Insight into the Binding of Argon to Cyclic Water Clusters from Symmetry-Adapted Perturbation Theory.

This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H2O clusters containing three-five water molecules (Ar(H2O)n=3-5). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple-ζ correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body-many-body (2b:Mb) and three-body-many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H2O)4 and three for (H2O)5. To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H2O)n clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol-1 and by nearly 6 kJ mol-1 for one Ar(H2O)5 complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm-1 for some hydrogen-bonded OH stretching frequencies.

Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision.

The bombardment of a protein multilayer target by an energetic argon cluster ion beam enables protein transfer onto a collector in the vacuum while preserving their bioactivity (iBEAM method). In parallel to this new soft-landing variant, protein transfer in the gas phase is a prerequisite for their characterization by mass spectrometry. The successful transfer of bioactive lysozymes (14 kDa) by cluster-induced soft landing and its mechanistic explanation by molecular dynamics (MD) simulations have sparked an important inquiry: Can heavier biomolecules be desorbed while maintaining their tridimensional structure and hence their bioactivity? To address this question, we employed MD simulations using a reactive force field (ReaxFF). Specifically, the Ar cluster-induced desorption of glucose oxidase from either a gold substrate or a lysozyme underlayer was modeled using the LAMMPS code. First, the force field parameters were trained by computing the dissociation energetics of a series of organic molecules with ReaxFF and DFT, in order to realistically describe N-S and O-S interactions in the bombarded glucose oxidase molecule. Second, bombardment simulations investigated the effects of cluster size (ranging from 1000 to 10000 Ar atoms) and kinetic energy (1.5 and 3.0 eV/atom) on the structural features and energetics of the desorbing glucose oxidase. Our results show that large argon clusters (≥7000) are needed to desorb glucose oxidase from a gold surface, yet protein fragmentation and/or pronounced denaturation occur. However, the transfer of structurally preserved glucose oxidase in the gas phase is predicted by the simulations when an organic layer is used as a substrate.

Infrared spectroscopic and theoretical investigations of novel iridium oxyfluorides.

The iridium oxyfluorides (OIrF, OIrF2 and FOIrF) were prepared for the first time by the reaction of IR-laser ablated iridium atoms and OF2, isolated in solid neon and argon matrices. The assignments of the main vibrational absorptions of these products were supported by a combined analysis of IR-matrix-isolation spectroscopy with 18OF2 substitution and quantum-chemical calculations. The OIrF molecule exhibits triple bond character. In contrast to terminal oxyl radical species OPtF2 and OAuF2, a much lower spin-density contribution at the oxygen atom was found in OIrF2.

Comparison study of mouse brain tissue by using ToF-SIMS within static limits and hybrid SIMS beyond static limits (dynamic mode).

In the study of degenerative brain diseases, changes in lipids, the main component of neurons, are particularly important because they are used as indicators of pathological changes. One method for the sensitive measurement of biomolecules, especially lipids, is time-of-flight secondary ion mass spectrometry (ToF-SIMS) using pulsed argon cluster ions. In this study, biomolecules including various lipids present in normal mouse brain tissue were measured using ToF-SIMS equipped with pulsed argon cluster primary ions. Based on the ToF-SIMS measurement results, hybrid SIMS (OrbiSIMS), which is a ToF-SIMS system with the addition of an orbitrap mass analyzer, was used to directly identify the biomolecules by the region in the real tissue samples. For this, the results of ToF-SIMS, which measured the tissue samples from a single mouse brain within static limits, were compared with those from OrbiSIMS measured beyond the static limits in terms of the differences in molecular profiling. From this analysis, two types of positive and negative ions were selected for identification, with the OrbiSIMS MS/MS results indicating that the positive ions were glycerophosphocholine and the negative ions were glycerophosphoinositol and sulfatide, a sphingolipid. Then, to confirm the identification of the molecular candidates, lipids were extracted from mirror image tissue samples, and LC-MS/MS also using an orbitrap mass analyzer was performed. As a result, the direct identification of molecular candidate groups distributed in particular regions of the tissue samples via OrbiSIMS was found to be consistent with the identification results by LC-MS/MS for extracted samples.

Structure, energetics, and spectroscopy of the K2+(X2Σ+g) interacting with the noble gas atoms Ar, Kr and Xe.

The structure, energetic, and spectroscopy properties of the ionic system K2+(X2Σ+g) interacting with the noble gas atoms Argon, Krypton and Xenon are studied. The computations are done by an accurate ab initio approach based on the pseudo-potential technique, Gaussian basis sets, parameterized l-dependent polarization potentials and an analytic potential form for the K+Ar, K+Kr and K+Xe interactions. These interactions are added via the CCSD(T) potential taken from literature and fitted applying the analytical expression of Tang and Toennies. The application of the pseudo-potential approach reduces the number of active electrons of each complex to only one electron. The potential energy surfaces are analyzed on a large range of the Jacobi coordinates, R and θ. By the general interpolation outline based on the RKHS (Reproducing Kernel Hilbert Space) procedure, we have reproduced for each complex from our ab initio results the two-dimensional contour plots of an analytical potential. To evaluate the stability of each complex, we have determined from the potential energy surfaces the equilibrium distance (Re), the well depth (De), the quantum energy (D0), the zero-point-energy (ZPE) and the ZPE%. The results showed that the linear configurations, where the noble gas atom connected to the K2+(X2Σ+g) system, are the more stable.

UV Laser-Induced Phototransformations of Matrix-Isolated 5-Chloro-3-nitro-2-hydroxyacetophenone.

Conformational changes of 5-chloro-3-nitro-2-hydroxyacetophenone were studied by experimental and theoretical methods. Phototransformations of the compound were induced in low-temperature argon matrices by using UV radiation, which was followed by FT-IR measurements. Two types of changes within the molecule were detected: rotations of the hydroxyl and acetyl groups. A new conformer without an intramolecular hydrogen bond was generated upon irradiation with λ = 330 nm, whereas the reverse reaction was observed at 415 nm.

Structure and IR spectroscopic properties of complexes of 1,2,4-triazole and 3-amino-1,2,4-triazole with dinitrogen isolated in solid argon.

Complexes of 1,2,4-triazole (TR) and 3-amino-1,2,4-triazole (AT) with N2 were studied computationally employing MP2 and B3LYPD3 methods and experimentally by FTIR matrix isolation technique. The results show that both triazoles interact specifically with dinitrogen in several different ways. For the 1:1 complexes of 1,2,4-triazole five stable minima were located on the potential energy surface. The most stable of them comprises a weak hydrogen bond formed between the NH group of the ring and the lone pair of the nitrogen molecule. The second most stable structure is bound by the N⋯π bond formed between one of the N atoms of the N2 molecule and the triazole ring. Three other complexes are stabilized by the C-H⋯N and N⋯N van der Waals interactions. In the case of 3-amino-1,2,4-triazole, the two most stable dinitrogen complexes are analogous to those found for the 1,2,4-triazole and involve N-H⋯N and N⋯π bonds. In other structures amino or CH groups act as proton donors to the N2 molecule. The N⋯N van der Waals interactions are also present. The analysis of the infrared spectra of low temperature matrices containing TR or AT and dinitrogen indicates that in both systems mostly 1:1 hydrogen-bonded complexes with the NH group interacting with N2 are present in solid argon.

Infrared Spectra and Phototransformations of meta-Fluorophenol Isolated in Argon and Nitrogen Matrices.

Monomers of meta-fluorophenol (mFP) were trapped from the gas phase into cryogenic argon and nitrogen matrices. The estimated relative energies of the two conformers are very close, and in the gas phase they have nearly equal populations. Due to the similarity of their structures (they only differ in the orientation of the OH group), the two conformers have also similar predicted vibrational signatures, which makes the vibrational characterization of the individual rotamers challenging. In the present work, it has been established that in an argon matrix only the most stable trans conformer of mFP exists (the OH group pointing away from the fluorine atom). On the other hand, the IR spectrum of mFP in a nitrogen matrix testifies to the simultaneous presence in this matrix of both the trans conformer and of the higher-energy cis conformer (the OH group pointing toward the fluorine atom), which is stabilized by interaction with the matrix gas host. We found that the exposition of the cryogenic N2 matrix to the Globar source of the infrared spectrometer affects the conformational populations. By collecting experimental spectra, either in the full mid-infrared range or only in the range below 2200 cm-1, we were able to reliably distinguish two sets of experimental bands originating from individual conformers. A comparison of the two sets of experimental bands with computed infrared spectra of the conformers allowed, for the first time, the unequivocal vibrational identification of each of them. The joint implementation of computational vibrational spectroscopy and matrix-isolation infrared spectroscopy proved to be a very accurate method of structural analysis. Some mechanistic insights into conformational isomerism (the quantum tunneling of hydrogen atom and vibrationally-induced conformational transformations) have been addressed. Finally, we also subjected matrix-isolated mFP to irradiations with UV light, and the phototransformations observed in these experiments are also described.

Low-temperature argon plasma jet with cascading electrode technique for biological applications.

In this study, the design, performance, and characteristics of a low-temperature argon plasma jet with cascading electrode technique (APJCE) are presented. APJCE is designed based on a tip-ring structure with a cascading ring. The effect of plasma jet driven by repetitive high-voltage microsecond pulses in APJCE structure was measured qualitatively in local surface temperature detection system. Then, by applying the generated plasma jet to biological surface and measuring and characterizing the electrical parameters, we obtained a plasma jet, which is electrically and thermally in the cold plasma regime. Simulation of the electric field distribution in the nozzle also yielded similar results to the experimental results. Finally, by cascading electrodes, we guided the plasma column to the nozzle output so that the plasma temperature within four centimeters of the nozzle output is 37 °C. The resulting plasma jets were studied by atomic emission spectroscopy and the intensity of the spectral lines of the atmospheric argon plasma jet spectra was obtained as a final experimental result at the output.

Spectroscopic evidence for 1,2-diiminoethane - a key intermediate in imidazole synthesis.

Simple imines and diimines are common building blocks in organic synthesis, but the compound class is spectroscopically not well characterized. Herein we report the formation of the simplest diimine, namely 1,2-diiminoethane, as well as spectroscopic characterization by cryogenic matrix isolation IR and UV/Vis spectroscopy. Three conformers of 1,2-diiminoethane form after UV irradiation of 1,2-diazidoethane by N2 extrusion at 3 K in solid argon and can be photochemically interconverted. In a matrix isolation pyrolysis experiment at 600 °C with 1,2-diazidoethane as the starting material we observe hydrogen cyanide and formaldimine as the main decomposition products. All experimental findings are supported by deuterium labeling experiments and B3LYP/6-311++G(2d,2p) calculations. Irradiation of 1,2-diazidoethane in aqueous solution leads to the formation of imidazoles as indicated by NMR spectroscopy and GC-MS analysis. Our results underline the key role of diimines as building blocks in N-heterocyclic chemistry.

Gas Cluster Ion Beams as a Versatile Soft-Landing Tool for the Controlled Construction of Thin (Bio)Films.

Surface biofunctionalization with proteins is the key to many biomedical applications. In this study, a solvent-free method for the controlled construction of protein thin films is reported. Using large argon gas cluster ion beams, proteins are sputtered from a target (a pool of pure proteins), and collected on a chosen substrate, being nearly any solid material. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) revealed the presence of intact protein molecules on the collectors. Furthermore, lowering the energy per atom in the cluster projectiles down to 1 eV/atom allowed more than 60% of bradykinin molecules to be transferred intact. This protein deposition method offers a precise control of the film thickness as the transferred protein quantity is proportional to the argon clusters ion dose reached for the transfer. This major feature enables building protein films from (sub)mono- to multilayers, without upper limitation of the thickness. A procedure was developed to measure the film thickness in situ the ToF-SIMS instrument. The versatility and potential of this soft-landing alternative for further applications is demonstrated on the one hand by building a protein thin film at the surface of paper, a substrate hardly compatible with solution-based adsorption methods. On the other hand, the possibility to achieve alternated multilayer buildup is demonstrated with the construction of a bilayer composed of bradykinin and Irganox, with the two layers well separated. These results lay the first stone toward original and complex multilayers that could previously not be considered with solution-based adsorption methods, and this regardless of the substrate nature.

Matrix Isolation Study of Fumaric and Maleic Acids in Solid Nitrogen.

Fumaric and maleic acids ((E)- and (Z)-HOOC-CH═CH-COOH, FA and MA) were studied experimentally by infrared spectroscopy in nitrogen matrixes and theoretically by quantum chemical calculations. The calculations, carried out at the DFT(B3LYP) and MP2 levels of theory, predicted the existence of at least 5 conformers of maleic acid and 10 conformers of fumaric acid. After the deposition of the matrixes, two conformers of maleic acid (I and II) and three conformers (I-III) of fumaric acid were observed and characterized vibrationally. Selective narrowband near-infrared (NIR) excitation of the first OH stretching overtones of the different conformers of maleic and fumaric acids initially present in the matrixes allowed the generation of higher-energy forms, never before observed experimentally. In the case of maleic acid, conformers I (a cis-trans form, where cis and trans designate the conformation of the carboxylic groups of the molecule) and II (cis-cis) were found to generate the novel conformers VI (trans-trans) and VII (cis-trans), respectively. The conversion of conformer II into the most stable conformer I was also observed. For fumaric acid, the cis-cis conformers I-III were found to give rise to the new cis-trans conformers IV-VII, respectively. The tunneling decay of the new conformers produced upon NIR excitation of the lowest-energy conformers initially trapped in the matrixes was observed, and their lifetimes in solid N2 were determined. The increased stability of all of the observed high-energy conformers of the studied acids in the N2 matrix, compared to the argon matrix, where they could not be observed experimentally, demonstrates the stabilizing effect of the interaction between the OH groups of the acids with the matrix N2 molecules, in line with previous observations for other carboxylic acids. In addition, the photochemistry of matrix-isolated maleic and fumaric acids upon broad-band UV irradiation (λ > 235 nm) was also investigated. UV-induced isomerization of both acids around the C═C double bond was observed, together with their decarboxylation to acrylic acid.

The Radiation Chemistry of NH3···CO Complex in Cryogenic Media as Studied by Matrix Isolation.

The NH3···CO complex can be considered an important building block for cold synthetic astrochemistry leading to the formation of complex organic molecules, including key prebiotic species. In this work, we have studied the radiation-induced transformations of this complex in Ar, Kr, and Xe matrices using FTIR spectroscopy. On the basis of comparison with the quantum chemical calculations at the CCSD(T)/L2a_3 level of theory, it was found that the initial complex had the configuration with hydrogen bonding through the carbon atom of CO. Irradiation of the matrix isolated complex with X-rays at 6 K leads to the formation of a number of synthetic products, namely, HNCO (in all matrices), formamide NH2CHO, NH2CO, and HNCO-H2 (in argon and krypton). The matrix effect on the product distribution was explained by the involvement of different excited states of the complex in their formation. It was suggested that formamide results from the singlet excited states while other species mainly originate from triplet excited states. The latter states are efficiently populated through ion-electron recombination (in all matrices) and through intersystem crossing (particularly, in xenon). High yield of the recombination triplet states is a feature of the processes induced by high-energy radiation (in contrast to direct photolysis). NCO, CN, and NO were found as minor secondary products at high adsorbed doses. The astrochemical implications of the obtained results are discussed.

Inactivation of Escherichia coli by atmospheric pressure plasma jet in water.

The main aim of this work is inactivation of Escherichia coli in water using a laboratory-scale radio-frequency atmospheric pressure Argon plasma jet. This bacterium is widely present in the environment, especially in drinking water, and its pathogenic effects are very harmful. For this purpose, an Argon flow rate of 3.5 slm, maximum plasma power of 200 W, and discharge frequency of 13.56 MHz was conducted to generate a uniform plasma plume for water treatment. 150 ml of drinking water contaminated by E. coli was exposed to the radiation of plasma placed about 3 cm within the water, the treatment time varied from 2 to 6 minutes at 100, 150, and 200 W of plasma input power. The temperature of the plume, discharge current and voltage, and electron density were all measured to characterize the plasma. Active species such as excited molecules, ions, and radicals produced in the plasma in water were detected using the optical emission spectroscopy method. The decreasing behavior of live bacteria versus exposure time and plasma jet input power was observed, and finally, at the discharge power of 200 W and 6 min, an effective inactivation was achieved and the number of bacteria reduced from 92×104 to less than 1.7 MPN/100 ml.

In-depth analysis of iodine in artificial biofilm model layers by variable excitation energy XPS and argon gas cluster ion sputtering XPS.

Here, we present a study on agarose thin-film samples that represent a model system for the exopolysaccharide matrix of biofilms. Povidone-iodide (PVP-I) was selected as an antibacterial agent to evaluate our x-ray photoelectron spectroscopy (XPS)-based methodology to trace specific marker elements, here iodine, commonly found in organic matrices of antibiotics. The in-depth distribution of iodine was determined by XPS analyses with variable excitation energies and in combination with argon gas cluster ion beam sputter cycles. On mixed agarose/PVP-I nanometer-thin films, both methods were found to solve the analytical task and deliver independently comparable results. In the mixed agarose/PVP-I thin film, we found the outermost surface layer depleted in iodine, whereas the iodine is homogeneously distributed in the depth region between this outermost surface layer and the interface between the thin film and the substrate. Depletion of iodine from the uppermost surface in the thin-film samples is assumed to be caused by ultrahigh vacuum exposure resulting in a loss of molecular iodine (I2) as reported earlier for other iodine-doped polymers.

Formation and Evolution of H2C3O+• Radical Cations: A Computational and Matrix Isolation Study.

The family of isomeric H2C3O+• radical cations is of great interest for physical organic chemistry and chemistry occurring in extraterrestrial media. In this work, we have experimentally examined a unique synthetic route to the generation of H2C3O+• from the C2H2···CO intermolecular complex and also considered the relative stability and monomolecular transformations of the H2C3O+• isomers through high-level ab initio calculations. The structures, energetics, harmonic frequencies, hyperfine coupling constants, and isomerization pathways for several of the most important H2C3O+• isomers were calculated at the UCCSD(T) level of theory. The complementary FTIR and EPR studies in argon matrices at 5 K have demonstrated that the ionized C2H2···CO complex transforms into the E-HCCHCO+• isomer, and this latter species is supposed to be the key intermediate in further chemical transformations, providing a remarkable piece of evidence for kinetic control in low-temperature chemistry. Photolysis of this species at λ = 410-465 nm results in its transformation to the thermodynamically most stable H2CCCO+• isomer. Possible implications of the results and potentiality of the proposed synthetic strategy to the preparation of highly reactive organic radical cations are discussed.

High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action.

In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs - a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia.

Simple and Scalable Chemical Surface Patterning via Direct Deposition from Immobilized Plasma Filaments in a Dielectric Barrier Discharge.

In this work, immobilization of the often unwanted filaments in dielectric barrier discharges (DBD) is achieved and used for one-step deposition of patterned coatings. By texturing one of the dielectric surfaces, a discharge containing stationary plasma filaments is ignited in a mix of argon and propargyl methacrylate (PMA) in a reactor operating at atmospheric pressure. From PMA, hydrophobic and hydrophilic chemical and topographical contrasts at sub-millimeter scale are obtained on silicon and glass substrates. Chemical and physical characterizations of the samples are performed by micrometer-scale X-ray photoelectron spectroscopy and infrared imaging and by water contact angle and profilometry, respectively. From the latter and additional information from high-speed imaging of the plasma phase and electrical measurements, it is suggested that filaments, denser in energetic species, lead to higher deposition rate with higher fragmentation of the precursor, while surface discharges igniting outwards the filaments are leading to smoother and slower deposition. This work opens a new route for a one-step large-area chemical and morphological patterning of surfaces at sub-millimeter scales. Moreover, the possibility to separately deposit coatings from filaments and the surrounding plasma phase can be helpful to better understand the processes occurring during plasma polymerization in filamentary DBD.

Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families.

Argon belongs to the group of chemically inert noble gases, which display a remarkable spectrum of clinically useful biological properties. In an attempt to better understand noble gases, notably argon's mechanism of action, we mined a massive noble gas modeling database which lists all possible noble gas binding sites in the proteins from the Protein Data Bank. We developed a method of analysis to identify among all predicted noble gas binding sites the potentially relevant ones within protein families which are likely to be modulated by Ar. Our method consists in determining within structurally aligned proteins the conserved binding sites whose shape, localization, hydrophobicity, and binding energies are to be further examined. This method was applied to the analysis of two protein families where crystallographic noble gas binding sites have been experimentally determined. Our findings indicate that among the most conserved binding sites, either the most hydrophobic one and/or the site which has the best binding energy corresponds to the crystallographic noble gas binding sites with the best occupancies, therefore the best affinity for the gas. This method will allow us to predict relevant noble gas binding sites that have potential pharmacological interest and thus potential Ar targets that will be prioritized for further studies including in vitro validation.

Low-energy Ar+ and N+ ion beam induced chemical vapor deposition using hexamethyldisilazane for the formation of nitrogen containing SiC and carbon containing SiN films.

We proposed an experimental methodology for producing films on substrates with an ion beam induced chemical vapor deposition (IBICVD) method using hexamethyldisilazane (HMDS) as a source material. In this study, both HMDS and ion beam were simultaneously injected onto a Si substrate. We selected Ar+ and N+ as the ion beam. The energy of the ion beam was 101 eV. Temperature of the Si substrate was set at 540 °C. After the experiments, films were found to be deposited on the substrates. The films were then analyzed by Fourier transform infrared (FTIR) spectroscopy, stylus profilometer, X-ray diffraction, atomic force microscopy, and X-ray photoelectron spectroscopy (XPS). The FTIR and XPS results showed that silicon carbide films containing small amount of nitrogen were formed when Ar+ ions were injected in conjunction with HMDS. On the other hand, in the cases of N+ ion beam irradiation, silicon nitride films involving small amount of carbon were formed. It was noted that no film deposition was observed when HMDS alone was supplied to the substrates without any ion beam injections.