Engineering topics
Carmichael, Ian
Publications and source records attributed to Carmichael, Ian.
Fragmentation dynamics through geometrical distortion in low-energy electron attachment to carbon disulfide
The dissociation dynamics of dissociative electron attachment to carbon disulfide is studied using the velocity map imaging technique. Ion yields of the S− and CS− fragments are measured as a function of incident electron energy between 2 and 12 eV. Energy and angle-differential yields of the S− fragments are analyzed to investigate the dynamics of the CS2− anion around the 3.8-eV peak. The resonances involved in this fragmentation are identified and characterized in calculations using the well-known R-matrix method. Based on our measurements and the geometry dependence of the calculated resonances, we propose that a geometrical distortion of the transient negative-ion state of CS2 is necessary for S-CS bond dissociation to occur.
MA’AT analysis of the O -glycosidic linkages of oligosaccharides using nonconventional NMR J -couplings: MA’AT and MD models of phi
The use of two-bond 13 C– 1 H spin-coupling constants as nonconventional constraints in MA'AT analyses of the phi torsion angles of O -glycosidic linkages improves the agreement between MA'AT - and MD-determined probability distributions of the angles.
Methyl α‐D‐galactopyranosyl‐(1→3)‐β‐D‐galactopyranoside and methyl β‐D‐galactopyranosyl‐(1→3)‐β‐D‐galactopyranoside: Glycosidic linkage conformation determined from MA'AT analysis
Abstract MA'ATanalysis has been applied to two biologically‐importantO‐glycosidic linkages in two disaccharides, α‐D‐Galp‐(1→3)‐β‐D‐GalpOMe (3) and β‐D‐Galp‐(1→3)‐β‐D‐GalpOMe (4). Using density functional theory (DFT) to obtain parameterized equations relating a group of trans‐O‐glycosidic NMR spin‐couplings to eitherphi(ϕ') orpsi(ψ'), and experimental 3 J COCH , 2 J COC , and 3 J COCC spin‐couplings measured in aqueous solution in 13 C‐labeled isotopomers, probability distributions ofϕ'andψ'in each linkage were determined and compared to those determined by aqueous 1‐μs molecular dynamics (MD) simulation. Good agreement was found between theMA'ATand single‐state MD conformational models of these linkages for the most part, with modest (approximately <15°) differences in the mean values ofϕ'andψ', although the envelope of allowed angles (encoded in circular standard deviations or CSDs) is consistently larger forϕ'determined fromMA'ATanalysis than from MD for both linkages. TheMA'ATmodel of the α‐Galp‐(1→3)‐β‐Galplinkage agrees well with those determined previously using conventional NMR methods ( 3 J COCH values and/or 1 H‐ 1 H NOEs), but some discrepancy was observed for the β‐Galp‐(1→3)‐β‐Galplinkage, which may arise from errors in the conventions used to describe the linkage torsion angles. Statistical analyses of X‐ray crystal structures show ranges ofϕ'andψ'for both linkages that include the mean angles determined fromMA'ATanalyses, although both angles adopt a wide range of values in the crystalline state, withϕ'in β‐Galp‐(1→3)‐β‐Galplinkages showing greater‐than‐expected conformational variability.
Dissociative electron attachment studies of gas-phase acetic acid using a velocity map imaging technique
Abstract Advancing instrumentation to explore dissociative electron attachment (DEA) studies allows previously unattainable information to be acquired. Using a newly constructed velocity map imaging spectrometer, we revisited a study on DEA to gas-phase acetic acid. We discuss possible fragmentation channels and compared the corresponding ion yields with previous high electron-energy resolution results. We focus on the channels occurring at higher energies, particularly near 10 eV, and calculate their thermodynamic thresholds. Moreover, we expand previous studies and perform time-sliced imaging near the 10 eV resonance to obtain the kinetic energy distribution of the fragment ions.
Persistent radicals in irradiated imidazolium ionic liquids probed by EPR spectroscopy
Long-lived radicals were observed in irradiated room temperature ionic liquids (RTILs) composed of the bis(trifluoromethylsulfonyl)imide anion (Tf 2 N - ) with 1-hexyl-3-methylimidazolium (hmim + ) and1-butyl-3-methylimidazolium (bmim+) cations. The EPR signal intensity increases within hours and the spectral pattern changes during the time after irradiation. The kinetics data obtained indicate the existence of at least two distinct radical cations that have different formation and decay rates. We demonstrate that oxygen does not react rapidly with the radical species formed. The bmim + Tf 2 N - was selectively deuterated at various positions which allowed us to suggest possible structures of the stable radicals formed. The first structure is a radical cation containing 2 nitrogens and 6 protons all with ca. 8.2 Gauss hyperfine splittings, and 2 protons with 2.8 Gauss splitting. The structure of the second radical cation is similar, but characterized by an odd number of hydrogens with ca. 8.2 Gauss splitting. Extensive quantum chemistry calculations were performed to attempt to identify the structure of these persistent radicals. The most likely candidates are imidazole radical cations having methyl groups at the nitrogen atoms and substituents in the second position of the imidazole ring.
One-bond 13 C– 13 C spin-coupling constants in saccharides: a comparison of experimental and calculated values by density functional theory using solid-state 13 C NMR and X-ray crystallography
Methyl aldohexopyranosides were 13 C-labeled at contiguous carbons, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13 C nuclear magnetic resonance (NMR) spectroscopy to examine the degree to which density functional theory (DFT) can calculate one-bond 13C–13C spin-coupling constants ( 1 J CC ) in saccharides with sufficient accuracy to permit their use in MA'AT analysis, a newly-reported hybrid DFT/NMR method that provides probability distributions of molecular torsion angles in solution (Zhang et al., J. Phys. Chem. B, 2017, 121, 3042–3058; Meredith et al., J. Chem. Inf. Model., 2022, 62, 3135–3141). Experimental 1 J CC values in crystalline samples of the doubly 13 C-labeled compounds were measured by solid-state 13 C NMR and compared to those calculated from five different DFT models: (1) 1 J CC values calculated from single structures identical to those observed in crystalline samples by X-ray crystallography (all atom refinement); (2) 1 J CC values calculated from the single structures in (1) but after Hirshfeld atom refinement (HAR); (3) 1 J CC values calculated from the single structures in (1) after DFT-optimization of hydrogen atoms only; and (4 and 5) 1 J CC values calculated in rotamers of torsion angle θ 2 (C1–C2–O2–O2H) or ω(C4–C5–C6–O6) from which either specific or generalized parameterized equations were obtained and used to calculate 1 J CC values in the specific θ 2 or ω rotamers observed in crystalline samples. Good qualitative agreement was observed between calculated 1 J CC values and those measured by solid-state 13 C NMR regardless of the DFT model, but in no cases were calculated 1 J CC values quantitative, differing (over-estimated) on average by 4–5% from experimental values. These findings, and those reported recently from solution NMR studies (Tetrault et al., J. Phys. Chem. B 2022, 126, 9506–9515), indicate that improvements in DFT calculations are needed before calculated 1 J CC values can be used directly as reliable constraints in MA'AT analyses of saccharides in solution.
Unveiling the Mechanism of Photodamage to Sphingolipid Molecules via Laser Flash Photolysis and EPR
Abstract Sphingolipids are involved in the maintenance of the skin barrier function and regulate cellular processes of keratinocytes. The work reported here is designed to uncover details of the mechanism of damage to such lipids by UV radiation. Our approach employs laser flash photolysis and electron paramagnetic resonance (EPR) spectrometry to explore the mechanism of the decay reactions, and to determine the associated kinetic parameters. To interpret our experiments, we computed both excitation energies and EPR parameters of radicals formed during photolysis. Employing the spin‐trap EPR method confirmed the formation of both carbon‐ and nitrogen‐centered radicals. Thus, we can conclude that the photodecomposition of sphingolipids and their analogues proceeds by Norrish type I reactions with the formation of both nitrogen‐centered and alkyl radicals.
Reactivity of Zn + aq in high-temperature water radiolysis
For this work, reactivity of transients involving Zn + in high-temperature water radiolysis has been studied in the temperature range of 25–300 °C. The reduced monovalent zinc species were generated from an electron transfer process between the hydrated electron and Zn 2+ ions using pulse radiolysis. The Zn + species can subsequently be oxidized by the radiolytically-produced oxidizing species: ˙OH, H 2 O 2 and ˙H. We find that the absorption of monovalent zinc is very sensitive to the pH of the medium. An absorption maximum at 306–311 nm is most pronounced at pH 7 and the signal then decreases in acidic media where the reducing electrons are competitively captured by protons. At pH values higher than 7, hydroxo-forms of Zn 2+ are created and the maximum of the absorption signal begins to shift to the red spectral region. We find that the optical spectrum of Zn + aq cannot be fully explained in terms of a charge-transfer to solvent (CTTS) process, which was previously proposed. Reaction rates of most of the recombination reactions investigated follow the empirical Arrhenius relationship at temperatures up to 200 °C and have been determined at higher temperatures for the first time. A bimolecular disproportionation reaction of Zn + aq is not observed under the conditions investigated.
Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations
Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA’AT modeling of the O-glycosidic linkages of oligosaccharides. Four ( 1 J C1',H1' , 1 J C1',C2' , 2 J C1',H2' , and 2 J C2',H1' ) and eight ( 1 J C4,H4 , 1 J C3,C4 , 1 J C4,C5 , 2 J C3,H4 , 2 J C4,H3 , 2 J C5,H4 , 2 J C4,H5 , and 2 J C3,C5 ) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C–O torsion angles, $\phi$ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either $\phi$ or ψ. Secondary effects of exocyclic (hydroxyl) C–O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA’AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C–O bonds. The findings also provide new insights into the general effects of exocyclic C–O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.
MA’AT Analysis of Aldofuranosyl Rings: Unbiased Modeling of Conformational Equilibria and Dynamics in Solution
Not provided.
Two-bond 13 C– 13 C spin-coupling constants in saccharides: dependencies on exocyclic hydroxyl group conformation
Seven doubly 13 C-labeled isotopomers of methyl β-D-glucopyranoside, methyl β-D-xylopyranoside, methyl β-D-galactopyranoside, methyl β-D-galactopyranosyl-(1→4)-β-D-glucopyranoside and methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside were prepared, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13 C NMR spectroscopy to determine experimentally the dependence of 2 J C1,C3 values in aldopyranosyl rings on the C1–C2–O2–H torsion angle, θ 2 , involving the C2 carbon of the C1–C2–C3 coupling pathway. Using X-ray crystal structures to determine θ 2 in crystalline samples and by selecting compounds that exhibit a relatively wide range of θ 2 values in the crystalline state, 2 J C1,C3 values measured in crystalline samples were plotted against θ 2 and the resulting plot compared to that obtained from density functional theory (DFT) calculations. For θ 2 values ranging from ~90° to ~240°, very good agreement was observed between the experimental and theoretical plots, providing strong validation of DFT-calculated spin-coupling dependencies on exocyclic C–O bond conformation involving the central carbon of geminal C–C–C coupling pathways. we report that these findings provide new experimental evidence supporting the use of 2 J CCC values as non-conventional spin-coupling constraints in MA'AT conformational modeling of saccharides in solution, and the use of NMR spin-couplings not involving coupled hydroxyl hydrogens as indirect probes of C–O bond conformation. Solvomorphism was observed in crystalline βGal-(1→4)-βGlcOCH 3 wherein the previously-reported methanol solvate form was found to spontaneously convert to a monohydrate upon air-drying, leading to small but discernible conformational changes in, and a new crystalline form of, this disaccharide.
Isopropyl 3-deoxy-α- D - ribo -hexopyranoside (isopropyl 3-deoxy-α-D-glucopyranoside): evaluating trends in structural parameters
Isopropyl 3-deoxy-α-D-ribo-hexopyranoside (isopropyl 3-deoxy-α-D-glucopyranoside), C 9 H 18 O 5 , (I), crystallizes from a methanol–ethyl acetate solvent mixture at room temperature in a 4C1 chair conformation that is slightly distorted towards the C5 S C1 twist-boat form. A comparison of the structural parameters in (I), methyl α-D-glucopyranoside, (II), α-D-glucopyranosyl-(1→4)-D-glucitol (maltitol), (III), and 3-deoxy-α-D-ribo-hexopyranose (3-deoxy-α-D-glucopyranose), (IV), shows that most endocyclic and exocyclic bond lengths, valence bond angles and torsion angles in the aldohexopyranosyl rings are more affected by anomeric configuration, aglycone structure and/or the conformation of exocyclic substituents, such as hydroxymethyl groups, than by monodeoxygenation at C3. The structural effects observed in the crystal structures of (I)–(IV) were confirmed though density functional theory (DFT) calculations in computed structures (I) c –(IV) c . Exocyclic hydroxymethyl groups adopt the gauche–gauche (gg) conformation (H5 anti to O6) in (I) and (III), and the gauche–trans (gt) conformation (C4 anti to O6) in (II) and (IV). The O-glycoside linkage conformations in (I) and (III) resemble those observed in disaccharides containing β-(1→4) linkages.