Phases of Solid Methanol

AQUILA: A laboratory facility for the irradiation of astrochemical ice analogs by keV ions

The detection of various molecular species, including complex organic molecules relevant to biochemical and geochemical processes, in astronomical settings, such as the interstellar medium or the outer solar system, has led to the increased need for a better understanding of the chemistry occurring in these cold regions of space. In this context, the chemistry of ices prepared and processed at cryogenic temperatures has proven to be of particular interest due to the fact that many interstellar molecules are believed to originate within the icy mantles adsorbed on nano- and micro-scale dust particles. The chemistry leading to the formation of such molecules may be initiated by ionizing radiation in the form of galactic cosmic rays or stellar winds, and thus, there has been an increased interest in commissioning experimental setups capable of simulating and better characterizing this solid-phase radiation astrochemistry. In this article, we describe a new facility called AQUILA (Atomki-Queen's University Ice Laboratory for Astrochemistry), which has been purposefully designed to study the chemical evolution of ices analogous to those that may be found in the dense interstellar medium or the outer solar system as a result of their exposure to keV ion beams. The results of some ion irradiation studies of CH3OH ice at 20 K are discussed to exemplify the experimental capabilities of the AQUILA as well as to highlight its complementary nature to another laboratory astrochemistry setup at our institute.

Infrared Spectral Signatures of Nucleobases in Interstellar Ices I: Purines

The purine nucleobases adenine and guanine are complex organic molecules that are essential for life. Despite their ubiquitous presence on Earth, purines have yet to be detected in observations of astronomical environments. This work therefore proposes to study the infrared spectra of purines linked to terrestrial biochemical processes under conditions analogous to those found in the interstellar medium. The infrared spectra of adenine and guanine, both in neat form and embedded within an ice made of H2O:NH3:CH4:CO:CH3OH (10:1:1:1:1), were analysed with the aim of determining which bands attributable to adenine and/or guanine can be observed in the infrared spectrum of an astrophysical ice analogue rich in other volatile species known to be abundant in dense molecular clouds. The spectrum of adenine and guanine mixed together was also analysed. This study has identified three purine nucleobase infrared absorption bands that do not overlap with bands attributable to the volatiles that are ubiquitous in the dense interstellar medium. Therefore, these three bands, which are located at 1255, 940, and 878 cm-1, are proposed as an infrared spectral signature for adenine, guanine, or a mixture of these molecules in astrophysical ices. All three bands have integrated molar absorptivity values (ψ) greater than 4 km mol-1, meaning that they should be readily observable in astronomical targets. Therefore, if these three bands were to be observed together in the same target, then it is possible to propose the presence of a purine molecule (i.e., adenine or guanine) there.

Low Temperature Multilayer Adsorption of Methanol and Ethanol on Platinum

Adsorption of methanol and ethanol on the clean Pt (111) surface was studied at temperatures between 80 and 130 K using polarization-modulation infrared reflection absorption spectroscopy (PM-IRRAS). It was shown that adsorption of methanol at 80 K leads to the formation of amorphous solid methanol, and fast crystallization of the amorphous phase occurs upon warming at 100 K. Vapor deposition of methanol at 100 K directly leads to the formation of well-crystallized layers of solid methanol. According to PM-IRRAS, these crystalline layers consist of chains of hydrogen-bonded methanol molecules lying in a plane oriented close to the normal to the platinum surface. Adsorbed methanol is removed completely from platinum after heating to 120 K. Vapor deposition of ethanol at 80 K also leads to the formation of amorphous solid ethanol. However, subsequent warming does not lead to ordering of the adsorption layers, and at 130 K, ethanol is also completely desorbed.

Comparative electron irradiations of amorphous and crystalline astrophysical ice analogues

Laboratory studies of the radiation chemistry occurring in astrophysical ices have demonstrated the dependence of this chemistry on a number of experimental parameters. One experimental parameter which has received significantly less attention is that of the phase of the solid ice under investigation. In this present study, we have performed systematic 2 keV electron irradiations of the amorphous and crystalline phases of pure CH₃OH and N₂O astrophysical ice analogues. Radiation-induced decay of these ices and the concomitant formation of products were monitored in situ using FT-IR spectroscopy. A direct comparison between the irradiated amorphous and crystalline CH₃OH ices revealed a more rapid decay of the former compared to the latter. Interestingly, a significantly lesser difference was observed when comparing the decay rates of the amorphous and crystalline N₂O ices. These observations have been rationalised in terms of the strength and extent of the intermolecular forces present in each ice. The strong and extensive hydrogen-bonding network that exists in crystalline CH₃OH (but not in the amorphous phase) is suggested to significantly stabilise this phase against radiation-induced decay. Conversely, although alignment of the dipole moment of N₂O is anticipated to be more extensive in the crystalline structure, its weak attractive potential does not significantly stabilise the crystalline phase against radiation-induced decay, hence explaining the smaller difference in decay rates between the amorphous and crystalline phases of N₂O compared to those of CH₃OH. Our results are relevant to the astrochemistry of interstellar ices and icy Solar System objects, which may experience phase changes due to thermally-induced crystallisation or space radiation-induced amorphisation.

Effects of mixing between short-chain and branched-chain alcohols in protonated clusters

The previous analysis of the neat protonated branched-chain alcohol clusters revealed the impact of steric repulsion and dispersion of the bulky alkyl group on the hydrogen-bonded (H-bonded) structures and their temperature-dependence. To further understand the influence of the alkyl groups in H-bonded clusters, we studied the mixing of the two extremes of alcohols, methanol (MeOH) and tert-butyl alcohol (t-BuOH), with an excess proton. Infrared spectroscopy and a structural search of first principles calculations on the size-selected clusters H⁺(MeOH)_m(t-BuOH)_t (m + t = 4 and 5) were conducted. Temperature-dependence of the dominant H-bonded structures was explored by the Ar-tagging technique and quantum harmonic superposition approach. By introducing the dispersion-corrected density functional theory methods, it was shown that the effects of dispersion due to the bulky alkyl groups in the mixed clusters cannot be ignored for t≥ 2. The computational results qualitatively depicted the characteristics of the observed IR spectra, but overestimation of the temperature-dependence with dispersion correction was clearly seen due to the unbalanced correction between linear H-bonded structures and compact cyclic ones. These results demonstrate the importance of extensive investigation and benchmarks on different levels of theory, and that a properly sampled structure database is crucial to evaluate theoretical models.

Internal electric fields in methanol [MeOH]2-6 clusters

Water and methanol are well known solvents showing cooperative hydrogen bonding, however the differences in the hydrogen bonding pattern in water and methanol are due to the presence of the methyl group in methanol. The presence of the methyl group leads to formation of C-HO hydrogen bonds apart from the usual O-HO hydrogen bonds. The electric fields evaluated along the hydrogen bonded donor OH and CH groups reveal that the C-HO hydrogen bonds can significantly influence the structure and energetics (by about 20%) of methanol clusters. A linear Stark effect was observed on the hydrogen bonded OH groups in methanol clusters with a Stark tuning rate of 3.1 cm^-1 (MV cm^-1)^-1 as an average behaviour. Furthermore, the Stark tuning of the OH oscillators in methanol depends on their hydrogen bonding environment wherein molecules with the DAA motif show higher rates than the rest. The present work suggests that the OH group of methanol has higher sensitivity as a vibrational probe relative to the OH group of water.

Towards reliable ab initio sublimation pressures for organic molecular crystals - are we there yet?

Knowledge of molecular crystal sublimation equilibrium data is vital in many industrial processes, but this data can be difficult to measure experimentally for low-volatility species. Theoretical prediction of sublimation pressures could provide a useful supplement to experiment, but the exponential temperature dependence of sublimation (or any saturated vapor) pressure curve makes this challenging. An uncertainty of only a few percent in the sublimation enthalpy or entropy can propagate to an error in the sublimation pressure exceeding several orders of magnitude for a given temperature interval. Despite this fundamental difficulty, this paper performs some of the first ab initio predictions of sublimation pressure curves. Four simple molecular crystals (ethane, methanol, benzene, and imidazole) have been selected for a case study showing the currently achievable accuracy of quantum chemistry calculations. Fragment-based ab initio techniques and the quasi-harmonic approximation are used for calculations of cohesive and phonon properties of the crystals, while the vapor phase is treated by the ideal gas model. Ab initio sublimation pressure curves for model compounds are compared against their experimental counterparts. The computational uncertainties are estimated, weak points of the computational methodology are identified, and further improvements are proposed.

Competition between hydrogen bonds and van der Waals forces in intermolecular structure formation of protonated branched-chain alcohol clusters

To investigate the influence of bulky alkyl groups on hydrogen-bonded (H-bonded) network structures of alcohols, infrared (IR) spectra of protonated clusters of 2-propanol (2-PrOH) and tert-butyl alcohol (t-BuOH) were observed in the OH and CH stretch regions. In addition, by varying the tag species, the temperature dependence profile of the isomer population of H+(t-BuOH)n was revealed. An extensive search for stable isomers was performed using dispersion-corrected density functional theory methods, and temperature-dependent IR spectral simulations were done on the basis of the harmonic superposition approximation. The computational results qualitatively agreed with the observed size and temperature dependence of the H-bonded network structures of these protonated bulky alcohol clusters. However, the difficulty in the quantitative evaluation of dispersion was also demonstrated. It was shown that H+(2-PrOH)n (n = 4-7) have essentially the same network structures as the protonated normal alcohol clusters studied so far. On the other hand, H+(t-BuOH)n (n = 4-8) showed a clear preference for the smaller-membered ring structures, that is very different from the preference of the protonated normal alcohol clusters. The origin of the different structure preferences was discussed in terms of the steric effect and dispersion.

Expedite random structure searching using objects from Wyckoff positions

Random structure searching has been proved to be a powerful approach to search and find the global minimum and the metastable structures. A true random sampling is in principle needed yet it would be highly time-consuming and/or practically impossible to find the global minimum for the complicated systems in their high-dimensional configuration space. Thus the implementations of reasonable constraints, such as adopting system symmetries to reduce the independent dimension in structural space and/or imposing chemical information to reach and relax into low-energy regions, are the most essential issues in the approach. In this paper, we propose the concept of "object" which is either an atom or composed of a set of atoms (such as molecules or carbonates) carrying a symmetry defined by one of the Wyckoff positions of space group and through this process it allows the searching of global minimum for a complicated system to be confined in a greatly reduced structural space and becomes accessible in practice. We examined several representative materials, including Cd₃As₂ crystal, solid methanol, high-pressure carbonates (FeCO₃), and Si(111)-7 × 7 reconstructed surface, to demonstrate the power and the advantages of using "object" concept in random structure searching.

Hydrogen bond network structures of protonated short-chain alcohol clusters

Protonated alcohol clusters enable extraction of the physical essence of the nature of hydrogen bond networks.

Ab initio thermodynamic properties and their uncertainties for crystalline α-methanol

To investigate the performance of quasi-harmonic electronic structure methods for modeling molecular crystals at finite temperatures and pressures, thermodynamic properties are calculated for the low-temperature α polymorph of crystalline methanol and their computational uncertainties are analyzed.

Infrared spectra and band strengths of CH3SH, an interstellar molecule

Three solid phases of CH₃SH (methanethiol or methyl mercaptan) have been prepared and their mid-infrared spectra recorded at 10–110 K, with an emphasis on the 17–100 K region.

Non-covalent interaction of benzene with methanol and diethyl ether solid surfaces

We have investigated the interactions involved at the interface of binary, layered ices (benzene on methanol and on diethyl ether) by means of laboratory experiments and ab initio calculations on model clusters.

Structure prediction of the solid forms of methanol: an ab initio random structure searching approach

Liquid methanol and methanol clusters have been comprehensively studied to reveal their local structure and hydrogen bond networks.

Spectroscopic constraints on CH3OH formation: CO mixed with CH3OH ices towards young stellar objects

The prominent infrared absorption band of solid CO - commonly observed towards young stellar objects (YSOs) - consists of three empirically determined components. The broad 'red component' (2136 cm-1, 4.681 μm) is generally attributed to solid CO mixed in a hydrogen-bonded environment. Usually, CO embedded in the abundantly present water is considered. However, CO:H2O mixtures cannot reproduce the width and position of the observed red component without producing a shoulder at 2152 cm-1, which is not observed in astronomical spectra. Cuppen et al. showed that CO:CH3OH mixtures do not suffer from this problem. Here, this proposition is expanded by comparing literature laboratory spectra of different CO-containing ice mixtures to high-resolution (R = λ/Δλ = 25000) spectra of the massive YSO AFGL 7009S and of the low-mass YSOL1489 IRS. The previously unpublished spectrum of AFGL 7009S shows a wide band of solid 13CO, the first detection of 13CO ice in the polar phase. In this source, both the 12CO and 13CO ice bands are well fitted with CO:CH3OH mixtures, while respecting the profiles and depths of the methanol bands at other wavelengths, whereas mixtures with H2O cannot. The presence of a gradient in the CO:CH3OH mixing ratio in the grain mantles is also suggested. Towards L1489 IRS, the profile of the 12CO band is also better fitted with CH3OH-containing ices, although the CH3OH abundance needed is a factor of 2.4 above previous measurements. Overall, however, the results are reasonably consistent with models and experiments about formation of CH3OH by the hydrogenation of CO ices.

Coverage Dependence of Methanol Dissociation on TiO2(110)

Although the photochemistry of methanol on TiO₂(110) has been widely investigated as a prototypical model of the photocatalytic reaction of organic molecules, the most fundamental question of the adsorption state of methanol on TiO₂(110) is still unclear. We have investigated the adsorption of methanol on TiO₂(110) using sum frequency generation vibrational spectroscopy (SFG-VS) and density functional theory (DFT) calculations. The SFG results indicate the dissociation of methanol is highly dependent on the coverage. The DFT calculations suggest that the methanol prefers the partially dissociated structure at low coverage, whereas the second layer methanol, which is hydrogen-bonded to the bridge-bonded oxygen site, largely blocks the dissociation of the first layer methanol. Our results not only resolves a long-standing debate regarding the adsorption state of methanol on TiO₂(110) but also provides a detailed insight into the adsorption structure and sheds light on the photochemistry on this surface at the molecular level.

Structure and energetics of hydrogen-bonded networks of methanol on close packed transition metal surfaces

Methanol is a versatile chemical feedstock, fuel source, and energy storage material. Many reactions involving methanol are catalyzed by transition metal surfaces, on which hydrogen-bonded methanol overlayers form. As with water, the structure of these overlayers is expected to depend on a delicate balance of hydrogen bonding and adsorbate-substrate bonding. In contrast to water, however, relatively little is known about the structures methanol overlayers form and how these vary from one substrate to another. To address this issue, herein we analyze the hydrogen bonded networks that methanol forms as a function of coverage on three catalytically important surfaces, Au(111), Cu(111), and Pt(111), using a combination of scanning tunneling microscopy and density functional theory. We investigate the effect of intermolecular interactions, surface coverage, and adsorption energies on molecular assembly and compare the results to more widely studied water networks on the same surfaces. Two main factors are shown to direct the structure of methanol on the surfaces studied: the surface coverage and the competition between the methanol-methanol and methanol-surface interactions. Additionally, we report a new chiral form of buckled hexamer formed by surface bound methanol that maximizes the interactions between methanol monomers by sacrificing interactions with the surface. These results serve as a direct comparison of interaction strength, assembly, and chirality of methanol networks on Au(111), Cu(111), and Pt(111) which are catalytically relevant for methanol oxidation, steam reforming, and direct methanol fuel cells.