220 results on '"J. Scott McIndoe"'
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2. PythoMS: A Python Framework To Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data.
- Author
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Lars P. E. Yunker, Sofia Donnecke, Michelle Ting, Darien Yeung, and J. Scott McIndoe
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- 2019
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3. Competitive Isomerization and Catalyst Decomposition During Ring-Closing Metathesis
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Charles Killeen, Jie Liu, Harmen Zijlstra, Florian Maass, James Piers, Reid Adams, Allen G. Oliver, and J. Scott McIndoe
- Abstract
Ring-closing metathesis (RCM) is an elegant means of forming cyclic structural elements in both simple and complex molecules. Mechanistically, the reaction cycle is well understood, though subtle details concerning the fate of the catalyst and the appearance of yield-reducing by-products remain to be fully deciphered. We applied real-time analysis using electrospray ionization mass spectrometry (ESI-MS) to probe the RCM reaction, including studying the dynamics of all charged species in the reaction mixture and investigating the nature of the by-products formed. The catalyst of choice was Grubbs’ second-generation catalyst. The principal findings included the fact that for slower reactions, by-products appeared that differed in mass from the starting material and product by increments of CH2; that isomerization reactions were responsible for these by-products; and that the catalyst decomposes to form charged products including [ClPCy3]+, [HPCy3]+, and the imidazolinium salt of the N-heterocyclic carbene (NHC) ligand. In cases where RCM is slow, isomerization reactions play a disproportionate part in affecting yield of the desired product.
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- 2023
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4. Understanding the color change of the solutions of Cp 2 TiCl upon addition of water
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Rosales Antonio, Martin Jaraiz, Lourdes Enríquez, Tanner Thiessen, Jaspreet Sidhu, J. Scott McIndoe, and Ignacio Rodriguez-Garcia
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Inorganic Chemistry ,General Chemistry - Published
- 2022
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5. Spectroscopic Studies of Synthetic Methylaluminoxane: Structure of Methylaluminoxane Activators
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Mikko Linnolahti, Elena Liles, J. Scott McIndoe, Anuj Joshi, Scott Collins, and Harmen S. Zijlstra
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010405 organic chemistry ,Chemistry ,Electrospray ionization ,Organic Chemistry ,Methylaluminoxane ,chemistry.chemical_element ,General Chemistry ,Nuclear magnetic resonance spectroscopy ,010402 general chemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Ion ,chemistry.chemical_compound ,Hydrolysis ,Activator (phosphor) ,Polymer chemistry ,Polar ,Boron - Abstract
Hydrolysis of trimethylaluminum (Me3 Al) in polar solvents can be monitored by electrospray ionization mass spectrometry (ESI-MS) using the donor additive octamethyltrisiloxane [(Me3 SiO)2 SiMe2 , OMTS]. Using hydrated salts, hydrolytic methylaluminoxane (h-MAO) features different anion distributions, depending on the conditions of synthesis, and different activator contents as measured by NMR spectroscopy. Non-hydrolytic MAO was prepared using trimethylboroxine. The properties of this material, which contains incorporated boron, differ significantly from h-MAO. In the case of MAO prepared by direct hydrolysis, oligomeric anions are observed to rapidly form, and then more slowly evolve into a mixture dominated by an anion with m/z 1375 with formula [(MeAlO)16 (Me3 Al)6 Me]- . Theoretical calculations predict that sheet structures with composition (MeAlO)n (Me3 Al)m are favoured over other motifs for MAO in the size range suggested by the ESI-MS experiments. A possible precursor to the m/z 1375 anion is a local minimum based on the free energy released upon hydrolysis of Me3 Al.
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- 2021
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6. Dynamic Ion Speciation during the Hydrolysis of Aryltrifluoroborates**
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Johanne Penafiel, Darlene Gitaari, Atzin San Roman, Isaac Omari, J. Scott McIndoe, and Lars P. E. Yunker
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010405 organic chemistry ,Chemistry ,Induction period ,Electrospray ionization ,Organic Chemistry ,Inorganic chemistry ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,Coupling reaction ,0104 chemical sciences ,Ion ,Ion speciation ,Reaction rate ,Transmetalation ,Hydrolysis - Abstract
Organotrifluoroborates serve as coupling partners during transmetalation in the Suzuki-Miyaura reaction but require hydrolysis prior to the coupling reaction. Their anionic nature allows study of their hydrolysis by electrospray ionization mass spectrometry (ESI-MS) through real-time monitoring, complemented by pH analysis. The induction period varied according to the borates employed, and a dynamic series of equilibria for numerous ions was observed during hydrolysis. We found that the induction periods and reaction rates were sensitive to the R group of the borates, the shape of the reaction vessel, and stir rate.
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- 2021
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7. Regio- and diastereoselective Pd-catalyzed aminochlorocyclization of allylic carbamates: scope, derivatization, and mechanism
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Alessandro Rodrigues, Elaine Miho Ariga, Jullyane Emi Matsushima, Isaac Omari, Priscila Machado Arruda Soares, Francisco Wanderson Moreira Ribeiro, J. Scott McIndoe, Elisângela Vinhato, Bruna Papa Spadafora, Diogo Oliveira-Silva, and Thiago C. Correra
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chemistry.chemical_classification ,Allylic rearrangement ,Alkene ,Organic Chemistry ,Diastereomer ,Cleavage (embryo) ,Biochemistry ,Medicinal chemistry ,Catalysis ,chemistry.chemical_compound ,chemistry ,Yield (chemistry) ,Physical and Theoretical Chemistry ,Derivatization ,Vicinal - Abstract
The regio- and diastereoselective synthesis of oxazolidinones via a Pd-catalyzed vicinal C–N/C–Cl bond-forming reaction from internal alkenes of allylic carbamates is reported. The oxazolidinones are obtained in yields of 44 to 95% with high to excellent diastereoselectivities (from 6 : 1 to >20 : 1 dr) from readily available precursors. This process is scalable, and the products are suitable for the synthesis of useful amino alcohols. A detailed theoretical and experimental mechanistic study was carried out to describe that the reaction proceeds through an anti-aminopalladation of the alkene followed by an oxidative C–Pd(II) cleavage with retention of the carbon stereochemistry to yield the major diastereomer. The role of Cu(II) in a C–Cl bond-forming mechanism step has also been proposed.
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- 2021
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8. The signal-to-noise issue in mass spectrometric analysis of polymers
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Gregory T. Russell, Ian C. Chagunda, and J. Scott McIndoe
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chemistry.chemical_classification ,Materials science ,Polymers and Plastics ,010405 organic chemistry ,Drop (liquid) ,Organic Chemistry ,Dispersity ,Analytical chemistry ,Signal Width ,Bioengineering ,Polymer ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Matrix (chemical analysis) ,chemistry ,Molar mass distribution ,Solubility - Abstract
Mass spectrometric approaches to polymer analysis become increasingly ineffective as the average molecular weight of the polymer increases. Why? The reasons are several-fold, and apply to both ESI and MALDI: the distribution of signal over an increasing number of different species, even for distributions of narrowest possible dispersity; each unique species has its own intensity broadened over a widening range of m/z values as polyisotopic contributions become more significant; individual signal width becomes larger as m/z increases; and solubility properties and solvent adducts can limit the analytical signal for polymer analysis. For MALDI analysis there is an additional reason: effective sample preparations require a certain weight percentage, causing the concentration of polymer in the matrix to drop. All these factors conspire to cause a signal-to-noise problem that fundamentally limits the ability of mass spectrometry to determine molecular weight distribution for high mass polymers.
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- 2021
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9. Real-time analysis of methylalumoxane formation
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Anuj Joshi, Harmen S. Zijlstra, Carina Concepcion, J. Scott McIndoe, Elena Liles, and Mikko Linnolahti
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010405 organic chemistry ,Electrospray ionization ,Mixing (process engineering) ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Pyrophoricity ,0104 chemical sciences ,3. Good health ,Gibbs free energy ,Ion ,Chemistry ,Hydrolysis ,symbols.namesake ,chemistry ,Aluminium ,symbols ,Physical chemistry ,Reactivity (chemistry) ,Real time analysis - Abstract
Methylalumoxane (MAO), a perennially useful activator for olefin polymerization precatalysts, is famously intractable to structural elucidation, consisting as it does of a complex mixture of oligomers generated from hydrolysis of pyrophoric trimethylaluminum (TMA). Electrospray ionization mass spectrometry (ESI-MS) is capable of studying those oligomers that become charged during the activation process. We have exploited that ability to probe the synthesis of MAO in real time, starting less than a minute after the mixing of H2O and TMA and tracking the first half hour of reactivity. We find that the process does not involve an incremental build-up of oligomers; instead, oligomerization to species containing 12–15 aluminum atoms happens within a minute, with slower aggregation to higher molecular weight ions. The principal activated product of the benchtop synthesis is the same as that observed in industrial samples, namely [(MeAlO)16(Me3Al)6Me]−, and we have computationally located a new sheet structure for this ion 94 kJ mol−1 lower in Gibbs free energy than any previously calculated., The activator methylaluminoxane is made by hydrolysis of trimethylaluminum. Analysis using ESI-MS reveals rapid formation of small oligomers is followed by slower aggregation to the larger precursors most capable of releasing [Me2Al]+.
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- 2021
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10. A mechanistic investigation of the Suzuki polycondensation reaction using MS/MS methods
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Michelle Y. C. Ting, Lars P. E. Yunker, Katherine Hatlelid, Ian C. Chagunda, Meghan Vieweg, and J. Scott McIndoe
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chemistry.chemical_classification ,Condensation polymer ,010405 organic chemistry ,Chemistry ,Selected reaction monitoring ,Polymer ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Combinatorial chemistry ,Decomposition ,Catalysis ,0104 chemical sciences ,chemistry.chemical_compound ,Monomer ,Polymerization - Abstract
Understanding catalytic reactions is inherently difficult because not only is the catalyst the least abundant component in the mixture, but it also takes many different forms as the reaction proceeds. Precatalyst is converted into active catalyst, short-lived intermediates, resting states, and decomposition products. Polymerization catalysis is harder yet to study, because as the polymer grows the identities of these species change with every turnover as monomers are added to the chain. Modern mass spectrometric methods have proved to be up to the challenge, with multiple reaction monitoring (MRM) in conjunction with pressurized sample infusion (PSI) used to continuously probe all stages of the Suzuki polycondensation (SPC) reaction. Initiation, propagation, and termination steps were tracked in real time, as well as the side products from undesirable aryl-phosphine scrambling. The outstanding sensitivity and low signal-to-noise of the approach has real promise with respect to the depth with which this reaction and others like it can be studied.
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- 2021
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11. Trichloro(Dinitrogen)Platinate(II)
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Irina Paci, Gilian T. Thomas, J. Scott McIndoe, and Sofia Donnecke
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Ethylene ,010405 organic chemistry ,Electrospray ionization ,Organic Chemistry ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,Catalysis ,0104 chemical sciences ,Bond length ,chemistry.chemical_compound ,chemistry ,Dimethylformamide ,Zeise's salt ,Platinum ,Palladium ,Carbon monoxide - Abstract
Zeise's salt, [PtCl 3 (H 2 C=CH 2 )] - , is the oldest known organometallic complex, featuring ethylene strongly bound to a platinum salt. Many derivatives are known, but none involving dinitrogen, and indeed dinitrogen complexes are unknown for both platinum and palladium. Electrospray ionization mass spectrometry of K 2 [PtCl 4 ] solutions generate ions corresponding to [PtCl 3 (N 2 )] - , whose identity was confirmed through ion mobility spectrometry and MS/MS experiments that proved it to be distinct from its isobaric counterparts [PtCl 3 (C 2 H 4 )] - and [PtCl 3 (CO)] - . Computational analysis established a gas-phase platinum-dinitrogen bond strength of 116 kJ mol -1 , substantially weaker than the ethylene and carbon monoxide analogues but stronger than for polar solvents such as water, methanol and dimethylformamide, and strong enough that the calculated N-N bond length of 1.119 A represents weakening to a degree typical of isolated dinitrogen complexes.
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- 2020
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12. Reactive metallocene cations as sensitive indicators of gas-phase oxygen and water
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Sofia Donnecke, Anuj Joshi, Scott Collins, Dongju Shin, Irina Paci, J. Scott McIndoe, and Ori Granot
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Inorganic Chemistry ,Hydrolysis ,chemistry.chemical_compound ,Fragmentation (mass spectrometry) ,chemistry ,Electrospray ionization ,Inorganic chemistry ,chemistry.chemical_element ,Oxygen ,Nitrogen ,Metallocene ,Titanium ,Ion - Abstract
Analysis of highly reactive compounds at very low concentration in solution using electrospray ionization mass spectrometry requires the use of exhaustively purified solvents. It has generally been assumed that desolvation gas purity needs to be similarly high, and so most chemists working in this space have relied upon high purity gas. However, the increasing competitiveness of nitrogen generators, which provide gas purity levels that vary inversely with flow rate, prompted an investigation of the effect of gas-phase oxygen on the speciation of ions. The most reactive species studied, the reduced titanium complex [Cp2Ti(NCMe)2]+[ZnCl3]− and the olefin polymerization pre-catalyst [Cp2Zr(μ-Me)2AlMe2]+[B(C6F5)4]−, only exhibited detectable oxidation when they were rendered coordinatively unsaturated through in-source fragmentation. Computational chemistry allowed us to find the most plausible pathways for the observed chemistry in the absence of observed intermediates. The results provide insight into the gas-phase oxidation or hydrolysis of these reactive species.
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- 2020
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13. Cover Picture: Pressurized Sample Infusion (Chem. Methods 1/2022)
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Ian Chagunda, J. Scott McIndoe, Gilian Thomas, and Sofia Donnecke
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General Medicine - Published
- 2022
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14. Pressurized Sample Infusion
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Ian Chagunda, J. Scott McIndoe, Gilian Thomas, and Sofia Donnecke
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General Medicine - Published
- 2021
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15. Handling considerations for the mass spectrometry of reactive organometallic compounds
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Anuj Joshi, Charles Killeen, Tanner Thiessen, Harmen S. Zijlstra, and J. Scott McIndoe
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Spectroscopy - Abstract
Mass spectrometry is a powerful tool in disparate areas of chemistry, but its characteristic strength of sensitivity can be an Achilles heel when studying highly reactive organometallic compounds. A quantity of material suitable for mass spectrometric analysis often represents a tiny grain or a very dilute solution, and both are highly susceptible to decomposition due to ambient oxygen or moisture. This complexity can be frustrating to chemists and analysts alike: the former being unable to get spectra free of decomposition products and the latter often being poorly equipped to handle reactive samples. Fortunately, many creative solutions to such problems have been developed. This review summarizes some key methods for handling reactive samples in conjunction with the various ionization methods most frequently employed for their analysis.
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- 2021
16. A mechanistic investigation of the Pd-catalyzed cross-coupling between
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Gilian T, Thomas, Kiera, Ronda, and J Scott, McIndoe
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The cross-coupling of
- Published
- 2021
17. A mechanistic investigation of the Pd-catalyzed cross-coupling between N-tosylhydrazones and aryl halides
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Gilian T. Thomas, Kiera Ronda, and J. Scott McIndoe
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Reaction mechanism ,010405 organic chemistry ,Aryl ,Halide ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Combinatorial chemistry ,0104 chemical sciences ,Catalysis ,Inorganic Chemistry ,Coupling (electronics) ,chemistry.chemical_compound ,chemistry ,Product formation - Abstract
The cross-coupling of N-tosylhydrazones and aryl halides forms carbon-carbon bonds, producing 1,1-disubstituted alkenes. Though it has proven extremely useful in several fields of chemistry, its mechanism remains experimentally unexplored. Combining benchtop NMR and real-time mass spectrometry afforded the ability to monitor the catalytic intermediates as well as the rate of product formation.
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- 2021
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18. Confounding contaminants in mass spectrometric reaction monitoring
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J Scott McIndoe, Lars Yunker, Rhonda L. Stoddard, Natalie L. Dean, Landon MacGillivray, and Gilian T. Thomas
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Chemistry ,Ion-mobility spectrometry ,010401 analytical chemistry ,010402 general chemistry ,Condensed Matter Physics ,Mass spectrometry ,01 natural sciences ,0104 chemical sciences ,Catalysis ,Metal ,Computational chemistry ,visual_art ,visual_art.visual_art_medium ,Physical and Theoretical Chemistry ,Instrumentation ,Spectroscopy - Abstract
Reactions carried out in the presence of rubber septa run the risk of additives being leached out by the solvent. Normally, such species are present at low enough levels that they do not interfere with the reaction significantly. However, when studying reactions using sensitive methods such as mass spectrometry, the appearance of even trace amounts of material can confuse dynamic analyses of reactions. A wide variety of additives are present in rubber along with the polymer: antioxidants, dyes, detergent, and vulcanization agents, and these are all especially problematic in negative ion mode. A redesigned Schlenk flask for pressurized sample infusion (PSI) is presented as a means of practically eliminating the presence of contaminants during reaction analyses.
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- 2019
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19. Structure, Anion, and Solvent Effects on Cation Response in ESI-MS
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Jenny Yu, Jaiya Randhawa, Isaac Omari, Parmissa Randhawa, and J. Scott McIndoe
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chemistry.chemical_classification ,Electrospray ionization ,010401 analytical chemistry ,Inorganic chemistry ,Protonation ,Mass spectrometry ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Ion ,Solvent ,chemistry.chemical_compound ,chemistry ,Structural Biology ,Mass spectrum ,Phosphonium ,Solvent effects ,Counterion ,Acetonitrile ,Spectroscopy - Abstract
The abundance of an ion in an electrospray ionization mass spectrum is dependent on many factors beyond just solution concentration. Even in cases where the analytes of interest are permanently charged (under study here are ammonium and phosphonium ions) and do not rely on protonation or other chemical processes to acquire the necessary charge, factors such as cation structure, molecular weight, solvent, and the identity of the anion can affect results. Screening of a variety of combinations of cations, anions, and solvents provided insight into some of the more important factors. Rigid cations and anions that conferred high conductivity tended to provide the highest responses. The solvent that most closely reflected actual solution composition was acetonitrile, while methanol, acetonitrile/water, and dichloromethane produced a higher degree of discrimination between different ions. Functional groups that had affinity for the solvent tended to depress response. These observations will provide predictive power when accounting for analytes that for reasons of high reactivity can not be isolated.
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- 2019
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20. Assigning the ESI mass spectra of organometallic and coordination compounds
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Krista L. Vikse and J. Scott McIndoe
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chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Electrospray ionization ,010401 analytical chemistry ,Context (language use) ,01 natural sciences ,3. Good health ,0104 chemical sciences ,Characterization (materials science) ,Coordination complex ,Ion ,chemistry.chemical_compound ,Computational chemistry ,Mass spectrum ,Spectroscopy ,Organometallic chemistry - Abstract
Electrospray ionization mass spectrometry (ESI-MS) is a useful technique for solving organometallic and coordination chemistry characterization problems that are difficult to address using traditional methods. However, assigning the ESI mass spectra of such compounds can be challenging, and the considerations involved in doing so are quite different from assigning the mass spectra of purely organic samples. This is a tutorial article for organometallic/coordination chemists using ESI-MS to analyze pure compounds or reaction mixtures. The fundamentals of assigning ESI mass spectra are discussed within the context of organometallic and coordination systems. The types of ions commonly observed by ESI-MS are categorized and described. Finally, a step-by-step guide for the assignment of organometallic and coordination chemistry ESI mass spectra is provided along with two case studies.
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- 2019
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21. Open-Source Laser-Cut-Model Kits for the Teaching of Molecular Geometry
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J. Scott McIndoe, Corrina J. K. Ewan, Natalie L. Dean, and Douglas Braden
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Structure (mathematical logic) ,Science instruction ,Engineering drawing ,010405 organic chemistry ,05 social sciences ,050301 education ,General Chemistry ,3D Molecular Structures ,01 natural sciences ,Session (web analytics) ,0104 chemical sciences ,Education ,Set (abstract data type) ,Open source ,0503 education - Abstract
Comprehension of the 3D structure of objects usually represented in 2D is a critical part of understanding molecular geometries. The frequency with which students actually get hands-on with 3D molecular structures is often limited to a singular laboratory session. We sought to develop a set of molecular shapes that were inexpensive enough not only to deploy in a first-year laboratory setting but also to allow the students to take the set home with them to study at their leisure. Laser-cut acrylic parts in five colors were used, and each set could be quickly assembled into the 13 different molecular shapes commonly encountered at the first-year level. The set of shapes was attractive, useful, and easy and fast to fabricate, and they were appreciated by our students. All files have been released in an open-source format, so any interested parties can deploy these models as soon as they secure access to a suitable laser cutter.
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- 2019
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22. Step-by-step real time monitoring of a catalytic amination reaction
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Harmen S. Zijlstra, Gilian T. Thomas, Eric Janusson, and J. Scott McIndoe
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Materials science ,010405 organic chemistry ,Inorganic chemistry ,Selected reaction monitoring ,Metals and Alloys ,chemistry.chemical_element ,General Chemistry ,Mass spectrometry ,010402 general chemistry ,01 natural sciences ,Combinatorial chemistry ,Catalysis ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Triple quadrupole mass spectrometer ,chemistry ,Reagent ,Materials Chemistry ,Ceramics and Composites ,Real time analysis ,Amination ,Palladium - Abstract
The multiple reaction monitoring mode of a triple quadrupole mass spectrometer is used to examine the Buchwald-Hartwig amination reaction at 0.1% catalyst loading in real-time using sequential addition of reagents to probe the individual steps in the cycle. This is a powerful new method for probing reactions under realistic conditions.
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- 2019
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23. Acid-selective mass spectrometric analysis of petroleum fractions
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Haoxuan Zhu, J. Scott McIndoe, G. Bryce McGarvey, and Isaac Omari
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Chromatography ,Electrospray ionization ,010401 analytical chemistry ,Fraction (chemistry) ,Context (language use) ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,Deprotonation ,chemistry ,Naphthenic acid ,Carboxylate ,Physical and Theoretical Chemistry ,Derivatization ,Instrumentation ,Spectroscopy ,Carbodiimide - Abstract
Naphthenic acids are cycloaliphatic carboxylic acids that are naturally-occurring constituents of petroleum. Analytical mass spectrometric methods aimed at carboxylic acids tend to involve deprotonation to generate carboxylate anions, but also produce detectable ions of every acidic component of the mixture. A charged tag carbodiimide is able to facilitate detection of model naphthenic acids as well as low levels of naphthenic acids in petroleum fractions via tandem electrospray ionization mass spectrometry. This approach exhibits greater selectivity than deprotonation, and a picture of the acidic components of a petroleum fraction emerges after a quick derivatization step and without the use of chromatographic separation. The method may prove useful in the context of characterizing the naphthenic acid components of complicated matrices.
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- 2019
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24. Mass Spectrometry of Inorganic and Organometallic Compounds: Tools - Techniques - Tips
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William Henderson, J. Scott McIndoe
- Published
- 2005
25. Are Methylaluminoxane Activators Sheets?
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Scott Collins, Galib Hasan, Anuj Joshi, Mikko Linnolahti, J. Scott McIndoe, INAR Physical Chemistry, and Department of Chemistry
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STRUCTURAL-CHARACTERIZATION ,sheets ,Materials science ,116 Chemical sciences ,Methylaluminoxane ,OLIGOMERIZATION ,methylaluminoxane ,02 engineering and technology ,010402 general chemistry ,OXIDATION ,anionization ,01 natural sciences ,Article ,chemistry.chemical_compound ,Polymer chemistry ,ionization ,CATALYTIC-ACTIVITY ,Physical and Theoretical Chemistry ,MASS-SPECTROMETRIC CHARACTERIZATION ,TRIMETHYLALUMINUM ,ESI-MS ,Articles ,ALUMINUM ,021001 nanoscience & nanotechnology ,HYDROLYSIS ,Atomic and Molecular Physics, and Optics ,3. Good health ,0104 chemical sciences ,POLYMERIZATION ,chemistry ,MAO ,0210 nano-technology - Abstract
Density functional theory calculations on neutral sheet models for methylaluminoxane (MAO) indicate that these structures, containing 5‐coordinate and 4‐coordinate Al, are likely precursors to ion‐pairs seen during the hydrolysis of trimethylaluminum (Me3Al) in the presence of donors such as octamethyltrisiloxane (OMTS). Ionization by both methide ([Me]−) and [Me2Al]+ abstraction, involving this donor, were studied by polarizable continuum model calculations in fluorobenzene (PhF) and o‐difluorobenzene (DFB) media. These studies suggest that low MW, 5‐coordinate sheets ionize by [Me2Al]+ abstraction, while [Me]− abstraction from Me3Al‐OMTS is the likely process for higher MW 4‐coordinate sheets. Further, comparison of anion stabilities per mole of aluminoxane repeat unit (MeAlO)n, suggest that anions such as [(MeAlO)7(Me3Al)4Me]−=[7,4]− are especially stable compared to higher homologues, even though their neutral precursors are unstable., Hydrolysis of trimethylaluminum (Me3Al): Viewed through the lenses of electrospray ionization mass spectrometry and density functional theory, methylaluminoxane activators adopt sheet structures while the larger sheets form chelated anions on reaction with neutral donors. Calculated ion‐pair stabilities in polar media agree well with experimental spectra collected during formation of activators.
- Published
- 2021
26. Standardized Stirring for Small Scale Surveys
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J. Scott McIndoe, Isaac Omari, and Mathias Paul
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Reaction rate ,3d printed ,Materials science ,Scale (ratio) ,Rectangular array ,technology, industry, and agriculture ,Analytical chemistry ,General Medicine ,equipment and supplies - Abstract
Stirring rates in heterogeneous catalytic reactions have an effect on reaction rates. When conducting small-scale surveys using a single central stir plate, reaction vessels in different positions experience slightly different levels and patterns of agitation. We probed this effect by running the same reaction 40 times, varying the stir rate (fast/slow) and the vial position using two 3D printed vial holders. We found variability of conversion (measured mass spectrometrically) to be approximately two times higher for vials placed at different distances, but the effect was relatively small and could be minimized by using a high stir rate. For those experimenters wishing to completely eliminate differential stirring as a cause for variation in results, the 3D printed circular array we designed is recommended over a conventional rectangular array.
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- 2021
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27. Inexpensive Open Source Laser Cut Model Kits for the Teaching of Molecular Geometry
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J. Scott McIndoe and Sean Adams
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Engineering drawing ,VSEPR theory ,Computer science ,Laser cutting ,Adobe ,Sorting ,cardboard ,engineering.material ,Laser ,law.invention ,Molecular geometry ,Open source ,law ,visual_art ,engineering ,visual_art.visual_art_medium - Abstract
We recently published an article in the Journal of Chemical Education on VSEPR model kits for helping teach molecular geometry. We have used these transparent acrylic models for several years now at the University of Victoria, but the challenges of COVID-19 meant that this year we needed to make a faster, less expensive version that could be easily mailed out to our students, without requiring any sorting and packaging steps. Accordingly, we designed a version that can be cut out of 2 mm thick recycled “chipboard” cardboard, in which all 26 parts for the 13 different models fit in one piece of card 175 × 120 mm (and 16 of these kits can be cut from one sheet in the laser cutter). The material cost is less than $0.25 per kit and the cutting time on our machine (Trotec Speedy360, 130 W) is 1 minute and 45 seconds per kit. These files are made freely available for all interested users as supporting information for this contribution, in CorelDraw, Adobe Illustrator, pdf and dxf formats.
- Published
- 2020
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28. Disulfonated Xantphos for Mass Spectrometric Mechanistic Analysis
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Mathias Paul, Katarina Lana Laketic, and J. Scott McIndoe
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Reaction conditions ,010405 organic chemistry ,Ligand ,Xantphos ,Organic Chemistry ,General Chemistry ,Bite angle ,010402 general chemistry ,01 natural sciences ,Mass spectrometric ,Catalysis ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Computational chemistry - Abstract
Xantphos is a wide bite angle bisphosphine ligand that finds wide application in catalysis. Tracking its behavior during reactions under realistic reaction conditions can be difficult at low concentrations, and although electrospray ionization mass spectrometry (ESI-MS) is effective at real-time monitoring of catalytic reactions, it can only observe ions. Accordingly, we experimented with the dianionic disulfonated version of xantphos as a charged tag for mechanistic analysis. It proved to behave exactly as hoped, providing good intensity and enabled the direct study of both an initial binding event (to copper, very fast) and a subsequent transfer to another metal (palladium). Its dianionic nature makes it especially promising for the study of reactions in which metals change charge state, because a cationic metal complex with an anionic ligand is an invisible zwitterion, whereas a dianionic ligand would instead make the same cationic complex appear due to the overall charge of −1. As such, disulfonated xantphos holds genuine promise as a mechanistic probe in real time analysis using mass spectrometry.
- Published
- 2020
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29. Dynamic Ion Speciation During Hydrolysis of Aryltrifluoroborates
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J Scott McIndoe, Atzin San Roman, Darlene Gitaari, Johanne Penafiel, Lars Yunker, and Isaac Omari
- Abstract
Organotrifluoroborates serve as a coupling partner during transmetallation in the Suzuki-Miyaura reaction but require hydrolysis prior to the coupling reaction. Their anionic nature allows study of their hydrolysis by electrospray ionization mass spectrometry (ESI-MS) by real-time monitoring, complemented by pH analysis. Induction periods varied according to the borates employed, and a dynamic series of equilibria for numerous ions was observed during hydrolysis. We found that the induction periods and reaction rates were sensitive to the R group of the borates, the shape of reaction vessel, and stir rate, and that after complete decay of all of the aryltrifluoroborate ion the solution contained a variety of partially hydrolyzed species.
- Published
- 2020
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30. Chromate Conversion Coating and Alternatives as Corrosion-Resistant Treatments for Metal Parts
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J Scott McIndoe, Johanne Penafiel, and Isaac Omari
- Abstract
Chromate conversion coating is an efficacious and fast means of protecting metal parts from corrosion, but problematic in that it uses the toxic and carcinogenic chromic acid as the reagent. This short report covers some key considerations and alternatives.
- Published
- 2020
- Full Text
- View/download PDF
31. Trichloro(Dinitrogen)platinate(II)
- Author
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J. Scott McIndoe, Irina Paci, Sofia Donnecke, and Gilian T. Thomas
- Subjects
Bond length ,chemistry.chemical_compound ,Ethylene ,chemistry ,Electrospray ionization ,chemistry.chemical_element ,Dimethylformamide ,Zeise's salt ,Platinum ,Medicinal chemistry ,Palladium ,Carbon monoxide - Abstract
Zeise’s salt, [PtCl3(H2C=CH2)]–, is the oldest known organometallic complex, featuring ethylene strongly bound to a platinum salt. Many derivatives are known, but none involving dinitrogen, and indeed dinitrogen complexes are unknown for both platinum and palladium. Electrospray ionization mass spectrometry of K2[PtCl4] solutions generate strong ions corresponding to [PtCl3(N2)]–, whose identity was confirmed through ion mobility spectroscopy and MS/MS experiments that proved it to be distinct from its isobaric counterparts [PtCl3(C2H4)]– and [PtCl3(CO)]–. Computational analysis established a gas-phase platinum-dinitrogen bond strength of 116 kJ mol-1, substantially weaker than the ethylene and carbon monoxide analogues but stronger than for polar solvents such as water, methanol and dimethylformamide, and strong enough that the calculated N-N bond length of 1.119 Å represents weakening to a degree typical of isolated dinitrogen complexes.
- Published
- 2020
- Full Text
- View/download PDF
32. Trichloro(Dinitrogen)platinate(II)
- Author
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J Scott McIndoe, Irina Paci, Sofia Donnecke, and Gilian T. Thomas
- Abstract
Zeise’s salt, [PtCl3(H2C=CH2)]–, is the oldest known organometallic complex, featuring ethylene strongly bound to a platinum salt. Many derivatives are known, but none involving dinitrogen, and indeed dinitrogen complexes are unknown for both platinum and palladium. Electrospray ionization mass spectrometry of K2[PtCl4] solutions generate strong ions corresponding to [PtCl3(N2)]–, whose identity was confirmed through ion mobility spectroscopy and MS/MS experiments that proved it to be distinct from its isobaric counterparts [PtCl3(C2H4)]– and [PtCl3(CO)]–. Computational analysis established a gas-phase platinum-dinitrogen bond strength of 116 kJ mol-1, substantially weaker than the ethylene and carbon monoxide analogues but stronger than for polar solvents such as water, methanol and dimethylformamide, and strong enough that the calculated N-N bond length of 1.119 Å represents weakening to a degree typical of isolated dinitrogen complexes.
- Published
- 2020
- Full Text
- View/download PDF
33. Catalyst Deactivation Processes During 1-Hexene Polymerization
- Author
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Harmen S. Zijlstra, Anuj Joshi, Scott Collins, and J. Scott McIndoe
- Subjects
Zirconium ,Electrospray ,010405 organic chemistry ,Electrospray ionization ,Inorganic chemistry ,chemistry.chemical_element ,General Chemistry ,Post-metallocene catalyst ,010402 general chemistry ,Mass spectrometry ,Photochemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,1-Hexene ,chemistry.chemical_compound ,chemistry ,Polymerization ,Ionization ,Olefin polymerization - Abstract
The catalyst [Cp2Zr(μ-Me)2AlMe2]+[B(C6F5)4]− (1) has been studied by electrospray ionisation mass spectrometry (ESI-MS) in order to better understand the complexities of catalyst deactivation in the polymerisation of 1-hexene. Using offline, online and flow-based methods, we observe that zirconium π-allyl species are unstable in solution and previously unobserved dimethylalane complexes are more stable. The dimethylalane complexes are resistant to further 1-hexene additions and their formation represent a new pathway for catalyst deactivation.
- Published
- 2020
- Full Text
- View/download PDF
34. Real-Time Monitoring of a Cobalt-Mediated One-Pot Transition Metal Catalyzed Multicomponent Reaction
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Antonio Crotti, Daniel Previdi, Paulo Donate, and J Scott McIndoe
- Abstract
In this paper, pressurized sample infusion electrospray ionization mass spectrometry (PSI-ESI-MS) and FTIR spectroscopy was used to investigate the mechanism of a like-Barbier cobalt-mediated one-pot transition metal-catalyzed multicomponent reaction (MCR). The use of charge-tagged aryl halides allowed for the detection of cobalt(II)-promoted hydrodehalogenation products. Although these products were also detected in the off-line ESI-MS monitoring, the ability of PSI-ESI-MS to track real-time changes in the reaction mixture composition proved cobalt(II) was responsible for the undesired transformation. The occurrence of cobalt(II)-promoted hydrodehalogenation as a side reaction in this MCR had not been considered in previous mechanistic proposals and represents an important mechanistic consideration.
- Published
- 2020
- Full Text
- View/download PDF
35. Gas-Phase Oxidation of Reactive Organometallic Ions
- Author
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Scott Collins, Dongju Shin, Irina Paci, J. Scott McIndoe, Anuj Joshi, Ori Granot, and Sofia Donnecke
- Subjects
chemistry ,Fragmentation (mass spectrometry) ,Electrospray ionization ,Inorganic chemistry ,chemistry.chemical_element ,Mass spectrometry ,Oxygen ,Decomposition ,Nitrogen ,Ion ,Titanium - Abstract
Analysis of highly reactive compounds at very low concentration in solution using electrospray ionization mass spectrometry requires the use of exhaustively purified solvents. It has generally been assumed that desolvation gas purity needs to be similarly high, and so most chemists working in this space have relied upon high purity gas. However, the increasingly competitiveness of nitrogen generators, which provide gas purity levels that vary inversely with flow rate, prompted an investigation of the effect of gas-phase oxygen on the speciation of ions. For moderately oxygen sensitive species such as phosphines, no gas-phase oxidation was observed. Even the most reactive species studied, the reduced titanium complex [Cp2Ti(NCMe)2]+[ZnCl3]– and the olefin polymerization precatalyst [Cp2Zr(µ-Me)2AlMe2]+ [B(C6F5)4]–, only exhibited detectable oxidation when they were rendered coordinatively unsaturated through in-source fragmentation. Computational chemistry allowed us to find the most plausible pathways for the observed chemistry in the absence of observed intermediates. The results provide insight into the gas-phase oxidation of reactive species and should assure experimentalists that evidence of significant oxidation is likely a solution rather than a gas-phase process, even when relatively low-purity nitrogen is used for desolvation.
- Published
- 2020
- Full Text
- View/download PDF
36. Real-time monitoring of a cobalt-mediated one-pot transition metal-catalyzed multicomponent reaction
- Author
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Antônio Eduardo Miller Crotti, J. Scott McIndoe, Daniel Previdi, and Paulo Marcos Donate
- Subjects
inorganic chemicals ,010405 organic chemistry ,Electrospray ionization ,Aryl ,technology, industry, and agriculture ,Side reaction ,chemistry.chemical_element ,Halide ,010402 general chemistry ,CATÁLISE ,01 natural sciences ,Combinatorial chemistry ,0104 chemical sciences ,Catalysis ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Transition metal ,Materials Chemistry ,Physical and Theoretical Chemistry ,Fourier transform infrared spectroscopy ,Cobalt - Abstract
In this paper, pressurized sample infusion electrospray ionization mass spectrometry (PSI-ESI-MS) and FTIR spectroscopy were used to investigate the mechanism of a like-Barbier cobalt-mediated one-pot transition metal-catalyzed multicomponent reaction (MCR). The use of charge-tagged aryl halides allowed for the detection of cobalt(II)-promoted hydrodehalogenation products. Although these products were also detected in the off-line ESI-MS monitoring, the ability of PSI-ESI-MS to track real-time changes in the reaction mixture composition proved cobalt(II) was responsible for the undesired transformation. The occurrence of cobalt(II)-promoted hydrodehalogenation as a side reaction in this MCR had not been considered in previous mechanistic proposals and represents an important mechanistic consideration.
- Published
- 2020
37. Magnesium-Accelerated Maillard Reactions Drive Differences in Adjunct and All-Malt Brewing
- Author
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Hannah Charnock, Euan Thomson, Isaac Omari, Alexa L. Fugina, and J. Scott McIndoe
- Subjects
0106 biological sciences ,business.industry ,Chemistry ,Magnesium ,technology, industry, and agriculture ,chemistry.chemical_element ,food and beverages ,04 agricultural and veterinary sciences ,Calcium ,040401 food science ,01 natural sciences ,Applied Microbiology and Biotechnology ,Maillard reaction ,symbols.namesake ,0404 agricultural biotechnology ,010608 biotechnology ,symbols ,Brewing ,Food science ,business ,Yeast metabolism ,Food Science ,Biotechnology - Abstract
Magnesium impacts key processes in brewing including yeast metabolism and mash pH but is typically overshadowed in brewing studies, owing to the established centrality of calcium. Using flame atomic absorption spectroscopy (FAAS), a 33.7% average increase in magnesium concentration in commercially available beers brewed with 100% barley malt versus those brewed with adjunct grains was identified. Parallel analysis of brewing grains implicates rice in driving this discrepancy. Given the known catalytic properties of magnesium, its role in beer color development via Maillard chemistry using model systems and wort (unfermented beer) was investigated. Kinetic data were obtained by ultraviolet-visible spectrometry and reaction species were identified by electrospray ionization mass spectrometry. Magnesium accelerated Maillard chemistry in all systems in a dose-dependent manner. These findings reveal a divergence in outcomes of all-malt and adjunct brewing driven by magnesium-catalyzed color formation in the brewhouse. It is proposed that magnesium inhibits water mobility and serves as a Lewis acid catalyst to facilitate Maillard reactions.
- Published
- 2020
- Full Text
- View/download PDF
38. Oxidation of Methylalumoxane Oligomers: A Theoretical Study Guided by Mass Spectrometry
- Author
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Mikko Linnolahti, Harmen S. Zijlstra, J. Scott McIndoe, Scott Collins, and Erik Endres
- Subjects
010405 organic chemistry ,Chemistry ,Electrospray ionization ,Organic Chemistry ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Redox ,0104 chemical sciences ,Catalysis ,Inorganic Chemistry ,Molecular level ,Polymerization ,Computational chemistry ,Impurity ,Oxidation process ,Physical and Theoretical Chemistry - Abstract
Methylalumoxane (MAO) plays a critical role in catalytic polymerization of olefins, both as activator of the precatalyst and scavenger of impurities. The latter involves oxidation of MAO, which is not well understood at a molecular level. On the basis of our previous computational explorations of the structure of MAO and electrospray ionization mass spectrometry (ESI-MS) studies of its oxidation, we report here a systematic theoretical study to shed light on the oxidation process. We identify the structural features of the MAO that are essential for oxidation by screening the thermodynamics of the oxidation reactions as a function of shape and size of the previously justified model MAOs. In correlation with previously reported ESI-MS studies of the corresponding anions ( Chem. Eur. J. 2018, 24, 5506−5512, DOI: 10.1002/chem.201705458), the calculations indicate that Al sites of high Lewis acidity could be of major relevance in the oxidation process. Such sites are abundant in the size domain observed relev...
- Published
- 2018
- Full Text
- View/download PDF
39. Fluoride-mediated rearrangement of phenylfluorosilanes
- Author
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Natalie L. Dean and J. Scott McIndoe
- Subjects
Electrospray ,010405 organic chemistry ,Chemistry ,Electrospray ionization ,Organic Chemistry ,Inorganic chemistry ,General Chemistry ,Fluorine-19 NMR ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Mass spectrometric ,Catalysis ,0104 chemical sciences ,Ion ,chemistry.chemical_compound ,Hiyama coupling ,Fluoride - Abstract
Combining Ph3SiF and fluoride ion under conditions used for the Hiyama coupling causes rapid formation of the expected [Ph3SiF2]−; however, real-time electrospray mass spectrometric analysis reveals that phenyl-fluoride exchange occurs concomitantly, also producing substantial quantities of [PhnSiF5–n]− (n = 0–2). The exchange process is verified using 19F NMR spectroscopy. This observation may have implications for Hiyama reaction protocols, which use transmetallation from triaryldifluorosilicates as a key step in cross-coupling.
- Published
- 2018
- Full Text
- View/download PDF
40. (Ge2P2)2−: a binary analogue of P4as a precursor to the ternary cluster anion [Cd3(Ge3P)3]3−
- Author
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J. Scott McIndoe, Jascha Bandemehr, Xiulan Xie, Florian Weigend, Stefanie Dehnen, Stefan Mitzinger, John F. Corrigan, and Kevin Reiter
- Subjects
Diffraction ,010405 organic chemistry ,Chemistry ,Metals and Alloys ,Binary number ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,3. Good health ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Ion ,Crystallography ,Materials Chemistry ,Ceramics and Composites ,Cluster (physics) ,Moiety ,Ternary operation - Abstract
The novel binary P4 analogue (Ge2P2)2- proved to be a suitable precursor for heteroatomic cluster synthesis. Over time in solution, it rearranges to form (Ge7P2)2-, as shown by NMR studies and X-ray diffraction. Reactions of (Ge2P2)2- with CdPh2 afford [K(crypt-222)]3[Cd3(Ge3P)3], containing an unprecedented ternary cluster anion with a triangular Cd3 moiety.
- Published
- 2018
- Full Text
- View/download PDF
41. Synthesis, characterization and mass-spectrometric analysis of [LSn(IV)F4−x]x+ salts [L = tris ((1-ethyl-benzoimidazol-2-yl)methyl)amine, x = 1–4]
- Author
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Ala'aeddeen Swidan, Riccardo Suter, J. Scott McIndoe, Charles L. B. Macdonald, Neil Burford, and Harmen S. Zijlstra
- Subjects
Tris ,010405 organic chemistry ,Electrospray ionization ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,Nitrogen ,Mass spectrometric ,0104 chemical sciences ,Inorganic Chemistry ,chemistry.chemical_compound ,Heteronuclear molecule ,chemistry ,Amine gas treating ,Single crystal ,Fluoride - Abstract
A series of complexes with the formulae [(BIMEt3)SnF4-x][OTf]x with x = 1-4 has been synthesized by successive fluoride abstraction from SnF4 with TMSOTf in the presence of the tetradentate nitrogen donor BIMEt3 (tris ((1-ethyl-benzoimidazol-2-yl)methyl)amine). Single crystal X-ray diffraction and heteronuclear NMR spectroscopic analysis provided insight into these new main group cations. Electrospray ionization mass spectrometric analysis on solutions containing the different salts allowed for successful detection of the cations [(BIMEt3)SnF]3+, [(BIMEt3)SnF2]2+ and [(BIMEt3)SnF3]+.
- Published
- 2018
- Full Text
- View/download PDF
42. Additive and Aging Effects on Methylalumoxane Oligomers
- Author
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J. Scott McIndoe, Scott Collins, Mikko Linnolahti, and Harmen S. Zijlstra
- Subjects
Period (periodic table) ,010405 organic chemistry ,Chemistry ,Electrospray ionization ,Organic Chemistry ,Analytical chemistry ,Ion pairs ,010402 general chemistry ,01 natural sciences ,Oligomer ,0104 chemical sciences ,Ion ,Inorganic Chemistry ,Crystallography ,chemistry.chemical_compound ,Ionization ,Degradation (geology) ,Physical and Theoretical Chemistry - Abstract
In the presence of the weak donor octamethyltrisiloxane (OMTS), methylalumoxane (MAO) undergoes ionization through [Me2Al]+ abstraction. The [Me2Al·OMTS]+[(MeAlO)x(Me3Al)yMe]− ion pairs formed can conveniently be studied by electrospray ionization mass spectrometry. The anion distribution changes with OMTS:Al ratio, with low molecular weight (MW) anions forming at high ratios due to oligomer degradation. Monitoring of room-temperature aging shows that MAO oligomers of low MW are slowly and systematically converted to species with higher MW through addition of (MeAlO) units, and intermediate oligomers are observed and assigned. This process occurs at room temperature but does not occur significantly over a period of months at low temperatures. Computational investigations of these species show large cagelike clusters with four-coordinate Al and three-coordinate O. All neutral structures have sites that could readily give up [Me2Al]+ to form the observed ions, though sites that can lose [Me2Al]+ without lea...
- Published
- 2017
- Full Text
- View/download PDF
43. Mass spectrometric characterization of oligomeric phosphaalkenes
- Author
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Matthew A. Henderson, J. Scott McIndoe, Bronwyn H. Gillon, Derek P. Gates, and Eric Janusson
- Subjects
chemistry.chemical_classification ,010405 organic chemistry ,Phosphorus ,Electrospray ionization ,Organic Chemistry ,Inorganic chemistry ,Analytical chemistry ,chemistry.chemical_element ,General Chemistry ,Polymer ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Mass spectrometric ,Catalysis ,0104 chemical sciences ,Ion ,Characterization (materials science) ,chemistry - Abstract
Oligomeric phosphaalkenes are readily characterized using electrospray ionization mass spectrometry (ESI-MS). The high affinity of phosphines for silver ions permits the detection of the unadulterated polymer as [M + xAg]x+ions (x = 2–3). When the oligomers are oxidized using H2O2, the resulting phosphine oxide polymer may be treated with sodium ions to produce [M + xNa]x+ions (x = 2–3). Both methods predict a similar distribution of oligomers: Mnvalues of 3450 ± 100 Da and a PDI of 1.09 ± 0.01 cover both analyses. This distribution represents oligomers of the general formula Me(PMesCPh2)nH from n = 4–20, maximizing at ∼n = 10.
- Published
- 2017
- Full Text
- View/download PDF
44. Determination of n-Alkanes in Jet Fuel by Cold-electron Ionization Gas Chromatography–Mass Spectrometry
- Author
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Ori Granot, J. Scott McIndoe, and Farhana Islam
- Subjects
N alkanes ,Chromatography ,010401 analytical chemistry ,Biochemistry (medical) ,Clinical Biochemistry ,Analytical chemistry ,Standard solution ,Jet fuel ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Analytical Chemistry ,Characterization (materials science) ,Hexane ,chemistry.chemical_compound ,chemistry ,Electrochemistry ,Sample preparation ,Gas chromatography–mass spectrometry ,Spectroscopy ,Electron ionization - Abstract
A rapid, easy, and reliable method was developed for the characterization of jet fuel with minimal sample preparation. A standard solution of 13 aliphatic n-alkanes in hexane was used to evaluate a...
- Published
- 2017
- Full Text
- View/download PDF
45. Mass transfer and convection effects in small-scale catalytic hydrogenation
- Author
-
Yang Wu, David A. Harrington, Harmen S. Zijlstra, J. Scott McIndoe, and Jingwei Luo
- Subjects
Convection ,010405 organic chemistry ,Chemistry ,Electrospray ionization ,Diffusion ,Analytical chemistry ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Reaction rate ,Laboratory flask ,Mass transfer - Abstract
Rhodium-catalyzed hydrogenation of alkynes was studied under conditions of low concentration of substrate and either one or two equivalents of hydrogen using pressurized sample infusion electrospray ionization mass spectrometry (PSI-ESI-MS). Four sample vials of the same volume but of different diameter enabled the investigation of the effects of surface area on reaction rates. Running the same experiments with stirring on or off allowed further details to emerge, notably the obvious effects of convection thanks to the localized sampling technique employed. Modelling of the system allowed for a better understanding of the relative importance of the various factors in play (reaction rate, surface area, mass transfer, convection). These factors should be carefully considered when studying or optimizing reactions involving narrow reaction flasks, especially when those flasks are unstirred.
- Published
- 2017
- Full Text
- View/download PDF
46. Phenol-selective mass spectrometric analysis of jet fuel
- Author
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J. Scott McIndoe, James Piers, Haoxuan Zhu, Eric Janusson, Allen G. Oliver, Farhana Islam, Ori Granot, Jingwei Luo, and G. Bryce McGarvey
- Subjects
Electrospray ionization ,010401 analytical chemistry ,Jet fuel ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Mass spectrometric ,3. Good health ,0104 chemical sciences ,Analytical Chemistry ,Williamson ether synthesis ,chemistry.chemical_compound ,chemistry ,Impurity ,Electrochemistry ,Mass spectrum ,Environmental Chemistry ,Organic chemistry ,Phenol ,Phenols ,Spectroscopy - Abstract
Bromobenzyl compounds react selectively with phenols via the Williamson ether synthesis. An imidazolium charge-tagged bromobenzyl compound can be used to reveal phenol impurities in jet fuel by analysis via electrospray ionization mass spectrometry. The complex matrix as revealed by Cold EI GC/MS analysis is reduced to a few simple sets of compounds in the charge-tagged ESI mass spectrum, primarily substituted phenols and thiols. Examination of jet fuels treated by different refinery methods reveals the efficacy of these approaches in removing these contaminants.
- Published
- 2017
- Full Text
- View/download PDF
47. Orbital Shaped Standing Waves Using Chladni Plates
- Author
-
J Scott McIndoe, Irina Paci, Shaun MacLean, Andrew Macdonald, Johanne Penafiel, and Eric Janusson
- Abstract
Chemistry students are often introduced to the concept of atomic orbitals with a representation of a one-dimensional standing wave. The classic example is the harmonic frequencies which produce standing waves on a guitar string; a concept which is easily replicated in class with a length of rope. From here, students are typically exposed to a more realistic three-dimensional model, which can often be difficult to visualize. Extrapolation from a two-dimensional model, such as the vibrational modes of a drumhead, can be used to convey the standing wave concept to students more easily. We have opted to use Chladni plates which may be tuned to give a two-dimensional standing wave which serves as a cross-sectional representation of atomic orbitals. The demonstration, intended for first year chemistry students, facilitates the examination of nodal and anti-nodal regions of a Chladni figure which students can then connect to the concept of quantum mechanical parameters and their relationship to atomic orbital shape.
- Published
- 2019
- Full Text
- View/download PDF
48. Experimental Strategies for Avoiding Saturation Effects in ESI-MS
- Author
-
J Scott McIndoe, Yuxuan Chen, Anuj Joshi, and Alan Wei
- Abstract
All instruments with detectors are prone to saturation effects at high concentration, and mass spectrometers are no exception. The very high sensitivity of mass spectrometry makes the onset of saturation occur at lower concentrations than other methods, and in cases where the analyte of interest is very reactive, concentrations at which saturation can be problematic may be necessary in order to ensure decomposition is mitigated. Indications that saturation is occurring are provided, and some data processing strategies are outlined, followed by a range of detuning strategies that may be employed to reduce saturation effects in the context of electrospray ionization mass spectrometry (ESI-MS), including lowering voltages on detector or capillary, increasing cone gas flow rates, or adjusting the probe position. A combination of strategies generally allows researchers to make the best possible compromises when studying compounds at relatively high concentration.
- Published
- 2019
- Full Text
- View/download PDF
49. An Information-Rich Graphical Representation of Catalytic Cycles
- Author
-
Brett Henderson, Sofia Donnecke, James McFarlane, and J. Scott McIndoe
- Subjects
education.field_of_study ,010405 organic chemistry ,Chemistry ,Interface (Java) ,Programming language ,Organic Chemistry ,Population ,Representation (systemics) ,010402 general chemistry ,computer.software_genre ,01 natural sciences ,0104 chemical sciences ,Catalysis ,Computational science ,Visualization ,Inorganic Chemistry ,Annotation ,Physical and Theoretical Chemistry ,education ,Representation (mathematics) ,computer - Abstract
Catalytic reactions are limited in their turnover by certain steps in the cycle. We present a free, open-source, web-based interface to generate visualizations of the rate constants of various steps in the cycle. Population of a web form using known data will generate a highly customizable graphic for annotation by the user to represent their chemistry.
- Published
- 2019
- Full Text
- View/download PDF
50. PythoMS: A Python Framework To Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data
- Author
-
Michelle Y. C. Ting, Darien Yeung, Sofia Donnecke, J. Scott McIndoe, and Lars P. E. Yunker
- Subjects
Data Analysis ,Computer science ,General Chemical Engineering ,Large dynamic range ,Overlay ,Library and Information Sciences ,computer.software_genre ,01 natural sciences ,Mass Spectrometry ,Histogram ,0103 physical sciences ,Zoom ,computer.programming_language ,Information retrieval ,010304 chemical physics ,Cheminformatics ,Experimental data ,General Chemistry ,Python (programming language) ,Mass spectrometric ,0104 chemical sciences ,Computer Science Applications ,010404 medicinal & biomolecular chemistry ,Scripting language ,Programming Languages ,computer ,Dimerization ,Palladium - Abstract
Mass spectrometric data are copious and generate a processing burden that is best dealt with programmatically. PythoMS is a collection of tools based on the Python programming language that assist researchers in creating figures and video output that is informative, clear, and visually compelling. The PythoMS framework introduces a library of classes and a variety of scripts that quickly perform time-consuming tasks: making proprietary output readable; binning intensity vs time data to simulate longer scan times (and hence reduce noise); calculating theoretical isotope patterns and overlaying them in histogram form on experimental data (an approach that works even for overlapping signals); rendering videos that enable zooming into the baseline of intensity vs time plots (useful to make sense of data collected over a large dynamic range) or that depict the evolution of different species in a time-lapse format; calculating aggregates; and providing a quick first-pass at identifying fragments in MS/MS spectra. PythoMS is a living project that will continue to evolve as additional scripts are developed and deployed.
- Published
- 2019
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