The reaction of the D1-silylidyne radical (SiD; X 2 Π) with phosphine (PH 3 ; X 1 A 1 ) was conducted in a crossed molecular beams machine under single collision conditions. Merging of the experimental results with ab initio electronic structure and statistical Rice–Ramsperger–Kassel–Marcus (RRKM) calculations indicates that the reaction is initiated by the barrierless formation of a van der Waals complex (i0) as well as intermediate (i1) formed via the barrierless addition of the SiD radical with its silicon atom to the non-bonding electron pair of phosphorus of the phosphine. Hydrogen shifts from the phosphorous atom to the adjacent silicon atom yield intermediates i2a, i2b, i3; unimolecular decomposition of these intermediates leads eventually to the formation of trans / cis -phosphinidenesilyl (HSiPH, p2/p4) and phosphinosilylidyne (SiPH 2 , p3) via hydrogen deuteride (HD) loss (experiment: 80 ± 11%, RRKM: 68.7%) and d - trans / cis -phosphinidenesilyl (DSiPH, p2′/p4′) plus molecular hydrogen (H 2 ) (experiment: 20 ± 7%, RRKM: 31.3%) through indirect scattering dynamics via tight exit transition states. Overall, the study reveals branching ratios of p2/p4/p2′/p4′ ( trans / cis HSiPH/DSiPH) to p3 (SiPH 2 ) of close to 4 : 1. The present study sheds light on the complex reaction dynamics of the silicon and phosphorous systems involving multiple atomic hydrogen migrations and tight exit transition states, thus opening up a versatile path to access the previously elusive phosphinidenesilyl and phosphinosilylidyne doublet radicals, which represent potential targets of future astronomical searches toward cold molecular clouds (TMC-1), star forming regions (Sgr(B2)), and circumstellar envelopes of carbon rich stars (IRC + 10216).
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Structural study of 1- and 2-naphthol: new insights into the non-covalent H–H interaction in cis -1-naphthol
Previous microwave studies of naphthol monomers were supplemented by measuring spectra of all 13 C mono-substituted isotopologues of the cis - and trans -conformers of 1-naphthol and 2-naphthol in their natural abundances. The resulting data were utilized to determine substitution structures and so-called semi-experimental effective structures. Results from electronic structure calculations show that the OH group of cis -1-naphthol points ≈6° out of plane, which is consistent with the inertial defect data of cis - and trans -1-naphthol. The non-planarity of cis -1-naphthol is a result of a close-contact H-atom–H-atom interaction. This type of H–H interaction has been the subject of much controversy in the past and we provide here an in-depth theoretical analysis of it. The naphthol system is particularly well-suited for such analysis as it provides internal standards with its four different isomers. The methods used include quantum theory of atoms in molecules, non-covalent interactions, independent gradient model, local vibrational mode, charge model 5, and natural bond orbital analyses. We demonstrate that the close-contact H–H interaction is neither a purely attractive nor repulsive interaction, but rather a mixture of the two.
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- Award ID(s):
- 1464906
- NSF-PAR ID:
- 10342517
- Date Published:
- Journal Name:
- Physical Chemistry Chemical Physics
- Volume:
- 24
- Issue:
- 6
- ISSN:
- 1463-9076
- Page Range / eLocation ID:
- 3722 to 3732
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The current work presents new experimental autoignition and speciation data on the two
cis ‐hexene isomers:cis ‐2‐hexene andcis ‐3‐hexene. The new data provide insights on the effects of carbon‐carbon double bond location and stereoisomeric structures on ignition delay times and reaction pathways for linear hexene isomers. Experiments were performed using the University of Michigan rapid compression facility to determine ignition delay times from pressure‐time histories. Stoichiometric (ϕ = 1.0) mixtures at dilution levels of inert gas to O2 = 7.5:1 (mole basis) were investigated at an average pressure of 11 atm and temperatures from 809 to 1052 K. Speciation experiments were conducted atT = 900 K for the twocis ‐hexene isomers, where fast‐gas sampling and gas chromatography were used to identify and quantify the twocis ‐hexene isomers and stable intermediate species. The ignition delay time data showed negligible sensitivity to the location of the carbon‐carbon double bond and the stereoisomeric structure (cis‐trans), and the species data showed no correlation with the stereoisomeric structure, but there was a strong correlation of some of the measured species with the location of the double bond in the hexene isomer. In particular, 2‐hexene showed strong selectivity to propene, acetaldehyde, and 1,3‐butadiene, and 3‐hexene showed selectivity to propanal. Model predictions of ignition delay times were in excellent agreement with the experimental data. There was generally good agreement for the model predictions of the species data for 2‐hexene; however, the mechanism overpredicted some of the small aldehyde (C2‐C4) species for 3‐hexene. Reaction pathway analysis indicates the hexenes are almost exclusively consumed by H‐atom abstraction reactions at the conditions studied (P = 11 atm,T > 900 K), and not by C3‐C4scission as observed in high‐temperature (>1300 K) hexene ignition studies. Improved estimates for 3‐hexene + OH reactions may improve model predictions for the species measured in this work. -
The conformational preferences of 28 sterically and electronically diverse N-aryl amides were detd. using d. functional theory (DFT), using the B3LYP functional and 6-31G(d) basis set. For each compd., both the cis and trans conformers were optimized, and the difference in ground state energy calcd. For six of the compds., the potential energy surface was detd. as a function of rotation about the N-aryl bond (by 5° increments) for both cis and trans conformers. A natural bond orbital (NBO) deletion strategy was also employed to det. the extent of the contribution of conjugation to the energies of each of the conformers. By comparing these computational results with previously reported exptl. data, an explanation for the divergent conformational preferences of 2° N-aryl amides and 3° N-alkyl-N-aryl amides was formulated. This explanation accounts for the obsd. relationships of both steric and electronic factors detg. the geometry of the optimum conformation, and the magnitude of the energetic difference between cis and trans conformers: except under the most extreme scenarios, 2° amides maintain a trans conformation, and the N-bound arene lies in the same plane as the amide unless it has ortho substituents; for 3° N-alkyl-N-aryl amides in which the alkyl and aryl substituents are connected in a small ring, trans conformations are also favored, for most cases other than formamides, and the arene and amide remain in conjugation; and for 3° N-alkyl-N-aryl amides in which the alkyl and aryl substituents are not connected in a small ring, allylic strain between the two N-bound substituents forces the aryl substituent to rotate out of the plane of the amide, and the trans conformation is destabilized with respect to the cis conformation due to repulsion between the π system of the arene and the lone pairs on the oxygen atom of the carbonyl. The cis conformation is increasingly more stable than the trans conformation as electron d. is increased on the arene because the more electron-rich arenes adopt a more orthogonal arrangement, increasing the interaction with the carbonyl oxygen, while simultaneously increasing the magnitude of the repulsion due to the increased electron d. in the π system. The trans conformation is favored for 2° amides even when the arene is orthogonal to the amide, in nearly all cases, because the C-N-C bond angle can expend at the expense of the C-N-H bond angles, while this is not favorable for 3° amides.more » « less
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High-resolution direct absorption infrared spectra of metastable cis-formic acid (HCOOH) trapped in a cis-well resonance behind a 15 kcal/mol barrier are reported for the first time, with the energetically unstable conformer produced in a supersonic slit plasma expansion of trans-formic acid/H 2 mixtures. We present a detailed high-resolution rovibrational analysis for cis-formic acid species in the OH stretch ( ν 1 ) fundamental, providing first precision vibrational band origin, rotational constants, and term values, which in conjunction with ab initio calculations at the couple-cluster with single, double, and perturbative triple [CCSD(T)]/ANOn (n = 0, 1, 2) level support the experimental assignments and establish critical points on the potential energy surface for internal rotor trans-to-cis isomerization. Relative intensities for a- and b-type transitions observed in the spectra permit the transition dipole moment components to be determined in the body fixed frame and prove to be in good agreement with ab initio CCSD(T) theoretical estimates but in poor agreement with simple bond-dipole predictions. The observed signal dependence on H 2 in the discharge suggests the presence of a novel H atom radical chemical mechanism for strongly endothermic “up-hill” internal rotor isomerization between trans- and cis-formic acid conformers.more » « less
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Non-covalent complexes of the short amyloid peptide motif Gly-Asn-Asn-Gln-Gln-Asn-Tyr (GNNQQNY) with peptide counterparts that were tagged with a diazirine ring at the N-termini (*GNNQQNY) were generated as singly charged ions in the gas phase. Specific laser photodissociation (UVPD) of the diazirine tag in the gas-phase complexes at 355 nm generated transient carbene intermediates that underwent covalent cross-linking with the target GNNQQNY peptide. The crosslinking yields ranged between 0.8 and 4.5%, depending on the combinations of peptide C-terminal amides and carboxylates. The covalent complexes were analyzed by collision-induced dissociation tandem mass spectrometry (CID-MS 3 ), providing distributions of cross-links at the target peptide amino acid residues. A general preference for cross-linking at the target peptide Gln-4-Gln-5-Asn-6-Tyr-7 segment was observed. Born–Oppenheimer molecular dynamics calculations were used to obtain 100 ps trajectories for nine lowest free-energy conformers identified by ωB97X-D/6-31+G(d,p) gradient geometry optimizations. The trajectories were analyzed for close contacts between the incipient carbene atom and the X–H bonds in the target peptide. The close-contact analysis pointed to the Gln-5 and Tyr-7 residues as the most likely sites of cross-linking, consistent with the experimental CID-MS 3 results. Non-covalent binding in the amide complexes was evaluated by DFT calculations of structures and energies. Although antiparallel arrangements of the GNNQQNY and *GNNQQNY peptides were favored in low-energy gas-phase and solvated complexes, the conformations and peptide–peptide interface surfaces were found to differ from the secondary structure of the dry interface in GNNQQNY motifs of amyloid aggregates.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D1CP05632H
