Chapter

Ab initio Calculation of Binding Energies of Interstellar Sulphur-Containing Species on Crystalline Water Ice Models

Authors:
To read the full-text of this research, you can request a copy directly from the authors.

Abstract

There are different environments in the interstellar medium (ISM), depending on the density, temperature and chemical composition. Among them, molecular clouds, often referred to as the cradle of stars, are paradigmatic environments relative to the chemical diversity and complexity in space. Indeed, there, radio to far-infrared observations revealed the presence of several molecules in the gas phase, while near-infrared spectroscopy detected the existence of submicron sized dust grains covered by \(\mathrm{H}_{2}\mathrm{O}\)-dominated ice mantles. The interaction between gas-phase species and the surfaces of water ices is measured by the binding energy (BE), a crucial parameter in astrochemical modelling. In this work, the BEs of a set of sulphur-containing species on water ice mantles have been computed by adopting a periodic ab initio approach using a crystalline surface model. The Density Functional Theory (DFT)-based B3LYP-D3(BJ) functional was used for the prediction of the structures and energetics. DFT BEs were refined by adopting an ONIOM-like procedure to estimate them at CCSD(T) level toward complete basis set extrapolation, in which a very good correlation between values has been found. Moreover, we show that geometry optimization with the computationally cheaper HF-3c method followed by single point energy calculations at DFT to compute the BEs is a suitable cost-effective recipe to arrive at BE values of the same quality as those computed at full DFT level. Finally, computed data were compared with the available literature data.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

ResearchGate has not been able to resolve any citations for this publication.
Article
Full-text available
One of the major obstacles to accurately modeling the interstellar chemistry is inadequate knowledge of the binding energy (BE) of interstellar species with dust grains. In denser regions of molecular clouds, where very complex chemistry is active, interstellar dust is predominantly covered by H2O molecules, thus it is essential to know the interaction of gas-phase species with water ice to trace realistic physical and chemical processes. To this end, we consider water (cluster) ice to calculate the BE of several atoms, molecules, and radicals of astrochemical interest. Systematic studies have been carried out to come up with a relatively more accurate BE of astrophysically relevant species on water ice. We increase the size of the water cluster methodically to capture the realistic situation. Sequentially, one, three, four, five, and six water molecules are considered to represent water ice analogs in increasing order of complexity. We note that for most of the species considered here, as we increase the cluster size, our calculated BE value starts to converge toward the experimentally obtained value. More specifically, our computed results with the water c-pentamer (average deviation from experiment ∼±15.8%) and c-hexamer (chair) (average deviation from experiment ∼±16.7%) configurations are found to be nearer to an experimentally obtained value other than the value found for the water clusters we consider. © 2018. The American Astronomical Society. All rights reserved..
Article
Full-text available
The latest release of the Crystal program for solid-state quantum-mechanical ab initio simulations is presented. The program adopts atom-centered Gaussian-type functions as a basis set, which makes it possible to perform all-electron as well as pseudopotential calculations. Systems of any periodicity can be treated at the same level of accuracy (from 0D molecules, clusters and nanocrystals, to 1D polymers, helices, nanorods, and nanotubes, to 2D monolayers and slab models for surfaces, to actual 3D bulk crystals), without any artificial repetition along nonperiodic directions for 0–2D systems. Density functional theory calculations can be performed with a variety of functionals belonging to several classes: local-density (LDA), generalized-gradient (GGA), meta-GGA, global hybrid, range-separated hybrid, and self-consistent system-specific hybrid. In particular, hybrid functionals can be used at a modest computational cost, comparable to that of pure LDA and GGA formulations, because of the efficient implementation of exact nonlocal Fock exchange. Both translational and point-symmetry features are fully exploited at all steps of the calculation, thus drastically reducing the corresponding computational cost. The various properties computed encompass electronic structure (including magnetic spin-polarized open-shell systems, electron density analysis), geometry (including full or constrained optimization, transition-state search), vibrational properties (frequencies, infrared and Raman intensities, phonon density of states), thermal properties (quasi-harmonic approximation), linear and nonlinear optical properties (static and dynamic [hyper]polarizabilities), strain properties (elasticity, piezoelectricity, photoelasticity), electron transport properties (Boltzmann, transport across nanojunctions), as well as X-ray and inelastic neutron spectra. The program is distributed in serial, parallel, and massively parallel versions. In this paper, the original developments that have been devised and implemented in the last 4 years (since the distribution of the previous public version, Crystal14, occurred in December 2013) are described.
Article
Full-text available
We report the detection of the 62 μm feature of crystalline water ice in emission toward the bow-shaped Herbig-Haro object HH 7. Significant amounts of far-infrared continuum emission are also detected between 10 and 200 μm, so that Herbig-Haro objects cease to be pure emission-line objects at far-infrared wavelengths. The formation of crystalline water ice mantles requires grain temperatures Tgr 100 K at the time of mantle formation, suggesting that we are seeing material processed by the HH 7 shock front. The deduced ice mass is ~2 × 10-5 M☉, corresponding to a water column density N(H2O) ~ 1018 cm-2; an estimate of the [H2O]/[H] abundance yields values close to the interstellar gas-phase oxygen abundance. The relatively high dust temperature and the copious amounts of gas-phase water needed to produce the observed quantity of crystalline water ice suggest a scenario in which both dissociative and nondissociative shocks coexist. The timescale for ice mantle formation is of the order of ~400 yr, so that the importance of gas-phase water cooling as a shock diagnostic may be greatly diminished.
Article
Full-text available
The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
Article
Carbon monoxide (CO) is the second most abundant molecule in the gas-phase of the interstellar medium. In dense molecular clouds, it is also present in the solid-phase as a constituent of the mixed water-dominated ices covering dust grains. Its presence in the solid-phase is inferred from its infrared (IR) signals. In experimental observations of solid CO/water mixed samples, its IR frequency splits into two components, giving rise to a blue- and a redshifted band. However, in astronomical observations, the former has never been observed. Several attempts have been carried out to explain this peculiar behaviour, but the question still remains open. In this work, we resorted to pure quantum mechanical simulations in order to shed some light on this problem. We adopted different periodic models simulating the CO/H2O ice system, such as single and multiple CO adsorption on water ice surfaces, CO entrapped into water cages and proper CO:H2O mixed ices. We also simulated pure solid CO. The detailed analysis of our data revealed how the quadrupolar character of CO and the dispersive forces with water ice determine the energetic of the CO/H2O ice interaction, as well as the CO spectroscopic behaviour. Our data suggest that the blueshifted peak can be assigned to CO interacting via the C atom with dangling H atoms of the water ice, while the redshifted one can actually be the result of CO involved in different reciprocal interactions with the water matrix. We also provide a possible explanation for the lack of the blueshifted peak in astronomical spectra. Our aim is not to provide a full account of the various interstellar ices, but rather to elucidate the sensitivity of the CO spectral features to different water ice environments.
Article
Advanced telescopes, such as ALMA and the James Webb Space Telescope, are likely to show that the chemical universe may be even more complex than currently observed, requiring astrochemical modelers to improve their models to account for the impact of new data. However, essential input information for gas−grain models, such as binding energies of molecules to the surface, have been derived experimentally only for a handful of species, leaving hundreds of species with highly uncertain estimates. We present in this paper a systematic study of the effect of uncertainties in the binding energies on an astrochemical two-phase model of a dark molecular cloud, using the rate equations approach. A list of recommended binding energy values based on a literature search of published data is presented. Thousands of simulations of dark cloud models were run, and in each simulation a value for the binding energy of hundreds of species was randomly chosen from a normal distribution. Our results show that the binding energy of H2 is critical for the surface chemistry. For high binding energies, H2 freezes out on the grain forming an H2 ice. This is not physically realistic, and we suggest a change in the rate equations. The abundance ranges found are in reasonable agreement with astronomical ice observations. Pearson correlation coefficients revealed that the binding energy of HCO, HNO, CH2, and C correlate most strongly with the abundance of dominant ice species. Finally, the formation route of complex organic molecules was found to be sensitive to the branching ratios of H2CO hydrogenation.
Article
Recent laboratory measurements have confirmed that chemical desorption (desorption of products due to exothermic surface reactions) can be an efficient process. The impact of including this process into gas-grain chemical models entirely depends on the formalism used and the associated parameters. Among these parameters, binding energies are probably the most uncertain ones for the moment. We propose a new model to compute binding energy of species to water ice surfaces. We have also compared the model results using either the new chemical desorption model proposed by Minissale et al. (2016) or the one of Garrod et al. (2007). The new binding energies have a strong impact on the formation of complex organic molecules. In addition, the new chemical desorption model from Minissale produces a much smaller desorption of these species and also of methanol. Combining the two effects, the abundances of CH3OH and COMs observed in cold cores cannot be reproduced by astrochemical models anymore.
Article
Freeze-out of the gas phase elements onto cold grains in dense interstellar and circumstellar media builds up ice mantles consisting of molecules that are mostly formed in situ (H2O, NH3, CO2, CO, CH3OH, and more). This review summarizes the detected infrared spectroscopic ice features and compares the abundances across Galactic, extragalactic, and solar system environments. A tremendous amount of information is contained in the ice band profiles. Laboratory experiments play a critical role in the analysis of the observations. Strong evidence is found for distinct ice formation stages, separated by CO freeze out at high densities. The ice bands have proven to be excellent probes of the thermal history of their environment. The evidence for the long-held idea that processing of ices by energetic photons and cosmic rays produces complex molecules is weak. Recent state of the art observations show promise for much progress in this area with planned infrared facilities.
Article
A quantum chemical method based on a Hartree-Fock calculation with a small Gaussian AO basis set is presented. Its main area of application is the computation of structures, vibrational frequencies, and noncovalent interaction energies in huge molecular systems. The method is suggested as a partial replacement of semiempirical approaches or density functional theory (DFT) in particular when self-interaction errors are acute. In order to get accurate results three physically plausible atom pair-wise correction terms are applied for London dispersion interactions (D3 scheme), basis set superposition error (gCP scheme), and short-ranged basis set incompleteness effects. In total nine global empirical parameters are used. This so-called Hartee-Fock-3c (HF-3c) method is tested for geometries of small organic molecules, interaction energies and geometries of noncovalently bound complexes, for supramolecular systems, and protein structures. In the majority of realistic test cases good results approaching large basis set DFT quality are obtained at a tiny fraction of computational cost. © 2013 Wiley Periodicals, Inc.
Article
A periodic Hartree-Fock ab initio study is presented concerning two proton-ordered structures of ordinary ice: one ferro-electric (C-ice), the other anti-ferro-electric (P-ice). The calculated energies are practically coincident, and in good agrement with the experimental stability of disordered ice Ih. Slabs are cut out from these crystals in order to formulate a model for studying the surface properties of ordinary ice. The stability of these two-dimensional periodic systems is discussed, and the relaxation of the P-ice slab formed by two bilayers parallel to the (001) face is considered. Finally, an embedded cluster method is adopted to calculate geometric and energetic properties of KOH and NaOH dissolved in C- and P-ice at low concentration. This study permits us to discuss the role of KOH in promoting the transition from disordered Ih to ordered C-ice, which has been observed to occur at 72 K [Leadbetter &etal;, J. Chem. Phys. 82, 424 (1985)].
Article
New models of the dense interstellar clouds chemistry in which both gas-phase and grain-surface chemistry occur are presented. The chemistry in quiescent clouds is described at the dust-grain and gas temperatures of 10 K and the gas density of 2 x 10 exp 4/cu cm. It is found that the synthesis of complex molecules on 10-K grain surfaces does not proceed even for models that are in atomic H and rich in H2, the activation energy of reactions of hydrocarbon radicals C(n) and C(n)H with H2 is 2100 K. Such a low activation energy allow tunnelling to take place and produce more saturated, less reactive molecular species. It is also found that cosmic ray desorption processes cannot prevent the bulk of the heavy gaseous material from accreting on to dust particles in sufficiently long times if the overall gas density is 2 x 10 exp 4/cu cm.
Article
Our Sun and planetary system were born about 4.5 billion years ago. How did this happen and what is our heritage from these early times? This review tries to address these questions from an astrochemical point of view. On the one hand, we have some crucial information from meteorites, comets and other small bodies of the Solar System. On the other hand, we have the results of studies on the formation process of Sun-like stars in our Galaxy. These results tell us that Sun-like stars form in dense regions of molecular clouds and that three major steps are involved before the planet formation period. They are represented by the pre-stellar core, protostellar envelope and protoplanetary disk phases. Simultaneously with the evolution from one phase to the other, the chemical composition gains increasing complexity. In this review, we first present the information on the chemical composition of meteorites, comets and other small bodies of the Solar System, which is potentially linked to the first phases of the Solar System's formation. Then we describe the observed chemical composition in the pre-stellar core, protostellar envelope and protoplanetary disk phases, including the processes that lead to them. Finally, we draw together pieces from the different objects and phases to understand whether and how much we inherited chemically from the time of the Sun's birth.
Article
The thermal desorption characteristics of 16 astrophysically relevant species from laboratory analogues of the icy mantles on interstellar dust grains have been surveyed in an extensive set of preliminary temperature programmed desorption experiments. The species can be separated into three categories based on behaviour. Water-like species have a single relevant desorption coincident with water. CO-like species show the volcano desorption and co-desorption of trapped molecules, monolayer desorption from the surface of water ice, and multilayer desorption if initially present in sufficient abundance in an outer layer separated from the water ice. Intermediate species show the two desorptions of trapped molecules, and may show a small monolayer desorption for molecules small enough to have a limited ability to diffuse through the structure of porous amorphous water ice. Methods by which the results obtained under laboratory conditions can be adapted for astrophysical situations are discussed.
Article
We report the detection of the 62 ensuremathmum feature of ensuremath crystallineensuremath<?iensuremath> water ice in emission toward the bow-shaped Herbig-Haro object HH 7. Significant amounts of far-infrared continuum emission are also detected between 10 and 200 ensuremathmum, so that Herbig-Haro objects cease to be pure emission-line objects at far-infrared wavelengths. The formation of crystalline water ice mantles requires grain temperatures Tensuremath grensuremath<?subensuremath>$gtrsim$100 K at the time of mantle formation, suggesting that we are seeing material processed by the HH 7 shock front. The deduced ice mass is textttchar1262 $times$ 10ensuremath -5ensuremath<?supensuremath> M?, corresponding to a water column density ensuremath Nensuremath<?iensuremath>(Hensuremath 2ensuremath<?subensuremath>O) textttchar126 10ensuremath 18ensuremath<?supensuremath> cmensuremath -2ensuremath<?supensuremath>; an estimate of the ?Hensuremath 2ensuremath<?subensuremath>O???H? abundance yields values close to the interstellar gas-phase oxygen abundance. The relatively high dust temperature and the copious amounts of gas-phase water needed to produce the observed quantity of crystalline water ice suggest a scenario in which both dissociative and nondissociative shocks coexist. The timescale for ice mantle formation is of the order of textttchar126400 yr, so that the importance of gas-phase water cooling as a shock diagnostic may be greatly diminished.
Article
We present the 1.9--4.2um spectra of the five bright (L<11.2) young stars associated with silhouette disks with moderate to high inclination angle of 39--80deg in the M42 and M43 regions. The water ice absorption is seen toward d121-1925 and d216-0939, while the spectra of d182-316, d183-405, and d218-354 show no water ice feature around 3.1um within the detection limits. By comparing the water ice features toward nearby stars, we find that the water ice absorption toward d121-1925 and d216-0939 most likely originates from the foreground material and the surrounding disk, respectively. The angle of the disk inclination is found to be mainly responsible for the difference of the optical depth of the water ice among the five young stars. Our results suggest that there is a critical inclination angle between 65deg and 75deg for the circumstellar disk where the water ice absorption becomes strong. The average density at the disk surface of d216-0939 was found to be 6.38x10^(-18) g cm^(-3). The water ice absorption band in the d216-0939 disk is remarkable in that the maximum optical depth of the water ice band is at a longer wavelength than detected before. It indicates that the primary carrier of the feature is purely crystallized water ice at the surface of the d216-0939 disk with characteristic size of ~0.8um, which suggests grain growth. This is the first direct detection of purely crystallized water ice in a silhouette disk.
Article
The IMOMM, IMOMO, and ONIOM methods have been proven to be powerful tools for the theoretical treatment of large molecular systems where different levels of theory are applied to different parts of a molecule. Within this framework we present a modified handling of the link atoms which are introduced to terminate the dangling bonds of the model system. Using this new scheme the definition of the combined energy gradient, the Hessian matrix, and the integration of higher derivatives of the energy with respect to nuclear coordinates and the electric field vector becomes straightforward. This allows for the first time the consistent combination of vibrational frequencies and the calculation of other molecular properties such as IR intensities, Raman intensities as well as dipole moments, polarizabilities, and hyperpolarizabilities. Test calculations for some typical as well as unusual examples and partitioning schemes are presented to demonstrate the power and limitations of the method and to provide guidelines for its applicability. Users of the method are strongly advised to test, calibrate and confirm for themselves the validity of the method combination and the model subsystem for the properties they want to calculate.
Article
Despite the remarkable thermochemical accuracy of Kohn–Sham density-functional theories with gradient corrections for exchange-correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional containing local-spin-density, gradient, and exact-exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first- and second-row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
Article
It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.
Article
Current gradient-corrected density-functional approximations for the exchange energies of atomic and molecular systems fail to reproduce the correct 1/r asymptotic behavior of the exchange-energy density. Here we report a gradient-corrected exchange-energy functional with the proper asymptotic limit. Our functional, containing only one parameter, fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
Article
A correlation-energy formula due to Colle and Salvetti [Theor. Chim. Acta 37, 329 (1975)], in which the correlation energy density is expressed in terms of the electron density and a Laplacian of the second-order Hartree-Fock density matrix, is restated as a formula involving the density and local kinetic-energy density. On insertion of gradient expansions for the local kinetic-energy density, density-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.
Article
Presented in this paper is an ab initio chemical model for dense interstellar clouds that incorporates 598 grain surface reactions, with small grains providing the reaction area. Gas-phase molecules are depleted through collisions with grains. The abundances of 372 chemical species are calculated as a function of time and are found to be of sufficient magnitude to explain most observations. Peak abundances are achieved on time scales of the order of 100,000 to 1 million years, depending on cloud density and kinetic temperature. The reaction rates for ion-molecule chemistry are approximately the same, indicating that surface and gas-phase chemistry may be coupled in certain regions. The composition of grain mantles is shown to be a function of grain radius. In certain grain-size ranges, large molecules containing two or more heavy atoms are more predominant than lighter 'ices' - H2O, NH3, and CH4. It is possible that absorption due to these large molecules in the mantle may contribute to the observed 3-micron band in astronomical spectra.
Gaussian16 Revision C.01
  • M J Frisch
Frisch, M.J., et al.: Gaussian16 Revision C.01. Gaussian Inc., Wallingford CT (2016)