Probing the interaction between solid benzene and water using vacuum ultraviolet and infrared spectroscopy

We present results of a combined vacuum ultravioloet (VUV) and infrared (IR) photoabsorption study of amorphous benzene:water mixtures and layers to investigate the benzene-water interaction in the solid phase. UV spectra of 1:1, 1:10 and 1:100 benzene:water mixtures at 24 K reveal a concentration dependent shift in the energies of the 1B2u, 1B1u and 1E1u electronic states of benzene. All the electronic bands blueshift from pure amorphous benzene towards gas phase energies with increasing water concentration. IR results reveal a strong dOH-π benzene-water interaction via the dangling OH stretch of water with the delocalised π system of the benzene molecule. Although this interaction influences the electronic states of benzene with the benzenewater interaction causing a redshift in the electronic states from that of the free benzene molecule, the benzene-benzene interaction has a more significant effect on the electronic states of benzene. VUV spectra of benzene and water layers show evidence of non-wetting between benzene and water, characterised by Rayleigh scattering tails at wavelengths greater than 220 nm. Our results also show evidence of benzene-water interaction at the benzene-water interface affecting both the benzene and the water electronic states. Annealing the mixtures and layers of benzene and water show that benzene remains trapped within in/under water ice until water desorption near 160 K. These first systematic studies of binary amorphous mixtures in the VUV, supported with complementary IR studies, provide a deeper insight into the influence of intermolecular interactions on intramolecular electronic states with significant implications for our understanding of photochemical processes in more realistic astrochemical environments

Ionic strength and calcium regulate membrane interactions of myelin basic protein and the cytoplasmic domain of myelin protein zero

The formation of a mature myelin sheath in the vertebrate nervous system requires specific protein-membrane interactions. Several myelin-specific proteins are involved in stacking lipid membranes into multilayered structures around axons, and misregulation of these processes may contribute to chronic demyelinating diseases. Two key proteins in myelin membrane binding and stacking are the myelin basic protein (MBP) and protein zero (P0). Other factors, including Ca2+, are important for the regulation of myelination. We studied the effects of ionic strength and Ca2+ on the membrane interactions of MBP and the cytoplasmic domain of P0 (P0ct). MBP and P0ct bound and aggregated negatively charged lipid vesicles, while simultaneously folding, and both ionic strength and calcium had systematic effects on these interactions. When decreasing membrane net negative charge, the level and kinetics of vesicle aggregation were affected by both salt and Ca2+. The effects on lipid membrane surfaces by ions can directly affect myelin protein-membrane interactions, in addition to signalling effects in myelinating glia.publishedVersio

Graphene oxide layer-by-layer films for sensors and devices

Funding Information: Funding: The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007–2013) CALIPSO under grant agreement number 312284 and from the Portuguese funding agency FCT—Fundação para a Ciência e a Tecnologia—within projects UID/EEA/50014/2019, UID/FIS/00068/2019, PTDC/FIS-NAN/0909/2014, UID/FIS/00068/2019, the Bilateral Project entitled “Deteção de Estrogénio-um Contaminante Emergente em Corpos Hídricos” within the scope of “Cooperação Transnacional_FCT (Portugal)-CAPES (Brazil) 2018”.Layer-by-layer films of poly (allylamine hydrochloride) (PAH) and graphene oxide (GO) were characterized, looking at growth with the number of bilayers, morphology, and electrical properties. The PAH/GO films revealed a linear increase in absorbance with the increase in the number of deposited bilayers, allowing the determination that 10.7 ± 0.1 mg m−2 of GO is adsorbed per unit of area of each bilayer. GO absorption bands at 146, 210, 247 and 299 nm, assigned to π-π* and n-π* transitions in the aromatic ring (phenol) and of the carboxylic group, respectively, were characterized by vacuum ultraviolet spectroscopy. The morphological characterization of these films demonstrated that they are not completely uniform, with a bilayer thickness of 10.5 ± 0.7 nm. This study also revealed that the films are composed of GO and/or PAH/GO fibers and that GO is completely adsorbed on top of PAH. The electrical properties of the films reveal that PAH/GO films present a semiconductor behavior. In addition, a slight decrease in conduction was observed when films were prepared in the presence of visible light, likely due to the presence of oxygen and moisture that contributes to the damage of GO molecules.publishersversionpublishe

Systematic investigation of CO₂ : NH₃ ice mixtures using mid-IR and VUV spectroscopy – part 1: thermal processing

The adjustment of experimental parameters in interstellar ice analogues can have profound effects on molecular synthesis within an ice system. We demonstrated this by systematically investigating the stoichiometric mixing ratios of CO2 : NH3 ices as a function of thermal processing using mid-IR and VUV spectroscopy. We observed that the type of CO2 bonding environment was dependent on the different stoichiometric mixing ratios and that this pre-determined the NH3 crystallite structure after phase change. The thermal reactivity of the ices was linked to the different chemical and physical properties of the stoichiometric ratios. Our results provide new details into the chemical and physical properties of the different stoichiometric CO2 : NH3 ices enhancing our understanding of the thermally induced molecular synthesis within this ice system

The ground and ionic states of cyclohepta-1,3,5-triene and their relationship to norcaradiene states. New 1H and 13C NMR spectra, and analysis of a new experimental photoelectron spectrum by ab initio methods

The strong inter-relationship between cyclohepta-1,3,5-triene (CHT) and norcaradiene (NCD) observed in some reactions, has been extended to include the energy surfaces for some low-lying ionic states. Whilst equilibrium structures of 2A/ symmetry containing the CHT skeleton were routinely found, the structures emerging with 2A// symmetry were found to be NCD ionic states. Surface studies, by variation of the C1 to C6 distance, showed minima for both state symmetries. Curve crossing which occurs in CS symmetry, is avoided by distortion to C1 symmetry. The CHT → NCD structural change is attributed to initial conrotatory closure of the singly occupied molecular orbital. A new synchrotron-based study of the photoelectron spectrum (PES) for CHT up to 25 eV shows little vibrational structure. We have assigned the overall PES up to 17 eV in considerable detail, using a variety of theoretical methods. The vertical ionization energy (VIE) sequence in the PES for CHT ions, is predicted to be: 12A/ < 12A// < 22A/ < 22A//. The calculated lowest ionic state, with lowest vibrational frequency 87 cm-1, leads to a high density of vibrational states. The Franck-Condon (FC) envelopes of the two lowest PES bands have been analysed. The identity of the PES spectrum, as derived from CHT rather than NCD, was demonstrated by 1H and 13C nuclear magnetic resonance (NMR) spectra of the sample; this agrees with the predicted PES spectra of CHT and NCD. The NCD predicted spectrum shows significant differences from CHT.PostprintPostprintPeer reviewe

On the electronic structure of methyl butyrate and methyl valerate

No. 2019-A0010806820 UIDB/00068/2020 PTDC/FIS-AQM/31281/2017Abstract: We present novel results of the analysis of the electronic structure of two aliphatic esters: methyl butyrate and methyl valerate. High-resolution photoabsorption spectra were collected and analyzed over the energy range 4.0–10.8 eV and showed for both the molecules not only a clear band of the HOMO to LUMO transition, but also vibronic structure associated with the first Rydberg-valence transition. Photoelectron spectra recorded from 9 to over 28 eV revealed many ionization states with the first adiabatic ionization energies found to be 9.977 eV and 9.959 eV for methyl butyrate and methyl valerate, respectively. Ab initio calculations have been performed in order to help assign the photoabsorption and photoelectron features. Photolysis life times in the atmosphere were calculated revealing that photolysis is not competitive over hydroxyl radical scavenging in the process of removal of these esters from the atmosphere. Graphical abstract: [Figure not available: see fulltext.]publishersversionpublishe

Electronic State Spectroscopy of Nitromethane and Nitroethane

Funding Information: L.V.S.D., A.S.B., and M.H.F.B. acknowledge support from the Brazilian agencies Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). L.V.S.D., A.S.B., and M.H.F.B. also acknowledge Prof. Carlos de Carvalho for computational support at LFTC-DFis-UFPR and at LCPAD-UFPR. The authors acknowledge the beam time at the ISA synchrotron, Aarhus University, Denmark. The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) CALIPSO under grant agreement n° 312284. P.L.V. acknowledges the Portuguese National Funding Agency (FCT) through research grant CEFITEC (UIDB/00068/2020), as well as his visiting professor position at Federal University of Paraná, Curitiba, Brazil. This contribution is also based upon work from the COST Action CA18212-Molecular Dynamics in the GAS phase (MD-GAS), supported by COST (European Cooperation in Science and Technology). Publisher Copyright: © 2023 The Authors. Published by American Chemical Society.High-resolution photoabsorption cross-sections in the 3.7-10.8 eV energy range are reinvestigated for nitromethane (CH3NO2), while for nitroethane (C2H5NO2), they are reported for the first time. New absorption features are observed for both molecules which have been assigned to vibronic excitations of valence, Rydberg, and mixed valence-Rydberg characters. In comparison with nitromethane, nitroethane shows mainly broad absorption bands with diffuse structures, which can be interpreted as a result of the side-chain effect contributing to an increased number of internal degrees of freedom. New theoretical quantum chemical calculations performed at the time-dependent density functional theory (TD-DFT) level were used to qualitatively help interpret the recorded photoabsorption spectra. From the photoabsorption cross-sections, photolysis lifetimes in the terrestrial atmosphere have been obtained for both compounds. Relevant internal conversion from Rydberg to valence character is noted for both molecules, while the nuclear dynamics of CH3NO2 and C2H5NO2 along the C-N reaction coordinate have been evaluated through potential energy curves at the TD-DFT level of theory, showing that the pre-dissociative character is more prevalent in nitromethane than in nitroethane.publishersversioninpres

A new endstation for extreme-ultraviolet spectroscopy of free clusters and nanodroplets

We present a new endstation for the AMOLine of the ASTRID2 synchrotron at Aarhus University, which combines a cluster and nanodroplet beam source with a velocity map imaging and time-of-flight spectrometer for coincidence imaging spectroscopy. Extreme-ultraviolet spectroscopy of free nanoparticles is a powerful tool for studying the photophysics and photochemistry of resonantly excited or ionized nanometer-sized condensed-phase systems. Here we demonstrate this capability by performing photoelectron-photoion coincidence (PEPICO) experiments with pure and doped superfluid helium nanodroplets. Different doping options and beam sources provide a versatile platform to generate various van der Waals clusters as well as He nanodroplets. We present a detailed characterization of the new setup and present examples of its use for measuring high-resolution yield spectra of charged particles, time-of-flight ion mass spectra, anion-cation coincidence spectra, multi-coincidence electron spectra and angular distributions. A particular focus of the research with this new endstation is on intermolecular charge and energy-transfer processes in heterogeneous nanosystems induced by valence-shell excitation and ionization.Comment: 28 pages, 17 figures, submitted to Review of Scientific Instrument

High-level studies of the ionic states of norbornadiene and quadricyclane, including analysis of new experimental photoelectron spectra by configuration interaction and coupled cluster calculations

Synchrotron-based photoelectron spectra (PES) of norbornadiene (NBD) and quadricyclane (QC) differ significantly from those in previous studies. The adiabatic ionization energy (AIE1) for NBD, assigned to the 2B1 state at 8.279 eV, shows a progression of 18 members with decreasing vibration frequency from 390 cm−1 to 340 cm−1; our calculated frequency is 381 cm−1. Similarly, the AIE1 for QC at 7.671 eV, assigned to the 2B2 state, discloses a vibrational progression of nine or more members with vibration frequency decreasing from 703 cm−1 to 660 cm−1; our calculated vibration frequency is 663 cm−1. These AIEs, determined by coupled cluster and fourth order Møller–Plesset perturbation theory, were very similar to the corresponding second order perturbation theory results. The calculated AIE symmetry sequences are 2B1 < 2A1 < 2A2 < 2B2 for NBD and 2B2 < 2A2 < 2B1 < 2A1 for QC. The overall PES vertical ionization energy profiles for both compounds were closely reproduced by Tamm–Dancoff approximation energies and intensities. The vibrational structure of the ionic states, determined using Franck–Condon methods, gave a good account of the observed spectra, but the observed envelopes for both IE1 are complex sets of vibrations, rather than single progressions. The NMR spectra for QC showed residual second order properties at 300 MHz; both QC and NBD have been theoretically analyzed in greater detail using AA/BB/CC/XX/ spectra, where all H are coupled; the magnetic shielding and spin–spin coupling constants obtained are similar to experimental values.PostprintPostprintPeer reviewe

A Novel Function

Funding Information: This work was supported by Fundação para a Ciência e Tecnologia, Ministério da Ciência, Tecnologia e Ensino Superior (FCT-MCTES), through the grant number PTDC/QUI/64248/2006 (to A.S.P.), the Radiation Biology and Biophysics Doctoral Training Programme—RaBBiT (PD/00193/2012), Applied Molecular Biosciences Unit—UCIBIO (UIDP/04378/2020, i4HB—Institute for Health and Bioeconomy (LA/P/0140/2020) and CEFITEC (UIDB/00068/2020). A.V.A. (PD/BD/135477/2017 and COVID/BD/152498/2022) is supported by the RaBBiT programme. This work benefited from STSM funding by COST Action (CA15126 MOBIEU) and by the project CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020. Publisher Copyright: © 2022 by the authors.Encapsulins are protein nanocages capable of harboring smaller proteins (cargo proteins) within their cavity. The function of the encapsulin systems is related to the encapsulated cargo proteins. The Myxococcus xanthus encapsulin (EncA) naturally encapsulates ferritin-like proteins EncB and EncC as cargo, resulting in a large iron storage nanocompartment, able to accommodate up to 30,000 iron atoms per shell. In the present manuscript we describe the binding and protection of circular double stranded DNA (pUC19) by EncA using electrophoretic mobility shift assays (EMSA), atomic force microscopy (AFM), and DNase protection assays. EncA binds pUC19 with an apparent dissociation constant of 0.3 ± 0.1 µM and a Hill coefficient of 1.4 ± 0.1, while EncC alone showed no interaction with DNA. Accordingly, the EncAC complex displayed a similar DNA binding capacity as the EncA protein. The data suggest that initially, EncA converts the plasmid DNA from a supercoiled to a more relaxed form with a beads-on-a-string morphology. At higher concentrations, EncA self-aggregates, condensing the DNA. This process physically protects DNA from enzymatic digestion by DNase I. The secondary structure and thermal stability of EncA and the EncA−pUC19 complex were evaluated using synchrotron radiation circular dichroism (SRCD) spectroscopy. The overall secondary structure of EncA is maintained upon interaction with pUC19 while the melting temperature of the protein (Tm) slightly increased from 76 ± 1 °C to 79 ± 1 °C. Our work reports, for the first time, the in vitro capacity of an encapsulin shell to interact and protect plasmid DNA similarly to other protein nanocages that may be relevant in vivo.publishersversionpublishe