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Corinti D, Gregori B, Guidoni L, Scuderi D, McMahon TB, Chiavarino B, Fornarini S, Crestoni ME. Complexation of halide ions to tyrosine: role of non-covalent interactions evidenced by IRMPD spectroscopy. Phys Chem Chem Phys 2018; 20:4429-4441. [PMID: 29372198 DOI: 10.1039/c7cp06657k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The binding motifs in the halide adducts with tyrosine ([Tyr + X]-, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950-1950 and 2800-3700 cm-1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm-1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]- and [nitroTyr + X]-, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, -2.1, -6.8 kJ mol-1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion-π interactions yielding ring isomers for [nitroTyr + X]-, where the anion is placed above the face of the aromatic ring.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy.
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2
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Paciotti R, Coletti C, Re N, Scuderi D, Chiavarino B, Fornarini S, Crestoni ME. Serine O-sulfation probed by IRMPD spectroscopy. Phys Chem Chem Phys 2016; 17:25891-904. [PMID: 26027702 DOI: 10.1039/c5cp01409c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sulfation of amino acids is a frequent post-translational modification. It is highly labile, though, and characterizing it by mass spectrometry, an otherwise powerful and widely exploited tool in analytical proteomics, is a challenge. The presently reported study is aimed at revealing the O-sulfation of l-serine and elucidating the effects of protonation and deprotonation on the structure and stability of the ensuing ionic species, [sSer + H](+) and [sSer - H](-). These ions are obtained as gaseous, isolated species by electrospray ionization, trapped in a Paul ion-trap, and sampled by IR multiple photon dissociation (IRMPD) spectroscopy in either the 750-1900 cm(-1) fingerprint range, or the 2900 and 3700 cm(-1) range encompassing the N-H and O-H stretching modes. The recorded IRMPD spectra present diagnostic signatures of the sulfate modification which are missing in the spectra of the native serine ions, [Ser + H](+) and [Ser - H](-). The experimental IRMPD features have been interpreted by comparison with the linear IR spectra of the lowest energy structures that are likely candidates for the sampled ions, calculated at the M06-2X/6-311+G(d,p) level of theory. Evidence is gathered that the most stable conformations of [sSer + H](+) are stabilized by hydrogen bonding interactions between the protonated amino group and both the carbonyl and sulfate oxygens. [sSer - H](-) ions possess a negatively charged sulfate group involved in either a S=O···HN or a S=O···HO hydrogen bond. The experimental IRMPD spectra are consistent with the presence of multiple low-lying structures in a thermally equilibrated population of several species particularly in the case of [sSer - H](-) ions, where the high structural flexibility combined with the presence of a negative charge favors the co-existence of several different H-bonding motifs.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
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3
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Corinti D, Mannina L, Chiavarino B, Steinmetz V, Fornarini S, Crestoni ME. IRMPD signature of protonated pantothenic acid, an ubiquitous nutrient. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Danikiewicz W, Zimnicka M. Negative ion gas-phase chemistry of arenes. MASS SPECTROMETRY REVIEWS 2016; 35:123-146. [PMID: 25851641 DOI: 10.1002/mas.21467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Abstract
Reactions of aromatic and heteroaromatic compounds involving anions are of great importance in organic synthesis. Some of these reactions have been studied in the gas phase and are occasionally mentioned in reviews devoted to gas-phase negative ion chemistry, but no reviews exist that collect all existing information about these reactions. This work is intended to fill this gap. In the first part of this review, methods for generating arene anions in the gas phase and studying their physicochemical properties and fragmentation reactions are presented. The main topics in this part are as follows: processes in which gas-phase arene anions are formed, measurements and calculations of the proton affinities of arene anions, proton exchange reactions, and fragmentation processes of substituted arene anions, especially phenide ions. The second part is devoted to gas-phase reactions of arene anions. The most important of these are reactions with electrophiles such as carbonyl compounds and α,β-unsaturated carbonyl and related compounds (Michael acceptors). Other reactions including oxidation of arene anions and halogenophilic reactions are also presented. In the last part of the review, reactions of electrophilic arenes with nucleophiles are discussed. The best known of these is the aromatic nucleophilic substitution (SN Ar) reaction; however, other processes that lead to the substitution of a hydrogen atom in the aromatic ring are also very important. Aromatic substrates in these reactions are usually but not always nitroarenes bearing other substituents in the ring. The first step in these reactions is the formation of an anionic σ-adduct, which, depending on the substituents in the aromatic ring and the structure of the attacking nucleophile, is either an intermediate or a transition state in the reaction path. In the present review, we attempted to collect the results of both experimental and computational studies of the aforementioned reactions conducted since the very beginning of gas-phase negative ion chemistry.
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Affiliation(s)
- Witold Danikiewicz
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Magdalena Zimnicka
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Nakata K, Fujio M, Siehl HU, Tsuno Y. Computational study of substituent effects on gas-phase stabilities of Meisenheimer complexes. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The total stabilization energies (TSEs) and anion stabilization energies (ASEs) of ring-substituted (X-) Meisenheimer complexes featuring two NO2 groups in the ring were determined using appropriate isodesmic reactions. The structures and energies of respective species were calculated at the B3LYP/6–311+G(2d,p) level of theory. Ten series of substituent effects were examined by varying substituent Y, which is connected to the sp3 carbon of the ring. The substituent effects were successfully analyzed using an extended Yukawa–Tsuno equation, [Formula: see text]. The r− values for the TSEs were identical to those for the ASEs, whereas the s values for the TSEs were significantly different from those for the ASEs. This shows that the effect of neutral species contributes to the s values of the TSEs. The r− and s values for the ASEs of all Meisenheimer complexes were distributed in a narrow range because substituent Y was insulated from the π-conjugation system. The r− values were large and the s values were small. This shows that the r− and s values were independent of each other and that the extended three-term Yukawa–Tsuno equation was intrinsic for substituent-effect analyses of anions. Although the variation was not substantial, the change in the r− values was clearly explained by the orbital interaction between substituent Y and the π-conjugation system. The r− values exhibited a good correlation with the bond lengths between the ring and the 4-NO2 group among all Meisenheimer complexes and benzylic anions. These facts provide a physical meaning: the r− value is a parameter that reveals the degree of the additional π interactions between the electron-withdrawing substituents and the π-conjugation systems of the ring.
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Affiliation(s)
- Kazuhide Nakata
- Science Research Center, Hosei University, 2-17-1 Fujimi, Chiyoda-ku, Tokyo 102-8160, Japan
| | - Mizue Fujio
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hans-Ullrich Siehl
- Institute for Organic Chemistry I, University of Ulm, Albert Einstein Allee 11, D-89069 Ulm, Germany
| | - Yuho Tsuno
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Zimnicka M, Danikiewicz W. Gas-Phase Anionic σ-Adduct (Trans)formations in Heteroaromatic Systems. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1191-1203. [PMID: 25895890 PMCID: PMC4475249 DOI: 10.1007/s13361-015-1122-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/28/2015] [Accepted: 02/28/2015] [Indexed: 06/04/2023]
Abstract
Anions of nitroderivatives of thiophene and furan were subjected to the reactions with selected C-H acids in the gas phase. Various structures and reaction pathways were proposed for the observed ionic products. In general, the reactions of heteroaromatic anions with C-H acids may be divided into three groups, depending on the proton affinity difference between C-H acid's conjugate base and heteroaromatic anion (ΔPA). The proton transfer from C-H acid to heteroaromatic anion is a dominant process in the reactions for which ΔPA < 0 kcal mol(-1), whereas the reactions with high ΔPA (ΔPA > 16 kcal mol(-1)) do not lead to any ionic products. The formation of σ-adducts and products of their further transformations according to the VNS, SNAr, cine, and tele substitution mechanisms have been proposed for reactions with moderate ΔPA. The other possible mechanisms as SN2 reaction, nucleophilic addition to the cyano group, ring-opening pathway, and halogenophilic reaction have also been discussed to contribute in the reactions between heteroaromatic anions and C-H acids.
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Affiliation(s)
- Magdalena Zimnicka
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Witold Danikiewicz
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Crestoni ME, Chiavarino B, Fornarini S. Nitrosyl–heme and anion–arene complexes: structure, reactivity and spectroscopy. PURE APPL CHEM 2015. [DOI: 10.1515/pac-2014-1203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractTwo topics are selected and illustrated to exemplify (i) a biological and (ii) an organic ionic intermediate. The reactivity behavior of NO adducts with ferric and ferrous hemes has shown remarkable similarities when examined in the gas phase, demonstrating that the largely different NO affinity displayed in solution and in biological media is due to the different coordination environment. In fact, ferrous hemes present a vacant or highly labile axial coordination site, prone to readily bind NO. The vibrational signatures of the NO ligand have also been probed in vacuo for the first time in the nitrosyl complexes deriving from ferrous and ferric hemes under strictly comparable five-coordination at the metal center. Negatively charged σ-adducts, from the association of anions with 1,3,5-trinitrobenzene, an exemplary π-electron-deficient arene, have been probed by IRMPD spectroscopy and found to display variable binding motifs from a strongly covalent σ-adduct (Meisenheimer complex) to a weakly covalent σ-complex, depending on the anion basicity.
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Affiliation(s)
- Maria Elisa Crestoni
- 1Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Barbara Chiavarino
- 1Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Simonetta Fornarini
- 1Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
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8
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Interaction of cisplatin with 5'-dGMP: a combined IRMPD and theoretical study. Inorg Chem 2015; 54:3513-22. [PMID: 25798661 DOI: 10.1021/acs.inorgchem.5b00070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
IR multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH3)2(5'-dGMP-H)](+) and cis-[PtCl(NH3)2(5'-dGMP)](+) ions (where 5'-dGMP is 2'-deoxyguanosine-5'-monophosphate), generated in the gas phase by electrospray ionization, was performed in two spectral regions, namely, 700-1900 cm(-1) and 2800-3800 cm(-1). For structural assignment, experimental IRMPD spectra were compared to IR spectra computed at the B3LYP/LACV3P/6-311G** level of theory. In agreement with computational results, the vibrational spectroscopic characterization of the cis-[Pt(NH3)2(5'-dGMP-H)](+) ion points to macrochelate species resulting from the simultaneous interaction of the metal with both the N7 atom of the guanine residue and an O atom of the phosphate group, structures that bear features in common with those characterized in solution by NMR spectroscopy. Concerning the cis-[PtCl(NH3)2(5'-dGMP)](+) ion, our study points to a monodentate complex involving exclusively the N7 position of guanine, as observed in solution. Also this species exhibits a compact form due to the formation of two hydrogen bonds involving the same ammonia ligand. For both complexes, IRMPD experiments show that a strong intramolecular hydrogen bond is established between one ammonia hydrogen and the carbonyl group of guanine. The strength of this particular interaction can be qualitatively estimated by looking at the redshift of the CO vibration with respect to an unperturbed C═O stretching mode in the fingerprint region. This point is also highlighted in the X-H (X = N, O) stretch region, by the shift of the N-H stretch frequency as a function of the number of hydrogen bonds involving the ammonia ligand.
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Affiliation(s)
- Barbara Chiavarino
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | | | - Jean-Yves Salpin
- ∥Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Boulevard François Mitterrand, 91025 Evry, France
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9
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Błaziak K, Mąkosza M, Danikiewicz W. Competition between Nucleophilic Substitution of Halogen (SNAr) versus Substitution of Hydrogen (SNArH)-A Mass Spectrometry and Computational Study. Chemistry 2015; 21:6048-51. [DOI: 10.1002/chem.201406542] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 11/11/2022]
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10
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De Petris A, Chiavarino B, Crestoni ME, Coletti C, Re N, Fornarini S. Exploring the Conformational Variability in the Heme b Propionic Acid Side Chains through the Effect of a Biological Probe: A Study of the Isolated Ions. J Phys Chem B 2015; 119:1919-29. [DOI: 10.1021/jp5113476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alberto De Petris
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Cecilia Coletti
- Dipartimento
di Farmacia, Università G. D’Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
| | - Nazzareno Re
- Dipartimento
di Farmacia, Università G. D’Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
| | - Simonetta Fornarini
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
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11
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Indra Neela Y, Narahari Sastry G. Theoretical investigation of anion (F−, Cl−) and cation (Na+) interactions with substituted benzene [C6H6 −nYn(Y = –F, –CN, –NO2;n= 1–6)]. Mol Phys 2014. [DOI: 10.1080/00268976.2014.948940] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Schulz J, Jašíková L, Škríba A, Roithová J. Role of Gold(I) α-Oxo Carbenes in the Oxidation Reactions of Alkynes Catalyzed by Gold(I) Complexes. J Am Chem Soc 2014; 136:11513-23. [DOI: 10.1021/ja505945d] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jiří Schulz
- Department of Organic Chemistry,
Faculty of Science, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Lucie Jašíková
- Department of Organic Chemistry,
Faculty of Science, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Anton Škríba
- Department of Organic Chemistry,
Faculty of Science, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Jana Roithová
- Department of Organic Chemistry,
Faculty of Science, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
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13
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Cairns AG, Senn HM, Murphy MP, Hartley RC. Expanding the palette of phenanthridinium cations. Chemistry 2014; 20:3742-51. [PMID: 24677631 PMCID: PMC4164275 DOI: 10.1002/chem.201304241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/03/2014] [Indexed: 01/01/2023]
Abstract
5,6-Disubstituted phenanthridinium cations have a range of redox, fluorescence and biological properties. Some properties rely on phenanthridiniums intercalating into DNA, but the use of these cations as exomarkers for the reactive oxygen species (ROS), superoxide, and as inhibitors of acetylcholine esterase (AChE) do not require intercalation. A versatile modular synthesis of 5,6-disubstituted phenanthridiniums that introduces diversity by Suzuki–Miyaura coupling, imine formation and microwave-assisted cyclisation is presented. Computational modelling at the density functional theory (DFT) level reveals that the novel displacement of the aryl halide by an acyclic N-alkylimine proceeds by an S(N)Ar mechanism rather than electrocyclisation. It is found that the displacement of halide is concerted and there is no stable Meisenheimer intermediate, provided the calculations consistently use a polarisable solvent model and a diffuse basis set.
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Affiliation(s)
- Andrew G Cairns
- WestCHEM School of Chemistry, University of GlasgowGlasgow, G12 8QQ (UK) E-mail:
| | - Hans Martin Senn
- WestCHEM School of Chemistry, University of GlasgowGlasgow, G12 8QQ (UK) E-mail:
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC BuildingCambridge, CB2 0XY (UK)
| | - Richard C Hartley
- WestCHEM School of Chemistry, University of GlasgowGlasgow, G12 8QQ (UK) E-mail:
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Lanucara F, Chiavarino B, Scuderi D, Maitre P, Fornarini S, Crestoni ME. Kinetic control in the CID-induced elimination of H3PO4 from phosphorylated serine probed using IRMPD spectroscopy. Chem Commun (Camb) 2014; 50:3845-8. [PMID: 24589658 DOI: 10.1039/c4cc00877d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy was used to assay the structural features of the fragment ions resulting from the elimination of H3PO4 in the Collision-Induced Dissociation (CID) of protonated serine. The results are interpreted with the aid of density functional theory calculations. Experiment and theory point to an aziridine-ring structure, implying participation of the vicinal amino group in the formation of this species. This finding constitutes a benchmark for investigating the same process in the CID of phosphorylated peptides.
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Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, M17DN Manchester, UK.
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Chiavarino B, Maitre P, Fornarini S, Crestoni ME. Cyanide-arene Meisenheimer complex generated in electrospray ionization mass spectrometry using acetonitrile as a solvent. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1603-1607. [PMID: 23954999 DOI: 10.1007/s13361-013-0703-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 06/02/2023]
Abstract
The C - C bond formation activated under negative electrospray ionization of an acetonitrile solution of 1,3,5-trinitrobenzene is reported. The solvent function is to provide a source of cyanide ion, a highly problematic reagent, which is found to attack the electron-deficient aromatic ring to form a covalently bound anionic complex (Meisenheimer complex). The structure of the complex is elucidated by means of collision induced dissociation mass spectrometry and IR multiple photon dissociation spectroscopy in the 'fingerprint' region.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Rome, Italy
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Affiliation(s)
| | - Steven R. Kass
- Department
of Chemistry, University of Minnesota,
Minneapolis, Minnesota 55455,
United States
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17
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Adriaenssens L, Estarellas C, Vargas Jentzsch A, Martinez Belmonte M, Matile S, Ballester P. Quantification of Nitrate−π Interactions and Selective Transport of Nitrate Using Calix[4]pyrroles with Two Aromatic Walls. J Am Chem Soc 2013; 135:8324-30. [DOI: 10.1021/ja4021793] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Louis Adriaenssens
- Institute of Chemical Research of Catalonia (ICIQ), Avda. Països Catalans
16, 43007 Tarragona, Spain
| | - Carolina Estarellas
- Department de Química, Universitat de les Illes Balears, crta. Valldemossa
km 7.5, 07122, Palma de Mallorca, Spain
| | | | - Marta Martinez Belmonte
- Institute of Chemical Research of Catalonia (ICIQ), Avda. Països Catalans
16, 43007 Tarragona, Spain
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ), Avda. Països Catalans
16, 43007 Tarragona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig Lluís
Companys 23, 08010 Barcelona, Spain
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18
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Bahou M, Witek H, Lee YP. Infrared identification of the σ-complex of Cl-C6H6 in the reaction of chlorine atom and benzene in solid para-hydrogen. J Chem Phys 2013; 138:074310. [DOI: 10.1063/1.4790860] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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19
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Interaction of Cisplatin with Adenine and Guanine: A Combined IRMPD, MS/MS, and Theoretical Study. J Am Chem Soc 2013; 135:1445-55. [DOI: 10.1021/ja309857d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie
del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Debora Scuderi
- Laboratoire de Chimie-Physique, Université Paris Sud Orsay, Avenue Georges Clémenceau,
91405 Orsay Cedex, France
- CNRS-UMR 8000
| | - Jean-Yves Salpin
- Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation
pour la Biologie et l’Environnement, Boulevard François
Mitterrand, 91025 Evry, France
- CNRS-UMR 8587
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20
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Lanucara F, Crestoni ME, Chiavarino B, Fornarini S, Hernandez O, Scuderi D, Maitre P. Infrared spectroscopy of nucleotides in the gas phase 2. The protonated cyclic 3′,5′-adenosine monophosphate. RSC Adv 2013. [DOI: 10.1039/c3ra41117f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Crestoni ME, Chiavarino B, Steinmetz V, Fornarini S. Communication: Vibrational study of a benzyl carbanion: Deprotonated 2,4-dinitrotoluene. J Chem Phys 2012; 137:181101. [DOI: 10.1063/1.4767393] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Wang DX, Fa SX, Liu Y, Hou BY, Wang MX. Anion-directed assembly of a rectangular supramolecular cage in the solid state with electron-deficient phenoxylated oxacalix[2]arene[2]triazine. Chem Commun (Camb) 2012; 48:11458-60. [DOI: 10.1039/c2cc36465d] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Kim DY, Geronimo I, Singh NJ, Lee HM, Kim KS. Anion Binding by Electron-Deficient Arenes Based on Complementary Geometry and Charge Distribution. J Chem Theory Comput 2011; 8:274-80. [DOI: 10.1021/ct200663x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dong Young Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Inacrist Geronimo
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - N. Jiten Singh
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Han Myoung Lee
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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24
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Raju RK, Bloom JWG, An Y, Wheeler SE. Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry. Chemphyschem 2011; 12:3116-30. [PMID: 21928437 DOI: 10.1002/cphc.201100542] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 02/01/2023]
Abstract
Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.
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Affiliation(s)
- Rajesh K Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
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25
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Chai Y, Jiang K, Sun C, Pan Y. Gas-Phase Nucleophilic Aromatic Substitution between Piperazine and Halobenzyl Cations: Reactivity of the Methylene Arenium Form of Benzyl Cations. Chemistry 2011; 17:10820-4. [DOI: 10.1002/chem.201101790] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Indexed: 11/10/2022]
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26
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Abstract
In the last decade, we have experienced massive progress in spectroscopic methods for mass-selected ions. The aim of this tutorial review is to present action spectroscopy as a powerful tool for the investigation of ionic reaction intermediates. Examples span from ultraviolet and infrared photodissociation spectroscopy of model reaction intermediates to applications of infrared multiphoton dissociation spectroscopy (IRMPD) to intermediates directly sampled from reaction mixtures. The first example of double resonance IR-UV spectroscopy of model intermediates in an organometallic reaction is also mentioned.
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Affiliation(s)
- Jana Roithová
- Charles University in Prague, Faculty of Science, Department of Organic and Nuclear Chemistry, Hlavova 2030, 128 43 Prague 2, Czech Republic.
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27
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Olson EJ, Xiong TT, Cramer CJ, Bühlmann P. Interaction of a Weakly Acidic Dinitroaromatic with Alkylamines: Avoiding the Meisenheimer Trap. J Am Chem Soc 2011; 133:12858-65. [DOI: 10.1021/ja205156r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric J. Olson
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Teng T. Xiong
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Philippe Bühlmann
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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28
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Garver JM, Yang Z, Kato S, Wren SW, Vogelhuber KM, Lineberger WC, Bierbaum VM. Gas phase reactions of 1,3,5-triazine: proton transfer, hydride transfer, and anionic σ-adduct formation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1260-1272. [PMID: 21953109 DOI: 10.1007/s13361-011-0133-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 05/31/2023]
Abstract
The gas phase reactivity of 1,3,5-triazine with several oxyanions and carbanions, as well as amide, was evaluated using a flowing afterglow-selected ion flow tube mass spectrometer. Isotopic labeling, H/D exchange, and collision induced dissociation experiments were conducted to facilitate the interpretation of structures and fragmentation processes. A multi-step (→ HCN + HC(2)N (2) (-) → CN(-) + 2 HCN) and/or single-step (→ CN(-) + 2 HCN) ring-opening collision-induced fragmentation process appears to exist for 1,3,5-triazinide. In addition to proton and hydride transfer reactions, the data indicate a competitive nucleophilic aromatic addition pathway (S(N)Ar) over a wide range of relative gas phase acidities to form strong anionic σ-adducts (Meisenheimer complexes). The significant hydride acceptor properties and stability of the anionic σ-adducts are rationalized by extremely electrophilic carbon centers and symmetric charge delocalization at the electron-withdrawing nitrogen positions. The types of anion-arene binding motifs and their influence on reaction pathways are discussed.
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Affiliation(s)
- John M Garver
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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29
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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30
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1172] [Impact Index Per Article: 90.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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31
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Lanucara F, Chiavarino B, Crestoni ME, Scuderi D, Sinha RK, Maı̂tre P, Fornarini S. Naked Five-Coordinate FeIII(NO) Porphyrin Complexes: Vibrational and Reactivity Features. Inorg Chem 2011; 50:4445-52. [DOI: 10.1021/ic200073v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Francesco Lanucara
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Debora Scuderi
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Rajeev K. Sinha
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Philippe Maı̂tre
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
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32
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Wheeler SE, Houk KN. Are anion/pi interactions actually a case of simple charge-dipole interactions? J Phys Chem A 2010; 114:8658-64. [PMID: 20433187 DOI: 10.1021/jp1010549] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Substituent effects in Cl(-)...C(6)H(6-n)X(n) complexes, models for anion/pi interactions, have been examined using density functional theory and robust ab initio methods paired with large basis sets. Predicted interaction energies for 83 model Cl(-)...C(6)H(6-n)X(n) complexes span almost 40 kcal mol(-1) and show an excellent correlation (r = 0.99) with computed electrostatic potentials. In contrast to prevailing models of anion/pi interactions, which rely on substituent-induced changes in the aryl pi-system, it is shown that substituent effects in these systems are due mostly to direct interactions between the anion and the substituents. Specifically, interaction energies for Cl(-)...C(6)H(6-n)X(n) complexes are recovered using a model system in which the substituents are isolated from the aromatic ring and pi-resonance effects are impossible. Additionally, accurate potential energy curves for Cl(-) interacting with prototypical anion-binding arenes can be qualitatively reproduced by adding a classical charge-dipole interaction to the Cl(-)...C(6)H(6) interaction potential. In substituted benzenes, binding of anions arises primarily from interactions of the anion with the local dipoles induced by the substituents, not changes in the interaction with the aromatic ring itself. When designing anion-binding motifs, phenyl rings should be viewed as a scaffold upon which appropriate substituents can be placed, because there are no attractive interactions between anions and the aryl pi-system of substituted benzenes.
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Affiliation(s)
- Steven E Wheeler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.
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33
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Bouchoux G, Winter JD, Flammang R, Gerbaux P. Aromatic Substitution Reactions between Ionized Benzene Derivatives and Neutral Methyl Isocyanide. J Phys Chem A 2010; 114:7408-16. [DOI: 10.1021/jp102794c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Guy Bouchoux
- Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Département de Chimie, Ecole Polytechnique, Palaiseau Cedex, France
| | - Julien De Winter
- Mass Spectrometry Research Group, CISMa, University of Mons-UMons, Place du Parc 20, B-7000 Mons, Belgium
| | - Robert Flammang
- Mass Spectrometry Research Group, CISMa, University of Mons-UMons, Place du Parc 20, B-7000 Mons, Belgium
| | - Pascal Gerbaux
- Mass Spectrometry Research Group, CISMa, University of Mons-UMons, Place du Parc 20, B-7000 Mons, Belgium
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34
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Mizuse K, Hasegawa H, Mikami N, Fujii A. Infrared and Electronic Spectroscopy of Benzene−Ammonia Cluster Radical Cations [C6H6(NH3)1,2]+: Observation of Isolated and Microsolvated σ-Complexes. J Phys Chem A 2010; 114:11060-9. [DOI: 10.1021/jp1009466] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kenta Mizuse
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hayato Hasegawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Naohiko Mikami
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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35
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Sinha RK, Maître P, Piccirillo S, Chiavarino B, Crestoni ME, Fornarini S. Cysteine radical cation: A distonic structure probed by gas phase IR spectroscopy. Phys Chem Chem Phys 2010; 12:9794-800. [DOI: 10.1039/c003576a] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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