energy Dissociation Pathways of Dinucleotides in the Gas-Phase. Int. J. Mass Spectrom. Ion Processes 1995, 148, 1-23. 5. Rodgers, M. T.; Campbell, S. A.; Beauchamp, J. L., Site-Specific Lithium Ion Attachment Directs Low-Energy Dissociation Pathways of Dinucleotides in the Gas Phase: Application to



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 22 of 40

22

Nucleic Acid Sequencing by Mass Spectrometry. Int. J. Mass Spectrom. Ion Processes 1997, 161, 193-216. 6. Nei, Y.-w.; Hallowita, N.; Steill, J. D.; Oomens, J.; Rodgers, M. T., Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated DNA Mononucleotides: Gas-Phase Conformations and Energetics. J. Phys. Chem. A 2013, 117, 1319-1335. 7. Nei, Y.-w.; Crampton, K. T.; Berden, G.; Oomens, J.; Rodgers, M. T., Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated RNA Mononucleotides: Gas-Phase Conformations and Energetics. J. Phys. Chem. A 2013, 117, 10634-10649. 8. Lovejoy, K. S.; Todd, R. C.; Zhang, S. Z.; McCormick, M. S.; D'Aquino, J. A.; Reardon, J. T.; Sancar, A.; Giacomini, K. M.; Lippard, S. J., Cis-Diammine(Pyridine)Chloroplatinum(II), a Monofunctional Platinum(II) Antitumor Agent: Uptake, Structure, Function, and Prospects. P. Natl. Acad. Sci. USA 2008, 105, 8902-8907. 9. Hambley, T. W., The Influence of Structure on the Activity and Toxicity of Pt Anti-Cancer Drugs. Coordin. Chem. Rev. 1997, 166, 181-223. 10. Yang, D. Z.; Vanboom, S. S. G. E.; Reedijk, J.; Vanboom, J. H.; Wang, A. H. J., Structure and Isomerization of an Intrastrand Cisplatin-Cross-Linked Octamer DNA Duplex by NMR Analysis. Biochemistry-US 1995, 34, 12912-12920. 11. Fichtingerschepman, A. M. J.; Vanderveer, J. L.; Denhartog, J. H. J.; Lohman, P. H. M.; Reedijk, J., Adducts of the Antitumor Drug Cis-Diamminedichloroplatinum(II) with DNA Formation, Identification, and Quantitation. Biochemistry-US 1985, 24, 707-713. 12. Sip, M.; Schwartz, A.; Vovelle, F.; Ptak, M.; Leng, M., Distortions Induced in DNA by Cisplatinum Interstrand Adducts. Biochemistry-US 1992, 31, 2508-2513. 13. Chiavarino, B.; Crestoni, M. E.; Fornarini, S.; Scuderi, D.; Salpin, J. Y., Interaction of Cisplatin with 5'-dGMP: A Combined IRMPD and Theoretical Study. Inorganic Chemistry 2015, 54, 3513-3522. 14. Chiavarino, B.; Crestoni, M. E.; Fornarini, S.; Scuderi, D.; Salpin, J. Y., Interaction of Cisplatin with Adenine and Guanine: A Combined IRMPD, MS/MS, and Theoretical Study. J. Am. Chem. Soc. 2013, 135, 1445-1455. 15. Dehand, J.; Jordanov, J., Interaction of Cis-Diaminotolueneplatinum(II) with NucleosidesEvidence for Guanosine O(6).N(7) Chelation by Platinum. J. Chem. Soc. Chem. Comm. 1976, 598-599. 16. Warnke, U.; Rappel, C.; Meier, H.; Kloft, C.; Galanski, M.; Hartinger, C. G.; Keppler, B. K.;


Page 23 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


23

Jaehde, U., Analysis of Platinum Adducts with DNA Nucleotides and Nucleosides by Capillary Electrophoresis Coupled to ESI-MS: Indications of Guanosine 5'-Monophosphate O-6-N7 Chelation. ChemBioChem 2004, 5, 1543-1549. 17. Farrell, N., Platinum-Based Drugs in Cancer Therapy. Humana Press Inc.: New York, 2000; p 341. 18. Chapman, E. G.; DeRose, V. J., Site-Specific Platinum(II) Cross-Linking in a Ribozyme Active Site. J. Am. Chem. Soc. 2012, 134, 256-262. 19. Wu, P. K.; Kharatishvili, M.; Qu, Y.; Farrell, N., A Circular Dichroism Study of Ethidium Bromide Binding to Z-DNA Induced by Dinuclear Platinum Complexes. J. Inorg. Biochem. 1996, 63, 9-18. 20. Perigaud, C.; Gosselin, G.; Imbach, J. L., Stereospecific Synthesis of Chiral Acyclic Analogs of Guanosine. Bioorg. Med. Chem. Lett. 1992, 2, 677-680. 21. Perigaud, C.; Gosselin, G.; Imbach, J. L., Nucleoside Analogs as Chemotherapeutic-Agents-a Review. Nucleos. Nucleot. Nucl. 1992, 11, 903-945. 22. Lyamichev, V. I.; Mirkin, S. M.; Frankkamenetskii, M. D., A pH-Dependent Structural Transition in the Homopurine-Homopyrimidine Tract in Superhelical DNA. J. Biomol. Struct. Dyn. 1985, 3, 327-338. 23. Mirkin, S. M.; Lyamichev, V. I.; Drushlyak, K. N.; Dobrynin, V. N.; Filippov, S. A.; Frankkamenetskii, M. D., DNA H-Form Requires a Homopurine-Homopyrimidine Mirror Repeat. Nature 1987, 330, 495-497. 24.

Vojtiskova,

M.;

Palecek,

E.,

Unusual

Protonated

Structure

in

the

Homopurine·Homopyrimidine Tract of Supercoiled and Linearized Plasmids Recognized by Chemical Probes. J. Biomol. Struct. Dyn. 1987, 5, 283-296. 25. Kohwi, Y.; Kohwishigematsu, T., Magnesium Ion-Dependent Triple-Helix Structure Formed by Homopurine-Homopyrimidine Sequences in Supercoiled Plasmid DNA. P. Natl. Acad. Sci. USA 1988, 85, 3781-3785. 26. Neidle, S.; Read, M. A., G-Quadruplexes as Therapeutic Targets. Biopolymers 2001, 56, 195-208. 27. Shalaby, T.; Fiaschetti, G.; Nagasawa, K.; Shin-ya, K.; Baumgartner, M.; Grotzer, M., GQuadruplexes as Potential Therapeutic Targets for Embryonal Tumors. Molecules 2013, 18, 12500-12537. 28. Lyonnais, S.; Hounsou, C.; Teulade-Fichou, M. P.; Jeusset, J.; Le Cam, E.; Mirambeau, G.,



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 24 of 40

24

G-Quartets Assembly within a G-rich DNA Flap: A Possible Event at the Center of the HIV-1 Genome. Nucleic Acids Res. 2002, 30, 5276-5283. 29. Sen, D.; Gilbert, W., Formation of Parallel 4-Stranded Complexes by Guanine-Rich Motifs in DNA and its Implications for Meiosis. Nature 1988, 334, 364-366. 30. Sundquist, W. I.; Klug, A., Telomeric DNA Dimerizes by Formation of Guanine Tetrads between Hairpin Loops. Nature 1989, 342, 825-829. 31. Parkinson, G. N.; Lee, M. P. H.; Neidle, S., Crystal Structure of Parallel Quadruplexes from Human Telomeric DNA. Nature 2002, 417, 876-880. 32. 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. 33. Gu, J. D.; Leszczynski, J., Origin of Na+/K+ Selectivity of the Guanine Tetraplexes in Water: The Theoretical Rationale. J. Phys. Chem. A 2002, 106, 529-532. 34. Hud, N. V.; Smith, F. W.; Anet, F. A. L.; Feigon, J., The Selectivity for K+ versus Na+ in DNA Quadruplexes is Dominated by Relative Free Energies of Hydration: A Thermodynamic Analysis by H-1 NMR. Biochemistry-US 1996, 35, 15383-15390. 35.

Wang,

C.;

Gao,

H.;

Gaffney,

B.

L.;

Jones,

R.

A.,

Nitrogen-15-Labeled

Oligodeoxynucleotides .3. Protonation of the Adenine N1 in the A-C and A-G Mispairs of the Duplexes (d[CG(15N1)AGAATTCCCG])2 and (d[CGGGAATTC(15N1)ACG])2. J. Am. Chem. Soc. 1991, 113, 5486-5488. 36. Leroy, J. L.; Gehring, K.; Kettani, A.; Gueron, M., Acid Multimers of Oligodeoxycytidine Strands-Stoichiometry,

Base-Pair

Characterization,

and

Proton-Exchange

Properties.

Biochemistry-US 1993, 32, 6019-6031. 37. Moser, H. E.; Dervan, P. B., Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation. Science 1987, 238, 645-650. 38. Delossantos, C.; Rosen, M.; Patel, D., NMR-Studies of DNA (R+)n·(Y-)n·(Y+)n Triple Helices in Solution: Imino and Amino Proton Markers of T·A·T and C·G·C+ Base-Triple Formation. Biochemistry-US 1989, 28, 7282-7289. 39. Xodo, L. E.; Manzini, G.; Quadrifoglio, F.; Vandermarel, G. A.; Vanboom, J. H., Effect of 5Methylcytosine on the Stability of Triple-Stranded DNA-A Thermodynamic Study. Nucleic Acids Res. 1991, 19, 5625-5631. 40. Singleton, S. F.; Dervan, P. B., Influence of pH on the Equilibrium Association Constants for Oligodeoxyribonucleotide-Directed Triple Helix Formation at Single DNA Sites. Biochemistry-


Page 25 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


25

US 1992, 31, 10995-11003. 41. Day, H. A.; Pavlou, P.; Waller, Z. A. E., i-Motif DNA: Structure, Stability and Targeting with Ligands. Bioorgan. Med. Chem. 2014, 22, 4407-4418. 42. Yang, B.; Rodgers, M. T., Base-Pairing Energies of Proton-Bound Heterodimers of Cytosine and Modified Cytosines: Implications for the Stability of DNA i-Motif Conformations. J. Am. Chem. Soc. 2014, 136, 282-290. 43. Yang, B.; Rodgers, M. T., Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m(5)dCyd: Implications for the Stability of DNA i-Motif Conformations. J. Am. Soc. Mass Spectrom. 2015, 26, 1394-1403. 44. Watson, J. D.; Crick, F. H. C., The Structure of DNA. Cold Spring Harb. Sym. 1953, 18, 123-131. 45. Bzowska, A.; Kulikowska, E.; Shugar, D., Purine Nucleoside Phosphorylases: Properties, Functions, and Clinical Aspects. Pharmacol. Therapeut. 2000, 88, 349-425. 46. Pelle, R.; Schramm, V. L.; Parkin, D. W., Molecular Cloning and Expression of a PurineSpecific N-Ribohydrolase from Trypanosoma Brucei Brucei-Sequence, Expression, and Molecular Analysis. J. Biol. Chem. 1998, 273, 2118-2126. 47. Versees, W.; Loverix, S.; Vandemeulebroucke, A.; Geerlings, P.; Steyaert, J., Leaving Group Activation by Aromatic Stacking: An Alternative to General Acid Catalysis. J. Mol. Biol. 2004, 338, 1-6. 48. Mol, C. D.; Parikh, S. S.; Putnam, C. D.; Lo, T. P.; Tainer, J. A., DNA Repair Mechanisms for the Recognition and Removal of Damaged DNA Bases. Annu. Rev. Bioph. Biom. 1999, 28, 101-128. 49. Cao, C. Y.; Kwon, K.; Jiang, Y. L.; Drohat, A. C.; Stivers, J. T., Solution Structure and Base Perturbation Studies Reveal a Novel Mode of Alkylated Base Recognition by 3-Methyladenine DNA Glycosylase I. J. Biol. Chem. 2003, 278, 48012-48020. 50. Mons, M.; Dimicoli, I.; Piuzzi, F.; Tardivel, B.; Elhanine, M., Tautomerism of the DNA Base Guanine and its Methylated Derivatives as Studied by Gas-Phase Infrared and Ultraviolet Spectroscopy. J. Phys. Chem. A 2002, 106, 5088-5094. 51. Alonso, J. L.; Pena, I.; Lopez, J. C.; Vaquero, V., Rotational Spectral Signatures of Four Tautomers of Guanine. Angew. Chem. Int. Ed. 2009, 48, 6141-6143. 52. Zhachkina, A.; Liu, M.; Sun, X. J.; Amegayibor, F. S.; Lee, J. K., Gas-Phase Thermochemical Properties of the Damaged Base O(6)-Methylguanine versus Adenine and



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 26 of 40

26

Guanine. J. Org. Chem. 2009, 74, 7429-7440. 53. Szczepaniak, K.; Szczesniak, M.; Szajda, W.; Person, W. B.; Leszczynski, J., InfraredSpectra of Tautomers and Rotamers of 9-Methylguanine: an Experimental and Theoretical-Study. Can. J. Chem. 1991, 69, 1705-1720. 54. Szczepaniak, K.; Szczesniak, M.; Person, W. B., Infrared Studies and the Effect of Ultraviolet-Irradiation on the Tautomers of 9-Methylguanine Isolated in an Argon Matrix. Chem. Phys. Lett. 1988, 153, 39-44. 55. Schoone, K.; Maes, G.; Adamowicz, L., Computational and Matrix-Isolation FT-IR Study of the Tautomeric and Vibrational Properties of Methylated Guanines. J. Mol. Struct. 1999, 481, 505-509. 56. Ahmadi, M. S.; Fattahi, A., DFT Study on Metal Cationization and O-6-Protonation on 2'Deoxyguanosine Configuration: Changes on Sugar Puckering and Strength of the N-Glycosidic Bond. J. Theor. Comput. Chem. 2010, 9, 585-609. 57. Ahmadi, M. S.; Shakourian-Fard, M.; Fattahi, A., Molecular Structure and Character of Bonding of Mono and Divalent Metal Cations (Li+, Na+, K+, Mg2+, Ca2+, Zn2+, and Cu+) with Guanosine: AIM and NBO Analysis. Struct. Chem. 2012, 23, 613-626. 58. Nei, Y.-w.; Akinyemi, T. E.; Kaczan, C. M.; Steill, J. D.; Berden, G.; Oomens, J.; Rodgers, M. T., Infrared Multiple Photon Dissociation Action Spectroscopy of Sodiated Uracil And Thiouracils: Effects of Thioketo-Substitution on Gas-Phase Conformation. Int. J. Mass Spectrom. 2011, 308, 191-202. 59. Nei, Y.-w.; Akinyemi, T. E.; Steill, J. D.; Oomens, J.; Rodgers, M. T., Infrared Multiple Photon Dissociation Action Spectroscopy of Protonated Uracil and Thiouracils: Effects of Thioketo-Substitution on Gas-Phase Conformation. Int. J. Mass Spectrom. 2010, 297, 139-151. 60. Crampton, K. T.; Rathur, A. I.; Nei, Y.-w.; Berden, G.; Oomens, J.; Rodgers, M. T., Protonation Preferentially Stabilizes Minor Tautomers of the Halouracils: IRMPD Action Spectroscopy and Theoretical Studies. J. Am. Soc. Mass Spectrom. 2012, 23, 1469-1478. 61. Kaczan, C. M.; Rathur, A. I.; Wu, R. R.; Chen, Y.; Austin, C. A.; Berden, G.; Oomens, J.; Rodgers, M. T., Infrared Multiple Photon Dissociation Action Spectroscopy of Sodium Cationized Halouracils: Effects of Sodium Cationization and Halogenation on Gas-Phase Conformation. Int. J. Mass Spectrom. 2015, 378, 76-85. 62. Oomens, J.; Moehlig, A. R.; Morton, T. H., Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy of the Proton-Bound Dimer of 1-Methylcytosine in the Gas Phase. J. Phys. Chem.


Page 27 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


27

Lett. 2010, 1, 2891-2897. 63. Yang, B.; Wu, R. R.; Berden, G.; Oomens, J.; Rodgers, M. T., Infrared Multiple Photon Dissociation Action Spectroscopy of Proton-Bound Dimers of Cytosine and Modified Cytosines: Effects of Modifications on Gas-Phase Conformations. J. Phys. Chem. B 2013, 117, 1419114201. 64. Salpin, J. Y.; Haldys, V.; Guillaumont, S.; Tortajada, J.; Hurtado, M.; Lamsabhi, A., GasPhase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple-Photon Dissociation Spectroscopy Study. ChemPhysChem 2014, 15, 2959-2971. 65. Yang, B.; Wu, R. R.; Polfer, N. C.; Berden, G.; Oomens, J.; Rodgers, M. T., IRMPD Action Spectroscopy of Alkali Metal Cation-Cytosine Complexes: Effects of Alkali Metal Cation Size on Gas Phase Conformation. J. Am. Soc. Mass Spectrom. 2013, 24, 1523-1533. 66. Wu, R. R.; Yang, B.; Berden, G.; Oomens, J.; Rodgers, M. T., Gas-Phase Conformations and Energetics of Protonated 2'-Deoxyguanosine and Guanosine: IRMPD Action Spectroscopy and Theoretical Studies. J. Phys. Chem. B 2014, 118, 14774-14784. 67. Wu, R. R.; Yang, B.; Berden, G.; Oomens, J.; Rodgers, M. T., Gas-Phase Conformations and Energetics of Protonated 2'-Deoxyadenosine and Adenosine: IRMPD Action Spectroscopy and Theoretical Studies. J. Phys. Chem. B 2015, 119, 2795-2805. 68. Wu, R. R.; Yang, B.; Frieler, C. E.; Berden, G.; Oomens, J.; Rodgers, M. T., Diverse Mixtures of 2,4-Dihydroxy Tautomers and O4 Protonated Conformers of Uridine and 2'Deoxyuridine Coexist in the Gas Phase. Phys. Chem. Chem. Phys. 2015, 17, 25978-25988. 69. Wu, R. R.; Yang, B.; Frieler, C. E.; Berden, G.; Oomens, J.; Rodgers, M. T., N3 and O2 Protonated Tautomeric Conformations of 2'-Deoxycytidine and Cytidine Coexist in the Gas Phase. J. Phys. Chem. B 2015, 119, 5773-5784. 70. Wu, R. R.; Yang, B.; Frieler, C. E.; Berden, G.; Oomens, J.; Rodgers, M. T., 2,4-Dihydroxy and O2 Protonated Tautomers of dThd and Thd Coexist in the Gas Phase: Methylation Alters Protonation Preferences versus dUrd and Urd. J. Am. Soc. Mass Spectrom. 2016, 27, 410-421. 71. Ung, H. U.; Huynh, K. T.; Poutsma, J. C.; Oomens, J.; Berden, G.; Morton, T. H., Investigation of Proton Affinities and Gas Phase Vibrational Spectra of Protonated Nucleosides, Deoxynucleosides, and their Analogs. Int. J. Mass Spectrom. 2015, 378, 294-302. 72. Filippi, A.; Fraschetti, C.; Rondino, F.; Piccirillo, S.; Steinmetz, V.; Guidoni, L.; Speranza, M., Protonated Pyrimidine Nucleosides Probed by IRMPD Spectroscopy. Int. J. Mass Spectrom. 2013, 354, 54-61.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 28 of 40

28

73. Zhu, Y.; Hamlow, L. A.; He, C. C.; Strobehn, S. F.; Lee, J. K.; Gao, J.; Berden, G.; Oomens, J.; Rodgers, M. T., Influence of Sodium Cationization versus Protonation on the Gas-Phase Conformations and Glycosidic Bond Stabilities of 2'-Deoxyadenosine and Adenosine. J. Phys. Chem. B 2016, 120, 8892-8904. 74. Wu, R. R. H., C. C.; Hamlow, L. A.; Nei, Y.-w.; Berden, G.; Oomens, J.; Rodgers, M. T., Protonation Induced Base Rotation of Purine Nucleotides pdGuo and pGuo. Phys. Chem. Chem. Phys. 2016, 18, 15081-15090. 75. Wu, R. R.; He, C. C.; Hamlow, L. A.; Nei, Y.-w.; Berden, G.; Oomens, J.; Rodgers, M. T., N3 Protonation Induces Base Rotation of 2'-Deoxyadenosine-5'-Monophosphate and Adenosine5'-Monophosphate. J. Phys. Chem. B 2016, 120, 4616-4624. 76. Chiavarino, B.; Crestoni, M. E.; Fornarini, S.; Lanucara, F.; Lemaire, J.; Maitre, P.; Scuderib, D., Infrared Spectroscopy of Isolated Nucleotides 1. The Cyclic 3',5'-Adenosine Monophosphate Anion. Int. J. Mass Spectrom. 2008, 270, 111-117. 77. Lanucara, F.; Crestoni, M. E.; Chiavarino, B.; Fornarini, S.; Hernandez, O.; Scuderi, D.; Maitre, P., Infrared Spectroscopy of Nucleotides in the Gas Phase 2. The Protonated Cyclic 3',5'Adenosine Monophosphate. Rsc. Adv. 2013, 3, 12711-12720. 78. Ligare, M. R.; Rijs, A. M.; Berden, G.; Kabelac, M.; Nachtigallova, D.; Oomens, J.; de Vries, M. S., Resonant Infrared Multiple Photon Dissociation Spectroscopy of Anionic Nucleotide Monophosphate Clusters. J. Phys. Chem. B 2015, 119, 7894-7901. 79. Salpin, J. Y.; MacAleese, L.; Chirot, F.; Dugourd, P., Structure of the Pb2+-Deprotonated dGMP Complex in the Gas Phase: A Combined MS-MS/IRMPD Spectroscopy/Ion Mobility Study. Phys. Chem. Chem. Phys. 2014, 16, 14127-14138. 80. Wu, R. R.; Hamlow, L. A.; He, C. C.; Nei, Y.-w.; Berden, G.; Oomens, J.; Rodgers, M. T., N3 and O2 Protonated Conformers of the Cytosine Mononulceotides Coexist in the Gas Phase. J. Am. Soc. Mass Spectrom. 2017. DOI: 10.1007/S13361-017-1653-8 81. Polfer, N. C.; Oomens, J.; Moore, D. T.; von Helden, G.; Meijer, G.; Dunbar, R. C., Infrared Spectroscopy of Phenylalanine Ag(I) and Zn(II) Complexes in the Gas Phase. J. Am. Chem. Soc. 2006, 128, 517-525. 82. Valle, J. J.; Eyler, J. R.; Oomens, J.; Moore, D. T.; van der Meer, A. F. G.; von Helden, G.; Meijer, G.; Hendrickson, C. L.; Marshall, A. G.; Blakney, G. T., Free Electron Laser-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Facility for Obtaining Infrared Multiphoton Dissociation Spectra of Gaseous Ions. Rev. Sci. Instrum. 2005, 76, 023103.


Page 29 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


29

83. Polfer, N. C.; Oomens, J., Reaction Products in Mass Spectrometry Elucidated with Infrared Spectroscopy. Phys. Chem. Chem. Phys. 2007, 9, 3804-3817. 84. Oepts, D.; Vandermeer, A. F. G.; Vanamersfoort, P. W., The Free-Electron-Laser User Facility Felix. Infrared Phys. Techn. 1995, 36, 297-308. 85. Memboeuf, A.; Nasioudis, A.; Indelicato, S.; Pollreisz, F.; Kuki, A.; Keki, S.; van den Brink, O. F.; Vekey, K.; Drahos, L., Size Effect on Fragmentation in Tandem Mass Spectrometry. Anal. Chem. 2010, 82, 2294-2302. 86. Derwa, F.; Depauw, E.; Natalis, P., New Basis for a Method for the Estimation of Secondary Ion Internal Energy-Distribution in Soft Ionization Techniques. Org. Mass Spectrom. 1991, 26, 117-118. 87. Guo, X. H.; Duursma, M. C.; Kistemaker, P. G.; Nibbering, N. M. M.; Vekey, K.; Drahos, L.; Heeren, R. M. A., Manipulating Internal Energy of Protonated Biomolecules in Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Mass Spectrom. 2003, 38, 597-606. 88. Memboeuf, A.; Jullien, L.; Lartia, R.; Brasme, B.; Gimbert, Y., Tandem Mass Spectrometric Analysis of a Mixture of Isobars Using the Survival Yield Technique. J. Am. Soc. Mass Spectrom. 2011, 22, 1744-1752. 89. Kertesz, T. M.; Hall, L. H.; Hill, D. W.; Grant, D. F., CE50: Quantifying Collision Induced Dissociation Energy for Small Molecule Characterization and Identification. J. Am. Soc. Mass Spectrom. 2009, 20, 1759-1767. 90. HyperChem Computational Chemistry Software Package, version 5.0; hypercube, Inc.: Gainsville, FL, 1997. 91. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G.A.; et al. Gaussian 09, revision C.01; Gaussian, Inc.: Wallingford, CT, 2009. 92. Wu, R. R.; Chen, Y.; Rodgers, M. T., Mechanisms and Energetics for N-Glycosidic Bond Cleavage of Protonated 2'-Deoxyguanosine and Guanosine. Phys. Chem. Chem. Phys. 2016, 18, 2968-2980. 93. Wu, R. R.; Rodgers, M. T., Mechanisms and Energetics for N-Glycosidic Bond Cleavage of Protonated Adenine Nucleosides: N3 Protonation Induces Base Rotation and Enhances NGlycosidic Bond Stability. Phys. Chem. Chem. Phys. 2016, 18, 16021-16032. 94. Wu, R. R.; Rodgers, M. T., O2 Protonation Controls Threshold Behavior for N-Glycosidic



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 30 of 40

30

Bond Cleavage of Protonated Cytosine Nucleosides. J. Phys. Chem. B 2016, 120, 4803-4811. 95. Wu, R. R.; Rodgers, M. T., Tautomerization Lowers the Activation Barriers for NGlycosidic Bond Cleavage of Protonated Uridine and 2'-Deoxyuridine. Phys. Chem. Chem. Phys. 2016, 18, 24451-24459. 96. Altona, C.; Sundaralingam, M., Conformational-Analysis of Sugar Ring in Nucleosides and Nucleotides: New Description Using Concept of Pseudorotation. J. Am. Chem. Soc. 1972, 94, 8205-8212.

Table 1. Geometric Details of the B3LYP/6-311+G(d,p) Ground B1(O6N7) Conformers of [dGuo+Na]+ and [Guo+Na]+ and Ground N7 Conformers of [dGuo+H]+ and [Guo+H]+.α

[dGuo+Na]+

[Guo+Na]+

Na+…N7

2.370 Å

2.371 Å

Na+…O6

2.274 Å

2.272 Å

C1′…N9

1.469 Å

1.463 Å

Bond Angle

∠N7Na+O6

81.7°

81.6°

Dihedral Angle

∠C4N9C1′O4′

237.3°

234.7°

∠O5′C5′C4′O4′

-65.5°

-65.6°

[dGuo+H]+

[Guo+H]+

H+…N7

1.012 Å

1.013 Å

C1′…N9

1.508 Å

1.498 Å

∠C5N7H+

125.6°

125.6°

∠C8N7H+

125.4°

125.4°

∠C4N9C1′O4′

203.0°

203.8°

∠O5′C5′C4′O4′

-62.6°

-63.0°

Bond Length

Bond Length

Bond Angle

Dihedral Angle

α

Structural information for [dGuo+H]+ and [Guo+H]+ are taken from reference 66.


Page 31 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


31 Table 2. Relative Enthalpies and Free Energies of Select Stable Low-Energy Conformers of [dGuo+Na]+ and [Guo+Na]+ at 0 and 298 K in kJ/molα Species

0.0 0.0 3.1 3.6 1.6 1.6 11.5 12.3 12.1 11.0 14.0 13.8 18.1 18.5 19.2 18.1 54.2 53.1 104.2 103.0 129.9 129.7

0.0 2.6 6.4 6.5 10.1 14.5 14.9 21.8 56.9 106.3 131.1

173.3° 12.1° 160.3° 146.7° 31.8° 199.8° 134.2° 35.2° 334.7° 188.3° 138.5°

Guanine Orientation anti anti syn anti anti anti anti syn syn syn anti

B1(O6N7) 1.1 1.9 B2(O6N7) 0.0 0.0 B3(O6N7) 3.7 4.4 B6(O6N7) 11.5 13.0 B11(O6N7) 11.0 10.8 B20(O6N7) 20.6 21.5 B25(O6N7) 27.7 28.8 T1(N3O4'O5') 75.2 75.0 B1(N3O2') 84.2 84.0 T1(N3NH2O2') 84.6 84.3 B1(N3O4') 98.5 99.2 B1(O2'O3') 118.2 119.1 B1(O3'O4') 120.0 119.9

0.0 0.5 3.3 7.0 11.0 19.4 23.6 77.4 82.7 83.5 96.8 115.2 121.4

169.0° 155.9° 14.4° 131.5° 44.4° 190.0° 36.5° 10.0° 174.6 72.9° 189.2° 164.7° 213.6°

anti syn anti anti syn anti anti syn anti anti syn syn anti

Conformer

[dGuo+Na]+ B1(O6N7) B6(O6N7) B9(O6N7) B10(O6N7) B14(O6N7) B15(O6N7) B16(O6N7) B27(O6N7) T1(N3O4'O5') B1(O4'O5') B1(N3O3') [Guo+Na]+

∆H0

∆H298 ∆G298

P

Sugar Puckering C2'-endo (2T3) C3′-endo (3T2) C2'-endo (2T1) C2′-endo (2T1) C3′-endo (3T4) C3′-exo (3E) C1′-exo (1T2) C3′-endo (3T4) C2′-exo (2T1) C3′-exo (3T2) C1′-exo (1T2) C2′-endo (2T3) C2′-endo (2T1) C3′-endo (3T2) C1′-exo (1T2) C4′-exo (4T3) C3′-exo (3T2) C3′-endo (43T) C3′-endo (3T2) C2′-endo (2T3) O4′-endo (4OT) C3′-exo (3T2) C2′-endo (2T3) C3′-exo (3T4)

α

Energetics based on single-point energy calculations performed at the B3LYP/6-311+G(2d,2p)

level of theory, including ZPE and thermal corrections based on the B3LYP/6-311+G(d,p) optimized structures and vibrational frequencies.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 32 of 40

32

Table 3. Vibrational Assignments for the Ground B1(O6N7) Conformers of [dGuo+Na]+ and [Guo+Na]+ α Vibrational Mode

[dGuo+Na]+

[Guo+Na]+

Sugar ring bending C2′-C3′ stretching Sugar ring stretching Sugar hydrogen bending Nucleobase ring stretching Nucleobase ring stretching NH2 scissoring

650 938 970 to 1145 1145 to 1280 1280 to 1480 1526 1588 1628 1685 3420 3440 3542

− − 976 to 1153 1153 to 1267 1287 to 1443 1526 1586 1629 1687 3417 3435 3543 3577 3662

C−NH2 stretching C=O stretching N1−H stretching NH2 symmetric stretching NH2 asymmetric stretching 2′-hydroxyl stretching 3′- and 5′-hydroxyl stretching

− 3658

α

All values are given in cm-1.


Page 33 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


33

Figure Captions Figure 1. Chemical structures of 2′-deoxyguanosine (dGuo) and guanosine (Guo) indicating the numbering of each atom. The ground-state structures of [dGuo+Na]+ and [Guo+Na]+ predicted at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. The sodium cation binding mode, guanine orientation, and sugar puckering are also given for each structure. Ground structures of [dGuo+H]+ and [Guo+H]+ are shown for comparison and taken from reference 66. The Na+−O6, Na+−N7, H+−N7 and the C1'−N9 N-glycosidic bond lengths are also given. Figure 2. IRMPD action spectra of [dGuo+Na]+ and [Guo+Na]+ in the IR fingerprint and hydrogen-stretching regions. IRMPD action spectra of [dGuo+H]+ and [Guo+H]+ previously reported are overlaid in grey for comparison and taken from reference 66. Figure 3. CID mass spectra of [dGuo+H]+, [Guo+H]+, [dGuo+Na]+, and [Guo+Na]+ at an rf excitation amplitude (EA) that produces ~50% dissociation. Figure 4. Comparison of the experimental IRMPD action spectrum of [dGuo+Na]+ with the B3LYP/6-311+G(d,p) optimized structures and calculated linear IR spectra for the most stable B(O6N7) binding conformers with anti and syn orientations computed for [dGuo+Na]+ populated in the experiments. The B3LYP/6-311+G(2d,2p) relative Gibbs free energies at 298 K, guanine orientation, and sugar puckering are also shown. Figure 5. Comparison of the experimental IRMPD action spectrum of [Guo+Na]+ with the B3LYP/6-311+G(d,p) optimized structures and calculated linear IR spectra for the most stable B(O6N7) binding conformers with anti and syn orientations computed for [Guo+Na]+ populated in the experiments. The B3LYP/6-311+G(2d,2p) relative Gibbs free energies at 298 K, guanine orientation, and sugar puckering are also shown. Figure 6. Survival yield curves of [dGuo+H]+, [Guo+H]+, [dGuo+Na]+ and [Guo+Na]+ and the corresponding CID50% values and uncertainties determined from fits to the data using eq 2.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58

Page 34 of 40

34

Figure 1

2.370 Å

2.274 Å

[dGuo+Na]+ B1(O6N7) anti, C2′-endo (2T3) C1′-N9: 1.469 Å 1.012 Å

2.371 Å

2.272 Å

[Guo+Na]+ B1(O6N7) anti, C2′-endo (2T3) C1′-N9: 1.463 Å 1.013 Å

[dGuo+H]+ [Guo+H]+ N7 N7 anti, C3′-endo (3ACS T2)Paragon Plus Environmentanti, C3′-endo (3T2) C1′-N9: 1.508 Å C1′-N9: 1.498 Å

Page 35 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58


35

Figure 2



36

Figure 3

100

rf EA: 0.18 V

[dGuo+H]+

[Gua+H]+ 50

0 100

Relative Intensity

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58

Page 36 of 40

rf EA: 0.21 V

[Guo+H]+

rf EA: 0.25 V

[dGuo+Na]+

50

0 100

[Gua+Na]+ 50

0 100

rf EA: 0.29 V

[Guo+Na]+

50

0 150

200

250

m/z


300

Page 37 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58


37

Figure 4 [dGuo+Na]+ IRMPD

B1(O6N7) 0.0 kJ/mol anti C2'-endo (2T3)


B9(O6N7) 6.4 kJ/mol syn C2'-endo (2T1)

B15(O6N7) 14.5 kJ/mol anti C3'-exo (3E)



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58

Page 38 of 40

38

Figure 5

[Guo+Na]+ IRMPD


B2(O6N7) 0.5 kJ/mol syn C2'-endo (2T1)



Page 39 of 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58


39

Figure 6



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58

Page 40 of 40

40

TOC Graphic

[dGuo+Na]+

[Guo+Na]+

TOC Graphic @ 3.25’’X1.85’’


Gas-Phase Conformations and N-Glycosidic Bond Stabilities of

Recommend Documents