1
|
Zhou S, Qi M, Luo Y, Li W, Liu Y, Guo C, Wei W, Chen G, Tu P, Feng H, Pan Y. Radical-Induced Dissociation for Oligonucleotide Sequencing by TiO 2/ZnAl-Layered Double Oxide-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2023; 95:16505-16513. [PMID: 37902600 DOI: 10.1021/acs.analchem.3c02166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
De novo sequencing of oligonucleotides remains challenging, especially for oligonucleotides with post-transcriptional or synthetic modifications. Mass spectrometry (MS) sequencing can reliably detect and locate all of the modification sites in oligonucleotides via m/z variance. However, current MS-based sequencing methods exhibit complex spectra and low ion abundance and usually require coupled instrumentation. Herein, we demonstrate a method of oligonucleotide sequencing using TiO2/ZnAl-layered double oxide (LDO)-assisted laser desorption/ionization (LDI)-MS based on radical-induced dissociation (RID). ·CH2OH radicals can be produced on the surface of a TiO2/ZnAl-LDO matrix via ultraviolet light, inducing an attack on the active site of the oligonucleotide phosphate skeleton to create typical "a-, a-B-, c·-, d-, w-, and y"-type fragments. Compared with the spectra obtained via collision-based methods, such as collision-induced dissociation and higher-energy collisional dissociation, the LDI-MS spectra based on RID exhibit single-charged signals, fewer types of fragments, and a lower proportion of unknown noise peaks. We demonstrate full sequence coverage for a 6-mer 2'-O-methyl-modified oligonucleotide and a 21-mer small interfering RNA and show that RID can sequence oligonucleotides with modifications. Importantly, the mechanism responsible for the RID of the oligonucleotide phosphate skeleton was investigated through offline experiments, demonstrating consistent results with density functional theory calculations.
Collapse
Affiliation(s)
- Shiwen Zhou
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| | - Menghui Qi
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| | - Yuanqing Luo
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| | - Wangyu Li
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| | - Yaqin Liu
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| | - Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou 310009, China
| | - Wei Wei
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| | - Guanru Chen
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| | - Peijun Tu
- Department of Environmental Medicine and Public Health, Mount Sinai Hospital, New York 10029, United States
| | - Hongru Feng
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou 310027, China
| |
Collapse
|
2
|
Douroudgari H, Zarepour H, Vahedpour M, Jaberi M, Zarepour M. The atmospheric relevance of primary alcohols and imidogen reactions. Sci Rep 2023; 13:9150. [PMID: 37277419 DOI: 10.1038/s41598-023-35473-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Organic alcohols as very volatile compounds play a crucial role in the air quality of the atmosphere. So, the removal processes of such compounds are an important atmospheric challenge. The main goal of this research is to discover the atmospheric relevance of degradation paths of linear alcohols by imidogen with the aid of simulation by quantum mechanical (QM) methods. To this end, we combine broad mechanistic and kinetic results to get more accurate information and to have a deeper insight into the behavior of the designed reactions. Thus, the main and necessary reaction pathways are explored by well-behaved QM methods for complete elucidation of the studying gaseous reactions. Moreover, the potential energy surfaces as a main factor are computed for easier judging of the most probable pathways in the simulated reactions. Our attempt to find the occurrence of the considered reactions in the atmospheric conditions is completed by precisely evaluating the rate constants of all elementary reactions. All of the computed bimolecular rate constants have a positive dependency on both temperature and pressure. The kinetic results show that H-abstraction from the α carbon is dominant relative to the other sites. Finally, by the results of this study, we conclude that at moderate temperatures and pressures primary alcohols can degrade with imidogen, so they can get atmospheric relevance.
Collapse
Affiliation(s)
- Hamed Douroudgari
- Department of Chemistry, University of Zanjan, PO Box 38791-45371, Zanjan, Iran.
| | - Hadi Zarepour
- Department of Chemistry, University of Zanjan, PO Box 38791-45371, Zanjan, Iran
| | - Morteza Vahedpour
- Department of Chemistry, University of Zanjan, PO Box 38791-45371, Zanjan, Iran.
| | - Mahdi Jaberi
- Department of Chemistry, University of Zanjan, PO Box 38791-45371, Zanjan, Iran
| | - Mahdi Zarepour
- Department of Chemistry, University of Zanjan, PO Box 38791-45371, Zanjan, Iran
| |
Collapse
|
3
|
Reaction pathways for palladium(I) reduction in laser-induced particle formation of Pd: An ab initio molecular orbital study. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
|
4
|
Espinosa-Garcia J, Rangel C. Analytical potential energy surface and dynamics for the OH + CH 3OH reaction. J Chem Phys 2023; 158:054302. [PMID: 36754788 DOI: 10.1063/5.0137372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Using as functional form a combination of valence bond and mechanic molecular terms a new full-dimensional potential energy surface was developed for the title reaction, named PES-2022, which was fitted to high-level ab initio calculations at the coupled-cluster singles, doubles, and perturbative triples-F12 explicitly correlated level on a representative number of points describing the reactive system. This surface simultaneously describes the two reaction channels, hydrogen abstraction from the methyl group [(R1) path] and from the alcohol group [(R2) path] of methanol to form water. PES-2022 is a smooth and continuous surface, which reasonably describes the topology of this reactive system from reactants to products, including the intermediate complexes present in the system. Based on PES-2022 an exhaustive dynamics study was performed using quasi-classical trajectory calculations under two different initial conditions: at a fixed room temperature, for direct comparison with the experimental evidence and at different collision energies, to analyze possible mechanisms of reaction. In the first case, the available energy was mostly deposited as water vibrational energy, with the vibrational population inverted in the stretching modes and not inverted in the bending modes, reproducing the experimental evidence. In the second case, the analysis of different dynamics magnitudes (excitation functions, product energy partitioning, and product scattering distributions), allows us to suggest different mechanisms for both (R1) and (R2) paths: a direct mechanism for the (R2) path vs an indirect one, related with "nearly trapped" trajectories in the intermediate complexes, for the (R1) path.
Collapse
Affiliation(s)
- J Espinosa-Garcia
- Área de Química Física and Instituto de Computación Científica Avanzada, Universidad de Extremadura, 06071 Badajoz, Spain
| | - C Rangel
- Área de Química Física and Instituto de Computación Científica Avanzada, Universidad de Extremadura, 06071 Badajoz, Spain
| |
Collapse
|
5
|
Ab initio characterization of the potential energy profiles for the multi-channel reactions: H/Cl + CH3OH. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
6
|
Nguyen QV, Frisbie CD. Hopping Conductance in Molecular Wires Exhibits a Large Heavy-Atom Kinetic Isotope Effect. J Am Chem Soc 2021; 143:2638-2643. [PMID: 33587628 DOI: 10.1021/jacs.0c12244] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We report a large kinetic isotope effect (KIE) for intramolecular charge transport in π-conjugated oligophenyleneimine (OPI) molecules connected to Au electrodes. 13C and 15N substitution on the imine bonds produces a conductance KIE of ∼2.7 per labeled atom in long OPI wires >4 nm in length, far larger than typical heavy-atom KIEs for chemical reactions. In contrast, isotopic labeling in shorter OPI wires <4 nm does not produce a conductance KIE, consistent with a direct tunneling mechanism. Temperature-dependent measurements reveal that conductance for a long 15N-substituted OPI wire is activated, and we propose that the exceptionally large conductance KIEs imply a thermally assisted, through-barrier polaron tunneling mechanism. In general, observation of large conductance KIEs opens up considerable opportunities for understanding microscopic conduction mechanisms in π-conjugated molecules.
Collapse
Affiliation(s)
- Quyen Van Nguyen
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - C Daniel Frisbie
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
7
|
Nguyen TL, Ruscic B, Stanton JF. A master equation simulation for the•OH + CH3OH reaction. J Chem Phys 2019; 150:084105. [DOI: 10.1063/1.5081827] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thanh Lam Nguyen
- Quantum Theory Project, Department of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, USA
| | - Branko Ruscic
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - John F. Stanton
- Quantum Theory Project, Department of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, USA
| |
Collapse
|
8
|
Wijker RS, Adamczyk P, Bolotin J, Paneth P, Hofstetter TB. Isotopic analysis of oxidative pollutant degradation pathways exhibiting large H isotope fractionation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:13459-13468. [PMID: 24175739 DOI: 10.1021/es403597v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Oxidation of aromatic rings and its alkyl substituents are often competing initial steps of organic pollutant transformation. The use of compound-specific isotope analysis (CSIA) to distinguish between these two pathways quantitatively, however, can be hampered by large H isotope fractionation that precludes calculation of apparent (2)H-kinetic isotope effects (KIE) as well as the process identification in multi-element isotope fractionation analysis. Here, we investigated the C and H isotope fractionation associated with the transformation of toluene, nitrobenzene, and four substituted nitrotoluenes by permanganate, MnO4(-), to propose a refined evaluation procedure for the quantitative distinction of CH3-group oxidation and dioxygenation. On the basis of batch experiments, an isotopomer-specific kinetic model, and density functional theory (DFT) calculations, we successfully derived the large apparent (2)H-KIE of 4.033 ± 0.20 for the CH3-group oxidation of toluene from H isotope fractionation exceeding >1300‰ as well as the corresponding (13)C-KIE (1.0324 ± 0.0011). Experiment and theory also agreed well for the dioxygenation of nitrobenzene, which was associated with (2)H- and (13)C-KIEs of 0.9410 ± 0.0030 (0.9228 obtained by DFT) and 1.0289 ± 0.0003 (1.025). Consistent branching ratios for the competing CH3-group oxidation and dioxygenation of nitrotoluenes by MnO4(-) were obtained from the combined modeling of concentration as well as C and H isotope signature trends. Our approach offers improved estimates for the identification of contaminant microbial and abiotic oxidation pathways by CSIA.
Collapse
Affiliation(s)
- Reto S Wijker
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | | | | | | | | |
Collapse
|
9
|
Giebel BM, Swart PK, Riemer DD. New insights to the use of ethanol in automotive fuels: a stable isotopic tracer for fossil- and bio-fuel combustion inputs to the atmosphere. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:6661-6669. [PMID: 21692481 DOI: 10.1021/es200982t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Ethanol is currently receiving increased attention because of its use as a biofuel or fuel additive and because of its influence on air quality. We used stable isotopic ratio measurements of (13)C/(12)C in ethanol emitted from vehicles and a small group of tropical plants to establish ethanol's δ(13)C end-member signatures. Ethanol emitted in exhaust is distinctly different from that emitted by tropical plants and can serve as a unique stable isotopic tracer for transportation-related inputs to the atmosphere. Ethanol's unique isotopic signature in fuel is related to corn, a C4 plant and the primary source of ethanol in the U.S. We estimated a kinetic isotope effect (KIE) for ethanol's oxidative loss in the atmosphere and used previous assumptions with respect to the fractionation that may occur during wet and dry deposition. A small number of interpretive model calculations were used for source apportionment of ethanol and to understand the associated effects resulting from atmospheric removal. The models incorporated our end-member signatures and ambient measurements of ethanol, known or estimated source strengths and removal magnitudes, and estimated KIEs associated with atmospheric removal processes for ethanol. We compared transportation-related ethanol signatures to those from biogenic sources and used a set of ambient measurements to apportion each source contribution in Miami, Florida-a moderately polluted, but well ventilated urban location.
Collapse
Affiliation(s)
- Brian M Giebel
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, Miami, Florida 33149, United States.
| | | | | |
Collapse
|
10
|
Nilsson EJK, Johnson MS, Nielsen CJ. Isotope Effects in the Reactions of Chloroform Isotopologues with Cl, OH, and OD. J Phys Chem A 2009; 113:1731-9. [DOI: 10.1021/jp807233x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Elna J. K. Nilsson
- Copenhagen Center for Atmospheric Research, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway
| | - Matthew S. Johnson
- Copenhagen Center for Atmospheric Research, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway
| | - Claus J. Nielsen
- Copenhagen Center for Atmospheric Research, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway
| |
Collapse
|