Automated Reaction Mechanism Generation Including Nitrogen as a Heteroatom

The open source rate‐based Reaction Mechanism Generator (RMG) software and its thermochemical and kinetics databases were extended to include nitrogen as a heteroatom. Specific changes to RMG and the mining of thermochemistry and reaction kinetics data are discussed. This new version of RMG has been tested by generating a detailed pyrolysis and oxidation model for ethylamine (EA, CH₃CH₂NH₂) at ∼1400 K and ∼2 bar, and comparing it to recent shock tube studies. Validation of the reaction network with recent experimental data showed that the generated model successfully reproduced the observed species as well as ignition delay measurements. During pyrolysis, EA initially decomposes via a C C bond scission, and the CH₂NH₂ product subsequently produces the first H radicals in this system via β‐scission. As the concentration of H increases, the major EA consuming reaction becomes H abstraction at the α‐site by H radicals, leading to a chain reaction since its product generates more H radicals. During oxidation, the dominant N₂‐producing route is mediated by NO and N₂O. The observables were found to be relatively sensitive to the C C and C N EA bond scission reactions as well as to the thermodynamic values of EA; thermodynamic data for EA were computed at the CBS‐QB3 level and reported herein. This work demonstrates the ability of RMG to construct adequate kinetic models for nitrogenous species and discusses the pyrolysis and oxidation mechanisms of EA.     

A theoretical kinetic study of the reactions of NH2 radicals with methanol and ethanol and their implications in kinetic modeling

Amino (NH₂) radicals play a central role in the pyrolysis and oxidation of ammonia. Several reports in the literature highlight the importance of the reactions of NH₂ radicals with fuel in NH₃-dual-fuel combustion. Therefore, we investigated the reactions of NH₂ radicals with methanol (CH₃OH) and ethanol (C₂H₅OH) theoretically. We explored the various reaction pathways by exploiting CCSD(T)/cc-pV(T, Q)Z//M06-2X/aug-cc-pVTZ level of theory. The reaction proceeds via complex formation at the entrance and exit channels in an overall exothermic process. We used canonical transition state theory to obtain the high-pressure limiting rate coefficients for various channels over the temperature range of 300–2000 K. We discerned the role of various channels in the potential energy surface (PES) of NH₂ + CH₃OH/C₂H₅OH reactions. For both reactions, the hydrogen abstraction pathway at the OH-site of alcohols plays a minor role in the entire T-range investigated. By including the title reactions into an extensive kinetic model, we demonstrated that the reaction of NH₂ radicals with alcohols plays a paramount role in accurately predicting the low-temperature oxidation kinetics of NH₃-alcohols dual fuel systems (e.g., shortening the ignition delay time). On the contrary, these reactions have negligible importance for high-temperature oxidation kinetics of NH₃-alcohol blends (e.g., not affecting the laminar flame speed). In addition, we calculated the rate coefficients for NH₂ + CH₄ = CH₃ + NH₃ reaction that are in excellent agreement with the experimental data.     

The methylamine radical cation [CH3NH2]+˙ and its stable isomer the methylenammonium radical cation [CH2NH3]+˙

The potential energy surface for the [CH₅N]^+˙ system has been investigated using ab initio molecular orbital calculations with large, polarization basis sets and incorporating valence-electron correlation. Two [CH₅N]^+˙ isomers can be distinguished: the well known methylamine radical cation, [CH₃NH₂]^+˙, and the less familiar methylenammonium radical cation, [CH₂NH₃]^+˙. The latter is calculated to lie 8 kJ mol^?1 lower in energy. A substantial barrier (176 kJ mol^?1) is predicted for rearrangement of [CH₂NH₃]^+˙ to [CH₃NH₂]^+˙. In addition, a large barrier (202 kJ mol^?1) is found for loss of a hydrogen radical from [CH₂NH₃]^+˙ via direct N—H bond cleavage to give the aminomethyl cation [CH₂NH₂]⁺. These results are consistent with the existence of the methylenammonium ion [CH₂NH₃]^+˙ as a stable observable species. The barrier to loss of a hydrogen radical from [CH₃NH₂]^+˙ is calculated to be 140 kJ mol^?1.     

Unimolecular reactions of the isolated immonium ions CH3CH = NH+C4H9, CH3CH2Ch = NH+C4H9 and (CH3)2C = NH+C4H9

The reactions of ten metastable immonium ions of general structure R¹R²C?NH⁺C₄H₉ (R¹ = H, R² = CH₃, C₂H₅; R¹ = R² = CH₃) are reported and discussed. Elimination of C₄H₈ is usually the dominant fragmentation pathway. This process gives rise to a Gaussian metastable peak; it is interpreted in terms of a mechanism involving ion-neutral complexes containing incipient butyl) cations. Metastable immonium ions ontaining an isobutyl group are unique in undergoing a minor amount of imine (R¹R²C?NH) loss. This decomposition route, which also produces a Gaussian metastable peak, decreases in importance as the basicity of the imine increases. The correlation between imine loss and the presence of an isobutyl group is rationalized by the rearrangement of the appropriate ion-neutral complexes in which there are isobutyl cations to the isomeric complexes containing the thermodynamically more stable tert-butyl cations. A sizeable amount of a third reaction, expulsion of C₃H₆, is observed for metastable n-C₄H₉ ⁺NH?CR¹R² ions; in contrast to C₄H₈ and R¹R²C?NH loss, C₃H₆ elimination occurs with a large kinetic energy release (40–48 kJ mol^?1) and is evidenced by a dish-topped metastable peak. This process is explained using a two-step mechanism involving a 1,5-hydride shift, followed by cleavage of the resultant secondary open-chain cations, CH₃CH⁺ CH₂CH₂NHCHR¹R².     

Direct dynamics study on the mechanism and the kinetics of the reaction of CH3NH2 with OH

A theoretical study of the mechanism and the kinetics for the hydrogen abstraction reaction of methylamine by OH radical has been presented at the CCSD(T)/6‐311 ++G(2d,2p)//CCSD/6‐31G(d) level of theory. Our theoretical calculations suggest a stepwise mechanism involving the formation of a prereactant complex in the entrance channel and a preproduct complex in the exit channel, for the two hydrogen abstraction channels involving the methyl and amine groups. For clarity, the diagram of potential for the reaction is given. The calculated standard reaction enthalpies are ?98.48 and ?76.50 kJ mol^?1 and barrier heights are 0.36 and 25.25 kJ mol^?1, respectively. The rate constants are evaluated by means of the improved canonical variational transition state theory with small‐curvature tunneling correction (ICVT/SCT) in the temperature range of 299–3000 K. The calculated results show that the rate constants at experimentally measured temperatures are in good agreement with the experimental values. It is shown that the calculated rate constants exhibit a non‐Arrhenius behavior. Moreover, the variational effect is obvious in the calculated temperature range. The dominant product channel is to form CH₂NH₂ and H₂O via hydrogen abstraction from the CH₃ group of CH₃NH₂ by OH in the calculated temperature range. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Reactive collisions in quadrupole cells. Part I. Reaction of [CH3NH2]+˙ with the isomeric butenes and pentenes

The reactions of mass-selected [CH₃NH₂]⁺˙ ions with the isomeric butenes and pentenes were studied at low collision energies in the radiofrequency-only quadrupole collision cell of a hybrid BEqQ tandem mass spectrometer. Characteristic iminium ions arising by addition of the methylamine to the olefin followed by fragmentation are observed for but-1-ene pent-1-ene and 3-methylbut-1-ene. However, for but-2-ene pent-2-ene 2-methylpropene 2-methylbut-1-ene and 2-methylbut-2-ene the major reaction channel of [CH₃NH₂]⁺˙ is charge exchange to form the olefinic molecular ion. The isomeric olefins are characterized to a considerable extent by the characteristic ion–molecule reactions that these molecular ions undergo with the neutral olefin.     

A comparative theoretical study of the reactivities of the Al+ and Cu+ ions toward methylamine and dimethylamine

A very recent laser ablation‐molecular beam experiment shows that an Al⁺ ion can react with a single methylamine (MA, CH₃NH₂) or dimethylamine (DMA, (CH₃)₂NH) molecule to form a 1:1 ion–molecule complex Al⁺[CH₃NH₂] or Al⁺[(CH₃)₂NH)], whereas a dehydrogenated complex ion Cu⁺[CH₃N] or Cu⁺[C₂H₅N] is detected, respectively, in the similar reaction for a Cu⁺ ion. Here, we show a comparative density functional theory study for the reactivities of the Al⁺ and Cu⁺ ions toward MA and DMA to reveal the intrinsic mechanism. It is found that the interactions of the Al⁺ ion with MA and DMA are mostly electrostatic, leading to the direct ion–molecule complexes, Al⁺? NH₂CH₃ and Al⁺? NH( CH₃)₂, in contrast to the non‐negligible covalent character in the corresponding Cu⁺‐containing complexes, Cu⁺? NH₂CH₃ and Cu⁺? NH( CH₃)₂. The general dehydrogenation mechanism for MA and DMA promoted by the Cu⁺ ion has been shown, and the preponderant structures contributing to the mass spectra of the product ions Cu⁺[CH₃N] and Cu⁺[C₂H₅N] are rationalized as Cu⁺? NHCH₂ and Cu⁺? N( CH₂)( CH₃). The presumed dehydrogenation reactions are also discussed for the Al⁺‐containing systems. However, the involved barriers are found to be too high to be overcome at low energy conditions. These results have rationalized all the experimental observations well. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

An experimental and modeling study of ethanol oxidation kinetics in an atmospheric pressure flow reactor

Experimental profiles of stable species concentrations and temperature are reported for the flow reactor oxidation of ethanol at atmospheric pressure, initial temperatures near 1100 K and equivalence ratios of 0.61–1.24. Acetaldehyde, ethene, and methane appear in roughly equal concentrations as major intermediate species under these conditions. A detailed chemical mechanism is validated by comparison with the experimental species profiles. The importance of including all three isomeric forms of the C₂H₅O radical in such a mechanism is demonstrated. The primary source of ethene in ethanol oxidation is verified to be the decomposition of the C₂H₄OH radical. The agreement between the model and experiment at 1100 K is optimized when the branching ratio of the reactions of C₂H₅OH with OH and H is defined by (30% C₂H₄OH + 50% CH₃CHOH + 20% CH₃CH₂O) + XH. As in methanol oxidation, HO₂ chemistry is very important, while the H + O₂ chain branching reaction plays only a minor role until late in fuel decay, even at temperatures above 1100 K.     

Methylamine‐Gas‐Induced Defect‐Healing Behavior of CH3NH3PbI3 Thin Films for Perovskite Solar Cells

We report herein the discovery of methylamine (CH₃NH₂) induced defect‐healing (MIDH) of CH₃NH₃PbI₃ perovskite thin films based on their ultrafast (seconds), reversible chemical reaction with CH₃NH₂ gas at room temperature. The key to this healing behavior is the formation and spreading of an intermediate CH₃NH₃PbI₃?xCH₃NH₂ liquid phase during this unusual perovskite–gas interaction. We demonstrate the versatility and scalability of the MIDH process, and show dramatic enhancement in the performance of perovskite solar cells (PSCs) with MIDH. This study represents a new direction in the formation of defect‐free films of hybrid perovskites.     

Reaction of dioxides derived from organosilicon thiocarbamides with ammonia and methylamine

Reactions of organosilicon thiocarbamide dioxides {[R₃Si(CH₂)₃NH]₂CSO₂, R = Et (I), O_1.5 (II)} with methylamine and ammonia were studied. The reaction of compound I with ammonia involves, along with the substitution of the NHC(SO₂)NH fragment by a guanidine residue, Si-C bond cleavage to form an oligomer comprising [O(Et)Si(CH₂)₃NH]₂C=NH and [O_1.5Si(CH₂)₃NH]₂C=NH elementary units. The reactions of compound II with methylamine and ammonia resulted in the synthesis of organosilicon polymers containing guanidine groups. These polymers exhibit a high sorption capacity toward Ag(I).     

Reactions of perfluoronitriles. II. Interactions with phenylphosphine

Treatment of perfluoro-n-octanonitrile with phenylphosphine gave tetraphenyltetraphosphine and a spectrum of reduction and interaction products. Fifteen compounds were identified. The imine, (R_fC₇F₁₅) R_fCHNH, and the amine, R_fCH₂NH₂, were the primary reduction products. Secondary phosphorus-free products, some formed following ammonia evolution, were the following: R_fCHNCH₂R_f, R_fCH₂CH(NH₂)R_f, R_fC(NH)NCR_f(NH₂), R_fCH₂NHCR_f(NH), (R_fCN)₃, R_fCHNCR_fNCR_f(NH), R_fCH₂NCR_fNHCH₂R_f, and R_fCH₂NCR_fNHCR_f(NH). Only three phosphorus-containing materials were definitely identified: R_fCH(NH₂)P(C₆H₅)H, R_fCH[P(C₆H₅)H]NCHR_f, and R_fC(NH)P(C₆H₅)CR_f(NH). Depending on reaction conditions, specific phosphorus-containing compounds could be preferentially produced. All the structure assignments are based solely on mass spectral breakdown patterns, since pure compounds were not isolated.     

Pyrolysis and Oxidation of Methane in a RF Plasma Reactor

The chemical kinetic effects of RF plasma on the pyrolysis and oxidation of methane were studied experimentally and computationally in a laminar flow reactor at 100 Torr and 373 K with and without oxygen addition into He/CH₄ mixtures. The formation of excited species as well as intermediate species and products in the RF plasma reactor was measured with optical emission spectrometer and Gas Chromatography and the data were used to validate the kinetic model. The kinetic analysis was performed to understand the key reaction pathways. The experimental results showed that H₂, C₂ and C₃ hydrocarbon formation was the major pathways for plasma assisted pyrolysis of methane. In contrast, with oxygen addition, C₂ and C₃ formation dramatically decreased, and syngas (H₂ and CO) became the major products. The above results revealed oxygen addition significantly modified the chemistry of plasma assisted fuel pyrolysis in a RF discharge. Moreover, an increase of E/n was found to be more beneficial for the formation of higher hydrocarbons while a small amount of oxygen was presented in a He/CH₄ mixture. A reaction path flux analysis showed that in a RF plasma, the formation of active species such as CH₃, CH₂, CH, H, O and O (¹D) via the electron impact dissociation reactions played a critical role in the subsequent processes of radical chain propagating and products formation. The results showed that the electronically excitation, ionization, and dissociation processes as well as the products formation were selective and strongly dependent on the reduced electric field.     

Kinetics and mechanisms of chlorine transfer from chloramine to amines in aqueous medium

The kinetics and the equilibrium constant of the chlorine transfer reaction between monochloramine NH₂Cl and the amines: C₂H₅NH₂, (CH₃)₂CHNH₂, (CH₃)₂NH, and (C₂H₅)₂NH are investigated by spectrophotometry in aqueous medium at 25°C, in the pH range from 8 to 13 and for an ionic strength equal to 1.03 ± 0.05M. For a concentration of total ammonia equal to 1M, the observed rate constant is pH independent below 8 and above 12.8 and reaches a maximum located between the pK_as of NH₄⁺ and RR'NH₂⁺. From these results and those obtained earlier for NH₂Cl and CH₃NH₂, the reaction is shown to involve an interaction between neutral molecules NH₂Cl and RR'NH, subject to general acid catalysis. The ability of an interaction corresponding to a specific catalysis and involving NH₃Cl⁺ and RR'NH rather than NH₂Cl and RR'NH₂⁺ is also discussed. The activation parameters are given for each reaction.     

Nitramine and nitrosamine formation is a minor pathway in the atmospheric oxidation of methylamine: A theoretical kinetic study of the CH3NH + O2 reaction

The atmospheric oxidation of amines proceeds via initial radical attack at C–H or N–H bonds to form carbon- and nitrogen-centered radicals, respectively. It is conventionally assumed that nitrogen-centered aminyl radicals react slowly with oxygen in the troposphere and associate predominantly with the radicals ^•NO and NO₂^• to form toxic nitrosamines and nitramines. We have used theoretical kinetic modeling techniques to study the prototypical CH₃N^•H + O₂ reaction and have shown that it proceeds to CH₂NH + HO₂^• under tropospheric conditions with a rate coefficient of 3.6 × 10⁻¹⁷ cm³ molecule⁻¹ s⁻¹. Although this value is low compared to the competing NO_x reactions (∼10⁻¹¹ cm³ molecule⁻¹ s⁻¹), the much higher concentration of O₂ versus NO_x in air makes it the dominant process in the atmospheric oxidation of methylamine for NO_x concentrations below 100 ppb. The mechanism identified here is available to amines with primary, secondary, and tertiary α carbons and suggests that they may be less likely to form nitramines and nitrosamines than is currently thought.     

Theoretical study on the ion–molecule reaction of NH+ with CH2O

An in‐depth theoretical study is carried out at the B3LYP/6‐311G(d,p), M062X/aug‐cc‐pVDZ and CCSD(T)/6‐311++G(3df,2dp) (single‐point) levels as an attempt to explore the mechanism of the little‐understood ion–molecule reaction between NH⁺ and CH₂O. Various possible reaction pathways are taken into account. It is shown that six dissociation products, including P ₁ (²N + CH₂OH⁺), P ₂ (⁴N + CH₂OH⁺), P ₃ (³NH + CH₂O⁺), P ₄ (NH₂ + HCO⁺), P ₅ (NH + CO), and P ₉ (H + CONH) are all accessible both kinetically and thermodynamically. Among these products, P ₄ is the most competitive product with predominant abundance, and the second most feasible product is P ₃ , followed by P ₂ and P ₁ . The remaining products, P ₅ and P ₉ , may have negligible yield under room temperature condition. As the intermediates and transition states involved in the NH⁺ + CH ₂ O reaction all stay below the reactant, the title reaction is expected to be rapid, which is consistent with the measured large rate constant in experiment. The present study will enrich our knowledge of the chemistry of NH⁺. Furthermore, our calculated result is compared with the previous experimental research, and, meanwhile, it provides a useful guide for understanding analogous reaction, NH⁺ with CH₂NH. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Reaction paths of some open-shell reactive intermediates

The intermolecular interaction energy for reacting systems in singlet, triplet and doublet states was partitioned by the perturbation expansion method into the chemically meaningful five interaction terms: the Coulomb, exchange-repulsion, induction, dispersion, and charge-transfer energies. In the local ZDO approximation, these energy terms were evaluated for the dimerization of methylenes (^1,3CH₂), the additions of carbenes (^1,3CH₂ and^1,3CF₂) as well as amino radicals (²NH₂ and²NF₂) toward ethylene, and the hydrogen abstractions by methylenes (^1,3CH₂), nitrene (³NH), and hydroxyl radical (²OH) from methane. It has been found that the reaction path is much influenced by the spinmultiplicity, and that the charge-transfer and exchange-repulsion terms play a dominant role in determining the course of reactions.     

Gas-phase proton-transport self-catalysed isomerisation of glutamine radical cation: The important role of the side-chain

The gas-phase isomerisation reaction of glutamine radical cation from [NH₂CH (CH₂CH₂CONH₂) COOH ]^+• to [ NH₂C (CH₂CH₂CONH₂) C (OH)₂]^+• has been studied theoretically using the MPWB1K functional approach. The [ NH₂ C (CH₂CH₂CONH₂) C (OH)₂]^+• diol species has been found to be the most stable isomer for glutamine radical cation. Moreover, it has been observed that glutamine has a long enough side-chain with basic groups that acts as a solvent molecule favouring the proton-transfer from C _α to COOH group. This fact reduces dramatically the isomerisation energy barriers compared to the same process for glycine radical cation in gas phase. Thus, this reaction can be considered as an example of gas-phase proton-transport catalysed reaction in which the proton-transport is carried out by the reactant molecule itself instead of any solvent. Contribution to the Serafin Fraga Memorial Issue.     

Prebiotic Synthesis and Isomerization in Interstellar Analog Ice: Glycinal,Acetamide, and Their Enol Tautomers

Glycinal (HCOCH₂NH₂) and acetamide (CH₃CONH₂) are simple molecular building blocks of biomolecules in prebiotic chemistry, though their origin on early Earth and formation in interstellar media remain a mystery. These molecules are formed with their tautomers in low temperature interstellar model ices upon interaction with simulated galactic cosmic rays. Glycinal and acetamide are accessed via barrierless radical-radical reactions of vinoxy (⋅CH₂CHO) and acetyl (⋅C(O)CH₃), and then undergo keto-enol tautomerization. Exploiting tunable photoionization reflectron time-of-flight mass spectroscopy and photoionization efficiency (PIE) curves, these results demonstrate fundamental reaction pathways for the formation of complex organics through non-equilibrium ice reactions in cold molecular cloud environments. These molecules demonstrate an unconventional starting point for abiotic synthesis of organics relevant to contemporary biomolecules like polypeptides and cell membranes in deep space.     

Properties of strong hydrogen-bonded systems: The formation of hydrogen-bonded ion pair in amine·HCL systems

The hydrogen-bonded complexes between CH₃NH₂ and (CH₃)₂NH with HCl have been studied by the ab initio molecular orbital method using the 4–31G basis set. Calculations show that the proton potential curve has a single minimum near to the nitrogen atom in both complexes. This means that the proton has been transferred from HCl to the amine. ΔE and the dipole moment of the complexes studied are as follows: ?18.2 kcal mol^?1, 10.3 D for methylamine ·HCl, and ?21.7 kcal mol^?1 11.1 D for the corresponding dimethylamine complex. Other properties of the hydrogen-bonded ion pairs are discussed.     

Acid–Base Chemistry at the Ice Surface: Reverse Correlation Between Intrinsic Basicity and Proton‐Transfer Efficiency to Ammonia and Methyl Amines

Proton transfer from the hydronium ion to NH₃, CH₃NH₂, and (CH₃)₂NH is examined at the surface of ice films at 60 K. The reactants and products are quantitatively monitored by the techniques of Cs⁺ reactive‐ion scattering and low‐energy sputtering. The proton‐transfer reactions at the ice surface proceed only to a limited extent. The proton‐transfer efficiency exhibits the order NH₃>(CH₃)NH₂=(CH₃)₂NH, which opposes the basicity order of the amines in the gas phase or aqueous solution. Thermochemical analysis suggests that the energetics of the proton‐transfer reaction is greatly altered at the ice surface from that in liquid water due to limited hydration. Water molecules constrained at the ice surface amplify the methyl substitution effect on the hydration efficiency of the amines and reverse the order of their proton‐accepting abilities.