CHO Substitution Effect Revisited in the Vibrationally Resolved Laser-Induced Fluorescence Spectra of Methoxycyclohexoxy Radicals.

The oxy-substituted alkoxy radicals have attracted wide attention due to the increasing application of oxygenated volatile organic compounds as fuel additives and solvents. Direct detection of these intermediate radicals is desired for measuring the reaction rate and investigating the oxidation mechanism of organic compounds in the atmosphere. A charge-transfer excited state induced by CHO substitution was identified in our previous study of 3-methoxy-1-propoxy radical [Xue, J.

Intramolecular charge transfer excitation induced by CHO substitution in the 3-methoxy-1-propoxy radical.

The oxy-substituted alkoxy radicals are generated from the oxidation of ethers. Their degradation path affects ozone production and the formation of the secondary organic aerosol in the atmosphere. In this work, three alkoxy radicals with methoxy (CH3O) substitution at β, γ, and δ carbon are studied using laser-induced fluorescence (LIF) spectroscopy and theoretical calculation methods.

Direct observation of the intermediate radical in the photodissociation of 1,3-cyclohexane dinitrite.

A two-step photodissociation mechanism was proposed in the literature for dinitrites in the absence of direct evidence of the intermediate species. In this work, photodissociation dynamics of cis and trans 1,3-cyclohexane dinitrites are investigated by laser-induced fluorescence (LIF) spectroscopy and theoretical calculation methods. Observation of the fluorescence spectra of the 3-nitrosooxy cyclohexoxy radical provides direct experimental evidence that the intermediate species exists.

Energetic switch of the proline effect in collision-induced dissociation of singly and doubly protonated peptide Ala-Ala-Arg-Pro-Ala-Ala.

Suppression of the selective cleavage at N-terminal of proline is observed in the peptide cleavage by proteolytic enzyme trypsin and in the fragment ion mass spectra of peptides containing Arg-Pro sequence. An insight into the fragmentation mechanism of the influence of arginine residue on the proline effect can help in prediction of mass spectra and in protein structure analysis. In this work, collision-induced dissociation spectra of singly and doubly charged peptide AARPAA were studied by ESI MS/MS and theoretical calculation methods.

Photodissociation dynamics of dinitrite at 355 nm: initiation of a reactive pathway.

Dinitrites are effective nitrosating reagents in preparative chemistry and their decomposition products are involved in the atmospheric reaction of volatile organic compounds with nitrogen oxides (NO). In this work, photodissociation dynamics of five alkyl dinitrites were investigated by detecting the LIF spectra of the dissociation products and theoretical calculations. The results showed that the C-C bond connecting the two nitrosooxy (-ONO) functional groups was the weakest bond in vicinal dinitrites and aldehydes were the dissociation products.

Methyl substitution effect on the jet-cooled laser-induced fluorescence spectrum of cyclohexoxy radical.

Understanding the structure and properties of cyclohexoxy radical and its substitutes is important because of their presence in combustion processes, in atmospheric chemistry, and as intermediates in the hydrocarbon reactions. In this work, jet-cooled laser-induced fluorescence (LIF) spectra of five dimethyl substituted cyclohexoxy radicals are obtained for the first time. The correlation between the spectral variations and the radical structural changes is studied with the assistance of theoretical calculations at the B3LYP/6-31+G(d) and CASSCF/6-31+G(d) levels.

The role of basic residues in the fragmentation process of the lysine rich cell-penetrating peptide TP10.

Selective cleavage effect of basic residues in the fragmentation of short peptides has been studied intensively. In contrast, the role of basic residues in the degradation of large peptides, such as cell-penetrating peptides, is largely unknown. In this work, the fragmentation of a 21 residues cell-penetrating peptide TP10 containing four lysine residues was studied by collision-induced dissociation mass spectrometry and computation methods.

Time-Resolved Fluorescence Anisotropy Study of the Interaction Between DNA and a Peptide Truncated from the p53 Protein Core Domain.

Time-resolved fluorescence anisotropy spectroscopy was applied to study the interaction between a peptide truncated from the binding site of tumor suppressor p53 protein and the DNAs covalently labeled with 6-carboxyfluorescein (FAM) dye. Fluorescence intensity quenching and changes of anisotropy decay lifetime were monitored when FAM labeled DNA formed complex with the peptide. The results demonstrated that the sequence of DNA could not define the binding specificity between the peptide and DNA.

Laser-induced fluorescence of isobutoxy in competition with ground state decomposition.

Spectroscopic detection is an important method to monitor alkoxy radicals in atmospheric photochemistry studies. In this work, we report the first observation of the laser-induced fluorescence (LIF) spectra of isobutoxy, 2-methyl-1-butoxy, and 3-methyl-1-butoxy in supersonic jet-cooled condition. Ground state unimolecular decomposition and isomerization as well as excited state relaxation dynamics of isobutoxy were discussed in combination with the theoretical calculations.

Selective cleavage enhanced by acetylating the side chain of lysine.

Selective cleavage is of great interest in mass spectrometry studies as it can help sequence identification by promoting simple fragmentation pattern of peptides and proteins. In this work, the collision-induced dissociation of peptides containing internal lysine and acetylated lysine residues were studied. The experimental and computational results revealed that multiple fragmentation pathways coexisted when the lysine residue was two amino acid residues away from N-terminal of the peptide.

Steady-state and time-resolved fluorescence of tetramethylrhodamine attached to DNA: correlation with DNA sequences.

Time-resolved fluorescence as well as steady-state absorption and fluorescence were detected in order to study the interactions between tetramethylrhodamine (TAMRA) and DNA when TAMRA was covalently labeled on single- and double-stranded oligonucleotides. Fluorescence intensity quenching and lifetime changes were characterized and correlated with different DNA sequences. The results demonstrated that the photoinduced electron transfer interaction between guanosine residues and TAMRA introduced a short lifetime fluorescence component when guanosine residues were at the TAMRA-attached terminal of the DNA sequences.

Vibrationally resolved LIF spectrum of tertiary methylcyclohexoxy radical.

Cyclohexoxy radical and its substitutes are intermediates of the combustion reaction in automobile engines, and hence play an important role in the atmospheric chemistry. Spectroscopic and conformational studies can provide convenient methods to monitor these species. In this work, we report the observation of the laser induced fluorescence (LIF) excitation spectrum of 1-methylcyclohexoxy, a tertiary ring alkoxy radical, in supersonic jet condition.

A LabVIEW-Based Virtual Instrument System for Laser-Induced Fluorescence Spectroscopy.

We report the design and operation of a Virtual Instrument (VI) system based on LabVIEW 2009 for laser-induced fluorescence experiments. This system achieves synchronous control of equipment and acquisition of real-time fluorescence data communicating with a single computer via GPIB, USB, RS232, and parallel ports. The reported VI system can also accomplish data display, saving, and analysis, and printing the results.

Conformation and spectroscopy study of cycloheptoxy radical.

Alkoxy radicals are important intermediates in the formation of tropospheric ozone. The spectroscopic identification and characterization of these species are important for understanding their chemistry in the atmosphere. In this work, we report the observation of the laser induced fluorescence (LIF) excitation spectrum of cycloheptoxy radical.

Selective cleavage of protonated penetratin and its substitutes under low-energy collision-induced dissociation condition.

An understanding of the dissociation of penetratin is important for improving its metabolic stability and cargo-delivery efficiency. In this study, we describe the selective cleavage of the K15-K16 amide bond of penetratin under the low-energy collision-induced dissociation condition in mass spectrometry. A variety of penetratin substitutes have been studied in which key basic amino acids have been substituted within the sequence.

Dissociation of protonated peptides containing adjacent arginines.

The dissociation of protonated peptides containing adjacent arginines has been studied by electrospray ionization-tandem mass spectrometry (ESI MS/MS) and theoretical calculations. The experimental results show that singly protonated peptides cleave at the Arg-Arg amide bond and generate the y(1) ion when adjacent arginines are the C-terminal residues. The major cleavage occurs at the C-terminal amide bond and produces the b(n-1) ion when adjacent arginines are not the C-terminal residues.

High resolution spectra and conformational analysis of 2-butoxy radical.

We have recorded five high resolution (200 MHz), rotationally resolved, vibrational bands of the B-X electronic transition of 2-butoxy. Two bands of the 2-butoxy spectrum have been rotationally analyzed and assigned to two different geometrical conformers of the molecule. The analyses allow the determination of the six experimental rotational constants defined by the geometry of the species in the ground (X) and excited (B) electronic states and also four spin-rotation constants for the X electronic state of the conformers.

Jet-cooled laser spectroscopy of the cyclohexoxy radical.

The laser-induced fluorescence and laser-excited dispersed fluorescence spectra of the cyclohexoxy radical has been observed under two sets of free-jet-cooling conditions, characterized by rotational temperatures of approximately 1 and 100 K. Although five conformers of cyclohexoxy are possible, it appears that all presently observed spectral bands can be accounted for by a single one. All cold spectral bands are assigned to the B-X electronic transition of the cyclohexoxy radical.