Low-temperature Matrices Research Articles

UV-promoted radical formation, and near-IR-induced and spontaneous conformational isomerization in monomeric 9-methylguanine isolated in low-temperature Ar matrices.

Three low-energy isomers of 9-methylguanine, the amino-oxo (AO) form and two amino-hydroxy (AH1 and AH2) conformers, were trapped from the gas phase into low-temperature argon matrices. The AH1 and AH2 isomers, differing in the orientation of the OH group, were found to transform into each other upon excitation with near-IR light. The population of the AO form of the compound was not changed upon any near-IR irradiation of the matrix samples. Using monochromatic near-IR light, generated by a frequency-tunable laser source, it was possible to selectively induce the AH1 → AH2 or AH2 → AH1 conversion. Photoreversibility of this conformational transformation was then demonstrated. Exposure of matrix-isolated monomers of 9-methylguanine to broadband near-IR light also led to conformational conversions within the amino-hydroxy tautomeric form; the final stage of this process was always the same photostationary state independent of the initial ratio of AH1 and AH2 populations. Spontaneous conformational conversion, transforming the higher-energy AH2 form into the lower-energy AH1 isomer, was observed for matrix-isolated monomers of 9-methylguanine kept in the dark. The mechanism of this process must rely on quantum tunneling of the light hydrogen atom. Irradiation of matrix-isolated 9-methylguanine with UV laser light at λ = 288 or 285 nm led to a substantial consumption of the two AH forms, while the amount of AO isomer remained unchanged. On the other hand, a decrease in the population of the AO isomer occurred upon excitations at shorter wavelengths, λ = 280 or 275 nm. The spectral changes observed after UV-irradiation suggest the generation (and stabilization in the matrix) of a radical species, resulting from the photocleavage of the O-H or N1-H bonds, in the AH or AO isomer, respectively.

UV-induced transformations of matrix-isolated 6-azacytosine

UV-induced transformations were studied for monomers of 6-azacytosine isolated in low-temperature Ar matrices. In contrast to cytosine, where the amino-hydroxy (AH) tautomer is the lowest-energy form, the amino-oxo (AO) and imino-oxo (IO) isomers of 6-azacytosine were found to be the most stable and most populated. Due to the high relative energy of the AH tautomer of 6-azacytosine, this form is not populated in low-temperature matrices after their formation and prior to any irradiation. Excitation of 6-azacytosine monomers with UV light from the 328-300 nm range led to structural transformations of AO and IO forms. The initially most populated AO tautomer was observed either to convert, in a phototautomeric reaction, into the AH product or to undergo photodecarbonylation to yield 4-amino-1,2,3-(2H)-triazole. The relative efficiencies of the two processes depend on the wavelength and on the pulsed or continuous-wave character of the UV light used for excitation. For the IO tautomer of 6-azacytosine, the excitation with UV 328-300 nm light induced the photoconversion of the initially more populated anti IO1 isomer into the syn IO2 form. This transformation was found to be partially photoreversible.

Hydrogen-bonded complexes of ethynethiol and hydrogen cyanide trapped in low-temperature argon matrices

Hydrogen bonding is one of the exciting and interesting research themes because it plays important roles in biomolecules, plant cells, and so on. Here we report hydrogen-bonded complexes among the photodecomposition products of thiazole, being studied by a joint use of infrared (IR) spectroscopy and density-functional-theory (DFT) calculations. Three types of hydrogen-bonded complexes of ethynethiol (HSCCH) and hydrogen cyanide (HCN), which are photodecomposed by two cleavages of the NC–SC and CN–CC single bonds of thiazole in argon matrices, have been identified by comparison of the observed IR spectra with the corresponding calculated spectral patterns. In addition, another complex with weak interaction between S atom and HCN, which are photoproduced by cleavages of the three single bonds of thiazole, is detected by comparison with the wavenumbers previously reported in literature. The reaction mechanisms to form these complexes are discussed based on the analysis of IR spectra and the DFT calculations.

Splitting of Hydrogen Sulfide by Group 14 Elements (Si, Ge, Sn, Pb) in Excess Argon at Cryogenic Temperatures.

The water gas reaction C + H2O → CO + H2 has been employed for centuries; however little is known for analogous reaction M + H2S → MS + H2 (M = Si, Ge, Sn, Pb). In addition, this latter reaction is intriguing in its function of converting pollutant H2S to clean energy source H2. We report herein the reactions of laser-ablated Group 14 atom M (M = Si, Ge, Sn, Pb) with H2S using matrix isolation infrared spectroscopy as well as the state-of-the-art quantum chemical calculations. Important reactive intermediates HMSH with high active H (protonic Hδ+ and hydridic Hδ-) are identified. In addition, the reaction mechanisms are established for insertion reaction M + H2S → HMSH, and photoinduced H2 elimination reactions of HMSH → MS+ H2 and H2SiS → SiS+ H2 in low-temperature matrices.

Matrix-isolation vibrational circular dichroism spectroscopy in structural studies of peptides: Conformational landscape of the Ac(-Ala)1–4-OMe depsipeptide series

Depsipeptides are naturally occurring peptide analogues containing ester functionalities and are in the focus of numerous pharmaceutical researches and clinical studies owing to their enzyme inhibitor properties and cytotoxic activity against human tumor cell lines. Exploring their conformational landscape could contribute to a better understanding of their mechanism of action and support further drug developments. In this article, we present a combined theoretical and experimental study of the Ac(-Ala)1–4-OMe depsipeptide series by means of matrix-isolation (MI) IR and VCD spectroscopy. The conformational spaces of these peptides were explored via molecular mechanics and DFT computations and the IR and VCD spectra of isolated molecules were recorded in low-temperature Ar matrices. It is demonstrated that MI-VCD spectroscopy can provide additional information even to well resolved MI-IR spectra and support the determination of conformer distributions. Three conformers of Ac-Ala-OMe were identified experimentally, in agreement with theoretical predictions, and their approximate relative ratios were determined. In the case of larger members of the series, the unambiguous identification of individual conformers was not possible in most cases. However, simultaneous analysis of MI-VCD and MI-IR spectra allowed the assignment of the spectral signatures of typical secondary structural elements and groups of similar conformers. The effects including empirical dispersion corrections in DFT computations on the conformer distribution were also examined.

Jahn-Teller Effect of the Benzene Radical Cation: A Direct ab Initio Molecular Dynamics Study.

The benzene radical cation (Bz+) is a typical model molecule of the Jahn-Teller (J-T) active species. Bz+ has two structural forms due to the J-T effect. These are the compressed and elongated forms, expressed as Bz+(comp) and Bz+(elong), respectively. In Bz+(comp), the hexagonal structure of the benzene ring is compressed up and down, and in Bz+(elong), it is pulled up and down. From electron spin resonance experiments, it was found that Bz+ takes a compressed form in low-temperature Freon matrices (CF3Cl and CF2ClCFCl2), whereas the elongated form was found in argon matrices. However, the selectivity of these structural forms is still unclear. In this study, the ionization dynamics of isolated benzene (Bz) and benzene-M complexes (where M denotes counter-molecules, M = NH3, H2O, CF3Cl, CH4, CH3OH, Ar, SH2, ammonia dimer, or water dimer) have been investigated by means of the direct ab initio molecular dynamics (AIMD) method in order to shed light on the Bz+ formation mechanism. The static ab initio calculations showed that Bz+(comp) is slightly more energetically stable than Bz+(elong), although the energy difference was only 0.1 kcal/mol at the CCSD/6-311++G(d,p) level. The direct AIMD calculations indicated that Bz+(comp) was formed from the Bz-M complexes when M was NH3, CF3Cl, or an ammonia dimer, whereas the ionization of Bz-M when M was H2O, CH4, CH3OH, SH2, or a water dimer formed Bz+(elong). In the case of complexes with an argon dimer, Bz(Ar)2, both forms were obtained from a slight orientation change of Ar on Bz. A selective rule is discussed on the basis of the calculated results.

Method and basis set dependence of the NICS indexes of aromaticity for benzene.

The role of theory level in prediction of benzene magnetic indexes of aromaticity is analysed and compared with calculated nuclear magnetic shieldings of 3 He used as NMR probe. Three closely related nucleus-independent chemical shift (NICS) based indexes were calculated for benzene at SCF-HF, MP2, and DFT levels of theory and the impact of basis set on these quantities was studied. The changes of benzene NICS(0), NICS(1), and NICS(1)zz parameters calculated using SCF-HF, MP2 and several density functionals were within 1 to 3ppm. Similar deviations between magnetic indexes of aromaticity were observed for values calculated with selected basis sets. Only very small effect of polar solvent on benzene aromaticity was predicted. The 3 He nuclear magnetic isotropic shielding (σ) and its zz-components (σzz ) of helium atom approaching the centre of benzene ring from above produced similar curves versus benzene-He distance to NICS parameters calculated for similarly moving Bq ghost atom. We also propose an experimental verification of NICS calculations by designing the 3 He NMR measurement for benzene saturated with helium gas or in low temperature matrices.

Photoinduced transformations of indole and 3-formylindole monomers isolated in low-temperature matrices.

Photochemical transformations were studied for monomers of indole and 3-formylindole isolated in low-temperature noble-gas matrices. Upon UV (λ > 270 nm) irradiation of indole trapped in argon and neon matrices, the initial 1H-form of the compound converted into the 3H-tautomer. Alongside this photoinduced hydrogen-atom transfer, an indolyl radical was also generated by photodetachment of the hydrogen atom from the N1-H bond. Excitation of 3-formylindole isolated in an argon matrix with UV (λ > 335 nm) light led to interconversion between the two conformers of the 1H-tautomer, differing from each other in the orientation of the formyl group (cis or trans). Parallel to this conformational phototransformation, the 3H-form of the compound was generated in the 1H → 3H phototautomeric conversion. The photoproducts emerging upon UV irradiation of indole and 3-formylindole were identified by comparison of their infrared spectra with the spectra calculated for candidate structures.

Infrared and density functional theory studies of isoprene-water complexes in noble gas matrices

The interaction of 2-methyl-1,3-butadiene (isoprene) with a H2O molecule in low-temperature noble gas matrices (Ar or Kr) was investigated using infrared absorption spectroscopy. Vibrational peaks arising from 1:1 isoprene-H2O adducts were assigned and compared with the results of quantum chemical calculations. The comparison led to the conclusion that the H2O molecule in the complex preferentially H-bonds to one of the two unsaturated CC bonds, and that the binding energy of the complex is comparable to that of the C6H6-H2O complex. The present study suggests that the change in the charge distribution of isoprene due to the formation of a complex with H2O may lead to alteration of the reactivity with respect to the insertion of OH radicals, thereby influencing the formation of aerosols in the atmosphere.

Structural and spectroscopic properties of complexes formed between HNCS and SO2 in low temperature matrices

Matrix isolation FTIR spectroscopy has been combined with quantum chemical calculations in the aim to characterize complexes of isothiocyanic acid HNCS with SO2. The geometries of the 1:1, 1:2 and 2:1 complexes were optimized at the MP2 and DFT (B3LYPD3) levels of theory with the 6-311++G(3df,3pd) basis set. Five different HNCS⋯SO2 structures of the 1:1 stoichiometry were optimized. Three of them involve a weak NH⋯O hydrogen bond whereas two other geometries are stabilized by van der Waals interactions of various types. The HNCS/SO2/Ar spectra analysis evidences that at least one of the three hydrogen bonded structure is present after deposition of the matrices whereas the most stable van der Waals HNCS⋯SO2 structure as well as complexes of the 1:2 stoichiometry were detected upon annealing.

Infrared spectra of 5-fluorouracil molecules isolated in inert Ar matrices, and their films on graphene oxide at 6 K

The FTIR spectra of 5-fluorouracil (5FU) molecules isolated in low-temperature (T = 6 K) argon matrices were observed in the infrared range of 3800–200 cm−1. The FTIR spectra of graphene oxide (GO) films on a copper mirror at a temperature of 6 K and the spectra of 5FU films grown on GO films were recorded for the first time. Estimates of the 5FU tautomer population using quantum-mechanical methods DFT/B3LYP and MP2, and calculations of the 5FU vibrational spectra using the DFT/B3LYP/6-311++G(df,pd) method with a correction to the calculated frequencies by a third-order polynomial were performed. It is found that the population of the minor 5FU tautomers at an evaporation temperature of 375 K does not exceed 0.1%. In the spectral range of 1900–500 cm−1 ten 5FU combination modes are registered, which are amplified by the Fermi resonance. In the region of fundamental vibrations νCO, triple Fermi resonance is observed. It is demonstrated that low temperatures have little effect on the spectral characteristics of GO films. Furthermore, multiple thermal cycling between 6 and 295 K does not violate the integrity of the GO films and their thermal contact with the copper mirror. The FTIR spectra of 5FU matrix and film samples grown on different substrates are compared. A gain in the absorption band of thin-film 5FU grown on GO, in comparison to samples grown on a Cu substrate, is recorded. It is established that the infrared spectrum changes when the 5FU deposited on GO film is annealed. The relationship between these spectral changes and the polymorphism of the 5FU crystal structure is discussed.

Flash Vacuum Pyrolysis of Azides, Triazoles, and Tetrazoles.

Flash vacuum pyrolysis (FVP) of azides is an extremely valuable method of generating nitrenes and studying their thermal rearrangements. The nitrenes can in many cases be isolated in low-temperature matrices and observed spectroscopically. NH and methyl, alkyl, aralkyl, vinyl, cyano, aryl and N-heteroaryl, acyl, carbamoyl, alkoxycarbonyl, imidoyl, boryl, silyl, phosphonyl, and sulfonyl nitrenes are included. FVP of triazoloazines generates diazomethylazines and azinylcarbenes, which often rearrange to the energetically more stable arylnitrenes. N2 elimination from monocyclic 1,2,3-triazoles can generate iminocarbenes, 1H-azirines, ketenimines, and cyclization products, and 1,2,4-triazoles are precursors of nitrile ylides. Benzotriazoles are preparatively useful precursors of cyanocyclopentadienes, carbazoles, and aza-analogues. FVP of 5-aryltetrazoles can result in double N2 elimination with formation of arylcarbenes or of heteroarylcarbenes, which again rearrange to arylnitrenes. Many 5-substituted and 2,5-disubstituted tetrazoles are excellent precursors of nitrile imines (propargylic, allenic, or carbenic), which are isolable at low temperatures in some cases (e.g., aryl- and silylnitrile imines) or rearrange to carbodiimides. 1,5-Disubstituted tetrazoles are precursors of imidoylnitrenes, which also rearrange to carbodiimides or add intramolecularly to aryl substituents to yield indazoles and related compounds. Where relevant for the mechanistic understanding, pyrolysis under flow conditions or in solution or the solid state will be mentioned. Results of photolysis reactions and computational chemistry complementing the FVP results will also be mentioned in several places.

The acetylacetone-water complex in a low-temperature solid argon matrix

A mixture of acetylacetone and water was condensed in low-temperature Ar matrices at 5K, and infrared spectra were observed. It was found that the H2O molecules formed hydrogen bonds with the acetylacetone. The structure of the H2O-C5H8O2 complex was estimated with the aid of a density functional calculation. A similar sample was prepared using deuterium-substituted water to confirm the structure of the complex. Upon annealing the matrix-isolated sample, aggregation of H2O molecules was observed and the amount of the complex remained unchanged.

A Very Short Be–Be Distance but No Bond: Synthesis and Bonding Analysis of Ng–Be2O2–Ng′ (Ng, Ng′=Ne, Ar, Kr, Xe)

Short interatomic distances below standard values for a single bond are usually identified with double or triple bonds. The synthesis and spectroscopic characterization of a molecule is reported where the distance between two beryllium atoms is shorter than a standard double bond but there is no bond. The cyclic diberyllium dioxide Be2 O2 molecule, which is coordinated by two noble gas atoms in Ng-Be2 O2 -Ng' (Ng, Ng'=Ne, Ar, Kr, Xe) was isolated and spectroscopically identified in low-temperature matrices. The complexes possess very short Be-Be distances, but the analysis of the electronic structure reveals that there is no chemical bond.

Activation of the B-F Bond by Diphenylcarbene: A Reversible 1,2-Fluorine Migration between Boron and Carbon.

Experiments in low-temperature matrices reveal that triplet diphenylcarbene inserts into the very strong B-F bond of BF3 in a two-step reaction. The first step is the formation of a strongly bound Lewis acid-base complex between the singlet state of diphenylcarbene and BF3 . This step involves an inversion of the spin state of the carbene from triplet to singlet. The second step requires visible-light photochemical activation to induce a 1,2-F migration from boron to the adjacent carbon atom under formation of the formal insertion product of the carbene center into BF3 . The 1,2-F migration is reversible under short-wavelength UV irradiation, thus leading back to the Lewis acid-base adduct.

Isocyano compounds newly recognized in photochemical reaction of thiazole: matrix-isolation FT-IR and theoretical studies

UV-induced photoreactions of thiazole isolated in low-temperature argon matrices have been investigated, leading to the conclusion that photoproducts identified newly, including three kind isocyano compounds, are produced by ring-opening reaction.

From clusters to condensed phase – FT IR studies of water

Intermolecular hydrogen bonding, which is formed between water molecules in the condensed state, causes a variety of unique properties of liquid water. In this paper the results of experimental FT IR studies of water trapped in an Ar matrix as well as condensed water at temperatures from 133 to 293K are presented. It is shown that the temperature evolution of the FTIR-spectra of water trapped in low-temperature matrices can be considered as an experimental model of the structure transformation of water during the phase transition from gas phase to condensed confined water. The comparison of the vibrational spectra of water in matrix isolation with the corresponding spectra of condensed water gives information about the peculiarities of H-bonded structures of water.

Vibrational spectra of water clusters, trapped in low temperature matrices

Recorded infrared absorption spectra of water, trapped in an argon matrix at temperatures ranging from 9 to 50 K. The observed spectral bands are assigned to water clusters composed of different numbers of molecules. The temperature dependence of the recorded spectra makes it possible to construct a model of the structural transformations that take place in the water during the phase transition from the gaseous to the condensed state.

Effect of low-temperature argon matrices on the IR spectra and structure of flexible N-acetylglycine molecules

A study of how the matrix environment impacts the structure and IR spectra of N-acetylglycine conformers. The conformational composition of this compound is determined according to an analysis of the FTIR spectra of N-acetylglycine isolated in low temperature argon matrices. Bands of three N-acetylglycine conformers are identified based on the spectra: one major and two minor. The structure of all observed conformers is stabilized by different intramolecular hydrogen bonds. The Gibbs free energies of the conformers were calculated (CCSD(T)/CBS method), and these energy values were used to calculate conformer population at a temperature of 360 K, of which 85.3% belonged to the main conformer, and 9.6% and 5.1% to the minor conformers. We also determined the size and shape of the cavities that form when the N-acetylglycine conformers are embedded in the argon crystal during matrix deposition. It is established that the most energetically favorable cavity for the planar main conformer is the cavity that forms when 7 argon atoms are replaced. At the same time, bulky minor conformers were embedded into cavities that correspond to 8 removed argon atoms. We calculated the complexation energy between argon clusters and conformers, and the deformation energy of the argon crystal and the N-acetylglycine conformers. The matrix-induced shifts to the conformer oscillation frequency are calculated.

Chemical-technological and mineralogical-geochemical aspects of the radioactive waste management

This paper considers various matrices that are able to incorporate components of radioactive wastes (RAW) of different origin. It is noted that attempts to develop the single phase crystalline matrix to immobilize all RAW components failed. The only single phase matrix brought to the industrial application is glass, which is able to accumulate practically all RAW components but in limited concentrations. Prospects are related with some types of ceramics for immobilization of narrow fractions of RAW or individual radionuclides (for instance, minor actinides), as well as some types of low-temperature matrices (iron-phosphate, magnesium–potassium–phosphate, and geopolymers). Approaches to choosing the technology of waste form synthesis are considered. Perspectives of application of both high-temperature (cold-crucible induction melting, self-propagating high-temperature synthesis) methods and modified cementation technologies are demonstrated. It is noted that the final isolation of RAW from the biosphere suggests their disposal in underground repositories. The most difficult technical problem is the disposal of RAW containing long-lived radionuclides. It is shown that the quantitative assessment of repository safety with allowance for their characteristics and all possible processes and phenomena is required to substantiate the safe disposal of long-lived radionuclides.