1
|
Raczyńska ED, Gal JF, Maria PC. Strong Bases and beyond: The Prominent Contribution of Neutral Push-Pull Organic Molecules towards Superbases in the Gas Phase. Int J Mol Sci 2024; 25:5591. [PMID: 38891779 PMCID: PMC11172071 DOI: 10.3390/ijms25115591] [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: 04/24/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In this review, the principles of gas-phase proton basicity measurements and theoretical calculations are recalled as a reminder of how the basicity PA/GB scale, based on Brønsted-Lowry theory, was constructed in the gas-phase (PA-proton affinity and/or GB-gas-phase basicity in the enthalpy and Gibbs energy scale, respectively). The origins of exceptionally strong gas-phase basicity of some organic nitrogen bases containing N-sp3 (amines), N-sp2 (imines, amidines, guanidines, polyguanides, phosphazenes), and N-sp (nitriles) are rationalized. In particular, the role of push-pull nitrogen bases in the development of the gas-phase basicity in the superbasicity region is emphasized. Some reasons for the difficulties in measurements for poly-functional nitrogen bases are highlighted. Various structural phenomena being in relation with gas-phase acid-base equilibria that should be considered in quantum-chemical calculations of PA/GB parameters are discussed. The preparation methods for strong organic push-pull bases containing a N-sp2 site of protonation are briefly reviewed. Finally, recent trends in research on neutral organic superbases, leaning toward catalytic and other remarkable applications, are underlined.
Collapse
Affiliation(s)
- Ewa Daniela Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, Parc Valrose, 06108 Nice, France;
| | - Pierre-Charles Maria
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, Parc Valrose, 06108 Nice, France;
| |
Collapse
|
2
|
Gozzo TA, Bush MF. Effects of charge on protein ion structure: Lessons from cation-to-anion, proton-transfer reactions. MASS SPECTROMETRY REVIEWS 2024; 43:500-525. [PMID: 37129026 DOI: 10.1002/mas.21847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Collision cross-section values, which can be determined using ion mobility experiments, are sensitive to the structures of protein ions and useful for applications to structural biology and biophysics. Protein ions with different charge states can exhibit very different collision cross-section values, but a comprehensive understanding of this relationship remains elusive. Here, we review cation-to-anion, proton-transfer reactions (CAPTR), a method for generating a series of charge-reduced protein cations by reacting quadrupole-selected cations with even-electron monoanions. The resulting CAPTR products are analyzed using a combination of ion mobility, mass spectrometry, and collisional activation. We compare CAPTR to other charge-manipulation strategies and review the results of various CAPTR-based experiments, exploring their contribution to a deeper understanding of the relationship between protein ion structure and charge state.
Collapse
Affiliation(s)
- Theresa A Gozzo
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| |
Collapse
|
3
|
Gámez F, Avilés-Moreno JR, Martens J, Berden G, Oomens J, Martínez-Haya B. Vibrational signatures of dynamic excess proton storage between primary amine and carboxylic acid groups. J Chem Phys 2024; 160:094311. [PMID: 38450729 DOI: 10.1063/5.0192331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
Ammonium and carboxylic moieties play a central role in proton-mediated processes of molecular recognition, charge transfer or chemical change in (bio)materials. Whereas both chemical groups constitute acid-base pairs in organic salt-bridge structures, they may as well host excess protons in acidic environments. The binding of excess protons often precedes proton transfer reactions and it is therefore of fundamental interest, though challenging from a quantum chemical perspective. As a benchmark for this process, we investigate proton storage in the amphoteric compound 5-aminovaleric acid (AV), within an intramolecular proton bond shared by its primary amine and carboxylic acid terminal groups. Infrared ion spectroscopy is combined with ab initio Molecular Dynamics (AIMD) calculations to expose and rationalize the spectral signatures of protonated AV and its deuterated isotopologues. The dynamic character of the proton bond confers a fluxional structure to the molecular framework, leading to wide-ranging bands in the vibrational spectrum. These features are reproduced with remarkable accuracy by AIMD computations, which serves to lay out microscopic insights into the excess proton binding scenario.
Collapse
Affiliation(s)
- F Gámez
- Department of Physical Chemistry, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J R Avilés-Moreno
- Department of Applied Physical Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - J Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - G Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - B Martínez-Haya
- Center for Nanoscience and Sustainable Technologies (CNATS), Universidad Pablo de Olavide, 41013 Seville, Spain
| |
Collapse
|
4
|
Weintraut T, Heiles S, Gerbig D, Henss A, Junck J, Düring RA, Rohnke M. Lipid-related ion suppression on the herbicide atrazine in earthworm samples in ToF-SIMS and matrix-assisted laser desorption ionization mass spectrometry imaging and the role of gas-phase basicity. Biointerphases 2024; 19:021003. [PMID: 38602440 DOI: 10.1116/6.0003437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
In mass spectrometry imaging (MSI), ion suppression can lead to a misinterpretation of results. Particularly phospholipids, most of which exhibit high gas-phase basicity (GB), are known to suppress the detection of metabolites and drugs. This study was initiated by the observation that the signal of an herbicide, i.e., atrazine, was suppressed in MSI investigations of earthworm tissue sections. Herbicide accumulation in earthworms was investigated by time-of-flight secondary ion mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Additionally, earthworm tissue sections without accumulation of atrazine but with a homogeneous spray deposition of the herbicide were analyzed to highlight region-specific ion suppression. Furthermore, the relationship of signal intensity and GB in binary mixtures of lipids, amino acids, and atrazine was investigated in both MSI techniques. The GB of atrazine was determined experimentally through a linear plot of the obtained intensity ratios of the binary amino acid mixtures, as well as theoretically. The GBs values for atrazine of 896 and 906 kJ/mol in ToF-SIMS and 933 and 987 kJ/mol in MALDI-MSI were determined experimentally and that of 913 kJ/mol by quantum mechanical calculations. Compared with the GB of a major lipid component, phosphatidylcholine (GBPC = 1044.7 kJ/mol), atrazine's experimentally and computationally determined GBs in this work are significantly lower, making it prone to ion suppression in biological samples containing polar lipids.
Collapse
Affiliation(s)
- Timo Weintraut
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Sven Heiles
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, Dortmund 44139, Germany
- Faculty of Chemistry, University of Duisburg-Essen, Universitaetsstrasse 5, Essen 45141, Germany
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Dennis Gerbig
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Anja Henss
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Johannes Junck
- Institute of Soil Science and Soil Conservation, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, Giessen 35392, Germany
| | - Rolf-Alexander Düring
- Institute of Soil Science and Soil Conservation, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, Giessen 35392, Germany
| | - Marcus Rohnke
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| |
Collapse
|
5
|
Nacsa AB, Kígyósi M, Czakó G. Protonation of serine: conformers, proton affinities and gas-phase basicities at the "gold standard" and beyond. Phys Chem Chem Phys 2023; 25:8891-8902. [PMID: 36916632 DOI: 10.1039/d3cp00612c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The potential energy surfaces (PESs) of serine and its protonated counterparts are investigated to determine the structures of the minima. A total of 95 neutral serine, 15 N-(amino-) and 46 O-(carbonyl-)protonated serine conformers are found. Their relative energies, geometries and harmonic vibrational frequencies are determined at the MP2/aug-cc-pVDZ level of theory. To obtain highly accurate thermodynamic values, further computations are performed: the ten conformers with the lowest relative energies from each molecule type (neutral, N- and O-protonated) are further optimized using the explicitly correlated CCSD(T)-F12a/cc-pVDZ-F12 method (for neutral serine, harmonic vibrational frequencies were also computed). In addition, auxiliary corrections were determined: basis-set effects up to CCSD(T)-F12b/cc-pVQZ-F12, electron correlation effects up to CCSDT(Q), core correlation and second-order Douglas-Kroll relativistic effects along with zero-point energy contributions. Two important thermodynamic parameters (at 298.15 K), proton affinity (PA)/gas-phase basicity (GB) are calculated considering the two different protonation sites: 218.05 ± 0.2/209.86 ± 0.6 kcal mol-1 and 205.87 ± 0.2/196.36 ± 0.3 kcal mol-1 for the amino and carbonyl sites, respectively. The uncertainty of the determined values was approximated based on various sources including auxiliary corrections, basis-set effects, harmonic vibrational frequencies.
Collapse
Affiliation(s)
- András B Nacsa
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Máté Kígyósi
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| |
Collapse
|
6
|
Dudek WM, Ostrowski S, Dobrowolski JC. On Aromaticity of the Aromatic α-Amino Acids and Tuning of the NICS Indices to Find the Aromaticity Order. J Phys Chem A 2022; 126:3433-3444. [PMID: 35617165 PMCID: PMC9189847 DOI: 10.1021/acs.jpca.2c00346] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The NICS aromaticity indices of the rings in flexible phenylalanine (Phe), tryptophan (Trp), tyrosine (Tyr), and histidine (His) chiral molecules were analyzed. These molecules have several dozens of conformers, and their rings are slightly non-planar. Therefore, the population-averaged NICSpav index was defined, and the NICS scans had to be performed with respect to planes found by the least-squares routine. A rule differentiating an obverse and a reverse ring face in aromatic amino acids was formulated. The NICS scan minima corresponding to the obverse and reverse face were unequal, which prompted us to use the term ring face aromaticity/ring face tropicity. It appeared that for Phe, Trp, Tyr, and His, the reverse face has always had higher ring face aromaticity/ring face tropicity than the obverse one. Despite the NICS modifications, uncertainty about the amino acid aromaticity order remained. This motivated us to use the integral INICS index newly proposed by Stanger as well. Then, the following sequence was obtained: Trp(phenyl) > Phe > Trp(pyrrole) > His > Tyr. The juxtaposition of the INICS indices of amino acids with that of some model rings revealed a fair transferability of the values. Finally, analysis of the substituent effect on INICS demonstrated that the aromaticity of Tyr is the lowest due to the strength of the OH group π-electron-donating effect able to perturb enough the ring charge distribution and its magnetic aromaticity. The NICS calculations were executed using the ARONICS program written within the project.
Collapse
Affiliation(s)
- Wojciech M Dudek
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Sławomir Ostrowski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| |
Collapse
|
7
|
Chiavarino B, Sinha RK, Crestoni ME, Corinti D, Filippi A, Fraschetti C, Scuderi D, Maitre P, Fornarini S. Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay. Chemistry 2021; 27:2348-2360. [PMID: 33175428 DOI: 10.1002/chem.202003555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Indexed: 11/06/2022]
Abstract
The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]+ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]+ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.
Collapse
Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Rajeev K Sinha
- Department of Atomic and Molecular Physics, Manipal University, Manipal, 576104, Karnataka, India
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Debora Scuderi
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Philippe Maitre
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| |
Collapse
|
8
|
Lamsabhi AM, Mó O, Yáñez M, Salpin JY. Combined Experimental and Theoretical Survey of the Gas-Phase Reactions of Serine-Ca 2+ Adducts. J Phys Chem A 2019; 123:6241-6250. [PMID: 31268328 DOI: 10.1021/acs.jpca.9b03977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The association of Ca2+ to serine and the subsequent gas-phase unimolecular reactivity of the [Ca(Ser)]2+ (Ser = Serine) adduct was investigated throughout the use of tandem mass spectrometry techniques and B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) density functional theory calculations. In a first step, the structure and relative stability of all possible conformers of serine were obtained and analyzed, as well as the most stable [serine-Ca]2+ adducts. For the analysis of the different potential energy surfaces associated with the gas-phase unimolecular reactivity of these adducts, only those that differ by less than 100 kJ·mol-1 from the global minimum were taken into account. In agreement with previous studies, the serine-Ca2+ global minimum corresponds to a charge-solvated structure in which Ca is tricoordinated to neutral serine. The major peaks observed in the nanoelectrospray-MS/MS spectrum of [Ca(Ser)]2+ adduct correspond to both Coulomb explosions, yielding either CaOH+ + [C3,H6,N,O2]+ or [C2,H4,O,N]+ + [Ca(C,H3,O2)]+, and to the loss of neutrals, namely, CH2O and H2O. Our theoretical survey of the energy profile allow us to conclude that, although all the aforementioned fragmentation processes can have their origin at the global minimum, similar fragmentations involving low-lying conformers, both zwitterionic and nonzwitterionic, compete and should be considered to account for the observed reactivity. We have also found that in some specific cases post-transition state dynamics similar to the ones described before in the literature for formamide-Ca2+ reactions, may also play a role.
Collapse
Affiliation(s)
- Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Otilia Mó
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Jean-Yves Salpin
- LAMBE, Univ Evry, CNRS, CEA , Université Paris-Saclay , F-91025 Evry-Courcouronnes , France.,LAMBE, UCP , Université Paris-Seine , F-91025 Evry-Courcouronnes , France
| |
Collapse
|
9
|
Shahriar I, Islam MKB, Iqfath M, Rahman A, Halim MA. Solvent effect on vibrational circular dichroism of chiral amino acids. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2419-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
10
|
Bouchoux G. Gas phase basicities of polyfunctional molecules. Part 6: Cyanides and isocyanides. MASS SPECTROMETRY REVIEWS 2018; 37:533-564. [PMID: 28621817 DOI: 10.1002/mas.21538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/15/2017] [Indexed: 05/26/2023]
Abstract
This paper gathers structural and thermochemical informations related to the gas-phase basicity of molecules containing cyanides (nitriles) and isocyanides (isonitriles) functional groups. It constitutes the sixth part of a general review devoted to gas-phase basicities of polyfunctional compounds. A large corpus of cyanides and isocyanides molecules is examined under seven major chapters. In the first one, a rapid overview of the definitions and methods leading to gas-phase basicity, GB, proton affinity, PA, and protonation entropy, Δp S°, is given. In the same chapter, several aspects of the gas phase chemistry of protonated cyanides and isocyanides are also presented. Chapters II-VI detail the protonation energetics of aliphatic, unsaturated, and heteroatom substituted (halogens, O, S, N, P) cyanides. A seventh chapter is devoted to isocyanides. Experimental data available in the literature (120 references) were reevaluated according to the presently adopted basicity scale that is the NIST database anchored to PA(NH3 ) = 853.6 kJ/mol and GB (NH3 ) = 819 kJ/mol. In this latter source, however, several erroneous values have been identified which were corrected in the present review. Structural and energetic information given by G4MP2 quantum chemistry computations on ca. 60 typical systems are presented. The present review includes the GB, PA, and Δp S° values of ca. 110 cyanides and isocyanides, and, for selected examples, is completed by a set of computed heats of formation (Δf H°) at 0 and 298 K.
Collapse
Affiliation(s)
- Guy Bouchoux
- Département de Chimie, Laboratoire de Chimie Moléculaire, UMR CNRS 9168, Ecole Polytechnique, Palaiseau, France
- Université Paris-Sud XI, ICMO, Orsay, France
| |
Collapse
|
11
|
Fraschetti C, Montagna M, Crestoni ME, Calcaterra A, Aiello F, Santi L, Filippi A. Kinetic enantioselectivity of a protonated bis(diamido)-bridged basket resorcin[4]arene towards alanine peptides. Org Biomol Chem 2018; 15:1183-1189. [PMID: 28084488 DOI: 10.1039/c6ob02734b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Efficient enantiodiscrimination of some alanine-containing di- and tri-peptides by using chiral protonated bis(diamido)-bridged basket resorcin[4]arenes depends on several factors, including the basicity of the amino acid residues at the C- and N-termini of the peptide.
Collapse
Affiliation(s)
- C Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, 00185 Roma, Italy.
| | - M Montagna
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, 00185 Roma, Italy.
| | - M E Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, 00185 Roma, Italy.
| | - A Calcaterra
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, 00185 Roma, Italy.
| | - F Aiello
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy
| | - L Santi
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, 00185 Roma, Italy.
| | - A Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, P.le A. Moro 5, 00185 Roma, Italy.
| |
Collapse
|
12
|
Bouchoux G, Eckert-Maksic M. Gas phase basicities of polyfunctional molecules. Part 5: Non-aromatic sp 2 nitrogen containing compounds. MASS SPECTROMETRY REVIEWS 2018; 37:139-170. [PMID: 27275644 DOI: 10.1002/mas.21511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 05/22/2016] [Indexed: 06/06/2023]
Abstract
This paper constitutes the fifth part of a general review of the gas-phase protonation thermochemistry of polyfunctional molecules (Part 1: Theory and methods, Mass Spectrom Rev 2007, 26:775-835, Part 2: Saturated basic sites, Mass Spectrom Rev 2012, 31:353-390, Part 3: Amino acids, Mass Spectrom Rev 2012, 31:391-435, Part 4: Carbonyl as basic site, Mass Spectrom Rev 2015, 34:493-534). This part is devoted to non-aromatic molecules characterized by a lone pair located on a sp2 nitrogen atom, it embraces functional groups such as imines, amidines, guanidines, diazenes, hydrazines, oximes, and phosphazenes. Specific examples are examined under five major chapters. In the first one, aliphatic and unsaturated (conjugated and cyclic) imines, hydrazones, and oximes are considered. A second chapter describes the protonation energetic of aliphatic, conjugated, or cyclic amidines. Guanidines, polyguanides, and biomolecules containing guanidine were examined in the third chapter. A fourth chapter describes the particular case of the phosphazene molecules. Finally, diazenes and azides were considered in the last chapter. Experimental data were re-evaluated according to the presently adopted basicity scale, i.e., PA(NH3 ) = 853.6 kJ/mol, GB (NH3 ) = 819 kJ/mol. Structural and energetic information given by G4MP2 quantum chemistry computations on typical systems are presented. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:139-170, 2018.
Collapse
Affiliation(s)
- Guy Bouchoux
- Département de Chimie, Laboratoire de Chimie Moléculaire, UMR CNRS 9168, Ecole Polytechnique, Palaiseau, 91120, France
- Université Paris-Sud XI, ICMO, Orsay, 91405, France
| | - Mirjana Eckert-Maksic
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute, Bijenicka 54, Zagreb, HR 1000, Croatia
| |
Collapse
|
13
|
Klyne J, Bouchet A, Ishiuchi SI, Fujii M, Dopfer O. Cation-Size-Dependent Conformational Locking of Glutamic Acid by Alkali Ions: Infrared Photodissociation Spectroscopy of Cryogenic Ions. J Phys Chem B 2018; 122:2295-2306. [DOI: 10.1021/acs.jpcb.7b12601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Johanna Klyne
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Aude Bouchet
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
- Laboratory
for Chemistry and Life Science, Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
| | - Shun-ichi Ishiuchi
- Laboratory
for Chemistry and Life Science, Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
| | - Otto Dopfer
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| |
Collapse
|
14
|
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.
Collapse
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.
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Fujiwara Y, Saito N. Time-of-flight secondary ion mass spectrometry using a new primary ion beam generated by vacuum electrospray of a protic ionic liquid, propylammonium nitrate. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1859-1867. [PMID: 28815824 DOI: 10.1002/rcm.7960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/10/2017] [Accepted: 08/13/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Protic ionic liquids have the potential to be useful materials for primary ion beams in terms of protonation, since they have active protons. Selecting protic ionic liquids suitable for primary ion beams is of great importance to increase molecular secondary ion yields. Propylammonium nitrate ([C3 H7 NH3 ][NO3 ]) seems promising in view of its proton affinity. It is likely that [C3 H7 NH3 ]+ cations can act as proton donors, and [NO3 ]- anions can work as proton acceptors. METHODS Time-of-flight secondary ion mass spectrometry (TOF-SIMS) experiments have been performed to verify the usefulness of [C3 H7 NH3 ][NO3 ]. A primary propylammonium nitrate cluster ion beam was generated by vacuum electrospray, and then used to analyze amino acids (arginine, glutamic acid, aspartic acid), angiotensin II and polyethylene glycol. Positive and negative secondary ion mass spectra were obtained to study both protonation and deprotonation. RESULTS The propylammonium nitrate cluster ion beam successfully generated protonated molecules [M + H]+ of all the analytes in positive ion mode. The primary ion beam also generated deprotonated molecules [M - H]- of glutamic acid, aspartic acid and angiotensin II in negative ion mode. Additionally, adduct ions related to [C3 H7 NH3 ][NO3 ] were detected in the case of arginine and polyethylene glycol. CONCLUSIONS The TOF-SIMS experiments confirmed that the propylammonium nitrate cluster ion beam was useful in generating molecular secondary ions, demonstrating that it is well suited for a primary ion beam in TOF-SIMS.
Collapse
Affiliation(s)
- Yukio Fujiwara
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba-shi, Ibaraki-ken, 305-8568, Japan
| | - Naoaki Saito
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba-shi, Ibaraki-ken, 305-8568, Japan
| |
Collapse
|
16
|
Pedraza-González L, Charry J, Quintero W, Alí-Torres J, Reyes A. Fast and accurate prediction of proton affinities: revisiting the extended Koopmans' theorem for protons. Phys Chem Chem Phys 2017; 19:25324-25333. [PMID: 28890980 DOI: 10.1039/c7cp04936f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we propose schemes based on the extended Koopmans' theorem for quantum nuclei (eKT), in the framework of the any particle molecular orbital approach (APMO/KT), for the quantitative prediction of gas phase proton affinities (PAs). The performance of these schemes has been tested on a set of 300 organic molecules containing diverse functional groups. The APMO/KT scheme scaled by functional group (APMO/KT-SC-FG) displays an overall mean absolute error of 1.1 kcal mol-1 with respect to experimental data. Its performance in PA calculations is similar to that of post-Hartree-Fock composite methods or that of the APMO second order proton propagator (APMO/PP2) approach. The APMO/KT-SC-FG scheme is also employed to predict PAs of polyfunctional molecules such as the Nerve Agent VX and the 20 common α-amino acids, finding excellent agreement with available theoretical and/or experimental data. The accuracy of the predictions demonstrates that the APMO/KT-SC-FG scheme is a low-cost alternative to adiabatic methods for the calculation of accurate PAs. One of the most appealing features of the APMO/KT-SC-FG scheme, is that PAs can be derived from one single-point APMO Hartree-Fock calculation.
Collapse
Affiliation(s)
- Laura Pedraza-González
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 # 45-03, Bogotá, Colombia.
| | | | | | | | | |
Collapse
|
17
|
Raczyńska ED, Gal JF, Maria PC. The guanylated bioamine agmatine – A theoretical investigation of its structure and exceptional high basicity in the gas phase. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
18
|
Nadler WM, Waidelich D, Kerner A, Hanke S, Berg R, Trumpp A, Rösli C. MALDI versus ESI: The Impact of the Ion Source on Peptide Identification. J Proteome Res 2017; 16:1207-1215. [PMID: 28176526 DOI: 10.1021/acs.jproteome.6b00805] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For mass spectrometry-based proteomic analyses, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are the commonly used ionization techniques. To investigate the influence of the ion source on peptide detection in large-scale proteomics, an optimized GeLC/MS workflow was developed and applied either with ESI/MS or with MALDI/MS for the proteomic analysis of different human cell lines of pancreatic origin. Statistical analysis of the resulting data set with more than 72 000 peptides emphasized the complementary character of the two methods, as the percentage of peptides identified with both approaches was as low as 39%. Significant differences between the resulting peptide sets were observed with respect to amino acid composition, charge-related parameters, hydrophobicity, and modifications of the detected peptides and could be linked to factors governing the respective ion yields in ESI and MALDI.
Collapse
Affiliation(s)
- Wiebke Maria Nadler
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | | | - Alexander Kerner
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Hanke
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Regina Berg
- Department of Chemistry, University of Zurich , Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Andreas Trumpp
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christoph Rösli
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| |
Collapse
|
19
|
Eyrilmez SM, Bernhardt E, Dávalos JZ, Lepšík M, Hobza P, Assaf KI, Nau WM, Holub J, Oliva-Enrich JM, Fanfrlík J, Hnyk D. Binary twinned-icosahedral [B21H18]− interacts with cyclodextrins as a precedent for its complexation with other organic motifs. Phys Chem Chem Phys 2017; 19:11748-11752. [DOI: 10.1039/c7cp01074e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A macropolyhedral boron hydride anion with two counterions can form stable complexes with β- and γ-cyclodextrin in the gas phase.
Collapse
Affiliation(s)
- Saltuk M. Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Flemingovo nam. 2
- CZ-16610 Prague 6
- Czech Republic
- Department of Physical Chemistry, Palacký University
| | - Eduard Bernhardt
- Bergische University Wuppertal, Gaussstrasse 20
- D-42097 Wuppertal
- Germany
| | - Juan Z. Dávalos
- Instituto de Química-Física “Rocasolano”, CSIC
- ES-28006 Madrid
- Spain
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Flemingovo nam. 2
- CZ-16610 Prague 6
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Flemingovo nam. 2
- CZ-16610 Prague 6
- Czech Republic
- Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University
| | - Khaleel I. Assaf
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1
- D-28759 Bremen
- Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1
- D-28759 Bremen
- Germany
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i. CZ-25068 Husinec-Řež
- Czech Republic
| | | | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Flemingovo nam. 2
- CZ-16610 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i. CZ-25068 Husinec-Řež
- Czech Republic
| |
Collapse
|
20
|
Ropo M, Blum V, Baldauf C. Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead. Sci Rep 2016; 6:35772. [PMID: 27808109 PMCID: PMC5093913 DOI: 10.1038/srep35772] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/03/2016] [Indexed: 12/16/2022] Open
Abstract
We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+. The underlying data set consists of more than 45,000 first-principles predicted conformers with relative energies up to ~4 eV (~400 kJ/mol). We show that only very few distinct backbone structures of isolated amino acids and their dipeptides emerge as lowest-energy conformers. The isolated amino acids predominantly adopt structures that involve an acidic proton shared between the carboxy and amino function. Dipeptides adopt one of two intramolecular-hydrogen bonded conformations C5 or . Upon complexation with a divalent cation, the accessible conformational space shrinks and intramolecular hydrogen bonding is prevented due to strong electrostatic interaction of backbone and side chain functional groups with cations. Clear correlations emerge from the binding energies of the six divalent ions with amino acids and dipeptides. Cd2+ and Hg2+ show the largest binding energies-a potential correlation with their known high acute toxicities. Ca2+ and Pb2+ reveal almost identical binding energies across the entire series of amino acids and dipeptides. This observation validates past indications that ion-mimicry of calcium and lead should play an important role in a toxicological context.
Collapse
Affiliation(s)
- M. Ropo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
- Department of Physics, Tampere University of Technology, Finland
- COMP, Department of Applied Physics, Aalto University, Finland
| | - V. Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
| | - C. Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| |
Collapse
|
21
|
Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
Collapse
Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| |
Collapse
|
22
|
Batoon P, Ren J. Proton Affinity of Isomeric Dipeptides Containing Lysine and Non-Proteinogenic Lysine Homologues. J Phys Chem B 2016; 120:7783-94. [DOI: 10.1021/acs.jpcb.6b03776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick Batoon
- Department of Chemistry, University of the Pacific, 3601 Pacific
Avenue, Stockton, California 95211, United States
| | - Jianhua Ren
- Department of Chemistry, University of the Pacific, 3601 Pacific
Avenue, Stockton, California 95211, United States
| |
Collapse
|
23
|
Hadadi N, Ataman M, Hatzimanikatis V, Panayiotou C. Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites. Phys Chem Chem Phys 2016; 17:10438-53. [PMID: 25799954 DOI: 10.1039/c4cp05825a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chemical calculations of the thermochemical quantities of relatively heavy metabolites such as amino acids/oligopeptides, nucleosides, saccharides and their derivatives in the ideal gas state. The results of this study will be combined with the corresponding hydration/solvation results in subsequent parts of this work in order to derive the desired thermochemical quantities in aqueous solutions. The above metabolites exist in a vast conformational/isomerization space including rotational conformers, tautomers or anomers exhibiting often multiple or cooperative intramolecular hydrogen bonding. We examine the challenges posed by these features for the reliable estimation of thermochemical quantities. We discuss conformer search, conformer distribution and averaging processes. We further consider neutral metabolites as well as protonated and deprotonated metabolites. In addition to the traditional presentation of gas-phase acidities, basicities and proton affinities, we also examine heats and free energies of ionic species. We obtain simple linear relations between the thermochemical quantities of ions and the formation quantities of their neutral counterparts. Furthermore, we compare our calculations with reliable experimental measurements and predictive calculations from the literature, when available. Finally, we discuss the next steps and perspectives for this work.
Collapse
Affiliation(s)
- N Hadadi
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | | | | | | |
Collapse
|
24
|
First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids. Sci Data 2016; 3:160009. [PMID: 26881946 PMCID: PMC4755128 DOI: 10.1038/sdata.2016.9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 01/15/2016] [Indexed: 11/24/2022] Open
Abstract
We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.
Collapse
|
25
|
Bain RM, Yan X, Raab SA, Ayrton ST, Flick TG, Cooks RG. On-line chiral analysis using the kinetic method. Analyst 2016; 141:2441-6. [PMID: 26979554 DOI: 10.1039/c6an00100a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chiral analysis of constituents in solution-phase reaction mixtures can be performed by tandem mass spectrometry using the kinetic method to determine the enantiomeric excess (ee).
Collapse
Affiliation(s)
- Ryan M. Bain
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Xin Yan
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | | | | | | | - R. Graham Cooks
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
- Center for Analytical Instrumentation Development
| |
Collapse
|
26
|
Mistarz UH, Brown JM, Haselmann KF, Rand KD. Probing the Binding Interfaces of Protein Complexes Using Gas-Phase H/D Exchange Mass Spectrometry. Structure 2015; 24:310-8. [PMID: 26749447 DOI: 10.1016/j.str.2015.11.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 12/20/2022]
Abstract
Fast gas-phase hydrogen/deuterium exchange mediated by ND3 gas and measured by mass spectrometry (gas-phase HDX-MS) is a largely unharnessed, fast, and sensitive method for probing primary- and higher-order polypeptide structure. Labeling of heteroatom-bound non-amide hydrogens in a sub-millisecond time span after electrospray ionization by ND3 gas can provide structural insights into protein conformers present in solution. Here, we have explored the use of gas-phase HDX-MS for probing the higher-order structure and binding interfaces of protein complexes originating from native solution conditions. Lysozyme ions bound by an oligosaccharide incorporated less deuterium than the unbound ion. Similarly, trypsin ions showed reduced deuterium uptake when bound by the peptide ligand vasopressin. Our results are in good agreement with crystal structures of the native protein complexes, and illustrate that gas-phase HDX-MS can provide a sensitive and simple approach to measure the number of heteroatom-bound non-amide side-chain hydrogens involved in the binding interface of biologically relevant protein complexes.
Collapse
Affiliation(s)
- Ulrik H Mistarz
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Jeffery M Brown
- Waters MS Technologies Centre, Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Kim F Haselmann
- Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv 2670, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark.
| |
Collapse
|
27
|
Laszlo KJ, Bush MF. Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2152-61. [PMID: 26323617 PMCID: PMC4655144 DOI: 10.1007/s13361-015-1245-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/23/2015] [Accepted: 08/01/2015] [Indexed: 05/08/2023]
Abstract
Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA.
| |
Collapse
|
28
|
Nadler W, Berg R, Walch P, Hanke S, Baalmann M, Kerner A, Trumpp A, Roesli C. Ion source-dependent performance of 4-vinylpyridine, iodoacetamide, and N-maleoyl derivatives for the detection of cysteine-containing peptides in complex proteomics. Anal Bioanal Chem 2015; 408:2055-67. [DOI: 10.1007/s00216-015-9113-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 10/05/2015] [Accepted: 10/09/2015] [Indexed: 01/03/2023]
|
29
|
Riffet V, Bouchoux G, Frison G. Microhydration of Protonated Nα-Acetylhistidine: A Theoretical Approach. J Phys Chem B 2015; 119:11527-39. [PMID: 26252717 DOI: 10.1021/acs.jpcb.5b05581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Extensive exploration of the potential energy surfaces of protonated Nα-acetylhistidine hydrated by 0-3 molecules of water was performed. The methodology combined hierarchical and genealogical (Darwin family tree) approaches using polarizable AMOEBA force field and M06 functional. It is demonstrated that this mixed approach allows recovering a larger number of conformers than the number recovered by using any one of the two methods alone. Hydration enthalpies of protonated Nα-acetylhistidine and of model compounds have been computed using higher theoretical methods, up to the G4MP2 procedure. Excellent agreement with experiment is observed for successive hydration of methylamonium and imidazolium cations using MP2/6-311++G(2d,2p)//M06/6-311++G(d,p) and G4MP2 methods, thereby validating the theory levels used for hydrated protonated Nα-acetylhistidine. It is found that the first hydration enthalpy of protonated Nα-acetylhistidine is ca. 10 kJ mol(-1) lower than that of imidazolium, a result explained by the local environment of the positively charged imidazolium moiety.
Collapse
Affiliation(s)
- Vanessa Riffet
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique and CNRS , 91128 Palaiseau cedex, France
| | - Guy Bouchoux
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique and CNRS , 91128 Palaiseau cedex, France
| | - Gilles Frison
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique and CNRS , 91128 Palaiseau cedex, France
| |
Collapse
|
30
|
Bouchoux G. Gas-phase basicities of polyfunctional molecules. Part 4: Carbonyl groups as basic sites. MASS SPECTROMETRY REVIEWS 2015; 34:493-534. [PMID: 24399766 DOI: 10.1002/mas.21416] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 06/03/2023]
Abstract
This article constitutes the fourth part of a general review of the gas-phase protonation thermochemistry of polyfunctional molecules (Part 1: Theory and methods, Mass Spectrom Rev 2007, 26:775-835, Part 2: Saturated basic sites, Mass Spectrom Rev 2012, 31:353-390, Part 3: Amino acids, Mass Spectrom Rev 2012, 31:391-435). This fourth part is devoted to carbonyl containing polyfunctional molecules. After a short reminder of the methods of determination of gas-phase basicity and the underlying physicochemical concepts, specific examples are examined under two major chapters. In the first one, aliphatic and unsaturated (conjugated and cyclic) ketones, diketones, ketoalcohols, and ketoethers are considered. A second chapter describes the protonation energetic of gaseous acids and derivatives including diacids, diesters, diamides, anhydrides, imides, ureas, carbamates, amino acid derivatives, and peptides. Experimental data were re-evaluated according to the presently adopted basicity scale. Structural and energetic information given by G3 and G4 quantum chemistry computations on typical systems are presented.
Collapse
Affiliation(s)
- Guy Bouchoux
- Département de Chimie, Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91120, Palaiseau, France
| |
Collapse
|
31
|
Alahmadi YJ, Gholami A, Fridgen TD. The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N-H and O-H stretching region and computational methods. Phys Chem Chem Phys 2015; 16:26855-63. [PMID: 25375752 DOI: 10.1039/c4cp03104k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD spectroscopy and computational chemistry techniques have been used to determine that the proton- and sodium-bound dimers of proline exist as a mixture of a number of different structures. Simulated annealing computations were found to be helpful in determining the unique structures of the protonated and sodiated dimers, augmenting chemical intuition. The experimental and computational results are consistent with the proton-bound dimer of N-protonated proline bound to zwitterionic proline. There was no spectroscopic evidence in the 3200-3800 cm(-1) region for a canonical structure which is predicted to have a weak N-H stretch at about 3440 cm(-1). A well resolved band at 1733 cm(-1) from a previous spectroscopic study (DOI: 10.1021/ja068715a ) was reassigned from a high energy canonical isomer to the C=O stretch of a lower energy zwitterionic structure. This band is a free carboxylate C=O stretch where protonated proline is hydrogen bonded to the other carboxylate oxygen which is also involved in an intramolecular hydrogen bond. Fifteen structures of the sodium bound proline dimer were computed to be within 10 kJ mol(-1) of Gibbs energy and eight structures were within 5 kJ mol(-1). None of these structures can be ruled out based on the experimental IRMPD spectrum. They all have an N-H stretching band predicted in a position that agrees with the experimental spectrum. However, only structures where one of the proline monomers is in the canonical form and having a free O-H bond can produce the band at ∼3600 cm(-1).
Collapse
|
32
|
Bourcier S, Chiaa RX, Mimbong RNB, Bouchoux G. Gas-phase lithium cation affinity of glycine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:149-159. [PMID: 26307695 DOI: 10.1255/ejms.1299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The gas-phase lithium cation binding thermochemistry of glycine has been determined theoretically by quantum chemical calculations at the G4 level and experimentally by the extended kinetic method using electrospray ionization quadrupole time-of-flight tandem mass spectrometry. The lithium cation affinity of glycine, ∆(Li)H°(298)(GLY), i.e. the∆(Li)H°(298) of the reaction GlyLi(+)→ Gly + Li(+)) given by the G4 method is equal to 241.4 kJ.mol(-1) if only the most stable conformer of glycine is considered or to 242.3 kJ.mol(-1) if the 298K equilibrium mixture of neutral conformers is included in the calculation. The ∆(Li)H°(298)(GLY) deduced from the extended kinetic method is obviously dependent on the choice of the Li(+) affinity scale, thus∆(Li)H°(298)(GLY) is equal to 228.7±0.9(2.0) kJ.mol(- 1) if anchored to the recently re-evaluated lithium cation affinity scale but shifted to 235.4±1.0 kJ.mol(-1) if G4 computed lithium cation affinities of the reference molecules is used. This difference of 6.3 kJ.mol(-1) may originate from a compression of the experimental lithium affinity scale in the high ∆(Li)H°(298) region. The entropy change associated with the reaction GlyLi(+)→Gly + Li(+) reveals a gain of approximately 15 J.mol(-) 1.K(-1) with respect to monodentate Li(+) acceptors. The origin of this excess entropy is attributed to the bidentate interaction between the Li(+) cation and both the carbonyl oxygen and the nitrogen atoms of glycine. The computed G4 Gibbs free energy,∆(Li)G°(298)(GLY) is equal to 205.3 kJ.mol(-1), a similar result, 201.0±3.4 kJ.mol(-1), is obtained from the experiment if the∆(Li)G°(298) of the reference molecules is anchored on the G4 results.
Collapse
Affiliation(s)
- Sophie Bourcier
- Laboratoire de Chimie Moléculaire. Ecole Polytechnique. UMR 9168 CNRS 91128 Palaiseau, France.
| | - Ru Xuan Chiaa
- N anyang Technological University. 21 Nanyang Link. 637371 Singapore
| | | | - Guy Bouchoux
- Laboratoire de Chimie Moléculaire. Ecole Polytechnique. UMR 9168 CNRS. 91128 Palaiseau, France. Université Paris-Sud XI. 91400 Orsay, France.
| |
Collapse
|
33
|
Li H, Li L, Jiang J, Lin Z, Luo Y. Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine. Phys Chem Chem Phys 2015; 17:24754-60. [DOI: 10.1039/c5cp03729h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The global minimum of the dipeptide ArgGly is found to be in the canonical form, rather than the zwitterionic form.
Collapse
Affiliation(s)
- Hongbao Li
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science and Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology
- Guizhou Normal College
- Guiyang
- China
| | - Leilei Li
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Zijing Lin
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Yi Luo
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science and Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology
- Guizhou Normal College
- Guiyang
- China
- Hefei National Laboratory for Physical Sciences at the Microscale
| |
Collapse
|
34
|
Todua NG, Tretyakov KV, Mikaia AI. Mass spectrometry of analytical derivatives. 1. Cyanide cations in the spectra of N- alkyl-N-perfluoroacyl- α-amino acids and their methyl esters. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:183-90. [PMID: 26307698 PMCID: PMC5094188 DOI: 10.1255/ejms.1374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The central mission for the development of the National Institute of Standards and Technology/National Institutes of Health/Environmental Protection Agency Mass Spectral Library is the acquisition of reference gas chromatography-mass spectrometry data for important compounds and their chemical modification products. The addition of reliable reference data of various derivatives of amino acids to The Library, and the study of their behavior under electron ionization conditions may be useful for their identification, structure elucidation and a better understanding of the data obtained when the same derivatives are subjected to other ionization methods. N-Alkyl-N-perfluoroacyl derivatives of amino acids readily produce previously unreported alkylnitrilium cations of composition [HC≡N-alkyl](+). Homologous [HC≡N-aryl](+) cations are typical for corresponding N-aryl analogs. The formation of other ions characteristic for these derivatives involves oxygen rearrangement giving rise to ions [C(n)F(2n+1)-C≡N(+)C(n)H(2n+1)] and [CnF(2n+1)-C≡N(+)-aryl]. The introduction of an N-benzyl substituent in a molecule favors a process producing benzylidene iminium cations. L-Threonine and L-cysteine derivatives exhibit more fragmentation pathways not typical for other α-amino acids; additionally, the N(ω)- amino group in L-lysine directs the dissociation process and provides structural information on the substitution at the amino functions in the molecule.
Collapse
Affiliation(s)
- Nino G Todua
- Na tional Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Kirill V Tretyakov
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Anzor I Mikaia
- Na tional Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| |
Collapse
|
35
|
Zwitterionic versus canonical amino acids over the various defects in zeolites: a two-layer ONIOM calculation. Sci Rep 2014; 4:6594. [PMID: 25307449 PMCID: PMC4194432 DOI: 10.1038/srep06594] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/17/2014] [Indexed: 12/01/2022] Open
Abstract
Defects are often considered as the active sites for chemical reactions. Here a variety of defects in zeolites are used to stabilize zwitterionic glycine that is not self-stable in gas phase; in addition, effects of acidic strengths and zeolite channels on zwitterionic stabilization are demonstrated. Glycine zwitterions can be stabilized by all these defects and energetically prefer to canonical structures over Al and Ga Lewis acidic sites rather than Ti Lewis acidic site, silanol and titanol hydroxyls. For titanol (Ti-OH), glycine interacts with framework Ti and hydroxyl sites competitively, and the former with Lewis acidity predominates. The transformations from canonical to zwitterionic glycine are obviously more facile over Al and Ga Lewis acidic sites than over Ti Lewis acidic site, titanol and silanol hydroxyls. Charge transfers that generally increase with adsorption energies are found to largely decide the zwitterionic stabilization effects. Zeolite channels play a significant role during the stabilization process. In absence of zeolite channels, canonical structures predominate for all defects; glycine zwitterions remain stable over Al and Ga Lewis acidic sites and only with synergy of H-bonding interactions can exist over Ti Lewis acidic site, while automatically transform to canonical structures over silanol and titanol hydroxyls.
Collapse
|
36
|
Meng L, Wang Z, Zhang J, Zhou M, Wu W. Low Energy Conformations and Gas-Phase Acidity and Basicity of Pyrrolysine. J Phys Chem A 2014; 118:7085-95. [DOI: 10.1021/jp503444h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lingbiao Meng
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Zhuo Wang
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Jicheng Zhang
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Minjie Zhou
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Weidong Wu
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| |
Collapse
|
37
|
Meng L, Lin Z. Complexations of alkali/alkaline earth metal cations with gaseous glutamic acid. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
38
|
Morrison LJ, Chamot-Rooke J, Wysocki VH. IR action spectroscopy shows competitive oxazolone and diketopiperazine formation in peptides depends on peptide length and identity of terminal residue in the departing fragment. Analyst 2014; 139:2137-43. [PMID: 24618890 PMCID: PMC6467643 DOI: 10.1039/c4an00064a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The interplay between the entropically and enthalpically favored products of peptide fragmentation is probed using a combined experimental and theoretical approach. These b2 ion products can take either an oxazolone or diketopiperazine structure. Cleavage after the second amide bond is often a favorable process because the products are small ring structures that are particularly stable. These structures are structurally characterized by action IRMPD spectroscopy and semi-quantified using gas-phase hydrogen-deuterium exchange. The formation of the oxazolone and diketopiperazine has been thought to be largely governed by the identity of the first two residues at the N-terminus of the peptide. We show here that the length of the precursor peptide and identity of the third residue play a significant role in the formation of the diketopiperazine structure in peptides containing an N-terminal asparagine residue. This is additionally the first instance showing an N-terminal residue with an amide side chain can promote formation of the diketopiperazine b2 ion structure.
Collapse
Affiliation(s)
- L J Morrison
- Department of Chemistry and Biochemistry, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, USA.
| | | | | |
Collapse
|
39
|
Marek A, Tureček F. Collision-induced dissociation of diazirine-labeled peptide ions. Evidence for Brønsted-acid assisted elimination of nitrogen. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:778-789. [PMID: 24549894 DOI: 10.1007/s13361-014-0832-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 12/26/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Gas-phase dissociations were investigated for several peptide ions containing the Gly-Leu* N-terminal motif where Leu* was a modified norleucine residue containing the photolabile diazirine ring. Collisional activation of gas-phase peptide cations resulted in facile N₂ elimination that competed with backbone dissociations. A free lysine ammonium group can act as a Brønsted acid to facilitate N₂ elimination. This dissociation was accompanied by insertion of a lysine proton in the side chain of the photoleucine residue, as established by deuterium labeling and gas-phase sequencing of the products. Electron structure calculations were used to provide structures and energies of reactants, intermediates, and transition states for Gly-Leu*-Gly-Gly-Lys amide ions that were combined with RRKM calculations of unimolecular rate constants. The calculations indicated that Brønsted acid-catalyzed eliminations were kinetically preferred over direct loss of N₂ from the diazirine ring. Mechanisms are proposed to explain the proton-initiated reactions and discuss the reaction products. The non-catalyzed diazirine ring cleavage and N₂ loss is proposed as a thermometer dissociation for peptide ion dissociations.
Collapse
Affiliation(s)
- Aleš Marek
- Department of Chemistry, University of Washington, Bagley Hall, Seattle, WA, 98195-1700, USA
| | | |
Collapse
|
40
|
In-spray supercharging of intact proteins by capillary electrophoresis–electrospray ionization–mass spectrometry using sheath liquid interface. Anal Chim Acta 2014; 813:97-105. [DOI: 10.1016/j.aca.2013.12.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/17/2013] [Accepted: 12/28/2013] [Indexed: 01/10/2023]
|
41
|
Harrison AG. Effect of the sarcosine residue on sequence scrambling in peptide b(5) ions. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:161-167. [PMID: 24464544 DOI: 10.1002/jms.3323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/24/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
The effect of N-methylation on sequence scrambling in the fragmentation of b5 ions has been investigated by studying a variety of peptides containing sarcosine (N-methylglycine). The product ion mass spectra for the b5 ions derived from Sar-A-A-A-Y-A and Sar-A-A-Y-A-A show only minor signals for non-direct sequence ions the major fragmentation reactions occurring from the unrearranged structures. This is in contrast to the b5 ions where the Sar residue is replaced by Ala and sequence scrambling occurs. The b5 ion derived from Y-Sar-A-A-A-A shows a product ion mass spectrum essentially identical to the spectrum of the b5 ion derived from Sar-A-A-A-Y-A, indicating that in the former case macrocyclization has occurred but the macrocyclic form shows a strong preference to reopen to put the Sar residue in the N-terminal position. Similar results were obtained in the comparison of b5 ions derived from A-Sar-A-A-Y-A and Sar-A-A-Y-A-A. The product ion mass spectra of the MH(+) ions of Y-Sar-A-A-A-A and A-Sar-A-A-Y-A show substantial signals for non-direct sequence ions indicating that fragmentation of the MH(+) ions channels extensively through the respective b5 ions and further fragmentation of these species.
Collapse
Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, Canada
| |
Collapse
|
42
|
Glasovac Z, Eckert-Maksić M. Effect of Intramolecular Hydrogen Bonds on the Gas-Phase Basicity of Guanidines. Aust J Chem 2014. [DOI: 10.1071/ch14182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Three series of novel trisubstituted guanidines containing at least one hydrogen bond accepting (HBA) group were modelled using B3LYP/6–311+G(2df,p)//B3LYP/6–31G(d) calculations. Their structure was modified by incorporating a variety of different HBA groups covering a wide range of hydrogen bond strengths. Calculated gas-phase basicities (GBs) ranged from 1035 to 1181 kJ mol–1 depending on the nature of the substituent. To rationalise changes in the GB, a correlation of GB against two independent variables (pKHB and σ4B) was conducted where pKHB served as the descriptor of the hydrogen bond strength and σ4B was introduced to describe changes in the GBs in the open-chain model systems, i.e. in the absence of intramolecular hydrogen bond (IMHB), caused by the electronic effect of the propyl-HBA substituent. A very good correlation of the calculated gas-phase basicities against these two independent variables was established for all three sets of the bases.
Collapse
|
43
|
Gupta M, da Silva EF, Svendsen HF. Explicit Solvation Shell Model and Continuum Solvation Models for Solvation Energy and pKa Determination of Amino Acids. J Chem Theory Comput 2013; 9:5021-37. [DOI: 10.1021/ct400459y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mayuri Gupta
- Department
of Chemical Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eirik F. da Silva
- Department
of Process Technology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway
| | - Hallvard F. Svendsen
- Department
of Chemical Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| |
Collapse
|
44
|
Thorough theoretical search of conformations of neutral, protonated and deprotonated glutamine in gas phase. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
45
|
Amorim Madeira PJ, Vaz PD, Bettencourt da Silva RJN, Florêncio MH. Can Semi-empirical Calculations Help Solve Mass Spectrometry Problems? Protonation Sites and Proton Affinities of Amino Acids. Chempluschem 2013; 78:1149-1156. [DOI: 10.1002/cplu.201300173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/19/2013] [Indexed: 11/10/2022]
|
46
|
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
| | | |
Collapse
|
47
|
Fraschetti C, Filippi A, Crestoni ME, Ema T, Speranza M. Multifunctional Macrocyclic Receptors as Templates for Aromatic Amino Acids: A Rare Example of a Highly Selective Multi-Input Multi-Output Chemo-"Logic Gate". Chempluschem 2013; 78:979-987. [PMID: 31986732 DOI: 10.1002/cplu.201300086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Indexed: 01/08/2023]
Abstract
Proton-bound [M⋅H⋅G]+ diastereomeric complexes between some chiral aromatic amino acids or dipeptides (G) and a chiral multifunctional macrocyclic receptor (M=Chirabite-A) undergo, in the gas phase, highly selective substitution and addition reactions by amines, such as 2-aminobutane and piperidine. All the [M⋅H⋅G]+ complexes follow time-dependent monoexponential decays. In some cases, the kinetic curves exhibit a plateau revealing the presence of unreactive [M⋅H⋅G]+ structures. In them, the amino acid is accommodated in the macrocycle cavity in the zwitterionic form by sharing its acidic hydrogen atoms with the pyridine nitrogen atoms of the host. The same interactions are structurally inaccessible to G=dipeptides or monofunctional amines, which then can be readily released from [M⋅H⋅G]+ . When the amino acid interacts with the amidocarbonyl oxygen atoms pointing outside the macrocycle cavity, it saves the canonical structure and can be readily displaced by the amine. The Chirabite-A may act as an efficient template for aromatic amino acids by releasing them or not depending upon the amino acid configuration and the basicity of the amine. These unique properties confer to the gas-phase diastereomeric [M⋅H⋅G]+ complexes the features of multi-input multi-output chemo-"logic gates".
Collapse
Affiliation(s)
- Caterina Fraschetti
- Dipartimento di Chimica e Tecnologia del Farmaco, Università "La Sapienza", P. le A. Moro, 5-00185 Roma (Italy), Fax: (+39) 06-49913602
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologia del Farmaco, Università "La Sapienza", P. le A. Moro, 5-00185 Roma (Italy), Fax: (+39) 06-49913602
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologia del Farmaco, Università "La Sapienza", P. le A. Moro, 5-00185 Roma (Italy), Fax: (+39) 06-49913602
| | - Tadashi Ema
- Graduate School of Natural Sciences and Technology, Okayama University, Tsushima, Okayama 700-8530 (Japan)
| | - Maurizio Speranza
- Dipartimento di Chimica e Tecnologia del Farmaco, Università "La Sapienza", P. le A. Moro, 5-00185 Roma (Italy), Fax: (+39) 06-49913602
| |
Collapse
|
48
|
Bouchoux G. From the mobile proton to wandering hydride ion: mechanistic aspects of gas-phase ion chemistry. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:505-518. [PMID: 23584944 DOI: 10.1002/jms.3204] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/06/2013] [Accepted: 03/06/2013] [Indexed: 06/02/2023]
Abstract
Structural characterization of molecular species by mass spectrometry supposes the knowledge of the type of ions generated and the mechanism by which they dissociate. In this context, a need for a rationalization of electrospray ionization(+)(-) mass spectra of small molecules has been recently expressed. Similarly, at the other end of the mass scale, efforts are currently made to interpret the major fragmentation processes of protonated and deprotonated peptides and their reduced forms produced in electron capture or electron transfer experiments. Most fragmentation processes of molecular and pseudo-molecular ions produced in the ion source of a mass spectrometer may be described by a combination of several key mechanistic steps: simple bond dissociation, formation of ion-neutral complex intermediates, hydrogen atom, hydride ion or proton migrations and nucleophilic attack. Selected crucial aspects of these elementary reactions, occurring inside positively charged ions, will be recalled and illustrated by examples taken in recent mass spectrometry literature. Emphasis will be given on the protonation process and its consequence in terms of structure and energetic.
Collapse
Affiliation(s)
- Guy Bouchoux
- Laboratoire des Mécanismes Réactionnels. Ecole Polytechnique. CNRS, Université Paris-sud, 91128, Palaiseau, France.
| |
Collapse
|
49
|
Wang C, Lin Z, Zhang R. Zwitterions are the most stable form for neutral arginylglycine in gas phase: Clear theoretical evidence. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
50
|
Riffet V, Bouchoux G. Gas-phase structures and thermochemistry of neutral histidine and its conjugated acid and base. Phys Chem Chem Phys 2013; 15:6097-106. [DOI: 10.1039/c3cp00043e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|