Slow photoelectron spectroscopy of δ-valerolactam and its dimer

Photoionization Dynamics and Proton Transfer within the Adenine-Thymine Nucleobase Pair

Studying the stability of hydrogen-bonded nucleobase pairs, at the heart of the genetic code, is of utmost importance for an in-depth understanding of basic mechanisms of life and biomolecular evolution. We present here a VUV single photon ionization dynamic study of the nucleobase pair adenine-thymine (AT), revealing its ionization and dissociative ionization thresholds via double imaging electron/ion coincidence spectroscopy. The experimental data, consisting of cluster mass-resolved threshold photoelectron spectra and photon energy-dependent ion kinetic energy release distributions, allow the unambiguous distinction of the dissociation of AT into protonated adenine AH⁺ and a dehydrogenated thymine radical T(-H) from dissociative ionization processes of other nucleobase clusters. Comparison to high-level ab initio calculations indicates that our experimental observations can be explained by a single hydrogen-bonded conformer present in our molecular beam and allows the estimation of an upper limit of the barrier of the proton transfer in the ionized AT pair.

Unimolecular decomposition of methyl ketene and its dimer in the gas phase: theory and experiment

We present a combined theoretical and experimental investigation on the single photoionization and dissociative photoionization of gas-phase methyl ketene (MKE) and its neutral dimer (MKE2). The performed experiments entail the recording of photoelectron photoion coincidence (PEPICO) spectra and slow photoelectron spectra (SPES) in the energy regime 8.7-15.5 eV using linearly polarized synchrotron radiation. We observe both dimerization and trimerization of the monomer which brings about significantly complex and abstruse dissociative ionization patterns. These require the implementation of theoretical calculations to explore the potential energy surfaces of the monomer and dimer's neutral and ionized geometries. To this end, explicitly correlated quantum chemical methodologies involving the coupled cluster with single, double and perturbative triple excitations (R)CCSD(T)-F12 method, are utilized. An improvement in the adiabatic ionization energy of MKE is presented (AIE = 8.937 ± 0.020 eV) as well as appearance energies for multiple fragments formed through dissociative ionization of either the MKE monomer or dimer. In this regard, the synergy of experiment and theory is crucial to interpreting the obtained results. We discuss the potential astrochemical implications of this work in the context of recent advances in the field of astrochemistry and speculate on the potential presence and eventual fate of interstellar MKE molecules.

Hydrogel Microparticles Functionalized with Engineered Escherichia coli as Living Lactam Biosensors

Recently there has been an increasing need for synthesizing valued chemicals through biorefineries. Lactams are an essential family of commodity chemicals widely used in the nylon industry with annual production of millions of tons. The bio-production of lactams can substantially benefit from high-throughput lactam sensing strategies for lactam producer screening. We present here a robust and living lactam biosensor that is directly compatible with high-throughput analytical means. The biosensor is a hydrogel microparticle encapsulating living microcolonies of engineered lactam-responsive Escherichia coli. The microparticles feature facile and ultra-high throughput manufacturing of up to 10,000,000 per hour through droplet microfluidics. We show that the biosensors can specifically detect major lactam species in a dose-dependent manner, which can be quantified using flow cytometry. The biosensor could potentially be used for high-throughput metabolic engineering of lactam biosynthesis.

Revisiting the spectroscopy of xanthine derivatives: theobromine and theophylline

We explore the influence of the relative position of the methyl substituent on the photophysics of theophylline and theobromine, two molecules that are structurally related to the DNA bases. Using a combination of spectroscopic techniques and quantum mechanical calculations, we show that moving the methyl group from N1 in theophylline to N7 in theobromine causes significant differences in their excited state properties, i.e., it produces pyramidalization of N7 in the excited state of the latter. Paradoxically, this modification seems to have little effect on the structural properties of the cation and the ionization process. It is suggested that similar effects may exist in the excited state properties of DNA bases.

Advances in spectroscopy and dynamics of small and medium sized molecules and clusters

Investigations of the spectroscopy and dynamics of small- and medium-sized molecules and clusters represent a hot topic in atmospheric chemistry, biology, physics, atto- and femto-chemistry and astrophysics.

Electronic, structural and vibrational induced effects upon ionization of 2-quinolinone

Using first principle methodologies, we characterize the lowest electronic states of 2-quinolinone(+) cation. The ground state of this ion is of X˜(2)A(″) nature. We deduce the adiabatic ionization energy of 2-quinolinone to be equal 8.249eV using the explicitly correlated coupled cluster level and where zero point vibrational energy, core-valence and scalar relativistic effects are taken into account. We examine also the ionization induced structural changes and vibrational shifts and analyze the electron density differences between the neutral and ionic species. These data show that the formation of 2-quinolinone(+)X˜(2)A(″) from 2-quinolinone affects strongly the HNCO group, whereas the carbon skeletal is perturbed when the upper electronic cationic states are populated. The comparison to 2-pyridone allows the elucidation of the effect of benzene ring fused with this heterocyclic ring. Since quinolones and pyridones are both model systems of DNA bases, these findings might help in understanding the charge redistribution in these biological entities upon ionization.

Vibrationally resolved photoelectron spectroscopy of electronic excited states of DNA bases: application to the ã state of thymine cation

For fully understanding the light-molecule interaction dynamics at short time scales, recent theoretical and experimental studies proved the importance of accurate characterizations not only of the ground (D0) but also of the electronic excited states (e.g., D1) of molecules. While ground state investigations are currently straightforward, those of electronic excited states are not. Here, we characterized the à electronic state of ionic thymine (T(+)) DNA base using explicitly correlated coupled cluster ab initio methods and state-of-the-art synchrotron-based electron/ion coincidence techniques. The experimental spectrum is composed of rich and long vibrational progressions corresponding to the population of the low frequency modes of T(+)(Ã). This work challenges previous numerous works carried out on DNA bases using common synchrotron and VUV-based photoelectron spectroscopies. We provide hence a powerful theoretical and experimental framework to study the electronic structure of ionized DNA bases that could be generalized to other medium-sized biologically relevant systems.

Identification of 2-piperidone as a biomarker of CYP2E1 activity through metabolomic phenotyping

Cytochrome P450 2E1 (CYP2E1) is a key enzyme in the metabolic activation of many low molecular weight toxicants and also an important contributor to oxidative stress. A noninvasive method to monitor CYP2E1 activity in vivo would be of great value for studying the role of CYP2E1 in chemical-induced toxicities and stress-related diseases. In this study, a mass spectrometry-based metabolomic approach was used to identify a metabolite biomarker of CYP2E1 through comparing the urine metabolomes of wild-type (WT), Cyp2e1-null, and CYP2E1-humanized mice. Metabolomic analysis with multivariate models of urine metabolites revealed a clear separation of Cyp2e1-null mice from WT and CYP2E1-humanized mice in the multivariate models of urine metabolomes. Subsequently, 2-piperidone was identified as a urinary metabolite that inversely correlated to the CYP2E1 activity in the three mouse lines. Backcrossing of WT and Cyp2e1-null mice, together with targeted analysis of 2-piperidone in mouse serum, confirmed the genotype dependency of 2-piperidone. The accumulation of 2-piperidone in the Cyp2e1-null mice was mainly caused by the changes in the biosynthesis and degradation of 2-piperidone because compared with the WT mice, the conversion of cadaverine to 2-piperidone was higher, whereas the metabolism of 2-piperidone to 6-hydroxy-2-piperidone was lower in the Cyp2e1-null mice. Overall, untargeted metabolomic analysis identified a correlation between 2-piperidone concentrations in urine and the expression and activity of CYP2E1, thus providing a noninvasive metabolite biomarker that can be potentially used in to monitor CYP2E1 activity.

State-selected unimolecular decomposition of δ-valerolactam+ and δ-valerolactam2+ cations: theory and experiment

The near threshold photofragmentation pattern of δ-valerolactam(+) and δ-valerolactam(2)(+) has been recorded combining electron/ion coincidence techniques and vacuum ultraviolet synchrotron radiation. The experimental method yields the fragment intensity as a function of the internal energy deposited into the parent cation, up to 3.1 eV above the first ionization threshold. In parallel, ab initio studies on the δ-valerolactam(+) and δ-valerolactam(2)(+) cations and their ionic and neutral fragmentation products have been performed with the aim of determining the isomers of the ionic products observed experimentally as well as of their neutral counterparts. These computations were performed using the PBE0 exchange-correlation functional and the aug-cc-pVDZ basis set. We found good agreement between the calculated reaction enthalpies and experimental appearance energies of the ions. More generally, our experimental and theoretical results reveal that the fragmentation of the ionic species of interest leads to a multitude of neutral and ionic fragments, which may be formed after intramolecular isomerization and complex decomposition processes. Multistep reaction pathways are expected.

A new double imaging velocity focusing coincidence experiment: i2PEPICO

The vacuum ultraviolet (VUV) beamline of the Swiss Light Source has been upgraded after two years of operation. A new, turntable-type monochromator was constructed at the Paul Scherrer Institut, which allows for fast yaw-alignment as well as quick grating change and exchange. In addition to the original imaging photoelectron photoion coincidence endstation (iPEPICO), a second, complementary double imaging setup (i(2)PEPICO) has been built. Volatile samples can be introduced at room temperature or in a molecular beam, a pyrolysis source allows for radical production, and non-volatile solids can be evaporated in a heated cell. Monochromatic VUV radiation ionizes the sample and both photoelectrons and photoions are velocity map imaged onto two fast position sensitive detectors and detected in delayed coincidence. High intensity synchrotron radiation leads to ionization rates above 10(5) s(-1). New data acquisition and processing approaches are discussed for recording coincidence processes at high rates. The setup is capable of resolving pulsed molecular beam profiles and the synchrotron time structure temporally. The latter is shown by photoelectron autocorrelation, which displays both the 1.04 MHz ring clock frequency as well as resolving the micro-pulses with a separation of 2 ns. Kinetic energy release analysis on the dissociative photoionization of CF(4) indicates a dissociation mechanism change in the Franck-Condon allowed energy range of the first ion state.