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Risoluti R, Caprari P, Gullifa G, Diana L, Luciani M, Amato A, Materazzi S. TGA/Chemometric Test Is Able to Detect the Presence of a Rare Hemoglobin Variant Hb Bibba. Front Mol Biosci 2019; 6:101. [PMID: 31632985 PMCID: PMC6781652 DOI: 10.3389/fmolb.2019.00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/17/2019] [Indexed: 11/13/2022] Open
Abstract
In this study the TGA/Chemometric test was applied for diagnosis of a case of congenital hemolytic anemia for which the common first level diagnostic tests were not able to find the erythrocyte congenital defect. A 6 years old girl presented chronic hemolytic anemia characterized by hyperbilirubinemia, increased spleen, negative Coombs tests, normal hemoglobin values, decreased mean corpuscular volume (MCV), increased red cell distribution width (RDW), reticulocytes and lactate dehydrogenase (LDH), and altered erythrocyte morphology (ovalocytes, spherocytes, and rare schizocytes). The diagnostic protocols for differential diagnosis of hereditary hemolytic anemia were carried out by the investigation of the congenital hemolytic anemias due to defects of membrane proteins and the most common erythrocyte enzymes, but no defect was found. The TGA/Chemometric test was applied and the PLS-DA model of prediction was used to process results. The thermogravimetric profile of the patient was very distinct from those of healthy subjects and comparable with those of thalassemia patients. The classification model applied to the patient identified a chronic hemolytic anemia due to a hemoglobin defect and the molecular characterization confirmed the TGA/Chemometrics results, demonstrating the presence of a very rare hemoglobin variant Hb Bibba (α2136(H19)Leu → Proβ2). In conclusion the TGA/Chemometric test proved to be a promising tool for the screening of the hemoglobin defects, in a short time and at low cost, of this case of congenital hemolytic anemia of difficult diagnosis. This method results particularly suitable in pediatric patients as it requires small sample volumes and is able to characterize patients subjected to transfusion.
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Affiliation(s)
- Roberta Risoluti
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Patrizia Caprari
- National Centre for the Control and Evaluation of Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Loretta Diana
- National Centre for the Control and Evaluation of Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Matteo Luciani
- UO Ematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy
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Abstract
This work aims to investigate possible interferences due to the presence of sodium carbonate on the photodegradation of the reactive Black 5 azoic dye, both in systems containing only titanium oxide and those containing titanium oxide and hydrogen peroxide. The role of hydrogen peroxide is explicitly treated. Sodium carbonate, in fact, is often present in the wastewater of textile industries as it is used in the fiber dyeing phases. The use of TiO2 nanoparticles is emphasized, and the possible danger is underlined. Each system was subjected to ultraviolet irradiation (UV) by varying the exposure time. After the photodegrading tests, the resulting solutions were analyzed by UV-vis spectrophotometry and High-Resolution Nuclear Magnetic Resonance to measure the residual concentrations of dye. The dye degradation curves and reaction rates for different UV exposure times were obtained and discussed as a function of the used additives. All the data are repeated three times, and they differ only by a maximum of 5%. The results indicated a reduction of about 50% of the initial concentration of Reactive Black 5 after 30 min under optimal experimental conditions. The NMR analysis indicated the formation of a series of aromatic structures that were generated by the UV-induced photochemical fragmentation of the original molecule.
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3
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Risoluti R, Pichini S, Pacifici R, Materazzi S. Miniaturized analytical platform for cocaine detection in oral fluids by MicroNIR/Chemometrics. Talanta 2019; 202:546-553. [DOI: 10.1016/j.talanta.2019.04.081] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022]
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Lico D, Vuono D, Siciliano C, B Nagy J, De Luca P. Removal of unleaded gasoline from water by multi-walled carbon nanotubes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 237:636-643. [PMID: 30851592 DOI: 10.1016/j.jenvman.2019.02.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 01/08/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
This article displays an efficient and cost effective technique for the removal of unleaded gasoline from water. Multi-walled carbon nanotubes (MWCNTs) were used as the sorbent material. Nanotubes were synthesized according to a well-known procedure and successfully used avoiding cumbersome purifications from traces of catalyst. A series of lab-scale experiments was performed on dispersions of commercial unleaded gasoline (20 mL) in water (30 mL), which were subjected to the action of variable amounts of MWCNTs at room temperature. Physicochemical characteristics and sorbent capacity of nanotubes were investigated by thermal analysis and FT-IR spectroscopy. The highest percentage of removed unleaded gasoline was obtained using small amounts (0.7 g) of MWCNTs, over very short stirring times (5 min). The composition of residual organic materials in water was investigated by 1H and 13C high-resolution NMR spectroscopy, which confirmed the almost complete removal of unleaded gasoline hydrocarbon components from polluted waters.
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Affiliation(s)
- Daniele Lico
- Dipartimento di Ingegneria per l'Ambiente e il Territorio e Ingegneria Chimica, Università della Calabria, I-87036, Arcavacata di Rende, CS, Italy
| | - Danilo Vuono
- Dipartimento di Ingegneria per l'Ambiente e il Territorio e Ingegneria Chimica, Università della Calabria, I-87036, Arcavacata di Rende, CS, Italy
| | - Carlo Siciliano
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria, I-87036, Arcavacata di Rende, CS, Italy
| | - Janos B Nagy
- Dipartimento di Ingegneria per l'Ambiente e il Territorio e Ingegneria Chimica, Università della Calabria, I-87036, Arcavacata di Rende, CS, Italy
| | - Pierantonio De Luca
- Dipartimento di Ingegneria Meccanica, Energetica e Gestionale, Università della Calabria, I-87036, Arcavacata di Rende, CS, Italy.
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5
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High-throughput determination of vitamin E in extra virgin olive oil by paper spray tandem mass spectrometry. Anal Bioanal Chem 2019; 411:2885-2890. [PMID: 30899998 DOI: 10.1007/s00216-019-01727-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/18/2019] [Accepted: 02/27/2019] [Indexed: 01/03/2023]
Abstract
Extra virgin olive oil provides an important intake of α-tocopherol, which is part of vitamin E complex. A fast analytical method for its quantification, based on paper spray mass spectrometry, has been developed. The methodology possesses the ability to record mass spectra without sample preparation or preseparation steps. The experiments were performed in Multiple Reaction Monitoring scan mode; in particular, the transitions m/z 429 → m/z 163 for α-tocopherol and m/z 435 → m/z 169 for the labeled internal standard were monitored, in order to obtain the greatest specificity and the best sensitivity. The accuracy of the method was tested analyzing spiked samples prepared at concentrations within the dynamic range of the calibration curve, which returned values near 100%. Furthermore, good values of LOQ and LOD were obtained, demonstrating that this approach can be applied for a rapid screening of tocopherols in different vegetable oils. The results were compared with analyses performed by traditional chromatographic methods. Graphical abstract.
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6
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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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7
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Cruz-Ortiz AF, Rossa M, Berthias F, Berdakin M, Maitre P, Pino GA. Fingerprints of Both Watson-Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H + Pair. J Phys Chem Lett 2017; 8:5501-5506. [PMID: 29064704 DOI: 10.1021/acs.jpclett.7b02140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Gas phase protonated guanine-cytosine (CGH+) pair was generated using an electrospray ionization source from solutions at two different pH (5.8 and 3.2). Consistent evidence from MS/MS fragmentation patterns and differential ion mobility spectra (DIMS) point toward the presence of two isomers of the CGH+ pair, whose relative populations depend strongly on the pH of the solution. Gas phase infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1900 cm-1 spectral range further confirms that the Watson-Crick isomer is preferentially produced (91%) at pH = 5.8, while the Hoogsteen isomer predominates (66%) at pH = 3.2). These fingerprint signatures are expected to be useful for the development of new analytical methodologies and to trigger isomer selective photochemical studies of protonated DNA base 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, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Maximiliano Rossa
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Francis Berthias
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Matías Berdakin
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Philippe Maitre
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , 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, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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9
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Wu RR, Yang B, Berden G, Oomens J, Rodgers MT. Gas-Phase Conformations and Energetics of Protonated 2′-Deoxyadenosine and Adenosine: IRMPD Action Spectroscopy and Theoretical Studies. J Phys Chem B 2015; 119:2795-805. [DOI: 10.1021/jp509267k] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- R. R. Wu
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Bo Yang
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - G. Berden
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - J. Oomens
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van’t Hoff
Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - M. T. Rodgers
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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10
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Rubino FM. Toxicity of Glutathione-Binding Metals: A Review of Targets and Mechanisms. TOXICS 2015; 3:20-62. [PMID: 29056650 PMCID: PMC5634692 DOI: 10.3390/toxics3010020] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/04/2014] [Accepted: 01/14/2015] [Indexed: 02/07/2023]
Abstract
Mercury, cadmium, arsenic and lead are among priority metals for toxicological studies due to the frequent human exposure and to the significant burden of disease following acute and chronic intoxication. Among their common characteristics is chemical affinity to proteins and non-protein thiols and their ability to generate cellular oxidative stress by the best-known Fenton mechanism. Their health effects are however diverse: kidney and liver damage, cancer at specific sites, irreversible neurological damages with metal-specific features. Mechanisms for the induction of oxidative stress by interaction with the cell thiolome will be presented, based on literature evidence and of experimental findings.
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Affiliation(s)
- Federico Maria Rubino
- LaTMA Laboratory for Analytical Toxicology and Metabonomics, Department of Health Sciences, Università degli Studi di Milano at "Ospedale San Paolo" v. A. di Rudinì 8, I-20142 Milano, Italy.
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11
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Palamarchuk GV, Shishkin OV, Gorb L, Leszczynski J. Nucleic acid bases in anionic 2'-deoxyribonucleotides: a DFT/B3LYP study of structures, relative stability, and proton affinities. J Phys Chem B 2013; 117:2841-9. [PMID: 23425497 DOI: 10.1021/jp311363c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protonation of nucleobases in anions of canonical 2'-deoxyribonucleotides has been investigated by the DFT computational study at the B3LYP/aug-cc-pvdz level of theory. It is demonstrated that the protonation leads to a significant decrease of conformational space of purine nucleotides while almost all conformers found for non-protonated molecules correspond to minima of the potential energy surface for protonated mdTMP and mdCMP. However, in all nucleotides, only one conformer is populated. This applies to all tautomers of protonated molecules except the mdTMP and mdCMP with the proton attached to the carbonyl group where a minor population of second conformer is observed. Protonation of nucleobase leads to significant elongation of the N-glycosidic bond. These findings agree well with suggestions that protonation of nucleobase is a first step in cleavage of the glycosidic bond. The oxygen atoms of both carbonyl groups of thymine and the N3 atom of the pyrimidine ring of cytosine, guanine, and adenine represent the most preferable sites for protonation of anions of 2'-deoxyrobonucleotides. The highest proton affinity is observed for the base in mdGMP and the lowest for the thymine moiety in mdTMP. It should be noted that calculated values of the proton affinities in anionic nucleotides are significantly higher (by 2-3 eV) than for nucleosides and neutral nucleotides. This allows assuming that the proton affinity of the base in DNA macromolecule may be tuned by changing the extent of shielding or neutralization of negative charge of the phosphate group.
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Affiliation(s)
- Gennady V Palamarchuk
- STC Institute for Single Crystals, National Academy of Sciences of Ukraine, 60 Lenina ave., Kharkiv 61001, Ukraine
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12
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Investigation of the Cu binding site at [dCdG] and [CG] base pairs in the absence of a DNA backbone. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Moser A, Range K, York DM. Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis. J Phys Chem B 2010; 114:13911-21. [PMID: 20942500 PMCID: PMC2970571 DOI: 10.1021/jp107450n] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benchmark quantum calculations of proton affinities and gas-phase basicities of molecules relevant to biochemical processes, particularly acid/base catalysis, are presented and compared for a variety of multilevel and density functional quantum models. Included are nucleic acid bases in both keto and enol tautomeric forms, ribose in B-form and A-form sugar pucker conformations, amino acid side chains and backbone molecules, and various phosphates and phosphoranes, including thio substitutions. This work presents a high-level thermodynamic characterization of biologically relevant protonation states and provides a benchmark database for development of next-generation semiempirical and approximate density functional quantum models and parametrization of methods to predict pK(a) values and relative solvation energies.
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Affiliation(s)
- Adam Moser
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
| | - Kevin Range
- Department of Chemistry, Lock Haven University of Pennsylvania, Lock Haven, PA 17745, USA
| | - Darrin M. York
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854-8087, USA
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14
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Kumari S, Devi CL, Prabhakar S, Bhanuprakash K, Vairamani M. Estimation of gas-phase acidities of deoxyribonucleosides: an experimental and theoretical study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:136-143. [PMID: 19892566 DOI: 10.1016/j.jasms.2009.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 09/22/2009] [Accepted: 09/23/2009] [Indexed: 05/28/2023]
Abstract
We determined the gas-phase acidities (DeltaH(acid)) of four deoxyribonucleosides, i.e., 2'-deoxyadenosine (dA), 2'-deoxyguanosine (dG), 2'-deoxycytidine (dC), and 2'-deoxythymidine (dT) by applying the extended kinetic method. The negatively charged proton-bound hetero-dimeric anions, [A - H - B](-) of the deoxyribonucleosides (A) and reference compounds (B) were generated under electrospray ionization conditions. Collision-induced dissociation spectra of [A - H - B](-) were recorded at four different collision energies using a triple quadrupole mass spectrometer. The abundance ratios of the individual monomeric product ions were used to determine the DeltaH(acid) of the deoxyribonucleosides. The obtained DeltaH(acid) value follows the order dA > dC > dT > dG. The DeltaG(acid) (298 K) values were determined by using DeltaG(acid) = DeltaH(acid) - TDeltaS(acid) where the DeltaH(acid) and DeltaS(acid) values were determined directly from the kinetic method plots. The DeltaH(acid) values were also predicted for the deoxyribonucleosides at the B3LYP/6-311+G**//B3LYP/6-311G** level of theory. The acidity trend obtained from the computational investigation shows good agreement with that obtained experimentally by the extended kinetic method. Theoretical calculations provided the most preferred deprotonation site as C5'-OH from sugar moiety in case of dA, and as -NH(2) (dC and dG) or -NH- (dT) from nitrogenous base moiety in the case of other deoxyribonucleosides.
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Affiliation(s)
- Sangeeta Kumari
- National Center for Mass Spectrometry, Indian Institute of Chemical Technology, Hyderabad 500 607, India
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15
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Touboul D, Bouchoux G, Zenobi R. Gas-Phase Protonation Thermochemistry of Adenosine. J Phys Chem B 2008; 112:11716-25. [DOI: 10.1021/jp804786e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David Touboul
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Guy Bouchoux
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
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16
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Salpin JY, Guillaumont S, Tortajada J, MacAleese L, Lemaire J, Maitre P. Infrared spectra of protonated uracil, thymine and cytosine. Chemphyschem 2007; 8:2235-44. [PMID: 17910021 DOI: 10.1002/cphc.200700284] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.
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Affiliation(s)
- Jean-Yves Salpin
- Laboratoire d'Analyse et de Modélisation pour la Biologie et l'Environnement (LAMBE), Université d'Evry Val d'Esonne-CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand, 91025 Evry, France.
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17
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Alves S, Woods A, Tabet JC. Charge state effect on the zwitterion influence on stability of non-covalent interaction of single-stranded DNA with peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:1613-1622. [PMID: 18085569 DOI: 10.1002/jms.1359] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Negative ion ESI mass spectrometry was used to study the gas-phase stability and dissociation pathways of peptide-DNA complexes. We show that bradykinin and three modified peptides containing the basic residue arginine or lysine form stable interactions with single-stranded oligonucleotides. ESI-MS/MS of complexes of T(8) with PPGFSPFRR resulted in a major dissociation pathway through cleavage of the peptide covalent bond. The stability of the complex is due to electrostatic interaction between the negatively charged phosphate group and the basic side chain of the arginine and lysine residues as demonstrated by Vertes et al. and Woods et al. In fact, the present work establishes the role played by zwitterions on complex stabilisation. The presence of protons in nucleobase and/or amino acid contributes in reinforcing the strength of the salt bridge (SB) interaction. The zwitterionic form of the most basic of amino acid residues, arginine, is assumed to form a strong SB interaction to the negatively charged phosphate groups of DNA. This non-covalent complex is stable enough to withstand disruption of the non-covalent interaction and to first break the covalent bond. Moreover, the dependence of fragmentation patterns upon the complex charge state is explained by the fact that the net number of negative charges modulates the number of zwitterionic sites, which stabilise the complexes. Finally, the weak influence of the nucleobase is assumed by the existence of competition for proton addition between the nucleobase and the R/K side chain leading to a decrease in the stabilisation of the SB interaction.
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Affiliation(s)
- Sandra Alves
- Laboratoire de Chimie Structurale Organique et Biologique, UMR 7613/BP45, Université Pierre et Marie Curie, 4 Place Jussieu, Paris 75252, France
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Raczyńska ED, Gal JF, Maria PC, Zientara K, Szelag M. Application of FT-ICR-MS for the study of proton-transfer reactions involving biomolecules. Anal Bioanal Chem 2007; 389:1365-80. [PMID: 17786415 DOI: 10.1007/s00216-007-1508-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 07/06/2007] [Accepted: 07/12/2007] [Indexed: 10/22/2022]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry, combined with modern ionization (fast atom bombardment , electrospray ionization, matrix-assisted laser desorption-ionization), fragmentation (collision-induced dissociation, surface-induced dissociation, one-photon ultraviolet photodissociation, infrared multiphoton dissociation, blackbody infrared radiative dissociation, electron-capture dissociation), and separation (high-performance liquid chromatography, liquid chromatography, capillary electrophoresis) techniques is now becoming one of the most attractive and frequently used instrumental platforms for gas-phase studies of biomolecules such as amino acids, bioamines, peptides, polypeptides, proteins, nucleobases, nucleosides, nucleotides, polynucleotides, nucleic acids, saccharides, polysaccharides, etc. Since it gives the possibilities to trap the ions from a few seconds up to thousands of seconds, it is often applied to study ion/molecule reactions in the gas phase, particularly proton-transfer reactions which provide important information on acid-base properties. These properties determine in part the three-dimensional structure of biomolecules, most of their intramolecular and intermolecular interactions, and consequently their biological activity. They also indicate the form (unionized, zwitterionic, protonated, or deprotonated) which the biomolecule may take in a nonpolar environment.
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Affiliation(s)
- E D Raczyńska
- Department of Chemistry, Warsaw University of Agriculture (SGGW), 02-726 Warsaw, Poland.
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Cheng P, Bohme DK. Gas-Phase Formation of Radical Cations of Monomers and Dimers of Guanosine by Collision-Induced Dissociation of Cu(II)−Guanosine Complexes. J Phys Chem B 2007; 111:11075-82. [PMID: 17715957 DOI: 10.1021/jp071933l] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An electrosprayed water/methanol solution of guanosine and Cu(NO3)2 was observed to give rise to gas-phase copper complexed ions of [CuLn]*2+, [CuL(MeOH)n]*2+, and [CuG n(NO3)]*+, as well as the ions [L]*+, [L+H]+, [G]*+, and [G+H]+ (L=guanosine, G=guanine). The Collision-Induced Dissociation (CID) of [CuL3]*2+ and [CuL(MeOH)n]*2+ (n=2, 3) generates guanosine radical cations [L]*+, while dimeric guanosine radical cations [L2]*+ are generated in the dissociation of [CuL4]*2+. Protonated guanosine [L+H]+ is one of the main products in the primary dissociation of [CuL2]*2+, while the dissociation of the higher-order [CuG2]*2+ produces the [G]*+ radical cation. The guanosine dimer radical cation, [L2]*+ presumably arises from the interaction of two guanosine molecules via proton and hydrogen bonding and is observed to dissociate into [L+H]+ and [L-H]* at low energies. We propose that the first two ligands bind strongly with Cu(II) through N7 and O6 to form a [CuL2]*2+ complex with a four-coordinated planar structure and that a third ligand binds loosely with copper to form [CuL3]*2+. Additional ligation observed in the formation of [CuLn]*2+ (n<or=6) ions is presumed to occur by hydrogen bonding. The ribose group of guanosine appears to play an important role in the stabilization of the doubly charged Cu-guanosine complex and in intraligand proton transfer upon CID. The molecular radical cations [L]*+ observed in the ESI-MS spectrum at low declustering potentials originate primarily from [CuL(MeOH)2,3]*2+ complexes which can dissociate more easily than [CuL3]*2+.
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Affiliation(s)
- Ping Cheng
- Department of Chemistry, Centre for Research in Mass Spectrometry and Centre for Research in Earth and Space Science, York University, Toronto, Ontario, Canada, M3J 1P3
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Kamel AM, Munson B. Collisionally-induced dissociation of substituted pyrimidine antiviral agents: mechanisms of ion formation using gas phase hydrogen/deuterium exchange and electrospray ionization tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1477-92. [PMID: 17583534 DOI: 10.1016/j.jasms.2007.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 05/04/2007] [Accepted: 05/05/2007] [Indexed: 05/15/2023]
Abstract
ESI and CID mass spectra were obtained for four pyrimidine nucleoside antiviral agents and the corresponding compounds in which the labile hydrogens were replaced by deuterium using gas-phase exchange. The number of labile hydrogens, x, was determined from a comparison of ESI spectra obtained with N(2) and with ND(3) as the nebulizer gas. CID mass spectra were obtained for [M + H](+) and [M - H](-) ions and the exchanged analogs, [M(D(x)) + D](+) and [M(D(x)) - D](-), produced by ESI using a SCIEX API-III(plus) mass spectrometer. Protonated pyrimidine antiviral agents dissociate through rearrangement decompositions of base-protonated [M + H](+) ions by cleavage of the glycosidic bonds to give the protonated bases with a sugar moiety as the neutral fragment. Cleavage of the glycosidic bonds with charge retention on the sugar moiety eliminates the base moiety as a neutral molecule and produces characteristic sugar ions. CID of protonated pyrimidine bases, [B + H](+), occurs through three major pathways: (1) elimination of NH(3) (ND(3)), (2) loss of H(2)O (D(2)O), and (3) elimination of HNCO (DNCO). Protonated trifluoromethyl uracil, however, dissociates primarily through elimination of HF followed by the loss of HNCO. CID mass spectra of [M - H](-) ions of all four antiviral agents show NCO(-) as the principal decomposition product. A small amount of deprotonated base is also observed, but no sugar ions. Elimination of HNCO, HN(3), HF, CO, and formation of iodide ion are minor dissociation pathways from [M - H](-) ions.
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Affiliation(s)
- Amin M Kamel
- Department of Exploratory Medical Sciences, Pfizer Global Research and Development, Groton Laboratories, Groton, Connecticut 06340, USA.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:693-704. [PMID: 15880598 DOI: 10.1002/jms.806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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