We have developed NiO/HM20, a matrix composed of NiO nanoparticles (NiO) loaded on zeolite surface, for matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). By photoexcitation, monovalent nickel ion (Ni+) was dominantly observed with high intensity. The mechanism of Ni+ production was studied by picosecond time-resolved emission spectroscopy. By loading NiO on the zeolite surface, a new relaxation pathway to other electronic excited states was observed, which increased the lifetime of electron–hole pairs and promoted the reduction of nickel. The long-lived charge-separated electronic excited state corresponding to the large polarization of NiO was confirmed by X-ray photoelectron spectroscopy (XPS) and X-ray diffraction spectroscopy (XRD). The correlation between the Auger parameter related to the polarization energy and the Ni+ peak intensity in the mass spectrum was confirmed. By applying the developed NiO/HM20 matrix to the MS measurement of small molecules, we found that molecules were ionized through complex formation with Ni+ using the coordination of lone electron pairs or π-electrons in the analyte molecules.
{"title":"Monovalent nickel ion as ionization probe in matrix-assisted laser desorption/ionization mass spectrometry","authors":"Toshiki Horikoshi , Jiawei Xu , Mengrui Yang , Wei Chang , Tatsuya Fujino","doi":"10.1016/j.ijms.2024.117354","DOIUrl":"10.1016/j.ijms.2024.117354","url":null,"abstract":"<div><div>We have developed NiO/HM20, a matrix composed of NiO nanoparticles (NiO) loaded on zeolite surface, for matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). By photoexcitation, monovalent nickel ion (Ni<sup>+</sup>) was dominantly observed with high intensity. The mechanism of Ni<sup>+</sup> production was studied by picosecond time-resolved emission spectroscopy. By loading NiO on the zeolite surface, a new relaxation pathway to other electronic excited states was observed, which increased the lifetime of electron–hole pairs and promoted the reduction of nickel. The long-lived charge-separated electronic excited state corresponding to the large polarization of NiO was confirmed by X-ray photoelectron spectroscopy (XPS) and X-ray diffraction spectroscopy (XRD). The correlation between the Auger parameter related to the polarization energy and the Ni<sup>+</sup> peak intensity in the mass spectrum was confirmed. By applying the developed NiO/HM20 matrix to the MS measurement of small molecules, we found that molecules were ionized through complex formation with Ni<sup>+</sup> using the coordination of lone electron pairs or π-electrons in the analyte molecules.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117354"},"PeriodicalIF":1.6,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142529483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-16DOI: 10.1016/j.ijms.2024.117353
David V. Sirbescu-Stanley , Kristina M. Lemmer , Daniel E. Austin , Nicholas R. Taylor
A new miniature coaxial ion trap mass analyzer with a rectilinear ion guide has been constructed using a combination of planar and cylindrical electrodes. The results reported here focus on characterizing the performance of the rectilinear ion guide and simplified toroidal ion trap components. The simplified toroidal ion trap was found to have an ion capacity in excess of 105 ions and mass spectral resolution of 0.5–0.6 when used as a mass analyzer. The ion storage efficiency within the toroidal trapping region was evaluated and found the stored ion population decreased exponentially with storage time. Ion losses depended slightly on the stored βz condition. Ion losses within the toroidal region are attributed primarily to field instabilities at the intersection point of the two components while charge exchange reactions were observed but considered a minor loss mechanism. The ability to mass selectively ejection ions of a specific mass from the toroidal trapping region was characterized and found to approach 100 % efficiency under appropriate ejection conditions.
{"title":"A simplified coaxial ion trap mass analyzer: Characterization of the simplified toroidal ion trap with a rectilinear ion guide","authors":"David V. Sirbescu-Stanley , Kristina M. Lemmer , Daniel E. Austin , Nicholas R. Taylor","doi":"10.1016/j.ijms.2024.117353","DOIUrl":"10.1016/j.ijms.2024.117353","url":null,"abstract":"<div><div>A new miniature coaxial ion trap mass analyzer with a rectilinear ion guide has been constructed using a combination of planar and cylindrical electrodes. The results reported here focus on characterizing the performance of the rectilinear ion guide and simplified toroidal ion trap components. The simplified toroidal ion trap was found to have an ion capacity in excess of 10<sup>5</sup> ions and mass spectral resolution of 0.5–0.6 when used as a mass analyzer. The ion storage efficiency within the toroidal trapping region was evaluated and found the stored ion population decreased exponentially with storage time. Ion losses depended slightly on the stored β<sub>z</sub> condition. Ion losses within the toroidal region are attributed primarily to field instabilities at the intersection point of the two components while charge exchange reactions were observed but considered a minor loss mechanism. The ability to mass selectively ejection ions of a specific mass from the toroidal trapping region was characterized and found to approach 100 % efficiency under appropriate ejection conditions.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117353"},"PeriodicalIF":1.6,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142529484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-12DOI: 10.1016/j.ijms.2024.117349
Charles Killeen, Antonia Kropp, Ian C. Chagunda, Emily C. Jackson, J. Scott McIndoe
Electrospray ionization mass spectrometry is capable of transferring ions from solution to the gas phase across a broad range of solvents. A systematic investigation of the relative performance of different solvents has not been previously conducted, and we sought to remedy this situation. Fourteen solvents across a wide range of polarities were investigated for their ability to provide strong signals for four permanently charged ions. We found the best solvents to be acetone, acetonitrile, dichloromethane, tetrahydrofuran, and the previously unused (in an ESI-MS context) trifluorotoluene.
{"title":"The amenability of different solvents to electrospray ionization mass spectrometry","authors":"Charles Killeen, Antonia Kropp, Ian C. Chagunda, Emily C. Jackson, J. Scott McIndoe","doi":"10.1016/j.ijms.2024.117349","DOIUrl":"10.1016/j.ijms.2024.117349","url":null,"abstract":"<div><div>Electrospray ionization mass spectrometry is capable of transferring ions from solution to the gas phase across a broad range of solvents. A systematic investigation of the relative performance of different solvents has not been previously conducted, and we sought to remedy this situation. Fourteen solvents across a wide range of polarities were investigated for their ability to provide strong signals for four permanently charged ions. We found the best solvents to be acetone, acetonitrile, dichloromethane, tetrahydrofuran, and the previously unused (in an ESI-MS context) trifluorotoluene.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117349"},"PeriodicalIF":1.6,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142446270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-11DOI: 10.1016/j.ijms.2024.117351
Yinan Li , Jonathan Martens , Wai Kit Tang , Giel Berden , Jos Oomens , Ivan K. Chu
We investigated the dissociation and characterization of radical cations of glycylglycyltyrosine [GGY]•+, focusing on β-radical-induced N–Cα peptide bond cleavage reactions at the tyrosyl residue. By combining density functional theory (DFT) calculations with experimental studies utilizing low-energy collision-induced dissociation (CID) mass spectrometry and deuterium labeling on the two β-hydrogen atoms of the tyrosyl residue in [GGY]•+, we elucidated the intricacies of the β-radical structure and its origin. Unlike tryptophan-containing [GGW]•+, which forms canonical π-radical precursors, infrared multiphoton dissociation (IRMPD) spectroscopy results reveal that the β-radical [GGYβ•]+ isomerizes from the phenoxy-radical [GGYo•]+, with the radical localized on the β-carbon of the tyrosyl residue and the phenolic oxygen atom, respectively. The isomerization barriers from [GGYo•]+ to [GGYβ•]+ are <109 kJ mol−1.
{"title":"Characterization of glycylglycyltyrosine radical cations: Insights into β-radical formation and N–Cα peptide bond dissociation at the tyrosine residue","authors":"Yinan Li , Jonathan Martens , Wai Kit Tang , Giel Berden , Jos Oomens , Ivan K. Chu","doi":"10.1016/j.ijms.2024.117351","DOIUrl":"10.1016/j.ijms.2024.117351","url":null,"abstract":"<div><div>We investigated the dissociation and characterization of radical cations of glycylglycyltyrosine [GGY]<sup>•+</sup>, focusing on β-radical-induced N–C<sub>α</sub> peptide bond cleavage reactions at the tyrosyl residue. By combining density functional theory (DFT) calculations with experimental studies utilizing low-energy collision-induced dissociation (CID) mass spectrometry and deuterium labeling on the two β-hydrogen atoms of the tyrosyl residue in [GGY]<sup>•+</sup>, we elucidated the intricacies of the β-radical structure and its origin. Unlike tryptophan-containing [GGW]<sup>•+</sup>, which forms canonical π-radical precursors, infrared multiphoton dissociation (IRMPD) spectroscopy results reveal that the β-radical [GGY<sub>β</sub><sup>•</sup>]<sup>+</sup> isomerizes from the phenoxy-radical [GGY<sub>o</sub><sup>•</sup>]<sup>+</sup>, with the radical localized on the β-carbon of the tyrosyl residue and the phenolic oxygen atom, respectively. The isomerization barriers from [GGY<sub>o</sub><sup>•</sup>]<sup>+</sup> to [GGY<sub>β</sub><sup>•</sup>]<sup>+</sup> are <109 kJ mol<sup>−1</sup>.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117351"},"PeriodicalIF":1.6,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1016/j.ijms.2024.117350
Zachary J. Devereaux , E.O. Soley , G. Berden , J. Oomens , M.T. Rodgers
Fluorinated nucleosides are well-established as anticancer and antiviral medications. As with many pharmaceuticals, the effects of fluorine modifications are often only partially understood. In this work, the effects of 5-fluorination of the cytosine nucleobase on the structures and glycosidic bond stabilities of the protonated canonical DNA and RNA cytidine nucleosides (dCyd and Cyd) are examined. Infrared multiple photon dissociation action spectroscopy experiments and electronic structure calculations are employed to probe the structural influences of 5-fluorination. Spectral signatures in the IR fingerprint and hydrogen-stretching regions indicate that 5-fluorination heavily directs for and solely produces O2 protonation para to the 5-fluoro substituent. This differs from the canonical cytidine nucleosides where roughly equal populations of O2 and N3 protonated structures were observed. Energy-resolved collision-induced dissociation experiments combined with survival yield analyses are performed to probe the influence of 5-fluorination on glycosidic bond stability. Trends in the energy-dependence of the survival yield curves indicate that 5-fluorination weakens the glycosidic bond, and that the influence of 5-fluorination on glycosidic bond stability is much greater for dCyd than Cyd. Theory also finds that 5-fluorination weakens the glycosidic bond but predicts that the influence of 5-fluorination on N-glycosidic bond stability is roughly the same for dCyd and Cyd. Oh, what a difference the 2′-hydroxy substituent makes?
{"title":"Influence of 5-fluorination on the structure and glycosidic bond stability of the protonated canonical DNA and RNA cytidine nucleosides: Oh, what a difference the 2′-hydroxy substituent makes?","authors":"Zachary J. Devereaux , E.O. Soley , G. Berden , J. Oomens , M.T. Rodgers","doi":"10.1016/j.ijms.2024.117350","DOIUrl":"10.1016/j.ijms.2024.117350","url":null,"abstract":"<div><div>Fluorinated nucleosides are well-established as anticancer and antiviral medications. As with many pharmaceuticals, the effects of fluorine modifications are often only partially understood. In this work, the effects of 5-fluorination of the cytosine nucleobase on the structures and glycosidic bond stabilities of the protonated canonical DNA and RNA cytidine nucleosides (dCyd and Cyd) are examined. Infrared multiple photon dissociation action spectroscopy experiments and electronic structure calculations are employed to probe the structural influences of 5-fluorination. Spectral signatures in the IR fingerprint and hydrogen-stretching regions indicate that 5-fluorination heavily directs for and solely produces O2 protonation <em>para</em> to the 5-fluoro substituent. This differs from the canonical cytidine nucleosides where roughly equal populations of O2 and N3 protonated structures were observed. Energy-resolved collision-induced dissociation experiments combined with survival yield analyses are performed to probe the influence of 5-fluorination on glycosidic bond stability. Trends in the energy-dependence of the survival yield curves indicate that 5-fluorination weakens the glycosidic bond, and that the influence of 5-fluorination on glycosidic bond stability is much greater for dCyd than Cyd. Theory also finds that 5-fluorination weakens the glycosidic bond but predicts that the influence of 5-fluorination on N-glycosidic bond stability is roughly the same for dCyd and Cyd. Oh, what a difference the 2′-hydroxy substituent makes?</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117350"},"PeriodicalIF":1.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-27DOI: 10.1016/j.ijms.2024.117348
Daiki Asakawa
The use of an oxidizing matrix for matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) specifically induces the cleavage of Cα-C bonds on the peptide backbone, except for bonds located on the N-terminal side of proline residues. To examine the effect of Pro residues on bond cleavage induced by MALDI-ISD with an oxidizing matrix, the small dipeptides AcAA-NH2 and AcAP-NH2 were used as models. As the fragmentation is initiated by electron transfer from the peptide to the oxidizing matrix, the dissociation chemistry of the cation radical forms of the model peptides [AcAA-NH2]+• and [AcAP-NH2]+• was investigated using quantum chemistry calculations. The [AcAA-NH2]+• can produce fragment ions not only due to Cα–C bond cleavage, but also peptide bond cleavage. Quantum chemistry calculations indicated that peptide bond cleavage of [AcAA-NH2]+• occurs more slowly compared to Cα–C bond cleavage. Instead of Cα–C bond cleavage, the bond on the N-terminal side of Pro residue undergoes peptide bond cleavage during MALDI-ISD with an oxidizing matrix, due to the lack of an amide hydrogen in the Pro residue. The [AcAP-NH2]+• undergoes proton migration from the δ-carbon of the Pro residue. Depending on the proton binding site in the peptide cation radical, the peptide bond cleavage of [AcAP-NH2]+• results in the formation of either [b1]+, and [y1]•, or [a1]• and [y1]+. These theoretical results are consistent with experimental findings, and the newly proposed mechanism involving peptide cation radical formation followed by proton migration provides a more accurate model for the MALDI-ISD processes.
{"title":"Theoretical investigation for the proline effect on peptide fragmentation induced by matrix-assisted laser desorption/ionization in-source decay with an oxidizing matrix","authors":"Daiki Asakawa","doi":"10.1016/j.ijms.2024.117348","DOIUrl":"10.1016/j.ijms.2024.117348","url":null,"abstract":"<div><div>The use of an oxidizing matrix for matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) specifically induces the cleavage of Cα-C bonds on the peptide backbone, except for bonds located on the N-terminal side of proline residues. To examine the effect of Pro residues on bond cleavage induced by MALDI-ISD with an oxidizing matrix, the small dipeptides AcAA-NH<sub>2</sub> and AcAP-NH<sub>2</sub> were used as models. As the fragmentation is initiated by electron transfer from the peptide to the oxidizing matrix, the dissociation chemistry of the cation radical forms of the model peptides [AcAA-NH<sub>2</sub>]<sup>+</sup>• and [AcAP-NH<sub>2</sub>]<sup>+</sup>• was investigated using quantum chemistry calculations. The [AcAA-NH<sub>2</sub>]<sup>+</sup>• can produce fragment ions not only due to Cα–C bond cleavage, but also peptide bond cleavage. Quantum chemistry calculations indicated that peptide bond cleavage of [AcAA-NH<sub>2</sub>]<sup>+</sup>• occurs more slowly compared to Cα–C bond cleavage. Instead of Cα–C bond cleavage, the bond on the N-terminal side of Pro residue undergoes peptide bond cleavage during MALDI-ISD with an oxidizing matrix, due to the lack of an amide hydrogen in the Pro residue. The [AcAP-NH<sub>2</sub>]<sup>+</sup>• undergoes proton migration from the δ-carbon of the Pro residue. Depending on the proton binding site in the peptide cation radical, the peptide bond cleavage of [AcAP-NH<sub>2</sub>]<sup>+</sup>• results in the formation of either [b<sub>1</sub>]<sup>+</sup>, and [y<sub>1</sub>]•, or [a<sub>1</sub>]• and [y<sub>1</sub>]<sup>+</sup>. These theoretical results are consistent with experimental findings, and the newly proposed mechanism involving peptide cation radical formation followed by proton migration provides a more accurate model for the MALDI-ISD processes.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117348"},"PeriodicalIF":1.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142357047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-24DOI: 10.1016/j.ijms.2024.117347
Solita M. Wilson , Brittney E. Petel , Michela L. Maiola , Dylan Forbes , Ellen M. Matson , Julia Laskin
Atom-by-atom substitution is a promising strategy for tailoring the electronic properties of transition metal oxide clusters. This approach typically generates a mixture of species that are difficult to separate using conventional methods. As a result, the characterization of their structures and electronic properties remains challenging. Herein, we use collision-induced dissociation (CID) to study the fragmentation of well-defined Fe- and W-doped Lindquist polyoxovanadate methoxides synthesized as a mixture of singly and doubly substituted species. Fragmentation reveals that Fe heteroatoms are efficiently retained within the metal oxide core. In contrast, one W atom is incorporated into the primary WO2(OCH3)2 neutral loss from both the singly and doubly substituted W-containing clusters. Collision energy-resolved CID provides insights into the fragmentation pathways, which are compared to those of the homometallic polyoxovanadate methoxide species. The incorporation of Fe into the cluster reduces its stability towards fragmentation, which could be attributed to the increase in the relative stability of Fe-containing fragment ions with four metal atoms in comparison with their homometallic analog. The observed fragmentation is rationalized by assuming that Fe atoms are incorporated within the low valent plane, while one W atom occupies the axial out-of-plane position in the cluster.
逐原子置换是调整过渡金属氧化物团簇电子特性的一种有前途的策略。这种方法通常会产生难以用传统方法分离的混合物。因此，对它们的结构和电子特性进行表征仍然具有挑战性。在本文中，我们利用碰撞诱导解离（CID）技术研究了作为单取代和双取代物种混合物合成的定义明确的铁掺杂和钨掺杂林奎斯特多氧化钒酸甲氧基化物的碎片。碎片分析表明，铁杂质原子被有效地保留在金属氧化物核心中。相比之下，单取代和双取代的含 W 原子簇中都有一个 W 原子掺入了主 WO2(OCH3)2 中性损失。碰撞能量分辨 CID 深入揭示了其破碎途径，并将其与同金属聚氧化钒甲氧化物物种的破碎途径进行了比较。在簇中加入铁会降低其碎裂的稳定性，这可能是因为与同金属类似物相比，含有四个金属原子的含铁碎片离子的相对稳定性增加了。假定铁原子在低价平面内结合，而一个 W 原子占据了簇中的轴向平面外位置，则观察到的碎裂现象是合理的。
{"title":"Mass spectrometry provides insights into the structures of polyoxovanadate alkoxide clusters substituted with Fe and W heterometals","authors":"Solita M. Wilson , Brittney E. Petel , Michela L. Maiola , Dylan Forbes , Ellen M. Matson , Julia Laskin","doi":"10.1016/j.ijms.2024.117347","DOIUrl":"10.1016/j.ijms.2024.117347","url":null,"abstract":"<div><div>Atom-by-atom substitution is a promising strategy for tailoring the electronic properties of transition metal oxide clusters. This approach typically generates a mixture of species that are difficult to separate using conventional methods. As a result, the characterization of their structures and electronic properties remains challenging. Herein, we use collision-induced dissociation (CID) to study the fragmentation of well-defined Fe- and W-doped Lindquist polyoxovanadate methoxides synthesized as a mixture of singly and doubly substituted species. Fragmentation reveals that Fe heteroatoms are efficiently retained within the metal oxide core. In contrast, one W atom is incorporated into the primary WO<sub>2</sub>(OCH<sub>3</sub>)<sub>2</sub> neutral loss from both the singly and doubly substituted W-containing clusters. Collision energy-resolved CID provides insights into the fragmentation pathways, which are compared to those of the homometallic polyoxovanadate methoxide species. The incorporation of Fe into the cluster reduces its stability towards fragmentation, which could be attributed to the increase in the relative stability of Fe-containing fragment ions with four metal atoms in comparison with their homometallic analog. The observed fragmentation is rationalized by assuming that Fe atoms are incorporated within the low valent plane, while one W atom occupies the axial out-of-plane position in the cluster.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117347"},"PeriodicalIF":1.6,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142357168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-24DOI: 10.1016/j.ijms.2024.117345
Virginia G. Rodriguez , Tucker W.R. Lewis , Thomas M. Miller , Shaun G. Ard , Albert A. Viggiano , Nicholas S. Shuman
Kinetics of the reactions of N3+ and N4+ with N(4S) and O(3P) are measured at room temperature using a flowing afterglow-selected ion flow tube apparatus. Oxygen atoms are produced by titrating NO against nitrogen atoms formed from a microwave discharge of N2. The reaction rate constants are generally well-described by assuming strict spin-conservation along with Langevin capture kinetics. N3+ + N occurs with k = 1.8 × 10−10 cm3 s−1, spin state counting indicates both doublet and quartet states of N2+ are formed. N4+ + N occurs with k = 2.2 × 10−10 cm3 s−1, yielding exclusively N3+. The N3+ + O reaction occurs with k = 2.5 × 10−10 cm3 s−1, yielding significant amounts of NO+ and N2+ products. N4+ + O, the only of these reactions without any spin-constraint, is the only reaction to occur near the Langevin capture rate with k = 5.6 × 10−10 cm3 s−1. The major product of the N4+ + O reaction is charge transfer to yield O+ (k = 4.1 × 10−10 cm3 s−1) with N2O+ (k = 7.7 × 10−11 cm3s−1) and probably NO + formed as minor products. The reaction of N4+ + NO minimally occurs with k < 6.5 × 10−12 cm3 s−1. A novel method of assessing uncertainties in rate constants derived from complicated chemical reaction networks is presented, yielding probability density curves as a function of each partial rate constant. The analysis obviates the need of assuming experimental errors of the rate constants are normally distributed.
使用流动的余辉选择离子流管仪器在室温下测量了 N3+ 和 N4+ 与 N(4S) 和 O(3P) 反应的动力学。氧原子是通过将 NO 与 N2 微波放电形成的氮原子进行滴定而产生的。通过假设严格的自旋守恒和朗格文捕获动力学，反应速率常数一般都能得到很好的描述。N3+ + N 的反应速率为 k = 1.8 × 10-10 cm3 s-1，自旋态计数表明 N2+ 的双态和四态均已形成。N4+ + N 的反应速度为 k = 2.2 × 10-10 cm3 s-1，生成的完全是 N3+。N3+ + O 反应在 k = 2.5 × 10-10 cm3 s-1 时发生，生成大量 NO+ 和 N2+ 产物。N4+ + O 是这些反应中唯一没有自旋约束的反应，也是唯一以 k = 5.6 × 10-10 cm3 s-1 发生在朗格文捕获率附近的反应。N4+ + O 反应的主要产物是电荷转移产生的 O+（k = 4.1 × 10-10 cm3 s-1），次要产物是 N2O+（k = 7.7 × 10-11 cm3 s-1）和可能形成的 NO+。N4+ + NO 的反应以 k < 6.5 × 10-12 cm3 s-1 的最小值发生。本文提出了一种新方法，用于评估从复杂化学反应网络中得出的速率常数的不确定性，得出了作为各部分速率常数函数的概率密度曲线。这种分析方法无需假设速率常数的实验误差呈正态分布。
{"title":"Kinetics of N3+ and N4+ with N(4S), O(3P), and NO","authors":"Virginia G. Rodriguez , Tucker W.R. Lewis , Thomas M. Miller , Shaun G. Ard , Albert A. Viggiano , Nicholas S. Shuman","doi":"10.1016/j.ijms.2024.117345","DOIUrl":"10.1016/j.ijms.2024.117345","url":null,"abstract":"<div><div>Kinetics of the reactions of N<sub>3</sub><sup>+</sup> and N<sub>4</sub><sup>+</sup> with N(<sup>4</sup>S) and O(<sup>3</sup>P) are measured at room temperature using a flowing afterglow-selected ion flow tube apparatus. Oxygen atoms are produced by titrating NO against nitrogen atoms formed from a microwave discharge of N<sub>2</sub>. The reaction rate constants are generally well-described by assuming strict spin-conservation along with Langevin capture kinetics. N<sub>3</sub><sup>+</sup> + N occurs with k = 1.8 × 10<sup>−10</sup> cm<sup>3</sup> s<sup>−1</sup>, spin state counting indicates both doublet and quartet states of N<sub>2</sub><sup>+</sup> are formed. N<sub>4</sub><sup>+</sup> + N occurs with k = 2.2 × 10<sup>−10</sup> cm<sup>3</sup> s<sup>−1</sup>, yielding exclusively N<sub>3</sub><sup>+</sup>. The N<sub>3</sub><sup>+</sup> + O reaction occurs with k = 2.5 × 10<sup>−10</sup> cm<sup>3</sup> s<sup>−1</sup>, yielding significant amounts of NO<sup>+</sup> and N<sub>2</sub><sup>+</sup> products. N<sub>4</sub><sup>+</sup> + O, the only of these reactions without any spin-constraint, is the only reaction to occur near the Langevin capture rate with k = 5.6 × 10<sup>−10</sup> cm<sup>3</sup> s<sup>−1</sup>. The major product of the N<sub>4</sub><sup>+</sup> + O reaction is charge transfer to yield O<sup>+</sup> (k = 4.1 × 10<sup>−10</sup> cm<sup>3</sup> s<sup>−1</sup>) with N<sub>2</sub>O<sup>+</sup> (k = 7.7 × 10<sup>−11</sup> cm<sup>3</sup>s<sup>−1</sup>) and probably NO <sup>+</sup> formed as minor products. The reaction of N<sub>4</sub><sup>+</sup> + NO minimally occurs with k < 6.5 × 10<sup>−12</sup> cm<sup>3</sup> s<sup>−1</sup>. A novel method of assessing uncertainties in rate constants derived from complicated chemical reaction networks is presented, yielding probability density curves as a function of each partial rate constant. The analysis obviates the need of assuming experimental errors of the rate constants are normally distributed.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117345"},"PeriodicalIF":1.6,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142357054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-24DOI: 10.1016/j.ijms.2024.117346
C. Ruth Wang , Paul J. Trim , Jacob XM. Truong , Marten F. Snel , Tara L. Pukala
Snake venoms are composed of bioactive proteins and peptides from various toxin families and elicit potent pharmacological activity. There is great interest in characterising these venom proteins for the development of effective antivenom treatment as well as utilisation for biomedical and therapeutic applications. However, a thorough structural understanding of the snake venom proteins is necessary. Higher-order protein complexes are known to form in snake venoms and lend structural and functional diversity, often eliciting greater activity than the sum of monomeric protein species. Despite the significance, the nature of these protein complexes is extremely underexplored. In this study, we demonstrate the use of mass spectrometry (MS)-based strategies to explore the toxins at a quaternary level in the venom from the medically significant forest cobra (Naja melanoleuca). Small toxins, mainly three finger toxins (3FTxs) and phospholipase A2s (PLA2s), were identified by comparison of intact and chemically reduced masses using matrix-assisted laser desorption ionisation (MALDI-MS) profiling. Notably, interrogation of these small toxins by native MS and collision-induced dissociation revealed the presence of various non-covalent 3FTx and PLA2 dimers, providing insight on the higher-order protein structures for a variety of N. melanoleuca toxins using a MS-based approach. Furthermore, phospholipid substrate specificity of N. melanoleuca PLA2 enzymes were explored, capturing the indiscriminate activity of these PLA2s towards a range of phospholipid classes for the first time.
蛇毒由来自不同毒素家族的生物活性蛋白质和肽组成，具有强大的药理活性。为了开发有效的抗蛇毒血清治疗方法，以及将蛇毒应用于生物医学和治疗领域，人们对研究这些蛇毒蛋白的特征有着浓厚的兴趣。然而，彻底了解蛇毒蛋白的结构是必要的。众所周知，蛇毒中会形成高阶蛋白复合物，这种复合物具有结构和功能多样性，通常比单体蛋白的总和具有更强的活性。尽管意义重大，但这些蛋白质复合物的性质却极少被探索。在这项研究中，我们展示了如何利用基于质谱的策略来探索具有重要医学价值的森林眼镜蛇（Naja melanoleuca）毒液中的四级毒素。利用基质辅助激光解吸电离（MALDI-MS）分析法，通过比较完整质量和化学还原质量，确定了小毒素，主要是三指毒素（3FTxs）和磷脂酶 A2s（PLA2s）。值得注意的是，通过本征质谱和碰撞诱导解离对这些小毒素进行检测，发现了各种非共价的 3FTx 和 PLA2 二聚体的存在，从而利用基于质谱的方法深入了解了多种 N. melanoleuca 毒素的高阶蛋白质结构。此外，研究人员还探索了 N. melanoleuca PLA2 酶的磷脂底物特异性，首次捕获了这些 PLA2 对一系列磷脂类别的无差别活性。
{"title":"Interrogation of three-finger toxin and phospholipase A2 higher order structures from the forest cobra (Naja melanoleuca) venom using a mass spectrometric approach","authors":"C. Ruth Wang , Paul J. Trim , Jacob XM. Truong , Marten F. Snel , Tara L. Pukala","doi":"10.1016/j.ijms.2024.117346","DOIUrl":"10.1016/j.ijms.2024.117346","url":null,"abstract":"<div><div>Snake venoms are composed of bioactive proteins and peptides from various toxin families and elicit potent pharmacological activity. There is great interest in characterising these venom proteins for the development of effective antivenom treatment as well as utilisation for biomedical and therapeutic applications. However, a thorough structural understanding of the snake venom proteins is necessary. Higher-order protein complexes are known to form in snake venoms and lend structural and functional diversity, often eliciting greater activity than the sum of monomeric protein species. Despite the significance, the nature of these protein complexes is extremely underexplored. In this study, we demonstrate the use of mass spectrometry (MS)-based strategies to explore the toxins at a quaternary level in the venom from the medically significant forest cobra (<em>Naja melanoleuca</em>). Small toxins, mainly three finger toxins (3FTxs) and phospholipase A<sub>2</sub>s (PLA<sub>2</sub>s), were identified by comparison of intact and chemically reduced masses using matrix-assisted laser desorption ionisation (MALDI-MS) profiling. Notably, interrogation of these small toxins by native MS and collision-induced dissociation revealed the presence of various non-covalent 3FTx and PLA<sub>2</sub> dimers, providing insight on the higher-order protein structures for a variety of <em>N. melanoleuca</em> toxins using a MS-based approach. Furthermore, phospholipid substrate specificity of <em>N. melanoleuca</em> PLA<sub>2</sub> enzymes were explored, capturing the indiscriminate activity of these PLA<sub>2</sub>s towards a range of phospholipid classes for the first time.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"506 ","pages":"Article 117346"},"PeriodicalIF":1.6,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142319203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-20DOI: 10.1016/j.ijms.2024.117344
R.R. Wu , M.T. Rodgers
Synergistic infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and electronic structure calculations revealed that both 2,4-dihydroxy tautomers and O2 protonated conformers of protonated thymidine, [dThd+H]+, and protonated 5-methyluridine, [Thd+H]+ coexist in the gas phase with the 2,4-dihydroxy tautomers dominating the population. In the current study, the kinetic energy dependence of the collision-induced dissociation behavior of [dThd+H]+ and [Thd+H]+ are examined in a guided ion beam tandem mass spectrometer. The primary dissociation pathways observed involve N-glycosidic bond cleavage leading to competitive elimination of either protonated or neutral thymine. The potential energy surfaces (PESs) for these N-glycosidic bond cleavage pathways are mapped via electronic structure calculations for the mixture of 2,4-dihydroxy tautomers and O2 protonated conformers of [dThd+H]+ and [Thd+H]+ populated in the IRMPD experiments. The activation energies and heats of reaction predicted for N-glycosidic bond cleavage at the B3LYP and MP2(full) levels of theory are compared to the measured values. The agreement between experiment and theory indicates that B3LYP provides better estimates of the energetics of the species along the PESs for N-glycosidic bond cleavage of [dThd+H]+ and [Thd+H]+ than MP2, and that the 2,4-dihydroxy tautomers, which are stabilized by strong hydrogen-bonding interactions, control the threshold dissociation behavior of [dThd+H]+ and [Thd+H]+.
{"title":"Protonation-induced tautomerization lowers the activation barriers for N-glycosidic bond cleavage of thymidine and 5-methyluridine","authors":"R.R. Wu , M.T. Rodgers","doi":"10.1016/j.ijms.2024.117344","DOIUrl":"10.1016/j.ijms.2024.117344","url":null,"abstract":"<div><div>Synergistic infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and electronic structure calculations revealed that both 2,4-dihydroxy tautomers and O2 protonated conformers of protonated thymidine, [dThd+H]<sup>+</sup>, and protonated 5-methyluridine, [Thd+H]<sup>+</sup> coexist in the gas phase with the 2,4-dihydroxy tautomers dominating the population. In the current study, the kinetic energy dependence of the collision-induced dissociation behavior of [dThd+H]<sup>+</sup> and [Thd+H]<sup>+</sup> are examined in a guided ion beam tandem mass spectrometer. The primary dissociation pathways observed involve N<em>-</em>glycosidic bond cleavage leading to competitive elimination of either protonated or neutral thymine. The potential energy surfaces (PESs) for these N<em>-</em>glycosidic bond cleavage pathways are mapped via electronic structure calculations for the mixture of 2,4-dihydroxy tautomers and O2 protonated conformers of [dThd+H]<sup>+</sup> and [Thd+H]<sup>+</sup> populated in the IRMPD experiments. The activation energies and heats of reaction predicted for N<em>-</em>glycosidic bond cleavage at the B3LYP and MP2(full) levels of theory are compared to the measured values. The agreement between experiment and theory indicates that B3LYP provides better estimates of the energetics of the species along the PESs for N<em>-</em>glycosidic bond cleavage of [dThd+H]<sup>+</sup> and [Thd+H]<sup>+</sup> than MP2, and that the 2,4-dihydroxy tautomers, which are stabilized by strong hydrogen-bonding interactions, control the threshold dissociation behavior of [dThd+H]<sup>+</sup> and [Thd+H]<sup>+</sup>.</div></div>","PeriodicalId":338,"journal":{"name":"International Journal of Mass Spectrometry","volume":"507 ","pages":"Article 117344"},"PeriodicalIF":1.6,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142652333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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