Low-temperature Argon Matrices Research Articles

Hydrogen-atom tunneling in small thioamides: N-methylthiourea, thiobenzamide and 2-cyanothioacetamide

The most stable thione tautomeric forms of N-methylthiourea, thiobenzamide and 2-cyanothioacetamide were isolated in low-temperature argon matrices. The higher-energy thiol tautomers of these compounds were generated upon irradiation of matrix-isolated monomers with UV (λ > 270 nm) light. For N-methylthiourea and thiobenzamide, kept in the dark at 3.5 K for a long period of time, a spontaneous thiol → thione hydrogen atom tunneling transformation occurred. Only the thiol isomers with the favorably oriented hydrogen atom of the imino group underwent these hydrogen-atom tunneling processes. The other thiol isomers, with the hydrogen atom of the imino group oriented towards the sulfur atom, did not undergo the thiol → thione conversion. For the photogenerated thiol forms of 2-cyanothioacetamide, no spontaneous thiol → thione tautomeric transformation was detected. Instead, only the spontaneous conformational change of one S-H rotamer of the thiol 2-cyanothioacetamide tautomer into the other S-H rotamer was observed.

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.

NIR and UV induced transformations of indazole-3-carboxylic acid isolated in low temperature matrices

The molecular structure and NIR and UV induced phototransformations of indazole-3-carboxylic acid were studied in low temperature argon and nitrogen matrices by FTIR spectroscopy and B3LYP/6–311++G(2d,2p) calculations. Eleven minima of IC were located on the S0 potential energy surface. The three most stable structures were detected experimentally in both matrices after deposition. Upon NIR irradiation a dominant process was rotamerization within the carboxylic group leading to changes in the population of the trans 1HIC1 and cis 1HIC2 forms. In turn, at UV irradiation at λ = 260 nm two new tautomers (2HIC2 and 2HIC3) were generated indicating that the hydrogen atom transfer in pyrazole ring took place. Based on the obtained kinetic curves, differences in the phototransformation rates in different matrices were indicated.

The influence of low-temperature argon matrix on embedded water clusters. A DFT theoretical study

Computer simulations of an argon fcc crystal fragment with embedded water clusters of different sizes are performed using the quantum mechanical DFT/M06-2X method. The effect of the argon matrix on the structural, energy, and spectral parameters of individual water clusters are investigated. The formation energies of (H2O)n@Arm complexes, as well as deformation energies of water clusters and of the argon crystal involved in the embedment, are computed for n = 1–7. Matrix shifts of the IR vibrational frequencies of water clusters isolated in argon matrices are predicted based on the results of the calculations. The predictions indicate a possibility of the formation of small stable water complexes in low-temperature argon matrices.

Phototransformations of 2-aminonicotinic acid resolved with matrix isolation infrared spectroscopy and ab initio calculations

The structure and phototransformations of 2-aminonicotinic acid (ANA) induced by tunable UV laser were studied in low-temperature argon matrices with the use of Fourier-transform infrared (FTIR) spectroscopy. After the deposition of the argon matrix, two amino isomers (ANA-1 and ANA-2) were detected, with populations of 96 % and 4 %, respectively. Electronic structure calculations confirm these to be the two most stable isomers of ANA. The irradiation of the amino isomers gives rise to an intricate system of photoinduced reactions, which involves amino-imino phototautomerism, and rotations of the carboxylic group. Following irradiation at 350 nm, a rotation of the carboxylic group of ANA-1 was detected leading to increase of the ANA-2 form. In turn, at 310 nm two new imino forms (INA-1 and INA-2) of 2-aminonicotinic acid were generated indicating that UV-induced hydrogen atom transfer between ANA and INA tautomeric forms took place. The corresponding reverse photorotamerizations were also detected at 390 nm, resulting in the recovery of the initial ANA-1 and ANA-2 isomers. On the basis of electronic structure calculations, we hypothesize that ANA-INA phototautomerization takes place in the vibrationally hot electronic ground state. Its occurrence appears to be contingent on the molecule being able to access a conical intersection between the lowest singlet excited state and the ground state.

Matrix isolation studies of vibrational structure of hemiporphycene

Parent, unsubstituted free base hemiporphycene, a constitutional isomer of porphyrin, was synthesized only a few years ago, and the detailed characterization of vibrational structure is lacking. We studied vibrations of hemiporphycene using site-selected fluorescence and IR measurements in low temperature argon and nitrogen matrices, combined with recording Raman spectra of polycrystalline samples. Temperature dependence of IR and Raman spectra was also investigated. The spectra were analysed with the help of DFT calculations of vibrational energies and transition intensities. Most of the bands observed in the 600-1600 cm−1 range could be reliably assigned. Moreover, it was possible to photoconvert the lowest energy trans1 tautomer, the only species present at low temperatures, into a higher energy trans2 form. However, this process is not efficient and strongly depends on the chromophore microenvironment.

Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations

The conformational equilibrium of thymidine and deuterothymidine molecules in low-temperature Ar matrices has been studied using low-temperature matrix-isolation Fourier IR spectroscopy and quantum-chemical calculations by the DFT/B3LYP and MP2 methods. It has been found that two anti-conformers ta2_0 and ta3_0 with different structures of the sugar ring, C2′-endo and C3′-endo, predominate in low-temperature matrices. In isolated state, each of these conformers has a few low-barrier satellites that can fully pass into more stable structures when a molecule enters the matrix. The main syn conformer ts2_0 is stabilized by an intramolecular hydrogen bond between the O5′H group of the sugar and the C2O group of the base (O5′H⋅⋅⋅O2), while C2′-endo is the predominant conformation of the deoxyribose ring. The considerably lower population of ts2_0 compared to the anti-conformers ta2_0, ta3_0 can be explained by the smaller population of satellite conformations. It has been shown that the absorption band of νN3D stretching vibration is split by the Fermi resonance.

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.

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.

FTIR study of acetylacetone, D2-acetylacetone and hexafluoroacetylacetone–water complexes in argon and nitrogen matrices

Association of acetylacetone molecules with water was studied by means of infrared absorption spectroscopy aided by matrix isolation technique. The spectra of acetylacetone–water mixtures isolated in low temperature argon and nitrogen matrices revealed additional spectral bands, not observed in the spectra of pure substances, thus confirming the formation of hydrogen bonded complexes. The precise assignment of the spectral bands was performed by varying the sample concentration, performing annealing experiments and DFT B3LYP 6-311++G(3df, 3pd) calculations. Positions of the associated water bands indicate a medium strength hydrogen bond comparable to the one observed in the water trimers. The effect of hydrogen bond formation is rather minimal for the acetylacetone molecule and our experiments confirm no significant influence on an internal hydrogen bond structure or dynamics in the acetylacetone molecule. Similar conclusions are valid in the case of the D2O D2-acetylacetone complex. Different situation is observed when CH3 groups in acetylacetone are replaced with CF3 groups. The calculated energy of the complex is twice as small. This is also confirmed by a very small bounded OH stretch shift. This observation confirms that the electronic structure of the molecular groups even relatively far away from the hydrogen bond accepting atom has a large influence on its possibility to form a hydrogen bond.

FTIR matrix isolation and theoretical studies of glycolic acid dimers

Glycolic acid (GA) dimers were studied in low temperature argon matrices by means of FTIR spectroscopy. Experimentally, the dimers were produced when monomeric glycolic acid molecules were thermally mobilized upon annealing of argon matrices at 25–35 K. The experimental spectra observed upon annealing indicate the presence of three different dimer structures. Computationally, MP2 and DFT calculations were used to study the potential dimer species in order to scrutinize the possible dimer structures, their energetics and their spectral features. Altogether 27 local minima were found for dimer structures for the three lowest conformers of glycolic acid considered based on previous studies on glycolic monomer in argon matrices. Comparing the computational and the experimental spectra especially in the OH and CO stretching regions it was possible to assign the experimental observations to the three most stable dimer species.

Controlled light-driven switching in 2-thiobenzimidazole

The optically-controllable reversible single-molecule photoswitching in 2-thiobenzimidazole (C7H6N2S; 2TBI) is experimentally demonstrated. Monomers of the target compound were isolated in low temperature argon matrices and investigated by infrared spectroscopy. After matrix deposition, only the thione tautomer of the compound was observed. Such result is in accordance with the predicted relative energy of the two tautomers (thione and thiol forms; ΔE(thiol-thione) = 44.6 kJ mol−1, as obtained at the DFT(B3LYP)/6−311 + +G(d,p) level of approximation). In situ irradiation of the initially deposited matrix at λ = 307 nm, using an UV tunable narrowband light source, led to conversion of the thione form of 2TBI into the thiol tautomer. In turn, subsequent irradiation at λ = 246 nm resulted in the reverse, thiol→thione, photoconversion, demonstrating that the two tautomers can be selectively interconverted through optical control. Noteworthy, both photoprocesses take place without simultaneous significant photodecomposition of the compound, thus making this chemical system a promising candidate for acting as a molecular switch. The observed phototautomerizations are rationalized in terms of the Photo-Induced hydrogen-atom Detachment-Association (PIDA) mechanism.

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.

Formation of coronene:water complexes: FTIR study in argon matrices and theoretical characterisation.

In this paper, we report a combined theoretical and experimental study of coronene:water interactions in low temperature argon matrices. The theoretical calculations were performed using the mixed density functional-based tight binding/force field approach. The results are discussed in the light of experimental matrix isolation FTIR spectroscopic data. We show that, in the solid phase, (C24H12)(H2O)n (n ≤ 6) σ-type complexes, i.e. with water molecules coordinated on the edge of coronene, are formed, whereas in the gas phase, π-interaction is preferred. These σ-complexes are characterised by small shifts in water absorption bands and a larger blue shift of the out-of-plane γ(CH) deformation of coronene, with the shift increasing with the number of complexed water molecules. Such σ interaction is expected to favour photochemical reaction between water and coronene at the edges of the coronene molecule, leading to the formation of oxidation products at low temperature, even in the presence of only a few water molecules and at radiation energies below the ionisation potential of coronene.

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.

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.

Degradation mechanism of γ-irradiated polytetrafluoroethylene (PTFE) powder by low-temperature matrix-isolation infrared spectroscopy and chemiluminescence spectroscopy

In order to elucidate the mechanism of degradation of γ-irradiated polytetrafluoroethylene (PTFE), gases evolved by isothermal heating under vacuum were trapped in low-temperature argon matrices. Infrared spectra of the evolved gases were assigned to COF2 and CF4 by comparison with the corresponding literatures. Kinetic analyses of the IR absorbance and chemiluminescence intensity changes against heating time were carried out to determine the rate constants of the thermal reactions, showing that CF4 was produced more rapidly than COF2. By comparison between the rate constants obtained by infrared spectroscopy and chemiluminescence spectroscopy, we propose a new thermal reaction mechanism of γ-irradiated PTFE at the molecular level. Thermal reaction mechanism of γ-irradiated polytetrafluoroethylene (PTFE) is elucidated at the molecular level by kinetic analysis, where a new multichannel Fourier-transform chemiluminescence spectrometer was used.

Infrared spectra and UV-induced photochemistry of methyl aziridine-2-carboxylate isolated in argon and xenon matrices

Methyl aziridine-2-carboxylate (MA2C) has been isolated in low temperature argon and xenon matrices and its structure and photochemistry were studied by FTIR spectroscopy. The reactant as well as the main photoproducts were characterized by comparison of their experimental IR spectra with spectra calculated at the DFT(B3LYP)/6-311++G(d,p) level. The theoretical calculations predicted the existence of two low energy MA2C conformers, differing by the orientation of the OCCN dihedral angle. Both conformers were identified in the studied matrices. Both narrowband tunable and broadband UV irradiations of matrix-isolated MA2C yielded isomerization photoproducts resulting from cleavage of the CC and weakest CN bonds of the aziridine ring. Irradiation with UV laser-light at λ=235nm resulted in the formation of the E isomer of methyl 2-(methylimino)-acetate (MMIA) and the Z isomer of methyl 3-iminopropanoate (M3IP). Subsequent irradiation at 290nm led to observation of new bands resulting from E→Z isomerization of MMIA, while bands due to M3IP remained unchanged. The photoproduced Z isomer of MMIA could be subsequently consumed upon higher-wavelength irradiation (λ=330nm). The initially produced MMIA conformer was found to obey the nonequilibrium of excited rotamers (NEER) principle. No photoproducts resulting from the cleavage of the strongest CN bond of the MA2C aziridine ring were observed, nor that of methyl 3-aminoacrylate (M3AA), which could in principle be obtained also by cleavage of the weakest CN bond of the MA2C aziridine ring, but would imply a different H-atom migration simultaneous with the ring opening process. These results indicate that both the differential electronic characteristics of the CN bonds of substituted aziridine rings and the type of required H-atom migration are major factors in determining the specific photochemistries of substituted aziridines. Photofragmentation reactions of MA2C were also observed, through identification of various related products, e.g., acetonitrile, methanol, methane, CO and CO2.

Thermal Decomposition of 2(3H) and 2(5H) Furanones: Theoretical Aspects.

The thermal decomposition reactions of 2(3H) and 2(5H) furanones and their methyl derivatives are explored. Theoretical calculations of the barriers, reaction enthalpies, and the properties of these and intermediate species are reported using the composite model chemistry CBS-QB3 and also the functional M06-2X allied to the 6-311++G(d,p) basis set. Thus, the bond dissociation enthalpies, ionization energies, and unimolecular chemical kinetic rate constants in the high-pressure limit were computed. We show that flow reactor experiments that intimated that heating the 2(3H) furanone converts it to the isomeric 2(5H) furanone occurs via a 1 → 2 H-transfer reaction to an open ring ketenoic aldehyde. The latter can then ring close to the other isomeric structure. The final products acrolein and carbon monoxide are only formed from 2(3H), and acrolein will further decompose to ethylene and CO. Comparable channels explain the interconversion of 5-methyl-2(3H) furanone to its 2(5H) isomer and to the formation of methyl vinyl ketone and CO. The influence of the methyl group at other positions on the ring is hardly of significance except in the case of 5-methyl-2(5H) furanone where a hydrogen atom transfer from the methyl group leads to the formation of a doubly unsaturated carboxylic compound, 2,4-pentadienoic acid. Studies of the UV photolysis of the parent compounds in both low-temperature inert argon matrices and in solution are broadly in accord with the thermal findings insofar as product formation is concerned and with our theoretical calculations. The dominant features of the early decomposition chemistry of these compounds are simple hydrogen transfer and simultaneous ring opening reactions, which do however result in some quite unusual species.

UV-light induced conformational changes of 2-pyridinecarboxylic acid in low-temperature argon matrices

Conformational changes of 2-pyridinecarboxylic acid (2-picolinic acid) upon UV irradiation have been investigated by low-temperature matrix-isolation infrared spectroscopy. Only one conformer having an intramolecular hydrogen bond of COOH⋯N in the pyridine ring is found to exist in argon matrices after deposition before UV irradiation, in contrast to a reported feature in the CCl4 solution. The hydrogen bond is broken by UV irradiation, resulting in two less stable conformers; one increases immediately at the early irradiation stage while the other increases slowly during the prolonged irradiation time. The conformations around the OCOH and CCOOH bonds of the photoproducts are identified by assignments of the IR bands measured in an argon matrix with an aid of the density-functional-theory calculation. The proposed photoreaction pathways of the conformational changes based on this observation are supported by a kinetic analysis of the IR absorbance changes with the reactants and the photoproducts against the irradiation time.