Recent synthetic strategies for the functionalization of fused bicyclic heteroaromatics using organo-Li, -Mg and -Zn reagents.

This review highlights the use of functionalized organo-Li, -Mg and -Zn reagents for the construction and selective functionalization of 5- and 6-membered fused bicyclic heteroaromatics. Special attention is given to the discussion of advanced syntheses for the preparation of highly functionalized heteroaromatic scaffolds, including quinolines, naphthyridines, indoles, benzofurans, benzothiophenes, benzoxazoles, benzothiazoles, benzopyrimidines, anthranils, thienothiophenes, purine coumarins, chromones, quinolones and phthalazines and their fused heterocyclic derivatives. The organometallic reagents used for the desired functionalizations of these scaffolds are generally prepared in situ using the following methods: (i) through directed selective metalation reactions (DoM), (ii) by means of halogen/metal exchange reactions, (iii) through oxidative metal insertions (Li, Mg, Zn), and (iv) by transmetalation reactions (organo-Li and Mg transmetalations with ZnCl2 or ZnO(Piv)2). The resulting reactive organometallic reagents allow a wide range of C-C, C-N and C-X cross-coupling reactions with different electrophiles, employing in particular Kumada or Negishi protocols among other transition metal (Pd, Ni, Co, Cu, Cr, Fe, etc.)-catalyzed processes. In addition, key developments concerning selective metalation techniques will be presented, which rely on the use of RLi, LDA and TMP metal bases. These methods are now widely employed in organic synthetic chemistry and have proven to be particularly valuable for drug development programs in the pharmaceutical industry. New and improved protocols have resulted in many Li, Mg and Zn organyls now being compatible with functionalized aryl, heteroaryl, alkenyl, alkynyl and alkyl compounds even in the presence of labile functional groups, making these reagents well-suited for C(sp2)-C(sp2), C(sp2)-C(sp) and C(sp2)-C(sp3) cross-coupling reactions with fused heteroaryl halides. In addition, the use of some transition metal-catalyzed processes occasionally allows a reversed role of the reactants in cross-coupling reactions, providing alternative synthetic routes for the preparation of fused heteroaromatic-based bioactive drugs and natural products. In line with this, this article points to novel methods for the functionalization of bicyclic heteroaromatic scaffolds by organometallic reagents that have been published in the period 2010-2023.

Time-Resolved X-ray Photoelectron Spectroscopy: Ultrafast Dynamics in CS2 Probed at the S 2p Edge.

Recent developments in X-ray free-electron lasers have enabled a novel site-selective probe of coupled nuclear and electronic dynamics in photoexcited molecules, time-resolved X-ray photoelectron spectroscopy (TRXPS). We present results from a joint experimental and theoretical TRXPS study of the well-characterized ultraviolet photodissociation of CS2, a prototypical system for understanding non-adiabatic dynamics. These results demonstrate that the sulfur 2p binding energy is sensitive to changes in the nuclear structure following photoexcitation, which ultimately leads to dissociation into CS and S photoproducts. We are able to assign the main X-ray spectroscopic features to the CS and S products via comparison to a first-principles determination of the TRXPS based on ab initio multiple-spawning simulations. Our results demonstrate the use of TRXPS as a local probe of complex ultrafast photodissociation dynamics involving multimodal vibrational coupling, nonradiative transitions between electronic states, and multiple final product channels.

Core spectroscopy of oxazole.

We have measured, analyzed, and simulated the ground state valence photoelectron spectrum, x-ray absorption (XA) spectrum, x-ray photoelectron (XP) spectrum as well as normal and resonant Auger-Meitner electron (AE) spectrum of oxazole at the carbon, oxygen, and nitrogen K-edge in order to understand its electronic structure. Experimental data are compared to theoretical calculations performed at the coupled cluster, restricted active space perturbation theory to second-order and time-dependent density functional levels of theory. We demonstrate (1) that both N and O K-edge XA spectra are sensitive to the amount of dynamical electron correlation included in the theoretical description and (2) that for a complete description of XP spectra, additional orbital correlation and orbital relaxation effects need to be considered. The normal AE spectra are dominated by a singlet excitation channel and well described by theory. The resonant AE spectra, however, are more complicated. While the participator decay channels, dominating at higher kinetic energies, are well described by coupled cluster theory, spectator channels can only be described satisfactorily using a method that combines restricted active space perturbation theory to second order for the bound part and a one-center approximation for the continuum.

Lanmodulin peptides - unravelling the binding of the EF-Hand loop sequences stripped from the structural corset.

Lanmodulin (LanM), a naturally lanthanide (Ln)-binding protein with a remarkable selectivity for Lns over Ca(ii) and affinities in the picomolar range, is an attractive target to address challenges in Ln separation. Why LanM has such a high selectivity is currently not entirely understood; both specific amino acid sequences of the EF-Hand loops and cooperativity effects have been suggested. Here, we removed the effect of cooperativity and synthesised all four 12-amino acid EF-Hand loop peptides, and investigated their affinity for two Lns (Eu(iii) and Tb(iii)), the actinide Cm(iii) and Ca(ii). Using isothermal titration calorimetry and time-resolved laser fluorescence spectroscopy (TRLFS) combined with parallel factor analysis, we show that the four short peptides behave very similarly, having affinities in the micromolar range for Eu(iii) and Tb(iii). Ca(ii) was shown not to bind to the peptides, which was verified with circular dichroism spectroscopy. This technique also revealed an increase in structural organisation upon Eu(iii) addition, which was supported by molecular dynamics simulations. Lastly, we put Eu(iii) and Cm(iii) in direct competition using TRLFS. Remarkably, a slightly higher affinity for Cm(iii) was found. Our results demonstrate that the picomolar affinities in LanM are largely an effect of pre-structuring and therefore a reduction of flexibility in combination with cooperative effects, and that all EF-Hand loops possess similar affinities when detached from the protein backbone, albeit still retaining the high selectivity for lanthanides and actinides over calcium.

Transforming Chemical Proteomics Enrichment into a High-Throughput Method Using an SP2E Workflow.

Protein post-translational modifications (PTMs) play a critical role in the regulation of protein catalytic activity, localization, and protein-protein interactions. Attachment of PTMs onto proteins significantly diversifies their structure and function, resulting in proteoforms. However, the sole identification of post-translationally modified proteins, which are often cell type and disease-specific, is still a highly challenging task. Substoichiometric amounts and modifications of low abundant proteins necessitate the purification or enrichment of the modified proteins. Although the introduction of mass spectrometry-based chemical proteomic strategies has enabled the screening of protein PTMs with increased throughput, sample preparation remains highly time-consuming and tedious. Here, we report an optimized workflow for the enrichment of PTM proteins in a 96-well plate format, which could be extended to robotic automation. This platform allows us to significantly lower the input of total protein, which opens up the opportunity to screen specialized and difficult-to-culture cell lines in a high-throughput manner. The presented SP2E protocol is robust and time- and cost-effective, as well as suitable for large-scale screening of proteoforms. The application of the SP2E protocol will thus enable the characterization of proteoforms in various processes such as neurodevelopment, neurodegeneration, and cancer. This may contribute to an overall acceleration of the recently launched Human Proteoform Project.

Photodissociation of the trichloromethyl radical: photofragment imaging and femtosecond photoelectron spectroscopy.

Halogen-containing radicals play a key role in catalytic reactions leading to stratospheric ozone destruction, thus their photochemistry is of considerable interest. Here we investigate the photodissociation dynamics of the trichloromethyl radical, CCl3 after excitation in the ultraviolet. While the primary processes directly after light absorption are followed by femtosecond-time resolved photoionisation and photoelectron spectroscopy, the reaction products are monitored by photofragment imaging using nanosecond-lasers. The dominant reaction is loss of a Cl atom, associated with a CCl2 fragment. However, the detection of Cl atoms is of limited value, because in the pyrolysis CCl2 is formed as a side product, which in turn dissociates to CCl + Cl. We therefore additionally monitored the molecular fragments CCl2 and CCl by photoionisation at 118.2 nm and disentangled the contributions from various processes. A comparison of the CCl images with control experiments on CCl2 suggest that the dissociation to CCl + Cl2 contributes to the photochemistry of CCl3.

Vacuum Ultraviolet Excited State Dynamics of the Smallest Ketone: Acetone.

We combined tunable vacuum-ultraviolet time-resolved photoelectron spectroscopy (VUV-TRPES) with high-level quantum dynamics simulations to disentangle multistate Rydberg-valence dynamics in acetone. A femtosecond 8.09 eV pump pulse was tuned to the sharp origin of the A1(n3dyz) band. The ensuing dynamics were tracked with a femtosecond 6.18 eV probe pulse, permitting TRPES of multiple excited Rydberg and valence states. Quantum dynamics simulations reveal coherent multistate Rydberg-valence dynamics, precluding simple kinetic modeling of the TRPES spectrum. Unambiguous assignment of all involved Rydberg states was enabled via the simulation of their photoelectron spectra. The A1(ππ*) state, although strongly participating, is likely undetectable with probe photon energies ≤8 eV and a key intermediate, the A2(nπ*) state, is detected here for the first time. Our dynamics modeling rationalizes the temporal behavior of all photoelectron transients, allowing us to propose a mechanism for VUV-excited dynamics in acetone which confers a key role to the A2(nπ*) state.

Directing excited state dynamics via chemical substitution: A systematic study of π-donors and π-acceptors at a carbon-carbon double bond.

Functional group substituents are a ubiquitous tool in ground-state organic chemistry often employed to fine-tune chemical properties and obtain desired chemical reaction outcomes. Their effect on photoexcited electronic states, however, remains poorly understood. To help build an intuition for these effects, we have studied ethylene, substituted with electron acceptor (cyano) and/or electron donor (methoxy) substituents, both theoretically and experimentally: using ab initio quantum molecular dynamics and time-resolved photoelectron spectroscopy. Our results show the consistent trend that photo-induced ethylenic dynamics is primarily localized to the carbon with the greater electron density. For doubly substituted ethylenes, the trend is additive when both substituents are located on opposite carbons, whereas the methoxy group (in concert with steric effects) dominates when both substituents are located on a single carbon atom. These results point to the development of rules for structure-dynamics correlations; in this case, a novel mechanistic ultrafast photochemistry for conjugated carbon chains employing long-established chemical concepts.

VUV excited-state dynamics of cyclic ethers as a function of ring size.

The vacuum ultraviolet (VUV) absorption spectra of cyclic ethers consist primarily of Rydberg ← n transitions. By studying three cyclic ethers of varying ring size (tetrahydropyran, tetrahydrofuran and trimethylene oxide, n = 6-4), we investigated the influence of ring size on the VUV excited-state dynamics of the 3d Rydberg manifold using time-resolved photoelectron spectroscopy (TRPES), time-resolved mass spectroscopy (TRMS) and ab initio electronic structure calculations. Whereas neither the electronic characters nor the term energies of the excited-states are substantially modified when the ring-size is reduced from n = 6 to 5 to 4, the excited-state lifetimes concomitantly decrease five-fold. TRPES and TRMS allow us to attribute the observed dynamics to a Rydberg cascade from the initially excited d-Rydberg manifold via the p-Rydberg manifold to the s-Rydberg state. Cuts through potential energy surfaces along the C-O bond reveal that a nσ* state crossing brings the s-Rydberg state along a path to the ring-opened ground state. The observed difference in excited-state lifetimes is attributed to an increasing slope along the repulsive C-O bond coordinate as ring size decreases.

Vacuum-Ultraviolet Absorption Spectrum of 3-Methoxyacrylonitrile.

The high-resolution absorption spectrum of 3-methoxyacrylonitrile (3MAN) was measured between 5.27 and 12.59 eV using a synchrotron-based Fourier-transform spectrometer. It was related to an absolute absorption cross-section scale. Complementary calculations at the DFT-MRCI/aug-cc-pVTZ level of theory document the vertical transition energies and oscillator strengths toward the first 19 states of both the E and Z geometrical isomers of 3MAN. Comparisons with the experimental absorption spectrum reveal the similarities and differences between 3MAN, a bifunctional molecule, with acrylonitrile and methylvinylether, where only one functional group is present. As in acrylonitrile, several broad valence transitions were observed up to the ionization limit. They are likely associated with the extended π-system induced by the nitrile group but might also involve σσ* transitions close to the ionization limit. As in methylvinylether, Rydberg series converging to the ionization limit are absent. This is attributed to a difference in neutral and cationic geometry due to a 60° rotation of the methyl group.

High-resolution vacuum ultraviolet absorption spectra of 2,3- and 2,5-dihydrofuran.

Using a synchrotron-based Fourier-transform spectrometer, the high-resolution absorption spectra of the C1-symmetric 2,3-dihydrofuran (23DHF) and C2v-symmetric 2,5-dihydrofuran (25DHF) have been measured from 5.5 eV to 9.4 eV with an absolute absorption cross section scale. Oscillator strengths and vertical excitation energies of the lowest 18 states have been computed using the average of the second- and third-order algebraic diagrammatic construction polarization propagator method and the equation-of-motion coupled-cluster method at the level of singles and doubles model. These show that the bright valence transitions of ππ*-character are embedded into Rydberg transitions, whose oscillator strengths are at least one order of magnitude lower. To account for intensity borrowing, the first broad valence transition between 5.5 eV and 6.8 eV was simulated using a nuclear ensemble, and the agreement between experiment and theory is excellent. Whereas 23DHF only exhibits one broad valence transition followed by d/f Rydberg series converging to the ionization energy, the absorption spectrum of 25DHF has four bands, attributed to a valence nπσ → π*-transition, nπσ → 3px,z/3dxz transitions, a second valence nπ → π*-transition followed by d/f Rydberg series converging to the ionization energy, respectively. All Rydberg series converging to the ionization energy have been characterized in terms of their quantum defects.

Threshold photoelectron spectroscopy of the HO2 radical.

We report a synchrotron radiation vacuum ultraviolet photoionization study of the hydroperoxyl radical (HO2), a key reaction intermediate in combustion and atmospheric chemistry as well as astrochemistry, using double imaging photoelectron photoion coincidence spectroscopy. The HO2 radical is formed in a microwave discharge flow tube reactor through a set of reactions initiated by F atoms in a CH4/O2/He gas mixture. The high-resolution threshold photoelectron spectrum of HO2 in the 11 eV-12 eV energy range is acquired without interferences from other species and assigned with the aid of theoretically calculated adiabatic ionization energies (AIEs) and Franck-Condon factors. The three vibrational modes of the radical cation HO2 +, the H-O stretch, the H-O-O bend, and the O-O stretch, have been identified, and their individual frequencies are measured. In addition, the AIEs of the X3A″ ground state and the a1A' first excited electronic state of HO2 + are experimentally determined at 11.359 ± 0.003 eV and 11.639 ± 0.005 eV, respectively, in agreement with high-level theoretically computed results. Furthermore, the former AIE value provides validation of thermochemical networks used to extract the enthalpy of formation of the HO2 radical.

A set of rhamnosylation-specific antibodies enables detection of novel protein glycosylations in bacteria.

Despite its potential importance for bacterial virulence, protein rhamnosylation has not yet been sufficiently studied. Specific anti-SerRha, anti-ThrRha and anti-AsnRha antibodies allowed the identification of previously unknown monorhamnosylated proteins in cytosol and membrane fractions of bacterial cell lysates. Mapping of the complete rhamnoproteome in pathogens should facilitate development of targeted therapies against bacterial infections.

Folding and Unfolding of the Short Light-Triggered ß-Hairpin Peptide AzoChignolin Occurs within 100 ns.

To map the underlying molecular mechanisms of folding dynamics in proteins, light-operated peptides have emerged as promising tools. In this study, we reveal the complete sequence of light-induced structural changes of AzoChignolin, a short ß-hairpin peptide containing an azobenzene photoswitch in its loop region. Light-triggered structural changes were monitored by time-resolved IR spectroscopy. Formation and destruction of the hairpin structure is very fast and occurs within 100 ns for AzoChignolin in methanol. Atomistic molecular dynamics simulations using two explicit solvents, methanol and water, revealed the underlying molecular processes and allowed us to gain further insight into the reaction mechanism. Despite its rapid reaction time, hairpin formation in these solvents is not force-driven by the molecular switch but proceeded via formation of interstrand hydrogen bonds and contacts between aromatic residues. Moreover, the combined experimental and theoretical study demonstrates that the solvent (methanol vs water) does not dictate the velocity of ß-hairpin formation in the AzoChignolin peptide comprising only a few hydrophobic residues in the strands.

Optical Control of Cytokine Production Using Photoswitchable Galactosylceramides.

α-Galactosylceramides are glycosphingolipids that show promise in cancer immunotherapy. After presentation by CD1d, they activate natural killer T cells (NKT), which results in the production of a variety of pro-inflammatory and immunomodulatory cytokines. Herein, we report the synthesis and biological evaluation of photochromic derivatives of KRN-7000, the activity of which can be modulated with light. Based on established structure-activity relationships, we designed photoswitchable analogues of this glycolipid that control the production of pro-inflammatory cytokines, such as IFN-γ. The azobenzene derivative α-GalACer-4 proved to be more potent than KRN-7000 itself when activated with 370 nm light. Photolipids of this type could improve our mechanistic understanding of cytokine production and could open new directions in photoimmunotherapy.

Exploring the Excited-State Dynamics of Hydrocarbon Radicals, Biradicals, and Carbenes Using Time-Resolved Photoelectron Spectroscopy and Field-Induced Surface Hopping Simulations.

Reactive hydrocarbon molecules like radicals, biradicals, and carbenes are not only key players in combustion processes and interstellar and atmospheric chemistry but also important intermediates in organic synthesis. These systems typically possess many low-lying, strongly coupled electronic states. After light absorption, this leads to rich photodynamics characterized by a complex interplay of nuclear and electronic motion, which is still not comprehensively understood and not easy to investigate both experimentally and theoretically. In order to elucidate trends and contribute to a more general understanding, we here review our recent work on excited-state dynamics of open-shell hydrocarbon species using time-resolved photoelectron spectroscopy and field-induced surface hopping simulations and report new results on the excited-state dynamics of the tropyl and the 1-methylallyl radical. The different dynamics are compared, and the difficulties and future directions of time-resolved photoelectron spectroscopy and excited-state dynamics simulations of open-shell hydrocarbon molecules are discussed.