Formation of 6-methyl-1,4-dihydronaphthalene in the reaction of the p-tolyl radical with 1,3-butadiene under single-collision conditions

Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins: Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band Maxima

A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds to a certain position of a charged or polar residue relative to the retinal chromophore. The proposed approach was evaluated against an example set consisting of twelve bovine rhodopsin and sodium pumping rhodopsin mutants. The limits of the applicability of the models are also discussed. The results of our study can be useful for the interpretation of experimental data and for the rational design of rhodopsins with required spectral properties.

In Situ Laser-Induced Fabrication of a Ruthenium-Based Microelectrode for Non-Enzymatic Dopamine Sensing

In this paper, we propose a fast and simple approach for the fabrication of the electrocatalytically active ruthenium-containing microstructures using a laser-induced metal deposition technique. The results of scanning electron microscopy and electrical impedance spectroscopy (EIS) demonstrate that the fabricated ruthenium-based microelectrode had a highly developed surface composed of 10 μm pores and 10 nm zigzag cracks. The fabricated material exhibited excellent electrochemical properties toward non-enzymatic dopamine sensing, including high sensitivity (858.5 and 509.1 μA mM⁻¹ cm⁻²), a low detection limit (0.13 and 0.15 μM), as well as good selectivity and stability.

On the formation and the isomer specific detection of methylacetylene (CH3CCH), propene (CH3CHCH2), cyclopropane (c-C3H6), vinylacetylene (CH2CHCCH), and 1,3-butadiene (CH2CHCHCH2) from interstellar methane ice analogues

Pure methane (CH4) ices processed by energetic electrons under ultra-high vacuum conditions to simulate secondary electrons formed via galactic cosmic rays (GCRs) penetrating interstellar ice mantles have been shown to produce an array of complex hydrocarbons with the general formulae: CnH2n+2 (n = 4-8), CnH2n (n = 3-9), CnH2n-2 (n = 3-9), CnH2n-4 (n = 4-9), and CnH2n-6 (n = 6-7). By monitoring the in situ chemical evolution of the ice combined with temperature programmed desorption (TPD) studies and tunable single photon ionization coupled to a reflectron time-of-flight mass spectrometer, specific isomers of C3H4, C3H6, C4H4, and C4H6 were probed. These experiments confirmed the synthesis of methylacetylene (CH3CCH), propene (CH3CHCH2), cyclopropane (c-C3H6), vinylacetylene (CH2CHCCH), 1-butyne (HCCC2H5), 2-butyne (CH3CCCH3), 1,2-butadiene (H2CCCH(CH3)), and 1,3-butadiene (CH2CHCHCH2) with yields of 2.17 ± 0.95 × 10-4, 3.7 ± 1.5 × 10-3, 1.23 ± 0.77 × 10-4, 1.28 ± 0.65 × 10-4, 4.01 ± 1.98 × 10-5, 1.97 ± 0.98 × 10-4, 1.90 ± 0.84 × 10-5, and 1.41 ± 0.72 × 10-4 molecules eV-1, respectively. Mechanistic studies exploring the formation routes of methylacetylene, propene, and vinylacetylene were also conducted, and revealed the additional formation of the 1,2,3-butatriene isomer. Several of the above isomers, methylacetylene, propene, vinylacetylene, and 1,3-butadiene, have repeatedly been shown to be important precursors in the formation of polycyclic aromatic hydrocarbons (PAHs), but until now their interstellar synthesis has remained elusive.

A combined crossed molecular beams and computational study on the formation of distinct resonantly stabilized C5H3 radicals via chemically activated C5H4 and C6H6 intermediates

The crossed molecular beams technique was utilized to explore the formation of three isomers of resonantly stabilized (C5H3) radicals along with their d2-substituted counterparts via the bimolecular reactions of singlet/triplet dicarbon [C2(X1Σ+g/a3Πu)] with methylacetylene [CH3CCH(X1A1)], d3-methylacetylene [CD3CCH(X1A1)], and 1-butyne [C2H5CCH(X1A')] at collision energies up to 26 kJ mol-1via chemically activated singlet/triplet C5H4/C5D3H and C6H6 intermediates. These studies exploit a newly developed supersonic dicarbon [C2(X1Σ+g/a3Πu)] beam generated via photolysis of tetrachloroethylene [C2Cl4(X1Ag)] by excluding interference from carbon atoms, which represent the dominating (interfering) species in ablation-based dicarbon sources. We evaluated the performance of the dicarbon [C2(X1Σ+g/a3Πu)] beam in reactions with methylacetylene [CH3CCH(X1A1)] and d3-methylacetylene [CD3CCH(X1A1)]; the investigations demonstrate that the reaction dynamics match previous studies in our laboratory utilizing ablation-based dicarbon sources involving the synthesis of 1,4-pentadiynyl-3 [HCCCHCCH(X2B1)] and 2,4-pentadiynyl-1 [H2CCCCCH(X2B1)] radicals via hydrogen (deuterium) atom elimination. Considering the C2(X1Σ+g/a3Πu)-1-butyne [C2H5CCH(X1A')] reaction, the hitherto elusive methyl-loss pathway was detected. This channel forms the previously unknown resonantly stabilized penta-1-yn-3,4-dienyl-1 [H2CCCHCC(X2A)] radical along with the methyl radical [CH3(X2A2'')] and is open exclusively on the triplet surface with an overall reaction energy of -86 ± 10 kJ mol-1. The preferred reaction pathways proceed first by barrierless addition of triplet dicarbon to the π-electronic system of 1-butyne, either to both acetylenic carbon atoms or to the sterically more accessible carbon atom, to form the methyl-bearing triplet C6H6 intermediates [i41b] and [i81b], respectively, with the latter decomposing via a tight exit transition state to penta-1-yn-3,4-dienyl-1 [(H2CCCHCC(X2A)] plus the methyl radical [CH3(X2A2'')]. The successful unraveling of this methyl-loss channel - through collaborative experimental and computational efforts - underscores the viability of the photolytically generated dicarbon beam as an unprecedented tool to access reaction dynamics underlying the formation of resonantly stabilized free radicals (RSFR) that are vital to molecular mass growth processes that ultimately lead to polycyclic aromatic hydrocarbons (PAHs).

Untangling the methane chemistry in interstellar and solar system ices toward ionizing radiation: a combined infrared and reflectron time-of-flight analysis

Pure methane (CH₄/CD₄) ices were exposed to three ionizing radiation sources at 5.5 K under ultrahigh vacuum conditions to compare the complex hydrocarbon spectrum produced across several interstellar environments. These irradiation sources consisted of energetic electrons to simulate secondary electrons formed in the track of galactic cosmic rays (GCRs), Lyman α (10.2 eV; 121.6 nm) photons simulated the internal VUV field in a dense cloud, and broadband (112.7-169.8 nm; 11.0-7.3 eV) photons which mimic the interstellar ultra-violet field. The in situ chemical evolution of the ices was monitored via Fourier transform infrared spectroscopy (FTIR) and during heating via mass spectrometry utilizing a quadrupole mass spectrometer with an electron impact ionization source (EI-QMS) and a reflectron time-of-flight mass spectrometer with a photoionization source (PI-ReTOF-MS). The FTIR analysis detected six small hydrocarbon products from the three different irradiation sources: propane [C₃H₈(C₃D₈)], ethane [C₂H₆(C₂D₆)], the ethyl radical [C₂H₅(C₂D₅)], ethylene [C₂H₄(C₂D₄)], acetylene [C₂H₂(C₂D₂)], and the methyl radical [CH₃(CD₃)]. The sensitive PI-ReTOF-MS analysis identified a complex array of products with different products being detected between experiments with general formulae: C_nH_2n+2 (n = 4-8), C_nH_2n (n = 3-9), C_nH_2n-2 (n = 3-9), C_nH_2n-4 (n = 4-9), and C_nH_2n-6 (n = 6-7) from electron irradiation and C_nH_2n+2 (n = 4-8), C_nH_2n (n = 3-10), C_nH_2n-2 (n = 3-11), C_nH_2n-4 (n = 4-11), C_nH_2n-6 (n = 5-11), and C_nH_2n-8 (n = 6-11) from broadband photolysis and Lyman α photolysis. These experiments show that even the simplest hydrocarbon can produce important complex hydrocarbons such as C₃H₄ and C₄H₆ isomers. Distinct isomers from these groups have been shown to be important reactants in the synthesis of polycyclic aromatic hydrocarbons like indene (C₉H₈) and naphthalene (C₁₀H₈) under interstellar conditions.

Formation of bicyclic polycyclic aromatic hydrocarbons (PAHs) from the reaction of a phenyl radical with cis-3-penten-1-yne

The formation of PAHs within 4-, 5-, 6- and 7-membered rings on the C₆H₅ + C₅H₆ potential energy surface.

Naphthalene formation pathways from phenyl radical via vinyl radical (C2H3) and vinylacetylene (C4H4): computational studies on reaction mechanisms and kinetics

The reaction mechanisms of PAH formation from phenyl radical (C6H5) to naphthalene via C2H3 (C2H3-Path) and C4H4 (C4H4-Path) were investigated by the G3(MP2, CC) method. The hydrogen abstraction, ring closure, cis–trans isomerization, and disproportionation reactions were considered, as well as their occurred sequence. The results showed that H-abstraction reactions occurred more easily than H-dissociation reactions. The cis–trans conversion reactions in sub-routes of C2H3-Path and C4H4-Path provided the largest barriers of 51, 53, and 36 kcal/mol along their routes, which illustrated that the cis–trans isomerization was energetically costly in the PAH formation process. The entrance barriers of C2H2-Path, C2H3-Path, and C4H4-Path are 6, 8, and 3 kcal/mol, respectively, which indicates that it is easier to add C4H4 to C6H5 compared with adding C2H2 to C2H3. C2H3 additions were highly exothermic with reaction energies greater than 110 kcal/mol, and compared with C2H2 additions, C2H3 additions were irreversible. However, C2H2-Path, C2H3-Path and C4H4-Path involved energy barriers of 20, 32, and 36 kcal/mol, respectively. Considering the high temperature in combustion and the approximate concentrations of C2H3 and C4H4, all three of these pathways could lead to naphthalene in some combustion flames.

On the formation of nitrogen-substituted polycyclic aromatic hydrocarbons (NPAHs) in circumstellar and interstellar environments

The chemical evolution of extraterrestrial environments leads to the formation of nitrogen substituted polycyclic aromatic hydrocarbons (NPAHs) via gas phase radical mediated aromatization reactions.

Oxidation of the para-Tolyl Radical by Molecular Oxygen under Single-Collison Conditions: Formation of the para-Toloxy Radical

Crossed molecular beam experiments were performed to elucidate the chemical dynamics of the para-tolyl (CH₃C₆H₄) radical reaction with molecular oxygen (O₂) at an average collision energy of 35.3 ± 1.4 kJ mol^-1. Combined with theoretical calculations, the results show that para-tolyl is efficiently oxidized by molecular oxygen to para-toloxy (CH₃C₆H₄O) plus ground-state atomic oxygen via a complex forming, overall exoergic reaction (experimental, -33 ± 16 kJ mol^-1; computational, -42 ± 8 kJ mol^-1). The reaction dynamics are analogous to those observed for the phenyl (C₆H₅) plus molecular oxygen system which suggests the methyl group is a spectator during para-tolyl oxidation and that application of phenyl thermochemistry and reaction rates to para-substituted aryls is likely a suitable approximation.