Unveiling the complex vibronic structure of the canonical adenine cation

Accurate Prediction of Adiabatic Ionization Energies for PAHs and Substituted Analogues

The accurate calculation of adiabatic ionization energies (AIEs) for polycyclic aromatic hydrocarbons (PAHs) and their substituted analogues is essential for understanding their electronic properties, reactivity, stability, and environmental/health implications. This study demonstrates that the M06-2X density functional theory method excels in predicting the AIEs of polycyclic aromatic hydrocarbons and related molecules, rivaling the (R)CCSD(T)-F12 method in terms of accuracy. These findings suggest that M06-2X, coupled with an appropriate basis set, represents a reliable and efficient method for studying polycyclic aromatic hydrocarbons and related molecules, aligning well with the experimental techniques. The set of molecules examined in this work encompasses numerous polycyclic aromatic hydrocarbons from m/z 67 up to m/z 1,176, containing heteroatoms that may be found in biofuels or nucleic acid bases, making the results highly relevant for photoionization experiments and mass spectrometry. For coronene-derivative molecular species with the C6n2H6n chemical formula, we give an expression to predict their AIEs (AIE (n) = 4.359 + 4.8743n-0.72057, in eV) upon extending the π-aromatic cloud until reaching graphene. In the long term, the application of this method is anticipated to contribute to a deeper understanding of the relationships between PAHs and graphene, guiding research in materials science and electronic applications and serving as a valuable tool for validating theoretical calculation methods.

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.

Process study of ceramic membrane-coupled mixed-cell fermentation for the production of adenine

In order to solve the problems of high complexity, many by-products, high pollution and difficult extraction of the existing adenine production process, in this study, ceramic membrane-coupled mixed cell fermentation was used to produce adenine while reducing the synthesis of by-products and simplifying the production process of adenine. Nucleoside hydrolase (encoded by the rihC gene) was used to produce adenine by coordinated fermentation with the adenosine-producing bacterium Bacillus Subtilis XGL. The adenosine hydrolase (AdHy)-expressing strain Escherichia coli BL21-AdHy was successfully employed and the highest activity of the crude enzyme solution was found by orthogonal experiments at 170 W power, 42% duty cycle, and 8 min of sonication. The highest AdHy activity was found after 18 h of induction incubation. E. coli BL21-AdHy was induced for 18 h and sonicated under the above ultrasonic conditions and the resulting crude enzyme solution was used for co-fermentation of the strain and enzyme. Moreover, 15% (v/v) of the AdHy crude enzyme solution was added to fermentation of B. subtilis XGL after 35 h. Finally, the whole fermentation system was dialyzed using coupled ceramic membranes for 45 and 75 h, followed by the addition of fresh medium. In contrast, the AdHy crude enzyme solution was added after 35, 65, and 90 h of B. subtilis fermentation, with three additions of 15, 15, and 10% of the B. subtilis XGL fermentation system. The process was validated in a 5 L fermenter and 14 ± 0.25 g/L of adenine was obtained, with no accumulation of adenosine and d-ribose as by-products. The enzymatic activity of the AdHy crude solution treated with ultrasound was greatly improved. It also reduced the cellular activity of E. coli BL21-AdHy and reduced effects on bacterial co-fermentation. Membrane-coupled dialysis solved the problem of decreased yield due to poor bacterial survival and decreased viability, and eliminated inhibition of the product synthesis pathway by adenosine. The batch addition of crude enzyme broth allowed the continuous conversion of adenosine to adenine. This production method provides the highest yield of biologically produced adenine reported to date, reduces the cost of adenine production, and has positive implications for the industrial production of adenine by fermentation. And it provides a reference for producing other high-value-added products made by fermentation.

Accounting for molecular flexibility in photoionization: case of tert-butyl hydroperoxide

tert-Butyl hydroperoxide (tBuOOH) is a common intermediate in the oxidation of organic compounds that needs to be accurately quantified in complex gas mixtures for the development of chemical kinetic models of low temperature combustion. This work presents a combined theoretical and experimental investigation on the synchrotron-based VUV single photon ionization of gas-phase tBuOOH in the 9.0 - 11.0 eV energy range, including dissociative ionization processes. Computations consist of the determination of the structures, vibrational frequencies and the energetics of neutral and ionic tBuOOH. The Franck-Condon spectrum for the tBuOOH⁺ (X⁺) + e^- ← tBuOOH (X) + hν transition is computed, where special treatment is undertaken because of the flexibility of tBuOOH, in particular regarding the OOH group. Through comparison of the experimental mass-selected threshold photoelectron spectra with explicitly correlated coupled cluster calculations and Franck-Condon simulations that account for the flexibility of the molecule, an estimation of the ionization energy is given. The appearance energy of the only fragment observed within the above-mentioned energy range, identified as the tert-butyl C₄H₉⁺, is also reported. Finally, the signal branching ratio between the parent and the fragment ions is provided as a function of photon energy, essential to quantify tBuOOH in gas-phase oxidation/combustion experiments via advanced mass spectrometry techniques.

Threshold photoelectron spectroscopy of 9-methyladenine: theory and experiment

We present a combined experimental and theoretical study of single-photon ionization of 9-methyladenine (9MA) in the gas phase. In addition to tautomerism, several rotamers due to the rotation of the methyl group may exist. Computations show, however, that solely one rotamer contributes because of low population in the molecular beam and/or unfavorable Franck-Condon factors upon ionization. Experimentally, we used VUV radiation available at the DESIRS beamline of the synchrotron radiation facility SOLEIL to record the threshold photoelectron spectrum of this molecule between 8 and 11 eV. This spectrum consists of a well-resolved band assigned mainly to vibronic levels of the D₀ cationic state, plus a contribution from the D₁ state, and two large bands corresponding to the D₁, D₂ and D₃ electronically excited states. The adiabatic ionization energy of 9MA is measured at 8.097 ± 0.005 eV in close agreement with the computed value using the explicitly correlated coupled cluster approach including core valence, scalar relativistic and zero-point vibrational energy corrections. This work sheds light on the complex pattern of the lowest doublet electronic states of 9MA⁺. The comparison to canonical adenine reveals that methylation induces further electronic structure complication that may be important to understand the effects of ionizing radiation and the charge distribution in these biological entities at different time scales.

UVPD spectroscopy of differential mobility-selected prototropic isomers of protonated adenine

Two prototropic isomers of adenine are formed in an electrospray ion source and are resolved spatially in a differential mobility spectrometer before detection in a triple quadrupole mass spectrometer. Each isomer is gated in CV space before being trapped in the linear ion trap of the modified mass spectrometer, where they are irradiated by the tuneable output of an optical parametric oscillator and undergo photodissociation to form charged fragments with m/z 119, 109, and 94. The photon-normalised intensity of each fragmentation channel is measured and the action spectra for each DMS-gated tautomer are obtained. Our analysis of the action spectra, aided by calculated vibronic spectra and thermochemical data, allow us to assign the two signals in our measured ionograms to specific tautomers of protonated adenine.

Isomer-sensitive characterization of low temperature oxidation reaction products by coupling a jet-stirred reactor to an electron/ion coincidence spectrometer: case of n-pentane

Using a tunable vacuum ultraviolet synchrotron beam line and first principle computations, a jet-stirred reactor was coupled for the first time to a photoionization mass spectrometer using electron/ion coincidence imaging.

Energetics and ionization dynamics of two diarylketone molecules: benzophenone and fluorenone

Single photon ionization and subsequent unimolecular ion decomposition were studied on jet-cooled benzophenone and fluorenone separately, using VUV synchrotron radiation in a photoion/photoelectron coincidence setup. Slow PhotoElectron Spectra (SPES) were recorded in coincidence with either the parent or the fragment ions for hν < 12.5 eV. Dissociative ionization is observed for benzophenone only. The full interpretation of the measurements, including the identification of the neutral and ionic species when dissociative ionization is at play, benefits from high level ab initio computations for determining the equilibrium structures and the energetics of the neutral and ionized molecules and of their fragments. Electronically excited states of the parent molecular ions were calculated also. From this analysis, an accurate experimental determination of the energetics of the benzophenone and fluorenone ions and of their fragmentation channels is available: adiabatic ionization energies of benzophenone at 8.923 ± 0.005 eV and of fluorenone at 8.356 ± 0.007 eV; and appearance energies of benzophenone fragment ions at 11.04 ± 0.02 eV (loss of C₆H₅), 11.28 ± 0.02 eV (loss of H) and 11.45 ± 0.02 eV (loss of CO). The corresponding fragmentation mechanisms are explored, showing likely concerted bonds rearrangement. Possible pre-ionizing fragmentation is discussed in light of the spectra presented. The structural rigidity of fluorenone diarylketone seems to be the origin of the inhibition of the fragmentation of its cation.

State-Dependent Fragmentation of Protonated Uracil and Uridine

Action spectroscopy using photon excitation in the VUV range (photon energy 4.5-9 eV) was performed on protonated uracil (UraH⁺) and uridine (UrdH⁺). The precursor ions with m/ z 113 and m/ z 245, respectively, were produced by an electrospray ionization source and accumulated inside a quadrupole ion trap mass spectrometer. After irradiation with tunable synchrotron radiation, product ion mass spectra were obtained. Fragment yields as a function of excitation energy show several maxima that can be attributed to the photoexcitation into different electronic states. For uracil, vertically excited states were calculated using the equation-of-motion coupled cluster approach and compared to the observed maxima. This allows to establish correlations between electronic states and the resulting fragment masses and can thus help to disentangle the complex de-excitation and fragmentation pathways of nucleic acid building blocks. Photofragmentation of the nucleoside uridine shows a significantly lower variety of fragments, indicating stabilization of the nucleobase by the attached sugar.

Single photon ionization of methyl isocyanide and the subsequent unimolecular decomposition of its cation: experiment and theory

Methyl isocyanide, CH₃NC, is a key compound in astrochemistry and astrobiology.