1
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Kou M, Oh YH, Lee S, Kong X. Distinguishing gas phase lactose and lactulose complexed with sodiated L-arginine by IRMPD spectroscopy and DFT calculations. Phys Chem Chem Phys 2023; 25:25116-25121. [PMID: 37676638 DOI: 10.1039/d3cp03406b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
We present the origin of the observed differentiation of lactose and lactulose achieved by complexation with sodiated L-arginine (ArgNa+). We find that the infrared multiphoton dissociation (IRMPD) bands in 3600-3650 and >3650 cm-1 regimes for gas phase lactose and lactulose, respectively, vanish when forming host-guest complexes with ArgNa+. We interpret these differences in the IRMPD spectra by scrutinizing the interactions between the functional groups (guanidium, -CO2-Na+) in ArgNa+ and -OHs in lactose/lactulose. Our calculated structures and infrared spectra of lactose/ArgNa+ and lactulose/ArgNa+ host-guest pairs indicate that the functional groups interact with the low- and high-frequency -OH stretch modes of lactose and lactulose, respectively, in the 3600-3720 cm-1 window.
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Affiliation(s)
- Min Kou
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, and Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Young-Ho Oh
- Department of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Republic of Korea.
| | - Sungyul Lee
- Department of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Republic of Korea.
| | - Xianglei Kong
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, and Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
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2
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Unveiling host-guest-solvent interactions in solution by identifying highly unstable host-guest configurations in thermal non-equilibrium gas phase. Sci Rep 2022; 12:8169. [PMID: 35581255 PMCID: PMC9114120 DOI: 10.1038/s41598-022-12226-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
We propose a novel scheme of examining the host-guest-solvent interactions in solution from their gas phase structures. By adopting the permethylated β-cyclodextrin (perm β-CD)-protonated L-Lysine non-covalent complex as a prototypical system, we present the infrared multiple photon dissociation (IRMPD) spectrum of the gas phase complex produced by electrospray ionization technique. In order to elucidate the structure of perm β-CD)/LysH+ complex in the gas phase, we carry out quantum chemical calculations to assign the two strong peaks at 3,340 and 3,560 cm-1 in the IRMPD spectrum, finding that the carboxyl forms loose hydrogen bonding with the perm β-CD, whereas the ammonium group of L-Lysine is away from the perm β-CD unit. By simulating the structures of perm β-CD/H+/L-Lysine complex in solution using the supramolecule/continuum model, we find that the extremely unstable gas phase structure corresponds to the most stable conformer in solution.
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3
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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4
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Boychuk BTA, Rebecca Jeong YE, Wetmore SD. Assessment of the Accuracy of DFT-Predicted Li +-Nucleic Acid Binding Energies. J Chem Theory Comput 2021; 17:5392-5408. [PMID: 34339194 DOI: 10.1021/acs.jctc.1c00401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding how lithium interacts with complex biosystems is crucial for uncovering the roles of this alkali metal in biology and designing extraction techniques for battery production and environmental remediation. In this light, fundamental information about Li+ binding to nucleic acids is required. Herein, a new database of Li+-nucleic acid interactions is presented that contains CCSD(T)/CBS benchmark energies for all nucleobase and phosphate binding locations. Furthermore, the performance of 54 DFT functionals in combination with three triple-zeta (TZ) basis sets (6-311+G(3df,2p), aug-cc-pVTZ, and def2-TZVPP) is tested. The results identify a range of functionals across different families (B2-PLYP, PBE-QIDH, ωB97, ωB97X-D, MN15, B3PW91, B97-2, TPSS, BP86-D3(BJ), and PBE) that can accurately describe coordinated Li+-nucleic acid interactions, with the average mean percent error (AMPE) across binding positions and basis sets being below 2%. Nevertheless, only three functionals tested (B2-PLYP, PBE-QIDH, and ωB97X-D) preserve this accuracy for metal cation-π interactions, suggesting that caution is warranted when choosing a functional to describe a diverse range of Li+-nucleic acid complexes. Removal of counterpoise corrections has very little impact on the reliability of most functionals, while the effect of empirical dispersion corrections varies depending on the functional choice and interaction type. While increasing the basis set to quadruple-zeta quality had little impact on the AMPE, the accuracy of double-zeta basis sets varies with family. Importantly, DFT methods reproduce the CCSD(T)/CBS trend in the preferred binding position for a given nucleic acid component and the global trend across components (phosphate ≫ G > C ≫ A ∼ T = U), as well as the geometries of the metal-nucleic acid complexes. The overall top performing functional is PBE-QIDH, which results in deviations from CCSD(T)/CBS values as small as ∼0.1 kcal/mol for nucleobase contacts and ∼1 kcal/mol for phosphate interactions. The most accurate DFT methods identified in the present work are recommended for future investigations of lithium interactions in larger nucleic acid systems to provide insights into the biological roles of this metal and the design of novel biosensing strategies.
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Affiliation(s)
- Briana T A Boychuk
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Ye Eun Rebecca Jeong
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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5
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Lee C, Choi YK, Lee S, Han SY. Hydrogen bonding influences collision-induced dissociation of Na + -bound guanine tetrads. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4582. [PMID: 33085179 DOI: 10.1002/jms.4582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Na+ -bound guanine (G)-tetrads possess square planar structures formed solely by noncovalent interactions including multiple hydrogen bonds. Unlike G-tetrads facilitated by other alkali metal ions, an intriguing behavior in collision-induced dissociation (CID) has been observed in Na+ -bound G-tetrads, which features a preferential, simultaneous loss of two G ligands in the low energy regime. To understand this unique behavior, we investigated the CID of Na+ -bound G-tetrads with mixed ligands of G and 9-methylguanine (9mG), [Na·Gm ·9mGn ]+ (m + n = 4), and [Li·9mG4 ]+ for comparison. In the CID experiments, the simultaneous losses of two ligands were by far more pronounced than the loss of a single ligand for all five Na+ -bound G-tetrads. However, it appeared that the CID of [Li·9mG4 ]+ prefers to lose single ligands sequentially. An analysis of the fragment abundances suggested that the generation of Na+ -bound dimeric fragments might have occurred with two adjacent ligands. This theoretical study predicted for [Li·9mG4 ]+ that the loss of a single ligand is more energetically favorable than the production of neutral hydrogen-bonded fragments by 35.5 kJ/mol (ΔG). This contradicts our previous calculations for [Na·9mG4 ]+ that a neutral loss of hydrogen-bonded dimers provides the lowest energy product state of Na+ -bound dimeric fragments, which is lower than that of Na+ -bound trimeric fragments by 15.6 kJ/mol. From the results, this comparative study suggests that the pronounced generation of Na+ -bound dimeric fragments in CID of the G-tetrads is likely promoted by the dissociation pathway associated with neutral loss of hydrogen-bonded dimers. It thus demonstrates that multiple hydrogen bonding participating in formation of Na+ -bound G-tetrads may also strongly influence the fate of dissociating complexes of G-tetrads.
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Affiliation(s)
- Chaewon Lee
- Department of Chemistry, Gachon University, Seongnam-si, Republic of Korea
| | - Yoon Kyung Choi
- Department of Chemistry, Gachon University, Seongnam-si, Republic of Korea
| | - Sanghun Lee
- Department of Chemistry, Gachon University, Seongnam-si, Republic of Korea
| | - Sang Yun Han
- Department of Chemistry, Gachon University, Seongnam-si, Republic of Korea
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6
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Cheng R, Martens J, Fridgen TD. A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G-C base pairs. Phys Chem Chem Phys 2020; 22:11546-11557. [PMID: 32395733 DOI: 10.1039/d0cp00069h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures and properties of metal cationized complexes of 9-ethylguanine (9eG) and 1-methylcytosine (1mC), (9eG:1mC)M+, where M+ = Li+, Na+, K+, Rb+, Cs+ as well as the protonated complex, (9eG:1mC)H+, have been studied using a combination of IRMPD spectroscopy and computational methods. For (9eG:1mC)H+, the dominant structure is a Hoogsteen type complex with the proton covalently bound to N3 of 1mC despite this being the third best protonation site of the two bases; based on proton affinities N7 of 9eG should be protonated. However, this structural oddity can be explained considering both the number of hydrogen bonds that can be formed when N3 of 1mC is protonated as well as the strong ion-induced dipole interaction that exists between an N3 protonated 1mC and 9eG due to the higher polarizability of 9eG. The anomalous dissociation of (9eG:1mC)H+, forming much more (1mC)H+ than would be predicted based on the computed thermochemistry, can be explained as being due to the structural oddity of the protonation site and that the barrier to proton transfer from N3 of 1mC to N7 of 9eG grows dramatically as the base pair begins to dissociate. For the (9eG:1mC)M+; M = Li+, Na+, K+, Rb+, Cs+ complexes, single unique structures could not be assigned. However, the experimental spectra were consistent with the computed spectra. For (9eG:1mC)Li+, the lowest energy structure is one in which Li+ is bound to O6 of 9eG and both O2 and N3 of 1mC; there is also an interbase hydrogen bond from the amine of 1mC to N7 of 9eG. For Na+, K+, and Rb+, similar binding of the metal cation to 1mC is calculated but, unlike Li+, the lowest energy structure is one in which the metal cation is bound to N7 of 9eG; there is also an interbase hydrogen bond between the amine of 1mC and the carbonyl of 9eG. The lowest energy structure for the Cs complex is the Watson-Crick type base pairing with Cs+ binding only to 9eG through O6 and N7 and with three hydrogen bonds between 9eG and 1mC. It also interesting to note that the Watson-Crick base pairing structure gets lower in Gibbs energy relative to the lowest energy complexes as the metal gets larger. This indicates that the smaller, more densely charged cations have a greater propensity to interfere with Watson-Crick base pairing than do the larger, less densely charged metal cations.
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Affiliation(s)
- Ruodi Cheng
- Department of Chemistry, Memorial University, St. John's, NL A1B 3X7, Canada.
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7
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Cheng R, Loire E, Martens J, Fridgen TD. An IRMPD spectroscopic and computational study of protonated guanine-containing mismatched base pairs in the gas phase. Phys Chem Chem Phys 2020; 22:2999-3007. [DOI: 10.1039/c9cp06393e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Infrared multiple photon dissociation spectroscopy has been used to probe the structures of the three protonated base-pair mismatches containing 9-ethylguanine (9eG) in the gas phase. Some of these protonated base-pairs have been identified in RNA.
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Affiliation(s)
- Ruodi Cheng
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | - Estelle Loire
- Laboratoire Chimie Physique – CLIO
- Campus Universite d’Orsay
- France
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Nijmegen
- The Netherlands
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8
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Stefan L, Monchaud D. Applications of guanine quartets in nanotechnology and chemical biology. Nat Rev Chem 2019. [DOI: 10.1038/s41570-019-0132-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Choi YK, Han SY. Facile Production of Hydrogen‐bonded Dimeric Fragments from Collision‐induced Dissociation of Na
+
‐bound G‐Tetrads Predicted by Thermochemistry. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yoon Kyung Choi
- Department of NanochemistryGachon University Seongnam‐si 13120 Republic of Korea
| | - Sang Yun Han
- Department of NanochemistryGachon University Seongnam‐si 13120 Republic of Korea
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10
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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.
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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.
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11
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Park JJ, Han SY. Alternated Branching Ratios by Anomaly in Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pairs of 1-Methylcytosine with 1-Methylguanine and 9-Methylguanine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:846-854. [PMID: 30911905 DOI: 10.1007/s13361-019-02161-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/26/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
A comparative study on the proton-bound complexes of 1-methylcytosine (1-mC) with 1-methylguanine (1-mG) and 9-methylguanine (9-mG), [1-mC:1-mG:H]+ and [1-mC:9-mG:H]+, respectively, was carried out using energy-resolved collision-induced dissociation (ER-CID) experiments in combination with quantum chemical calculations. In ER-CID experiments, the measured survival yields indicated an essentially identical stability for the two proton-bound complexes. In comparison with the lowest-energy structures and base-pairing energetics predicted at the B3LYP/6-311+G(2d,2p) theory level, both complexes produced in this study were suggested to be proton-bound Hoogsteen base pairs. Curiously, despite the similarity in structures, binding energetics, and potential energy surfaces predicted by the B3LYP theory, the fragment branching ratios exhibited an intriguing alternation between the two proton-bound Hoogsteen base pairs. The CID of [1-mC:1-mG:H]+ produced protonated cytosines, [1-mC:H]+, more abundantly than [1-mG:H]+, whereas that of [1-mC:9-mG:H]+ gave rise to a more pronounced production of protonated guanines, [9-mG:H]+. However, using the proton affinities of moieties predicted by the high-accuracy methods, including CBS-QB3 and the Guassian-4 theory, the anomaly known for [Cytosine:Guanine:H]+ (J. Am. Soc. Mass Spectrom. 29, 2368-2379 (2018)) successfully accounted for the alternated branching ratios. Thereby, the anomaly, more specifically, the production of proton-transferred fragments of O-protonated cytosines in the CID of proton-bound Hoogsteen base pairs, is indeed real, which is disclosed as the alternated branching ratios in the CID spectra of [1-mC:1-mG:H]+ and [1-mC:9-mG:H]+ in this study. Graphical Abstract .
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Affiliation(s)
- Jeong Ju Park
- Department of Nanochemistry, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea
| | - Sang Yun Han
- Department of Nanochemistry, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
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12
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Wollschläger JM, Schalley CA. Ion Mobility Mass Spectrometric Investigation on the Photoisomerization of a 4,4’‐Diamidoazobenzene Model. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jan M. Wollschläger
- Institut für Chemie und Biochemie der Freien Universität Berlin Takustr 3 14195 Berlin Germany
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie der Freien Universität Berlin Takustr 3 14195 Berlin Germany
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13
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Devereaux ZJ, Zhu Y, Rodgers MT. Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:16-29. [PMID: 30189754 DOI: 10.1177/1469066718798097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.
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Affiliation(s)
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, USA
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14
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Azargun M, Meister PJ, Gauld JW, Fridgen TD. The K2(9-ethylguanine)122+ quadruplex is more stable to unimolecular dissociation than the K(9-ethylguanine)8+ quadruplex in the gas phase: a BIRD, energy resolved SORI-CID, IRMPD spectroscopic, and computational study. Phys Chem Chem Phys 2019; 21:15319-15326. [DOI: 10.1039/c9cp01651a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of experimental trapped-ion mass spectrometric studies and computational chemistry has been used to assess the intrinsic properties of the potassiated 9-ethylguanine (9eG) self-assembled quadruplex, K2(9eG)122+, in the gas phase.
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Affiliation(s)
- Mohammad Azargun
- Department of Chemistry
- Memorial University of Newfoundland
- St. John's
- Canada
| | - Paul J. Meister
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - James W. Gauld
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - Travis D. Fridgen
- Department of Chemistry
- Memorial University of Newfoundland
- St. John's
- Canada
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15
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Park JJ, Lee CS, Han SY. Proton Transfer Accounting for Anomalous Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pair of Cytosine and Guanine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2368-2379. [PMID: 30215166 DOI: 10.1007/s13361-018-2060-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
To understand the anomalous collision-induced dissociation (CID) behavior of the proton-bound Hoogsteen base pair of cytosine (C) and guanine (G), C:H+∙∙∙G, we investigated CID of a homologue series of proton-bound heterodimers of C, 1-methylcytosine, and 5-methylcytosine with G as a common base partner. The CID experiments were performed in an energy-resolved way (ER-CID) under both multiple and near-single collision conditions. The relative stabilities of the protonated complexes examined by ER-CID suggested that the proton-bound complexes produced by electrospray ionization in this study are proton-bound Hoogsteen base pairs. On the other hand, in contrast to the other base pairs, CID of C:H+∙∙∙G exhibited more abundant productions of C:H+, the fragment protonated on the moiety with a smaller proton affinity, than that of G:H+. This appeared to contradict general prediction based on the kinetic method. However, further theoretical exploration of potential energy surfaces found that there can be facile proton transfers in the proton-bound Hoogsteen base pairs during the CID process, which makes the process accessible to an additional product state of O-protonated C for C:H+ fragments. The presence of an additional dissociation channel, which in other words corresponds to twofold degeneracy in the transition state leading to C:H+ fragments, effectively doubles the apparent reaction rate for production of C:H+. In this way, the process gives rise to the anomaly, the observed pronounced formation of C:H+ in the CID of the proton-bound Hoogsteen base pair, C:H+∙∙∙G. Graphical Abstract ᅟ.
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Affiliation(s)
- Jeong Ju Park
- Department of Nanochemistry, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea
| | - Choong Sik Lee
- Scientific Investigation Laboratory, Ministry of National Defense, 22 Itaewon-ro, Yongsan-gu, Seoul, 04383, Republic of Korea
| | - Sang Yun Han
- Department of Nanochemistry, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
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16
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Streciwilk W, Terenzi A, Cheng X, Hager L, Dabiri Y, Prochnow P, Bandow JE, Wölfl S, Keppler BK, Ott I. Fluorescent organometallic rhodium(I) and ruthenium(II) metallodrugs with 4-ethylthio-1,8-naphthalimide ligands: Antiproliferative effects, cellular uptake and DNA-interaction. Eur J Med Chem 2018; 156:148-161. [PMID: 30006161 DOI: 10.1016/j.ejmech.2018.06.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 12/28/2022]
Abstract
Fluorescent 4-ethylthio-1,8-naphthalimides containing rhodium(I) N-heterocyclic carbene (NHC) and ruthenium (II) NHC fragments were synthesised and evaluated for their antiproliferative effects, cellular uptake and DNA-binding activity. Both types of organometallics triggered ligand dependent efficient cytotoxic effects against tumor cells with the rhodium(I) NHC derivatives causing stronger effects than the ruthenium (II) NHC analogues. Antiproliferative effects could also be observed against several pathogenic Gram-positive bacterial strains, whereas the growth of Gram-negative bacteria was not substantially affected. Cellular uptake was confirmed by atomic absorption spectroscopy as well as by fluorescence microscopy indicating a general ligand dependent accumulation in the cells. An in-depth study on the interaction with DNA confirmed insertion of the naphthalimide moiety between the planar bases of B-DNA via an intercalation mechanism, as well as its stacking on top of the quartets of G-quadruplex structures. Furthermore, additional coordinative binding of the organometallic complexes to the model DNA base 9-ethylguanine could be detected. The studied compounds thus represent promising bioorganometallics featuring strong pharmacological effects in combination with excellent cellular imaging properties.
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Affiliation(s)
- Wojciech Streciwilk
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethoven Straße 55, 38106, Braunschweig, Germany
| | - Alessio Terenzi
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Straße 42, A-1090, Vienna, Austria
| | - Xinlai Cheng
- Department of Pharmacy and Molecular Biotechnology, Division of Pharmaceutical Biology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120, Heidelberg, Germany
| | - Laura Hager
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Straße 42, A-1090, Vienna, Austria
| | - Yasamin Dabiri
- Department of Pharmacy and Molecular Biotechnology, Division of Pharmaceutical Biology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120, Heidelberg, Germany
| | - Pascal Prochnow
- Applied Microbiology, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Julia Elisabeth Bandow
- Applied Microbiology, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Stefan Wölfl
- Department of Pharmacy and Molecular Biotechnology, Division of Pharmaceutical Biology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120, Heidelberg, Germany
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Straße 42, A-1090, Vienna, Austria
| | - Ingo Ott
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethoven Straße 55, 38106, Braunschweig, Germany.
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17
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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.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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18
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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.
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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.
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19
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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.
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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.
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20
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Azargun M, Jami-Alahmadi Y, Fridgen TD. The intrinsic stabilities and structures of alkali metal cationized guanine quadruplexes. Phys Chem Chem Phys 2017; 19:1281-1287. [DOI: 10.1039/c6cp07301h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures and stabilities of self-assembled guanine quadruplexes, M(9eG)8+ (M = Na, K, Rb, Cs; 9eG = 9-ethylguanine), have been studied in the gas phase by blackbody infrared radiative dissociation kinetics to determine the effect the metal cations have on the decomposition energies and reactions of the quadruplex.
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Affiliation(s)
- M. Azargun
- Department of Chemistry
- Memorial University
- St John's
- Canada
| | | | - T. D. Fridgen
- Department of Chemistry
- Memorial University
- St John's
- Canada
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21
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Power B, Rowe S, Fridgen TD. Ammoniated Complexes of Uracil and Transition Metal Ions: Structures of [M(Ura-H)(Ura)(NH3)]+ by IRMPD Spectroscopy and Computational Methods (M = Fe, Co, Ni, Cu, Zn, Cd). J Phys Chem B 2016; 121:58-65. [DOI: 10.1021/acs.jpcb.6b09614] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Barry Power
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
| | - Steven Rowe
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
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22
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Power B, Haldys V, Salpin JY, Fridgen TD. Structures of [M(Ura-H)(H2 O)n ](+) (M = Mg, Ca, Sr, Ba; n = 1-3) complexes in the gas phase by IRMPD spectroscopy and theoretical studies. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:236-244. [PMID: 26956390 DOI: 10.1002/jms.3739] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 06/05/2023]
Abstract
The structures of singly and doubly (and for Mg, triply) hydrated group 2 metal dications bound to deprotonated uracil were explored in the gas phase using infrared multiple photon dissociation spectroscopy in the mid-infrared region (1000-1900 cm(-1) ) and the O-H/N-H stretching region (2700-3800 cm(-1) ) in a Fourier transform ion cyclotron resonance mass spectrometer. The infrared multiple photon dissociation spectra were then compared with the computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6-31 + G(d,p) basis set for all atoms except Ba(2+) and Sr(2+) , for which the LANL2DZ or the def2-TZVPP basis sets with relativistic core potentials were used. Atoms-in-molecules analysis was conducted for all lowest energy structures. The lowest energy isomers in all cases are those in which the one uracil is deprotonated at the N3 position, and the metal is coordinated to the N3 and O4 of uracil. Regardless of the degree of solvation, all water molecules are bound to the metal ion and participate in a hydrogen bond with a carbonyl of the uracil moiety.
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Affiliation(s)
- Barry Power
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7, Canada
| | - Violette Haldys
- Université d'Evry Val d'Essonne - Laboratoire d'Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Bâtiment Maupertuis, Boulevard François Mitterrand, 91025, Evry, France
- CNRS UMR 8587
| | - Jean-Yves Salpin
- Université d'Evry Val d'Essonne - Laboratoire d'Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Bâtiment Maupertuis, Boulevard François Mitterrand, 91025, Evry, France
- CNRS UMR 8587
| | - Travis D Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7, Canada
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23
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Peters GM, Skala LP, Davis JT. A Molecular Chaperone for G4-Quartet Hydrogels. J Am Chem Soc 2015; 138:134-9. [DOI: 10.1021/jacs.5b08769] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Gretchen Marie Peters
- Department of Chemistry and
Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Luke P. Skala
- Department of Chemistry and
Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery T. Davis
- Department of Chemistry and
Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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