1
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Armentrout PB. Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation. Phys Chem Chem Phys 2024. [PMID: 39042103 DOI: 10.1039/d4cp00897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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2
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de Miranda DB, Quintal S, Ferreira GB. Electronic analysis of n-propyl xanthate complexes with group 12 metals: a theoretical-experimental study. J Mol Model 2024; 30:163. [PMID: 38730058 DOI: 10.1007/s00894-024-05950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024]
Abstract
CONTEXT Xanthates are organic compounds of great interest in coordination chemistry due to their different basic sites, which allow them to form complexes with different coordination modes and geometries. These compounds are relevant in the environment and act as heavy metal collectors in aqueous environments. In this theoretical-experimental work, electronic spectroscopy studies of n-propyl xanthate complexes with group 12 metals were performed. This study verified structural differences in these systems, depending on the environment in which they are inserted. In addition, structural differences were observed when the solid was changed to an n-hexane solution. Thus, it was observed that the complexes assume a mononuclear structure in solution, while they present a polymeric form in the solid phase. The electronic spectra obtained through TD-DFT calculations were compared to those of the previously synthesized complexes. In the final theoretical analysis, the main orbitals involved in these transitions were assigned using population analysis calculations. The synthesis of the complexes was confirmed through infrared (MID and FAR), UV‒Vis, Raman, and NMR-1H spectroscopic analyses. METHODS The structures of the mononuclear and polymeric complexes were optimized in vacuum and n-hexane. Under vacuum, DFT levels M06L/6-311 + + G** + LANL2TZ and M06L/def2-TZVP were used for the mononuclear complexes, and M06L/LANL2DZ + LANL2 were used for the polymer complexes. For the calculations of the mononuclear complexes in n-hexane, the same level of theory was used for the solid state. TD-DFT calculations for 300 excited states were performed with the same levels of theory and used the optimized structures of the complexes. Furthermore, population analysis was carried out on all the systems studied. Gaussian 09 software was used for the structure optimization, TD-DFT, and population analysis calculations. GaussSum software was used to evaluate the molecular orbitals and electronic spectra.
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Affiliation(s)
- Daniella B de Miranda
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal Fluminense, Outeiro de S. João Batista s/n., Centro, Niterói, RJ, 24210-130, Brazil
| | - Susana Quintal
- Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense, Outeiro de S. João Batista s/n., Centro, Niterói, RJ, 24210-130, Brazil
| | - Glaucio B Ferreira
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal Fluminense, Outeiro de S. João Batista s/n., Centro, Niterói, RJ, 24210-130, Brazil.
- Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense, Outeiro de S. João Batista s/n., Centro, Niterói, RJ, 24210-130, Brazil.
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3
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Stevenson BC, Berden G, Martens J, Oomens J, Armentrout PB. Spectroscopic Investigation of the Metal Coordination of the Aromatic Amino Acids with Zinc and Cadmium. J Phys Chem A 2023; 127:3560-3569. [PMID: 37053556 DOI: 10.1021/acs.jpca.2c08940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl+ and CdCl+, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl+(Phe), CdCl+(Phe), ZnCl+(Tyr), CdCl+(Tyr), and ZnCl+(Trp) species were examined because the CdCl+(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed. In the case of MCl+(Phe) and MCl+(Tyr), these comparisons indicated the dominant binding motif is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. These observations are consistent with the predicted ground states at the B3LYP, B3P86, B3LYP-GD3BJ, and MP2 levels of theory. For the ZnCl+(Trp) system, the experimental spectrum indicates a similar binding motif, with the zinc atom coordinating with the backbone nitrogen and carbonyl oxygen and either the pyrrole ring or the benzene ring of the indole side chain. These observations are consistent with the predicted low-lying conformers identified by the aforementioned levels of theory, with the B3LYP and B3P86 levels predicting the metal-pyrrole ring interaction is more favorable than the metal-benzene ring interactions and the opposite at the B3LYP-GD3BJ and MP2 levels.
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Affiliation(s)
- Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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4
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Corinti D, Paciotti R, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Elusive intermediates in cisplatin reaction with target amino acids: Platinum(II)-cysteine complexes assayed by IR ion spectroscopy and DFT calculations. J Inorg Biochem 2022; 237:112017. [PMID: 36209532 DOI: 10.1016/j.jinorgbio.2022.112017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 01/18/2023]
Abstract
The reactivity of a widely used metal based antineoplastic drug, cisplatin, cis-PtCl2(NH3)2, with L-cysteine (Cys) has been investigated using a combination of electrospray ionization mass spectrometry (ESI-MS), IRMPD gas phase ion spectroscopy and DFT calculations. The cysteine lateral chain represents one of the main platination sites in proteins, which is believed to be related to the resistance mechanisms to cisplatin. The vibrational features of the mass-selected substitution product cis-[PtCl(NH3)2(Cys)]+ and the intercepted cis-[PtCl(NH3)2(H2O)(Cys)]+ intermediate complex were compared to calculated IR spectra, enabling the assessment of the sampled ions structures. In cis-[PtCl(NH3)2(Cys)]+, cysteine was found to bind platinum through the sulfur atom as a thiolate zwitterion, highlighting the enhanced acidity of the cysteine thiol group upon metal coordination. The cis-[PtCl(NH3)2(H2O)(Cys)]+ structure complies with the non-covalent encounter complex, formed by cis-[PtCl(NH3)2(H2O)]+ and neutral cysteine. This species is able to undergo the substitution process to produce cis-[PtCl(NH3)2(Cys)]+ when activated as a mass-isolated ion suggesting its participation in the reaction mechanism of cisplatin with cysteine in solution. Finally, the DFT-calculated energy profile for the substitution reaction was correlated with the peculiar gas-phase reactivity of this non-covalent complex, resulting to be 10-fold less reactive toward substitution than the corresponding methionine complex.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy.
| | - Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy.
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
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5
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Merx J, van Outersterp RE, Engelke UFH, Hendriks V, Wevers RA, Huigen MCDG, Waterval HWAH, Körver-Keularts IMLW, Mecinović J, Rutjes FPJT, Oomens J, Coene KLM, Martens J, Boltje TJ. Identification of Δ-1-pyrroline-5-carboxylate derived biomarkers for hyperprolinemia type II. Commun Biol 2022; 5:997. [PMID: 36131087 PMCID: PMC9492674 DOI: 10.1038/s42003-022-03960-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
Hyperprolinemia type II (HPII) is an inborn error of metabolism due to genetic variants in ALDH4A1, leading to a deficiency in Δ-1-pyrroline-5-carboxylate (P5C) dehydrogenase. This leads to an accumulation of toxic levels of P5C, an intermediate in proline catabolism. The accumulating P5C spontaneously reacts with, and inactivates, pyridoxal 5’-phosphate, a crucial cofactor for many enzymatic processes, which is thought to be the pathophysiological mechanism for HPII. Here, we describe the use of a combination of LC-QTOF untargeted metabolomics, NMR spectroscopy and infrared ion spectroscopy (IRIS) to identify and characterize biomarkers for HPII that result of the spontaneous reaction of P5C with malonic acid and acetoacetic acid. We show that these biomarkers can differentiate between HPI, caused by a deficiency of proline oxidase activity, and HPII. The elucidation of their molecular structures yields insights into the disease pathophysiology of HPII. Combined metabolomics, NMR, and, IRIS identify biomarkers of hyperprolinemia type II (HPII) distinct from HPI and similar metabolic signatures as in patients with pyridoxine-dependent epilepsy.
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Affiliation(s)
- Jona Merx
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Udo F H Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands
| | - Veronique Hendriks
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands
| | - Marleen C D G Huigen
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands
| | - Huub W A H Waterval
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Irene M L W Körver-Keularts
- United for Metabolic Disease, UMD, Amsterdam, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Floris P J T Rutjes
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands.,Department of Clinical Chemistry and Hematology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands.
| | - Thomas J Boltje
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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6
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Lu L, Li RZ, Xu XY. Interaction of Cysteine with Li + and LiF in the Presence of (H 2O) n ( n = 0-6) Clusters. ACS OMEGA 2022; 7:18646-18659. [PMID: 35694486 PMCID: PMC9178773 DOI: 10.1021/acsomega.2c01315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The interaction between cysteine with Li+ and LiF in the microcosmic water environment was investigated to elucidate how ions interact with amino acids and the cation-anion correlation effect involved. The structures of Cys·Li+(H2O) n and Cys·LiF(H2O) n (n = 0-6) were characterized using ab initio calculations. Our studies show that the water preferentially interacts with Li+/LiF. In Cys·Li+(H2O)0-6, Li+ interacts with amino nitrogen, carbonyl oxygen, and hydrophobic sulfur of Cys to form a tridentate mode, whereas in Cys·LiF(H2O) n , Li+ and F- work in cooperation and interact with carbonyl oxygen and hydroxyl hydrogen of Cys to form a bidentate type. The neutral and zwitterionic forms are essentially isoenergetic when the water number reaches three in the presence of Li+, whereas this occurs at four water molecules in the presence of LiF. Further research revealed that the interaction between Li+/LiF and Cys was mainly electrostatic, followed by dispersion, and the weakest interaction occurs at the transition from the neutral form to zwitterionic form. Natural population analysis charge analyses show that for Cys·Li+(H2O) n , the positive charge is mostly concentrated on Li+ except for the system containing three water molecules. For Cys·LiF(H2O) n , the positive charge is centered on the LiF unit in the range n = 0-6, and at n = 5, electron transfer from Cys to water occurs. Our study shows that the contribution of anions in zwitterionic state stabilization should be addressed more generally along with cations.
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7
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van Outersterp R, Engelke UF, Merx J, Berden G, Paul M, Thomulka T, Berkessel A, Huigen MC, Kluijtmans LA, Mecinović J, Rutjes FP, van Karnebeek CD, Wevers RA, Boltje TJ, Coene KL, Martens J, Oomens J. Metabolite Identification Using Infrared Ion Spectroscopy─Novel Biomarkers for Pyridoxine-Dependent Epilepsy. Anal Chem 2021; 93:15340-15348. [PMID: 34756024 PMCID: PMC8613736 DOI: 10.1021/acs.analchem.1c02896] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022]
Abstract
Untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics strategies are being increasingly applied in metabolite screening for a wide variety of medical conditions. The long-standing "grand challenge" in the utilization of this approach is metabolite identification─confidently determining the chemical structures of m/z-detected unknowns. Here, we use a novel workflow based on the detection of molecular features of interest by high-throughput untargeted LC-MS analysis of patient body fluids combined with targeted molecular identification of those features using infrared ion spectroscopy (IRIS), effectively providing diagnostic IR fingerprints for mass-isolated targets. A significant advantage of this approach is that in silico-predicted IR spectra of candidate chemical structures can be used to suggest the molecular structure of unknown features, thus mitigating the need for the synthesis of a broad range of physical reference standards. Pyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine metabolism, resulting from a mutation in the ALDH7A1 gene that leads to an accumulation of toxic levels of α-aminoadipic semialdehyde (α-AASA), piperideine-6-carboxylate (P6C), and pipecolic acid in body fluids. While α-AASA and P6C are known biomarkers for PDE in urine, their instability makes them poor candidates for diagnostic analysis from blood, which would be required for application in newborn screening protocols. Here, we use combined untargeted metabolomics-IRIS to identify several new biomarkers for PDE-ALDH7A1 that can be used for diagnostic analysis in urine, plasma, and cerebrospinal fluids and that are compatible with analysis in dried blood spots for newborn screening. The identification of these novel metabolites has directly provided novel insights into the pathophysiology of PDE-ALDH7A1.
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Affiliation(s)
- Rianne
E. van Outersterp
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Udo F.H. Engelke
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jona Merx
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Mathias Paul
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Thomas Thomulka
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Albrecht Berkessel
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Marleen C.D.G. Huigen
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo A.J. Kluijtmans
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jasmin Mecinović
- University
of Southern Denmark, Department of Physics,
Chemistry and Pharmacy, Campusvej 55, 5230 Odense, Denmark
| | - Floris P.J.T. Rutjes
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Clara D.M. van Karnebeek
- Department
of Pediatrics-Metabolic Diseases, Radboud Center for Mitochondrial
Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Thomas J. Boltje
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Karlien L.M. Coene
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 908, 1098XH Amsterdam, The Netherlands
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8
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Corinti D, Chiavarino B, Scuderi D, Fraschetti C, Filippi A, Fornarini S, Crestoni ME. Molecular Properties of Bare and Microhydrated Vitamin B5-Calcium Complexes. Int J Mol Sci 2021; 22:ijms22020692. [PMID: 33445631 PMCID: PMC7826572 DOI: 10.3390/ijms22020692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]−, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Debora Scuderi
- Institut de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France;
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
- Correspondence: ; Tel.: +39-06-4991-3596
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9
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Stevenson BC, Martens J, Berden G, Oomens J, Schäfer M, Armentrout PB. IRMPD Spectroscopic and Theoretical Structural Investigations of Zinc and Cadmium Dications Bound to Histidine Dimers. J Phys Chem A 2020; 124:10266-10276. [PMID: 33241937 DOI: 10.1021/acs.jpca.0c08861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallated gas-phase structures consisting of a deprotonated and an intact histidine (His) ligand, yielding M(His-H)(His)+, where M = Zn and Cd, were examined with infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light from a free-electron laser (FEL). In parallel, quantum chemical calculations identified several low-energy isomers for each complex. Experimental action spectra were compared to linear spectra calculated at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for the zinc and cadmium complexes, respectively. For both Zn and Cd species, the definitive assignment is complicated by conflicting relative energetics, which were calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels. Spectral comparison for both species indicates that the dominant conformation, [Nα,Nπ,CO-][CO2-](NπH+), has the deprotonated His chelating the metal at the amine nitrogen, π nitrogen of the imidazole ring, and the deprotonated carbonyl oxygen and that the intact His ligand adopts a salt-bridge bidentate binding motif, coordinating the metal with both carboxylate oxygens. There is also evidence for a conformation where the deprotonated His coordination is maintained, but the intact His ligand adopts a more canonical structure, coordinating with the metal atom at the amine nitrogen and π nitrogen, [Nα,Nπ,CO-][Nα,Nπ]gtgg. For both metallated species, B3LYP, B3P86, and B3LYP-GD3BJ levels of theory appear to describe the relative stability of the dominant zwitterionic species more accurately than the MP2(full) level.
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Affiliation(s)
- Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL, 1098 XH Amsterdam, The Netherlands
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, 50939 Cologne, Germany
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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10
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Boles GC, Stevenson BC, Hightower RL, Berden G, Oomens J, Armentrout PB. Zinc and cadmium complexation of L-methionine: An infrared multiple photon dissociation spectroscopy and theoretical study. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4580. [PMID: 32677757 DOI: 10.1002/jms.4580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Methionine (Met) cationized with Zn2+ , forming Zn (Met-H)+ (ACN) where ACN = acetonitrile, Zn (Met-H)+ , and ZnCl+ (Met), as well as Cd2+ , forming CdCl+ (Met), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from the FELIX free electron laser. A series of low-energy conformers for each complex was found using quantum-chemical calculations in order to identify the structures formed experimentally. For all four complexes, spectral comparison indicated that the main binding motif observed is a charge solvated, tridentate structure where the metal center binds to the backbone amino group nitrogen, backbone carbonyl oxygen (where the carboxylic acid is deprotonated in two of the Zn2+ complexes), and side-chain sulfur. For all species, the predicted ground structures reproduce the experimental spectra well, although low-lying conformers characterized by similar binding motifs may also contribute in each system. The current work provides valuable information regarding the binding interaction between Met and biologically relevant metals. Further, the comparison between the current work and previous analyses involving alkali metal cationized Met as well as cysteine (the other sulfur containing amino acid) cationized with Zn2+ and Cd2+ allows for the elucidation of important metal dependent trends associated with physiologically important metal-sulfur binding.
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Affiliation(s)
- Georgia C Boles
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | | | - Randy L Hightower
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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11
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Boles GC, Hightower RL, Berden G, Oomens J, Armentrout PB. Zinc and Cadmium Complexation of l-Threonine: An Infrared Multiple Photon Dissociation Spectroscopy and Theoretical Study. J Phys Chem B 2019; 123:9343-9354. [DOI: 10.1021/acs.jpcb.9b08184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgia C. Boles
- Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Randy L. Hightower
- Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
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12
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McNary CP, Nei YW, Maitre P, Rodgers MT, Armentrout PB. Infrared multiple photon dissociation action spectroscopy of protonated glycine, histidine, lysine, and arginine complexed with 18-crown-6 ether. Phys Chem Chem Phys 2019; 21:12625-12639. [PMID: 31155616 DOI: 10.1039/c9cp02265a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Complexes of 18-crown-6 ether (18C6) with four protonated amino acids (AAs) are examined using infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by the infrared free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO). The AAs examined in this work include glycine (Gly) and the three basic AAs: histidine (His), lysine (Lys), and arginine (Arg). To identify the (AA)H+(18C6) conformations present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP/6-311+G(d,p) level of theory. Relative energies of various conformers and isomers are provided by single point energy calculations carried out at the B3LYP, B3P86, M06, and MP2(full) levels using the 6-311+G(2p,2d) basis set. The comparisons between the IRMPD and theoretical IR spectra indicate that 18C6 binds to Gly and His via the protonated backbone amino group, whereas protonated Lys prefers binding via the protonated side-chain amino group. Results for Arg are less definitive with strong evidence for binding to the protonated guanidino side chain (the calculated ground conformer at most levels of theory), but contributions from backbone binding to a zwitterionic structure are likely.
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Affiliation(s)
- Christopher P McNary
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, Utah 84112, USA.
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Philippe Maitre
- Université Paris Sud, Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Bâtiment 350, 91405 Orsay Cedex, France
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, Utah 84112, USA.
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13
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Corinti D, Maccelli A, Chiavarino B, Maitre P, Scuderi D, Bodo E, Fornarini S, Crestoni ME. Vibrational signatures of curcumin's chelation in copper(II) complexes: An appraisal by IRMPD spectroscopy. J Chem Phys 2019; 150:165101. [PMID: 31042893 DOI: 10.1063/1.5086666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Curcumin (Cur) is a natural polyphenol with a wide spectrum of biological activities and appealing therapeutic potential. Herein, it has been delivered by electrospray ionization as gaseous protonated species, [Cur + H]+, and as a Cu(ii) complex, [Cu(Cur - H)]+, a promising antioxidant and radical scavenger. The gas phase structures were assayed by infrared multiple photon dissociation (IRMPD) spectroscopy in both the fingerprint (800-2000 cm-1) and hydrogen stretching (3100-3750 cm-1) ranges. Comparison between the experimental features and linear IR spectra of the lowest energy structures computed at the B3LYP/6-311+G(d,p) level reveals that bare [Cu(Cur - H)]+ exists in a fully planar and symmetric arrangement, where the metal interacts with the two oxygens of the syn-enolate functionality of deprotonated Cur and both OCH3 groups are engaged in H-bonding with the ortho OH. The effect of protonation on the energetic and geometric determinants of Cur has been explored as well, revealing that bare [Cur + H]+ may exist as a mixture of two close-lying isomers associated with the most stable binding motifs. The additional proton is bound to either the diketo or the keto-enol configuration of Cur, in a bent or nearly planar arrangement, respectively.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Alessandro Maccelli
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Enrico Bodo
- Dipartimento di Chimica, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
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14
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Owen CJ, Boles GC, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of lysine complexes with Zn 2+ and Cd 2. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:97-111. [PMID: 30526028 DOI: 10.1177/1469066718792902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The gas-phase structures of zinc and cadmium complexes of lysine (Lys) are investigated via a combination of infrared multiple photon dissociation action spectroscopy and ab initio quantum chemical calculations. In order to unambiguously identify the experimentally observed species, [Zn(Lys-H)]+ and CdCl+(Lys), the action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using 6-311+G(d,p) and def2-TVZP basis sets for the zinc and cadmium systems, respectively. Single point energies were also calculated at the B3LYP, B3P86, MP2, and B3LYP-GD3BJ (accounting for empirical dispersion) levels of theory using larger basis sets. Identification of the experimentally formed isomers is possible through good agreement between infrared multiple photon dissociation action spectra and the theoretically predicted spectra. The [Zn(Lys-H)]+ complex adopts a tridentate orientation involving the amino acid backbone amine and deprotonated carboxylic acid groups as well as the side-chain amine group, [Nα,CO-,Nɛ]. The CdCl+(Lys) complex similarly adopts a tridentate chelation involving the amino acid backbone amine and carbonyl groups, as well as the side-chain amine group, [Nα,CO,Nɛ]. In both cases, the identified complexes are the lowest energy gas-phase structures at all levels of theory.
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Affiliation(s)
- Cameron J Owen
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| | - Georgia C Boles
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| | - Giel Berden
- 2 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- 2 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- 3 Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P B Armentrout
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
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15
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McPherson JN, Elton TE, Colbran SB. A Strain-Deformation Nexus within Pincer Ligands: Application to the Spin States of Iron(II) Complexes. Inorg Chem 2018; 57:12312-12322. [DOI: 10.1021/acs.inorgchem.8b02038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- James N. McPherson
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Timothy E. Elton
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Stephen B. Colbran
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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16
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Smith ZM, Steinmetz V, Martens J, Oomens J, Poutsma JC. Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation †. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 429:158-173. [PMID: 29962900 PMCID: PMC6020040 DOI: 10.1016/j.ijms.2017.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH+, CavLi+, and CavNa+; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK+ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs+ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa+ and ArgK+. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na+, K+, and Cs+. A major difference between the zwitterionic forms of ArgM+ and CavM+ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.
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Affiliation(s)
- Zachary M Smith
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris Sud, Université Paris Saclay, CNRS, Orsay France
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences University of Amsterdam, Amsterdam, The Netherlands
| | - John C Poutsma
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
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17
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Cao W, Hewage D, Yang DS. Spectroscopy and formation of lanthanum-hydrocarbon radicals formed by association and carbon-carbon bond cleavage of isoprene. J Chem Phys 2018; 148:194302. [PMID: 30307187 DOI: 10.1063/1.5026899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
La atom reaction with isoprene is carried out in a laser-vaporization molecular beam source. The reaction yields an adduct as the major product and C-C cleaved and dehydrogenated species as the minor ones. La(C5H8), La(C2H2), and La(C3H4) are characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectra of all three species exhibit a strong origin band and several weak vibronic bands corresponding to La-ligand stretch and ligand-based bend excitations. La(C5H8) is a five-membered metallacycle, whereas La(C2H2) and La(C3H4) are three-membered rings. All three metallacycles prefer a doublet ground state with a La 6s1-based valence electron configuration and a singlet ion. The five-membered metallacycle is formed through La addition and isoprene isomerization, whereas the two three-membered rings are produced by La addition and insertion, hydrogen migration, and carbon-carbon bond cleavage.
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Affiliation(s)
- Wenjin Cao
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Dilrukshi Hewage
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Dong-Sheng Yang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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18
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Jadhav PD, Zuo Y, Shim YY, Shen J, Reaney MJT, Zhang N, Wang Y. Metal binding novel flaxseed peptides (linusorbs). Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.13786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Pramodkumar D. Jadhav
- Department of Plant Sciences; University of Saskatchewan; 51 Campus Drive Saskatoon SK S7N 5A8 Canada
| | - Yang Zuo
- Department of Plant Sciences; University of Saskatchewan; 51 Campus Drive Saskatoon SK S7N 5A8 Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory; Department of Food Science and Engineering; Jinan University; 601 Huangpu Avenue West Guangzhou Guangdong 510632 China
| | - Youn Young Shim
- Department of Plant Sciences; University of Saskatchewan; 51 Campus Drive Saskatoon SK S7N 5A8 Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory; Department of Food Science and Engineering; Jinan University; 601 Huangpu Avenue West Guangzhou Guangdong 510632 China
- Prairie Tide Chemicals Inc.; 102 Melville Street Saskatoon SK S7J 0R1 Canada
| | - Jianheng Shen
- Department of Plant Sciences; University of Saskatchewan; 51 Campus Drive Saskatoon SK S7N 5A8 Canada
| | - Martin J. T. Reaney
- Department of Plant Sciences; University of Saskatchewan; 51 Campus Drive Saskatoon SK S7N 5A8 Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory; Department of Food Science and Engineering; Jinan University; 601 Huangpu Avenue West Guangzhou Guangdong 510632 China
- Prairie Tide Chemicals Inc.; 102 Melville Street Saskatoon SK S7J 0R1 Canada
| | - Ning Zhang
- Guangdong Saskatchewan Oilseed Joint Laboratory; Department of Food Science and Engineering; Jinan University; 601 Huangpu Avenue West Guangzhou Guangdong 510632 China
| | - Yong Wang
- Guangdong Saskatchewan Oilseed Joint Laboratory; Department of Food Science and Engineering; Jinan University; 601 Huangpu Avenue West Guangzhou Guangdong 510632 China
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19
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Fraschetti C, Guarcini L, Zazza C, Mannina L, Circi S, Piccirillo S, Chiavarino B, Filippi A. Real time evolution of unprotected protonated galactosamine probed by IRMPD spectroscopy. Phys Chem Chem Phys 2018. [PMID: 29536991 DOI: 10.1039/c7cp07642h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conformational characterization of single α- and β-epimers of galactosamine in solution still remains an intriguing task because of their flexibility and ability to interconvert. This difficulty was circumvented by recording several "snapshots" of the epimerization process by means of fast ESI vaporization of a galactosamine·HCl sample solution at different times. Consequently, the so generated gaseous mixtures were spectroscopically investigated and the specific conformational features of both α- and β-epimers were assigned, despite the overlapping of several IR signals. Interestingly, from a comparison with time-resolved 1H-NMR data obtained for the same solutions, the catalyzing effect of the applied ESI technique in the anomerization process clearly emerges. Finally, the experimental data were supported using both the Density Functional Theory (DFT) and Block-Localized Wavefunction (BLW) approaches: the latter method was applied here for the first time for the investigation of charged species.
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Affiliation(s)
- C Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza-Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy.
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20
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Boles GC, Hightower RL, Coates RA, McNary CP, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Aspartic Acid Complexes with Zn2+ and Cd2+. J Phys Chem B 2018; 122:3836-3853. [DOI: 10.1021/acs.jpcb.8b00801] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Georgia C. Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Randy L. Hightower
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Christopher P. McNary
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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21
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Chalifoux AM, Boles GC, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of arginine complexes with Zn2+ and Cd2+. Phys Chem Chem Phys 2018; 20:20712-20725. [DOI: 10.1039/c8cp03484b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arginine (Arg) complexes with Zn2+ and Cd2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light from a free electron laser.
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Affiliation(s)
| | | | - Giel Berden
- Radboud University
- FELIX Laboratory
- Institute for Molecules and Materials
- NL-6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- FELIX Laboratory
- Institute for Molecules and Materials
- NL-6525 ED Nijmegen
- The Netherlands
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22
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Boles GC, Owen CJ, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of glutamic acid complexes with Zn2+and Cd2+. Phys Chem Chem Phys 2017; 19:12394-12406. [DOI: 10.1039/c7cp01786c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD of [Zn(Glu-H)ACN]+was particularly interesting because fragmentation of the amino acid was favored, rather than dissociation of the ACN ligand.
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Affiliation(s)
| | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
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23
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Power B, Rowe S, Fridgen TD. Ammoniated Complexes of Uracil and Transition Metal Ions: Structures of [M(Ura-H)(Ura)(NH3)]+ by IRMPD Spectroscopy and Computational Methods (M = Fe, Co, Ni, Cu, Zn, Cd). J Phys Chem B 2016; 121:58-65. [DOI: 10.1021/acs.jpcb.6b09614] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Barry Power
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
| | - Steven Rowe
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University, St. John’s, Newfoundland and Labrador, Canada A1B 3X7
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24
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Boles GC, Coates RA, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Asparagine Complexes with Zn2+ and Cd2+ and Their Deamidation Processes. J Phys Chem B 2016; 120:12486-12500. [DOI: 10.1021/acs.jpcb.6b10326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgia C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- van‘t
Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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25
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Scuderi D, Bodo E, Chiavarino B, Fornarini S, Crestoni ME. Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations. Chemistry 2016; 22:17239-17250. [PMID: 27808437 DOI: 10.1002/chem.201603298] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 01/02/2023]
Abstract
The redox activity of cysteine sulfur allows numerous post-translational protein modifications involved in the oxidative regulation of metabolism, in metal binding, and in signal transduction. A combined approach based on infrared multiple photon dissociation spectroscopy at the Centre Laser Infrarouge d'Orsay (CLIO) free electron laser facility, calculations of IR frequencies, and finite temperature ab initio molecular dynamics simulations has been employed to characterize the gas-phase structures of deprotonated cysteine sulfenic, sulfinic, and sulfonic acids, [cysSOx ]- (x=1, 2, 3, representing the number of S-bound oxygen atoms), which are key intermediates in the redox-switching chemistry of proteins. The ions show different structural motifs owing to preferential binding of the proton to either the carboxylate or sulfur-containing group. Due to the decreasing basicity of the sulfenic, sulfinic, and sulfonic terminals, the proton bound to SO- in [cysSO]- migrates to the carboxylate in [cysSO3 ]- , whereas it turns out to be shared in [cysSO2 ]- . Evidence is gathered that a mixture of close-lying low-energy conformers is sampled for each cysteine oxo form in a Paul ion trap at room temperature.
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Affiliation(s)
- Debora Scuderi
- Laboratoire de Chimie Physique d'Orsay, Faculté des Sciences, Université Paris Sud, UMR8000 CNRS, Bât 350, 91405, Orsay Cedex, France
| | - Enrico Bodo
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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Nieto P, Günther A, Berden G, Oomens J, Dopfer O. IRMPD Spectroscopy of Metalated Flavins: Structure and Bonding of Lumiflavin Complexes with Alkali and Coinage Metal Ions. J Phys Chem A 2016; 120:8297-8308. [PMID: 27690438 DOI: 10.1021/acs.jpca.6b08281] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavins are a fundamental class of biomolecules, whose photochemical properties strongly depend on their environment and their redox and metalation state. Infrared multiphoton dissociation (IRMPD) spectra of mass-selected isolated metal-lumiflavin ionic complexes (M+LF) are analyzed in the fingerprint range (800-1830 cm-1) to determine the bonding of lumiflavin with alkali (M = Li, Na, K, Cs) and coinage (M = Cu, Ag) metal ions. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron resonance mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by comparison to quantum chemical calculations at the B3LYP/cc-pVDZ level, yielding structure, binding energy, bonding mechanism, and spectral properties of the complexes. The most stable binding sites identified in the experiments involve metal bonding to the oxygen atoms of the two available CO groups of LF. Hence, CO stretching frequencies are a sensitive indicator of both the metal binding site and the metal bond strength. More than one isomer is observed for M = Li, Na, and K, and the preferred CO binding site changes with the size of the alkali ion. For Cs+LF, only one isomer is identified, although the energies of the two most stable structures differ by less than 7 kJ/mol. While the M+-LF bonds for alkali ions are mainly based on electrostatic forces, substantial covalent contributions lead to stronger bonds for the coinage metal ions. Comparison between lumiflavin and lumichrome reveals substantial differences in the metal binding motifs and interactions due to the different flavin structures.
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Affiliation(s)
- Pablo Nieto
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
| | - Alan Günther
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
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27
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Lesslie M, Lau JKC, Lawler JT, Siu KWM, Steinmetz V, Maître P, Hopkinson AC, Ryzhov V. Cysteine Radical/Metal Ion Adducts: A Gas-Phase Structural Elucidation and Reactivity Study. Chempluschem 2016; 81:444-452. [DOI: 10.1002/cplu.201500558] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Michael Lesslie
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| | - Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
- Department of Chemistry and Biochemistry; University of Windsor; Windsor ON N9B 3P4 Canada
| | - John T. Lawler
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
- Department of Chemistry and Biochemistry; University of Windsor; Windsor ON N9B 3P4 Canada
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique; Université Paris-Sud; UMR8000 CNRS; 91405 Orsay France
| | - Philippe Maître
- Laboratoire de Chimie Physique; Université Paris-Sud; UMR8000 CNRS; 91405 Orsay France
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
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28
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Coates RA, Boles GC, McNary CP, Berden G, Oomens J, Armentrout PB. Zn2+ and Cd2+ cationized serine complexes: infrared multiple photon dissociation spectroscopy and density functional theory investigations. Phys Chem Chem Phys 2016; 18:22434-45. [DOI: 10.1039/c6cp03805k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zinc and cadmium dications bind serine in tridentate structures at the amine and carbonyl groups and side-chain hydroxyl group.
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Affiliation(s)
| | | | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525ED Nijmegen
- The Netherlands
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29
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Ieritano C, Carr PJJ, Hasan M, Burt M, Marta RA, Steinmetz V, Fillion E, McMahon TB, Scott Hopkins W. The structures and properties of proton- and alkali-bound cysteine dimers. Phys Chem Chem Phys 2016; 18:4704-10. [DOI: 10.1039/c5cp07414b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proton-, lithium-, and sodium-bound cysteine dimers have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study.
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Affiliation(s)
| | | | - Moaraj Hasan
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | - Michael Burt
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | - Rick A. Marta
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | - Vincent Steinmetz
- Laboratoire Chimie Physique – CLIO
- Campus Universitaire
- d'Orsay
- Orsay
- France
| | - Eric Fillion
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
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30
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Boles GC, Coates RA, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Glutamine Complexes with Zn2+ and Cd2+. J Phys Chem B 2015; 119:11607-17. [DOI: 10.1021/acs.jpcb.5b06528] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgia C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- Van‘t
Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
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