Matrix Isolation Research Articles

Characterization of competing halogen-bonding and hydrogen-bonding motifs in the acetonitrile/hydrogen iodide dimer

Three different C3v configurations of the CH3CN/HI dimer have been characterized using MP2 and CCSD(T) methods with large correlation consistent basis sets. All three stationary points are minima. The hydrogen bonded CH3CN⋯HI configuration is the global minimum (GM) with an electronic dissociation energy exceeding 4 kcal mol−1 near the CCSD(T) complete basis set (CBS) limit. A strongly bound halogen-bonded form of the dimer, CH3CN⋯IH, lies within 0.9 kcal mol−1 of the GM according to CCSD(T) electronic energies extrapolated to the CBS limit. The energetic separation between the two minima decreases by approximately 0.1 kcal mol−1 at all levels of theory when the harmonic zero-point vibrational energies are included. A third minimum was identified in which iodine interacts with the hydrogens of the methyl group (HI⋯CH3CN). This minimum is significantly higher in energy than the GM, almost within 1 kcal mol−1 of the dissociation limit. The GM has been previously identified via matrix isolation infrared spectroscopy. The energetics, vibrational frequencies, and infrared intensities computed here corroborate the tentative assignment of a second feature in the HI stretching region of the experimental infrared spectrum to the halogen-bonded configuration.

The effects of conformation and intermolecular hydrogen bonding on the structure and IR spectra of flutamide; a study based on the matrix isolation technique, ab initio and DFT calculations

In this study, stable conformers of flutamide referred to as an anticancer drug were searched through a relaxed potential energy surface scan carried out at the B3LYP/6-31G(d) level of theory. This was followed by geometry optimization and thermochemistry calculations performed with the HF-SCF, MP2, B3LYP methods and the 6-31G(d), 6–311++G(d,p), aug-cc-pvTZ basis sets for each of the determined minimum energy conformers. The results revealed that flutamide has at least five stable conformers and two of them provide the major contribution to the observed matrix isolation infrared (IR) spectra of the molecule. The effects of conformational variety and intermolecular hydrogen bonding interactions on the observed IR spectra of flutamide were interpreted in the light of the vibrational spectral data obtained for the most stable monomer and dimer forms of the molecule at the same levels of theory. Pulay’s “Scaled Quantum Mechanical-Force Field (SQM-FF)” method was used in the refinement of the calculated harmonic wavenumbers, IR intensities and potential energy distributions. This scaling method which proved its superiority to both anharmonic frequency calculations and other scaling methods helped us to correctly interpret the remarkable differences between the matrix IR spectra of flutamide in argon and the condensed phase IR spectra of the molecule in solvents such as KBr, H2O, D2O, ethanol and methanol.

Radiation-induced transformations of isolated phosphine molecules at cryogenic temperatures: Spectroscopic and chemical aspects

The radiation-induced transformations of isolated phosphine molecules in a series of solid noble gas matrices occurring under the action of X-rays at 4.5 K were studied by FTIR spectroscopy. It was shown that decomposition was quite efficient (the corresponding radiation-chemical yields of PH3 degradation were estimated as 5.8, 4.2, 3.5, and 2.0 molecules per 100 eV for neon, argon, krypton, and xenon, respectively). The radiolysis proceeds via two channels yielding PH2• and PH, respectively (the spectroscopic and kinetic data suggest that the latter species is partially trapped in the same cage with hydrogen molecules). Comparative studies using direct activation of isolated phosphine molecules in matrices at λ = 185 nm revealed similarity in the degradation pathways under radiolysis and VUV photolysis. Spectroscopic characteristics of the observed products and possible astrochemical implications of the results are discussed.

Collective stabilization through n→π* and P…π phosphorous bonding with cooperative halogen and hydrogen bonding in POCl3-Nitrile dimers: Matrix isolation infrared spectroscopic and ab initio computational studies

In the present study, the interaction between phosphoryl chloride (POCl3) with acetonitrile (CH3CN) and benzonitrile (C6H5CN) was explored using matrix isolation infrared spectroscopy and quantum chemical computations. The computations performed at MP2 and B3LYP-GD3 levels of theory with aug-cc-pVDZ basis set indicated the dominant mode of stabilization in POCl3-CH3CN (PACN) dimer is through n→π* (lp(O)…π*(CN)) interaction and for the POCl3-C6H5CN (PBCN) dimer it is predominantly by P…π phosphorous bonding interaction. Computations revealed that the nitrile moiety plays a significant role towards the stability in both the class of dimers. PACN heterodimer appears to be the first prototype, with the -CN moiety playing the acceptor through n→π* charge transfer interaction. The characteristic geometries of the heterodimers stabilized by n→π* and/or P…π interactions have been generated within inert gas matrixes at the cryogenic temperature of 12 K and identified using infrared spectroscopy. The interactions have been comprehensively characterized using quantum theory of atoms in molecules, natural bond orbital analysis, electrostatic potential mapping, energy decomposition and non-covalent interaction analyses.

F2BMF (M = B and Al) Molecules: A Matrix Infrared Spectra and Theoretical Calculations Investigation.

Reactions of laser-ablated B and Al atoms with BF3 have been explored in the 4 K excess neon through the matrix isolation infrared spectrum, isotopic substitutions and quantum chemical calculations. The inserted complexes F2BMF (M = B, Al) were identified by anti-symmetric and symmetric stretching modes of F-B-F, and the F-11B-F stretch modes are at 1336.9 and 1202.4 cm-1 for F211B11BF and at 1281.5 and 1180.8 cm-1 for F211BAlF. The CASSCF analysis, EDA-NOCV calculation and the theory of atoms-in-molecules (AIM) are applied to investigate the bonding characters of F2BBF and F2BAlF molecules. The bonding difference between boron and aluminum complexes reveals interesting chemistries, and the FB species stabilization by a main group atom was first observed in this article.

Matrix effects in MI-VCD spectra of two chiral oxiranes and their potential microscopic origin.

Combining vibrational circular dichroism (VCD) spectroscopy with the matrix isolation (MI) technique opens up interesting possibilities to study chiral molecules. MI involves the isolation of guest species in inert solid matrices at cryogenic temperatures. Hence, MI-VCD measures are solid-state VCD measurements, and as such, can suffer from mostly birefringance-related artefacts in the same way as common solid-state VCD measurements. In this contribution, we demonstrate that the sample preparation condition have tremendous impact on the quality and reliability of the recorded MI-VCD spectra. While MI-IR spectra are basically blind to these artefacts, the variation of deposition temperatures and host flow rates seem to control whether high quality MI-VCD spectra are obtained or if depolarization effects lead to completely obscured spectra. For two selected examples, styrene oxide (SO) and 1-phenyl propylene oxide (PPO), we discuss how the various experimental conditions may lead to the aforementioned effects and give a microscopic description of their origin.

Reactions of oxygen atoms with fluoroform and its radiolysis products: matrix isolation and ab initio study.

The investigation of the reactions of oxygen atoms with fluoroform (CHF3) molecules and products of their degradation present significant interest for better understanding of the impact of chemically inert fluorinated compounds on atmospheric chemistry and may provide a deeper insight into mechanisms of chemical processes occurring under the action of hard UV and ionizing radiation. In the present study we applied a matrix isolation technique with FTIR spectroscopic detection combined with ab initio calculations to address this issue. It was found that the reactions of "hot" (translationally excited) O(1D) atoms produced by X-ray or UV radiation from appropriate precursors (N2O or H2O) resulted in the formation of carbonyl fluoride (COF2) and its complex with HF. The complex was detected and characterized for the first time. Singlet oxygen atoms also probably react with the products of radiation-induced degradation of fluoroform (CF3 and CF2). Additionally, the reaction of "hot" O(3P) atoms with fluoroform may occur to a certain extent yielding the CF3 radical. No evidence for the reactions of thermal O(3P) atoms with CHF3 or products of its degradation was found under the experimental conditions used. The implications of the results of this model study for understanding the evolution of fluoroform in the upper layers of the stratosphere and ionosphere are discussed.

Spectroscopic identification of interstellar relevant 2-iminoacetaldehyde.

Imines play a fundamental role in organic synthesis and some of them have been detected in space. However, the simplest imines are spectroscopically not well-characterized. Herein we present the infrared and UV/Vis spectroscopic characterization of 2-iminoacetaldehyde using cryogenic matrix isolation techniques. After UV irradiation of 2-azidoacetaldehyde in solid argon at 3 K we identified two conformers of 2-iminoacetaldehyde, which can be photochemically interconverted. Deuterium labelling experiments and high level ab initio coupled cluster calculations at the CCSD(T)/CBS level of theory provide further evidence for the formation of 2-iminoacetaldehyde.

Matrix-isolation vibrational circular dichroism (VCD) spectroscopy of chiral 1-phenyl-1-propanol.

Matrix Isolation IR and VCD spectroscopy is used to characterize the self-aggregation of the title compound. It is shown that only the IR spectral region of the OH-/CH-stretching modes is sensitive to hydrogen bonding interactions and that the fingerprint region is not notably affected. In contrast, some characteristic VCD spectral features can be identified in the fingerprint region.

Accurate calculation of the interaction of a barium monofluoride molecule with an argon atom: A step towards using matrix isolation of BaF for determining the electron electric dipole moment

Calculations of the BaF–Ar triatomic system are performed with a relativistic Hamiltonian and coupled cluster theory at the CCSD(T) level for 1386 positions of the Ar atom relative to the BaF molecule. Calculations are repeated with increasing basis sets (double-, triple-, quadruple- and quintuple-zeta), and these are extrapolated to estimate the complete-basis-set limit. The resulting energies provide a potential energy for the interaction of an Ar atom with a BaF molecule. A fit is presented that parametrizes this potential. This work is needed for an understanding of the position, modes of motion and energy shifts of BaF isolated in an Ar matrix. This understanding will guide the EDM3 collaboration in its pursuit of a precision measurement of the electron electric dipole moment using BaF isolated in a cryogenic Ar matrix.

Simultaneous observation of halogen-lone pair and halogen-π interactions of ferrocene derivatives under cryogenic conditions.

Contrasting cryosolutions and matrix isolation infrared spectroscopy, we investigate weak intermolecular interactions in complexes of iodo trifluoroethene (C2F3I) and N,N-dimethyl ferrocenyl amine as well as the parent ferrocene. In liquid xenon, solely the C-I⋯N halogen bond can be observed, while the confined environment in solid argon allows for the characterization of C-I⋯π and π⋯π bonded complexes.

Hydrogen bond properties of Se in [ROH-Se(CH3)2] complexes (R = H, CH3, C2H5): matrix-isolation infrared spectroscopy and theoretical calculations.

Se is now considered as a potential centre for hydrogen bond interactions. The hydrogen bond acceptor ability of Se has been investigated in [ROH-Se(CH3)2] complexes (R = H, CH3, and C2H5) using matrix-isolation infrared spectroscopy and electronic structure calculations. The first impression of the IR spectra of the hydrogen bond complexes of [ROH-Se(CH3)2] in N2 and Ar matrices is presented here. Moreover, no spectroscopic data are available for the [HOH-Se(CH3)2] complex. Vibrational spectra in the OH stretching region indicate the formation of the [ROH-Se(CH3)2] complex under the matrix-isolation conditions. Comparison of the experimental spectra with the simulated vibrational frequencies at different levels of theory confirms the formation of the 1 : 1 cluster of [ROH-Se(CH3)2] stabilised by O-H⋯Se hydrogen bond interactions. Multiple conformers of the [CH3OH-Se(CH3)2] complex having marginally different stabilisation energies have been predicted from electronic structure calculations and signatures of the same have been observed under the cold conditions of matrix isolation. Conformer specific assignment of the 1 : 1 cluster of [C2H5OH-Se(CH3)2] (anti and gauche forms) has been carried out in both the matrices. Concentration dependent experiments indicate the formation of higher order clusters and/or mixed clusters along with the formation of a 1 : 1 cluster for CH3OH and C2H5OH. The nature of the selenium centred hydrogen bond has been delineated using AIM, NBO and energy decomposition analysis. A comparison of similar complexes of H2O, CH3OH, and C2H5OH with O, S and Se indicates that Se is not far away in hydrogen bond acceptor ability compared to O and S.

Photochemical study and vibrational spectra of propiolamide isolated in low-temperature Ar, Xe, and N2 matrices

Propiolamide (HCCCONH2, PA) has been isolated in low-temperature matrices (Ar, Xe, and N2) and studied by matrix isolation infrared (IR) spectroscopy and quantum chemical calculations undertaken at the DFT(B3LYP)/6-311++G(d,p) level of theory. In situ broadband UV light (λ > 235 nm) irradiation of matrix-isolated PA led to the observation of new bands ascribed to different photoproducts resulting from three distinct photoreaction pathways: (i) tautomerization to propiolimidic acid (HCCC(OH)NH), (ii) CC bond cleavage, with formation of acetylene (HCCH) and isocyanic acid (HNCO), and (iii) decarbonylation, leading to generation of ethynamine (HCCNH2). Pathways (i) and (ii) were observed in all matrices, while (iii) was only observed in the matrices of the rare gases. Observation of characteristic bands due to the different photoproducts has been established, and the assignment of the IR spectra for all the species was carried out. As a whole, the detailed structural, vibrational, and photochemical data reported in this article appear relevant to the rational practical use of PA in its multiple application areas (in particular in the pharmaceutical and materials sciences domains) as well as for its analytical determination, including its search in the interstellar space.

A charged diatomic triple-bonded U≡N species trapped in C82 fullerene cages

Actinide diatomic molecules are ideal models to study elusive actinide multiple bonds, but most of these diatomic molecules have so far only been studied in solid inert gas matrices. Herein, we report a charged U≡N diatomic species captured in fullerene cages and stabilized by the U-fullerene coordination interaction. Two diatomic clusterfullerenes, viz. UN@Cs(6)-C82 and UN@C2(5)-C82, were successfully synthesized and characterized. Crystallographic analysis reveals U-N bond lengths of 1.760(7) and 1.760(20) Å in UN@Cs(6)-C82 and UN@C2(5)-C82. Moreover, U≡N was found to be immobilized and coordinated to the fullerene cages at 100 K but it rotates inside the cage at 273 K. Quantum-chemical calculations show a (UN)2+@(C82)2− electronic structure with formal +5 oxidation state (f1) of U and unambiguously demonstrate the presence of a U≡N bond in the clusterfullerenes. This study constitutes an approach to stabilize fundamentally important actinide multiply bonded species.

Breaking and Formation of Intramolecular Hydrogen Bonds in Dihydroxybenzaldehydes through UV-Induced Conformational Changes in a Low-Temperature Matrix.

Hydrogen bonding (HB) has been receiving attention from both experimental and theoretical researchers since its discovery in the 1920s due to its impact on many chemical and biological processes. However, despite the large number of investigations conducted on this topic, the nature of the HBs and, in particular, the estimation of intramolecular HB energies are still very active subjects of research. In this context, here we report a matrix isolation infrared spectroscopy study of 2,3-dihydroxybenzaldehyde (2,3-DHBA) and 2,4-dihydroxybenzaldehyde (2,4-DHBA), which contain two [one resonance-assisted HB (RAHB) and one conventional HB] and one (RAHB) intramolecular hydrogen bonds, respectively, in their most stable conformer. After isolation of the compounds in cryogenic (15 K) krypton matrices, ultraviolet irradiation led to the formation of higher-energy conformers (by a 180° rotation of the hydroxyl and aldehyde groups), which implies breaking of the intramolecular HBs initially existing in the isolated species and, in the case of 2,3-DHBA, to the formation of a new intramolecular HB. In this way, we were able to manipulate the structure of the molecules, allowing to characterize a diversity of intramolecular HBs in which the OH groups participate (from strong intramolecular RAHBs to weaker conventional HBs, and also no intramolecular HBs) through the corresponding vibrational signatures. The spectroscopic studies were complemented by natural bond orbital analysis and the molecular tailoring approach method, in order to estimate the relative intramolecular HB energies and explore the substitution effects on HB strength.

Fluorescence Excitation and Dispersed Fluorescence Spectra of the 1-Hydronaphthyl Radical (1-C10H9) in Solid para-Hydrogen.

Matrix isolation spectroscopy with para-hydrogen (p-H2) has previously been employed to record IR absorption spectra of hydrogenated and protonated polycyclic aromatic hydrocarbons (PAHs), prospective carriers of unidentified infrared and diffuse interstellar bands. Despite the promising prospects of p-H2 as matrix host, especially the rather weak interaction with the guest molecules and the resulting small matrix shifts, p-H2 matrix isolation spectroscopy has rarely been applied to study electronic transitions of guest molecules. Here, we present the dispersed fluorescence and fluorescence excitation spectrum of the 1-hydronaphthyl radical (1-C10H9) isolated in solid p-H2. We observed a strong 000 band associated with the electronic transition to the first excited electronic state at 18881 cm-1, red-shifted by ∼68 cm-1 relative to a value reported for jet-cooled 1-C10H9. From a comparison of our experimental results to simulated vibrationally resolved electronic absorption and emission spectra computed on the basis of (TD-)DFT geometry optimizations and scaled harmonic vibration calculations using the FCclasses code, we derived assignments for observed vibronic transitions. The dispersed fluorescence spectrum of 1-C10H9 is new; it complements the infrared spectrum and identified many vibrational modes unidentifiable with infrared. The excitation spectrum covers a much wider spectral range than previous reports. We compare the excitation spectrum in solid p-H2 to the reported electronic absorption spectrum of jet-cooled gaseous 1-C10H9 and that of 1-C10H9 isolated in solid Ne to assess the influence of p-H2 as a matrix host on the electronic transition of 1-C10H9 and discuss a potential contribution of 1-C10H9 to the diffuse interstellar bands.

Advances in Regenerative Medicine and Biomaterials.

The low regenerative potential of the human body hinders proper regeneration of dysfunctional or lost tissues and organs due to trauma, congenital defects, and diseases. Tissue or organ transplantation has hence been a major conventional option for replacing the diseased or dysfunctional body parts of the patients. In fact, a great number of patients on waiting lists would benefit tremendously if tissue and organs could be replaced with biomimetic spare parts on demand. Herein, regenerative medicine and advanced biomaterials strive to reach this distant goal. Tissue engineering aims to create new biological tissue or organ substitutes, and promote regeneration of damaged or diseased tissue and organs. This approach has been jointly evolving with the major advances in biomaterials, stem cells, and additive manufacturing technologies. In particular, three-dimensional (3D) bioprinting utilizes 3D printing to fabricate viable tissue-like structures (perhaps organs in the future) using bioinks composed of special hydrogels, cells, growth factors, and other bioactive contents. A third generation of multifunctional biomaterials could also show opportunities for building biomimetic scaffolds, upon which to regenerate stem cells in vivo. Besides, decellularization technology based on isolation of extracellular matrix of tissue and organs from their inhabiting cells is presented as an alternative to synthetic biomaterials. Today, the gained knowledge of functional microtissue engineering and biointerfaces, along with the remarkable advances in pluripotent stem cell technology, seems to be instrumental for the development of more realistic microphysiological 3D in vitro tissue models, which can be utilized for personalized disease modeling and drug development. This chapter will discuss the recent advances in the field of regenerative medicine and biomaterials, alongside challenges, limitations, and potentials of the current technologies.

Structural and physicochemical characterization of an aminosugar-rich exopolysaccharide isolated from a Chlorella sp.

In the present work an aminosugar-rich exopolysaccharide (EPS) of a novel Chlorella sp. strain was isolated and characterized. Isolation of the EPS matrix was a fast and financially viable procedure based upon consecutive centrifugation and resuspension steps without the use of hazardous chemicals. After acidic hydrolysis, the EPS matrix was examined by Nuclear Magnetic Resonance (NMR) Spectroscopy as well as Electrospray Ionization Tandem Mass Spectrometry (ESI-MS/MS), and it was shown that it is a heteropolysaccharide. Aminosugar moieties, mainly glucosamine and galactosamine, constituted >40 % of the structure's relative molar ratio, followed by rhamnose, arabinose, galactose, xylose and mannose. Differential scanning calorimetry (DSC) analysis showed that the EPS matrix exhibited specific thermal transitions in the range of 59–88 °C corresponding to crystallization steps, while thermogravimetric analysis showed that the polysaccharide presented exceptional thermal stability at temperatures up to 600 °C. Powder X-ray diffraction analysis showed that the polymer exhibited high crystallinity after one DSC cycle. The isolated EPS exhibited a maximum total antioxidant capacity of 11.5 mg ascorbic acid equivalents·g−1 and a reducing power of 11.2 mg ascorbic acid equivalents·g−1, while the ferric reducing antioxidant power of the EPS reached 37.2 μM Fe2+·g−1. In all cases the antioxidant and reducing power of the EPS was dose-dependent. The EPS exhibited a moderate hydrogen peroxide and hydroxyl radical scavenging activity reaching a maximum of approximately 40 % at 2 mg mL−1 concentration. All these structural and physicochemical characteristics, along with the strong antioxidant profile, make this macromolecule a strong candidate for further exploitation in commercial applications in the pharmaceutical, nutraceutical and bioplastic industries.

Structure, conformational landscape and UV-induced selective rotamerization of 2-aminoacetanilide

The molecular structure, conformational space and UV-induced rotamerization and decarbonylation of 2-aminoacetanilide (2AA) were investigated by matrix isolation infrared spectroscopy and quantum chemical electronic structure calculations. The compound was isolated in a cryogenic (15 K) argon matrix, and four conformers were spectroscopically identified: two trans-amide (OCNH dihedral ∼ 180°) conformers (trans-I and trans-II), and two higher-energy cis-amide (OCNH dihedral ∼ 0°) conformers (cis-I and cis-II). These four conformers were found to be present in the as-deposited matrix of 2AA in a population ratio matching well that predicted by the calculations for the gas-phase equilibrium at the temperature of the vapor of the compound before deposition (60 °C = 333.15 K). The calculations predicted also the existence of an additional higher-energy trans-amide conformer (trans-III) which was not observed experimentally. In situ broadband UV irradiation (λ > 235 nm) of the matrix-isolated compound was found to induce selective conversion of conformer trans-I into conformer trans-II, in a few minutes (55 % after 2 min. of irradiation; 70 % after 10 min.), while the populations of the cis-amide conformers did not change. Prolonged UV irradiation was found to result in decomposition of the compound, leading to generation of carbon monoxide and 2-amine-N-methylaniline. The infrared spectra of the experimentally relevant conformers of 2AA were interpreted and assigned with help of normal coordinate analysis, and the different behavior of the conformers of 2AA upon UV-irradiation of the argon matrix was explained with help of time-dependent DFT (TD-DFT) calculations.

Communication: Electronic transition of the l-C6 + cation at 417 nm.

A new electronic transition is reported for the linear C6 + cation with an origin at 416.8nm. This spectrum can be compared to the matrix isolation spectra at lower energies reported previously by Fulara et al. [J. Chem. Phys. 123, 044305 (2005)], which assigned linear and cyclic isomers, and to the gas phase spectrum reported previously by Campbell and Dunk [Rev. Sci. Instrum. 90, 103101 (2019)], which detected the same cyclic-isomer spectrum reported by Fulara. Comparisons to electronically excited states and vibrations predicted by various forms of theory allow assignment of the spectrum to a new electronic state of linear C6 +. The spectrum consists of a strong origin band, two vibronic progression members at higher energy and four hot bands at lower energies. The hot bands provide the first gas phase information on ground state vibrational frequencies. The vibrational and electronic structure of C6 + provide a severe challenge to computational chemistry.