Time-dependent chemistry in dense molecular clouds. II - Ultraviolet photoprocessing and infrared spectroscopy of grain mantles
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Dhendecourt, L. B.↗
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Time dependent chemistry in dense molecular clouds. III - Infrared band cross sections of molecules in the solid state at 10 K
Thin film transmission infrared spectra and a list of integrated absorbance values (band strengths) of bands in the 2.5 to 20 micron range of various molecular solids deposited on a CsI window cooled to 10 K are presented. These solids include molecules known or suspected to be present on interstellar grains such as H2O, CO, NH3 and CH4 and mixtures of these molecules as well as various hydrocarbons. The method is described by which the absorbance values derived can be used to estimate column densities of species adsorbed on interstellar grains and other solids associated with celestial IR sources.
Dhendecourt, L. B.↗
Shock chemistry in the molecular clouds associated with SNR IC 443
Observations of several interstellar molecules toward the highly perturbed B and G clouds associated with SNR IC 443 are reported. The results suggest that hot and dense material is present in the SNR, and that shocks are present in both regions. The HCO(+) abundance is shown to be a few times greater that found in cold quiescent gas, in contradiction with previous results. The SO, CS, CN, and NH3 abundances are similar to those found in cold dark clouds.
Ziurys, L. M.↗
Molecular dynamics based chemistry models of hypervelocity collisions of O(3P) + SO2( X , 1 A 1) in DSMC
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Neal Parsons↗
Developing Reaction Chemistry Models from Reactive Molecular Dynamics: TATB
Reactive Molecular Dynamic (RMD) are used to simulate the cook-off chemistry of TATB at a variety of fixed density and fixed temperature conditions. The chemical transformations are monitored using a Coordination Geometry Analysis (CGA) approach which tracks which atom types are bonded to each specific atom. This particularly identifies oxidation state changes that occur during the transformations. Correlations between these different chemical changes are identified using a Non-negative Matrix Factorization (NMF) approach. These identify reduced order chemistry models for the TATB system which contains six components whose concentration profiles are a function of both the temperature and density/pressure. The time histories of these transformations appear to show exponential growth/decay properties that could be fit with Arrhenius rates. These components should form the basis of deflagration rate models for these materials which could then be used in mesoscale simulations to analyze accidental initiation, shock-to-detonation and detonation propagation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular Magnetism in North America Conference
The report provides information on the Molecular Magnetism in North America (MAGNA) conference that the DOE funding supported. It was held 2/21/2020 - 2/24/2020 at the King and Prince Hotel on St. Simon’s Island in southern Georgia. It brought together workers from academic institutions and government laboratories working in the field of molecular magnetism, including synthetic chemistry of molecular and 1D-3D molecule-based materials, and the various physical and spectroscopic methods for their study. The oral program spanned 3½ days and comprised 32 talks (30 mins each) by faculty and government scientists, and 12 talks (15 mins each) by junior people (graduate students and postdoctorals). The poster session took place at 6 pm on Saturday, Feb 22nd, and comprised 21 posters. Total registrations for the meeting were 68.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The Chemistry and Excitation of Water in Molecular Clouds
We model the chemistry and thermal balance of opaque molecular clouds exposed to an external flux of ultraviolet photons. We include the processes of gas phase and grain surface chemical reactions; in particular we examine closely the freezing of atoms and molecules onto grain surfaces and the desorption of molecules from grain surfaces as a function of depth into a molecular cloud. We find that on the surface of a molecular cloud the gas phase water abundances are low because of photodissociation, and the grain phase water (ice) abundance is low because of photodesorption of water from the grain surfaces. Deeper into the cloud, at A(sub v) less than or approximately 2-8 depending on the strength of the external ultraviolet flux, the gas phase water abundance increases with depth as the photodissociation rates decline due to dust attenuation of the ultraviolet field. However, beyond A(sub v) less than or approximately 2-8 the gas phase water abundance declines because the water freezes as water ice on the grains, and photodesorption is no longer effective in clearing the ice. A peak water abundance of about 10(exp -6) to 10(exp -7) occurs at about A(sub v) approximately 2-8, relatively independent of the gas density and the ultraviolet field. We show that such a model matches very closely the observations of the Submillimeter Wave Astronomical Satellite (SWAS), a NASA Small Explorer Mission. The model elucidates several mechanisms that have been recently invoked to understand gas phase chemistry in clouds, including-the freeze-out of molecules onto grain surface, the desorption of these molecules from the surfaces, and the abundance gradients of molecules as functions of depth into molecular clouds.
Hollenbach, David↗
Ice Chemistry in Interstellar Dense Molecular Clouds, Protostellar Disks, and Comets
Despite the low temperatures (T less than 20K), low pressures, and low molecular densities found in much of the cosmos, considerable chemistry is expected to occur in many astronomical environments. Much of this chemistry happens in icy grain mantles on dust grains and is driven by ionizing radiation. This ionizing radiation breaks chemical bonds of molecules in the ices and creates a host of ions and radicals that can react at the ambient temperature or when the parent ice is subsequently warmed. Experiments that similar these conditions have demonstrated a rich chemistry associated with these environments that leads to a wide variety of organic products. Many of these products are of considerable interest to astrobiology. For example, the irradiation of simple ices has been shown to abiotically produce amino acids, nucleobases, quinones, and amphiphiles, all compounds that play key roles in modern biochemistry. This suggests extraterrestrial chemistry could have played a role in the origin of life on Earth and, by extension, do so on planets in other stellar systems.
Ice Irradiation↗
Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers
Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).
Jaffe, Richard↗
A non-mass-dependent oxygen isotope effect in the production of ozone from molecular oxygen - The role of molecular symmetry in isotope chemistry
It was previously reported that the reaction products from the synthesis of ozone in an electric discharge through molecular oxygen display a nonmass-dependent (NoMaDic) oxygen isotope effect. In this paper, a detailed characterization of the isotope effect, including the effect of molecular oxygen pressure, and the presence of a chemically inert third body (helium), is reported. The NoMaDic effect is due to an isotopically selective stabilization of the O3 formation reaction intermediate, possibly resulting from the ability of the different isotopomers to exhibit different molecular symmetries.
Heidenreich, J. E., III↗
The chemical evolution of molecular clouds
The nonequilibrium chemistry of dense molecular clouds (10,000 to 1 million hydrogen molecules per cu cm) is studied in the framework of a model that includes the latest published chemical data and most of the recent theoretical advances. In this model the only important external source of ionization is assumed to be high-energy cosmic-ray bombardment; standard charge-transfer reactions are taken into account as well as reactions that transfer charge from molecular ions to trace-metal atoms. Schemes are proposed for the synthesis of such species as NCO, HNCO, and CN. The role played by adsorption and condensation of molecules on the surface of dust grains is investigated, and effects on the chemical evolution of a dense molecular cloud are considered which result from varying the total density or the elemental abundances and from assuming negligible or severe condensation of gaseous species on dust grains. It is shown that the chemical-equilibrium time scale is given approximately by the depletion times of oxygen and nitrogen when the condensation efficiency is negligible; that this time scale is probably in the range from 1 to 4 million years, depending on the elemental composition and initial conditions in the cloud; and that this time scale is insensitive to variations in the total density.
Iglesias, E.↗
Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O-Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila
Mucins, heavily O-glycosylated glycoproteins, are a key component of mucus, and certain gut microbiota, including Akkermansia muciniphila , can utilise mucin glycans as a carbon source. Akkermansia muciniphila produces the O-glycopeptidase enzyme OgpA, which cleaves peptide bonds at the N-terminus of serine (Ser) or threonine (Thr) residues carrying O-glycan substitutions, with selectivity influenced by the O-glycan functional groups. Using molecular dynamics (MD) simulations and quantum chemistry calculations, we explored how different O-glycan groups affect OgpA's selectivity. Our results show that peptides bind to the enzyme via hydrogen bonds, π–π interactions, van der Waals forces and electrostatic interactions, with key residues, including Tyr90, Val138, Gly176, Tyr210 and Glu91, playing important roles. The primary determinant of selectivity is the interaction between the peptide's functional group and the enzyme's binding cavity, while peptide–enzyme interface interactions are secondary. Quantum chemistry calculations reveal that OgpA prefers peptides with a lower electrophilic character. This study provides new insights into mucin degradation by gut microbiota enzymes, advancing our understanding of this critical biological process.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
X-ray ionization and the chemistry of the Orion molecular cloud
The collection of unusually strong stellar X-ray sources in the vicinity of the Orion molecular cloud together bathe the gas with such an intensity of X-rays that they, rather than cosmic rays, dominate the ionization and heating of the gas. Estimates of the ionization rate and the elevation in temperature are presented, and the consequences for the gas chemistry are discussed. Strong small-scale inhomogeneities in molecular abundances and temperature are a distinguishing feature of ionization by stellar X-rays.
Krolik, J. H.↗
Can electric fields drive chemistry for an aqueous microdroplet?
Abstract Reaction rates of common organic reactions have been reported to increase by one to six orders of magnitude in aqueous microdroplets compared to bulk solution, but the reasons for the rate acceleration are poorly understood. Using a coarse-grained electron model that describes structural organization and electron densities for water droplets without the expense of ab initio methods, we investigate the electric field distributions at the air-water interface to understand the origin of surface reactivity. We find that electric field alignments along free O–H bonds at the surface are ~16 MV/cm larger on average than that found for O–H bonds in the interior of the water droplet. Furthermore, electric field distributions can be an order of magnitude larger than the average due to non-linear coupling of intramolecular solvent polarization with intermolecular solvent modes which may contribute to even greater surface reactivity for weakening or breaking chemical bonds at the droplet surface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A DSMC Surface Chemistry Model for Carbon-Based Ablators
A detailed molecular surface chemistry model for the DSMC (Direct Simulation Monte Carlo) method is proposed and implemented into the SPARTA (Stochastic PArallel Rarefied-gas Time-accurate Analyzer) DSMC solver. Molchanova et al. constructed a molecular model for surface recombination in DSMC that includes different surface processes (adsorption, desoprtion, Eley-Rideal and Langmuir-Hinshelwood). All surface processes can be divided into two groups: surface mechanisms, which involve only the particle adsorbed by the surface (desorption and Langmuir-Hinshelwood), and impact mechanisms, which also involve gas-phase particles (adsorption, Eley-Rideal). Using a similar approach, the 14-reaction kinetic model of oxygen-carbon interaction suggested by Zhlukhtov and Abe, as well as more recent models by Alba et al., Poovathinghal et al., and a new model developed in the scope of this work, are implemented in SPARTA. The computational results for the different oxidation models are compared with experimental results from Murray et al. (oxidation of a vitreous carbon surface due to a hyperthermal beam of O and O2), with a particular focus on fluxes, angular and Time-Of-Flight distributions of scattered particles.
oxidation↗
The MolSSI QCArchive project: An open-source platform to compute, organize, and share quantum chemistry data
The Molecular Sciences Software Institute's (MolSSI) Quantum Chemistry Archive (QCArchive) project is an umbrella name that covers both a central server hosted by MolSSI for community data and the Python-based software infrastructure that powers automated computation and storage of quantum chemistry (QC) results. The MolSSI-hosted central server provides the computational molecular sciences community a location to freely access tens of millions of QC computations for machine learning, methodology assessment, force-field fitting, and more through a Python interface. Facile, user-friendly mining of the centrally archived quantum chemical data also can be achieved through web applications found at the website. The software infrastructure can be used as a standalone platform to compute, structure, and distribute hundreds of millions of QC computations for individuals or groups of researchers at any scale. The QCArchiveInfrastructure is open-source (BSD-3C), code repositories can be found at github, and releases can be downloaded via PyPI and Conda. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry Data Science > Computer Algorithms and Programming
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The evolution of HCO + in molecular clouds using a novel chemical post-processing algorithm
Modelling the chemistry of molecular clouds is critical to accurately simulating their evolution. To reduce computational cost, 3D simulations generally restrict their chemistry to species with strong heating and cooling effects. Time-dependent information about the evolution of other species is therefore often neglected. We address this gap by post-processing tracer particles in the SILCC-Zoom molecular cloud simulations. Using a chemical network of 39 species and 301 reactions (including freeze-out of CO and H 2 O) and a novel algorithm to reconstruct a density grid from sparse tracer particle data, we produce time-dependent density distributions for various species. We focus upon the evolution of HCO + , which is a critical formation reactant of CO but is not typically modelled on the fly. We find that ∼ 90 per cent of the HCO + content of the cold molecular gas forms in situ around n HCO + ∼ 10 3 –10 4 cm −3 , over a time-scale of approximately 1 Myr. The remaining ∼ 10 per cent forms at high extinction sites, with minimal turbulent mixing out into the less dense gas. We further show that the dominant HCO + formation pathway is dependent on the visual extinction, with the reaction H 3 + + CO contributing 90 per cent of the total HCO + production above A V, 3D = 3. We produce the very first maps of the HCO + column density, N(HCO + ), and show that it reaches values as high as 10 15 cm −2 . We find that 50 per cent of the HCO + mass is located within AV ∼ 10–30 in a density range of 10 3.5 –10 4.5 cm −3 . Our maps of N(HCO + ) are shown to be in good agreement with recent observations of the W49A star-forming region.
79 ASTRONOMY AND ASTROPHYSICS↗
Aluminum Based Solvent-Free Organic–Inorganic Hybrid Materials
In emerging materials, molecular hybrids are especially promising, as they have molecular level mixing of the organic and inorganic components, producing homogeneous materials without interfaces that can deteriorate properties. However, the current methods of manufacturing molecular hybrids are based on solution processing, which is impractical for bulk materials such as may be used for optically clear radiation and electromagnetic shielding components or photonics. Here we examine molecular hybrids composed of aluminum isopropoxide (AIP) and epoxy resins aiming to understand the molecular scale chemistry and manufacturability of these hybrid materials. DSCmonitored cure revealed the ideal cure temperature for these materials is 160−170 °C and demonstrated that an AIP concentration of 16.7 wt % maximizes the extent of reaction. Kinetic analysis of the curing reaction showed the Sestak−Berggren autocatalytic model is effective at temperatures over 140 °C but the reaction has diffusion limitations at a temperature of 120 °C. Mechanical testing with custom resin molds revealed a decrease in properties of the bulk samples with increasing AIP content due to an increase in defects but further testing with nanoindentation demonstrated comparable or improved mechanical properties of AIP-epoxy hybrids compared to epoxy resin with a standard hardener. Ultimately, this work lays the foundation for hardener-free epoxy-aluminum inorganic/organic hybrids and presents opportunities to expand on properties for specific applications such as thermal conductivity, optical clarity, and dielectric constant.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗