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Nguan HS, Chen JL, Ni CK. Collision-Induced Dissociation of Fucose and Identification of Anomericity. J Phys Chem A 2024; 128:3812-3820. [PMID: 38690855 PMCID: PMC11103703 DOI: 10.1021/acs.jpca.4c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Structural determination of carbohydrates using mass spectrometry remains challenging, particularly, the differentiation of anomeric configurations. In this work, we studied the collision-induced dissociation (CID) mechanisms of sodiated α- and β-l-fucose using an experimental method and quantum chemistry calculations. The calculations show that α-l-fucose is more likely to undergo dehydration due to the fact that O1 and O2 are on the same side of the sugar ring. In contrast, β-l-fucose is more prone to the ring-opening reaction because more OH groups are on the same side of the sugar ring as O1. These differences suggest a higher preference for the dehydration reaction in sodiated α-l-fucose but a lower preference for ring-opening compared to that of β-l-fucose. The calculation results, which are used to assign the CID mass spectra of α- and β-l-fucose separated by high-performance liquid chromatography, are supported by the fucose produced from the CID of disaccharides Fuc-β-(1 → 3)-GlcNAc and Fuc-α-(1 → 4)-GlcNAc. This study demonstrates that the correlation of cis- and trans-configurations of O1 and O2 to the relative branching ratios of dehydration and cross-ring dissociation in CID, observed in aldohexose and ketohexose in the pyranose form, can be extended to deoxyhexoses for anomericity determination.
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Affiliation(s)
- Hock-Seng Nguan
- Institute
of Atomic and Molecular Sciences, Academia
Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Jien-Lian Chen
- Institute
of Atomic and Molecular Sciences, Academia
Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute
of Atomic and Molecular Sciences, Academia
Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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Phan HT, Tsou PK, Hsu PJ, Kuo JL. A first-principles exploration of the conformational space of sodiated di-saccharides assisted by semi-empirical methods and neural network potentials. Phys Chem Chem Phys 2024; 26:9556-9567. [PMID: 38456454 DOI: 10.1039/d3cp05362h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Previous exploration of the conformational space of sodiated mono-saccharides using a random search algorithm leads to ∼103 structurally distinct conformers covering an energy range of ∼150 kJ mol-1. Thus, it is reasonable to expect that the number of distinct conformers for a given disaccharide would be on the order of 106. Efficient identification of distinct conformers at the first-principles level has been demonstrated with the assistance of neural network potential (NNP) with an accuracy of ∼1 kJ mol-1 compared to DFT. Leveraging a local minima database of neutral and sodiated glucose (Glc), we develop algorithms to systematically explore the conformation landscape of 19 Glc-based sodiated disaccharides. To accelerate the exploration, the NNP method is implemented. The NNP achieves an accuracy of ∼2.3 kJ mol-1 compared to DFT, offering a comparable quality to that of DFT. Through a multi-model approach integrating DFTB3, NNP and DFT, we can rapidly locate low-energy disaccharide conformers at the first-principles level. The methodology we show here can be used to efficiently explore the potential energy landscape of any di-saccharides when first-principles accuracy is required.
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Affiliation(s)
- Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Pei-Kang Tsou
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
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Tsai ST, Hsu HC, Ni CK. A simple tandem mass spectrometry method for structural identification of pentose oligosaccharides. Analyst 2023; 148:1712-1731. [PMID: 36929945 DOI: 10.1039/d3an00068k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Differentiation of stereoisomers that are only dissimilar in the orientation of chemical bonds in space by mass spectrometry remains challenging. Structural determination of carbohydrates by mass spectrometry is difficult, mainly due to the large number of stereoisomers in carbohydrates. Arabinose and xylose are pentose stereoisomers typically present in plant polysaccharides and exist in α- and β-anomeric configurations of furanose and pyranose forms. Conventional methods used to determine the structures of polysaccharides include hydrolysis of polysaccharides into oligosaccharides followed by identification of these oligosaccharides' structures individually through nuclear magnetic resonance spectroscopy (NMR). Although the sensitivity of mass spectrometry is much higher than that of NMR, conventional mass spectrometry provides only limited useful information on oligosaccharide structure determination, only the linkage positions of glycosidic bonds. In this study, we demonstrated a mass spectrometry method for the identification of linkage positions, anomeric configurations, and monosaccharide stereoisomers of intact oligosaccharides consisting of arabinose and xylose. We separated arabinose and xylose monosaccharides into α-furanose, β-furanose, α-pyranose, and β-pyranose forms through high-performance liquid chromatography and obtained the corresponding collision-induced dissociation mass spectra. Using these monosaccharide spectra and a flow chart consisting of the proper CID sequences derived from the dissociation mechanisms of pentose, a simple multi-stage tandem mass spectrometry method for structural identification of intact oligosaccharides consisting of arabinose and xylose was developed. The new mass spectrometry method provides a simple method for determining the structure of polysaccharides consisting of arabinose and xylose. The flow chart can be used in computer coding for automation, an ultimate goal for oligosaccharide structure determination.
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Affiliation(s)
- Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan.
| | - Hsu-Chen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan.
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan. .,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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Nguan HS, Ni CK. Collision-Induced Dissociation of α-Isomaltose and α-Maltose. J Phys Chem A 2022; 126:8799-8808. [DOI: 10.1021/acs.jpca.2c04278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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Nguan HS, Tsai ST, Ni CK. Collision-Induced Dissociation of Cellobiose and Maltose. J Phys Chem A 2022; 126:1486-1495. [PMID: 35212541 DOI: 10.1021/acs.jpca.1c10046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure determination is a longstanding bottleneck of carbohydrate research. Tandem mass spectrometry (MS/MS) is one of the most widely used methods for carbohydrate structure determination. However, the effectiveness of MS/MS depends on how the precursor structures are derived from the observed fragments. Understanding the dissociation mechanisms is crucial for MS/MS-based structure determination. Herein, we investigate the collision-induced dissociation mechanism of β-cellobiose and β-maltose sodium adducts using quantum chemical calculations and experimental measurements. Four dissociation channels are studied. Dehydration mainly occurs through the transfer of an H atom to O1 of the sugar at the reducing end, followed by a C1-O1 bond cleavage; cross-ring dissociation starts with a ring-opening reaction, which occurs through the transfer of an H atom from O1 to O5 of the sugar at the reducing end. These two dissociation channels are analogous to that of glucose monosaccharide. The third channel, generation of B1 and Y1 ions, occurs through the transfer of an H atom from O3 (cellobiose) or O2 (maltose) to O1 of the sugar at the nonreducing end, followed by a glycosidic bond cleavage. The fourth channel, C1-Z1 fragmentation, has two mechanisms: (1) the transfer of an H atom from O3 or O2 to O4 of the sugar at the reducing end to generate C ions in the ring form and (2) the transfer of an H atom from O3 of the sugar at the reducing end to O5 of the sugar at the nonreducing end to produce C ions in the linear form. The results of calculations are supported by experimental collision-induced dissociation spectral measurements.
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Affiliation(s)
- Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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Wang J, Zhao J, Nie S, Xie M, Li S. Mass spectrometry for structural elucidation and sequencing of carbohydrates. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Tsai S, Ni C. Differentiation of aldohexoses and ketohexoses through collision‐induced dissociation. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shang‐Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica Taipei Taiwan
| | - Chi‐Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica Taipei Taiwan
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
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Tsai ST, Nguan HS, Ni CK. Identification of Anomericity and Linkage of Arabinose and Ribose through Collision-Induced Dissociation. J Phys Chem A 2021; 125:6109-6121. [PMID: 34256570 DOI: 10.1021/acs.jpca.1c03854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arabinose and ribose are two common pentoses that exist in both furanose and pyranose forms in plant and bacteria oligosaccharides. In this study, each pentose isomer, namely α-furanose, β-furanose, α-pyranose, and β-pyranose, was first separated through high-performance liquid chromatography followed by an investigation of collision-induced dissociation in an ion trap mass spectrometer. The major dissociation channels, dehydration and cross-ring dissociation, were analyzed by using high-level quantum chemistry calculations and transition state theory. The branching ratio of major dissociation channels was governed by two geometrical features: one being the cis or trans configuration of O1 and O2 atoms determining dehydration preferability and the other being the number of hydroxyl groups on the same side of the ring as the O1 atom determining the preferability of cross-ring dissociation. The relative branching ratios of the major channels were used to identify anomericity and the linkages of arabinose and ribose. Arabinose in the β-configuration and ribose in the α-configuration are predicted to have larger relative dehydration branching ratios than arabinose in the α-configuration and ribose in the β-configuration, respectively. Arabinose and ribose at the reducing end of oligosaccharides with 1 → 2 (pyranose and furanose), 1 → 3 (pyranose and furanose), 1 → 4 (pyranose only), and 1 → 5 (furanose only) linkages are predicted to undergo 0,2X, 0,3X, 0,2A, and 0,2A/0,3A cross-ring dissociation, respectively. Application of the dissociation mechanism to the disaccharide linkage determination is demonstrated.
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Affiliation(s)
- Shang-Ting Tsai
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Hock-Seng Nguan
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Chi-Kung Ni
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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