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1. Directed gas-phase preparation of the elusive phosphinosilylidyne (SiPH ₂ , X ² A′′) and cis / trans phosphinidenesilyl (HSiPH; X ² A′) radicals under single-collision conditions

   https://doi.org/10.1039/D1CP02812J  

   He, Chao ; Goettl, Shane J. ; Yang, Zhenghai ; Doddipatla, Srinivas ; Kaiser, Ralf I. ; Silva, Mateus Xavier ; Galvão, Breno R. ( September 2021 , Physical Chemistry Chemical Physics)

   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 onmore »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).« less
2.  Why Do N-Alkylated Anilides Bend Over? The Factors Dictating the Divergent Conformational Preferences of 2° and 3° N-Aryl Amides

   https://doi.org/DOI:10.1021/acs.jpca.9b04555  

   Pros, Gabrielle J. Bloomfield ( September 2019 , The journal of physical chemistry)

   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 substituentsmore »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.« less
3. Non-covalent complexes of the peptide fragment Gly-Asn-Asn-Gln-Gln-Asn-Tyr in the gas-phase. Photodissociative cross-linking, Born–Oppenheimer molecular dynamics, and ab initio computational binding study

   https://doi.org/10.1039/c8cp06893c  

   Huang, Shu R. ; Liu, Yang ; Tureček, František ( January 2019 , Physical Chemistry Chemical Physics)

   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. Althoughmore »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.« less
4. Glycosidic linkage, N -acetyl side-chain, and other structural properties of methyl 2-acetamido-2-deoxy-β- D -glucopyranosyl-(1→4)-β- D -mannopyranoside monohydrate and related compounds

   https://doi.org/10.1107/S2053229620001515  

   Zhang, Wenhui ; Meredith, Reagan J. ; Oliver, Allen G. ; Carmichael, Ian ; Serianni, Anthony S. ( March 2020 , Acta Crystallographica Section C Structural Chemistry)

   The crystal structure of methyl 2-acetamido-2-deoxy-β-D-glycopyranosyl-(1→4)-β-D-mannopyranoside monohydrate, C 15 H 27 NO 11 ·H 2 O, was determined and its structural properties compared to those in a set of mono- and disaccharides bearing N -acetyl side-chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N -acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen-bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis – trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter-residue hydrogen bonding and some bond angles in or proximal to β-(1→4) O -glycosidic linkages on linkage torsion angles ϕ and ψ. Hypersurfaces correlating ϕ and ψ with the linkage C—O—C bond anglemore »and total energy are sufficiently similar to render the former a proxy of the latter.« less
5. Insights into the Alkene Triol Conundrum: Characterization and Quantitation of Isoprene-Derived C5H10O3 Reactive Uptake Products

   FRAUENHEIM, MOLLY ; Beaver, Melinda ; Offenberg, John ; Zhang, Zhenfa ; Surratt, Jason ; Gold, Avram ( October 2022 , AAAR 40th Annual Conference)

   2-Methyltetrols and a group of C5H10O3 isomers referred to as “alkene triols,” are chemical tracers used to estimate the contribution of isoprene oxidation to atmospheric PM2.5. The molecular structures and the mass contribution of alkene triols are uncertain, and their origin as analytical artifacts is contentious. Here, we report that the alkene triols are uptake products and present evidence of partitioning into the gas phase. Based on the hypothesis that rearrangement of IEPOX yields C5H10O3 isomers on reactive uptake, we synthesized “alkene triol” candidates and investigated their behavior under conventional derivatization gas chromatography/electron impact mass spectrometry (GC/EI-MS) and, in parallel, by non-destructive hydrophilic interaction liquid chromatography coupled with high-resolution quadrupole time-of-flight electrospray mass spectrometry (HILIC/ESI-HR-QTOFMS). Synthetic targets were 3-methyltetrahydrofuran-2,4-diol (1) and 3-methylene-1,2,4-trihydroxybutane (2). Using the standards, we confirmed 1 and 2 in chamber-generated cis- and trans-β-IEPOX SOA both by HILIC/ESI-HR-QTOFMS and derivatization GC/EI-MS. In ambient SOA collected in Research Triangle Park, NC, 1 and 2 were confirmed and quantitatively estimated by GC-EI/MS. Trimethylsilyl derivatization of 1 is problematic, yielding predominantly bis- but also a small amount (<10%) of tris-trimethylsilyl forms. Our findings are consistent with reports that the tris-trimethylsilyl derivatives 1 and 2 represent largely thermal decomposition of 2-methyltetrol sulfatemore »esters; however, based on HILIC/ESI-HR-QTOFMS analysis of chamber-generated SOA, we estimate up to 10% and 50% of 1 and 2, respectively are not artifact-derived, and may arise from isomerization of IEPOX upon reactive uptake. Significant quantities of 1 and 2 were detected in impinger samples downstream from a denuder in series with a filter indicating partitioning into the gas phase. Results suggest that isoprene-derived “alkene triols” do form and are preferentially in the gas phase rather than particle phase, warranting studies on partitioning and gas-phase oxidation pathways.« less