Gas-phase Model Research Articles

Understanding the influence of external perturbation on aziridinium ion formation

ABSTRACT A density functional theory study is performed to understand the effect of discrete water molecules during Az+ ion formation in nitrogen mustards. A comparative study in gas phase, and implicit and explicit solvation models of three drug molecules (mustine, chlorambucil and melphalan) is reported. Noteworthy changes in the structure and C–N stretching frequencies of the transition states have been observed in the presence of explicit water molecules. Presence of explicit water molecules reduces the positive charge around the tricyclic Az+ ring, and hence stabilising it. Both activation energy and rate constants are seen to be significantly affected in the presence of discrete water molecules.

General mass-transfer model for gas phase in structured packings

Volumetric mass-transfer coefficient in the gas phase, kGa, for Mellapak 250.X and 250.Y structured packings has been measured by standard method of absorption of SO2 from carrier gas to aqueous solution of NaOH in the i.d. 150.6mm absorption column. Three carrier gases – He, N2 and SF6 – have been utilized providing wide range of ScG from 0.49 to 2.32. The gas-phase mass-transfer coefficient, kG, has been calculated from the experimental kGa data as the ratio of kGa and of the effective interfacial area, a, measured utilizing CO2/NaOH system. The experimental and literature kG data for Mellapak 250.X, 250.Y, 350.Y and 500.Y have been correlated by dimensionless correlation ShG=2.7+0.038⋅ReLG0.88⋅ScGβ with β=0.33+0.9⋅exp(−0.6⋅ScG). The correlation fits the data in the wide range of ReLG and ScG covering the process conditions of common absorption and distillation columns.

CFD modeling of a small-scale cyclonic combustor chamber using biomass powder

Thermal energy in the form of heat generally is produced and provided through thermal plants by combustion using coal, a type of fuel which impacts the environment severely. The use of biomass to provide heat and power as an alternative fuel is growing and can reduce the percentage use of the fossil fuels. However, the performance of the combustion systems with biomass as fuel needs evaluation, which is not an easy task. Modeling a fluidized biomass chamber involves the simulations of both solid-air combustion within the fluidized bed, and at the same time the gas phase reactions into the combustion chamber. Commercial CFD software packages usually have strong built-in capacities that facilitate gas phase modeling. The current study presents the computational modeling of a horizontal cyclonic combustor chamber burning biomass powder using ANSYS FLUENT software in conjunction with experimental biomass data. The mathematical models selected for the simulation were described as well as the boundary conditions. The obtained results are presented through velocity profiles and vectors, temperature fields and species mass fractions distribution. The temperature fields showed a maximum close to 1600 K, while mass fraction of species have demonstrated that, with the combustible and initial conditions set, the combustion reaction occurs completely at 0.55 m, leaving the remaining 1.5 m long for radial heat transfer in gas phase and eventually for a heat transfer to the chamber wall (in the boiler case). This extra length is directly related to the NOx formation, increasing the residence time of the product combustion gases at higher temperatures. The main mechanism of NOx formation was identified as the thermal mechanism.

Watson-Crick Base Pair Radical Cation as a Model for Oxidative Damage in DNA.

The deleterious cellular effects of ionizing radiation are well-known, but the mechanisms causing DNA damage are poorly understood. The accepted molecular events involve initial oxidation and deprotonation at guanine sites, triggering hydrogen atom abstraction reactions from the sugar moieties, causing DNA strand breaks. Probing the chemistry of the initially formed radical cation has been challenging. Here, we generate, spectroscopically characterize, and examine the reactivity of the Watson-Crick nucleobase pair radical cation in the gas phase. We observe rich chemistry, including proton transfer between the bases and propagation of the radical site in deoxyguanosine from the base to the sugar, thus rupturing the sugar. This first example of a gas-phase model system providing molecular-level details on the chemistry of an ionized DNA base pair paves the way toward a more complete understanding of molecular processes induced by radiation. It also highlights the role of radical propagation in chemistry, biology, and nanotechnology.

Simple model of inhibition of chain-branching combustion processes

A simple kinetic model has been suggested to describe the inhibition and extinction of flame propagation in reaction systems with chain-branching reactions typical for hydrocarbon systems. The model is based on the generalised model of the combustion process with chain-branching reaction combined with the one-stage reaction describing the thermal mode of flame propagation with the addition of inhibition reaction steps. Inhibitor addition suppresses the radical overshoot in flame and leads to the change of reaction mode from the chain-branching reaction to a thermal mode of flame propagation. With the increase of inhibitor the transition of chain-branching mode of reaction to the reaction with straight-chains (non-branching chain reaction) is observed. The inhibition part of the model includes a block of three reactions to describe the influence of the inhibitor. The heat losses are incorporated into the model via Newton cooling. The flame extinction is the result of the decreased heat release of inhibited reaction processes and the suppression of radical overshoot with the further decrease of the reaction rate due to the temperature decrease and mixture dilution. A comparison of the results of modelling laminar premixed methane/air flames inhibited by potassium bicarbonate (gas phase model, detailed kinetic model) with the results obtained using the suggested simple model is presented. The calculations with the detailed kinetic model demonstrate the following modes of combustion process: (1) flame propagation with chain-branching reaction (with radical overshoot, inhibitor addition decreases the radical overshoot down to the equilibrium level); (2) saturation of chemical influence of inhibitor, and (3) transition to thermal mode of flame propagation (non-branching chain mode of reaction). The suggested simple kinetic model qualitatively reproduces the modes of flame propagation with the addition of the inhibitor observed using detailed kinetic models.

Synthesis, spectroscopic characterization, biological activity and theoretical studies of (E)-N3-(2-chlorobenzylidene)-H-1,2,4-triazole-3,5-diamine

The Schiff base (E)-N3-(2-chlorobenzylidene)-H-1,2,4-triazole-3,5-diamine was synthesised and characterized by FT-IR, Raman, 1H &13C NMR, UV–Vis and mass spectrometry. A density functional theory based quantum chemical calculations were performed at B3LYP/6-311++G(d,p) level of theory. A comparative analysis of calculated vibrational frequencies with experimental vibrational frequencies was carried out and prominent bands were assigned. The theoretical UV–Vis spectral studies were carried out using time dependent-DFT method in gas phase and IEFPCM model with solvent field calculation. Atomic charges at selected atoms were calculated by Mulliken population analyses (MPA), Hirshfeld population analyses (HPA) and Natural population analyses (NPA) schemes. The molecular electrostatic potential (MEP) map was calculated to assign reactive site on the surface of the molecule. The conceptual DFT based global and local reactivity descriptors were calculated to obtain an insight into the structure-activity relationship. For instance, the results indicate that the C11 of compound is more prone to nucleophilic attack as it has found maximum value of electrophilic reactivity descriptors and thus favours the formation of new heterocyclic compounds. The frontier molecular orbital analysis was carried out to study the charge transfer within the molecule. The NBO analysis was performed to get an insight into the intramolecular conjugative electronic interactions. The titled compound was screened for in vitro antimicrobial activity against four bacterial and five fungal strains.

Reaction of Aniline with Singlet Oxygen (O21Δg).

Dissolved organic matter (DOM) acts as an effective photochemical sensitizer that produces the singlet delta state of molecular oxygen (O21Δg), a powerful oxidizer that removes aniline from aqueous solutions. However, the exact mode of this reaction, the p- to o-iminobenzoquinone ratio, and the selectivity of one over the other remain largely speculative. This contribution resolves these uncertainties. We report, for the first time, a comprehensive mechanistic and kinetic account of the oxidation of aniline with the singlet delta oxygen using B3LYP and M06 functionals in both gas and aqueous phases. Reaction mechanisms have been mapped out at E, H, and G scales. The 1,4-cycloaddition of O21Δg to aniline forms a 1,4-peroxide intermediate (M1), which isomerizes via a closed-shell mechanism to generate a p-iminobenzoquinone molecule. On the other hand, the O21Δg ene-type reaction forms an o-iminobenzoquinone product when the hydroperoxyl bond breaks, splitting hydroxyl from the 1,2-hydroperoxide (M3) moiety. The gas-phase model predicts the formation of both p- and o-iminobenzoquinones. In the latter model, the M1 adduct displays the selectivity of up to 96%. A water-solvation model predicts that M1 decomposes further, forming only p-iminobenzoquinone with a rate constant of k = 1.85 × 109 (L/(mol s)) at T = 313 K. These results corroborate the recent experimental findings of product concentration profile in which p-iminobenzoquinonine represents the only detected product.

Technical note: Conversion of isoprene hydroxy hydroperoxides (ISOPOOHs) on metal environmental simulation chamber walls

Abstract. Sources and sinks of isoprene oxidation products from low-NOx isoprene chemistry have been studied at the CERN CLOUD (Cosmics Leaving Outdoor Droplets) chamber with a custom-built selective reagent ion time-of-flight mass spectrometer (SRI-ToF-MS), which allows quantitative measurement of isoprene hydroxy hydroperoxides (ISOPOOHs). The measured concentrations of the main oxidation products were compared to chemical box model simulations based on the Leeds Master Chemical Mechanism (MCM) v3.3. The modeled ISOPOOH concentrations are a factor of 20 higher than the observed concentrations, and methyl vinyl ketone (MVK) and methacrolein (MACR) concentrations are up to a factor of 2 lower compared to observations, despite the artifact-free detection method. Addition of catalytic conversion of 1,2-ISOPOOH and 4,3-ISOPOOH to methyl vinyl ketone (MVK) and methacrolein (MACR) on the stainless-steel surface of the chamber to the chemical mechanism resolves the discrepancy between model predictions and observation. This suggests that isoprene chemistry in a metal chamber under low-NOx conditions cannot be described by a pure gas phase model alone. Biases in the measurement of ISOPOOH, MVK, and MACR can be caused not only intra-instrumentally but also by the general experimental setup. The work described here extends the role of heterogeneous reactions affecting gas phase composition and properties from instrumental surfaces, described previously, to general experimental setups. The role of such conversion reactions on real environmental surfaces is yet to be explored.

On the chemistry of the young massive protostellar core NGC 2264 CMM3

We present the first gas-grain astrochemical model of the NGC 2264 CMM3 protostellar core. The chemical evolution of the core is affected by changing its physical parameters such as the total density and the amount of gas-depletion onto grain surfaces as well as the cosmic ray ionisation rate, $\zeta$ . We estimated $\zeta_{\text{CMM3}} = 1.6 \times 10^{-17}~\mbox{s}^{-1}$ . This value is 1.3 times higher than the standard CR ionisation rate, $\zeta _{\text{ISM}} = 1.3 \times 10^{-17}~\mbox{s}^{-1}$ . Species response differently to changes into the core physical conditions, but they are more sensitive to changes in the depletion percentage and CR ionisation rate than to variations in the core density. Gas-phase models highlighted the importance of surface reactions as factories of large molecules and showed that for sulphur bearing species depletion is important to reproduce observations. Comparing the results of the reference model with the most recent millimeter observations of the NGC 2264 CMM3 core showed that our model is capable of reproducing the observed abundances of most of the species during early stages ( $\le 3\times10^{4}~\mbox{yrs}$ ) of their chemical evolution. Models with variations in the core density between $1\mbox{--}20 \times 10^{6}~\mbox{cm}^{-3}$ are also in good agreement with observations during the early time interval $1 \times 10^{4} < t\ (\mbox{yr}) < 5 \times 10^{4}$ . In addition, models with higher CR ionisation rates $(5\mbox{--}10) \times\zeta_{\text{ISM}}$ are often overestimating the fractional abundances of the species. However, models with $\zeta_{\text{CMM3}} = 5 \zeta_{\text{ISM}}$ may best fit observations at times $\sim 2 \times 10^{4}~\mbox{yrs}$ . Our results suggest that CMM3 is $(1\mbox{--}5) \times 10^{4}~\mbox{yrs}$ old. Therefore, the core is chemically young and it may host a Class 0 object as suggested by previous studies.

Characterization of fluorine-centred `F...O' σ-hole interactions in the solid state.

In the current study, the crystal structure of 1-(3-nitrophenyl)-2,2,2-trifluoroethanone (A1) and (E)-4-((4-fluorophenyl) diazenyl)phenol (A2) has been analyzed for the characterization of the presence of a `unique' and `rare' intermolecular C(sp3/sp2)-F...O contact, which has been observed to play a significant role in the crystal packing. Theoretical charge-density calculations have been performed to study the nature and strength associated with the existence of this intermolecular F...O contact, wherein the F atom is attached to an sp3-hybridized C atom in the case of A1 and to an sp2 hybridized carbon in the case of A2. The crystal packing of the former contains two `electronically different' Csp3-F...O contacts which are present across and in between the layers of molecules. In the latter case, it is characterized by the presence of a very `short' (2.708 Å) and `highly directional' (168° at ∠C4-F1...O1 and 174° at ∠C10-O1...F1) Csp2-F...O contact. According to the Cambridge Structural Database (CSD) study, it is a rare example in molecular crystals. Topological features of F...O contacts in the solid state were compared with the gas-phase models. The two-dimensional and three-dimensional static deformation density obtained from theoretical multipole modeling confirm the presence of a charge depleted region on the F atoms. Minimization of the electrostatic repulsion between like charges are observed through subtle arrangements in the electronic environment in two of the short intermolecular F...O contacts. These contacts were investigated using inputs from pair energy decomposition analysis, Bader's quantum theory of atoms in molecules (QTAIM), Hirshfeld surface analysis, delocalization index, reduced density gradient (RDG) plot, electrostatic potential surface and distributed atomic polarizability. The intermolecular energy decomposition (PIXEL) and RDG-NCI (non-covalent interaction) analysis of the F...O contacts establish the interaction to be dispersive in nature. The mutual polarization of an O atom by fluorine and vice versa provides real physical insights into the role of atomic polarizability in interacting atoms in molecules in crystals.

Dissociative Water Adsorption by Al3O4+ in the Gas Phase.

We use cryogenic ion trap vibrational spectroscopy in combination with density functional theory (DFT) to study the adsorption of up to four water molecules on Al3O4+. The infrared photodissociation spectra of [Al3O4(D2O)1-4]+ are measured in the O-D stretching (3000-2000 cm-1) as well as the fingerprint spectral region (1300-400 cm-1) and are assigned based on a comparison with simulated harmonic infrared spectra for global minimum-energy structures obtained with DFT. We find that dissociative water adsorption is favored in all cases. The unambiguous assignment of the vibrational spectra of these gas phase model systems allows identifying characteristic spectral regions for O-D and O-H stretching modes of terminal (μ1) and bridging (μ2) hydroxyl groups in aluminum oxide/water systems, which sheds new light on controversial assignments for solid Al2O3 phases.

Molecular modelling approach to elucidate the thermal decomposition routes of vanillin

Gas phase pyrolytic studies of vanillin, which is a promising model compound of lignin-derived bio-oil, were performed using the B3LYP/6-311+g(d,p) level of theory under the DFT framework. This theoretical study unravels and elucidates the competitive reaction pathways for the production of various products and their kinetics. The reaction kinetics are presented using both gas phase and solvation models.

Unifying the microscopic picture of His-containing turns: from gas phase model peptides to crystallized proteins.

The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, was assessed by the comparison of protein structures with relevant isolated model peptides. Gas phase laser spectroscopy, combined with relevant quantum chemistry methods, was used to characterize the γ- and β-turn structures in these model peptides. A conformer-selective NH stretch infrared study provided evidence for the formation in vacuo of two types of short-range H-bonded motifs, labelled ε-6δ and δ-δ7/πH, bridging the His side chain (in its gauche+ rotamer) to the neighbouring NH(i) and CO(i) sites of the backbone; each side chain-backbone motif was found to be specific of the tautomer (ε or δ) adopted by the His side chain in its neutral form. A close comparison between β- and γ-turns, selected from the Protein Data Bank, and the gas phase models demonstrated that a significant proportion of the gauche+ His rotamer distribution of proteins was well described by the corresponding gas phase H-bonded structures. This is consistent with the persistence of local 6δ and δ7/πH intramolecular interactions in proteins, emphasizing the relevance of gas phase data to secondary structures that are poorly accessible to solvents, e.g., in the case of a specific compact topology (Xxx-His β-turns). Deviations from the gas phase structures were also observed, mainly in His-Xxx β-turns, and assigned to solvent accessible turn structures. They were well accounted for by theoretical models of microhydrated turns, in which a few solvent molecules take over the gas phase motifs, constituting a water-mediated local anchoring of the His side chain to the backbone. Finally, the present gas phase benchmark models also pinpointed weaknesses in the protein structure determination by X-ray diffraction analysis; in particular, besides the lack of tautomer information, inaccuracies in the description of imidazole ring flip rotamerism were identified.

An experimental and numerical study on fire behaviors of charring materials frequently used in buildings

The single biggest market barriers of building materials is their fire risks, suffering from easily burning and generating a large amount of smoke and toxic gases. Fire behaviors of typical charring materials, including timber (Cherry) and polymer (acrylonitrile butadiene styrene, ABS), were investigated both experimentally and numerically. The proposed numerical model has considered both solid (the area inside sample slab) and gas (the area above sample surface) phases, addressing some previously usually-ignored fire processes, such as water evaporation, gases and liquids transportation inside solids, and volume change. Numerical results of timber and polymer were validated by cone calorimeter experiments. From both experimental and numerical results, three different stages of mass loss rate histories of charring materials were observed under external heat flux. In the gas phase, three high temperature areas were observed: two are near the walls of the two heaters due to the convection heat transfer; and one represents diffusion flame above sample surface, in which temperature increases with the intensity of external heat flux. This study provides not only an attempt to combine both solid and gas phases modeling for building materials, but also a platform for fire behavior modeling. Future research will focus on the validation of gas phase modeling and implementation of flame radiation.

Crystal structure determination as part of an undergraduate laboratory experiment: 1',3',3'-tri-methyl-spiro-[chromene-2,2'-indoline] and 1',3',3'-trimethyl-4-[(E)-(1,3,3-tri-methyl-indolin-2-yl-idene)meth-yl]spiro-[chroman-2,2'-indoline

The crystal structures of the title compounds, C19H19NO and C31H34N2O, were determined as part of an experiment in an undergraduate teaching laboratory that demonstrates the relationship between mol-ecular structure and function. 1',3',3'-Tri-methyl-spiro-[chromene-2,2'-indoline] is both a photoswitch and thermochromic mol-ecule. Students synthesized it and a bis-indoline adduct and compared the crystallographically determined structures to computed gas-phase models.

Raman optical activity of a flavone C-diglycoside: Aqueous solution conformations and absolute configuration

The combination of experimental and theoretical Raman optical activity data for the flavone C-diglycoside isoswertisin-4′-methyl-ether-2′′α-l-rhamnoside provided detailed information about its conformational preferences in aqueous solution as well as the absolute configuration of the glycosidic linkage. This work also demonstrated the importance of explicit solvation for accurate predictions of the conformational ensemble and vibrational optical activity properties of natural products in water, as opposed to gas-phase or polarizable continuum model calculations.

Mechanistic Aspects of Using Formate as a Hydrogen Donor in Aqueous Transfer Hydrogenation

Asymmetric transfer hydrogenation of ketones is an important chemical reaction. In aqueous solution, Ru(p-cymene)[TsDPEN] is an efficient catalyst for asymmetric transfer hydrogenation via a metal–ligand bifunctional mechanism with either 2-propanol or formate as hydrogen donors. Here, we provide novel insight for two key steps in the catalytic cycle of transfer hydrogenation cycle, using a computational model of Ru(p-cymene)[TsDPEN] with an explicit aqueous solvent. Employing ab initio molecular dynamics simulations, we model the hydride transfer between formate and the protonated and deprotonated catalyst, and the dissociation of the ruthenium-formato complex. It is shown that the aqueous solvent provides a significant contribution to the reaction barriers, increasing the hydride transfer barrier, while decreasing the dissociation barrier for ruthenium-formato complex, when compared with a gas-phase model. These effects can be attributed to hydrogen-bond structure around the formate, which favors the fo...

The effect of model fidelity on prediction of char burnout for single-particle coal combustion

Practical simulation of industrial-scale coal combustion relies on the ability to accurately capture the dynamics of coal subprocesses while also ensuring the computational cost remains reasonable. The majority of the residence time occurs post-devolatilization, so it is of great importance that a balance between the computational efficiency and accuracy of char combustion models is carefully considered. In this work, we consider the importance of model fidelity during char combustion by comparing combinations of simple and complex gas and particle-phase chemistry models. Detailed kinetics based on the GRI 3.0 mechanism and infinitely-fast chemistry are considered in the gas-phase. The Char Conversion Kinetics model and nth-Order Langmuir–Hinshelwood model are considered for char consumption. For devolatilization, the Chemical Percolation and Devolatilization and Kobayashi-Sarofim models are employed. The relative importance of gasification versus oxidation reactions in air and oxyfuel environments is also examined for various coal types. Results are compared to previously published experimental data collected under laminar, single-particle conditions. Calculated particle temperature histories are strongly dependent on the choice of gas phase and char chemistry models, but only weakly dependent on the chosen devolatilization model. Particle mass calculations were found to be very sensitive to the choice of devolatilization model, but only somewhat sensitive to the choice of gas chemistry and char chemistry models. High-fidelity models for devolatilization generally resulted in particle temperature and mass calculations that were closer to experimentally observed values.

UV Photolysis of Hydrogenated Amorphous Carbons of Astrophysical Interest

ABSTRACTIn the gas phase, most of the ionized or neutral molecules detected in the interstellar and circumstellar media contain at least one carbon atom. Carbon chemistry plays thus a dominant role in the understanding of the structure and evolution of the interstellar medium (ISM). One particular zone of interest to observe small carbonaceous radicals and molecules, are the sharp molecular clouds edges exposed to energetic photons. These photon-dominated regions are rich in these hydrocarbons (like CCH, c-C3H2, C4H), and provide tests for the chemistry models in the diffuse to molecular transition. The pure gas phase models generally fail in reproducing the abundance of many of the observed species, and several authors suggest such abundances may arise from the products of the VUV photodissociation of carbonaceous grains or PAHs. Hydrogenated amorphous carbons (a-C:H or HAC), abundantly observed in the ISM, could also be at the origin of many of these small carbonaceous radicals. Experimentally, this work investigates the production and release of hydrocarbons from the VUV photolysis of a-C:H interstellar analogues under ultra-high vacuum. The experimental results are applied to a Photon Dominated Region model to constrain the impact of this release on the observed gas phase species.

DPM simulation in an underground entry: Comparison between particle and species models

The diesel particulate matter (DPM) emission from diesel powered equipment in underground mines can cause health hazards including cancer to the miners. The understanding of the DPM propagation pattern under realistic mining condition is required for selecting proper DPM control strategies and to improve working practices in underground mines. In this paper, three dimensional simulations of DPM emission from the exhaust tail pipe of a load-haul-dump (LHD) vehicle and its subsequent distribution inside an isolated zone in the typical underground mine are carried out using two different solution models available in Ansys Fluent. The incoming fresh air into the isolated zone is treated as a continuous phase and DPM is treated either as a continuous phase (gas) or as a secondary discrete phase (particle). Species transport model is used when DPM is treated as gas and discrete phase model is used when DPM is assumed to behave like a particle. The distributions of DPM concentration inside the isolated zone obtained from each method are presented and compared. From the comparison results, an accurate and economical solution technique for DPM evaluation can be selected.