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Neumann J, Schmidtsdorff S, Schmidt AH, Parr MK. Controlling the elution order of insulin and its analogs in sub-/supercritical fluid chromatography using methanesulfonic acid and 18-crown-6 as mobile phase additives. J Sep Sci 2023; 46:e2300520. [PMID: 37775313 DOI: 10.1002/jssc.202300520] [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: 07/21/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 10/01/2023]
Abstract
The purity analysis of therapeutic peptides can often be challenging, demanding the application of more than a single analytical technique. Supercritical fluid chromatography nowadays is a promising alternative to reversed-phase liquid chromatography, providing orthogonal and complementary information. This study investigated its applicability for the separation of human insulin, its analogs and degradation products. A previously published method development protocol for peptides up to 2000 Da was successfully applied to the higher molecular weight insulins (6 kDa). A single gradient method was optimized for all insulins using a Torus DEA column (100 × 3.0 mm, 1.7 μm), carbon dioxide and a modifier consisting of methanol/acetonitrile/water/methanesulfonic acid (65:35:2:0.1, v/v/v/v). Consecutively, the crown ether 18-crown-6, which is well known to complex charged lysine sidechains and other amino functionalities, was added to the modifier to evaluate its impact on selectivity. A decreased retention and a shift in the elution order for the insulins were observed. An inverse effect on retention was found when combined with a neutral stationary phase chemistry (Viridis BEH).
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Affiliation(s)
- Jonas Neumann
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
- Chromicent GmbH, Berlin, Germany
| | - Sebastian Schmidtsdorff
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
- Chromicent GmbH, Berlin, Germany
| | | | - Maria K Parr
- Department of Biology, Chemistry, and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
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2
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Maity D. Recent advances in the modulation of amyloid protein aggregation using the supramolecular host-guest approaches. Biophys Chem 2023; 297:107022. [PMID: 37058879 DOI: 10.1016/j.bpc.2023.107022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Misfolding of proteins is associated with many incurable diseases in human beings. Understanding the process of aggregation from monomers to fibrils, the characterization of all intermediate species, and the origin of toxicity is very challenging. Extensive research including computational and experimental shed some light on these tricky phenomena. Non-covalent interactions between amyloidogenic domains of proteins play a major role in their self-assembly which can be disrupted by designed chemical tools. This will lead to the development of inhibitors of detrimental amyloid formations. In supramolecular host-guest chemistry approaches, different macrocycles function as hosts for encapsulating hydrophobic guests, i.e. phenylalanine residues of proteins, in their hydrophobic cavities via non-covalent interactions. In this way, they can disrupt the interactions between adjacent amyloidogenic proteins and prevent their self-aggregation. This supramolecular approach has also emerged as a prospective tool to modify the aggregation of several amyloidogenic proteins. In this review, we discussed recent supramolecular host-guest chemistry-based strategies for the inhibition of amyloid protein aggregation.
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Affiliation(s)
- Debabrata Maity
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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3
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Zhou L, Liu Z, Guo Y, Liu S, Zhao H, Zhao S, Xiao C, Feng S, Yang X, Wang F. Ultraviolet Photodissociation Reveals the Molecular Mechanism of Crown Ether Microsolvation Effect on the Gas-Phase Native-like Protein Structure. J Am Chem Soc 2023; 145:1285-1291. [PMID: 36584399 DOI: 10.1021/jacs.2c11210] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Maintaining the protein high-order structures and interactions during the transition from aqueous solution to gas phase is essential to the structural analysis of native mass spectrometry (nMS). Herein, we systematically interrogate the effects of charge state and crown ether (CE) complexation on the gas-phase native-like protein structure by integrating nMS with 193 nm ultraviolet photodissociation (UVPD). The alterations of photofragmentation yields of protein residues and the charge site distribution of fragment ions reveal the specific sites and sequence regions where charge and CE take effect. Our results exhibit the CE complexation on protonated residues can largely alleviate the structure disruption induced by the intramolecular solvation of charged side chains. The influences of CE complexation and positive charge on gas-phase protein structure exhibit generally opposite trends because the CE microsolvation avoids the hydrogen-bonding formation between the charged side chains with backbone carbonyls. Thus, CE complexation leads to a more stable and native-like protein structure in the gas phase.
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Affiliation(s)
- Lingqiang Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.,CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjie Guo
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shiwen Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunlei Xiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shun Feng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Rodgers MT, Seidu YS, Israel E. Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1697-1715. [PMID: 35921530 DOI: 10.1021/jasms.2c00137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA nanotechnology has been employed to develop devices based on i-motif structures. The protonated cytosine-cytosine base pairs that stabilize i-motif conformations are favored under slightly acidic conditions. This unique property has enabled development of the first DNA molecular motor driven by pH changes. The ability to alter the stability and pH transition range of such DNA molecular motors is desirable. Understanding how i-motif structures are influenced by modifications, and which modifications enhance stability and/or affect the pH characteristics, are therefore of great interest. Here, the influence of 5-halogenation of the cytosine nucleobases on the base pairing of protonated cytidine nucleoside analogue base pairs is examined using complementary threshold collision-induced dissociation techniques and computational methods. The nucleoside analogues examined here include the 5-halogenated forms of the canonical DNA and RNA cytidine nucleosides. Comparisons among these systems and to the analogous canonical base pairs previously examined enable the influence of 5-halogenation and the 2'-hydroxy substituent on the base pairing to be elucidated. 5-Halogenation of the cytosine nucleobases is found to enhance the strength of base pairing of DNA base pairs and generally weakens the base pairing for RNA base pairs. Trends in the strength of base pairing indicate that both inductive and polarizability effects influence the strength of base pairing. Overall, the present results suggest that 5-halogenation, and in particular, 5-fluorination and 5-iodination, provide effective means of stabilizing DNA i-motif conformations for applications in nanotechnology, whereas only 5-iodination is effective for stabilizing RNA i-motif conformations but the enhancement in stability is less significant.
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Affiliation(s)
- M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Yakubu S Seidu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - E Israel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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5
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Zhang Z, Yao Y, He L, Hong T, Li S, Huang F, Stang PJ. Coordination-driven self-assembly of dibenzo-18-crown-6 functionalized Pt(II) metallacycles. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Zhu B, Yang J, Van R, Yang F, Yu Y, Yu A, Ran K, Yin K, Liang Y, Shen X, Yin W, Choi SH, Lu Y, Wang C, Shao Y, Shi L, Tanzi RE, Zhang C, Cheng Y, Zhang Z, Ran C. Epitope alteration by small molecules and applications in drug discovery. Chem Sci 2022; 13:8104-8116. [PMID: 35919434 PMCID: PMC9278120 DOI: 10.1039/d2sc02819k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/07/2022] [Indexed: 11/22/2022] Open
Abstract
Small molecules and antibodies are normally considered separately in drug discovery, except in the case of covalent conjugates. We unexpectedly discovered several small molecules that could inhibit or enhance antibody–epitope interactions which opens new possibilities in drug discovery and therapeutic modulation of auto-antibodies. We first discovered a small molecule, CRANAD-17, that enhanced the binding of an antibody to amyloid beta (Aβ), one of the major hallmarks of Alzheimer's disease, by stable triplex formation. Next, we found several small molecules that altered antibody–epitope interactions of tau and PD-L1 proteins, demonstrating the generality of this phenomenon. We report a new screening technology for ligand discovery, screening platform based on epitope alteration for drug discovery (SPEED), which is label-free for both the antibody and small molecule. SPEED, applied to an Aβ antibody, led to the discovery of a small molecule, GNF5837, that inhibits Aβ aggregation and another, obatoclax, that binds Aβ plaques and can serve as a fluorescent reporter in brain slices of AD mice. We also found a small molecule that altered the binding between Aβ and auto-antibodies from AD patient serum. SPEED reveals the sensitivity of antibody–epitope interactions to perturbation by small molecules and will have multiple applications in biotechnology and drug discovery. A screening platform based on epitope alteration for drug discovery (SPEED).![]()
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Affiliation(s)
- Biyue Zhu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
- Key Laboratory of Drug Targeting and Drug Delivery Systems, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jing Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Richard Van
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Fan Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Yue Yu
- Department of Chemistry and Chemical Biology, University of California, Merced, California, 95343, USA
| | - Astra Yu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Kathleen Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Keyi Yin
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Yingxia Liang
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Xunuo Shen
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Wei Yin
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Se Hoon Choi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Liang Shi
- Department of Chemistry and Chemical Biology, University of California, Merced, California, 95343, USA
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Can Zhang
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
| | - Yan Cheng
- Key Laboratory of Drug Targeting and Drug Delivery Systems, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Zhirong Zhang
- Key Laboratory of Drug Targeting and Drug Delivery Systems, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, Massachusetts, USA, 02129
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7
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Roy HA, Rodgers MT. 1-Alkyl-3-methylimidazolium cation binding preferences in hexafluorophosphate ionic liquid clusters determined using competitive TCID measurements and theoretical calculations. Phys Chem Chem Phys 2021; 23:18145-18162. [PMID: 34612278 DOI: 10.1039/d1cp02928b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ionic liquids (ILs) exhibit unique properties that have led to their development and widespread use for a variety of applications. Development efforts have generally focused on achieving desired macroscopic properties via tuning of the IL through variation of the cations and anions. Both the macroscopic and microscopic properties of an IL influence its tunability and thus feasibility of use for selected applications. Works geared toward a microscopic understanding of the nature and strength of the intrinsic cation-anion interactions of ILs have been limited to date. Specifically, the intrinsic strength of the cation-anion interactions in ILs is largely unknown. In previous work, we employed threshold collision-induced dissociation (TCID) approaches supported and enhanced by electronic structure calculations to determine the bond dissociation energies (BDEs) and characterize the nature of the cation-anion interactions in a series of four 2 : 1 clusters of 1-alkyl-3-methylimidazolium cations with the hexafluorophosphate anion, [2Cnmim:PF6]+. To examine the effects of the 1-alkyl chain on the structure and energetics of binding, the cation was varied over the series: 1-ethyl-3-methylimidazolium, [C2mim]+, 1-butyl-3-methylimidazolium, [C4mim]+, 1-hexyl-3-methylimidazolium, [C6mim]+, and 1-octyl-3-methylimidazolium, [C8mim]+. The variation in the strength of binding among these [2Cnmim:PF6]+ clusters was found to be similar in magnitude to the average experimental uncertainty in the measurements. To definitively establish an absolute order of binding among these [2Cnmim:PF6]+ clusters, we extend this work again using TCID and electronic structure theory approaches to include competitive binding studies of three mixed 2 : 1 clusters of 1-alkyl-3-methylimidazolium cations and the hexafluorophosphate anion, [Cn-2mim:PF6:Cnmim]+ for n = 4, 6, and 8. The absolute BDEs of these mixed [Cn-2mim:PF6:Cnmim]+ clusters as well as the absolute difference in the strength of the intrinsic binding interactions as a function of the cation are determined with significantly improved precision. By combining the thermochemical results of the previous independent and present competitive measurements, the BDEs of the [2Cnmim:PF6]+ clusters are both more accurately and more precisely determined. Comparisons are made to results for the analogous [2Cnmim:BF4]+ and [Cn-2mim:BF4:Cnmim]+ clusters previously examined to elucidate the effects of the [PF6]- and [BF4]- anions on the binding.
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Affiliation(s)
- H A Roy
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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8
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Roy HA, Rodgers MT. Nature and strength of intrinsic cation-anion interactions of 1-alkyl-3-methylimidazolium hexafluorophosphate clusters. Phys Chem Chem Phys 2021; 23:13405-13418. [PMID: 34105537 DOI: 10.1039/d1cp01130h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Imidazolium-based cations and the hexafluorophosphate anion are among the most commonly used ionic liquids (ILs). Yet, the nature and strength of the intrinsic cation-anion interactions, and how they influence the macroscopic properties of these ILs are still not well understood. Threshold collision-induced dissociation is utilized to determine the bond dissociation energies (BDEs) of the 2 : 1 clusters of 1-alkyl-3-methylimidazolium cations and the hexafluorophosphate anion, [2Cnmim:PF6]+. The cation, [Cnmim]+, is varied across the series, 1-ethyl-3-methylimidazolium [C2mim]+, 1-butyl-3-methylimidazolium [C4mim]+, 1-hexyl-3-methylimidazolium [C6mim]+, 1-octyl-3-methylimidazolium [C8mim]+, to examine the structural and energetic effects of the size of the 1-alkyl substituent of the cation on the binding to [PF6]-. Complementary electronic structure methods are employed for the [Cnmim]+ cations, (Cnmim:PF6) ion pairs, and [2Cnmim:PF6]+ clusters to elucidate details of the cation-anion interactions and their impact on structure and energetics. Multiple levels of theory are benchmarked with the measured BDEs including B3LYP, B3LYP-GD3BJ, and M06-2X each with the 6-311+G(d,p) basis set for geometry optimizations and frequency analyses and the 6-311+G(2d,2p) basis set for energetic determinations. The modest structural variation among the [Cnmim]+ cations produces only minor structural changes and variation in the measured BDEs of the [2Cnmim:PF6]+ clusters. Present results are compared to those previously reported for the analogous 1-alkyl-3-methylimidazolium tetrafluoroborate IL clusters to compare the effects of these anions on the nature and strength of the intrinsic binding interactions.
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Affiliation(s)
- H A Roy
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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9
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Abdelmouleh M, Lalande M, Nicol E, Frison G, van der Rest G, Poully JC. Chemical Processes Involving 18-Crown-6-Ether in Activated Noncovalent Complexes with Protonated Peptides. Chemphyschem 2021; 22:1243-1250. [PMID: 33881793 DOI: 10.1002/cphc.202100075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Indexed: 11/10/2022]
Abstract
These last decades, it has been widely assumed that 18-crown-6-ether (CE) plays a spectator role during the chemical processes occurring in isolated host-guest complexes between peptides or proteins and CE after activation in mass spectrometers. Our present experimental and theoretical results challenge this hypothesis by showing that CE can abstract a proton or a protonated molecule from protonated peptides after activation by collisions in argon or electron capture/transfer. Furthermore, thanks to comparison between experimental and calculated values of collision cross-sections, we demonstrate that CE can change binding site after electron transfer. We also propose detailed mechanisms for these processes.
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Affiliation(s)
- Marwa Abdelmouleh
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Mathieu Lalande
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Edith Nicol
- Laboratoire de Chimie Moléculaire, Ecole Polytech, Inst Polytech Paris, CNRS, 91128, Palaiseau, France
| | - Gilles Frison
- Laboratoire de Chimie Moléculaire, Ecole Polytech, Inst Polytech Paris, CNRS, 91128, Palaiseau, France.,Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, 75005, Paris, France
| | - Guillaume van der Rest
- Institut de Chimie Physique, Université Paris Saclay, CNRS, Bâtiment 349, 91405, Orsay, France
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
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10
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Roy HA, Rodgers MT. Absolute Trends and Accurate and Precise Gas-Phase Binding Energies of 1-Alkyl-3-Methylimidazolium Tetrafluoroborate Ionic Liquid Clusters from Combined Independent and Competitive TCID Measurements. J Phys Chem A 2020; 124:10199-10215. [PMID: 33231458 DOI: 10.1021/acs.jpca.0c07246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ionic liquid (IL) development efforts have focused on achieving desired properties via tuning of the IL through variation of the cations and anions. However, works geared toward a microscopic understanding of the nature and strength of the intrinsic cation-anion interactions of ILs have been rather limited such that the intrinsic strength of the cation-anion interactions in ILs is largely unknown. In previous work, we employed threshold collision-induced dissociation approaches supported and enhanced by electronic structure calculations to characterize the nature of the cation-anion interactions in and determine the bond dissociation energies (BDEs) of a series of four 2:1 clusters of 1-alkyl-3-methylimidazolium cations and tetrafluoroborate anions, [2Cnmim:BF4]+. The cation was varied over the series: 1-ethyl-3-methylimidazolium, [C2mim]+, 1-butyl-3-methylimidazolium, [C4mim]+, 1-hexyl-3-methylimidazolium, [C6mim]+, and 1-octyl-3-methylimidazolium, [C8mim]+, to determine the structural and energetic effects of the size of the 1-alkyl substituent on the binding. The variation in the strength of binding determined for these [2Cnmim:BF4]+ clusters was found to be similar in magnitude to the average experimental uncertainty in these determinations. To definitively establish an absolute order of binding among these [2Cnmim:BF4]+ clusters, we extend this work here to include competitive binding studies of three mixed 2:1 clusters of 1-alkyl-3-methylimidazolium cations and tetrafluoroborate anions, [Cn-2mim:BF4:Cnmim]+ for n = 4, 6, and 8. Importantly, the results of the present work simultaneously provide the absolute BDEs of these mixed [Cn-2mim:BF4:Cnmim]+ clusters and the absolute relative order of the intrinsic binding interactions as a function of the cation with significantly improved precision. Further, by combining the thermochemical results of the previous and present studies, the BDEs of the [2Cnmim:BF4]+ clusters are more accurately and precisely determined.
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Affiliation(s)
- H A Roy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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11
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Roy HA, Hamlow LA, Rodgers MT. Gas-Phase Binding Energies and Dissociation Dynamics of 1-Alkyl-3-Methylimidazolium Tetrafluoroborate Ionic Liquid Clusters. J Phys Chem A 2020; 124:10181-10198. [PMID: 33231466 DOI: 10.1021/acs.jpca.0c06297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ionic liquids (ILs) have become increasingly popular due to their useful and unique properties, yet there are still many unanswered questions regarding their fundamental interactions. In particular, details regarding the nature and strength of the intrinsic cation-anion interactions and how they influence the macroscopic properties of ILs are still largely unknown. Elucidating the molecular-level details of these interactions is essential to the development of better models for describing ILs and enabling the purposeful design of ILs with properties tailored for specific applications. Current uses of ILs are widespread and diverse and include applications for energy storage, electrochemistry, designer/green solvents, separations, and space propulsion. To advance the understanding of the energetics, conformations, and dynamics of gas-phase IL clustering relevant to space propulsion, threshold collision-induced dissociation approaches are used to measure the bond dissociation energies (BDEs) of the 2:1 clusters of 1-alkyl-3-methylimidazolium cations and tetrafluoroborate, [2Cnmim:BF4]+. The cation, [Cnmim]+, is varied across the series, 1-ethyl-3-methylimidazolium [C2mim]+, 1-butyl-3-methylimidazolium [C4mim]+, 1-hexyl-3-methylimidazolium [C6mim]+, and 1-octyl-3-methylimidazolium [C8mim]+, to examine the structural and energetic effects of the size of the 1-alkyl substituent on binding. Complementary electronic structure calculations are performed to determine the structures and energetics of the [Cnmim]+ and [BF4]- ions and their binding preferences in the (Cnmim:BF4) ion pairs and [2Cnmim:BF4]+ clusters. Several levels of theory, B3LYP, B3LYP-GD3BJ, and M06-2X, using the 6-311+G(d,p) basis set for geometry optimizations and frequency analyses and the 6-311+G(2d,2p) basis set for energetics, are benchmarked to examine their abilities to properly describe the nature of the binding interactions and to reproduce the measured BDEs. The modest structural variation among these [Cnmim]+ cations produces only minor structural changes and variation in the measured BDEs of the [2Cnmim:BF4]+ clusters. Present findings indicate that the dominant cation-anion interactions involve the 3-methylimidazolium moieties and that these clusters are sufficiently small that differences in packing effects associated with the variable length of the 1-alkyl substituents are not yet significant.
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Affiliation(s)
- H A Roy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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12
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Silzel JW, Murphree TA, Paranji RK, Guttman MM, Julian RR. Probing the Stability of Proline Cis/Trans Isomers in the Gas Phase with Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1974-1980. [PMID: 32808771 DOI: 10.1021/jasms.0c00242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although most peptide bonds in proteins exist in the trans configuration, when cis peptide bonds do occur, they can have major impact on protein structure and function. The rapid identification of cis peptide bonds is therefore an important task. Peptide bonds containing proline are more likely to adopt the cis configuration because the ring connecting the side chain and backbone in proline flattens the energetic landscape relative to amino acids with free side chains. Examples of cis proline isomers have been identified in both solution and in the gas phase by a variety of structure-probing methods. Mass spectrometry is an attractive potential method for identifying cis proline due to its speed and sensitivity; however, the question remains of whether cis/trans proline isomers originating in solution are preserved during ionization and manipulation within a mass spectrometer. Herein, we investigate the gas-phase stability of isolated solution-phase cis and trans proline isomers using a synthetic peptide sequence with a Tyr-Pro-Pro motif. A variety of dissociation methods were explored to evaluate their potential to distinguish cis/trans configuration, including collision-induced dissociation, radical-directed dissociation, and photodissociation. Only photodissociation employed in conjunction with extremely gentle electrospray and charge solvation by 18-crown-6 ether was able to distinguish cis/trans isomers for our model peptide, suggesting that any thermal activation during transfer or while in the gas phase leads to isomer scrambling. Furthermore, the necessity for 18-crown-6 suggests that intramolecular charge solvation taking place during electrospray ionization can override cis/trans isomer homogeneity. Overall, the results suggest that solution-phase cis/trans proline isomers are fragile and easily lost during electrospray, requiring careful selection of instrument parameters and consideration of charge solvation to prevent cis/trans scrambling.
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Affiliation(s)
- Jacob W Silzel
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rajan K Paranji
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos M Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan R Julian
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
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13
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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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14
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Complexes of Crown Ether Macrocycles with Methyl Guanidinium: Insights into the Capture of Charge in Peptides. Chemphyschem 2018; 19:2169-2175. [PMID: 29944200 DOI: 10.1002/cphc.201800596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 11/08/2022]
Abstract
Crown ethers are well known as modulating agents of protein function and interactions. The action of crown ethers is driven by an alteration of the charged moieties of proteins through the capping of cationic amino acid side chains. This study evaluates the conformational features involved in the binding of crown ethers to the side chain of arginine. For this purpose, isolated complexes of methyl guanidinium with 12-crown-4 and 18-crown-6 are characterized with infrared action vibrational spectroscopy and quantum chemical computations. The conformational landscapes of the two complexes comprise an extensive ensemble of conformations close in energy. In the 12-crown-4 complex, the crown ether has the plane of its backbone approximately perpendicular to that of the guanidinium moiety and coordinates to two or three of its NHδ+ bonds. In the 18-crown-6 complex, the crown ether backbone is partially folded and tilted with respect to guanidinium and fixes its position in order to facilitate up to a four-fold coordination in the complex. The access of the complexes to multiple conformations leads to broad band structures in the N-H stretching region of their vibrational spectra.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013, Seville, Spain
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013, Seville, Spain
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15
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Wan Q, Chen S, Badu-Tawiah AK. An integrated mass spectrometry platform enables picomole-scale real-time electrosynthetic reaction screening and discovery. Chem Sci 2018; 9:5724-5729. [PMID: 30079181 PMCID: PMC6050606 DOI: 10.1039/c8sc00251g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/29/2018] [Indexed: 12/21/2022] Open
Abstract
The identification of new electrosynthetic pathways enables environmentally friendly synthetic applications. However, the development of miniaturized screening procedures/platforms to expedite the discovery of electrooxidation reactions remains challenging. Herein, we developed an integrated system that serves as a reactor and ion source in a single experimental step using only picomole-scale reactants to monitor electrooxidation in real-time. This reaction screening platform utilizes the intrinsic electrochemical capabilities of nano-electrospray ionization mass spectrometry. We validated the feasibility of this method by reproducing three known electrochemical reactions. We also discovered two new electroorganic reaction pathways: (i) C-N dehydrodimerization of 8-methyl-1,2,3,4-tetrahydroquinoline to construct a novel quinoline skeleton, and (ii) TEMPO-mediated accelerated electrooxidative dehydrogenation of tetrahydroisoquinolines. Moreover, the radical cations and key intermediates captured by this screening platform provided direct evidence for the mechanism of these novel electrochemical reactions.
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Affiliation(s)
- Qiongqiong Wan
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , USA .
| | - Suming Chen
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , USA .
| | - Abraham K Badu-Tawiah
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , USA .
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16
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Mistarz UH, Rand KD. Installation, validation, and application examples of two instrumental setups for gas-phase HDX-MS analysis of peptides and proteins. Methods 2018; 144:113-124. [PMID: 29753788 DOI: 10.1016/j.ymeth.2018.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/17/2018] [Accepted: 05/04/2018] [Indexed: 01/15/2023] Open
Abstract
Gas-phase hydrogen/deuterium exchange measured by mass spectrometry in a millisecond timeframe after ESI (gas-phase HDX-MS) is a fast and sensitive, yet unharnessed method to analyze the primary- and higher-order structure, intramolecular and intermolecular interactions, surface properties, and charge location of peptides and proteins. During a gas-phase HDX-MS experiment, heteroatom-bound non-amide hydrogens are made to exchange with deuterium during a millisecond timespan after electrospray ionization (ESI) by reaction with the highly basic reagent ND3, enabling conformational analysis of protein states that are pertinent to the native solution-phase. Here, we describe two different instrumental approaches to enable gas-phase HDX-MS for analysis of peptides and proteins on high-resolution Q-TOF mass spectrometers. We include a description of the procedure and equipment required for successful installation as well as suggested procedures for testing, validation, and troubleshooting of a gas-phase HDX-MS setup. In the two described approaches, gas-phase HDX-MS are performed either immediately after ESI in the cone exit region by leading N2-gas over a deuterated ND3/D2O solution, or by leading purified ND3-gas into different traveling wave ion guides (TWIG) of the mass spectrometer. We envision that a detailed description of the two gas-phase HDX-MS setups and their practical implementation and validation can pave the way for gas-phase HDX-MS to become a more routinely used MS technique for structural analysis of peptides and proteins.
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Affiliation(s)
- Ulrik H Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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17
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Yuan GJ, Liu SX, Tian ZF, Ren XM. A high temperature reversible phase transition in a supramolecular complex of 15-crown-5 with tetraphenylboron sodium. NEW J CHEM 2018. [DOI: 10.1039/c8nj02754d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High temperature (391 K) reversible phase transition and large thermal hysteresis (19 K) was observed in 15-crown-5 clathrates: [Na(15-crown-5)][BPh4] (15-crown-5 = 1,4,7,10,13-pentaoxacyclopentadecane, NaBPh4 = sodium tetraphenylboron).
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Affiliation(s)
- Guo-Jun Yuan
- Key Laboratory of Advanced Functional Materials of Nanjing
- Department of Chemistry
- Nanjing Xiaozhuang University
- Nanjing 211171
- P. R. China
| | - Shao-Xian Liu
- Key Laboratory of Advanced Functional Materials of Nanjing
- Department of Chemistry
- Nanjing Xiaozhuang University
- Nanjing 211171
- P. R. China
| | - Zheng-Fang Tian
- School of Chemical Engineer
- Huanggang Normal University
- Huanggang 438000
- P. R. China
| | - Xiao-Ming Ren
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Chemistry & Molecular Engineering
- Nanjing Tech University
- Nanjing 210009
- P. R. China
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18
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Pereverzev AY, Kopysov V, Boyarkin OV. High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy. Angew Chem Int Ed Engl 2017; 56:15639-15643. [DOI: 10.1002/anie.201709437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
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19
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Pereverzev AY, Kopysov V, Boyarkin OV. High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
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20
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Wang J, Zhu HT, Chen S, Luan C, Xia Y, Shen Y, Li YX, Hua Y, Liang YM. Electrophilic Cyclization and Intermolecular Acetalation of 2-(4-Hydroxybut-1-yn-1-yl)benzaldehydes: Synthesis of Diiodinated Diepoxydibenzo[c,k][1,9]dioxacyclohexadecines. J Org Chem 2017; 82:10641-10649. [PMID: 28862460 DOI: 10.1021/acs.joc.7b01646] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An expedient strategy for the preparation of diiodinated diepoxydibenzo[c,k][1,9]dioxacyclohexadecines from readily available 2-(4-hydroxybut-1-yn-1-yl)benzaldehydes through electrophile-triggered tandem cyclization/intermolecular acetalation sequence has been presented. The electrophilic macrocyclization can be performed under mild conditions and in up to gram quantities. Moreover, palladium-catalyzed coupling and reduction reactions of the resulting iodides could efficiently afford oxa-macrocycles.
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Affiliation(s)
- Jia Wang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, People's Republic of China
| | - Hai-Tao Zhu
- Shannxi Key Laboratory of Phytochemistry, Baoji University of Arts and Sciences , Baoji 721013, People's Republic of China
| | - Si Chen
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, People's Republic of China
| | - Cheng Luan
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, People's Republic of China
| | - Yu Xia
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, People's Republic of China
| | - Yi Shen
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, People's Republic of China
| | - Ying-Xiu Li
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, People's Republic of China
| | - Yingxi Hua
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, People's Republic of China
| | - Yong-Min Liang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, People's Republic of China
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21
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Wu RR, Chen Y, Rodgers MT. Mechanisms and energetics for N-glycosidic bond cleavage of protonated 2'-deoxyguanosine and guanosine. Phys Chem Chem Phys 2016; 18:2968-80. [PMID: 26740232 DOI: 10.1039/c5cp05738h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental and theoretical investigations suggest that hydrolysis of N-glycosidic bonds generally involves a concerted SN2 or a stepwise SN1 mechanism. While theoretical investigations have provided estimates for the intrinsic activation energies associated with N-glycosidic bond cleavage reactions, experimental measurements to validate the theoretical studies remain elusive. Here we report experimental investigations for N-glycosidic bond cleavage of the protonated guanine nucleosides, [dGuo+H](+) and [Guo+H](+), using threshold collision-induced dissociation (TCID) techniques. Two major dissociation pathways involving N-glycosidic bond cleavage, resulting in production of protonated guanine or the elimination of neutral guanine are observed in competition for both [dGuo+H](+) and [Guo+H](+). The detailed mechanistic pathways for the N-glycosidic bond cleavage reactions observed are mapped via electronic structure calculations. Excellent agreement between the measured and B3LYP calculated activation energies and reaction enthalpies for N-glycosidic bond cleavage of [dGuo+H](+) and [Guo+H](+) in the gas phase is found indicating that these dissociation pathways involve stepwise E1 mechanisms in analogy to the SN1 mechanisms that occur in the condensed phase. In contrast, MP2 is found to significantly overestimate the activation energies and slightly overestimate the reaction enthalpies. The 2'-hydroxyl substituent is found to stabilize the N-glycosidic bond such that [Guo+H](+) requires ∼25 kJ mol(-1) more than [dGuo+H](+) to activate the glycosidic bond.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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22
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Bonner JG, Hendricks NG, Julian RR. Structural Effects of Solvation by 18-Crown-6 on Gaseous Peptides and TrpCage after Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1661-1669. [PMID: 27506205 DOI: 10.1007/s13361-016-1456-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 06/06/2023]
Abstract
Significant effort is being employed to utilize the inherent speed and sensitivity of mass spectrometry for rapid structural determination of proteins; however, a thorough understanding of factors influencing the transition from solution to gas phase is critical for correct interpretation of the results from such experiments. It was previously shown that combined use of action excitation energy transfer (EET) and simulated annealing can reveal detailed structural information about gaseous peptide ions. Herein, we utilize this method to study microsolvation of charged groups by retention of 18-crown-6 (18C6) in the gas phase. In the case of GTP (CEGNVRVSRE LAGHTGY), solvation of the 2+ charge state leads to reduced EET, whereas the opposite result is obtained for the 3+ ion. For the mini-protein C-Trpcage, solvation by 18C6 leads to dramatic increase in EET for the 3+ ion. Examination of structural details probed by molecular dynamics calculations illustrate that solvation by 18C6 alleviates the tendency of charged side chains to seek intramolecular solvation, potentially preserving native-like structures in the gas phase. These results suggest that microsolvation may be an important tool for facilitating examination of native-like protein structures in gas phase experiments. Graphical Abstract ᅟ.
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Affiliation(s)
- James G Bonner
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Nathan G Hendricks
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, CA, 92521, USA.
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23
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Wu RR, Rodgers MT. Tautomerization lowers the activation barriers for N-glycosidic bond cleavage of protonated uridine and 2'-deoxyuridine. Phys Chem Chem Phys 2016; 18:24451-9. [PMID: 27536972 DOI: 10.1039/c6cp03620a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The gas-phase conformations of protonated uridine, [Urd+H](+), and its 2'-deoxy form, protonated 2'-deoxyuridine, [dUrd+H](+), have been examined in detail previously by infrared multiple photon dissociation action spectroscopy techniques. Both 2,4-dihydroxy tautomers and O4 protonated conformers of [Urd+H](+) and [dUrd+H](+) were found to coexist in the experiments with the 2,4-dihydroxy tautomers dominating the population. In the present study, the kinetic energy dependence of the collision-induced dissociation behavior of [Urd+H](+) and [dUrd+H](+) are examined using a guided ion beam tandem mass spectrometer to probe the mechanisms and energetics for activated dissociation of these protonated nucleosides. The primary dissociation pathways observed involve N-glycosidic bond cleavage leading to competitive elimination of protonated or neutral uracil. The potential energy surfaces (PESs) for these N-glycosidic bond cleavage pathways are mapped out via electronic structure calculations for the mixture of 2,4-dihydroxy tautomers and O4 protonated conformers of [Urd+H](+) and [dUrd+H](+) populated in the experiments. The calculated activation energies (AEs) and heats of reaction (ΔHrxns) for N-glycosidic bond cleavage at both the B3LYP and MP2(full) levels of theory are compared to the measured values. The agreement between experiment and theory indicates that B3LYP provides better estimates of the energetics of the species along the PESs for N-glycosidic bond cleavage than MP2, and that the 2,4-dihydroxy tautomers, which are stabilized by strong hydrogen-bonding interactions, predominantly influence the observed threshold dissociation behavior of [Urd+H](+) and [dUrd+H](+).
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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24
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Wu RR, Rodgers MT. O2 Protonation Controls Threshold Behavior for N-Glycosidic Bond Cleavage of Protonated Cytosine Nucleosides. J Phys Chem B 2016; 120:4803-11. [PMID: 27159774 DOI: 10.1021/acs.jpcb.6b04388] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
IRMPD action spectroscopy studies of protonated 2'-deoxycytidine and cytidine, [dCyd+H](+) and [Cyd+H](+), have established that both N3 and O2 protonated conformers coexist in the gas phase. Threshold collision-induced dissociation (CID) of [dCyd+H](+) and [Cyd+H](+) is investigated here using guided ion beam tandem mass spectrometry techniques to elucidate the mechanisms and energetics for N-glycosidic bond cleavage. N-Glycosidic bond cleavage is observed as the major dissociation pathways resulting in competitive elimination of either protonated or neutral cytosine for both protonated cytosine nucleosides. Electronic structure calculations are performed to map the potential energy surfaces (PESs) for both N-glycosidic bond cleavage pathways observed. The molecular parameters derived from theoretical calculations are employed for thermochemical analysis of the energy-dependent CID data to determine the minimum energies required to cleave the N-glycosidic bond along each pathway. B3LYP and MP2(full) computed activation energies for N-glycosidic bond cleavage associated with elimination of protonated and neutral cytosine, respectively, are compared to measured values to evaluate the efficacy of these theoretical methods in describing the dissociation mechanisms and PESs for N-glycosidic bond cleavage. The 2'-hydroxyl of [Cyd+H](+) is found to enhance the stability of the N-glycosidic bond vs that of [dCyd+H](+). O2 protonation is found to control the threshold energies for N-glycosidic bond cleavage as loss of neutral cytosine from the O2 protonated conformers is found to require ∼25 kJ/mol less energy than the N3 protonated analogues, and the activation energies and reaction enthalpies computed using B3LYP exhibit excellent agreement with the measured thresholds for the O2 protonated conformers.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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25
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Mallon M, Dutt S, Schrader T, Crowley PB. Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin. Chembiochem 2016; 17:774-83. [PMID: 26818656 DOI: 10.1002/cbic.201500477] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 11/11/2022]
Abstract
Progress in the field of bio-supramolecular chemistry, the bottom-up assembly of protein-ligand systems, relies on a detailed knowledge of molecular recognition. To address this issue, we have characterised complex formation between human ubiquitin (HUb) and four supramolecular anions. The ligands were: pyrenetetrasulfonic acid (4PSA), p-sulfonato-calix[4]arene (SCLX4), bisphosphate tweezers (CLR01) and meso-tetrakis (4-sulfonatophenyl)porphyrin (TPPS), which vary in net charge, size, shape and hydrophobicity. All four ligands induced significant changes in the HSQC spectrum of HUb. Chemical shift perturbations and line-broadening effects were used to identify binding sites and to quantify affinities. Supporting data were obtained from docking simulations. It was found that these weakly interacting ligands bind to extensive surface patches on HUb. A comparison of the data suggests some general indicators for the protein-binding specificity of supramolecular anions. Differences in binding were observed between the cavity-containing and planar ligands. The former had a preference for the arginine-rich, flexible C terminus of HUb.
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Affiliation(s)
- Madeleine Mallon
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Som Dutt
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.
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26
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Rodgers MT, Armentrout PB. Cationic Noncovalent Interactions: Energetics and Periodic Trends. Chem Rev 2016; 116:5642-87. [PMID: 26953819 DOI: 10.1021/acs.chemrev.5b00688] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this review, noncovalent interactions of ions with neutral molecules are discussed. After defining the scope of the article, which excludes anionic and most protonated systems, methods associated with measuring thermodynamic information for such systems are briefly recounted. An extensive set of tables detailing available thermodynamic information for the noncovalent interactions of metal cations with a host of ligands is provided. Ligands include small molecules (H2, NH3, CO, CS, H2O, CH3CN, and others), organic ligands (O- and N-donors, crown ethers and related molecules, MALDI matrix molecules), π-ligands (alkenes, alkynes, benzene, and substituted benzenes), miscellaneous inorganic ligands, and biological systems (amino acids, peptides, sugars, nucleobases, nucleosides, and nucleotides). Hydration of metalated biological systems is also included along with selected proton-based systems: 18-crown-6 polyether with protonated peptides and base-pairing energies of nucleobases. In all cases, the literature thermochemistry is evaluated and, in many cases, reanchored or adjusted to 0 K bond dissociation energies. Trends in these values are discussed and related to a variety of simple molecular concepts.
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Affiliation(s)
- M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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27
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Nichols CM, Wang ZC, Yang Z, Lineberger WC, Bierbaum VM. Experimental and Theoretical Studies of the Reactivity and Thermochemistry of Dicyanamide: N(CN)2–. J Phys Chem A 2016; 120:992-9. [DOI: 10.1021/acs.jpca.5b12496] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Charles M. Nichols
- Department of Chemistry and
Biochemistry, JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Zhe-Chen Wang
- Department of Chemistry and
Biochemistry, JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Zhibo Yang
- Department of Chemistry and
Biochemistry, JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - W. Carl Lineberger
- Department of Chemistry and
Biochemistry, JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Veronica M. Bierbaum
- Department of Chemistry and
Biochemistry, JILA, University of Colorado, Boulder, Colorado 80309, United States
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28
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Wu RR, Rodgers MT. Mechanisms and energetics for N-glycosidic bond cleavage of protonated adenine nucleosides: N3 protonation induces base rotation and enhances N-glycosidic bond stability. Phys Chem Chem Phys 2016; 18:16021-32. [DOI: 10.1039/c6cp01445c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
N3 protonation induces base rotation and stabilizes the syn orientation of the adenine nucleobase of [dAdo+H]+ and [Ado+H]+via formation of a strong intramolecular N3H+⋯O5′ hydrogen-bonding interaction, which in turn influences the mechanisms and energetics for N-glycosidic bond cleavage.
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Affiliation(s)
- R. R. Wu
- Department of Chemistry
- Wayne State University
- Detroit
- USA
| | - M. T. Rodgers
- Department of Chemistry
- Wayne State University
- Detroit
- USA
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29
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Ye Q, Wang HT, Zhou L, Kong LH, Ye HY, Fu DW, Zhang Y. Phase transition metal–crown ether coordination compounds tuned by metal ions. Dalton Trans 2016; 45:1000-6. [DOI: 10.1039/c5dt02631h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
(15-Crown-5)(BiCl3) and (15-crown-5)(SbCl3) are discovered to show phase transitions above room temperature, where the phase transition temperature relates to the metal center.
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Affiliation(s)
- Qiong Ye
- Ordered Matter Science Research Center
- Southeast University
- Nanjing
- China
| | - Hui-Ting Wang
- Ordered Matter Science Research Center
- Southeast University
- Nanjing
- China
| | - Lin Zhou
- Ordered Matter Science Research Center
- Southeast University
- Nanjing
- China
| | - Li-Hui Kong
- Ordered Matter Science Research Center
- Southeast University
- Nanjing
- China
| | - Heng-Yun Ye
- Ordered Matter Science Research Center
- Southeast University
- Nanjing
- China
| | - Da-Wei Fu
- Ordered Matter Science Research Center
- Southeast University
- Nanjing
- China
| | - Yi Zhang
- Ordered Matter Science Research Center
- Southeast University
- Nanjing
- China
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30
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Qi Y, Volmer DA. Electron-capture dissociation for investigating host/guest complexes of 18-crown-6-ether and peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2316-2318. [PMID: 26522326 DOI: 10.1002/rcm.7399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/18/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Yulin Qi
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Dietrich A Volmer
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
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31
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Wang R, Yang B, Wu RR, Rodgers MT, Schäfer M, Armentrout PB. Guided ion beam and computational studies of the decomposition of a model thiourea protein cross-linker. J Phys Chem B 2015; 119:3727-42. [PMID: 25660315 DOI: 10.1021/jp512997z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The dissociation of protonated methyl-d3 thiourea-4-butyric acid methyl amide (1), a model of thiourea-based protein cross-linking compounds, is examined both experimentally and computationally. Using a guided ion beam tandem mass spectrometer (GIBMS), the threshold collision-induced dissociation (TCID) of [1 + H](+) with Xe is examined as a function of collision energy. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for four primary and four secondary dissociation pathways, after accounting for competition between channels, sequential dissociations, unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. Computations are used to explore the pathways for the various processes and elucidation of their rate-limiting transition states. These results indicate that dissociation is initiated by migration of the excess proton from sulfur to one of three nitrogen atoms in 1, similar to the "mobile proton" model of peptide fragmentation. The computational energies for the rate-limiting transition states are generally in good agreement with the experimentally derived threshold energies, with MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) results being particularly favorable. This good comparison validates the mechanisms explored theoretically and allows identification of the structures of the various product ions and neutrals.
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Affiliation(s)
- Ran Wang
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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32
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Marek A, Shaffer CJ, Pepin R, Slováková K, Laszlo KJ, Bush MF, Tureček F. Electron transfer reduction of the diazirine ring in gas-phase peptide ions. On the peculiar loss of [NH4O] from photoleucine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:415-431. [PMID: 25515220 DOI: 10.1007/s13361-014-1047-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/22/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
Electron transfer to gas-phase peptide ions with diazirine-containing amino acid residue photoleucine (L*) triggers diazirine ring reduction followed by cascades of residue-specific radical reactions. Upon electron transfer, substantial fractions of (GL*GGR +2H)(+[Symbol: see text]) cation-radicals undergo elimination of [NH(4)O] radicals and N(2)H(2) molecules from the side chain. The side-chain dissociations are particularly prominent on collisional activation of long-lived (GL*GGR +2H)(+[Symbol: see text]) cation-radicals formed by electron transfer dissociation of noncovalent peptide-18-crown-6-ether ion complexes. The ion dissociation products were characterized by multistage tandem mass spectrometry (MS(n)) and ion mobility measurements. The elimination of [NH(4)O] was elucidated with the help of (2)H, (15) N, and (18)O-labeled peptide ions and found to specifically involve the amide oxygen of the N-terminal residue. The structures, energies, and electronic states of the peptide radical species were elucidated by a combination of near-UV photodissociation experiments and electron structure calculations combining ab initio and density functional theory methods. Electron transfer reaching the ground electronic states of charge reduced (GL*GGR +2H)(+[Symbol: see text]) cation-radicals was found to reduce the diazirine ring. In contrast, backbone N - Cα bond dissociations that represent a 60%-75% majority of all dissociations because of electron transfer are predicted to occur from excited electronic states.
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Affiliation(s)
- Aleš Marek
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, 98195-1700, USA
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33
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Bythell BJ. Cα hydrogen atom transfer in post-cleavage radical-cation complexes: short and steep versus long winding road. J Phys Chem A 2014; 118:10797-803. [PMID: 25329622 DOI: 10.1021/jp507865h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recently, I explored structurally straightforward pathways to Cα hydrogen atom, H(•), transfer reactions in the radical cation complex following electron capture/transfer of a series of polyprotonated peptides (J. Phys. Chem. A 2013, 117, 1189-1196). Here, I extend my analysis to incorporate detailed rearrangement processes potentially occurring prior to H(•) transfer. This comprises intracomplex isomerization of the initial iminol-terminated (-C(OH)═NH) form of the cn' species to the energetically more favorable, amide-terminated form (-C(O)-NH2) prior to Cα H(•) abstraction by the zm(•) species. The data indicate that the previously published H(•) transfer barriers are more energetically demanding than those of this multistep alternative. The rate-determining step is typically the intracomplex iminol isomerization, consistent with the substantial energetic favorability of the amide form of the cn species. The barriers to H(•) transfer still rise steeply as a function of the charge state. In agreement with experiment, evidence for product separation without H(•) transfer at a higher charge state is also provided.
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Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis , St. Louis, Missouri 63121, United States
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34
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Tian Y, Zhang X, Li Y, Shoup TM, Teng X, Elmaleh DR, Moore A, Ran C. Crown ethers attenuate aggregation of amyloid beta of Alzheimer's disease. Chem Commun (Camb) 2014; 50:15792-5. [PMID: 25372154 DOI: 10.1039/c4cc06029f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this report, we reasoned that non-covalent modification of amyloid beta (Aβ) by crown ethers could inhibit its aggregation. We demonstrated that PiB-C, a conjugate PiB and crown ether, could significantly reduce the aggregation in vitro. Additionally, two-photon imaging showed that PiB-C could efficiently label Aβ plaques and CAAs in AD mice.
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Affiliation(s)
- Yanli Tian
- Molecular Imaging Laboratory, A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Building 75, Charlestown, Massachusetts 02129, USA.
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35
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Far J, Delvaux C, Kune C, Eppe G, de Pauw E. The Use of Ion Mobility Mass Spectrometry for Isomer Composition Determination Extracted from Se-Rich Yeast. Anal Chem 2014; 86:11246-54. [DOI: 10.1021/ac503142u] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Johann Far
- Department
of Chemistry, Laboratory of Mass Spectrometry, University of Liège, 3 Allée
de la chimie, B6C, Liege (Sart Tilman), B-4000, Belgium
| | - Cédric Delvaux
- Department
of Chemistry, Laboratory of Mass Spectrometry, University of Liège, 3 Allée
de la chimie, B6C, Liege (Sart Tilman), B-4000, Belgium
| | - Christopher Kune
- Department
of Chemistry, Laboratory of Mass Spectrometry, University of Liège, 3 Allée
de la chimie, B6C, Liege (Sart Tilman), B-4000, Belgium
| | - Gauthier Eppe
- Department
of Chemistry, Laboratory of Mass Spectrometry, University of Liège, 3 Allée
de la chimie, B6C, Liege (Sart Tilman), B-4000, Belgium
- Centre
of Analytical Research and Technology (CART) - LSM/Inorganic Analytical
Chemistry, Department of Chemistry, University of Liège, 3, Allee de la Chimie
B6C, Liege, 4000, Belgium
| | - Edwin de Pauw
- Department
of Chemistry, Laboratory of Mass Spectrometry, University of Liège, 3 Allée
de la chimie, B6C, Liege (Sart Tilman), B-4000, Belgium
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36
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Austin CA, Rodgers MT. Alkali Metal Cation–Hexacyclen Complexes: Effects of Alkali Metal Cation Size on the Structure and Binding Energy. J Phys Chem A 2014; 118:5488-500. [DOI: 10.1021/jp502275q] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. A. Austin
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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37
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Armentrout PB, Austin CA, Rodgers MT. Alkali Metal Cation Interactions with 15-Crown-5 in the Gas Phase: Revisited. J Phys Chem A 2014; 118:8088-97. [DOI: 10.1021/jp4116172] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. B. Armentrout
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - C. A. Austin
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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38
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Armentrout PB, Yang B, Rodgers MT. Metal Cation Dependence of Interactions with Amino Acids: Bond Dissociation Energies of Rb+ and Cs+ to the Acidic Amino Acids and Their Amide Derivatives. J Phys Chem B 2014; 118:4300-14. [DOI: 10.1021/jp5001754] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 E, Room 2020, Salt Lake City, Utah 84112, United States
| | - Bo Yang
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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39
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Zhang Q, Yu HZ, Fu Y. NHC-catalyzed homoenolate reaction of enals and nitroalkenes: computational study of mechanism, chemoselectivity and stereoselectivity. Org Chem Front 2014. [DOI: 10.1039/c4qo00036f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mechanistic study on the NHC-catalyzed homoenolate reaction of enals and nitroalkenes has been performed with the aid of DFT calculations.
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Affiliation(s)
- Qi Zhang
- Department of Chemistry
- University of Science and Technology of China
- Hefei, China
| | - Hai-Zhu Yu
- Department of Polymer Science and Engineering
- University of Science and Technology Beijing
- Beijing 100083, PR China
| | - Yao Fu
- Department of Chemistry
- University of Science and Technology of China
- Hefei, China
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40
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Yang B, Rodgers MT. Base-pairing energies of proton-bound heterodimers of cytosine and modified cytosines: implications for the stability of DNA i-motif conformations. J Am Chem Soc 2013; 136:282-90. [PMID: 24320604 DOI: 10.1021/ja409515v] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The DNA i-motif conformation was discovered in (CCG)•(CGG)n trinucleotide repeats, which are associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The DNA i-motif is a four-stranded structure whose strands are held together by proton-bound dimers of cytosine (C(+)•C). The stronger base-pairing interactions in C(+)•C proton-bound dimers as compared to Watson-Crick G•C base pairs are the major forces responsible for stabilization of i-motif conformations. Methylation of cytosine results in silencing of the FMR1 gene and causes fragile X syndrome. However, the influence of methylation or other modifications such as halogenation of cytosine on the base-pairing energies (BPEs) in the i-motif remains elusive. To address this, proton-bound heterodimers of cytosine and 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, and 5-iodocytosine are probed in detail. Experimentally, the BPEs of proton-bound heterodimers of cytosine and modified cytosines are determined using threshold collision-induced dissociation (TCID) techniques. All modifications at the 5-position of cytosine are found to lower the BPE and therefore would tend to destabilize DNA i-motif conformations. However, the BPEs in these proton-bound heterodimers still significantly exceed those of the Watson-Crick G•C and neutral C•C base pairs, suggesting that C(+)•C mismatches are still energetically favored such that i-motif conformations are preserved. Excellent agreement between TCID measured BPEs and B3LYP calculated values is found with the def2-TZVPPD and 6-311+G(2d,2p) basis sets, suggesting that calculations at these levels of theory can be employed to provide reliable energetic predictions for related systems.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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41
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Tao Y, Julian RR. Factors that influence competitive intermolecular solvation of protonated groups in peptides and proteins in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1634-40. [PMID: 23836378 PMCID: PMC3806280 DOI: 10.1007/s13361-013-0684-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/17/2013] [Accepted: 05/19/2013] [Indexed: 05/13/2023]
Abstract
The ability of 18-crown-6 (18C6) to form noncovalent complexes with cationic groups in the gas phase has been leveraged in numerous, largely orthogonal mass spectrometry-based applications. Although the fundamental interaction between 18C6 and a charged group in the gas phase is quite strong, the strength of attachment of 18C6 to large molecules is more difficult to predict because intramolecular binding of the cation can be competitive. Herein, we demonstrate in experiments with model peptides that 18C6 adducts are not strongly attached to flexible molecules with numerous potential hydrogen bonding sites. 18C6 adduct stability is increased if intramolecular charge complexation is inhibited by sterics or competitive binding. It is demonstrated with molecular mechanics that significant structural changes occur upon loss of 18C6 in model peptides. Examination of the loss of 18C6 adducts from proteins following collisional activation reveals that lower charge states lose the most 18C6. The degree of 18C6 adduct stability may reflect the degree of structural reorganization that occurs following collisional activation, suggesting that lower charge states represent structures that are not similar to gas phase idealized states. In this regard, 18C6 may serve the function of protecting solution phase protein structure. Collisional activation of holomyoglobin with 18C6 adducts attached reveals that heme loss occurs primarily after 18C6 loss, further supporting the notion that 18C6 protects native structure by solvating charged sites.
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Affiliation(s)
- Yuanqi Tao
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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42
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Chen Y, Chinthaka SDM, Rodgers MT. Silver cation affinities of monomeric building blocks of polyethers and polyphenols determined by guided ion beam tandem mass spectrometry. J Phys Chem A 2013; 117:8274-84. [PMID: 23914909 DOI: 10.1021/jp402224t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Energy-resolved collision-induced dissociation (CID) of seven silver cation-ligand complexes, Ag(+)(L), with Xe is studied using guided ion beam tandem mass spectrometry techniques. The ligands, L, investigated are monomeric building blocks of polyethers and polyphenols including phenol, 2-hydroxyphenol, 3-hydroxyphenol, 4-hydroxyphenol, 2-hydroxymethyl phenol, 3-hydroxymethyl phenol, and 4-hydroxymethyl phenol. In all cases, Ag(+) is observed as the primary CID product, corresponding to endothermic loss of the intact neutral ligand. The kinetic-energy-dependent cross sections for CID of these Ag(+)(L) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298 K Ag(+)-L bond dissociation energies (BDEs). Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of the neutral ligands and their complexes to Ag(+) using either the Stuttgart RSC 1997 valence basis set and effective core potential (SRSC ECP) or DZVP-DFT to describe Ag(+). Theoretical BDEs are determined at the B3LYP/6-311+G(2d,2p) level of theory again using the SRSC ECP or DZVP-DFT for Ag(+). For all systems, the most stable binding conformations found involve cation-π interactions when the SRSC ECP is used to describe Ag(+). When DZVP-DFT is employed, the most stable binding geometries remain cation-π complexes except for the complex to 2HP, where the ground-state conformer involves bidentate binding of Ag(+) to the hydroxyl oxygen atoms of both substituents. The agreement between the measured and calculated BDEs is excellent with a MAD of 2.9 ± 1.7 kJ/mol when the SRSC ECP is used to describe Ag(+) and less satisfactory for DZVP-DFT, which underestimates the strength of binding in these systems by ~14% or 26.0 ± 6.7 kJ/mol.
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Affiliation(s)
- Y Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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43
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Nose H, Rodgers MT. Energy-Resolved Collision-Induced Dissociation Studies of 2,2'-Bipyridine Complexes of the Late First-Row Divalent Transition-Metal Cations: Determination of the Third-Sequential Binding Energies. Chempluschem 2013; 78:1109-1123. [PMID: 31986729 DOI: 10.1002/cplu.201300156] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Indexed: 11/08/2022]
Abstract
The third-sequential binding energies of the late first-row divalent transition-metal cations with 2,2'-bipyridine (Bpy) are determined using guided-ion-beam tandem mass spectrometry (GIBMS) techniques. The metal cations investigated include the late first-row divalent transition-metal cations, Fe2+ , Co2+ , Ni2+ , Cu2+ , and Zn2+ . The kinetic-energy-dependent cross sections for collision-induced dissociation (CID) of the M2+ (Bpy)3 complexes are analyzed to extract absolute 0 and 298 K bond dissociation energies (BDEs) for the loss of an intact Bpy ligand. Theoretical electronic structure calculations at the B3LYP, BHandHLYP, and M06 levels of theory are performed to determine stable geometries and sequential BDEs of the M2+ (Bpy)x complexes (x=1-3). BDEs computed using the M06 functional are the largest, BHandHLYP values are intermediate, whereas B3LYP produces the smallest values. Very good agreement between the B3LYP theoretically calculated and threshold collision-induced dissociation experimentally determined BDEs is found, which suggests that the B3LYP functional is capable of accurately describing the binding in these M2+ (Bpy)3 complexes. Periodic trends in the binding of the M2+ (Bpy)x complexes are examined and compared to the analogous complexes with 1,10-phenanthroline (Phen), M2+ (Phen)x . Comparisons are also made to the analogous Bpy complexes, M+ (Bpy)x , with the late first-row monovalent transition-metal cations, Co+ , Ni+ , Cu+ , and Zn+ investigated previously.
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Affiliation(s)
- Holliness Nose
- Department of Chemistry, Wayne State University, Detroit, MI 48202 (USA), Fax: (+1) 313-577-8822
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI 48202 (USA), Fax: (+1) 313-577-8822
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44
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Nose H, Chen Y, Rodgers MT. Energy-resolved collision-induced dissociation studies of 1,10-phenanthroline complexes of the late first-row divalent transition metal cations: determination of the third sequential binding energies. J Phys Chem A 2013; 117:4316-30. [PMID: 23565706 DOI: 10.1021/jp401711c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated.
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Affiliation(s)
- Holliness Nose
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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45
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Armentrout PB, Rodgers MT. Thermochemistry of non-covalent ion-molecule interactions. Mass Spectrom (Tokyo) 2013; 2:S0005. [PMID: 24349924 PMCID: PMC3810359 DOI: 10.5702/massspectrometry.s0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 01/09/2013] [Indexed: 11/23/2022] Open
Abstract
The thermochemistry of non-covalent ion-molecule complexes has been examined by measuring quantitative bond dissociation energies using threshold collision-induced dissociation in guided ion beam tandem mass spectrometers (GIBMS). The methods used are briefly reviewed and several examples of the types of information and insight that can be obtained from such thermodynamic information are discussed. The hydration of metal cations, both singly and doubly charged, is reviewed and the trends elucidated, mainly on the basis of electrostatic contributions. The binding of alkali metal cations to amino acids has been examined for a range of systems, with both the overall polarizability of the amino acid and the local dipole moment of heteroatomic side-chains shown to be important contributors. The gas-phase interactions of the 12-crown-4 (12C4) polyether with alkali metal cations, classic molecular recognition systems in solution, have been newly compared to previous GIBMS work. These results validate the previous hypothesis that excited conformers were present for Rb(+)(12C4) and Cs(+)(12C4) and offer clues as to how and why they are formed.
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Armentrout PB, Yang B, Rodgers MT. Metal Cation Dependence of Interactions with Amino Acids: Bond Energies of Rb+ and Cs+ to Met, Phe, Tyr, and Trp. J Phys Chem B 2013; 117:3771-81. [DOI: 10.1021/jp401366g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake
City, Utah 84112, United States
| | - Bo Yang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United
States
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United
States
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Stedwell CN, Galindo JF, Roitberg AE, Polfer NC. Structures of biomolecular ions in the gas phase probed by infrared light sources. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:267-285. [PMID: 23560933 DOI: 10.1146/annurev-anchem-062012-092700] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.
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Affiliation(s)
- Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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Armentrout PB, Citir M, Chen Y, Rodgers MT. Thermochemistry of Alkali Metal Cation Interactions with Histidine: Influence of the Side Chain. J Phys Chem A 2012; 116:11823-32. [DOI: 10.1021/jp310179c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East,
Room 2020, Salt Lake City, Utah 84112, United States
| | - Murat Citir
- Department of Chemistry, University of Utah, 315 South 1400 East,
Room 2020, Salt Lake City, Utah 84112, United States
| | - Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan
48202, United States
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan
48202, United States
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Stedwell CN, Patrick AL, Gulyuz K, Polfer NC. Screening for Phosphorylated and Nonphosphorylated Peptides by Infrared Photodissociation Spectroscopy. Anal Chem 2012; 84:9907-12. [DOI: 10.1021/ac3023058] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Corey N. Stedwell
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Amanda L. Patrick
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Kerim Gulyuz
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Nicolas C. Polfer
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
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50
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Chen Y, Rodgers MT. Structural and energetic effects in the molecular recognition of acetylated amino acids by 18-crown-6. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2020-2030. [PMID: 22926972 DOI: 10.1007/s13361-012-0466-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 07/25/2012] [Accepted: 07/31/2012] [Indexed: 06/01/2023]
Abstract
Absolute 18-crown-6 (18C6) binding affinities of four protonated acetylated amino acids (AcAAs) are determined using guided ion beam tandem mass spectrometry techniques. The AcAAs examined in this work include: N-terminal acetylated lysine (N(α)-AcLys), histidine (N(α)-AcHis), and arginine (N(α)-AcArg) as well as side chain acetylated lysine (N(ε)-AcLys). The kinetic-energy-dependent cross sections for collision-induced dissociation (CID) of the (AcAA)H(+)(18C6) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298 K (AcAA)H(+)-18C6 bond dissociation energies (BDEs) after accounting for the effects of multiple collisions, kinetic and internal energy distributions of the reactants, and unimolecular dissociation lifetimes. Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AcAAs as well as the proton bound complexes of these species, (AcAA)H(+)(18C6), at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31 G* and M06/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory. For all four (AcAA)H(+)(18C6) complexes, loss of neutral 18C6 corresponds to the most favorable dissociation pathway. At elevated energies, products arising from sequential dissociation of the primary CID product, H(+)(AcAA), are also observed. Protonated N(α)-AcLys exhibits a greater 18C6 binding affinity than other protonated N(α)-AcAAs, suggesting that the side chains of Lys residues are the preferred binding sites for 18C6 complexation to peptides and proteins. N(α)-AcLys exhibits a greater 18C6 binding affinity than N(ε)-AcLys, suggesting that binding of 18C6 to the side chain of Lys residues is more favorable than to the N-terminal amino group of Lys.
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Affiliation(s)
- Yu Chen
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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