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Bachir N, Kenouche S, Martínez-Araya JI. The effect of {O,N}=X⋯M={Ti,Zr,Hf} interactions on the sensitivity of CNO 2 trigger bonds in FOX-7: Approach based on the QTAIM/EDA-NOCV analysis. J Mol Graph Model 2024; 126:108645. [PMID: 37812869 DOI: 10.1016/j.jmgm.2023.108645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
The local chemical reactivity of FOX-7 (1,1-diamino-2,2-nitroethylene, also known as DADNE from DiAminoDiNitroEthylene) was elucidated through a quantitative study of the electrostatic potential on the molecular surface, topological analysis based on Bader's theory, and the EDA-NOCV method. Unlike (O2N)2CC(NH2)H2N⋯Cp2MCH3+ complexes, which exhibit both σ-donor and π-acceptor features, the situation is different concerning the (H2N)2CC(NO2)(O)NO⋯Cp2MCH3+ complexes, where both charge transfers correspond to the σ-donation. The two charge transfers reinforce each other, resulting in increased stability for (H2N)2CC(NO2)(O)NO⋯Cp2MCH3+. This seems to strengthen the (H2N)2CC(NO2)(O)NO⋯M={Ti,Zr,Hf} bond, which may explain the high stability of (H2N)2CC(NO2)(O)NO⋯Cp2MCH3+ compared to (O2N)2CC(NH2)-H2N⋯Cp2MCH3+. Results from topological analysis revealed that the decreased sensitivity to decomposition of CNO2 bonds depends on the chemical nature of the interacting metal, and the best achievements are obtained for the Hf-based complex. Our results demonstrate that the interaction of M={Ti,Zr,Hf} with CNO2 is more favourable than that with CNH2, this specific action on the trigger bond may support the use of Metallocene Methyl Cations (MMC) as possible neutralisers.
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Affiliation(s)
- Nassima Bachir
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory (LCA). University M. Khider of Biskra, 07000 Biskra, Algeria
| | - Samir Kenouche
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory (LCA). University M. Khider of Biskra, 07000 Biskra, Algeria
| | - Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Av. República 275, 8370146 Santiago, Chile; Centro de Química Teórica y Computacional (CQT&C). Facultad de Ciencias Exactas, Santiago, Chile.
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Bachir N, Kenouche S, Martínez-Araya JI. Theoretical investigation of the effect of O⋯M={Ti,Zr,Hf} interactions on the sensitivity of energetic N-nitro compounds. J Mol Graph Model 2022; 118:108341. [DOI: 10.1016/j.jmgm.2022.108341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
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3
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Lin X, Li X, Lu S, Wang F, Chen T, Yan J. Influence of organic and inorganic flocculants on the formation of PCDD/Fs during sewage sludge incineration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:14629-14636. [PMID: 25028327 DOI: 10.1007/s11356-014-3294-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 07/04/2014] [Indexed: 06/03/2023]
Abstract
Flocculants are widely used to improve the properties of sludge dewatering in industrial wastewater treatment. However, there have been no studies conducted on the influence of flocculants on the formation of polychlorinated dibenzo-p-dioxin and dibenzofurans (PCDD/Fs) during sewage sludge incineration. This paper selected three typical kinds of flocculants, including polyacrylamide (PAM), poly-ferric chloride (PFC), and polyaluminum chloride (PAC) flocculant, to study their influences on the formation of PCDD/Fs during sewage sludge incineration. The results indicated that PAM flocculant, which is an organic flocculant, inhibited the formation of PCDD/Fs in sewage sludge incineration, while inorganic flocculant, such as PFC and PAC flocculant, promoted the formation. The most probable explanation is that the amino content in the PAM flocculant acted as an inhibitor in the formation of PCDD/Fs, while the chlorine content, especially the metal catalyst in the PFC and PAC flocculants, increased the formation rate. The addition of flocculants nearly did not change the distribution of PCDD/F homologues. The PCDFs contributed the most toxic equivalent (TEQ) value, especially 2, 3, 4, 7, 8-PeCDF. Therefore, the use of inorganic flocculants in industrial wastewater treatment should be further assessed and possibly needs to be strictly regulated if the sludge is incinerated. From this aspect, a priority to the use of organic flocculants should be given.
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Affiliation(s)
- Xiaoqing Lin
- State Key Laboratory of Clean Energy Utilization, Institute for Thermal Power Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xiaodong Li
- State Key Laboratory of Clean Energy Utilization, Institute for Thermal Power Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Shengyong Lu
- State Key Laboratory of Clean Energy Utilization, Institute for Thermal Power Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Fei Wang
- State Key Laboratory of Clean Energy Utilization, Institute for Thermal Power Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Tong Chen
- State Key Laboratory of Clean Energy Utilization, Institute for Thermal Power Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jianhua Yan
- State Key Laboratory of Clean Energy Utilization, Institute for Thermal Power Engineering, Zhejiang University, Hangzhou, 310027, China
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WANG NANA, LI PING, HU YI, BU YUXIANG, WANG WEIHUA, XIE XIAOYAN. ASSOCIATION OF URACIL WITH Zn2+ AND THE HYDRATED Zn2+: A DFT INVESTIGATION. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633607002927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The association behaviors between Uracil and Zn 2+ in vacuum and in the presence of extra water molecules have been investigated systematically using the density functional theory (DFT). In these systems, the interaction of Zn 2+ with the carbonyl oxygen O 4 is systematically favored relative to O 2. For Uracil- Zn 2+ complexes, the more stable coordination mode among the possible complexes corresponds to the bidentate one, where the monodentate coordination mode is about 37 kcal/mol higher in energy relative to the bidentate case. Correspondingly, the stabilities of these structures are enhanced due to the formations of the four-membered chelate ring in the bidentate coordination processes. In the monodentate coordination complexes, the hydration effects are larger than those in the bidentate coordination complexes. The most basic center in the Uracil remains the same regardless of whether introducing the water molecules to Zn 2+ or not. The calculated Zn 2+ bonding energies in Uracil- Zn 2+( H 2 O ) complexes are reduced in comparison to those of the unhydrated Uracil- Zn 2+ complexes. Moreover, investigations of stepwise hydration of Zn 2+ in the most stable Uracil- Zn 2+ complex suggest that the successive hydration effect on the Zn 2+ site can enhance the strength of C = O bond in the Uracil- Zn 2+ complexes and reduce the association interaction of Uracil with Zn 2+. Additionally, the most acidic site of Uracil has been changed from N 1- to N 3– H group before and after introducing the Zn 2+ and there is a significant increase in the overall acidity of the system.
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Affiliation(s)
- NANA WANG
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
| | - PING LI
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
| | - YI HU
- High-performance Computational Center, Shandong University, Jinan, 250100, P. R. China
| | - YUXIANG BU
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
- Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China
| | - WEIHUA WANG
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
| | - XIAOYAN XIE
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
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Lu X, Wei S, Guo W, Wu CML. Mechanistic Insight into the Gas-Phase Reactions of Methylamine with Ground State Co+(3F) and Ni+(2D). J Phys Chem A 2010; 114:12490-7. [DOI: 10.1021/jp106397g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Xiaoqing Lu
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, People’s Republic of China, and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Shuxian Wei
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, People’s Republic of China, and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Wenyue Guo
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, People’s Republic of China, and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Chi-Man Lawrence Wu
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, People’s Republic of China, and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, People’s Republic of China
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Lamsabhi AM, Mó O, Yáñez M. Serine–Ca2+ versus serine–Cu2+ complexes — A theoretical perspective. CAN J CHEM 2010. [DOI: 10.1139/v10-038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The association of Ca2+ and Cu2+ to serine was investigated by means of B3LYP DFT calculations. The [serine–M]2+ (M = Ca, Cu) potential energy surfaces include, as does the neutral serine, a large number of conformers, in which a drastic reorganization of the electron density of the serine moiety is observed. This leads to significant changes in the number and strength of the intramolecular hydrogen bonds existing in the neutral serine tautomers. In some cases, a proton is transferred from the carboxylic OH group to the amino group and accordingly, some of the more stable [serine–M]2+ complexes can be viewed as the result of the interaction of the zwiterionic form of serine with the doubly charged metal ion. Whereas the interaction between Ca2+ and serine is essentially electrostatic, that between Cu2+ and serine has a non-negligible covalent character, reflected in larger electron densities at the bond critical points between the metal and the base, in the negative values of the electron density between the two interacting systems, and in much larger Cu2+ than Ca2+ binding energies. More importantly, the interaction with Cu2+ is followed by a partial oxidation of the base, which is not observed when the metal ion is Ca2+. The main consequence is that in Cu2+ complexes a significant acidity enhancement of the serine moiety takes place, which strongly favors the deprotonation of the [serine–Cu]2+ complexes. This is not the case for Ca2+ complexes. Thus, [serine–Ca]2+ complexes, like those formed by urea, thiourea, selenourea, or glycine, should be detected in the gas phase. Conversely, the complexes with Cu2+ should deprotonate spontaneously and therefore only [(serine–H)–Cu]+ monocations should be experimentally accessible.
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Affiliation(s)
- Al Mokhtar Lamsabhi
- Departamento de Química, C-9. Universidad Autónoma de Madrid. (Campus de Excelencia UAM-CSIC). Cantoblanco, 28049-Madrid, Spain
| | - Otilia Mó
- Departamento de Química, C-9. Universidad Autónoma de Madrid. (Campus de Excelencia UAM-CSIC). Cantoblanco, 28049-Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, C-9. Universidad Autónoma de Madrid. (Campus de Excelencia UAM-CSIC). Cantoblanco, 28049-Madrid, Spain
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7
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Safi ZS, Lamsabhi AM. A theoretical density functional study of association of Zn2+with oxazolidine and its thio derivatives in the gas phase. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Cheng W, Jiang H, Zhang D, Zhang C. A DFT study of the reactions of the Cu+ ion with methylamine and dimethylamine. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.10.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Wang P, Ohanessian G, Wesdemiotis C. Cu(II)-catalyzed reactions in ternary [Cu(AA)(AA - H)]+ complexes (AA = Gly, Ala, Val, Leu, Ile, t-Leu, Phe). EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:325-335. [PMID: 19423917 DOI: 10.1255/ejms.987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The unimolecular chemistry of [Cu(II)AA(AA - H)](+) complexes, composed of an intact and a deprotonated amino acid (AA) ligand, have been probed in the gas phase by tandem and multistage mass spectrometry in an electrospray ionization quadrupole ion trap mass spectrometer. The amino acids examined include Gly, Ala, Val, Leu, Ile, t-Leu and Phe. Upon collisionally-activated dissociation (CAD), the [Cu(II)AA(AA - H)](+) complexes undergo decarboxylation with simultaneous reduction of Cu(II) to Cu(I); during this process, a radical site is created at the alpha-carbon of the decarboxylated ligand (H(2)N(1) - (*)C(alpha)H - C(beta)H(2) - R; R = side chain substituent). The radical site is able to move along the backbone of the decarboxylated amino acid to form two new radicals (HN(1)(*) - C(alpha)H(2) - C(beta)H(2) - R and H(2)N(1) - C(alpha)H(2) - (*)C(beta)H - R). From the complexes of Gly and t-Leu, only C(alpha) and N(1) radicals can be formed. The whole radical ligand can be lost to form [Cu(I)AA](+) from these three isomeric radicals. Alternatively, further radical induced dissociations can take place along the backbone of the decarboxylated amino acid ligand to yield [Cu(II)AA(AA - 2H - CO(2))](+), [Cu(I)AA((*)NH(2))](+), [Cu(I)AA(HN = C(alpha)H(2))](+), or [Cu(I)AA(H(2)N - C(alpha)H = C(beta)H - R'](+) (R' = partial side chain substituent). The sodiated copper complexes, [Cu(II)(AA - H + Na)(AA - H)](+), show the same fragmentation patterns as their non-sodiated counterparts; sodium ion is retained on the intact amino acid ligand and is not involved in the CAD pathways. The amino groups of both AA units, the carbonyl group of the intact amino acid, and the deprotonated hydroxyl oxygen coordinate Cu(II) in square-planar fashion. Ab initio calculations indicate that the metal ion facilitates hydrogen atom shuttling between the N(1), C(alpha) and C(beta) atoms of the decarboxylated amino acid ligand. The dissociations of the decarboxylated radical ions unveil important insight about the so far largely unknown intrinsic chemistry of alpha-amino acid and peptide radicals, which are implicated as intermediates in numerous pathogenic biological processes.
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Affiliation(s)
- Ping Wang
- The Dow Chemical Company, 2301 N. Brazosport Blvd, B-1219 Freeport, TX 77541-3257, USA
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10
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Lu X, Guo W, Yang T, Zhao L, Du S, Wang L, Shan H. Gas-Phase Reactions of Co+ with Ethylamine: A Theoretical Approach to the Reaction Mechanisms of Transition Metal Ions with Primary Amines. J Phys Chem A 2008; 112:5312-21. [DOI: 10.1021/jp801653t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xiaoqing Lu
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, PR China
- College of Chemistry and Chemical Engineering, China University of Petroleum, Dongying, Shandong 257061, PR China
| | - Wenyue Guo
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, PR China
- College of Chemistry and Chemical Engineering, China University of Petroleum, Dongying, Shandong 257061, PR China
| | - Tianfang Yang
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, PR China
- College of Chemistry and Chemical Engineering, China University of Petroleum, Dongying, Shandong 257061, PR China
| | - Lianming Zhao
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, PR China
- College of Chemistry and Chemical Engineering, China University of Petroleum, Dongying, Shandong 257061, PR China
| | - Senchang Du
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, PR China
- College of Chemistry and Chemical Engineering, China University of Petroleum, Dongying, Shandong 257061, PR China
| | - Ling Wang
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, PR China
- College of Chemistry and Chemical Engineering, China University of Petroleum, Dongying, Shandong 257061, PR China
| | - Honghong Shan
- College of Physics Science and Technology, China University of Petroleum, Dongying, Shandong 257061, PR China
- College of Chemistry and Chemical Engineering, China University of Petroleum, Dongying, Shandong 257061, PR China
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11
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Wang W, Wang N, Li P, Bu Y, Xie X, Song R. Theoretical studies on the properties of uracil and its dimer upon thioketo substitution. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0442-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Pavelka M, Shukla MK, Leszczynski J, Burda JV. Theoretical Study of Hydrated Copper(II) Interactions with Guanine: A Computational Density Functional Theory Study. J Phys Chem A 2008; 112:256-67. [DOI: 10.1021/jp074891+] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Mó O, Yáñez M, Salpin JY, Tortajada J. Thermochemistry, bonding, and reactivity of Ni+ and Ni2+ in the gas phase. MASS SPECTROMETRY REVIEWS 2007; 26:474-516. [PMID: 17492664 DOI: 10.1002/mas.20134] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In this review, we present a general overview on the studies carried out on Ni(+-)- and Ni(2+)-containing systems in the gas phase since 1996. We have focused our attention in the determination of binding energies in parallel with an analysis of the structure and bonding of the complexes formed by the interaction of Ni(+) with one ligand, or in clusters where this metal ion binds several identical or different ligands. Solvation of Ni(2+) by different ligands is also discussed, together with the theoretical information available of doubly charged Ni-containing species. The final section of this review is devoted to an analysis of the gas-phase uni- and bimolecular reactivity of Ni(+) and Ni(2+) complexes.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
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Turecek F. Copper-biomolecule complexes in the gas phase. The ternary way. MASS SPECTROMETRY REVIEWS 2007; 26:563-82. [PMID: 17474124 DOI: 10.1002/mas.20137] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This review deals with copper complexes of a variety of organic and bioorganic molecules that have been produced as gas-phase ions by electrospray and other ionization methods and studied experimentally by mass spectrometry and theoretically by ab initio and density functional theory computations. Ternary complexes of Cu((II)) allow one to modify the oxidation state and coordination sphere of the copper ion and thus induce novel fragmentations that involve redox and radical-based reactions. Structure elucidation, distinction, and quantitation of leucine and isoleucine isomers in peptides, distinction of enantiomers in chiral compounds, and sensitive detection of antibiotics are some of the highlights of mass spectrometry of ternary copper complexes. Binary copper complexes are mainly represented by Cu((I)) species in which the copper ion displays the properties of a weak Lewis acid.
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Affiliation(s)
- Frantisek Turecek
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA 98195-1700, USA.
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15
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Safi Z, Lamsabhi AM. Gas-phase reactivity of 2,7-dimethyl-[1,2,4]-triazepine thio derivatives toward Cu+ cation: a DFT study. J Phys Chem A 2007; 111:2213-9. [PMID: 17388292 DOI: 10.1021/jp068642h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gas-phase interactions of 2,7-dimethyl-[1,2,4]-triazepine and its thio derivatives with Cu+ were studied through the use of high-level density functional theory (DFT) calculations. The structure of all possible tautomers and their conformers was optimized at the B3LYP/6-31G(d) level of theory. Final energies were obtained at the B3LYP/6-311+G(2df,2p) level. It has been found that the direct association of Cu+ occurs at the oxygen atom attached to position 3 in the case of the dioxo derivative and at the sulfur atom in all other cases. For the dithio derivatives, the global minimum of the PES corresponds to the structure in which the metal ion bridges between the heteroatom at position 3 and the nitrogen atom at position 4 of the corresponding enolic tautomer, forming a four-membered ring structure; for the dioxo derivative, this conformer competes with the ketone tautomer. Moreover, the isomerization processes leading from the most stable adduct to the other stable conformers were investigated. Among all the considered compounds, the 3,5-dithiotriazepines-Cu+ is found to be the one that associates Cu+ more tightly in the gas phase. The calculated Cu+ binding energies show a good correlation with the experimental proton affinities.
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Affiliation(s)
- Zaki Safi
- Department of Chemistry, Faculty of Science, Al-Azhar University of Gaza, Gaza, Palestine
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16
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Luna A, Mó O, Yáñez M, Gal JF, Maria PC, Guillemin JC. Gas-Phase Protonation and Deprotonation of Acrylonitrile Derivatives NCCHCHX (X=CH3, NH2, PH2, SiH3). Chemistry 2006; 12:9254-61. [PMID: 16991171 DOI: 10.1002/chem.200600154] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A combined experimental and theoretical study on the gas-phase basicity and acidity of a series of cyanovinyl derivatives is presented. The gas-phase basicities and acidities of (N[triple chemical bond]C--CH==CH--X, X=CH(3), NH(2)) were obtained by means of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry techniques. The corresponding calculated values were obtained at the G3B3 level of theory. The effects of exchanging CH(3) for SiH(3), and NH(2) for PH(2), were analyzed at the same level of theory. For the neutral molecules, the Z isomer is always the dominant species under standard gas-phase conditions at 298 K. The loss of the proton from the substituent X was found systematically to be much more favorable than deprotonation of the HC==CH linking group. The corresponding isomeric E ion is much more stable than the Z ion, so that only the former should be found in the gas phase. The most significant structural changes upon deprotonation occur for the methyl and amino derivatives because, in both cases, deprotonation of X leads to a significant charge delocalization in the corresponding anion. Protonation takes place systematically at the cyano group, whereby the isomeric E ion is again more stable than the Z ion. Push-pull effects explain the preference of aminoacrylonitrile to be protonated at the cyano group, which also explains the high basicity of this derivative relative to other members of the analyzed series that present rather similar gas-phase basicities, GB approximately 780 kJ mol(-1), indicating that the different nature of the substituents has only a weak effect on the intrinsic basicity of the cyano group. The cyanovinyl derivatives have a significantly stronger gas-phase acidity than that of the corresponding vinyl compounds CH(2)==CH--X. This acidity-strengthening effect of the cyano group is attributed to the greater stabilization of the anion with respect to the corresponding neutral compound.
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Affiliation(s)
- Alberto Luna
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
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Operti L, Rabezzana R. Gas-phase ion chemistry in organometallic systems. MASS SPECTROMETRY REVIEWS 2006; 25:483-513. [PMID: 16365877 DOI: 10.1002/mas.20075] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This review essentially deals with positive ion/molecule reactions occurring in gas-phase organometallic systems, and encompasses a period of time of approximately 7 years, going from 1997 to early 2004. Following the example of the excellent review by Eller & Schwarz (1991; Chem Rev 91:1121-1177), in the first part, results of reaction of naked ions are presented by grouping them according to the neutral substrate, while in the second part, ligated ions are grouped according to the different ligands. Whenever possible, comparison among similar studies is attempted, and general trends of reactivities are evidenced.
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Affiliation(s)
- Lorenza Operti
- Dipartimento di Chimica Generale ed Organica Applicata and NIS Centre of Excellence, Università degli Studi di Torino, Corso M. d'Azeglio 48, 10125 Torino, Italy
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18
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Lamsabhi AM, Alcamí M, Mó O, Yáñez M, Tortajada J. Gas-Phase Deprotonation of Uracil−Cu2+ and Thiouracil−Cu2+ Complexes. J Phys Chem A 2006; 110:1943-50. [PMID: 16451028 DOI: 10.1021/jp055163u] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The deprotonation of Cu2+ complexes with uracil, 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil has been investigated by means of B3LYP/ 6-311+G(2df,2p)//6-31G(d) calculations. The most stable [(uracil-H)Cu]+ and [(thiouracil-H)Cu]+ complexes correspond to bidentate structures in which Cu interacts with the deprotonated ring-nitrogen atom and with the oxygen or the sulfur atom of the adjacent carbonyl or thiocarbonyl group. For 2- and 4-thiouracil derivatives, the structures in which the metal cation interacts with the thiocarbonyl group are clearly favored with respect to those in which Cu interacts with the carbonyl group. This is at variance with what was found to be the most stable structure of the corresponding Cu2+ complexes, where association to the carbonyl oxygen was always preferred over the association to the thiocarbonyl group. The [(uracil-H)Cu]+ and [(thiouracil-H)Cu]+ complexes can be viewed as the result of Cu+ attachment to the uracil-H and thiouracil-H radicals formed by the deprotonation of the corresponding uracil+* and thiouracil+* radical cations. As a matter of fact their relative stability is dictated by the intrinsic stability of the corresponding uracil-H and thiouracil-H radical and by the fact that, in general, the N3-deprotonated site is a better electron donor than the N1. In all complexes, the bonding of Cu both to nitrogen and sulfur and to nitrogen and oxygen has a significantly large covalent character.
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Affiliation(s)
- Al Mokhtar Lamsabhi
- Departamento de Química C-9, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
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García R, Seco JM, Vázquez SA, Quiñoá E, Riguera R. Role of Barium(II) in the Determination of the Absolute Configuration of Chiral Amines by 1H NMR Spectroscopy. J Org Chem 2006; 71:1119-30. [PMID: 16438530 DOI: 10.1021/jo0522207] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assignment of the absolute configuration of alpha-chiral primary amines by complexation of their MPA derivatives with Ba2+ and NMR analysis of the changes generated is presented. All that is required is (a) the derivatization of the amine of unknown configuration with one enantiomer of the auxiliary reagent (MPA), either (R) or (S)-alpha-methoxyphenylacetic acid, (b) the recording of the 1H NMR spectrum of the resulting amide in MeCN-d3, (c) the addition of Ba(ClO4)2 to the NMR tube, and (d) the recording of a second spectrum after a few minutes of shaking. The above steps take a few minutes and are followed by an analysis of the shifts (measured as Deltadelta(Ba)) produced on the L1 and L2 substituents of the amine by the addition of Ba2+ and their comparison with those expected from the conformational changes produced by the complexation. The conformational changes initiated by complexation have been subjected to NMR and CD studies, which showed that the formation of the complex shifts the equilibrium from an antiperiplanar (AP) to a synperiplanar (SP) form, leading to an increase of the shielding by the phenyl group of MPA of the substituent of the amine located on the same side. In addition, theoretical calculations [density functional theory (DFT)] provide further support for the formation, structure, and stability of the complexes. The general applicability of this method and the trustworthiness of the resulting configurational assignment were guaranteed with a series of amines of known absolute configuration and varied structures, used as test compounds. The method proposed is simple, fast, and inexpensive, and it requires a very small amount of sample, only one derivatization, and the recording of just two 1H NMR spectra at room temperature. A graphical guide to simplify the application of this method is included.
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Affiliation(s)
- Rosa García
- Departamento de Química Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
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Lamsabhi AM, Alcamí M, Mó O, Yáñez M, Tortajada J. Association of Cu2+with Uracil and Its Thio Derivatives: A Theoretical Study. Chemphyschem 2004; 5:1871-8. [PMID: 15648135 DOI: 10.1002/cphc.200400208] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The structures and relative stabilities of the complexes between Cu2+ and uracil, 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil were investigated by B3LYP/6-311+G(2df,2p)//B3LYP/6-31G* DFT calculations. In those systems in which both types of basic centers, that is, a carbonyl and a thiocarbonyl group, are present, association of Cu2+ with the oxygen atom is systematically favored, in contrast to what was found for the corresponding Cu+ complexes. This can be understood by considering that association of Cu2+ is immediately followed by oxidation of the base, which accumulates the negative charge at the oxygen atoms. Similarly, for 2,4-dithiouracil the most basic site for Cu+ attachment is the sulfur atom at the 4-position, while for association of Cu2+ it is sulfur at the 2-position. In contrast, differences between uracil-Cu+ and uracil-Cu2+ complexes are very small, and in both cases the oxygen atom at the 4-position is the most basic. Cu2+ binding energies are about 4 and 1.2 times larger than Cu+ binding energies and proton affinities, respectively. Uracil- and thiouracil-Cu2+ complexes are thermodynamically unstable but kinetically stable with respect to their dissociation into uracil*+ + Cu+ or thiouracil*+ + Cu+. The Cu2+ binding energies vary with the difference between the second ionization potential of the metal and the first ionization potential of the base. regardless of the reference acid (H+, Cu+, Cu2+) the basicity trend is 2,4-dithiouracil > 4-thiouracil > 2-thiouracil > uracil.
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Affiliation(s)
- Al Mokhtar Lamsabhi
- Departamento de Química C-9, Facultad de Ciencias Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid, Spain
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Hoppilliard Y, Ohanessian G, Bourcier S. Fragmentation Mechanisms of Glycine-Cu+in the Gas Phase. An Experimental and Theoretical Study†. J Phys Chem A 2004. [DOI: 10.1021/jp047905+] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Corral I, Mó O, Yáñez M, Salpin JY, Tortajada J, Radom L. Gas-Phase Reactions between Urea and Ca2+: The Importance of Coulomb Explosions. J Phys Chem A 2004. [DOI: 10.1021/jp046624z] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Inés Corral
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, Laboratoire Analyse et Environnement, UMR CNRS 8587, Université d’Evry Val d'Essonne, Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY CEDEX, France, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Otilia Mó
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, Laboratoire Analyse et Environnement, UMR CNRS 8587, Université d’Evry Val d'Essonne, Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY CEDEX, France, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Manuel Yáñez
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, Laboratoire Analyse et Environnement, UMR CNRS 8587, Université d’Evry Val d'Essonne, Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY CEDEX, France, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Jean-Yves Salpin
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, Laboratoire Analyse et Environnement, UMR CNRS 8587, Université d’Evry Val d'Essonne, Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY CEDEX, France, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Jeanine Tortajada
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, Laboratoire Analyse et Environnement, UMR CNRS 8587, Université d’Evry Val d'Essonne, Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY CEDEX, France, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Leo Radom
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, Laboratoire Analyse et Environnement, UMR CNRS 8587, Université d’Evry Val d'Essonne, Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY CEDEX, France, School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia, and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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Rodríguez-Santiago L, Noguera M, Sodupe M, Salpin JY, Tortajada J. Gas Phase Reactivity of Ni+ with Urea. Mass Spectrometry and Theoretical Studies. J Phys Chem A 2003. [DOI: 10.1021/jp036216f] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Rodríguez-Santiago
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, and Laboratoire Analyze et Environnement. CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Boulevard François Mitterrand 91025 Evry Cedex, France
| | - M. Noguera
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, and Laboratoire Analyze et Environnement. CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Boulevard François Mitterrand 91025 Evry Cedex, France
| | - M. Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, and Laboratoire Analyze et Environnement. CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Boulevard François Mitterrand 91025 Evry Cedex, France
| | - J. Y. Salpin
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, and Laboratoire Analyze et Environnement. CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Boulevard François Mitterrand 91025 Evry Cedex, France
| | - J. Tortajada
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, and Laboratoire Analyze et Environnement. CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Boulevard François Mitterrand 91025 Evry Cedex, France
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24
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Corral I, Mó O, Yáñez M. The importance of agostic-type interactions for the binding energies of Ni+to saturated and α,β-unsaturated alkanes, silanes and germanes. NEW J CHEM 2003. [DOI: 10.1039/b305532a] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Boutreau L, Léon E, Rodríguez-Santiago L, Toulhoat P, Mó O, Tortajada J. Gas-Phase Reactivity of Cu+and Ag+with Glycerol: an Experimental and Theoretical Study. J Phys Chem A 2002. [DOI: 10.1021/jp020092+] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Cheng MJ, Hu CH, Yeh CS. Reactions of 2-Propanol with Cu+ in the Gas Phase: A Density Functional Theory Study. J Phys Chem A 2002. [DOI: 10.1021/jp0211335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mu-Jeng Cheng
- Department of Chemistry, National Changhua University of Education, Changhua 500, Taiwan
| | - Ching-Han Hu
- Department of Chemistry, National Changhua University of Education, Changhua 500, Taiwan
| | - Chen-Sheng Yeh
- Department of Chemistry, National Chen Kung University, Tainan 701, Taiwan
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Boutreau L, Toulhoat P, Tortajada J, Luna A, Mó O, Yáñez M. Reactions between Glycolic Acid and Cu+ in the Gas Phase. An Experimental and Theoretical Study. J Phys Chem A 2002. [DOI: 10.1021/jp026378w] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Galiano L, Alcamí M, Mó O, Yáñez M. Gas-Phase Chemistry of Ethyl and Vinyl Amines, Phosphines, and Arsines: A DFT Study of the Structure and Stability of Their Cu+ Complexes. J Phys Chem A 2002. [DOI: 10.1021/jp026386c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- L. Galiano
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco 28049, Madrid, Spain
| | - M. Alcamí
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco 28049, Madrid, Spain
| | - O. Mó
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco 28049, Madrid, Spain
| | - M. Yáñez
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco 28049, Madrid, Spain
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29
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García R, Seco JM, Vázquez SA, Quiñoá E, Riguera R. Absolute configuration of secondary alcohols by 1H NMR: in situ complexation of alpha-methoxyphenylacetic acid esters with barium(II). J Org Chem 2002; 67:4579-89. [PMID: 12076161 DOI: 10.1021/jo0256989] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel methodology that allows the assignment of the absolute configuration of chiral secondary alcohols by NMR using only one derivative is presented. All that is needed is (a) the derivatization of the alcohol of unknown configuration with one enantiomer--either the (R)- or the (S)--of alpha-methoxyphenylacetic acid (MPA), (b) the recording of the 1H NMR spectrum of the resulting ester in MeCN-d3, and (c) addition of a barium(II) salt [i.e. Ba(ClO4)2] to the NMR tube till saturation and recording of a second spectrum. The assignment of the R/S configuration to the alcohol takes a few minutes and consists on the comparison of the signs of the shifts (Deltadelta(Ba)) produced by addition of the barium(II) with those predicted for the (R) and the (S) enantiomers in accordance to a simplified model that reflects the conformational changes produced by the complexation with barium and their consequences in the chemical shifts. These conformational changes are based on experimental NMR and CD results showing that the formation of a barium(II) complex with the MPA ester moves the conformational equilibrium between syn- (sp) and anti-periplanar (ap) forms toward the most stable ones (sp), and that this leads to the increase of the shielding caused by the MPA phenyl group on a certain substituent of the alcohol. In addition, ab initio Hartree-Fock (HF) and density functional theory (DFT) calculations provide further evidence on the formation, structure, and stability of the complexes with Ba2+, Mg2+, and the influence of the solvent. The general applicability of this methodology and the reliability of the configurational assignment were assured by the study of about twenty alcohols of known configuration and diverse structural features. Its scope and limitations have also being established and other representative cations (i.e. Li+, Rb+, Cs+, Mg2+, Ca2+, Sc3+, V3+, Zn2+) were also evaluated. The procedure proposed is simple, fast, and cheap because it requires a very small amount of sample, only one derivatization, and the recording of only two 1H NMR spectra at rt. A graphical guide to facilitate the application of this new method is included at the end of the paper.
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Affiliation(s)
- Rosa García
- Departamento de Química Orgánica, Facultad de Química and Instituto de Acuicultura, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
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Alcamí M, Luna A, Mó O, Yáñez M, Boutreau L, Tortajada J. Experimental and Theoretical Investigation of the Reactions between Glucose and Cu+ in the Gas Phase. J Phys Chem A 2002. [DOI: 10.1021/jp0131471] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Alcamí
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, and Laboratoire Analyze et Environnement, UMR CNRS 8587, Université d'Evry Val d'Essonne Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY Cedex, France
| | - Alberto Luna
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, and Laboratoire Analyze et Environnement, UMR CNRS 8587, Université d'Evry Val d'Essonne Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY Cedex, France
| | - Otilia Mó
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, and Laboratoire Analyze et Environnement, UMR CNRS 8587, Université d'Evry Val d'Essonne Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY Cedex, France
| | - M. Yáñez
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, and Laboratoire Analyze et Environnement, UMR CNRS 8587, Université d'Evry Val d'Essonne Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY Cedex, France
| | - Laurence Boutreau
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, and Laboratoire Analyze et Environnement, UMR CNRS 8587, Université d'Evry Val d'Essonne Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY Cedex, France
| | - Jeanine Tortajada
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, and Laboratoire Analyze et Environnement, UMR CNRS 8587, Université d'Evry Val d'Essonne Institut des Sciences, Boulevard François Mitterrand, 91025 EVRY Cedex, France
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Pantazis DA, Tsipis AC, Tsipis CA. Ab Initio Quantum Chemical Study of the Coordination Preferences and Catalytic Role of Cu+ Ions in the Dehydration Reactions of Hydroxyformaldoxime Conformers and the Oxidation of HCN to Hydroxyformaldoxime by Hydrogen Peroxide. J Phys Chem A 2002. [DOI: 10.1021/jp013700e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dimitrios A. Pantazis
- Laboratory of Applied Quantum Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 540 06 Thessaloniki, Greece
| | - Athanassios C. Tsipis
- Laboratory of Applied Quantum Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 540 06 Thessaloniki, Greece
| | - Constantinos A. Tsipis
- Laboratory of Applied Quantum Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 540 06 Thessaloniki, Greece
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Alcamí M, Mó O, Yáñez M. Computational chemistry: a useful (sometimes mandatory) tool in mass spectrometry studies. MASS SPECTROMETRY REVIEWS 2001; 20:195-245. [PMID: 11835306 DOI: 10.1002/mas.10005] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this review, we present a brief summary of the theoretical methods most frequently used in gas-phase ion chemistry. In subsequent sections, the performance of these methods is analyzed, paying attention to the reliability of geometries, vibrational frequencies, energies, and entropies. The possible pathologies of the different methods, in the form of instabilities of the wave function or spin contamination problems, are discussed. Several examples are presented to illustrate the usefulness of ab initio or density functional theory (DFT) methods to predict the existence of elusive molecules and/or to characterize non-conventional structures, and to rationalize the charge redistributions normally associated with ion-molecule interactions and which result in bond-weakening or bond-reinforcement effects. Finally, the role of non-classical structures in ion-molecule interactions is also illustrated with different examples.
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Affiliation(s)
- M Alcamí
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
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Rodriguez-Santiago L, Sodupe M, Tortajada J. Gas-Phase Reactivity of Ni+ with Glycine. J Phys Chem A 2001. [DOI: 10.1021/jp004461i] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Rodriguez-Santiago
- Laboratoire Analyse et Environnement, CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Boulevard Françoise Mitterrand 91025 Evry Cedex, and Departament de Quimica, Universitat Autonoma de Barcelona, Bellaterra 08193 Barcelona
| | - M. Sodupe
- Laboratoire Analyse et Environnement, CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Boulevard Françoise Mitterrand 91025 Evry Cedex, and Departament de Quimica, Universitat Autonoma de Barcelona, Bellaterra 08193 Barcelona
| | - J. Tortajada
- Laboratoire Analyse et Environnement, CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Boulevard Françoise Mitterrand 91025 Evry Cedex, and Departament de Quimica, Universitat Autonoma de Barcelona, Bellaterra 08193 Barcelona
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Nakao Y, Hirao K, Taketsugu T. Theoretical study of the water activation by a cobalt cation: Ab initio multireference theory versus density functional theory. J Chem Phys 2001. [DOI: 10.1063/1.1336568] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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36
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Shields SJ, Bluhm BK, Russell DH. Fragmentation chemistry of [M + Cu]+ peptide ions containing an N-terminal arginine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2000; 11:626-638. [PMID: 10883818 DOI: 10.1016/s1044-0305(00)00128-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
[M + Cu]+ peptide ions formed by matrix-assisted laser desorption/ionization from direct desorption off a copper sample stage have sufficient internal energy to undergo metastable ion dissociation in a time-of-flight mass spectrometer. On the basis of fragmentation chemistry of peptides containing an N-terminal arginine, we propose the primary Cu+ ion binding site is the N-terminal arginine with Cu+ binding to the guanidine group of arginine and the N-terminal amine. The principal decay products of [M + Cu]+ peptide ions containing an N-terminal arginine are [a(n) + Cu - H]+ and [b(n) + Cu - H]+ fragments. We show evidence to suggest that [a(n) + Cu - H]+ fragment ions are formed by elimination of CO from [b(n) + Cu - H]+ ions and by direct backbone cleavage. We conclude that Cu+ ionizes the peptide by attaching to the N-terminal arginine residue; however, fragmentation occurs remote from the Cu+ ion attachment site involving metal ion promoted deprotonation to generate a new site of protonation. That is, the fragmentation reactions of [M + Cu]+ ions can be described in terms of a "mobile proton" model. Furthermore, proline residues that are adjacent to the N-terminal arginine do not inhibit formation of [b(n) + Cu - H]+ ion, whereas proline residues that are distant to the charge carrying arginine inhibit formation of [b(n) + Cu - H]+ ions. An unusual fragment ion, [c(n) + Cu + H]+, is also observed for peptides containing lysine, glutamine, or asparagine in close proximity to the Cu+ carrying N-terminal arginine. Mechanisms for formation of this fragment ion are also proposed.
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Affiliation(s)
- S J Shields
- Department of Chemistry, Texas A&M University, College Station 77842, USA
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Luna A, Amekraz B, Morizur JP, Tortajada J, Mó O, Yáñez M. Reactions of Urea with Cu+ in the Gas Phase: An Experimental and Theoretical Study. J Phys Chem A 2000. [DOI: 10.1021/jp9934634] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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38
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Luna A, Gevrey S, Tortajada J. Modeling the Interaction of the Phosphate Group in Nucleotides with Copper(I) in the Gas Phase: Reactivity of Cu+ with Orthophosphoric Acid and Its Monomethyl Ester. J Phys Chem B 1999. [DOI: 10.1021/jp991050x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Luna
- Laboratoire de Chimie Organique Structurale, Universite Pierre et Marie Curie, CNRS UMR 8587, 4 Place Jussieu, Boîte 45, 75252 Paris Cedex 05, France
| | - S. Gevrey
- Laboratoire de Chimie Organique Structurale, Universite Pierre et Marie Curie, CNRS UMR 8587, 4 Place Jussieu, Boîte 45, 75252 Paris Cedex 05, France
| | - J. Tortajada
- Laboratoire de Chimie Organique Structurale, Universite Pierre et Marie Curie, CNRS UMR 8587, 4 Place Jussieu, Boîte 45, 75252 Paris Cedex 05, France
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Nakao Y, Taketsugu T, Hirao K. Theoretical study of ammonia activation by M+ (M=Sc, Ni, Cu). J Chem Phys 1999. [DOI: 10.1063/1.479027] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Wu J, Wesdemiotis C. Cu(NH3)1–2 complexes: formation and characterization in the gas phase by neutralization–reionization mass spectrometry. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)00204-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bertrán J, Rodríguez-Santiago L, Sodupe M. The Different Nature of Bonding in Cu+-Glycine and Cu2+-Glycine. J Phys Chem B 1999. [DOI: 10.1021/jp984534m] [Citation(s) in RCA: 184] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Bertrán
- Departament de Química, Unitat de Química Física, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - L. Rodríguez-Santiago
- Departament de Química, Unitat de Química Física, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - M. Sodupe
- Departament de Química, Unitat de Química Física, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Satterfield M, Brodbelt JS. Sites of reaction of pilocarpine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1999; 10:209-216. [PMID: 10069045 DOI: 10.1016/s1044-0305(98)00141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Analysis of the sites of reaction of a biologically important compound, pilocarpine, a molecule with imidazole and butyrolactone rings connected by a methylene bridge, has been accomplished in a quadrupole ion trap with the aim of characterizing its structure/reactivity relationships. Ion-molecule reactions of pilocarpine with chemical ionizing agents, dimethyl ether (DME), 2-methoxyethanol, and trimethyl borate (TMB), along with collision-activated dissociation elucidated the reaction sites of pilocarpine and made possible the comparison of structural features that affect sites of reaction. Based on MS/MS experiments, methylation occurs on the imidazole ring upon reactions with CH3OCH2+ or (CH3OCH2CH2OH)H+ ions but methylation occurs on the lactone ring for reactions with (CH3O)2B+ ions. Bracketing experiments with two model compounds, alpha-methyl-gamma-butyrolactone and N-methyl imidazole, show the imidazole ring to have a greater gas-phase basicity and methyl cation affinity than the lactone ring. The contrast of methylation by TMB ions on the lactone ring is explained by initial addition of the dimethoxyborinium ion, (CH3O)2B+, on the imidazole ring with subsequent collisional activation promoting an intramolecular transfer of a methyl group to the lactone ring with concurrent loss of CH3OBO. Semiempirical molecular orbital calculations are undertaken to further address the favored reaction sites.
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Affiliation(s)
- M Satterfield
- Department of Chemistry and Biochemistry, University of Texas at Austin 78712, USA
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MANUEL MERCEDES, MÓ OTILIA, YÁÑEZ MANUEL. The reactions of Cl + ( 3P) and Cl + ( 1D) with hydrogen sulphide. A G2 molecular orbital study. Mol Phys 1999. [DOI: 10.1080/00268979909482955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- MERCEDES MANUEL
- a Departamento de Química, C-9 , Universidad Autónoma de Madrid , Cantoblanco, 28049 , Madrid , Spain
| | - OTILIA MÓ
- a Departamento de Química, C-9 , Universidad Autónoma de Madrid , Cantoblanco, 28049 , Madrid , Spain
| | - MANUEL YÁÑEZ
- a Departamento de Química, C-9 , Universidad Autónoma de Madrid , Cantoblanco, 28049 , Madrid , Spain
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Alcamí M, Mó O, Yáñez M, Luna A, Morizur JP, Tortajada J. Exploring the Potential Energy Surface of the Association of Cu+ to Oxaziridine, Nitrosomethane, and Formaldoxime. J Phys Chem A 1998. [DOI: 10.1021/jp982796i] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Luna A, Amekraz B, Tortajada J, Morizur JP, Alcamí M, Mó O, Yáñez M. Modeling the Interactions between Peptide Functions and Cu(I): Formamide−Cu+ Reactions in the Gas Phase. J Am Chem Soc 1998. [DOI: 10.1021/ja971623o] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Luna
- Contribution from the Laboratoire de Chimie Organique Structurale, Université Pierre et Marie Curie, CNRS UMR 172, Boite 45, 4 Place Jussieu, F-75252 Paris Cedex 05, and Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
| | - B. Amekraz
- Contribution from the Laboratoire de Chimie Organique Structurale, Université Pierre et Marie Curie, CNRS UMR 172, Boite 45, 4 Place Jussieu, F-75252 Paris Cedex 05, and Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
| | - J. Tortajada
- Contribution from the Laboratoire de Chimie Organique Structurale, Université Pierre et Marie Curie, CNRS UMR 172, Boite 45, 4 Place Jussieu, F-75252 Paris Cedex 05, and Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
| | - J. P. Morizur
- Contribution from the Laboratoire de Chimie Organique Structurale, Université Pierre et Marie Curie, CNRS UMR 172, Boite 45, 4 Place Jussieu, F-75252 Paris Cedex 05, and Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
| | - M. Alcamí
- Contribution from the Laboratoire de Chimie Organique Structurale, Université Pierre et Marie Curie, CNRS UMR 172, Boite 45, 4 Place Jussieu, F-75252 Paris Cedex 05, and Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
| | - O. Mó
- Contribution from the Laboratoire de Chimie Organique Structurale, Université Pierre et Marie Curie, CNRS UMR 172, Boite 45, 4 Place Jussieu, F-75252 Paris Cedex 05, and Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
| | - M. Yáñez
- Contribution from the Laboratoire de Chimie Organique Structurale, Université Pierre et Marie Curie, CNRS UMR 172, Boite 45, 4 Place Jussieu, F-75252 Paris Cedex 05, and Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain
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Luna A, Morizur JP, Tortajada J, Alcamí M, Mó O, Yáñez M. Role of Cu+ Association on the Formamide → Formamidic Acid → (Aminohydroxy)carbene Isomerizations in the Gas Phase. J Phys Chem A 1998. [DOI: 10.1021/jp980629c] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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