1
|
Dezalay J, Grégoire G, Broquier M, Soorkia S. IR and UV Spectroscopy of Gas-Phase Monohydrated Protonated Guanine. J Phys Chem A 2024; 128:8457-8465. [PMID: 39297670 DOI: 10.1021/acs.jpca.4c04976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
We use UV and infrared photodissociation spectroscopy to study monohydrated protonated guanine in a dual cryogenic ion trap spectrometer. The monohydrated complexes are formed through helium-mediated collisions between bare electrosprayed protonated guanine and low-pressure water vapor in a clustering trap maintained at 180 K, before being transferred to a quadrupole ion trap at 10 K. The spectrum of the monohydrated complex exhibits sharp vibronic transitions at the band origin and becomes broader and higher in intensity further in blue, which is very similar to protonated guanine but with a notable blue shift of ∼1850 cm-1 (∼0.23 eV). The UV hole-burning experiments showed that the vibronic bands recorded in the region of the band origin belong to a single conformer under our experimental conditions. The IR photodissociation spectrum in the 3000-3600 cm-1 range, with the aid of theoretical calculations (SCS-CC2/aug-cc-pVDZ), allowed us to assign the structure to the lowest energy N7-O conformer.
Collapse
Affiliation(s)
- J Dezalay
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - G Grégoire
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - M Broquier
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - S Soorkia
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| |
Collapse
|
2
|
Lee J, Tantillo DJ, Wang LP, Fiehn O. Impact of Protonation Sites on Collision-Induced Dissociation-MS/MS Using CIDMD Quantum Chemistry Modeling. J Chem Inf Model 2024. [PMID: 39329341 DOI: 10.1021/acs.jcim.4c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Protonation is the most frequent adduct found in positive electrospray ionization collision-induced mass spectra (CID-MS/MS). In a parallel report Lee, J. J. Chem. Inf. Model. 2024, 10.1021/acs.jcim.4c00760, we developed a quantum chemistry framework to predict mass spectra by collision-induced dissociation molecular dynamics (CIDMD). As different protonation sites affect fragmentation pathways of a given molecule, the accuracy of predicting tandem mass spectra by CIDMD ultimately depends on the choice of its protomers. To investigate the impact of molecular protonation sites on MS/MS spectra, we compared CIDMD-predicted spectra to all available experimental MS/MS spectra by similarity matching. We probed 10 molecules with a total of 43 protomers, the largest study to date, including organic acids (sorbic acid, citramalic acid, itaconic acid, mesaconic acid, citraconic acid, and taurine) as well as aromatic amines including uracil, aniline, bufotenine, and psilocin. We demonstrated how different protomers can converge different fragmentation pathways to the same fragment ions but also may explain the presence of different fragment ions in experimental MS/MS spectra. For the first time, we used in silico MS/MS predictions to test the impact of solvents on proton affinities, comparing the gas phase and a mixture of acetonitrile/water (1:1). We also extended applications of in silico MS/MS predictions to investigate the impact of protonation sites on the energy barriers of isomerization between protomers via proton transfer. Despite our initial hypothesis that the thermodynamically most stable protomer should give the best match to the experiment, we found only weak inverse relationships between the calculated proton affinities and corresponding entropy similarities of experimental and CIDMD-predicted MS/MS spectra. CIDMD-predicted mechanistic details of fragmentation reaction pathways revealed a clear preference for specific protomer forms for several molecules. Overall, however, proton affinity was not a good predictor corresponding to the predicted CIDMD spectra. For example, for uracil, only one protomer predicted all experimental MS/MS fragment ions, but this protomer had neither the highest proton affinity nor the best MS/MS match score. Instead of proton affinity, the transfer of protons during the electrospray process from the initial protonation site (i.e., mobile proton model) better explains the differences between the thermodynamic rationale and experimental data. Protomers that undergo fragmentation with lower energy barriers have greater contributions to experimental MS/MS spectra than their thermodynamic Boltzmann populations would suggest. Hence, in silico predictions still need to calculate MS/MS spectra for multiple protomers, as the extent of distributions cannot be readily predicted.
Collapse
Affiliation(s)
- Jesi Lee
- Department of Chemistry, University of California, Davis, California 95616, United States
- West Coast Metabolomics Center, University of California, Davis, California 95616, United States
| | - Dean Joseph Tantillo
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, California 95616, United States
| |
Collapse
|
3
|
Chiavarino B, Rotari L, Crestoni ME, Corinti D, Fornarini S, Scuderi D, Salpin JY. Binding Motifs of Carboplatin and Oxaliplatin with Guanine: A Combined MS/MS, IRMPD, and Theoretical Study. Inorg Chem 2023; 62:14546-14558. [PMID: 37647164 DOI: 10.1021/acs.inorgchem.3c01438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Complexes generated in the gas phase involving the purine nucleobase guanine bound to second and third generation platinum drugs, namely, carboplatin (CarboPt) and oxaliplatin (OxaliPt), were investigated by combining tandem mass spectrometry, collision-induced dissociation (CID), infrared multiple photon dissociation spectroscopy (IRMPD), and density functional theory (DFT) calculations. As the first step, a spectroscopic characterization of the protonated platinum drugs was accomplished. Protonation of both CarboPt and OxaliPt in the gas phase occurs on one of the two carbonyl groups of the cyclobutanedicarboxylate and oxalate ligand, respectively. Such protonation has been postulated by several theoretical studies as a key preliminary step in the hydrolysis of Pt drugs under acidic conditions. Subsequently, the protonated drugs react with guanine in solution to generate a complex of general formula [Pt drug + H + guanine]+, which was then mass-selected. CID experiments provided evidence of the presence of strong binding between guanine and platinum-based drugs within the complexes. The structures of the two complexes have also been examined by comparing the experimental IRMPD spectra recorded in two spectral regions with DFT-computed IR spectra. For each system, the IRMPD spectra agree with the vibrational spectra calculated for the global minimum structures, which present a monodentate complexation of Pt at the N7 position of canonical guanine. This binding scheme is therefore akin to that observed for cisplatin, while other coordination sites yield substantially less stable species. Interestingly, in the case of oxaliplatin, the IRMPD spectra are consistent with the presence of two isomeric forms very close in energy.
Collapse
Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, Roma I-00185, Italy
| | - Lucretia Rotari
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, Roma I-00185, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, Roma I-00185, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, Roma I-00185, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, Roma I-00185, Italy
| | - Debora Scuderi
- CNRS, Institut de Chimie Physique, Université Paris-Saclay, Orsay 91405, France
| | - Jean-Yves Salpin
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, Evry-Courcouronnes 91025, France
| |
Collapse
|
4
|
Alhajji E, Boulghobra A, Bonose M, Berthias F, Moussa F, Maître P. Multianalytical Approach for Deciphering the Specific MS/MS Transition and Overcoming the Challenge of the Separation of a Transient Intermediate, Quinonoid Dihydrobiopterin. Anal Chem 2022; 94:12578-12585. [PMID: 36074025 DOI: 10.1021/acs.analchem.2c00924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite recent technological developments in analytical chemistry, separation and direct characterization of transient intermediates remain an analytical challenge. Among these, separation and direct characterization of quinonoid dihydrobiopterin (qH2Bip), a transient intermediate of tetrahydrobiopterin (H4Bip)-dependent hydroxylation reactions, essential in living organisms, with important and varied human pathophysiological impacts, are a clear illustration. H4Bip regeneration may be impaired by competitive nonenzymatic autoxidation reactions, such as isomerization of qH2Bip into a more stable 7,8-H2Bip (H2Bip) isomer, and subsequent nonenzymatic oxidation reactions. The quinonoid qH2Bip intermediate thus plays a key role in H4Bip-dependent hydroxylation reactions. However, only a few experimental results have indirectly confirmed this finding while revealing the difficulty of isolating qH2Bip from H4Bip-containing solutions. As a result, no current H4Bip assay method allows this isomer to be quantified even by liquid chromatography-tandem mass spectrometry (MS/MS). Here, we report isolation, structural characterization, and abundance of qH2Bip formed upon H4Bip autoxidation using three methods integrated into MS/MS. First, we characterized the structure of the two observed H2B isomers using IR photodissociation spectroscopy in conjunction with quantum chemical calculations. Then, we used differential ion mobility spectrometry to fully separate all oxidized forms of H4Bip including qH2Bip. These data are consistent and show that qH2Bip can also be unambiguously identified thanks to its specific MS/MS transition. This finding paves the way for the quantification of qH2Bip with MS/MS methods. Most importantly, the half-life value of this intermediate is nearly equivalent to that of H4Bip (tens of minutes), suggesting that an accurate method of H4Bip analysis should include the quantification of qH2Bip.
Collapse
Affiliation(s)
- Eskander Alhajji
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Ayoub Boulghobra
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Myriam Bonose
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Francis Berthias
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Fathi Moussa
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Philippe Maître
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay Cedex, France
| |
Collapse
|
5
|
Rabus JM, Guan S, Schultz LM, Abutokaikah MT, Maître P, Bythell BJ. Protonated α- N-Acetyl Galactose Glycopeptide Dissociation Chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1745-1752. [PMID: 36018613 DOI: 10.1021/jasms.2c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We recently provided mass spectrometric, H/D labeling, and computational evidence of pyranose to furanose N-acetylated ion isomerization reactions that occurred prior to glycosidic bond cleavage in both O- and N-linked glycosylated amino acid model systems (Guan et al. Phys. Chem. Chem. Phys., 2021, 23, 23256-23266). These reactions occurred irrespective of the glycosidic linkage stereochemistry (α or β) and the N-acetylated hexose structure (GlcNAc or GalNAc). In the present article, we test the generality of the preceding findings by examining threonyl α-GalNAc-glycosylated peptides. We utilize computational chemistry to compare the various dissociation and isomerization pathways accessible with collisional activation. We then interrogate the structure(s) of the resulting charged glycan and peptide fragments with infrared "action" spectroscopy. Isomerization of the original pyranose, the protonated glycopeptide [AT(GalNAc)A+H]+, is predicted to be facile compared to direct dissociation, as is the glycosidic bond cleavage of the newly formed furanose form, i.e., furanose oxazolinium ion structures are predicted to predominate. IR action spectra for the m/z 204, C8H14N1O5+, glycan fragment population support this prediction. The IR action spectra of the complementary m/z 262 peptide fragment were assigned as a mixture of the lowest-energy structures of [ATA+H]+ consistent with the literature. If general, the change to a furanose m/z 204 product ion structure fundamentally alters the ion population available for MS3 dissociation and glycopeptide sequence identification.
Collapse
Affiliation(s)
- Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Lauren M Schultz
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Philippe Maître
- Institut de Chimie Physique, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| |
Collapse
|
6
|
Zheng L, Cuny J, Zamith S, L'Hermite JM, Rapacioli M. Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:27404-27416. [PMID: 34859809 DOI: 10.1039/d1cp03228c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Collision-induced dissociation experiments of hydrated molecular species can provide a wealth of important information. However, they often need a theoretical support to extract chemical information. In the present article, in order to provide a detailed description of recent experimental measurements [Braud et al., J. Chem. Phys., 2019, 150, 014303], collision simulations between low-energy protonated uracil water clusters (H2O)1-7,11,12UH+ and an Ar atom were performed using a quantum mechanics/molecular mechanics formalism based on the self-consistent-charge density-functional based tight-binding method. The theoretical proportion of formed neutral vs. protonated uracil containing clusters, total fragmentation cross sections as well as the mass spectra of charged fragments are consistent with the experimental data which highlights the accuracy of the present simulations. They allow to probe which fragments are formed on the short time scale and rationalize the location of the excess proton on these fragments. We demonstrate that this latter property is highly influenced by the nature of the aggregate undergoing the collision. Analyses of the time evolution of the fragments populations and of their relative abundances demonstrate that, up to 7 water molecules, a direct dissociation mechanism occurs after collision whereas for 11 and 12 water molecules a statistical mechanism is more likely to participate. Although scarce in the literature, the present simulations appear as a useful tool to complement collision-induced dissociation experiments of hydrated molecular species.
Collapse
Affiliation(s)
- Linjie Zheng
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Sébastien Zamith
- Laboratoire Collisions Agrégats Réactivié LCAR/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jean-Marc L'Hermite
- Laboratoire Collisions Agrégats Réactivié LCAR/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| |
Collapse
|
7
|
Chan RCT, Chan CTL, Ma C, Gu KY, Xie HX, Wong AKW, Xiong QW, Wang ML, Kwok WM. Long living excited state of protonated adenosine unveiled by ultrafast fluorescence spectroscopy and density functional theoretical study. Phys Chem Chem Phys 2021; 23:6472-6480. [PMID: 33729247 DOI: 10.1039/d0cp06439d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenosine (Ado) possesses ultrafast nonradiative dynamics accounting for its remarkably high photostability. The deactivation dynamics of Ado after protonation in an aqueous solution remains an elusive issue. Herein we report an investigation of the excited state dynamics of protonated Ado (AdoH+) performed using ultrafast time-resolved fluorescence spectroscopy combined with density functional theoretical calculation. The result obtained from comparison of conformers with protonation at different sites revealed that the syn-conformer with protonation occurring at the N3 position (syn-N3) is the predominant form of AdoH+ in the ground state, similar to that of Ado. In contrast, the fluorescence of AdoH+ with maximum intensity at 385 nm, significantly red-shifted from that of Ado, displaying decay dynamics composed of an ultrafast component with the lifetime of ∼0.5 ps and a slower one of ∼2.9 ns. The former is because of the decay of the syn-N3 conformer, similar to that reported for AdoH+ under the gas phase condition. The latter is due to the syn-N1 conformer formed via ultrafast proton transfer of the syn-N3. The excited state of syn-N1 has a peculiar nonplanar conformation over the purine molecule, which is responsible for the substantial Stokes shift showed in the fluorescence spectrum and correlates with a large energy barrier for nonradiative decay likely involving a reversed proton transfer. This study demonstrates the importance of protonation and solvent environment in altering dramatically the excited states of Ado, providing insight for better understanding nonradiative dynamics of both the monomeric bases and the oligomeric or polymeric DNAs.
Collapse
Affiliation(s)
- Ruth Chau-Ting Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China.
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Olmedo WE, Jimenez LB, Cruz-Ortiz AF, Maitre P, Pino GA, Rossa M. Infrared Multiple Photon Dissociation Spectroscopy of Protonated Cyameluric Acid. J Phys Chem A 2021; 125:607-614. [PMID: 33410690 DOI: 10.1021/acs.jpca.0c09394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The present study reports the first structural characterization of protonated cyameluric acid ([CA + H]+) in the gas phase, which paves the way for prospective bottom-up research on the condensed-phase chemistry of CA in the protonated form. A number of [CA + H]+ keto-enol isomers can a priori be produced as a result of protonation at available N and O positions of precursor neutral CA tautomers, yet ab initio computations predict different reduced [CA + H]+ isomer populations dominating the solution and gas phases that are involved in the ion generation process (i.e., electrospray ionization). Infrared multiple photon dissociation spectra were recorded in the 990-1900 and 3300-3650 cm-1 regions and compared with theoretical [B3LYP/6-311++G(d,p)] IR absorption spectra of several [CA + H]+ isomers, providing a satisfactory agreement for the most stable monohydroxy form in the gas phase, [1358a]+, yet the contribution of its nearly isoenergetic OH rotamer, [1358b]+, cannot be neglected. This is indicative of the occurrence of [CA + H]+ isomer interconversion reactions, assisted by protic solvent molecules, during their transfer into the gas phase. The results suggest that available O positions on neutral CA are energetically favored protonation sites in the gas phase.
Collapse
Affiliation(s)
- Walter E Olmedo
- INFIQC (CONICET - Universidad Nacional de Córdoba), Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Liliana B Jimenez
- INFIQC (CONICET - Universidad Nacional de Córdoba), Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Andrés F Cruz-Ortiz
- INFIQC (CONICET - Universidad Nacional de Córdoba), Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Philippe Maitre
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Gustavo A Pino
- INFIQC (CONICET - Universidad Nacional de Córdoba), Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Maximiliano Rossa
- INFIQC (CONICET - Universidad Nacional de Córdoba), Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| |
Collapse
|
9
|
Omidyan R, Abedini F, Shahrokh L, Azimi G. Excited State Deactivation Mechanism in Protonated Uracil: New Insights from Theoretical Studies. J Phys Chem A 2020; 124:5089-5097. [PMID: 32469520 DOI: 10.1021/acs.jpca.0c02284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have conducted here a theoretical exploration, discussing the distinct excited state lifetimes reported experimentally for the two lowest lying protonated isomers of uracil. In this regard, the first-principal computational levels as well as the nonadiabatic surface hopping dynamics have been employed. It has been revealed that relaxation of the 1ππ* state of enol-enol form (EE+) to the ground is barrier-free via out-of-plane coordinates, resulting in an ultrashort S1 lifetime of this species. For the second most stable isomer (EK+), however, a significant barrier predicted in the CASPT2 S1 potential energy profile along the twisting coordinate has been proposed to explain the relevant long lifetime reported experimentally.
Collapse
Affiliation(s)
- Reza Omidyan
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Fatemeh Abedini
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Leila Shahrokh
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Gholamhassan Azimi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| |
Collapse
|
10
|
Chiavarino B, Dopfer O, Crestoni ME, Corinti D, Maître P, Fornarini S. IRMPD Spectra of Protonated Hydroxybenzaldehydes: Evidence of Torsional Barriers in Carboxonium Ions. Chemphyschem 2020; 21:749-761. [PMID: 31951044 DOI: 10.1002/cphc.202000041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 11/09/2022]
Abstract
Protonation at the formyl oxygen atom of benzaldehydes leading to the formation of carboxonium ions yields two distinct isomers, depending on the relative orientation of the proton either cis or trans with respect to the hydrogen atom on the adjacent carbon. In this context, the IR multiple photon dissociation (IRMPD) spectra of protonated ortho, meta, and para-hydroxybenzaldehydes (OH-BZH+ ), delivered into the gas phase by electrospray ionization of hydro-alcoholic solutions, are reported in the 3200-3700 cm-1 spectral range. This range is characteristic of O-H stretching modes and thus able to differentiate cis and trans carboxonium isomers. Comparison between IRMPD spectra and DFT calculations at the B3LYP/6-311++G(2df2p) level suggests that for both p-OH-BZH+ and m-OH-BZH+ only cis conformers are present in the ion population analyzed. For o-OH-BZH+ , IRMPD spectroscopy points to a mixture comprising one trans and more than one cis conformers. The energy barrier for cis-trans isomerization calculated for each OH-BZH+ isomer is a measure of the degree of π-electron delocalization. Furthermore, IRMPD spectra of p-OH-BZH+ , m-OH-BZH+ and protonated phenol (this last used as reference) were recorded also in the fingerprint range. Both the observed C-O and O-H stretching vibrations appear to be a measure of π-electron delocalization in the ions.
Collapse
Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Philippe Maître
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| |
Collapse
|
11
|
Dvores MP, Çarçabal P, Maître P, Simons JP, Gerber RB. Gas phase dynamics, conformational transitions and spectroscopy of charged saccharides: the oxocarbenium ion, protonated anhydrogalactose and protonated methyl galactopyranoside. Phys Chem Chem Phys 2020; 22:4144-4157. [PMID: 32039431 DOI: 10.1039/c9cp06572e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a d-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl d-galactopyranoside-H+. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ∼300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.
Collapse
Affiliation(s)
- M P Dvores
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel.
| | - P Çarçabal
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - P Maître
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - J P Simons
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, UK
| | - R B Gerber
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel. and Department of Chemistry, University of California Irvine, CA 92697, USA
| |
Collapse
|
12
|
Abedini F, Omidyan R, Salehi M. Theoretical insights on nonradiative deactivation mechanisms of protonated xanthine. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.112067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
13
|
He CC, Hamlow LA, Zhu Y, Nei YW, Fan L, McNary CP, Maître P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2318-2334. [PMID: 31435890 DOI: 10.1007/s13361-019-02300-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]+, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]+ and [Nuo+H]+, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.
Collapse
Affiliation(s)
- C C He
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L Fan
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - C P McNary
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - P Maître
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
| |
Collapse
|
14
|
|
15
|
Cheng R, Loire E, Fridgen TD. Hydrogen bonding in alkali metal cation-bound i-motif-like dimers of 1-methyl cytosine: an IRMPD spectroscopic and computational study. Phys Chem Chem Phys 2019; 21:11103-11110. [PMID: 31094375 DOI: 10.1039/c9cp01223k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The structures of alkali metal cation bound 1-methylcytosine (1-mCyt) dimers were explored using vibrational spectroscopy in the form of infrared multiple photon dissociation (IRMPD) spectroscopy and by computational methods. For the smaller alkali metal cations, Li+ and Na+, only non-hydrogen bonded symmetric anti-parallel structures were observed in agreement with the lowest energy computed structures. For K+, Rb+, and Cs+ the vibrational spectra in the N-H stretch region showed strong evidence for hydrogen bonding in agreement with the lowest energy structures which contained hydrogen bonding interactions between the amine group of one cytosine and the carbonyl oxygen of the other cytosine. The lowest energy structures for these complexes were compared to previously studied cytosine complexes [(Cyt)2M]+ where M = Li, Na, and K. The calculations are in agreement that only the non-hydrogen bonded structures would be observed for these cytosine complexes.
Collapse
Affiliation(s)
- Ruodi Cheng
- Department of Chemistry, Memorial University, St. John's, NL A1B 3 × 7, Canada.
| | - Estelle Loire
- Laboratoire Chimie Physique - CLIO, Batiment 201, Porte 2, Campus Universite d'Orsay, 91405, France
| | - Travis D Fridgen
- Department of Chemistry, Memorial University, St. John's, NL A1B 3 × 7, Canada.
| |
Collapse
|
16
|
Gad SF, El-Demerdash SH, El-Mehasseb IM, El-Nahas AM. Structure, stability and conversions of tautomers and rotamers of azulene-based uracil analogue. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
17
|
Observation of complex formation between l-histidine and heterocyclic compounds in water and aqueous buffer solution using calorimetric and spectroscopic methods. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
18
|
Braud I, Zamith S, Cuny J, Zheng L, L’Hermite JM. Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study. J Chem Phys 2019; 150:014303. [DOI: 10.1063/1.5044481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Isabelle Braud
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Sébastien Zamith
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC) UMR5626, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Linjie Zheng
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC) UMR5626, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jean-Marc L’Hermite
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| |
Collapse
|
19
|
Willms JA, Vidic J, Barthelmes J, Steinmetz V, Bredow T, Maître P, Engeser M. Probing the gas-phase structure of charge-tagged intermediates of a proline catalyzed aldol reaction – vibrational spectroscopy distinguishes oxazolidinone from enamine species. Phys Chem Chem Phys 2019; 21:2578-2586. [DOI: 10.1039/c8cp04905j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Charge-tagging enables the detection of reaction intermediates which are probed by IRMPD spectroscopy in combination with theory.
Collapse
Affiliation(s)
- J. Alexander Willms
- Kekulé-Institute of Organic Chemistry and Biochemistry
- University of Bonn
- D-53121 Bonn
- Germany
| | - Jandro Vidic
- Mulliken Center for Theoretical Chemistry
- Institute of Physical und Theoretical Chemistry
- University of Bonn
- D-53115 Bonn
- Germany
| | - Janosch Barthelmes
- Kekulé-Institute of Organic Chemistry and Biochemistry
- University of Bonn
- D-53121 Bonn
- Germany
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique
- Université Paris-Sud
- CNRS, Université Paris-Saclay
- Orsay
- France
| | - Thomas Bredow
- Mulliken Center for Theoretical Chemistry
- Institute of Physical und Theoretical Chemistry
- University of Bonn
- D-53115 Bonn
- Germany
| | - Philippe Maître
- Laboratoire de Chimie Physique
- Université Paris-Sud
- CNRS, Université Paris-Saclay
- Orsay
- France
| | - Marianne Engeser
- Kekulé-Institute of Organic Chemistry and Biochemistry
- University of Bonn
- D-53121 Bonn
- Germany
| |
Collapse
|
20
|
Molano-Arevalo JC, Gonzalez W, Jeanne Dit Fouque K, Miksovska J, Maitre P, Fernandez-Lima F. Insights from ion mobility-mass spectrometry, infrared spectroscopy, and molecular dynamics simulations on nicotinamide adenine dinucleotide structural dynamics: NAD +vs. NADH. Phys Chem Chem Phys 2018; 20:7043-7052. [PMID: 29473073 DOI: 10.1039/c7cp05602h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is found in all living cells where the oxidized (NAD+) and reduced (NADH) forms play important roles in many enzymatic reactions. However, little is known about NAD+ and NADH conformational changes and kinetics as a function of the cell environment. In the present work, an analytical workflow is utilized to study NAD+ and NADH dynamics as a function of the organic content in solution using fluorescence lifetime spectroscopy and in the gas-phase using trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) and infrared multiple photon dissociation (IRMPD) spectroscopy. NAD solution time decay studies showed a two-component distribution, assigned to changes from a "close" to "open" conformation with the increase of the organic content. NAD gas-phase studies using nESI-TIMS-MS displayed two ion mobility bands for NAD+ protonated and sodiated species, while four and two ion mobility bands were observed for NADH protonated and sodiated species, respectively. Changes in the mobility profiles were observed for NADH as a function of the starting solution conditions and the time after desolvation, while NAD+ profiles showed no dependence. IRMPD spectroscopy of NAD+ and NADH protonated species in the 800-1800 and 3200-3700 cm-1 spectral regions showed common and signature bands between the NAD forms. Candidate structures were proposed for NAD+ and NADH kinetically trapped intermediates of the protonated and sodiated species, based on their collision cross sections and IR profiles. Results showed that NAD+ and NADH species exist in open, stack, and closed conformations and that the driving force for conformational dynamics is hydrogen bonding of the N-H-O and O-H-O forms with ribose rings.
Collapse
|
21
|
He CC, Hamlow LA, Devereaux ZJ, Zhu Y, Nei YW, Fan L, McNary CP, Maitre P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Purine Nucleosides. J Phys Chem B 2018; 122:9147-9160. [PMID: 30203656 DOI: 10.1021/acs.jpcb.8b07687] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The chemical difference between DNA and RNA nucleosides is their 2'-hydrogen versus 2'-hydroxyl substituents. Modification of the ribosyl moiety at the 2'-position and 2'-O-methylation in particular, is common among natural post-transcriptional modifications of RNA. 2'-Modification may alter the electronic properties and hydrogen-bonding characteristics of the nucleoside and thus may lead to enhanced stabilization or malfunction. The structures and relative glycosidic bond stabilities of the protonated forms of the 2'-O-methylated purine nucleosides, 2'-O-methyladenosine (Adom) and 2'-O-methylguanosine (Guom), were examined using two complementary tandem mass spectrometry approaches, infrared multiple photon dissociation action spectroscopy and energy-resolved collision-induced dissociation. Theoretical calculations were also performed to predict the structures and relative stabilities of stable low-energy conformations of the protonated forms of the 2'-O-methylated purine nucleosides and their infrared spectra in the gas phase. Low-energy conformations highly parallel to those found for the protonated forms of the canonical DNA and RNA purine nucleosides are also found for the protonated 2'-O-methylated purine nucleosides. Importantly, the preferred site of protonation, nucleobase orientation, and sugar puckering are preserved among the DNA, RNA, and 2'-O-methylated variants of the protonated purine nucleosides. The 2'-substituent does however influence hydrogen-bond stabilization as the 2'-O-methyl and 2'-hydroxyl substituents enable a hydrogen-bonding interaction between the 2'- and 3'-substituents, whereas a 2'-hydrogen atom does not. Further, 2'-O-methylation reduces the number of stable low-energy hydrogen-bonded conformations possible and importantly inverts the preferred polarity of this interaction versus that of the RNA analogues. Trends in the CID50% values extracted from survival yield analyses of the 2'-O-methylated and canonical DNA and RNA forms of the protonated purine nucleosides are employed to elucidate their relative glycosidic bond stabilities. The glycosidic bond stability of Adom is found to exceed that of its DNA and RNA analogues. The glycosidic bond stability of Guom is also found to exceed that of its DNA analogue; however, this modification weakens this bond relative to its RNA counterpart. The glycosidic bond stability of the protonated purine nucleosides appears to be correlated with the hydrogen-bond stabilization of the sugar moiety.
Collapse
Affiliation(s)
- C C He
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - L A Hamlow
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Zachary J Devereaux
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Y Zhu
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Y-W Nei
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - L Fan
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - C P McNary
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - P Maitre
- Laboratoire de Chimie Physique (UMR8000), CNRS, Université Paris-Sud, Université Paris-Saclay , 91405 Orsay , France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), CNRS, Université Paris-Sud, Université Paris-Saclay , 91405 Orsay , France
| | - B Schindler
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - I Compagnon
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - P B Armentrout
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - M T Rodgers
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| |
Collapse
|
22
|
Smith ZM, Steinmetz V, Martens J, Oomens J, Poutsma JC. Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation †. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 429:158-173. [PMID: 29962900 PMCID: PMC6020040 DOI: 10.1016/j.ijms.2017.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH+, CavLi+, and CavNa+; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK+ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs+ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa+ and ArgK+. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na+, K+, and Cs+. A major difference between the zwitterionic forms of ArgM+ and CavM+ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.
Collapse
Affiliation(s)
- Zachary M Smith
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris Sud, Université Paris Saclay, CNRS, Orsay France
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences University of Amsterdam, Amsterdam, The Netherlands
| | - John C Poutsma
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
| |
Collapse
|
23
|
Wu RR, Hamlow LA, He CC, Nei YW, Berden G, Oomens J, Rodgers MT. The intrinsic basicity of the phosphate backbone exceeds that of uracil and thymine residues: protonation of the phosphate moiety is preferred over the nucleobase for pdThd and pUrd. Phys Chem Chem Phys 2018; 19:30351-30361. [PMID: 29099122 DOI: 10.1039/c7cp05521h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gas-phase conformations of the protonated forms of thymidine-5'-monophosphate and uridine-5'-monophosphate, [pdThd+H]+ and [pUrd+H]+, are investigated by infrared multiple photon dissociation (IRMPD) action spectroscopy and electronic structure calculations. The IRMPD action spectra of [pdThd+H]+ and [pUrd+H]+ are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Low-energy conformations of [pdThd+H]+ and [pUrd+H]+ and their relative stabilities are computed at the MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers indicate that the dominant conformers of [pdThd+H]+ and [pUrd+H]+ populated in the experiments are protonated at the phosphate oxo oxygen atom, with a syn nucleobase orientation that is stabilized by strong P[double bond, length as m-dash]OH+O2 and P-OHO4' hydrogen-bonding interactions, and C2'-endo sugar puckering. Minor abundance of conformers protonated at the O2 carbonyl of the nucleobase residue may also contribute for [pdThd+H]+, but do not appear to be important for [pUrd+H]+. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of thymidine and uridine, [dThd+H]+ and [Urd+H]+, and the deprotonated forms of pdThd and pUrd, [pdThd-H]- and [pUrd-H]-, provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Most interestingly, the thymine and uracil nucleobases remain in their canonical forms for [pdThd+H]+ and [pUrd+H]+, unlike [dThd+H]+ and [Urd+H]+, where protonation occurs on the nucleobases and induces tautomerization of the thymine and uracil residues.
Collapse
Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | | | | | | | | | | | | |
Collapse
|
24
|
Bezzina JP, Prendergast MB, Blanksby SJ, Trevitt AJ. Gas-Phase Oxidation of the Protonated Uracil-5-yl Radical Cation. J Phys Chem A 2018; 122:890-896. [PMID: 29295616 DOI: 10.1021/acs.jpca.7b09411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study targets the kinetics and product detection of the gas-phase oxidation reaction of the protonated 5-dehydrouracil (uracil-5-yl) distonic radical cation using ion-trap mass spectrometry. Protonated 5-dehydrouracil radical ions (5-dehydrouracilH+ radical ion, m/z 112) are produced within an ion trap by laser photolysis of protonated 5-iodouracil. Storage of the 5-dehydrouracilH+ radical ion in the presence of controlled concentration of O2 reveals two main products. The major reaction product pathway is assigned as the formation of protonated 2-hydroxypyrimidine-4,5-dione (m/z 127) + •OH. A second product ion (m/z 99), putatively assigned as a five-member-ring ketone structure, is tentatively explained as arising from the decarbonylation (-CO) of protonated 2-hydroxypyrimidine-4,5-dione. Because protonation of the 5-dehydrouracil radical likely forms a dienol structure, the O2 reaction at the 5 position is ortho to an -OH group. Following this addition of O2, the peroxyl-radical intermediate isomerizes by H atom transfer from the -OH group. The ensuing hydroperoxide then decomposes to eliminate •OH radical. It is shown that this elimination of •OH radical (-17 Da) is evidence for the presence of an -OH group ortho to the initial phenyl radical site, in good accord with calculations. The subsequent CO loss mechanism, to form the aforementioned five-member-ring structure, is unclear, but some pathways are discussed. By following the kinetics of the reaction, the room temperature second-order rate coefficient of the 5-dehydrouracilH+ distonic radical cation with molecular oxygen is measured at 7.2 × 10-11 cm3 molecule-1 s-1, Φ = 12% (with ±50% total accuracy). For aryl radical reactions with O2, the presence of the •OH elimination product pathway, following the peroxyl-radical formation, is an indicator of an -OH group ortho to the radical site.
Collapse
Affiliation(s)
- James P Bezzina
- School of Chemistry, University of Wollongong , Wollongong, Australia 2522
| | | | - Stephen J Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology , Brisbane, Australia 4001
| | - Adam J Trevitt
- School of Chemistry, University of Wollongong , Wollongong, Australia 2522
| |
Collapse
|
25
|
Cheng R, Rose VE, Power B, Fridgen TD. Self-assembled uracil complexes containing tautomeric uracils: an IRMPD spectroscopic and computation study of the structures of gaseous uracilnCa2+ (n = 4, 5, or 6) complexes. Phys Chem Chem Phys 2018; 20:572-580. [DOI: 10.1039/c7cp07128k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structures of doubly-charged uracil (U) complexes with Ca2+, UnCa2+ (n = 4, 5, 6), were studied by infrared multiphoton dissociation (IRMPD) spectroscopy and computational methods.
Collapse
Affiliation(s)
- Ruodi Cheng
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | | | - Barry Power
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | | |
Collapse
|
26
|
Zhu Y, Roy HA, Cunningham NA, Strobehn SF, Gao J, Munshi MU, Berden G, Oomens J, Rodgers MT. IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Studies of Sodium Cationized Thymidine and 5-Methyluridine: Kinetic Trapping During the ESI Desolvation Process Preserves the Solution Structure of [Thd+Na]<sup/>. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2423-2437. [PMID: 28836109 DOI: 10.1007/s13361-017-1753-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/01/2017] [Accepted: 07/02/2017] [Indexed: 05/25/2023]
Abstract
Thymidine (dThd) is a fundamental building block of DNA nucleic acids, whereas 5-methyluridine (Thd) is a common modified nucleoside found in tRNA. In order to determine the conformations of the sodium cationized thymine nucleosides [dThd+Na]+ and [Thd+Na]+ produced by electrospray ionization, their infrared multiple photon dissociation (IRMPD) action spectra are measured. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations and frequency analyses are performed at the B3LYP/6-311+G(d,p) level of theory, whereas energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory. As protonation preferentially stabilizes minor tautomers of dThd and Thd, tautomerization facilitated by Na+ binding is also considered. Comparisons of the measured IRMPD and computed IR spectra find that [dThd+Na]+ prefers tridentate (O2,O4',O5') coordination to the canonical 2,4-diketo form of dThd with thymine in a syn orientation. In contrast, [Thd+Na]+ prefers bidentate (O2,O2') coordination to the canonical 2,4-diketo tautomer of Thd with thymine in an anti orientation. Although 2,4-dihydroxy tautomers and O2 protonated thymine nucleosides coexist in the gas phase, no evidence for minor tautomers is observed for the sodium cationized species. Consistent with experimental observations, the computational results confirm that the sodium cationized thymine nucleosides exhibit a strong preference for the canonical form of the thymine nucleobase. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized dThd and Thd follow the order [dThd+H]+ < [Thd+H]+ < [dThd+Na]+ < [Thd+Na]+. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - S F Strobehn
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - J Gao
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - M U Munshi
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
| |
Collapse
|
27
|
Filippi A, Fraschetti C, Guarcini L, Zazza C, Ema T, Speranza M. Spectroscopic Discrimination of Diastereomeric Complexes Involving an Axially Chiral Receptor. Chemphyschem 2017; 18:2475-2481. [DOI: 10.1002/cphc.201700732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Antonello Filippi
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| | - Caterina Fraschetti
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| | - Laura Guarcini
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| | - Costantino Zazza
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| | - Tadashi Ema
- Graduate School of Natural Sciences and Technology; Okayama University; Tsushima Okayama 700-8530 Japan
| | - Maurizio Speranza
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| |
Collapse
|
28
|
Bull JN, Coughlan NJA, Bieske EJ. Protomer-Specific Photochemistry Investigated Using Ion Mobility Mass Spectrometry. J Phys Chem A 2017; 121:6021-6027. [DOI: 10.1021/acs.jpca.7b05800] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- James N. Bull
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Evan J. Bieske
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
29
|
Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Undervalued N3 Coordination Revealed in the Cisplatin Complex with 2'-Deoxyadenosine-5'-monophosphate by a Combined IRMPD and Theoretical Study. Inorg Chem 2017; 56:8793-8801. [PMID: 28718635 DOI: 10.1021/acs.inorgchem.7b00570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex obtained by the reaction of cisplatin and 2'-deoxyadenosine-5'-monophosphate (5'-dAMP) in water has been isolated and detected by electrospray ionization mass spectrometry. The so-formed cis-[PtCl(NH3)2(5'-dAMP)]+ complex has been studied in detail by infrared multiple photon dissociation (IRMPD) spectroscopy in two spectral ranges, namely, 700-1900 and 2800-3800 cm-1, backed by quantum-chemical calculations at the B3LYP/LACV3P/6-311G** level of theory. In agreement with the computational results, the vibrational spectroscopic characterization of cis-[PtCl(NH3)2(5'-dAMP)]+ shows that the sampled ionic population comprises two major isomers, differentiated in the X-H stretching region by their distinct fragmentation patterns. One of these species presents coordination of the platinum moiety at the N3 position of adenine, whereas in the second one, platinum is bound at the N1 position of adenine. IRMPD kinetics have allowed an estimation of their relative proportions. Surprisingly, the most abundant component of cis-[PtCl(NH3)2(5'-dAMP)]+ is the N3 isomer, although it is slightly less stable than the other potential isomers in the gas phase. In contrast, the lowest-energy species, namely, the one showing cisplatin binding to the N7 position of adenine, seems to be the one less represented in the sampled ionic population. These findings suggest that the reaction of cisplatin with 5'-dAMP is governed by the kinetics of the process occurring in solution rather than by the thermodynamic factors.
Collapse
Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Debora Scuderi
- LCP, Université Paris Sud Orsay, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Jean-Yves Salpin
- LAMBE, Université d'Evry Val d'Essonne, CEA, CNRS, Université Paris-Saclay , F-91025 Evry, France.,LAMBE, Université Cergy-Pontoise, Université Paris-Seine , F-91025 Evry, France
| |
Collapse
|
30
|
Zhu Y, Roy HA, Cunningham NA, Strobehn SF, Gao J, Munshi MU, Berden G, Oomens J, Rodgers MT. Effects of sodium cationization versus protonation on the conformations and N-glycosidic bond stabilities of sodium cationized Urd and dUrd: solution conformation of [Urd+Na] + is preserved upon ESI. Phys Chem Chem Phys 2017; 19:17637-17652. [PMID: 28665436 DOI: 10.1039/c7cp02377d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Uridine (Urd) is one of the naturally occurring pyrimidine nucleosides of RNA. 2'-Deoxyuridine (dUrd) is a naturally occurring modified form of Urd, but is not one of the canonical DNA nucleosides. In order to understand the effects of sodium cationization on the conformations and energetics of Urd and dUrd, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and density functional theory (DFT) calculations are performed. By comparing the calculated IR spectra of [Urd+Na]+ and [dUrd+Na]+ with the measured IRMPD spectra, the stable low-energy conformers populated in the experiments are determined. Anti oriented bidentate O2 and O2' binding conformers of [Urd+Na]+ are the dominant conformers populated in the experiments, whereas syn oriented tridentate O2, O4', and O5' binding conformers of [dUrd+Na]+ are dominantly populated in the experiments. The 2'-hydroxyl substituent of Urd stabilizes the anti oriented O2 binding conformers of [Urd+Na]+. Significant differences between the measured IRMPD and calculated IR spectra for complexes of [Urd+Na]+ and [dUrd+Na]+ involving minor tautomeric forms of the nucleobase make it obvious that none are populated in the experiments. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized Urd and dUrd follow the order: [dUrd+H]+ < [Urd+H]+ < [dUrd+Na]+ < [Urd+Na]+. The 2'-deoxy modification is found to weaken the glycosidic bond of dUrd versus that of Urd for the sodium cationized uridine nucleosides.
Collapse
Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
| | - N A Cunningham
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
| | - S F Strobehn
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
| | - J Gao
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - M U Munshi
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - G Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
| |
Collapse
|
31
|
Lim SF, Harris BL, Khairallah GN, Bieske EJ, Maître P, da Silva G, Adamson BD, Scholz MS, Coughlan NJA, O'Hair RAJ, Rathjen M, Stares D, White JM. Seleniranium Ions Undergo π-Ligand Exchange via an Associative Mechanism in the Gas Phase. J Org Chem 2017; 82:6289-6297. [PMID: 28530810 DOI: 10.1021/acs.joc.7b00877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Collision-induced dissociation mass spectrometry of the ammonium ions 4a and 4b results in the formation of the seleniranium ion 5, the structure and purity of which were verified using gas-phase infrared spectroscopy coupled to mass spectrometry and gas-phase ion-mobility measurements. Ion-molecule reactions between the ion 5 (m/z = 261) and cyclopentene, cyclohexene, cycloheptene, and cyclooctene resulted in the formation of the seleniranium ions 7 (m/z = 225), 6 (m/z = 239), 8 (m/z = 253), and 9 (m/z = 267), respectively. Further reaction of seleniranium 6 with cyclopentene resulted in further π-ligand exchange giving seleniranium ion 7, confirming that direct π-ligand exchange between seleniranium ion 5 and cycloalkenes occurs in the gas phase. Pseudo-first-order kinetics established relative reaction efficiencies for π-ligand exchange for cyclopentene, cyclohexene, cycloheptene. and cyclooctene as 0.20, 0.07, 0.43, and 4.32. respectively. DFT calculations at the M06/6-31+G(d) level of theory provide the following insights into the mechanism of the π-ligand exchange reactions; the cycloalkene forms a complex with the seleniranium ion 5 with binding energies of 57 and 62 kJ/mol for cyclopentene and cyclohexene, respectively, with transition states for π-ligand exchange having barriers of 17.8 and 19.3 kJ/mol for cyclopentene and cyclohexene, respectively.
Collapse
Affiliation(s)
- S Fern Lim
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Benjamin L Harris
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - George N Khairallah
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia.,Accurate Mass Scientific Pty Ltd., P.O. Box 92, Keilor, VIC 3036, Australia
| | - E J Bieske
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Gabriel da Silva
- Chemical and Biomolecular Engineering, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Brian D Adamson
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Michael S Scholz
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Neville J A Coughlan
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Richard A J O'Hair
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Michael Rathjen
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Daniel Stares
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| | - Jonathan M White
- School of Chemistry and Bio21 Institute, University of Melbourne , Parkville, Melbourne 3010, Australia
| |
Collapse
|
32
|
Lesslie M, Lawler JT, Dang A, Korn JA, Bím D, Steinmetz V, Maître P, Tureček F, Ryzhov V. Cytosine Radical Cations: A Gas‐Phase Study Combining IRMPD Spectroscopy, UVPD Spectroscopy, Ion–Molecule Reactions, and Theoretical Calculations. Chemphyschem 2017; 18:1293-1301. [DOI: 10.1002/cphc.201700281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Michael Lesslie
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - John T. Lawler
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Andy Dang
- Department of Chemistry University of Washington Bagley Hall, Box 351700 Seattle Washington 98195 USA
| | - Joseph A. Korn
- Department of Chemistry University of Washington Bagley Hall, Box 351700 Seattle Washington 98195 USA
| | - Daniel Bím
- Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic 166 10 Prague 6 Czech Republic
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique Université Paris-Sud UMR8000 CNRS 91405 Orsay France
| | - Philippe Maître
- Laboratoire de Chimie Physique Université Paris-Sud UMR8000 CNRS 91405 Orsay France
| | - Frantisek Tureček
- Department of Chemistry University of Washington Bagley Hall, Box 351700 Seattle Washington 98195 USA
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| |
Collapse
|
33
|
Latrous L, Salpin JY, Haldys V, Léon E, Correia C, Lamsabhi AM. Gas-phase interactions of organotin compounds with cysteine. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1006-1015. [PMID: 27428725 DOI: 10.1002/jms.3812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/02/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
The gas-phase interactions of cysteine with di-organotin and tri-organotin compounds have been studied by mass spectrometry experiments and quantum calculations. Positive-ion electrospray spectra show that the interaction of di- and tri-organotins with cysteine results in the formation of [(R)2 Sn(Cys-H)]+ and [(R)3 Sn(Cys)]+ ions, respectively. MS/MS spectra of [(R)2 Sn(Cys-H)]+ complexes are characterized by numerous fragmentation processes, notably associated with elimination of NH3 and (C,H2 ,O2 ). Several dissociation routes are characteristic of each given organic species. Upon collision, both the [(R)3 Sn(Gly)]+ and [(R)3 Sn(Cys)]+ complexes are associated with elimination of the intact amino acid, leading to the formation of [(R)3 Sn]+ cation. But for the latter complex, two additional fragmentation processes are observed, associated with the elimination of NH3 and C3 H4 O2 S. Calculations indicate that the interaction between organotins and cysteine is predominantly electrostatic but also exhibits a considerable covalent character, which is slightly more pronounced in tri-organotin complexes. A preferred bidentate interaction of the type -η2 -S-NH2 , with sulfur and the amino group, is observed. As for the [(R)3 Sn(Cys)]+ complexes, their stability is due to the combination of the hydrogen bond taking place between the amino group and the sulfur lone pair and the interaction between the carboxylic oxygen atom and the metal. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Latifa Latrous
- Laboratoire de Chimie Analytique et Electrochimie Campus Universitaire, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092, Tunis, Tunisia.
| | - Jean-Yves Salpin
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Violette Haldys
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Emmanuelle Léon
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Catarina Correia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Ciencias, M-13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049, Madrid, Spain
| |
Collapse
|
34
|
Jeanne Dit Fouque K, Lavanant H, Zirah S, Steinmetz V, Rebuffat S, Maître P, Afonso C. IRMPD Spectroscopy: Evidence of Hydrogen Bonding in the Gas Phase Conformations of Lasso Peptides and their Branched-Cyclic Topoisomers. J Phys Chem A 2016; 120:3810-6. [DOI: 10.1021/acs.jpca.6b04496] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Hélène Lavanant
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Séverine Zirah
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Sylvie Rebuffat
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| |
Collapse
|
35
|
Salpin JY, Scuderi D. Structure of protonated thymidine characterized by infrared multiple photon dissociation and quantum calculations. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1898-1904. [PMID: 26411511 DOI: 10.1002/rcm.7296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/23/2015] [Accepted: 07/29/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Many fundamental studies are motivated by the probable relationship between the presence of rare enol tautomers of nucleobases and point mutation developing during nucleic acid replication. The evaluation of the tautomeric behaviour of nucleobases is therefore of fundamental importance. This can be probed in the gas phase by combining action spectroscopy and mass spectrometry. METHODS Experimental Infrared Multiple Photon Dissociation spectra in the fingerprint region of electrospray-generated and subsequently selected ions were recorded at the CLIO free electron laser (FEL) facility, by coupling the FEL to a quadrupole ion trap, and compared to calculated harmonic vibrational infrared spectra of the different low-lying isomers computed at the B3LYP/6-31++G(d,p) level. Relative energies were refined using the extended basis set 6-311++G(3df,2p). RESULTS The Density Functional Theory (DFT) study shows that, as for protonated thymine, the global energy minimum of protonated thymidine corresponds to an enol tautomer, whose infrared absorption spectrum is found to be in very good agreement with the experimental IRMPD spectrum. A very weak IRMPD signal observed at ~1780 cm(-1) is very likely the signature of an oxo tautomer. Consequently, as for thymine, protonated thymidine generated by electrospray corresponds to a mixture of at least two tautomeric forms. CONCLUSIONS Tautomerization can be characterized by IRMPD spectroscopy. Interestingly, the dominant enolic tautomeric form(s) presently observed cannot be directly generated from the most stable neutral tautomer of the thymine residue.
Collapse
Affiliation(s)
- Jean-Yves Salpin
- Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587
| | - Debora Scuderi
- Université Paris Sud Orsay, Laboratoire de Chimie Physique, Bâtiment 350, 91405, Orsay, France
- CNRS - UMR 8000
| |
Collapse
|
36
|
Lamsabhi AM, Gutiérrez-Oliva S, Mó O, Toro-Labbé A, Yáñez M. Effects of the ionization in the tautomerism of uracil: A reaction electronic flux perspective. J Comput Chem 2015; 36:2135-45. [DOI: 10.1002/jcc.24054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 07/22/2015] [Accepted: 07/31/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Al Mokhtar Lamsabhi
- Departamento De Química C-13; Universidad Autónoma De Madrid; Cantoblanco 28049 Spain Madrid
| | - Soledad Gutiérrez-Oliva
- Facultad De Química, Nucleus Millennium Chemical Processes and Catalysis (CPC); Laboratorio De Química Teórica Computacional (QTC), Pontificia Universidad Católica De Chile; Santiago Chile
| | - Otilia Mó
- Departamento De Química C-13; Universidad Autónoma De Madrid; Cantoblanco 28049 Spain Madrid
| | - Alejandro Toro-Labbé
- Facultad De Química, Nucleus Millennium Chemical Processes and Catalysis (CPC); Laboratorio De Química Teórica Computacional (QTC), Pontificia Universidad Católica De Chile; Santiago Chile
| | - Manuel Yáñez
- Departamento De Química C-13; Universidad Autónoma De Madrid; Cantoblanco 28049 Spain Madrid
| |
Collapse
|
37
|
Hernandez O, Isenberg S, Steinmetz V, Glish GL, Maitre P. Probing Mobility-Selected Saccharide Isomers: Selective Ion-Molecule Reactions and Wavelength-Specific IR Activation. J Phys Chem A 2015; 119:6057-64. [PMID: 25827317 DOI: 10.1021/jp511975f] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Differential Ion Mobility Spectrometry (DIMS) provides orthogonal separation to mass spectrometry, and DIMS combined with the high sensitivity of a quadrupole ion-trap is shown to be useful for the separation and identification of saccharides. A comprehensive analysis of the separation of anomers (α- and β-methylated glucose) and epimers (α-methylated glucose and mannose) ionized with Li(+), Na(+), and K(+) is performed. DIMS separation is found to be better for saccharides cationized with the two latter species. The corresponding resolving power for the two glucose anomers with Na(+) is found to be very close to the corresponding drift-tube IMS value. The lithiated complexes are investigated further using a combination of infrared spectroscopy integrated to ion-trap mass spectrometry and quantum chemical calculations. Together with DIMS, consistent results are obtained. It is found that two competing structural motifs might be at play, depending on the subtle balance between the maximization of the coordination of the metal cation and the intrinsic conformational energetics of the saccharide, which is for a large part driven by hydrogen bonding. The comparison of simulated and observed spectra clearly shows that a band at ∼3400 cm(-1) is specific to a structural motif found in the lithiated glucose complexes, which could explain the trends observed in the DIMS spectra of the saccharide complexes. It is shown that DIMS-MS/MS using wavelength specific IR activation would provide a new orthogonal dimension to mass spectrometry.
Collapse
Affiliation(s)
- Oscar Hernandez
- †Laboratoire de Chimie Physique, Université Paris Sud, 91400 Orsay, France
| | - Samantha Isenberg
- ‡Department of Chemistry, University of North Carolina, 320 Caudill Laboratories, Chapel Hill, North Carolina 27599-3290, United States
| | - Vincent Steinmetz
- †Laboratoire de Chimie Physique, Université Paris Sud, 91400 Orsay, France
| | - Gary L Glish
- ‡Department of Chemistry, University of North Carolina, 320 Caudill Laboratories, Chapel Hill, North Carolina 27599-3290, United States
| | - Philippe Maitre
- †Laboratoire de Chimie Physique, Université Paris Sud, 91400 Orsay, France
| |
Collapse
|
38
|
Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Interaction of cisplatin with 5'-dGMP: a combined IRMPD and theoretical study. Inorg Chem 2015; 54:3513-22. [PMID: 25798661 DOI: 10.1021/acs.inorgchem.5b00070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
IR multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH3)2(5'-dGMP-H)](+) and cis-[PtCl(NH3)2(5'-dGMP)](+) ions (where 5'-dGMP is 2'-deoxyguanosine-5'-monophosphate), generated in the gas phase by electrospray ionization, was performed in two spectral regions, namely, 700-1900 cm(-1) and 2800-3800 cm(-1). For structural assignment, experimental IRMPD spectra were compared to IR spectra computed at the B3LYP/LACV3P/6-311G** level of theory. In agreement with computational results, the vibrational spectroscopic characterization of the cis-[Pt(NH3)2(5'-dGMP-H)](+) ion points to macrochelate species resulting from the simultaneous interaction of the metal with both the N7 atom of the guanine residue and an O atom of the phosphate group, structures that bear features in common with those characterized in solution by NMR spectroscopy. Concerning the cis-[PtCl(NH3)2(5'-dGMP)](+) ion, our study points to a monodentate complex involving exclusively the N7 position of guanine, as observed in solution. Also this species exhibits a compact form due to the formation of two hydrogen bonds involving the same ammonia ligand. For both complexes, IRMPD experiments show that a strong intramolecular hydrogen bond is established between one ammonia hydrogen and the carbonyl group of guanine. The strength of this particular interaction can be qualitatively estimated by looking at the redshift of the CO vibration with respect to an unperturbed C═O stretching mode in the fingerprint region. This point is also highlighted in the X-H (X = N, O) stretch region, by the shift of the N-H stretch frequency as a function of the number of hydrogen bonds involving the ammonia ligand.
Collapse
Affiliation(s)
- Barbara Chiavarino
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | | | - Jean-Yves Salpin
- ∥Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Boulevard François Mitterrand, 91025 Evry, France
| |
Collapse
|
39
|
Berdakin M, Steinmetz V, Maitre P, Pino GA. On the Ag+–cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory. Phys Chem Chem Phys 2015; 17:25915-24. [DOI: 10.1039/c5cp02221e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single water molecule hydration stabilizes two quasi-isoenergetic complexes of cytosine⋯Ag+.
Collapse
Affiliation(s)
- Matias Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba)
- Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- Centro Láser de Ciencias Moleculares
- Universidad Nacional de Córdoba
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique
- Université Paris Sud
- UMR8000 CNRS
- Faculté des Sciences
- 91405 Orsay Cedex
| | - Philippe Maitre
- Laboratoire de Chimie Physique
- Université Paris Sud
- UMR8000 CNRS
- Faculté des Sciences
- 91405 Orsay Cedex
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba)
- Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- Centro Láser de Ciencias Moleculares
- Universidad Nacional de Córdoba
| |
Collapse
|
40
|
Bacchus-Montabonel MC, Calvo F. Nanohydration of uracil: emergence of three-dimensional structures and proton-induced charge transfer. Phys Chem Chem Phys 2015; 17:9629-33. [DOI: 10.1039/c5cp00611b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stepwise hydration of uracil proceeds three dimensionally above three molecules and qualitatively changes the response to proton damage.
Collapse
Affiliation(s)
| | - Florent Calvo
- Laboratoire Interdisciplinaire de Physique
- Rue de La Piscine
- Campus Saint Martin d'Hères
- 38000 Grenoble
- France
| |
Collapse
|
41
|
Wincel H. Hydration energies of protonated and sodiated thiouracils. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2134-2142. [PMID: 25270881 PMCID: PMC4221615 DOI: 10.1007/s13361-014-0987-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 08/13/2014] [Accepted: 08/19/2014] [Indexed: 06/03/2023]
Abstract
Hydration reactions of protonated and sodiated thiouracils (2-thiouracil, 6-methyl-2-thiouracil, and 4-thiouracil) generated by electrospray ionization have been studied in a gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH(o)n, ΔS(o)n, and ΔG(o)n, for the hydrated systems were obtained by equilibrium measurements. The water binding energies of protonated thiouracils, [2SU]H(+) and [6Me2SU]H(+), were found to be of the order of 51 kJ/mol for the first, and 46 kJ/mol for the second water molecule. For [4SU]H(+), these values are 3-4 kJ/mol lower. For sodiated complexes, these energies are similar for all studied systems, and varied between 62 and 68 kJ/mol for the first and between 48 and 51 kJ/mol for the second water molecule. The structural aspects of the precursors for hydrated complexes are discussed in conjunction with available literature data.
Collapse
Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland,
| |
Collapse
|
42
|
Valadbeigi Y, Farrokhpour H. Effect of hydration on the stability and tautomerisms of different isomers of uracil. RSC Adv 2014. [DOI: 10.1039/c4ra09733e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
|
43
|
Abstract
Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.
Collapse
|
44
|
Féraud G, Berdakin M, Dedonder C, Jouvet C, Pino GA. Excited states of proton-bound DNA/RNA base homodimers: pyrimidines. J Phys Chem B 2014; 119:2219-28. [PMID: 25046334 DOI: 10.1021/jp505756a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We are presenting the electronic photofragment spectra of the protonated pyrimidine DNA base homodimers. Only the thymine dimer exhibits a well structured vibrational progression, while the protonated monomer shows broad vibrational bands. This shows that proton bonding can block some nonradiative processes present in the monomer.
Collapse
Affiliation(s)
- Géraldine Féraud
- Physique des Interactions Ioniques et Moléculaires (PIIM), UMR 7345, CNRS, Aix-Marseille Université , 13397 Marseille Cedex 20, France
| | | | | | | | | |
Collapse
|
45
|
Butler M, Mañez PA, Cabrera GM, Maître P. Gas phase structure and reactivity of doubly charged microhydrated calcium(II)-catechol complexes probed by infrared spectroscopy. J Phys Chem A 2014; 118:4942-54. [PMID: 24963704 DOI: 10.1021/jp503789j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Doubly charged microhydrated adducts formed from catechol and calcium(II) were produced in the gas phase using electrospray ionization (ESI) appearing as the most important ions in the mass spectra recorded. The gas phase structures of [Ca(catechol)2(H2O)](2+) and [Ca(catechol)2(H2O)2](2+) have been assayed by IR multiphoton dissociation (IRMPD) spectroscopy, recording their vibrational spectra in the 3450-3750 cm(-1) range (OH stretching region) and in the 900-1700 cm(-1) fingerprint spectral region. The agreement between experimental and calculated IR spectra of the selected cluster ions confirmed the suitability of the proposed geometries. In addition, quantum chemical calculations at the B3LYP/6-311+G(d,p) level of theory were performed for [Ca(catechol)2(H2O)](2+) to gain insight into the major routes of dissociation. The results suggest that loss of the water molecule is the lowest energy fragmentation channel followed by charge separation products and neutral loss of one catechol molecule, in agreement with the product ions observed upon collision-induced dissociation (CID).
Collapse
Affiliation(s)
- Matias Butler
- Departamento de Química Orgánica, UMyMFOR-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pabellón II, 3° piso, C1428EHA, Buenos Aires, Argentina
| | | | | | | |
Collapse
|
46
|
Pedersen SØ, Byskov CS, Turecek F, Nielsen SB. Structures of Protonated Thymine and Uracil and Their Monohydrated Gas-Phase Ions from Ultraviolet Action Spectroscopy and Theory. J Phys Chem A 2014; 118:4256-65. [DOI: 10.1021/jp504153p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Øvad Pedersen
- Department
of Physics and Astronomy, Aarhus University, DK-8000 Aarhus
C, Denmark
| | | | - Frantisek Turecek
- Department
of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | | |
Collapse
|
47
|
Sadr-Arani L, Mignon P, Chermette H, Douki T. Theoretical and experimental study of the fragmentation of protonated uracil. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
48
|
Scuderi D, Lepere V, Piani G, Bouchet A, Zehnacker-Rentien A. Structural Characterization of the UV-Induced Fragmentation Products in an Ion Trap by Infrared Multiple Photon Dissociation Spectroscopy. J Phys Chem Lett 2014; 5:56-61. [PMID: 26276181 DOI: 10.1021/jz402348n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protonated cinchona alkaloids and their dimers undergo photochemical reaction in the gas phase, leading to UV-specific photofragments, not observed by collision-induced dissociation. Simultaneous coupling of UV and IR lasers with a Paul ion trap has been achieved for obtaining the vibrational spectrum of the fragments arising from the photodissociation. The structure of the photoproduced radical has been fully characterized by comparing the experimental spectrum to that simulated by DFT calculations.
Collapse
Affiliation(s)
- Debora Scuderi
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| | - Valeria Lepere
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| | - Giovanni Piani
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| | - Aude Bouchet
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| | - Anne Zehnacker-Rentien
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| |
Collapse
|
49
|
Berdakin M, Féraud G, Dedonder-Lardeux C, Jouvet C, Pino GA. Excited states of protonated DNA/RNA bases. Phys Chem Chem Phys 2014; 16:10643-50. [DOI: 10.1039/c4cp00742e] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited state lifetime of protonated DNA/RNA bases is strongly dependent on the tautomeric form.
Collapse
Affiliation(s)
- Matias Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba) Dpto. de Fisicoquímica – Facultad de Ciencias Químicas – Centro Láser de Ciencias Moleculares – Universidad Nacional de Córdoba
- Ciudad Universitaria
- X5000HUA Córdoba, Argentina
| | - Géraldine Féraud
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 13397 Marseille, France
| | - Claude Dedonder-Lardeux
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 13397 Marseille, France
| | - Christophe Jouvet
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 13397 Marseille, France
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba) Dpto. de Fisicoquímica – Facultad de Ciencias Químicas – Centro Láser de Ciencias Moleculares – Universidad Nacional de Córdoba
- Ciudad Universitaria
- X5000HUA Córdoba, Argentina
| |
Collapse
|
50
|
Galvão TLP, Rocha IM, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. Is Uracil Aromatic? The Enthalpies of Hydrogenation in the Gaseous and Crystalline Phases, and in Aqueous Solution, as Tools to Obtain an Answer. J Phys Chem A 2013; 117:5826-36. [DOI: 10.1021/jp404938u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiago L. P. Galvão
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Inês M. Rocha
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Maria D. M. C. Ribeiro da Silva
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Manuel A. V. Ribeiro da Silva
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| |
Collapse
|