Hydrophobic hydration of the hydrocarbon adamantane in amorphous ice

Hydrophobic molecules are by definition difficult to hydrate. Previous studies in the area of hydrophobic hydration have therefore often relied on using amphiphilic molecules where the hydrophilic part of a molecule enabled the solubility in liquid water. Here, we show that the hydrophobic adamantane (C10H16) molecule can be fully hydrated through vapour codeposition with water onto a cryogenic substrate at 80 K resulting in the matrix isolation of adamantane in amorphous ice. Using neutron diffraction in combination with the isotopic substitution method and the empirical potential structure refinement technique, we find that the first hydration shell of adamantane is well structured consisting of a hydrogen-bonded cage of 28 water molecules that is also found in cubic structure II clathrate hydrates. The four hexagonal faces of the 51264 cage are situated above the four methine (CH) groups of adamantane whereas the methylene (CH2) groups are positioned below the edges of two adjoining pentagonal faces. The oxygen atoms of the 28 water molecules can be categorised on the basis of symmetry equivalences as twelve A, twelve B and four C oxygens. The water molecules of the first hydration shell display orientations consistent with those expected for a clathrate-hydrate-type cage, but also unfavourable ones with respect to the hydrogen bonding between the water molecules. Annealing the samples at 140 K, which is just below the crystallisation temperature of the matrix, removes the unfavourable orientations and leads to a slight increase in the structural order of the first hydration shell. The very closest water molecules display a tendency for their dipole moments to point towards the adamantane which is attributed to steric effects. Other than this, no significant polarisation effects are observed which is consistent with weak interactions between adamantane and the amorphous ice matrix. FT-IR spectroscopy shows that the incorporation of adamantane into amorphous ice leads to a weakening of the hydrogen bonds. In summary, the matrix-isolation of the highly symmetric adamantane in amorphous ice provides an interesting test case for hydrophobic hydration. Studying the structure and spectroscopic properties of water at the interface with hydrophobic hydrocarbons is also relevant for astrophysical environments, such as comets or the interstellar medium, where amorphous ice and hydrocarbons have been shown to coexist in large quantities.

Structures and stabilities of PAH clusters solvated by water aggregates: The case of the pyrene dimer

Although clusters made of polycyclic aromatic hydrocarbon and water monomers are relevant objects in both atmospheric and astrophysical science, little is known about their energetic and structural properties. In this work, we perform global explorations of the potential energy landscapes of neutral clusters made of two pyrene units and one to ten water molecules using a density-functional-based tight-binding (DFTB) potential followed by local optimizations at the density-functional theory level. We discuss the binding energies with respect to various dissociation channels. It shows that cohesion energies of the water clusters interacting with a pyrene dimer are larger than those of the pure water clusters, reaching for the largest clusters an asymptotic limit similar to that of pure water clusters and that, although the hexamer and octamer can be considered magic numbers for isolated water clusters, it is not the case anymore when they are interacting with a pyrene dimer. Ionization potentials are also computed by making use of the configuration interaction extension of DFTB, and we show that in cations, the charge is mostly carried by the pyrene molecules.

Prediction of •OH-Initiated and •NO3-Initiated Transformation Products of Polycyclic Aromatic Hydrocarbons by Electronic Structure Approaches

The abiotic reaction products of polycyclic aromatic hydrocarbons (PAHs) with hydroxyl radicals (^•OH) and nitrate radicals (^•NO₃) are nitro-, oxygen-, and hydroxyl-containing PAHs (NPAHs, OPAHs, and OHPAHs). Four methods of the highest occupied molecular orbital (HOMO), Fukui function (FF), dual descriptor (DD), and population of π electrons (PP-π) are selected to predict the chemical reactivity of PAHs attacked by ^•OH and ^•NO₃ in this study. The predicted ^•OH-initiated and ^•NO₃-initiated transformation products are compared with the main PAH transformation products (PAH-TPs) observed in the laboratory. The results indicate that PP-π and DD approaches fail to predict the transformation products of fused PAHs containing five-membered rings. By predicting the PAH-TPs of 13-14 out of the 15 parent PAHs accurately, HOMO and FF methods were shown to be suitable for predicting the transformation products formed from the abiotic reactions of fused PAHs with ^•OH and ^•NO₃.

Effect of Microhydration on the Temporary Anion States of Pyrene

The influence of incremental hydration (≤4) on the electronic resonances of the pyrene anion is studied using two-dimensional photoelectron spectroscopy. The photoexcitation energies of the resonances do not change; therefore, from the anion's perspective, the resonances remain the same, but from the neutral's perspective of the electron-molecule reaction, the resonances decrease in energy by the binding energy of the water molecules. The autodetachment of the resonances shows that hydration has very little effect, showing that even the dynamics of most of the resonances are not impacted by hydration. Two specific resonances do show changes that are explained by the closing of specific autodetachment channels. The lowest-energy resonance leads to efficient electron capture as observed through thermionic emission and evaporation of water molecules (dissociative electron attachment). The implications of low-energy electron capture in dense molecular interstellar clouds are discussed.

Infrared Spectroscopy and Photochemistry of Anthracoronene in Cosmic Water Ice

We present a laboratory study of the polycyclic aromatic hydrocarbon (PAH) anthracoronene (AntCor, C₃₆H₁₈) in simulated interstellar ices in order to determine its possible contribution to the broad infrared absorption bands in the 5-8 μm wavelength interval. The Fourier transform infrared (FTIR) spectrum of AntCor, codeposited with water ice, was collected. The FTIR spectrum of the sample irradiated with ultraviolet photons was also collected. Unirradiated and UV-irradiated AntCor embedded in water ice have not been studied before; therefore, the molecule's band positions and intensities were compared to published data on AntCor in an argon matrix and theoretical calculations (DFT), as well as the published results of its parent molecules, coronene and anthracene, in water ice. The experimental band strengths for unirradiated AntCor exhibit variability as a function of PAH:H₂O concentration, with two distinct groupings of band intensities. AntCor clustering occurs for all concentrations and has a significant effect on PAH degradation rates and photoproduct variability. Near-IR spectra of irradiated AntCor samples show that AntCor⁺ production increases as the concentration of AntCor in water ice decreases. Photoproduct bands are assigned to AntCor⁺, cationic alcohols, protonated AntCor, and ketones. We report the rate constants of the photoproduct production for the 1:1280 AntCor:H₂O concentration. CO₂ production from AntCor is much less than what was previously reported for Ant and Cor and exhibits two distinct regimes as a function of AntCor:H₂O concentration. The contribution of AntCor photoproducts to astronomical spectra can be estimated by comparison with the observed intensities in the 7.4-8.0 μm range.

Density-functional tight-binding: basic concepts and applications to molecules and clusters

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.

On the formation of phosphorous polycyclic aromatics hydrocarbons (PAPHs) in astrophysical environments

The formation of phosphorous-containing polycyclic aromatic hydrocarbons (PAPHs) in astrophysical contexts is proposed and analyzed by means of computational methods [B3LYP-D3BJ/ma-def2-TZVPP, MP2-F12, CCSD-F12b and CCSD(T)-F12b levels of theory]. A "bottom-up" approach based on a radical-neutral reaction scheme between acetylene (C₂H₂) and the CP radical was used investigating: (a) the synthesis of the first PAPH (C₅H₅P) "phosphinine"; (b) PAPH growth by addition of C₂H₂ to the C₅H₄P radical; (c) PAPH synthesis by addition reactions of one CP radical and nC₂H₂ to a neutral PAH. Results show: (I) the formation of the phosphinine radical has a strong thermodynamic tendency (-133.3 kcal mol^-1) and kinetic barriers ≤5.4 kcal mol^-1; (II) PAPH growth by nC₂H₂ addition on the radical phosphinine easily and exothermically produces radicals (1a- or 1-phospha-naphtalenes with kinetic barriers ≤7.1 kcal mol^-1 and reaction free energies ≤-102.5 kcal mol^-1); (III) the addition of a single CP + nC₂H₂ to a neutral benzene generates a complex chemistry where the main product is 2-phospha-naphtalene; (IV) because of the CP radical character, its barrierless addition to a PAH produces a resonant stabilized PAPH, becoming excellent candidates for addition reactions with neutral or radical hydrocarbons and PAHs; (V) the same energy trend between all four levels of theory continues a well-calibrated computational protocol to analyze complex organic reactions with astrochemical interest using electronic structure theory.

A multifunctional setup to record FTIR and UV-vis spectra of organic molecules and their photoproducts in astronomical ices

This article describes a new, multi-functional, high-vacuum ice setup that allows to record the in situ and real-time spectra of vacuum UV (VUV)-irradiated non-volatile molecules embedded in a low-temperature (10 K) amorphous solid water environment. Three complementary diagnostic tools-UV-visible (UV-vis) and Fourier Transform Infrared (FTIR) spectroscopy and temperature-programmed desorption quadrupole mass spectrometry-can be used to simultaneously study the physical and chemical behavior of the organic molecules in the ice upon VUV irradiation. The setup is equipped with a temperature-controlled sublimation oven that enables the controlled homogeneous deposition of solid species such as amino acids, nucleobases, and polycyclic aromatic hydrocarbons (PAHs) in ice mixtures prepared from precursor gases and/or liquids. The resulting ice is photo-processed with a microwave discharge hydrogen lamp, generating VUV radiation with a spectral energy distribution representative for the interstellar medium. The characteristics, performance, and future potential of the system are discussed by describing three different applications. First, a new method is introduced, which uses broadband interference transmission fringes recorded during ice deposition, to determine the wavelength-dependent refractive index, n_λ, of amorphous solid water. This approach is also applicable to other solids, pure and mixed. Second, the UV-vis and FTIR spectroscopy of an VUV-irradiated triphenylene:water ice mixture is discussed, monitoring the ionization efficiency of PAHs in interstellar ice environments. The third and final example investigates the stability of solid glycine upon VUV irradiation by monitoring the formation of dissociation products in real time.

Theoretical determination of adsorption and ionisation energies of polycyclic aromatic hydrocarbons on water ice

In dense interstellar environments, Polycyclic Aromatic Hydrocarbons (PAHs) are likely to condense onto or integrate into water ice mantles covering dust grains. Understanding the role of ice in the photo-induced processes involving adsorbed PAHs is therefore a key issue in astrochemistry. This requires (i) the knowledge of PAH-ice interactions, i.e. PAH-ice adsorption energies and local structures at the PAH-ice interface, as well as (ii) the understanding of the fate of electrons in the PAH-ice system upon excitation. Regarding (i), in this work, we determined the lowest energy structures of PAH-ice systems for a variety of PAHs ranging from naphthalene to ovalene on three types of ice - crystalline (Ih and Ic) and amorphous (low density) - using an explicit description of the electrons and a finite-sized system. The electronic structure was determined using the Self Consistent Charge Density Functional based Tight Binding (SCC-DFTB) scheme with modified Mulliken charges in order to ensure a good description of the studied systems. Regarding (ii), the influence of the interaction with ice on the Vertical Ionisation Potentials (VIPs) of the series of PAHs was determined using the constrained SCC-DFTB scheme benchmarked against correlated wavefunction results for PAH-(H₂O)_n (n = 1-6, 13) clusters. The results show a deviation equal, at most, to ∼1.4 eV of the VIPs of PAHs adsorbed on ice with respect to the gas phase values. Our results are discussed in the light of experimental data and previous theoretical studies.

Adsorption of PAHs on interstellar ice viewed by classical molecular dynamics

The present work represents a complete description of PAH–ice interaction in the ground electronic state and at low temperature, providing the binding energies and barrier heights necessary to the ongoing improvement of astrochemical models.

Photochemistry of coronene in cosmic water ice analogs at different concentrations

This work presents the photochemistry of ultraviolet (UV) irradiated coronene in water ices at 15 K, studied using mid-infrared Fourier transform (FTIR) spectroscopy for C24H12:H2O at concentrations of (1:50), (1:150), (1:200), (1:300) and (1:400). Previous UV irradiation studies of anthracene:H2O, pyrene:H2O and benzo[ghi]perylene:H2O ices at 15 K have shown that aromatic alcohols and ketones, as well as CO2 and H2CO are formed at very low temperatures. Like-wise, here, in addition to the coronene cation, hydroxy-, keto-, and protonated coronene (coronene-H+) are formed. The rate constants for the decay of neutral coronene and for the formation of photoproducts have been derived. It is shown that PAHs and their UV-induced PAH:H2O photoproducts have mid-infrared spectroscopic signatures in the 5-8 μm region that can contribute to the interstellar ice components described by Boogert et al. (2008) as C1-C5. Our results suggest that oxygenated and hydrogenated PAHs could be in UV-irradiated regions of the ISM where water-rich ices are important.

Mechanisms of the Formation of Adenine, Guanine, and Their Analogues in UV-Irradiated Mixed NH3:H2O Molecular Ices Containing Purine

We investigated the formation mechanisms of the nucleobases adenine and guanine and the nucleobase analogues hypoxanthine, xanthine, isoguanine, and 2,6-diaminopurine in a UV-irradiated mixed 10:1 H₂O:NH₃ ice seeded with precursor purine by using ab initio and density functional theory computations. Our quantum chemical investigations suggest that a multistep reaction mechanism involving purine cation, hydroxyl and amino radicals, together with water and ammonia, explains the experimentally obtained products in an independent study. The relative abundances of these products appear to largely follow from relative thermodynamic stabilities. The key role of the purine cation is likely to be the reason why purine is not functionalized in pure ammonia ice, where cations are promptly neutralized by free electrons from NH₃ ionization. Amine group addition to purine is slightly favored over hydroxyl group attachment based on energetics, but hydroxyl is much more abundant due to higher abundance of H₂O. The amino group is preferentially attached to the 6 position, giving 6-aminopurine, that is, adenine, while the hydroxyl group is preferentially attached to the 2 position, leading to 2-hydroxypurine. A second substitution by hydroxyl or amino group occurs at either the 6 or the 2 position depending on the first substitution. Given that H₂O is far more abundant than NH₃ in the experimentally studied ices (as well as based on interstellar abundances), xanthine and isoguanine are expected to be the most abundant bi-substituted photoproducts. Key Words: Astrophysical ice-Abiotic organic synthesis-Nucleic acids-Origin of life-RNA world. Astrobiology 17, 771-785.

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

Coronene preferentially forms σ-type rather than π-type complexes with water in low temperature argon matrices.

Vibrational spectroscopy and molecular dynamics of water monomers and dimers adsorbed on polycyclic aromatic hydrocarbons

This paper reports structures, energetics, dynamics and spectroscopy of H2O and (H2O)2 systems adsorbed on coronene (C24H12), a compact polycyclic aromatic hydrocarbon (PAH). On-the-fly Born-Oppenheimer molecular dynamics simulations are performed for temperatures T varying from 10 to 300 K, on a potential energy surface obtained within the self-consistent-charge density-functional based tight-binding (SCC-DFTB) approach. Anharmonic infrared (IR) spectra are extracted from these simulations. We first benchmark the SCC-DFTB semi-empirical hamiltonian vs. DFT (Density Functional Theory) calculations that include dispersion, on (C6H6)(H2O)1,2 small complexes. We find that charge corrections and inclusion of dispersion contributions in DFTB are necessary to obtain consistent structures, energetics and IR spectra. Using this Hamiltonian, the structures, energetics and IR features of the low-energy isomers of (C24H12)(H2O)1,2 are found to be similar to the DFT ones, with evidence for a stabilizing edge-coordination. The temperature dependence of the motions of H2O and (H2O)2 on the surface of C24H12 is analysed, revealing ultra-fast periodic motion. The water dimer starts diffusing at a higher temperature than the water monomer (150 K vs. 10 K respectively), which appears to be consistent with the binding energies. Qualitative and quantitative analyses of the effects of T on the IR spectra are performed. Anharmonic factors in particular are derived and it is shown that they can be used as signatures for the presence of PAH-water complexes. Finally, this paper lays the foundations for the studies of larger (PAH)m(H2O)n clusters, that can be treated with the efficient computational approach benchmarked in this paper.