1
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Stochastic dynamic quantitative and 3D structural matrix assisted laser desorption/ionization mass spectrometric analyses of mixture of nucleosides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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2
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Paciotti R, Chiavarino B, Coletti C, Scuderi D, Re N, Corinti D, Rotari L, Fornarini S, Crestoni ME. IRMPD Spectroscopy of Bare Monodeprotonated Genistein, an Antioxidant Flavonoid. ACS OMEGA 2022; 7:19535-19544. [PMID: 35721943 PMCID: PMC9202291 DOI: 10.1021/acsomega.2c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/17/2022] [Indexed: 05/11/2023]
Abstract
Genistein is a naturally occurring polyphenol belonging to the family of flavonoids with estrogenic properties and proven antioxidant, anti-inflammatory, and hormonal effects. Genistein and its derivatives are involved in radical scavenging activity by way of mechanisms based on sequential proton-loss electron transfer. In view of this role, a detailed structural characterization of its bare deprotonated form, [geni-H]-, generated by electrospray ionization, has been performed by tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy in the 800-1800 cm-1 spectral range. Quantum chemical calculations at the B3LYP/6-311+G(d,p) level of theory were carried out to determine geometries, thermochemical data, and anharmonic vibrational properties of low-lying isomers, enabling to interpret the experimental spectrum. Evidence is gathered that the conjugate base of genistein exists as a single isomeric form, which is deprotonated at the most acidic site (7-OH) and benefits from a strong intramolecular H-bond interaction between 5-OH and the adjacent carbonyl oxygen in the most stable arrangement.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Cecilia Coletti
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Debora Scuderi
- Institut
de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Nazzareno Re
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Lucretia Rotari
- 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
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
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3
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Cruz-Ortiz AF, Jara-Toro RA, Aranguren JP, Scuderi D, Pino GA. Inter- and Intramolecular Proton Transfer in an Isolated (Cytosine-Guanine)H + Pair: Direct Evidence from IRMPD Spectroscopy. J Phys Chem A 2022; 126:1403-1411. [PMID: 35175052 DOI: 10.1021/acs.jpca.1c10651] [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
The collision-induced dissociation of the protonated cytosine-guanine pair was studied using tandem mass spectrometry (MS3) coupled to infrared multiple photon dissociation spectroscopy with the free electron laser at Orsay (CLIO) to determine the structure of the CH+ and GH+ ionic fragments. The results were rationalized with the help of electronic structure calculations at the density functional theory level with the B3LYP/6-311++G(3df,2p) method. Several tautomers of each fragment were identified for the first time, some of which were previously predicted by other authors. In addition, two unexpected and minor tautomers were also found: cytosine keto-imino [CKI(1,2,3,4)H+] and guanine keto-amino [GKA(1,3,7)H+]. These results highlight the importance of the DNA base tautomerization assisted by inter- and intramolecular proton or hydrogen transfer within the protonated pairs.
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Affiliation(s)
- Andrés F Cruz-Ortiz
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET─UNC, 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
| | - Rafael A Jara-Toro
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET─UNC, 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
| | - Juan P Aranguren
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET─UNC, 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
| | - Debora Scuderi
- Institut de Chimie Physique, CNRS-Université Paris Saclay, UMR8000, F-91405 Orsay, France
| | - Gustavo A Pino
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET─UNC, 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
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4
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Pedroza-Montero JN, Calaminici P, Köster AM. First-principle polarizabilities of nanosystems from auxiliary density perturbation theory with MINRES. Theor Chem Acc 2022. [DOI: 10.1007/s00214-021-02864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Structural Diversity of Di-Metalized Arginine Evidenced by Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy in the Gas Phase. Molecules 2021; 26:molecules26216546. [PMID: 34770955 PMCID: PMC8587954 DOI: 10.3390/molecules26216546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022] Open
Abstract
Although metal cations are prevalent in biological media, the species of multi-metal cationized biomolecules have received little attention so far. Studying these complexes in isolated state is important, since it provides intrinsic information about the interaction among them on the molecular level. Our investigation here demonstrates the unexpected structural diversity of such species generated by a matrix-assisted laser desorption ionization (MALDI) source in the gas phase. The photodissociation spectroscopic and theoretical study reflects that the co-existing isomers of [Arg+Rb+K−H]+ can have energies ≥95 kJ/mol higher than that of the most stable one. While the result can be rationalized by the great isomerization energy barrier due to the coordination, it strongly reminds us to pay more attention to their structural diversities for multi-metalized fundamental biological molecules, especially for the ones with the ubiquitous alkali metal ions.
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6
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Moe MM, Benny J, Sun Y, Liu J. Experimental and theoretical assessment of protonated Hoogsteen 9-methylguanine-1-methylcytosine base-pair dissociation: kinetics within a statistical reaction framework. Phys Chem Chem Phys 2021; 23:9365-9380. [PMID: 33885080 DOI: 10.1039/d0cp06682f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We investigated the collision-induced dissociation (CID) reactions of a protonated Hoogsteen 9-methylguanine-1-methylcytosine base pair (HG-[9MG·1MC + H]+), which aims to address the mystery of the literature reported "anomaly" in product ion distributions and compare the kinetics of a Hoogsteen base pair with its Watson-Crick isomer WC-[9MG·1MC + H]+ (reported recently by Sun et al.; Phys. Chem. Chem. Phys., 2020, 22, 24986). Product ion cross sections and branching ratios were measured as a function of center-of-mass collision energy using guided-ion beam tandem mass spectrometry, from which base-pair dissociation energies were determined. Product structures and energetics were assessed using various theories, of which the composite DLPNO-CCSD(T)/aug-cc-pVTZ//ωB97XD/6-311++G(d,p) was adopted as the best-performing method for constructing a reaction potential energy surface. The statistical Rice-Ramsperger-Kassel-Marcus theory was found to provide a useful framework for rationalizing the dominating abundance of [1MC + H]+ over [9MG + H]+ in the fragment ions of HG-[9MG·1MC + H]+. The kinetics analysis proved the necessity for incorporating into kinetics modeling not only the static properties of reaction minima and transition states but more importantly, the kinetics of individual base-pair conformers that have formed in collisional activation. The analysis also pinpointed the origin of the statistical kinetics of HG-[9MG·1MC + H]+vs. the non-statistical behavior of WC-[9MG·1MC + H]+ in terms of their distinctively different intra-base-pair hydrogen-bonds and consequently the absence of proton transfer between the N1 position of 9MG and the N3' of 1MC in the Hoogsteen base pair. Finally, the Hoogsteen base pair was examined in the presence of a water ligand, i.e., HG-[9MG·1MC + H]+·H2O. Besides the same type of base-pair dissociation as detected in dry HG-[9MG·1MC + H]+, secondary methanol elimination was observed via the SN2 reaction of water with nucleobase methyl groups.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA.
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7
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Cui X, Zhao Y, Li Z, Meng Q, Zhang C. Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP. Front Chem 2020; 8:605117. [PMID: 33330400 PMCID: PMC7734142 DOI: 10.3389/fchem.2020.605117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 11/13/2022] Open
Abstract
Recently, the successful incorporation of artificial base pairs in genetics has made a significant progress in synthetic biology. The present work reports the proton transfer and photoisomerization of unnatural base pair ZP, which is synthesized from the pyrimidine analog 6-amino-5-nitro-3-(1-β-D-2'-deoxyribo-furanosyl)-2 (1H)-pyridone (Z) and paired with its Watson-Crick complement, the purine analog 2-amino-8-(1'-β-D-2'- deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P). To explain the mechanism of proton transfer process, we constructed the relaxed potential energy surfaces (PESs) linking the different tautomers in both gas phase and solution. Our results show that the double proton transfer in the gas phase occurs in a concerted way both in S0 and S1 states, while the stepwise mechanism becomes more favorable in solution. The solvent effect can promote the single proton transfer, which undergoes a lower energy barrier in S1 state due to the strengthened hydrogen bond. In contrast to the excited state ultrafast deactivation process of the natural bases, there is no conical intersection between S0 and S1 states along the proton transfer coordinate to activate the decay mechanism in ZP. Of particular relevance to the photophysical properties, charge-transfer character is obviously related to the nitro rotation in S1 state. We characterized the molecular vibration effect on the electronic properties, which reveals the electronic excitation can be tuned by the rotation-induced structural distortion accompanied with the electron localization on nitro group.
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Affiliation(s)
- Xixi Cui
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Yu Zhao
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Zhibing Li
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qingtian Meng
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Changzhe Zhang
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan, China
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8
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Sun Y, Moe MM, Liu J. Is non-statistical dissociation a general feature of guanine–cytosine base-pair ions? Collision-induced dissociation of a protonated 9-methylguanine–1-methylcytosine Watson–Crick base pair, and comparison with its deprotonated and radical cation analogues. Phys Chem Chem Phys 2020; 22:24986-25000. [DOI: 10.1039/d0cp04243a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Non-statistical dissociation of a protonated guanine–cytosine Watson–Crick base pair.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
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