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Benny J, Saito T, Liu J. Nitrosation mechanisms, kinetics, and dynamics of the guanine and 9-methylguanine radical cations by nitric oxide-Radical-radical combination at different electron configurations. J Chem Phys 2024; 161:125101. [PMID: 39319660 DOI: 10.1063/5.0230367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 09/06/2024] [Indexed: 09/26/2024] Open
Abstract
As a precursor to various reactive nitrogen species formed in biological systems, nitric oxide (•NO) participates in numerous processes, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. Forming guanine radical cations is another common DNA lesion resulting from ionization and oxidation damage. As such, the interaction of •NO with guanine radical cations (G•+) may contribute to the radiosensitization of •NO. An intriguing aspect of this process is the participation of multiple spin configurations in the reaction, including open-shell singlet 1,OS[G•+(↑)⋯(↓)•NO], closed-shell singlet 1,CS[G(↑↓)⋯NO+], and triplet 3[G•+(↑)⋯(↑)•NO]. In this study, the reactions of •NO with both unsubstituted guanine radical cations (in the 9HG•+ conformation) and 9-methylguanine radical cations (9MG•+, a guanosine-mimicking model compound) were investigated in the absence and presence of monohydration of radical cations. Kinetic-energy dependent reaction product ions and cross sections were measured using an electrospray ionization guided-ion beam tandem mass spectrometer. The reaction mechanisms, kinetics, and dynamics were comprehended by interpreting the reaction potential energy surface using spin-projected density functional theory, coupled cluster theory, and multiconfiguration complete active space second-order perturbation theory, followed by RRKM kinetics modeling. The combined experimental and computational findings revealed closed-shell singlet 1,CS[7-NO-9MG]+ as the major, exothermic product and triplet 3[8-NO-9MG]+ as the minor, endothermic product. Singlet biradical products were not detected due to high reaction endothermicities, activation barriers, and inherent instability.
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Affiliation(s)
- Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, the Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 731-3194 Hiroshima, Japan
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, the Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
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2
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Sergent I, Schutz T, Lutz JF, Charles L. Using ion mobility spectrometry to understand signal dilution during tandem mass spectrometry sequencing of digital polymers: Experimental evidence of intramolecular cyclization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9852. [PMID: 38924174 DOI: 10.1002/rcm.9852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
RATIONALE Optimizing the structure of digital polymers is an efficient strategy to ensure their tandem mass spectrometry (MS/MS) readability. In block-truncated poly(phosphodiester)s, homolysis of C-ON bonds in long chains permits the release of smaller blocks amenable to sequencing. Yet the dissociation behavior of diradical blocks was observed to strongly depend on their charge state. METHODS Polymers were ionized in negative mode electrospray and activated in-source so that blocks released as primary fragments can be investigated using ion mobility spectrometry (IMS) or sequenced in the post-IMS collision cell. Collision cross sections (CCS) were derived from arrival times using a calibration procedure developed for polyanions using the IMSCal software. A multistep protocol based on quantum methods and classical molecular dynamics was implemented for molecular modeling and calculation of theoretical CCS. RESULTS Unlike their triply charged homologues, dissociation of diradical blocks at the 2- charge state produces additional fragments, with +1 m/z shift for those holding the nitroxide α-termination and -1 m/z for those containing the carbon-centered radical ω-end. These results suggest cyclization of these diradical species, followed by H• transfer on activated reopening of this cycle. This assumption was validated using IMS resolution of the cyclic/linear isomers and supported by molecular modeling. CONCLUSIONS Combining IMS with molecular modeling provided new insights into how the charge state of digital blocks influences their dissociation. These results permit to define new guidelines to improve either ionization conditions or the structural design of these digital polymers for best MS/MS readability.
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Affiliation(s)
- Isaure Sergent
- Aix Marseille Université, CNRS, UMR7273, Institut de Chimie Radicalaire, Marseille, France
| | - Thibault Schutz
- Université de Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Strasbourg, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Strasbourg, France
| | - Laurence Charles
- Aix Marseille Université, CNRS, UMR7273, Institut de Chimie Radicalaire, Marseille, France
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Jurček O, Chattopadhyay S, Kalenius E, Linnanto JM, Kiesilä A, Jurček P, Radiměřský P, Marek R. Unsymmetric Chiral Ligands for Large Metallo-Macrocycles: Selectivity of Orientational Self-Sorting. Angew Chem Int Ed Engl 2024; 63:e202409134. [PMID: 38845398 DOI: 10.1002/anie.202409134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Indexed: 08/02/2024]
Abstract
Nature uses various chiral and unsymmetric building blocks to form substantial and complex supramolecular assemblies. In contrast, the majority of organic ligands used in metallosupramolecular chemistry are symmetric and achiral. Here we extend the group of unsymmetric chiral bile acids used as a scaffold for organic bispyridyl ligands by employing chenodeoxycholic acid (CDCA), an epimer of the previously used ursodeoxycholic acid (UDCA). The epimerism, flexibility, and bulkiness of the ligands leads to large structural differences in coordination products upon reaction with Pd(NO3)2. The UDCA-bispyridyl ligand self-assembles quantitatively into a single crown-like Pd3L6 complex, whereas the CDCA ligand provides a mixture of coordination complexes of general formula PdnL2n, i.e., Pd2L4, Pd3L6, Pd4L8, Pd5L10, and even Pd6L12 containing an impressive 120 chiral centers. The coordination products were studied by a combination of analytical methods, with ion-mobility mass spectrometry (IM-MS) providing valuable details on their structure and allowed an effective separation of m/z 1461 to individual signals according to the arrival time distribution, thereby revealing four different ions of [Pd3L6(NO3)3]3+, [Pd4L8(NO3)4]4+, [Pd5L10(NO3)5]5+, and [Pd6L12(NO3)6]6+. The structures of all the complexes were modelled using DFT calculations. Finally, the challenges and conclusions in determining the specific structural identity of these unsymmetric species are discussed.
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Affiliation(s)
- Ondřej Jurček
- Department of Natural Drugs, Faculty of Pharmacy, Masaryk University, Palackého 1946/1, CZ-61200, Brno, Czechia
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| | - Subhasis Chattopadhyay
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| | - Elina Kalenius
- Department of Chemistry, University of Jyvaskyla P. O. Box 35, FI-40014, Jyväskylä, Finland
| | - Juha M Linnanto
- Institute of Physics, University of Tartu, W. Ostwald Street 1, 50411, Tartu, Estonia
| | - Anniina Kiesilä
- Department of Chemistry, University of Jyvaskyla P. O. Box 35, FI-40014, Jyväskylä, Finland
| | - Pia Jurček
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| | - Petr Radiměřský
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| | - Radek Marek
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
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4
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Zhou W, Liu J, Chambreau SD, Vaghjiani GL. Dynamics and thermochemistry of the negatively charged clusters in a 2-hydroxyethylhydrazinium nitrate ionic liquid system. Phys Chem Chem Phys 2024; 26:21697-21711. [PMID: 39092620 DOI: 10.1039/d4cp02329c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The formation and fragmentation of negatively charged 2-hydroxyethylhydrazinium nitrate ([HOCH2CH2NH2NH2]+NO3-, HEHN) ionic liquid clusters were examined using a guided-ion beam tandem mass spectrometer furnished with collision-induced dissociation of selected ions with Xe atoms. Measurements included the compositions of cluster ions formed in the ionization source, and the dissociation products, cross sections, and 0 K threshold energies for individually selected cluster ions. To identify the structures of the main cluster ion series [(HEHN)n(HNO3)0-1NO3]- formed, molecular dynamics simulations were employed to create initial geometry guesses, followed by optimization at the ωB97XD/6-31+G(d,p) level of theory, from which global minimum structures were identified for reaction thermodynamics analyses. A comparison was made between the cluster formation and fragmentation in the negatively charged 2-hydroxyethylhydrazinium nitrate with those in the positive mode (reported by W. Zhou et al., Phys. Chem. Chem. Phys., 2023, 25, 17370). In both modes, the cluster ions were predominantly composed of m/z below 350; loss of a neutral 2-hydroxyethylhydrazinium nitrate ion pair represents the most important cluster fragmentation pathway, followed by intra-ion pair proton transfer-mediated 2-hydroxyethylhydrazine and HNO3 elimination; and all clusters started to dissociate at threshold energies less than 1.5 eV. The overwhelming similarities in the formation and fragmentation chemistry of positively vs. negatively charged 2-hydroxyethylhydrazinium nitrate clusters may be attributed to their inherent ionic nature and high electric conductivities.
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Affiliation(s)
- Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA.
- PhD Program in Chemistry, the Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA.
- PhD Program in Chemistry, the Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Steven D Chambreau
- Jacobs Technology, Inc., Air Force Research Laboratory, Edwards Air Force Base, California 93524, USA
| | - Ghanshyam L Vaghjiani
- In-Space Propulsion Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRS, Edwards Air Force Base, California 93524, USA
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Imagawa T, Ito S, Hennrich F, Neumaier M, Weis P, Koyasu K, Kappes MM, Tsukuda T. Revisiting the structure of [PdAu9(PPh3)8(CN)]2+ produced by atmospheric pressure plasma irradiation of [PdAu8(PPh3)8]2+ in methanol. J Chem Phys 2024; 161:024303. [PMID: 38980089 DOI: 10.1063/5.0219959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
Some of the authors of the present research group have previously reported mass spectrometric detection of [PdAu9(PPh3)8(CN)]2+ (PdAu9CN) by atmospheric pressure plasma (APP) irradiation of [MAu8(PPh3)8]2+ (PdAu8) in methanol and proposed based on density functional theory (DFT) calculations that PdAu9CN is constructed by inserting a CNAu or NCAu unit into the Au-PPh3 bond of PdAu8 [Emori et al., J. Chem. Phys. 155, 124312 (2021)]. In this follow-up study, we revisited the structure of PdAu9CN by high-resolution ion mobility spectrometry on an isolated sample of PdAu9CN with the help of dispersion-corrected DFT calculation. In contradiction to the previous proposal, we conclude that isomers in which an AuCN unit is directly bonded to the central Pd atom of PdAu8 are better candidates. This assignment was supported by Fourier transform infrared and ultraviolet-visible spectroscopies of isolated PdAu9CN. The simultaneous formation of [Au(PPh3)2]+ and PdAu9CN suggests that the AuCN species are formed by APP irradiation at the expense of a portion of PdAu8. These results indicate that APP may offer a unique method for transforming metal clusters into novel ones by generating in situ active species that were not originally added to the solution.
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Affiliation(s)
- Takumi Imagawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shun Ito
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Frank Hennrich
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
- Institute of Quantum Materials and Technologies, Karlsruhe Institute of Technology, Hermann-von- Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Marco Neumaier
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Kiichirou Koyasu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
- Institute of Quantum Materials and Technologies, Karlsruhe Institute of Technology, Hermann-von- Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Tatsuya Tsukuda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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6
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Ross DH, Bhotika H, Zheng X, Smith RD, Burnum-Johnson KE, Bilbao A. Computational tools and algorithms for ion mobility spectrometry-mass spectrometry. Proteomics 2024; 24:e2200436. [PMID: 38438732 DOI: 10.1002/pmic.202200436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/06/2024]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.
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Affiliation(s)
- Dylan H Ross
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Harsh Bhotika
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aivett Bilbao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
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7
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Sergent I, Schutz T, Oswald L, Obeid G, Lutz JF, Charles L. Using Nitroxides To Model the Ion Mobility Behavior of Nitroxide-Ended Oligomers: A Bottom-up Approach To Predict Mobility Separation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:534-541. [PMID: 38345914 DOI: 10.1021/jasms.3c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Block-truncated poly(phosphodiester)s are digital macromolecules storing binary information that can be decoded by MS/MS sequencing of individual blocks released as primary fragments of the entire polymer. As such, they are ideal species for the serial sequencing methodology enabled by MS-(CID)-IMS-(CID)-MS coupling, where two activation stages are combined in-line with ion mobility spectrometry (IMS) separation. Yet, implementation of this coupling still requires efforts to achieve IMS resolution of inner blocks, that can be considered as small oligomers with α termination composed of one nitroxide decorated with a different tag. As shown by molecular dynamics simulation, these oligomers adopt a conformation where the tag points out of the coil formed by the chain. Accordingly, the sole nitroxide termination was investigated here as a model to reduce the cost of calculation aimed at predicting the shift of collision cross-section (CCS) induced by new tag candidates and extrapolate this effect to nitroxide-terminated oligomers. A library of 10 nitroxides and 7 oligomers was used to validate our calculation methods by comparison with experimental IMS data as well as our working assumption. Based on conformation predicted by theoretical calculation, three new tag candidates could be proposed to achieve the +40 Å2 CCS shift required to ensure IMS separation of oligomers regardless of their coded sequence.
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Affiliation(s)
- Isaure Sergent
- Aix Marseille Université, CNRS, UMR 7273, Institut de Chimie Radicalaire (ICR), 13397 Marseille Cedex 20, France
| | - Thibault Schutz
- Université de Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), 67000 Strasbourg, France
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 67034 Strasbourg Cedex 2, France
| | - Laurence Oswald
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 67034 Strasbourg Cedex 2, France
| | - Georgette Obeid
- Université de Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), 67000 Strasbourg, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), 67000 Strasbourg, France
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 67034 Strasbourg Cedex 2, France
| | - Laurence Charles
- Aix Marseille Université, CNRS, UMR 7273, Institut de Chimie Radicalaire (ICR), 13397 Marseille Cedex 20, France
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8
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Hennrich F, Ito S, Weis P, Neumaier M, Takano S, Tsukuda T, Kappes MM. Cyclic ion mobility of doped [MAu 24L 18] 2- superatoms and their fragments (M = Ni, Pd and Pt; L = alkynyl). Phys Chem Chem Phys 2024; 26:8408-8418. [PMID: 38407473 DOI: 10.1039/d3cp06192b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Collision-induced dissociation and high-resolution cyclic ion mobility mass spectrometry, along with quantum chemical calculations and trajectory simulations, were used to compare the structures of isolated [MAu24(CCR)18]2-, M = Ni, Pd, or Pt, and their associated fragment ions. The three different alkynyl ligand-stabilized (CCR, R = 3,5-(CF3)2C6H3), transition metal-doped, gold cluster dianions showed mutually resolvable collision cross sections (CCS), which were ordered consistently with their molecular structures from X-ray crystallography. All three [MAu24(CCR)18]2- species fragment by sequential diyne loss to form [MAu24(CCR)18-n]2-, with n up to 12. The resultant fragment isomer distributions are significantly n- and M-dependent, and hint at a process involving concerted elimination of adjacent ligands. In particular [NiAu24(CCR)18]2- also fragments to generate alkyne-oligomers, an inference supported by the parallel observation of precursor dianion isomerization as collision energy is increased.
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Affiliation(s)
- Frank Hennrich
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, Karlsruhe 76131, Germany.
- Institute of Quantum Materials and Technologies, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Shun Ito
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, Karlsruhe 76131, Germany.
| | - Marco Neumaier
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, Karlsruhe 76131, Germany.
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Shinjiro Takano
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tatsuya Tsukuda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, Karlsruhe 76131, Germany.
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
- Institute of Quantum Materials and Technologies, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
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Williams OHL, Rusli O, Ezzedinloo L, Dodgen TM, Clegg JK, Rijs NJ. Automated Structural Activity Screening of β-Diketonate Assemblies with High-Throughput Ion Mobility-Mass Spectrometry. Angew Chem Int Ed Engl 2024; 63:e202313892. [PMID: 38012094 DOI: 10.1002/anie.202313892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 11/29/2023]
Abstract
Embracing complexity in design, metallo-supramolecular self-assembly presents an opportunity for fabricating materials of economic significance. The array of accessible supramolecules is alluring, along with favourable energy requirements. Implementation is hampered by an inability to efficiently characterise complex mixtures. The stoichiometry, size, shape, guest binding properties and reactivity of individual components and combinations thereof are inherently challenging to resolve. A large combinatorial library of four transition metals (Fe, Cu, Ni and Zn), and six β-diketonate ligands at different molar ratios and pH was robotically prepared and directly analysed over multiple timepoints with electrospray ionisation travelling wave ion mobility-mass spectrometry. The dataset was parsed for self-assembling activity without first attempting to structurally assign individual species. Self-assembling systems were readily categorised without manual data-handling, allowing efficient screening of self-assembly activity. This workflow clarifies solution phase supramolecular assembly processes without manual, bottom-up processing. The complex behaviour of the self-assembling systems was reduced to simpler qualities, which could be automatically processed.
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Affiliation(s)
| | - Olivia Rusli
- School of Chemistry, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Lida Ezzedinloo
- School of Chemistry, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Tyren M Dodgen
- Waters Corporation Australia, Rydalmere, NSW, 2116, Australia
| | - Jack K Clegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Nicole J Rijs
- School of Chemistry, UNSW Sydney, Sydney, NSW, 2052, Australia
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10
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Moe MM, Tsai M, Liu J. Effects of Intra-Base Pair Proton Transfer on Dissociation and Singlet Oxygenation of 9-Methyl-8-Oxoguanine-1-Methyl-Cytosine Base-Pair Radical Cations. Chemphyschem 2023; 24:e202300511. [PMID: 37738022 DOI: 10.1002/cphc.202300511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
8-Oxoguanosine is the most common oxidatively generated base damage and pairs with complementary cytidine within duplex DNA. The 8-oxoguanosine-cytidine lesion, if not recognized and removed, not only leads to G-to-T transversion mutations but renders the base pair being more vulnerable to the ionizing radiation and singlet oxygen (1 O2 ) damage. Herein, reaction dynamics of a prototype Watson-Crick base pair [9MOG ⋅ 1MC]⋅+ , consisting of 9-methyl-8-oxoguanine radical cation (9MOG⋅+ ) and 1-methylcystosine (1MC), was examined using mass spectrometry coupled with electrospray ionization. We first detected base-pair dissociation in collisions with the Xe gas, which provided insight into intra-base pair proton transfer of 9MOG⋅+ ⋅ 1MC← → ${{\stackrel{ {\rightarrow} } { {\leftarrow} } } }$ [9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ and subsequent non-statistical base-pair separation. We then measured the reaction of [9MOG ⋅ 1MC]⋅+ with 1 O2 , revealing the two most probable pathways, C5-O2 addition and HN7 -abstraction at 9MOG. Reactions were entangled with the two forms of 9MOG radicals and base-pair structures as well as multi-configurations between open-shell radicals and 1 O2 (that has a mixed singlet/triplet character). These were disentangled by utilizing approximately spin-projected density functional theory, coupled-cluster theory and multi-referential electronic structure modeling. The work delineated base-pair structural context effects and determined relative reactivity toward 1 O2 as [9MOG - H]⋅>9MOG⋅+ >[9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ ≥9MOG⋅+ ⋅ 1MC.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY 11101, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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11
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Liu Z, Roy M, DeYonker NJ, Gopalakrishnan R. Neutral gas pressure dependence of ion-ion mutual neutralization rate constants using Landau-Zener theory coupled with trajectory simulations. J Chem Phys 2023; 159:114111. [PMID: 37724728 DOI: 10.1063/5.0168609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
In this computational study, we describe a self-consistent trajectory simulation approach to capture the effect of neutral gas pressure on ion-ion mutual neutralization (MN) reactions. The electron transfer probability estimated using Landau-Zener (LZ) transition state theory is incorporated into classical trajectory simulations to elicit predictions of MN cross sections in vacuum and rate constants at finite neutral gas pressures. Electronic structure calculations with multireference configuration interaction and large correlation consistent basis sets are used to derive inputs to the LZ theory. The key advance of our trajectory simulation approach is the inclusion of the effect of ion-neutral interactions on MN using a Langevin representation of the effect of background gas on ion transport. For H+ - H- and Li+ - H(D)-, our approach quantitatively agrees with measured speed-dependent cross sections for up to ∼105 m/s. For the ion pair Ne+ - Cl-, our predictions of the MN rate constant at ∼1 Torr are a factor of ∼2 to 3 higher than the experimentally measured value. Similarly, for Xe+ - F- in the pressure range of ∼20 000-80 000 Pa, our predictions of the MN rate constant are ∼20% lower but are in excellent qualitative agreement with experimental data. The paradigm of using trajectory simulations to self-consistently capture the effect of gas pressure on MN reactions advanced here provides avenues for the inclusion of additional nonclassical effects in future work.
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Affiliation(s)
- Zhibo Liu
- Department of Mechanical Engineering, The University of Memphis, Memphis, Tennessee 38152, USA
| | - Mrittika Roy
- Department of Mechanical Engineering, The University of Memphis, Memphis, Tennessee 38152, USA
| | - Nathan J DeYonker
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152, USA
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12
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Kartowikromo KY, Olajide OE, Hamid AM. Collision cross section measurement and prediction methods in omics. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4973. [PMID: 37620034 PMCID: PMC10530098 DOI: 10.1002/jms.4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Omics studies such as metabolomics, lipidomics, and proteomics have become important for understanding the mechanisms in living organisms. However, the compounds detected are structurally different and contain isomers, with each structure or isomer leading to a different result in terms of the role they play in the cell or tissue in the organism. Therefore, it is important to detect, characterize, and elucidate the structures of these compounds. Liquid chromatography and mass spectrometry have been utilized for decades in the structure elucidation of key compounds. While prediction models of parameters (such as retention time and fragmentation pattern) have also been developed for these separation techniques, they have some limitations. Moreover, ion mobility has become one of the most promising techniques to give a fingerprint to these compounds by determining their collision cross section (CCS) values, which reflect their shape and size. Obtaining accurate CCS enables its use as a filter for potential analyte structures. These CCS values can be measured experimentally using calibrant-independent and calibrant-dependent approaches. Identification of compounds based on experimental CCS values in untargeted analysis typically requires CCS references from standards, which are currently limited and, if available, would require a large amount of time for experimental measurements. Therefore, researchers use theoretical tools to predict CCS values for untargeted and targeted analysis. In this review, an overview of the different methods for the experimental and theoretical estimation of CCS values is given where theoretical prediction tools include computational and machine modeling type approaches. Moreover, the limitations of the current experimental and theoretical approaches and their potential mitigation methods were discussed.
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Affiliation(s)
| | - Orobola E Olajide
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
| | - Ahmed M Hamid
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
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13
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Benny J, Liu J. Spin-orbit charge transfer from guanine and 9-methylguanine radical cations to nitric oxide radicals and the induced triplet-to-singlet intersystem crossing. J Chem Phys 2023; 159:085102. [PMID: 37638623 DOI: 10.1063/5.0160921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023] Open
Abstract
Nitric oxide (●NO) participates in many biological activities, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. To help understand the radiosensitization of ●NO, we report reaction dynamics between ●NO and the radical cations of guanine (a 9HG●+ conformer) and 9-methylguanine (9MG●+). On the basis of the formation of 9HG●+ and 9MG●+ in the gas phase and the collisions of the radical cations with ●NO in a guided-ion beam mass spectrometer, the charge transfer reactions of 9HG●+ and 9MG●+ with ●NO were examined. For both reactions, the kinetic energy-dependent product ion cross sections revealed a threshold energy that is 0.24 (or 0.37) eV above the 0 K product 9HG (or 9MG) + NO+ asymptote. To interrogate this abnormal threshold behavior, the reaction potential energy surface for [9MG + NO]+ was mapped out at closed-shell singlet, open-shell singlet, and triplet states using density functional and coupled cluster theories. The results showed that the charge transfer reaction requires the interaction of a triplet-state surface originating from a reactant-like precursor complex 3[9MG●+(↑)⋅(↑)●NO] with a closed-shell singlet-state surface evolving from a charge-transferred complex 1[9MG⋅NO+]. During the reaction, an electron is transferred from π∗(NO) to perpendicular π∗(9MG), which introduces a change in orbital angular momentum. The latter offsets the change in electron spin angular momentum and facilitates intersystem crossing. The reaction threshold in excess of the 0 K thermochemistry and the low charge-transfer efficiency are rationalized by the vibrational excitation in the product ion NO+ and the kinetic shift arising from a long-lived triplet intermediate.
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Affiliation(s)
- Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
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14
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Cajahuaringa S, Caetano DLZ, Zanotto LN, Araujo G, Skaf MS. MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies. J Chem Inf Model 2023; 63:3557-3566. [PMID: 37184925 PMCID: PMC10269586 DOI: 10.1021/acs.jcim.3c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Ion mobility mass spectrometry (IM-MS) techniques have become highly valued as a tool for structural characterization of biomolecular systems since they yield accurate measurements of the rotationally averaged collision cross-section (CCS) against a buffer gas. Despite its enormous potential, IM-MS data interpretation is often challenging due to the conformational isomerism of metabolites, lipids, proteins, and other biomolecules in the gas phase. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS data. In this work, we present MassCCS, a parallelized open-source code for computing CCS of molecules ranging from small organic compounds to massive protein assemblies at the trajectory method level of description using atomic and molecular buffer gas particles. The performance of the code is comparable to other available software for small molecules and proteins but is significantly faster for larger macromolecular assemblies. We performed extensive tests regarding accuracy, performance, and scalability with system size and number of CPU cores. MassCCS has proven highly accurate and efficient, with execution times under a few minutes, even for large (84.87 MDa) virus capsid assemblies with very modest computational resources. MassCCS is freely available at https://github.com/cces-cepid/massccs.
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Affiliation(s)
- Samuel Cajahuaringa
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Daniel L. Z. Caetano
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
- Institute
of Chemistry, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Leandro N. Zanotto
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Guido Araujo
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Munir S. Skaf
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
- Institute
of Chemistry, University of Campinas, Campinas, São Paulo 13083-970, Brazil
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15
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Naylor CN, Schaefer C, Kirk AT, Zimmermann S. The origin of isomerization of aniline revealed by high kinetic energy ion mobility spectrometry (HiKE-IMS). Phys Chem Chem Phys 2023; 25:1139-1152. [PMID: 36515135 DOI: 10.1039/d2cp01994a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although aniline is a relatively simple small molecule, the origin of its two peaks observed in ion mobility spectrometry (IMS) has remained under debate for at least 30 years. First hypothesized as a difference in protonation site (amine vs. benzene ring), each ion mobility peak differs by one Dalton when coupled with mass spectrometry where the faster mobility peak is the molecular ion peak, and the slower mobility peak is protonated. To complicate the deconvolution of structures, some previous literature shows the peaks as unresolved and thus proposes these species exist in equilibrium. In this work, we show that when measured with high kinetic energy ion mobility spectrometry (HiKE-IMS), the two peaks observed in spectra of both aniline and all n-fluoroanilines are fully separated (chromatographic resolution from 2-7, Rp > 110) and therefore not in equilibrium. The HiKE-IMS is capable of changing ionization conditions independently of drift region conditions, and our results agree with previous literature showing that ionization source settings (including possible fragmentation at this stage) are the only influence determining the speciation of the two aniline peaks. Finally, when the drift and reactant gas are changed to nitrogen, a third peak appears at high E/N for 2-fluoroaniline and 4-fluoroaniline for the first time in reported literature. As observed by HiKE-IMS-MS, the new third peak is also protonated showing that the para-protonated aniline and resulting fragment ion, molecular ion aniline, can be fully separated in the mobility domain for the first time. The appearance of the third peak is only possible due to the increased separation of the other two peaks within the HiKE-IMS.
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Affiliation(s)
- Cameron N Naylor
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Christoph Schaefer
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Ansgar T Kirk
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Stefan Zimmermann
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
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16
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Quesada JV, Chmela J, Greisch JF, Klopper W, Harding ME. A litmus test for the balanced description of dispersion interactions and coordination chemistry of lanthanoids. Phys Chem Chem Phys 2022; 24:25106-25117. [PMID: 35920212 DOI: 10.1039/d2cp01414a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of long-range interactions on the structure of complexes of Eu(III) with four 9-hydroxy-phenalen-1-one ligands (HPLN) and one alkaline earth metal dication [Eu(PLN)4AE]+ (AE: Mg, Ca, Sr, and Ba) is analyzed. Through the [Eu(PLN)4Ca]+ complex, which is a charged complex with two metals-one of them a lanthanoid-and with four relatively fluxional π-ligands, the difficulties of describing such systems are identified. The inclusion of the D3(BJ) or D4 corrections to different density functionals introduces significant changes in the structure, which are shown to stem from the interaction between pairs of PLN ligands. This interaction is studied further with a variety of density functionals, wave-function based methods, and by means of the random phase approximation. By comparing the computed results with those from experimental evidence of gas-phase photoluminescence and ion mobility measurements it is concluded that the inclusion of dispersion corrections does not always yield structures that are in agreement with the experimental findings.
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Affiliation(s)
- Juana Vázquez Quesada
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany.
| | - Jiří Chmela
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany.
| | - Jean-François Greisch
- Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
| | - Wim Klopper
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany. .,Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
| | - Michael E Harding
- Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
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17
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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18
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Harrilal CP, Gandhi VD, Nagy G, Chen X, Buchanan MG, Wojcik R, Conant CR, Donor MT, Ibrahim YM, Garimella SVB, Smith RD, Larriba-Andaluz C. Measurement and Theory of Gas-Phase Ion Mobility Shifts Resulting from Isotopomer Mass Distribution Changes. Anal Chem 2021; 93:14966-14975. [PMID: 34726890 DOI: 10.1021/acs.analchem.1c01736] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unanticipated discovery of recent ultra-high-resolution ion mobility spectrometry (IMS) measurements revealing that isotopomers─compounds that differ only in the isotopic substitution sites─can be separated has raised questions as to the physical basis for their separation. A study comparing IMS separations for two isotopomer sets in conjunction with theory and simulations accounting for ion rotational effects provides the first-ever prediction of rotation-mediated shifts. The simulations produce observable mobility shifts due to differences in gas-ion collision frequency and translational-to-rotational energy transfer. These differences can be attributed to distinct changes in the moment of inertia and center of mass between isotopomers. The simulations are in broad agreement with the observed experiments and consistent with relative mobility differences between isotopomers. These results provide a basis for refining IMS theory and a new foundation to obtain additional structural insights through IMS.
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Affiliation(s)
- Christopher P Harrilal
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Viraj D Gandhi
- Department of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States.,Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan Street, Indianapolis, Indiana 46202, United States
| | - Gabe Nagy
- Chemistry Department, University of Utah, Salt Lake City, Utah 84112, United States
| | - Xi Chen
- Department of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States.,Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan Street, Indianapolis, Indiana 46202, United States
| | - Michael G Buchanan
- Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan Street, Indianapolis, Indiana 46202, United States
| | - Roza Wojcik
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Christopher R Conant
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Micah T Donor
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Carlos Larriba-Andaluz
- Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan Street, Indianapolis, Indiana 46202, United States
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19
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Pham KN, Fernandez-Lima F. Structural Characterization of Human Histone H4.1 by Tandem Nonlinear and Linear Ion Mobility Spectrometry Complemented with Molecular Dynamics Simulations. ACS OMEGA 2021; 6:29567-29576. [PMID: 34778628 PMCID: PMC8582071 DOI: 10.1021/acsomega.1c03744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Extracellular histone H4 is an attractive drug target owing to its roles in organ failure in sepsis and other diseases. To identify inhibitors using in silico methods, information on histone H4 structural dynamics and three-dimensional (3D) structural coordinates is required. Here, DNA-free histone H4 type 1 (H4.1) was characterized by utilizing tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry (MS) complemented with molecular dynamics (MD) simulations. The gas-phase structures of H4.1 are dependent on the starting solution conditions, evidenced by differences in charge state distributions, mobility distributions, and collision-induced unfolding (CIU) pathways. The experimental results show that H4.1 adopts diverse conformational types from compact (C) to partially folded (P) and subsequently elongated (E) structures. Molecular dynamics simulations provided candidate structures for the histone H4.1 monomer in solution and for the gas-phase structures observed using FAIMS-IMS-TOF MS as a function of the charge state and mobility distribution. A combination of the FAIMS-TIMS experimental results with theoretical dipole calculations reveals the important role of charge distribution in the dipole alignment of H4.1 elongated structures at high electric fields. A comparison of the secondary and primary structures of DNA-free H2A.1 and H4.1 is made based on the experimental IMS-MS and MD findings.
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Affiliation(s)
- Khoa N. Pham
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United States
- Biomolecular
Science Institute, Florida International
University, Miami, Florida 33199, United
States
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20
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Edwards AN, Tran HM, Gallagher ES. Propagating Error through Traveling-Wave Ion Mobility Calibration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2621-2630. [PMID: 34662111 DOI: 10.1021/jasms.1c00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Native mass spectrometry (MS) is used to elucidate the stoichiometry of protein complexes and quantify binding interactions by maintaining native-like, noncovalent interactions in the gas phase. However, ionization forces proteins into specific conformations, losing the solution-phase dynamics associated with solvated protein structures. Comparison of gas-phase structures to those in solution, or to other gas-phase ion populations, has many biological implications. For one, analyzing the variety of conformations that are maintained in the gas-phase can provide insight into a protein's solution-phase energy landscape. The gas-phase conformations of proteins and complexes can be investigated using ion mobility (IM) spectrometry. Specifically, drift tube (DT)-IM utilizes uniform electric fields to propel a population of gas-phase ions through a region containing a neutral gas. By measuring the mobility (K) of gas-phase ions, users are able to calculate an average momentum transfer cross section (DTCCS), which provides structural information on the ion. Conversely, in traveling-wave ion mobility spectrometry (TWIMS), TWCCS values cannot be derived directly from an ion's mobility but must be determined following calibration. Though the required calibration adds uncertainty, it is common to report only an average and standard deviation of the calculated TWCCS, accounting for uncertainty associated with replicate measurements, which is a fraction of the overall uncertainty. Herein, we calibrate a TWIMS instrument and derive TWCCSN2 and TWCCSN2→He values for four proteins: cytochrome c, ubiquitin, apo-myoglobin, and holo-myoglobin. We show that compared to reporting only the standard deviation of TWCCS, propagating error through the calibration results in a significant increase in the number of calculated TWCCS values that agree within experimental error with literature values (DTCCS). Incorporating this additional uncertainty provides a more thorough assessment of a protein ion's gas-phase conformations, enabling the structures sampled by native IM-MS to be compared against other reported structures, both experimental and computational.
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Affiliation(s)
- Alexis N Edwards
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Hien M Tran
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
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21
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White N, Seelig JD, Loyalka SK. Computation of drag and diffusion coefficient for coronavirus: I. JOURNAL OF AEROSOL SCIENCE 2021; 157:105806. [PMID: 33976456 PMCID: PMC8103743 DOI: 10.1016/j.jaerosci.2021.105806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Monte Carlo simulations and integral equation techniques allow for the flexible and efficient computation of drag and diffusion coefficients for virus mimetic particles. We highlight a Monte Carlo method that is useful for computing the drag on biomimetic particles in the free-molecular regime and a numerical technique to solve a boundary integral equation (related to the Stokes equation) in the hydrodynamic limit. The free-molecular and the continuum results allow the construction of an approximation for the drag applicable over the full range of Knudsen numbers. Finally, we outline how this work will be useful in modeling viral transport in air and fluids and in viral morphology measurements and in viral separations via electrospray-differential mobility analyzers (ES-DMA).
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Affiliation(s)
- Nathan White
- Department of Mechanical & Aerospace Engineering, Lafferre Hall, University of Missouri, Columbia, MO, 65211, USA
| | | | - Sudarshan K Loyalka
- Department of Mechanical & Aerospace Engineering, Lafferre Hall, University of Missouri, Columbia, MO, 65211, USA
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22
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Connolly JRFB, Munoz-Muriedas J, Lapthorn C, Higton D, Vissers JPC, Webb A, Beaumont C, Dear GJ. Investigation into Small Molecule Isomeric Glucuronide Metabolite Differentiation Using In Silico and Experimental Collision Cross-Section Values. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1976-1986. [PMID: 34296869 DOI: 10.1021/jasms.0c00427] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Identifying isomeric metabolites remains a challenging and time-consuming process with both sensitivity and unambiguous structural assignment typically only achieved through the combined use of LC-MS and NMR. Ion mobility mass spectrometry (IMMS) has the potential to produce timely and accurate data using a single technique to identify drug metabolites, including isomers, without the requirement for in-depth interpretation (cf. MS/MS data) using an automated computational pipeline by comparison of experimental collision cross-section (CCS) values with predicted CCS values. An ion mobility enabled Q-Tof mass spectrometer was used to determine the CCS values of 28 (14 isomeric pairs of) small molecule glucuronide metabolites, which were then compared to two different in silico models; a quantum mechanics (QM) and a machine learning (ML) approach to test these approaches. The difference between CCS values within isomer pairs was also assessed to evaluate if the difference was large enough for unambiguous structural identification through in silico prediction. A good correlation was found between both the QM- and ML-based models and experimentally determined CCS values. The predicted CCS values were found to be similar between ML and QM in silico methods, with the QM model more accurately describing the difference in CCS values between isomer pairs. Of the 14 isomeric pairs, only one (naringenin glucuronides) gave a sufficient difference in CCS values for the QM model to distinguish between the isomers with some level of confidence, with the ML model unable to confidently distinguish the studied isomer pairs. An evaluation of analyte structures was also undertaken to explore any trends or anomalies within the data set.
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Affiliation(s)
- John R F B Connolly
- RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin D02 YN77, Ireland
| | | | - Cris Lapthorn
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - David Higton
- Waters Corporation, Stamford Ave, Wilmslow SK9 4AX, United Kingdom
| | | | - Alison Webb
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Claire Beaumont
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Gordon J Dear
- GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom
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23
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Pham KN, Mamun Y, Fernandez-Lima F. Structural Heterogeneity of Human Histone H2A.1. J Phys Chem B 2021; 125:4977-4986. [PMID: 33974801 PMCID: PMC8568062 DOI: 10.1021/acs.jpcb.1c00335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Histones are highly basic chromatin proteins that tightly package and order eukaryotic DNA into nucleosomes. While the atomic structure of the nucleosomes has been determined, the three-dimensional structure of DNA-free histones remains unresolved. Here, we combine tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry in parallel with molecular modeling to study the conformational space of a DNA-free histone H2A type 1 (H2A.1). Experimental results showed the dependence of the gas-phase structures on the starting solution conditions, characterized by charge state distributions, mobility distributions, and collision-induced-unfolding pathways. The measured H2A.1 gas-phase structures showed a high diversity of structural features ranging from compact (C) to partially folded (P) and then highly elongated (E) conformations. Molecular dynamics simulations provided candidate structures for the solution H2A.1 native conformation with folded N- and C-terminal tails, as well as gas-phase candidate structures associated with the mobility trends. Complementary collision cross section and dipole calculations showed that the charge distribution in the case of elongated gas-phase structures, where basic and acidic residues are mostly exposed (e.g., z > 15+), is sufficient to induce differences in the dipole alignment at high electric fields, in good agreement with the trends observed during the FAIMS-TIMS experiments.
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Affiliation(s)
- Khoa N Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Yasir Mamun
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.,Biomolecular Science Institute, Florida International University, Miami, Florida 33199, United States
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24
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Ligare MR, Morrison KA, Hewitt MA, Reveles JU, Govind N, Hernandez H, Baker ES, Clowers BH, Laskin J, Johnson GE. Ion Mobility Spectrometry Characterization of the Intermediate Hydrogen-Containing Gold Cluster Au 7(PPh 3) 7H 52. J Phys Chem Lett 2021; 12:2502-2508. [PMID: 33667097 DOI: 10.1021/acs.jpclett.0c03664] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We employ ion mobility spectrometry and density functional theory to determine the structure of Au7(PPh3)7H52+ (PPh3 = triphenylphosphine), which was recently identified by high mass resolution mass spectrometry. Experimental ion-neutral collision cross sections represent the momentum transfer between the ionic clusters and gas molecules averaged over the relative thermal velocities of the colliding pair, thereby providing structural insights. Theoretical calculations indicate the geometry of Au7(PPh3)7H52+ is similar to Au7(PPh3)7+, with three hydrogen atoms bridging two gold atoms and two hydrogen atoms forming single Au-H bonds. Collision-induced dissociation products observed during IMS experiments reveal that smaller hydrogen-containing clusters may be produced through fragmentation of Au7(PPh3)7H52+. Our findings indicate that hydrogen-containing species like Au7(PPh3)7H52+ act as intermediates in the formation of larger phosphine ligated gold clusters. These results advance the understanding and ability to control the mechanisms of size-selective cluster formation, which is necessary for scalable synthesis of clusters with tailored properties.
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Affiliation(s)
- Marshall R Ligare
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Kelsey A Morrison
- Department of Chemistry, Washington State University, P.O. Box 644630, Pullman, Washington 99164, United States
| | - Michael A Hewitt
- Department of Chemistry, Grinnell College, Grinnell, Iowa 50112, United States
| | - J Ulises Reveles
- Advanced Career Education (ACE) Center at Highland Springs, Highland Springs, Virginia 23075, United States
| | - Niranjan Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Heriberto Hernandez
- Department of Chemistry, Grinnell College, Grinnell, Iowa 50112, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, P.O. Box 644630, Pullman, Washington 99164, United States
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Grant E Johnson
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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25
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Naylor CN, Clowers BH. Reevaluating the Role of Polarizability in Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:618-627. [PMID: 33533630 DOI: 10.1021/jasms.0c00338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the expanding commercial availability of gas-phase separation systems that incorporate gas-phase mobility, there is a concurrent rise in efforts to cast the gas-phase mobility coefficient in terms of an ion-neutral collision cross-section (CCS). The motivating factors for this trend are varied, but many aim to complement experimental results with computationally generated CCS values from in silico structural approximations. Unfortunately, the current paradigm for relating experimental mobility results to computationally derived structures relies upon empirical approaches, including a myriad of variables that do not realistically bound the comparison. In this Critical Insight, we advocate for the development of a self-consistent experimental and computational framework that uses laboratory results to constrain the scope of the modeling effort. This paper aims to prompt discussion, challenge assumptions, and promote the development of more efficient, accurate computational techniques within the gas-phase ion measurement community. Specifically, we postulate whether experimental deviations from Langevin's polarization limit (Kpol) are suitable to estimate the relative contributions of hard-sphere collisions and long-range interactions within CCS values. Not surprisingly, different molecule classes exhibit different trends in the K/Kpol ratio when normalized for reduced mass, and the most common IMS calibrants (e.g., tune mix, polyalanine, tetraalkylammonium salts) follow different polarizability trends than many of the analytes probed in the literature. Succinctly, if gas-phase ion structure is largely invariant based upon the colliding neutral and newly developed experimental efforts can quantitatively capture ion polarizability, then modeling efforts describing a target analyte must be self-consistent as the collision neutral is changed in silico.
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Affiliation(s)
- Cameron N Naylor
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
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26
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Nielson FF, Colby SM, Thomas DG, Renslow RS, Metz TO. Exploring the Impacts of Conformer Selection Methods on Ion Mobility Collision Cross Section Predictions. Anal Chem 2021; 93:3830-3838. [PMID: 33606495 DOI: 10.1021/acs.analchem.0c04341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50 000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire data set. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property: the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good trade-off between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.
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Affiliation(s)
- Felicity F Nielson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington United States
| | - Sean M Colby
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington United States
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington United States
| | - Ryan S Renslow
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington United States
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27
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Ross DH, Xu L. Determination of drugs and drug metabolites by ion mobility-mass spectrometry: A review. Anal Chim Acta 2021; 1154:338270. [PMID: 33736803 DOI: 10.1016/j.aca.2021.338270] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/04/2023]
Abstract
Ion mobility-mass spectrometry (IM-MS) has gained increased applications in the characterization and identification of drugs and drug metabolites, largely owning to the complementary separation of analyte ions based on their gas-phase size and shape in the IM dimension in addition to their mass-to-charge ratios. In this review, we discuss recent advances in such applications. We first introduce various types of IM techniques, focusing on those that allow the measurement of collision cross section (CCS), the physical property of an ion that reflects its gas-phase size and shape. Next, we discuss the IM-MS landscape of the large chemical space of drugs and multimodal distributions of certain drugs in IM separation due to the presence of protomers. We then review drug metabolism reactions and discuss the application of IM-MS in separation and identification of isomeric drug metabolites. Subsequently, we discuss various approaches to generate theoretical and predicted CCS data, including theory-based calculation methods and data-driven prediction models, and currently available resources on these approaches. Finally, current limitations and future directions of application of IM-MS are discussed.
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Affiliation(s)
- Dylan H Ross
- Department of Medicinal Chemistry, University of Washington, 1959, NE Pacific Street, HSB H-172, Seattle, WA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, 1959, NE Pacific Street, HSB H-172, Seattle, WA, USA.
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28
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Kalenius E, Malola S, Matus MF, Kazan R, Bürgi T, Häkkinen H. Experimental Confirmation of a Topological Isomer of the Ubiquitous Au 25(SR) 18 Cluster in the Gas Phase. J Am Chem Soc 2021; 143:1273-1277. [PMID: 33444006 PMCID: PMC8023650 DOI: 10.1021/jacs.0c11509] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
High-resolution electrospray ionization
ion mobility mass spectrometry
has revealed a gas-phase isomer of the ubiquitous, extremely well-studied
Au25(SR)18 cluster both in anionic and cationic
form. The relative abundance of the isomeric structures can be controlled
by in-source activation. The measured collision cross section of the
new isomer agrees extremely well with a recent theoretical prediction
(MatusM. F.; et al. 2020, 56, 8087) corresponding to a Au25(SR)18– isomer that is energetically close and topologically connected to
the known ground-state structure via a simple rotation of the gold
core without breaking any Au–S bonds. The results imply that
the structural dynamics leading to isomerization of thiolate-protected
gold clusters may play an important role in their gas-phase reactions
and that isomerization could be controlled by external stimuli.
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Affiliation(s)
- Elina Kalenius
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Sami Malola
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - María Francisca Matus
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Rania Kazan
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Thomas Bürgi
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Hannu Häkkinen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.,Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
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29
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Maillard JF, Le Maître J, Rüger CP, Ridgeway M, Thompson CJ, Paupy B, Hubert-Roux M, Park M, Afonso C, Giusti P. Structural analysis of petroporphyrins from asphaltene by trapped ion mobility coupled with Fourier transform ion cyclotron resonance mass spectrometry. Analyst 2021; 146:4161-4171. [PMID: 34047731 DOI: 10.1039/d1an00140j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Molecular characterization of compounds present in highly complex mixtures such as petroleum is proving to be one of the main analytical challenges. Heavy fractions, such as asphaltenes, exhibit immense molecular and isomeric complexity. Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) with its unequalled resolving power, mass accuracy and dynamic range can address the isobaric complexity. Nevertheless, isomers remain largely inaccessible. Therefore, another dimension of separation is required. Recently, ion mobility mass spectrometry has revealed great potential for isomer description. In this study, the combination of trapped ion mobility and Fourier transform ion cyclotron resonance mass spectrometry (TIMS-FTICR) is used to obtain information on the structural features and isomeric diversity of vanadium petroporphyrins present in heavy petroleum fractions. The ion mobility spectra provided information on the isomeric diversity of the different classes of porphyrins. The determination of the collision cross section (CCS) from the peak apex allows us to hypothesize about the structural aspects of the petroleum molecules. In addition, the ion mobility signal full width at half maximum (FWHM) was used as a measure for isomeric diversity. Finally, theoretical CCS determinations were conducted first on core structures and then on alkylated petroporphyrins taking advantage of the linear correlation between the CCS and the alkylation level. This allowed the proposal of putative structures in agreement with the experimental results. The authors believe that the presented workflow will be useful for the structural prediction of real unknowns in highly complex mixtures.
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Affiliation(s)
- Julien F Maillard
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Johann Le Maître
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and TOTAL Refining & Chemicals, Total Research & Technology Gonfreville, BP 27, 76700 Harfleur, France and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Christopher P Rüger
- International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France and Joint Mass Spectrometry Centre/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany and Department Life, Light & Matter (LLM), University of Rostock, 18051 Rostock, Germany
| | | | | | - Benoit Paupy
- TOTAL Refining & Chemicals, Total Research & Technology Gonfreville, BP 27, 76700 Harfleur, France and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Marie Hubert-Roux
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | | | - Carlos Afonso
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Pierre Giusti
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen-Normandie, CNRS, IRCOF, Mont Saint Aignan Cedex, France. and TOTAL Refining & Chemicals, Total Research & Technology Gonfreville, BP 27, 76700 Harfleur, France and International Joint Laboratory - iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
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30
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Larriba-Andaluz C, Prell JS. Fundamentals of ion mobility in the free molecular regime. Interlacing the past, present and future of ion mobility calculations. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1826708] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Carlos Larriba-Andaluz
- Department of Mechanical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - James S. Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
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31
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Hale OJ, Sisley EK, Griffiths RL, Styles IB, Cooper HJ. Native LESA TWIMS-MSI: Spatial, Conformational, and Mass Analysis of Proteins and Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:873-879. [PMID: 32159346 PMCID: PMC7147347 DOI: 10.1021/jasms.9b00122] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/13/2020] [Accepted: 02/18/2020] [Indexed: 05/18/2023]
Abstract
We have previously demonstrated native liquid extraction surface analysis (LESA) mass spectrometry imaging of small intact proteins in thin tissue sections. We also showed calculation of collision cross sections for specific proteins extracted from discrete locations in tissue by LESA traveling wave ion mobility spectrometry (TWIMS). Here, we demonstrate an integrated native LESA TWIMS mass spectrometry imaging (MSI) workflow, in which ion mobility separation is central to the imaging experiment and which provides spatial, conformational, and mass information on endogenous proteins in a single experiment. The approach was applied to MSI of a thin tissue section of mouse kidney. The results show that the benefits of integration of TWIMS include improved specificity of the ion images and the capacity to calculate collision cross sections for any protein or protein complex detected in any pixel (without a priori knowledge of the presence of the protein).
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Affiliation(s)
- Oliver J. Hale
- School of Biosciences, University of
Birmingham, Edgbaston B15 2TT, U.K.
| | - Emma K. Sisley
- School of Biosciences, University of
Birmingham, Edgbaston B15 2TT, U.K.
| | - Rian L. Griffiths
- School of Biosciences, University of
Birmingham, Edgbaston B15 2TT, U.K.
| | - Iain B. Styles
- School of Computer Science, University of
Birmingham, Edgbaston B15 2TT, U.K.
| | - Helen J. Cooper
- School of Biosciences, University of
Birmingham, Edgbaston B15 2TT, U.K.
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32
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Hale OJ, Cramer R. Atmospheric Pressure Ultraviolet Laser Desorption and Ionization from Liquid Samples for Native Mass Spectrometry. Anal Chem 2019; 91:14192-14197. [PMID: 31651149 PMCID: PMC7007007 DOI: 10.1021/acs.analchem.9b03875] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Understanding protein structure is vital for evaluating protein interactions with drugs, proteins, and other ligands. Native mass spectrometry (MS) is proving to be invaluable for this purpose, enabling analysis of "native-like" samples that mimic physiological conditions. Native MS is usually performed by electrospray ionization (ESI) with its soft ionization processes and the generation of multiply charged ions proving favorable for conformation retention and high mass analysis, respectively. There is scope to expand the currently available toolset, specifically to other soft ionization techniques such as soft laser desorption, for applications in areas like high-throughput screening and MS imaging. In this Letter, observations made from native MS experiments using an ultraviolet (UV) laser-based ion source operating at atmospheric pressure are described. The ion source is capable of producing predominately multiply charged ions similar to ESI. Proteins and protein complexes were analyzed from a native-like sample droplet to investigate the technique. Ion mobility-mass spectrometry (IM-MS) measurements showed that folded protein conformations were detected for ions with low charge states. This observation indicates the source is suitable for native MS analysis and should be further developed for higher mass analysis in the future.
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Affiliation(s)
- Oliver J Hale
- Department of Chemistry , University of Reading , Whiteknights, Reading RG6 6AD , United Kingdom
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights, Reading RG6 6AD , United Kingdom
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33
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Pukala T. Importance of collision cross section measurements by ion mobility mass spectrometry in structural biology. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:72-82. [PMID: 30265417 DOI: 10.1002/rcm.8294] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
The field of ion mobility mass spectrometry (IM-MS) has developed rapidly in recent decades, with new fundamental advances underpinning innovative applications. This has been particularly noticeable in the field of biomacromolecular structure determination and structural biology, with pioneering studies revealing new structural insight for complex protein assemblies which control biological function. This perspective offers a review of recent developments in IM-MS which have enabled expanding applications in protein structural biology, principally focusing on the quantitative measurement of collision cross sections and their interpretation to describe higher order protein structures.
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Affiliation(s)
- Tara Pukala
- Discipline of Chemistry, University of Adelaide, North Terrace, Adelaide, South Australia, 5005
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34
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Comby-Zerbino C, Perić M, Bertorelle F, Chirot F, Dugourd P, Bonačić-Koutecký V, Antoine R. Catenane Structures of Homoleptic Thioglycolic Acid-Protected Gold Nanoclusters Evidenced by Ion Mobility-Mass Spectrometry and DFT Calculations. NANOMATERIALS 2019; 9:nano9030457. [PMID: 30893867 PMCID: PMC6474107 DOI: 10.3390/nano9030457] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/13/2019] [Accepted: 03/16/2019] [Indexed: 11/17/2022]
Abstract
Thiolate-protected metal nanoclusters have highly size- and structure-dependent physicochemical properties and are a promising class of nanomaterials. As a consequence, for the rationalization of their synthesis and for the design of new clusters with tailored properties, a precise characterization of their composition and structure at the atomic level is required. We report a combined ion mobility-mass spectrometry approach with density functional theory (DFT) calculations for determination of the structural and optical properties of ultra-small gold nanoclusters protected by thioglycolic acid (TGA) as ligand molecules, Au10(TGA)10. Collision cross-section (CCS) measurements are reported for two charge states. DFT optimized geometrical structures are used to compute CCSs. The comparison of the experimentally- and theoretically-determined CCSs allows concluding that such nanoclusters have catenane structures.
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Affiliation(s)
- Clothilde Comby-Zerbino
- Institut Lumière Matière UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon, F-69100 Villeurbanne, France.
| | - Martina Perić
- Center of Excellence for Science and Technology-Integration of Mediterranean region (STIM) at Interdisciplinary Center for Advanced Sciences and Technology (ICAST), University of Split, Poljička cesta 35, HR-21000 Split, Croatia.
| | - Franck Bertorelle
- Institut Lumière Matière UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon, F-69100 Villeurbanne, France.
| | - Fabien Chirot
- Institut des Sciences Analytiques UMR 5280, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, Univ Lyon, 5 rue de la Doua, F-69100 Villeurbanne, France.
| | - Philippe Dugourd
- Institut Lumière Matière UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon, F-69100 Villeurbanne, France.
| | - Vlasta Bonačić-Koutecký
- Center of Excellence for Science and Technology-Integration of Mediterranean region (STIM) at Interdisciplinary Center for Advanced Sciences and Technology (ICAST), University of Split, Poljička cesta 35, HR-21000 Split, Croatia.
- Department of Chemistry, Humboldt Universitat zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany.
| | - Rodolphe Antoine
- Institut Lumière Matière UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon, F-69100 Villeurbanne, France.
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35
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Prell JS. Modelling Collisional Cross Sections. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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36
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Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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37
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Duez Q, Metwally H, Konermann L. Electrospray Ionization of Polypropylene Glycol: Rayleigh-Charged Droplets, Competing Pathways, and Charge State-Dependent Conformations. Anal Chem 2018; 90:9912-9920. [DOI: 10.1021/acs.analchem.8b02115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Quentin Duez
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
- Organic Synthesis and Mass Spectrometry Laboratory, University of Mons, Place du Parc, 23, Mons, 7000, Belgium
| | - Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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38
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Canzani D, Laszlo KJ, Bush MF. Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure. J Phys Chem A 2018; 122:5625-5634. [DOI: 10.1021/acs.jpca.8b04474] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Daniele Canzani
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Kenneth J. Laszlo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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39
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Di Giovanni JP, Barkley RM, Jones DNM, Hankin JA, Murphy RC. Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1231-1241. [PMID: 29687419 PMCID: PMC6004252 DOI: 10.1007/s13361-018-1927-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 05/05/2023]
Abstract
Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H2O-CO2]- and [M-H-H2O]- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H2O]- ion from LTB4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H2O]- product ions from LTB4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.
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Affiliation(s)
- James P Di Giovanni
- Department of Pharmacology, University of Colorado Denver, Mail Stop 8303, 12801 E. 17th Ave, Aurora, CO, 80045, USA
| | - Robert M Barkley
- Department of Pharmacology, University of Colorado Denver, Mail Stop 8303, 12801 E. 17th Ave, Aurora, CO, 80045, USA
| | - David N M Jones
- Department of Pharmacology, University of Colorado Denver, Mail Stop 8303, 12801 E. 17th Ave, Aurora, CO, 80045, USA
| | - Joseph A Hankin
- Department of Pharmacology, University of Colorado Denver, Mail Stop 8303, 12801 E. 17th Ave, Aurora, CO, 80045, USA
| | - Robert C Murphy
- Department of Pharmacology, University of Colorado Denver, Mail Stop 8303, 12801 E. 17th Ave, Aurora, CO, 80045, USA.
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40
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Greisch JF, Weis P, Brendle K, Kappes MM, Haler JRN, Far J, De Pauw E, Albers C, Bay S, Wurm T, Rudolph M, Schulmeister J, Hashmi ASK. Detection of Intermediates in Dual Gold Catalysis Using High-Resolution Ion Mobility Mass Spectrometry. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00128] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jean-François Greisch
- Institute of Physical Chemistry, KIT, D-76131 Karlsruhe, Germany
- Institute of Nanotechnology, KIT, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Patrick Weis
- Institute of Physical Chemistry, KIT, D-76131 Karlsruhe, Germany
| | - Katrina Brendle
- Institute of Physical Chemistry, KIT, D-76131 Karlsruhe, Germany
| | - Manfred M. Kappes
- Institute of Physical Chemistry, KIT, D-76131 Karlsruhe, Germany
- Institute of Nanotechnology, KIT, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Jean R. N. Haler
- Mass Spectrometry Laboratory, University of Liège, MolSys Research Unit, B-4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, University of Liège, MolSys Research Unit, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, University of Liège, MolSys Research Unit, B-4000 Liège, Belgium
| | | | - Sarah Bay
- Organic Chemistry Institute, Heidelberg University, D-69120 Heidelberg, Germany
| | - Thomas Wurm
- Organic Chemistry Institute, Heidelberg University, D-69120 Heidelberg, Germany
| | - Matthias Rudolph
- Organic Chemistry Institute, Heidelberg University, D-69120 Heidelberg, Germany
| | - Jürgen Schulmeister
- Organic Chemistry Institute, Heidelberg University, D-69120 Heidelberg, Germany
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41
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Ickert S, Hofmann J, Riedel J, Beck S, Pagel K, Linscheid MW. Charge-induced geometrical reorganization of DNA oligonucleotides studied by tandem mass spectrometry and ion mobility. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2018; 24:225-230. [PMID: 29228798 DOI: 10.1177/1469066717746896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n = 15-40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence.
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Affiliation(s)
- Stefanie Ickert
- 1 Department of Chemistry, 9373 Humboldt-Universitaet zu Berlin , Berlin, Germany
- 2 Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Johanna Hofmann
- 3 Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
- 4 Institute of Chemistry and Biochemistry, Free University, Berlin, Germany
| | - Jens Riedel
- 2 Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Sebastian Beck
- 1 Department of Chemistry, 9373 Humboldt-Universitaet zu Berlin , Berlin, Germany
| | - Kevin Pagel
- 3 Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
- 4 Institute of Chemistry and Biochemistry, Free University, Berlin, Germany
| | - Michael W Linscheid
- 1 Department of Chemistry, 9373 Humboldt-Universitaet zu Berlin , Berlin, Germany
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42
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Majuta SN, Maleki H, Kiani Karanji A, Attanyake K, Loch E, Valentine SJ. Magnifying ion mobility spectrometry-mass spectrometry measurements for biomolecular structure studies. Curr Opin Chem Biol 2018; 42:101-110. [PMID: 29241076 PMCID: PMC6500794 DOI: 10.1016/j.cbpa.2017.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) provides information about the structures of gas-phase ions in the form of a collision cross section (CCS) with a neutral buffer gas. Indicating relative ion size, a CCS value alone is of limited utility. Although such information can be used to propose different conformer types, finer details of structure are not captured. The increased accessibility of IMS-MS measurements with commercial instrumentation in recent years has ballooned its usage in combination with separate measurements to provide enhanced data from which greater structural inferences can be drawn. This short review presents recent outstanding developments in scientific research that employs complementary measurements that when combined with IMS-MS data are used to characterize the structures of a wide range of compounds.
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Affiliation(s)
- Sandra N Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Hossein Maleki
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Ahmad Kiani Karanji
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Kushani Attanyake
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Elinore Loch
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States.
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43
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Ben-Nissan G, Sharon M. The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes. Curr Opin Chem Biol 2018; 42:25-33. [PMID: 29128665 PMCID: PMC5796646 DOI: 10.1016/j.cbpa.2017.10.026] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 12/16/2022]
Abstract
Ion-mobility mass spectrometry (IM-MS) is an approach that can provide information on the stoichiometry, composition, protein contacts and topology of protein complexes. The power of this approach lies not only in its sensitivity and speed of analysis, but also in the fact that it is a technique that can capture the repertoire of conformational states adopted by protein assemblies. Here, we describe the array of available IM-MS based tools, and demonstrate their application to the structural characterization of various protein complexes, including challenging systems as amyloid aggregates and membrane proteins. We also discuss recent studies in which IM-MS was applied towards investigations of conformational transitions and stabilization effects induced by protein interactions.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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44
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Re S, Watabe S, Nishima W, Muneyuki E, Yamaguchi Y, MacKerell AD, Sugita Y. Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase. Sci Rep 2018; 8:1644. [PMID: 29374210 PMCID: PMC5786100 DOI: 10.1038/s41598-018-20012-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/10/2018] [Indexed: 12/18/2022] Open
Abstract
Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changes of biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us to separate carbohydrate isomers with subtle conformational differences, but the relationship between CCS and atomic structure remains elusive. Here, we characterize conformational ensembles of gas-phase N-glycans under the electrospray ionization condition using molecular dynamics simulations with enhanced sampling. We show that the separation of CCSs between isomers reflects folding features of N-glycans, which are determined both by chemical compositions and protonation states. Providing a physicochemical basis of CCS for N-glycans helps not only to interpret IM-MS measurements but also to estimate CCSs of complex glycans.
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Affiliation(s)
- Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shigehisa Watabe
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Wataru Nishima
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Eiro Muneyuki
- Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, 21201, USA
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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45
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Lee JW, Lee HHL, Davidson KL, Bush MF, Kim HI. Structural characterization of small molecular ions by ion mobility mass spectrometry in nitrogen drift gas: improving the accuracy of trajectory method calculations. Analyst 2018; 143:1786-1796. [DOI: 10.1039/c8an00270c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An accurate theoretical collision cross section calculation method in nitrogen was developed for reliable structural ion mobility mass spectrometry.
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Affiliation(s)
- Jong Wha Lee
- Center for Analytical Chemistry
- Division of Chemical and Medical Metrology
- Korea Research Institute of Standards and Science (KRISS)
- Daejeon 34113
- Republic of Korea
| | - Hyun Hee L. Lee
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
| | | | | | - Hugh I. Kim
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
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46
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Laszlo KJ, Bush MF. Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas: Results from Trajectory Method Calculations. J Phys Chem A 2017; 121:7768-7777. [PMID: 28910102 DOI: 10.1021/acs.jpca.7b08154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Collision cross section (Ω) values of gas-phase ions of proteins and protein complexes are used to probe the structures of the corresponding species in solution. Ions of many proteins exhibit increasing Ω-values with increasing charge state but most Ω-values calculated for protein ions have used simple collision models that do not explicitly account for charge. Here we use a combination of ion mobility mass spectrometry experiments with helium gas and trajectory method calculations to characterize the extents to which increases in experimental Ω-values with increasing charge state may be attributed to increased momentum transfer concomitant with enhanced long-range interactions between the protein ion and helium atoms. Ubiquitin and C-to-N terminally linked diubiquitin ions generated from different solution conditions exhibit more than a 2-fold increase in Ω with increasing charge state. For native and energy-relaxed models of the proteins and most methods for distributing charge, Ω-values calculated using the trajectory method increase by less than 1% over the range of charge states observed from typical solution conditions used for native mass spectrometry. However, the calculated Ω-values increase by 10% to 15% over the full range of charge states observed from all solution conditions. Therefore, contributions from enhanced ion-induced dipole interactions with increasing charge state are significant but without additional structural changes can account for only a fraction of the increase in Ω observed experimentally. On the basis of these results, we suggest guidelines for calculating Ω-values in the context of applications in biophysics and structural biology.
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Affiliation(s)
- Kenneth J Laszlo
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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47
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Maiβer A, Hogan CJ. Examination of Organic Vapor Adsorption onto Alkali Metal and Halide Atomic Ions by using Ion Mobility Mass Spectrometry. Chemphyschem 2017; 18:3039-3046. [PMID: 28834069 PMCID: PMC5704694 DOI: 10.1002/cphc.201700747] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 11/19/2022]
Abstract
We utilize ion mobility mass spectrometry with an atmospheric pressure differential mobility analyzer coupled to a time‐of‐flight mass spectrometer (DMA‐MS) to examine the formation of ion‐vapor molecule complexes with seed ions of K+, Rb+, Cs+, Br−, and I− exposed to n‐butanol and n‐nonane vapor under subsaturated conditions. Ion‐vapor molecule complex formation is indicated by a shift in the apparent mobility of each ion. Measurement results are compared to predicted mobility shifts based upon the Kelvin–Thomson equation, which is commonly used in predicting rates of ion‐induced nucleation. We find that n‐butanol at saturation ratios as low as 0.03 readily binds to all seed ions, leading to mobility shifts in excess of 35 %. Conversely, the binding of n‐nonane is not detectable for any ion for saturation ratios in the 0–0.27 range. An inverse correlation between the ionic radius of the initial seed and the extent of n‐butanol uptake is observed, such that at elevated n‐butanol concentrations, the smallest ion (K+) has the smallest apparent mobility and the largest (I−) has the largest apparent mobility. Though the differences in behavior of the two vapor molecules types examined and the observed effect of ionic seed radius are not accounted for by the Kelvin–Thomson equation, its predictions are in good agreement with measured mobility shifts for Rb+, Cs+, and Br− in the presence of n‐butanol (typically within 10 % of measurements).
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Affiliation(s)
- Anne Maiβer
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, USA.,The Cyprus Institute, Aglandjia, Cyprus
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, USA
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48
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Root K, Wittwer Y, Barylyuk K, Anders U, Zenobi R. Insight into Signal Response of Protein Ions in Native ESI-MS from the Analysis of Model Mixtures of Covalently Linked Protein Oligomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1863-1875. [PMID: 28593376 DOI: 10.1007/s13361-017-1690-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 05/28/2023]
Abstract
Native ESI-MS is increasingly used for quantitative analysis of biomolecular interactions. In such analyses, peak intensity ratios measured in mass spectra are treated as abundance ratios of the respective molecules in solution. While signal intensities of similar-size analytes, such as a protein and its complex with a small molecule, can be directly compared, significant distortions of the peak ratio due to unequal signal response of analytes impede the application of this approach for large oligomeric biomolecular complexes. We use a model system based on concatenated maltose binding protein units (MBPn, n = 1, 2, 3) to systematically study the behavior of protein mixtures in ESI-MS. The MBP concatamers differ from each other only by their mass while the chemical composition and other properties remain identical. We used native ESI-MS to analyze model mixtures of MBP oligomers, including equimolar mixtures of two proteins, as well as binary mixtures containing different fractions of the individual components. Pronounced deviation from a linear dependence of the signal intensity with concentration was observed for all binary mixtures investigated. While equimolar mixtures showed linear signal dependence at low concentrations, distinct ion suppression was observed above 20 μM. We systematically studied factors that are most often used in the literature to explain the origin of suppression effects. Implications of this effect for quantifying protein-protein binding affinity by native ESI-MS are discussed in general and demonstrated for an example of an anti-MBP antibody with its ligand, MBP. Graphical Abstract ᅟ.
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Affiliation(s)
- Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Yves Wittwer
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrike Anders
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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49
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Shrivastav V, Nahin M, Hogan CJ, Larriba-Andaluz C. Benchmark Comparison for a Multi-Processing Ion Mobility Calculator in the Free Molecular Regime. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1540-1551. [PMID: 28477243 DOI: 10.1007/s13361-017-1661-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
A benchmark comparison between two ion mobility and collision cross-section (CCS) calculators, MOBCAL and IMoS, is presented here as a standard to test the efficiency and performance of both programs. Utilizing 47 organic ions, results are in excellent agreement between IMoS and MOBCAL in He and N2, when both programs use identical input parameters. Due to a more efficiently written algorithm and to its parallelization, IMoS is able to calculate the same CCS (within 1%) with a speed around two orders of magnitude faster than its MOBCAL counterpart when seven cores are used. Due to the high computational cost of MOBCAL in N2, reaching tens of thousands of seconds even for small ions, the comparison between IMoS and MOBCAL is stopped at 70 atoms. Large biomolecules (>10000 atoms) remain computationally expensive when IMoS is used in N2 (even when employing 16 cores). Approximations such as diffuse trajectory methods (DHSS, TDHSS) with and without partial charges and projected area approximation corrections can be used to reduce the total computational time by several folds without hurting the accuracy of the solution. These latter methods can in principle be used with coarse-grained model structures and should yield acceptable CCS results. Graphical Abstract ᅟ.
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Affiliation(s)
- Vaibhav Shrivastav
- Department of Mechanical Engineering, IUPUI, Indianapolis, IN, 46202, USA
| | - Minal Nahin
- Department of Mechanical Engineering, IUPUI, Indianapolis, IN, 46202, USA
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
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50
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Abstract
In this review, we focus on an important aspect of ion mobility (IM) research, namely the reporting of quantitative ion mobility measurements in the form of the gas-phase collision cross section (CCS), which has provided a common basis for comparison across different instrument platforms and offers a unique form of structural information, namely size and shape preferences of analytes in the absence of bulk solvent. This review surveys the over 24,000 CCS values reported from IM methods spanning the era between 1975 to 2015, which provides both a historical and analytical context for the contributions made thus far, as well as insight into the future directions that quantitative ion mobility measurements will have in the analytical sciences. The analysis was conducted in 2016, so CCS values reported in that year are purposely omitted. In another few years, a review of this scope will be intractable, as the number of CCS values which will be reported in the next three to five years is expected to exceed the total amount currently published in the literature.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
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