Intramolecular Hydrogen Transfer Reactions Research Articles

Reactive molecular dynamics insight into the thermal decomposition mechanism of 2,6-Bis(picrylamino)-3,5-dinitropyridine

2,6-bis(picrylamino)-3,5-dinitropyridine (PYX) has excellent thermostability, which makes its thermal decomposition mechanism receive much attention. In this paper, the mechanism of PYX thermal decomposition was investigated thoroughly by the ReaxFF-lg force field combined with DFT-B3LYP(6–311++G) method. The detailed decomposition mechanism, small-molecule product evolution, and cluster evolution of PYX were mainly analyzed. In the initial stage of decomposition, the intramolecular hydrogen transfer reaction and the formation of dimerized clusters are earlier than the denitration reaction. With the progress of the reaction, one side of the bitter amino group is removed from the pyridine ring, and then the pyridine ring is cleaved. The final products produced in the thermal decomposition process are CO2, H2O, N2, and H2. Among them, H2O has the earliest generation time, and the reaction rate constant (k3) is the largest. Many clusters are formed during the decomposition of PYX, and the formation, aggregation, and decomposition of these clusters are strongly affected by temperature. At low temperatures (2500 K–2750 K), many clusters are formed. At high temperatures (2750 K–3250 K), the clusters aggregate to form larger clusters. At 3500 K, the large clusters decompose and become small. In the late stage of the reaction, H and N in the clusters escaped almost entirely, but more O was trapped in the clusters, which affected the auto-oxidation process of PYX. PYX’s initial decomposition activation energy (Ea) was calculated to be 126.58 kJ/mol. This work contributes to a theoretical understanding of PYX’s entire thermal decomposition process.

Atomic insights into the thermal decomposition mechanism and cluster growth law of nanoscale HMX and LLM-126 mixture: A ReaxFF-lg molecular dynamics study

In this paper, the thermal decomposition process and cluster growth law of the HMX/LLM-126 nanoscale mixture system were studied by ReaxFF-lg combined with DFT, and the thermostability of the mixture system with a molar ratio of 1:1 was investigated. The results show that clusters can be formed between HMX and LLM-126 in the mixture system, which effectively delays the cracking speed of the HMX structure. Meanwhile, NO2 generated from the initial decomposition of HMX will accelerate the denitration process of LLM-126. The decomposition process of HMX is mainly a continuous denitration until the structural ring-opening disintegration, the initial decomposition step is C4H8O8N8 => C4H8O6N7 + NO2. In contrast, the initial decomposition of LLM-126 is dominated by intramolecular hydrogen transfer reactions and the generation of dimer clusters, followed by the detachment of nitro and bitter amino groups, and finally the cleavage of the pyridine ring. The intramolecular hydrogen transfer process of LLM-126 is the transfer of H on -NH- to the adjacent nitro group. After LLM-126 was added to the HMX system, the oxygen balance of the system increased, and the N content, exothermic rate, and the number of final products decreased significantly compared with the HMX pure component system. Also, the number of clusters generated, and the maximum cluster weight increased significantly. These phenomena are important reasons for the improved thermostability of the mixture system compared to the pure HMX system. This work can provide a theoretical basis for the design and application of nanoscale high-energy thermostable mixed explosives.

Theoretical Investigations of State Specific Hydrogen Atom Transfer in 8-Formyl-7-hydroxy-4-methylcoumarin

Excited state intramolecular hydrogen transfer (ESIHT) reaction of 8-formyl-7-hydroxy-4-methyl coumarin (FC) in its pure and hydrated state FC-(H2O)4 (FCH) has been studied by implementing state specific time dependent density functional theory (SS-TDDFT) along with the effective fragment potential (EFP1) method for solvation with discrete water molecules. The intramolecular hydrogen bond formed between hydroxyl hydrogen (H18) and formyl oxygen (O15) and intermolecular hydrogen bonds formed due to microsolvation were explored. The studies of electrostatic potential, natural charge analysis, difference electron density map and UV-Vis spectra of both FC and FCH molecules establish the intramolecular charge transfer (ICT) states of the molecules. The vertical excitation from S0 to S1 state causes the transfer of hydroxyl hydrogen to formyl oxygen and from S1 to S3 causes the transfer of the hydrogen atom back to hydroxyl oxygen. Potential energy surface scans along intramolecular hydrogen bonding at the ground and excited states confirm the state specific ESIHT reaction in both FC and FCH molecules.

Quantum Chemistry Calculation Study on Chain Reaction Mechanisms and Thermodynamic Characteristics of Coal Spontaneous Combustion at Low Temperatures.

The coal spontaneous combustion phenomenon seriously affects the safety production of coal mines. Aiming at the problem of complex coal molecular structure and incomplete reaction sequences at present, the mechanisms and thermodynamic parameters of coal spontaneous combustion chain reactions were explored by combining experimental detections and molecular simulations. First, the active groups on the surface of coal were obtained by Fourier transform infrared spectroscopy (FTIR), mainly including methyl (−CH3), methylene (−CH2), methyne (−CH), phenolic hydroxyl (−ArOH), alcohol hydroxyl (−ROH), carboxyl (−COOH), aldehyde (−CHO), and ether (−O−), and the coal molecular models containing functional groups and radicals were established. According to the charge density, electrostatic potential, and frontier orbital theories, the active sites and active bonds were obtained, and a series of reactions were given. The thermodynamic and structural parameters of each reaction were explored. In the chain initiation reaction stage, O2 chemisorption and the self-reaction of radicals play a leading role. In this stage, heat gradually accumulates and various radicals begin to generate, where the intramolecular hydrogen transfer reaction of a peroxide radical (−C–O–O·) can produce the key hydroxyl radical (−O·). In the chain propagation reaction stage, O2 and −O· continuously consume active sites to accelerate the reaction sequences and increase the temperature of coal, and index gases such as CO and CO2 generate, causing the chain cycle reactions to gradually form. The chain termination reaction stage is the formation of stable compounds such as ethers, esters, and quinones, which can inhibit the development of chain reactions. The results can further explain the reaction mechanism of coal spontaneous combustion and provide references for the development and utilization of chemical inhibitors.

Theoretical study on the feasibility of intramolecular hydrogen transfer reaction of 5-hydroxymethylfurfural

• Intramolecular hydrogen transfer reaction (IHTR) mechanism within 5-HMF is proposed. • The feasibility of IHTR reaction on Cu, Pd and Cu 3 Pd 2 was studied by DFT. • The favorable pathways for IHTR reaction on different catalysts were determined. • Cu 3 Pd 2 is predicted to be the most active catalyst for IHTR reaction of 5-HMF. The intramolecular hydrogen transfer reaction (IHTR) of 5-hydroxymethylfurfural can potentially reach a 100% atomic economic efficiency, which is of great significance to the utilization of biomass raw materials. In this work, the feasibility of IHTR on Cu, Pd and Cu 3 Pd 2 bimetallic catalysts was investigated by density functional theory (DFT) calculations. Eight intramolecular hydrogen-transfer pathways, consisting of four elementary reactions each, are proposed. The elementary reactions were categorized and discussed as follows: C-H bond cleavage, C 2 (H)=C 3 hydrogenation, O-H bond cleavage and C 2 =C 3 (H) hydrogenation. The relevant adsorption, activation and reaction energies were calculated and compared. Results reveal that the C-H bond is not easy to break on Cu(111) . On the surface of Pd(111), both the O-H bond cleavage and C=C bond hydrogenation reactions require higher energy barriers to overcome. Cu 3 Pd 2 (111) demonstrates high activity for both hydrogenation and dehydrogenation reactions. The reaction steps of the lowest energy path on Cu 3 Pd 2 (111) involve C-H bond cleavage, C 2 =C 3 (H) hydrogenation, O-H bond cleavage and C 2 (H)=C 3 hydrogenation. The rate-limiting step is the cleavage of the C-H bond, and its activation barrier is 0.89 eV. As a result, the Cu 3 Pd 2 (111) catalyst is predicted to be the most active catalyst for intramolecular hydrogen migration, while the Cu(111) surface is also conducive to the IHTR reaction with slightly higher energy barrier. The calculation results provide valuable theoretical basis for the optimization of experimental research.

Kinetic Study of Gas-Phase Reactions of Pyruvic Acid with HO2

Gas-phase reactions between pyruvic acid (PA) and HO2 radicals were examined using ab initio quantum chemistry and transition state theory. The rate coefficients were determined over a temperature range of 200-400 K including tunneling contributions. Six potential reaction pathways were identified. The two hydrogen abstraction reactions yielding the H2O2 product were found to have high barriers. The HO2 radical was also found to have a catalytic effect on the intramolecular hydrogen transfer reactions occurring by three distinct routes. These hydrogen-shift reactions are very interesting mechanistically although they are highly endothermic. The only reaction that contributes significantly to the consumption of PA is a multistep pathway involving a peroxy-radical intermediate, PA + HO2 → CH3COOH + OH + CO2. This exothermic process has potential atmospheric relevance because it produces an OH radical as a product. Atmospheric models currently have difficulty predicting accurate OH concentrations for certain atmospheric conditions, such as environments free of NOx and the nocturnal boundary layer. Reactions of this sort, although not necessary with PA, may account for a portion of this deficit. The present study helps settle the issue of the relative roles of reaction and photolysis in consumption of PA in the troposphere.

Mechanistic insight into the catalytic cracking mechanism of α-olefin on H-Y zeolite: A DFT study

In the bifunctional catalyst for Fischer-Tropsch synthesis, the distribution of products in the secondary catalytic reaction of intermediate products is affected by the Brønsted acid sites in zeolites. Linear α-olefins are the intermediates of Fischer-Tropsch synthesis. In this work, density functional theory (DFT) calculation was carried out to understand further Brønsted Acid Sites’ mechanism in the secondary reaction of Fischer-Tropsch synthesis. The adsorption energy of linear α-olefins on H-Y zeolite decreased with the increase of the carbon chain. Besides, four essential reactions were simulated by the DFT method. The four elementary reactions' energy barriers are: β bond-breaking reaction > skeleton isomerization reaction > intramolecular hydrogen transfer reaction > protonation reaction. Then, a complete reaction network of straight-chain α-Nonylene on H-Y zeolite was designed. The β bond-breaking reaction is a key step to determine the type and distribution of products.

Thermochemistry and kinetics of the 2‐butanone‐4‐yl CH3C(=O)CH2CH2• + O2 reaction system

AbstractThermochemistry and kinetic pathways on the 2‐butanone‐4‐yl (CH3C(=O)CH2CH2•) + O2 reaction system are determined. Standard enthalpies, entropies, and heat capacities are evaluated using the G3MP2B3, G3, G3MP3, CBS‐QB3 ab initio methods, and the B3LYP/6‐311g(d,p) density functional calculation method. The CH3C(=O)CH2CH2• radical + O2 association reaction forms a chemically activated peroxy radical with 35 kcal mol−1 excess of energy. The chemically activated adduct can undergo RO−O bond dissociation, rearrangement via intramolecular hydrogen transfer reactions to form hydroperoxide‐alkyl radicals, or eliminate HO2 and OH. The hydroperoxide‐alkyl radical intermediates can undergo further reactions forming ketones, cyclic ethers, OH radicals, ketene, formaldehyde, or oxiranes. A relatively new path showing a low barrier and resulting in reactive product sets involves peroxy radical attack on a carbonyl carbon atom in a cyclic transition state structure. It is shown to be important in ketones when the cyclic transition state has five or more central atoms.

Density functional tight-binding and infrequent metadynamics can capture entropic effects in intramolecular hydrogen transfer reactions.

Infrequent metadynamics uses biased simulations to estimate the unbiased kinetics of a system, facilitating the calculation of rates and barriers. Here the method is applied to study intramolecular hydrogen transfer reactions involving peroxy radicals, a class of reactions that is challenging to model due to the entropic contributions of the formation of ring structures in the transition state. Using the self-consistent charge density-functional based tight-binding (DFTB) method, we applied infrequent metadynamics to the study of four intramolecular H-transfer reactions, demonstrating that the method can qualitatively reproduce these high entropic contributions, as observed in experiments and those predicted by transition state theory modeled by higher levels of theory. We also show that infrequent metadynamics and DFTB are successful in describing the relationship between transition state ring size and kinetic coefficients (e.g., activation energies and the pre-exponential factors).

Methylation of toluene with methanol over HZSM-5: A periodic density functional theory investigation

Periodic density functional theory was applied to investigate the reaction mechanism for the methylation of toluene with methanol over HZSM-5. The results indicated that toluene could be methylated at its para, meta, ortho and geminal positions via a concerted or stepwise pathway. For the concerted pathway, the calculated free energy barriers for the para, meta, ortho and geminal methylation reactions were 167, 138, 139 and 183 kJ/mol, respectively. For the stepwise pathway, the dehydration of methanol was found to be the rate-determining step with a free energy barrier of 145 kJ/mol, whereas the free energy barriers for the methylation of toluene at its para, meta, ortho and geminal positions were 127, 105, 106 and 114 kJ/mol, respectively. Both pathways led to the formation of C8H11+ species as important intermediates, which could back-donate a proton to the zeolite framework via a reorientation process or form gaseous products through demethylation. Methane was formed via an intramolecular hydrogen transfer reaction from a ring carbon of the C8H11+ species to the carbon of the methyl group, with calculated energy barriers of 136, 132 and 134 kJ/mol for the para, meta and ortho C8H11+ species, respectively. The calculated free energy barriers for the formation of para-, meta- and ortho-xylene indicated that the formation of the para-xylene had the highest energy barrier for both pathways.

Intramolecular hydrogen transfer reactions catalyzed by pentamethylcyclopentadienyl rhodium and cobalt olefin complexes: Mechanistic studies

Intramolecular hydrogen transfer reactions catalyzed by pentamethylcyclopentadienyl rhodium and cobalt olefin complexes: Mechanistic studies

Methane formation mechanism in methanol to hydrocarbon process: A periodic density functional theory study

Methane is an important product in methanol to hydrocarbon (MTH) process and its formation mechanism over HZSM-5 was investigated by applying periodic density functional theory. The results show that the carbocations of C7H9+–C12H19+ are important intermediates in MTH process and methane is formed via one intramolecular hydrogen transfer reaction of these intermediates from ring carbon to the carbon of methyl group. The activation energies for methane formation increase from 101 to 174kJ/mol with increasing methyl groups in protonated methylbenzenes. The data indicate that methane has similar formation mechanism as ethene and propene, i.e. via hydrocarbon pool mechanism.

Intramolecular hydrogen transfer reactions catalyzed by pentamethylcyclopentadienyl rhodium and cobalt olefin complexes: Mechanistic studies

The mechanism of intramolecular transfer dehydrogenation catalyzed by [Cp∗M(VTMS)2] (1, M=Rh, 2, M=Co, Cp∗=C5Me5, VTMS=vinyltrimethylsilane) complexes has been studied using vinyl silane protected alcohols as substrates. Deuterium-labeled substrates have been synthesized and the regioselectivity of H/D transfers investigated using 1H and 2H NMR spectroscopy. The labeling studies establish a regioselective pathway consisting of alkene directed α C–H activation, 2,1 alkene insertion, and finally β-hydride elimination to give silyl enol ether products.

Thermal Cracking of Virgin and Waste Plastics of PP and LDPE in a Semibatch Reactor under Atmospheric Pressure

Study of the decomposition kinetics, pyrolysis products, and even reaction mechanisms plays an important role for the development of polymer recycling. In the present research, the kinetics of virgin and waste polypropylene (PP) and low-density polyethylene (LDPE) were studied by a modified Coats–Redfern method. Afterward, thermal cracking of them in a semibatch reactor under atmospheric pressure in nitrogen has been investigated. Both virgin and waste plastics are decomposed at 420–460 °C, and the products have been characterized using GC, FT-IR, 1H NMR, and GC-MS. The reaction path and the degradation mechanism for the thermal cracking of polymer in this study were also discussed. The lower activation energy of waste PP and LDPE indicates that waste plastics degrade at lower initial temperature and may favor mild conditions. Due to the short residence time, the higher gaseous and liquid yields were obtained for virgin PP and LDPE. A large amount of residues for waste polymer indicates that it is a favorable way to degrade waste plastics in a semibatch reactor without further separation. Chain scission reactions are the predominant degradation mechanism in this thermal cracking process. The significant content of unsaturated hydrocarbons in PP thermal cracking products shows the intramolecular hydrogen transfer and β-scission reactions are predominant. In the case of LDPE, intermolecular hydrogen transfer and β-disproportionate reactions also occur. For thermal cracking polymer in a semibatch reactor under atmospheric pressure, the high yields of gasoline (C6–C12) and diesel (C13–C22) fraction in liquid products confirm that it is a desirable way to realize waste plastics recovery.

Reactive simulation of the chemistry behind the condensed-phase ignition of RDX from hot spots.

Chemical events that lead to thermal initiation and spontaneous ignition of the high-pressure phase of RDX are presented using reactive molecular dynamics simulations. In order to initiate the chemistry behind thermal ignition, approximately 5% of RDX crystal is subjected to a constant temperature thermal pulse for various time durations to create a hot spot. After application of the thermal pulse, the ensuing chemical evolution of the system is monitored using reactive molecular dynamics under adiabatic conditions. Thermal pulses lasting longer than certain time durations lead to the spontaneous ignition of RDX after an incubation period. For cases where the ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. Contrary to the widely accepted unimolecular models of initiation chemistry, N-N bond dissociations that produce NO2 species are suppressed in the condensed phase. The gradual temperature and pressure increase in the incubation period is accompanied by the accumulation of short-lived, heavier polyradicals. The polyradicals contain intact triazine rings from the RDX molecules. At certain temperatures and pressures, the polyradicals undergo ring-opening reactions, which fuel a series of rapid exothermic chemical reactions leading to a thermal runaway regime with stable gas-products such as N2, H2O and CO2. The evolution of the RDX crystal throughout the thermal initiation, incubation and thermal runaway phases observed in the reactive simulations contains a rich diversity of condensed-phase chemistry of nitramines under high-temperature/pressure conditions.

Kinetics, mechanism and thermodynamics of reactions of CH3NHNH2 with OOH

Reactions between CH3NHNH2 and OOH radical were studied using computational methods. The activation energies (Ea) and Gibbs free energies of activation (ΔG#) were calculated at the MP2 and B3LYP levels of theory. The calculated activation energies of the hydrogen abstraction reactions were less than 100 kJ/mol and those for the substitution reactions were about 150–250 kJ/mol. The calculated activation energies for the intra-molecular hydrogen transfer reactions in CH3NHNH, CH2NNH2 and CH3NN molecules were 210–250 kJ/mol. Catalytic effect of the water molecule on the intra-molecular hydrogen transfer reactions was studied. It was found that the water molecule decreases the activation energies by about 70–100 kJ/mol. Rate constants of the reactions were calculated using transition state theory in the temperature range of 298–2000 K. Consecutive hydrogen abstraction reactions from CH3NHNH2 led to the formation of CH2NN, which was a very stable molecule.

Controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby

Although the local environment of a molecule can play an important role in its chemistry, rarely has it been examined experimentally at the level of individual molecules. Here we report the precise control of intramolecular hydrogen-transfer (tautomerization) reactions in single molecules using scanning tunnelling microscopy. By placing, with atomic precision, a copper adatom close to a porphycene molecule, we found that the tautomerization rates could be tuned up and down in a controlled fashion, surprisingly also at rather large separations. Furthermore, we extended our study to molecular assemblies in which even the arrangement of the pyrrolic hydrogen atoms in the neighbouring molecule influences the tautomerization reaction in a given porphycene, with positive and negative cooperativity effects. Our results highlight the importance of controlling the environment of molecules with atomic precision and demonstrate the potential to regulate processes that occur in a single molecule.

Theoretical study on intramolecular hydrogen transfer of 1-methylbutyl peroxide radical

The density functional theory method has been used to study the mechanism for the intramolecular hydrogen transfer (IHT) reaction of 1-methylbutly peroxide radical [n-C3H7CH(CH3)OO·]. The B3LYP method was used in conjunction with 6-31+G**, 6-311++G** and aug-cc-pVDZ basis sets. The geometrical configurations of reactants, productions and transition states were fully optimized on the potential energy surfaces. The results suggest that the IHT reactions involve the formation of transition states with five-, six- and seven-member rings when the transferring hydrogen atoms are at different initial positions related to the peroxide oxygen. The activation energies for the IHT reactions of β-, γ- and α-H migrations are 90.0, 100.8, and 140–152 kJ/mol at the B3LYP/6-311++G** level, respectively. The α-H is easier to transfer than the α- and γ-H. Both the activation energy and rate constant for β-H migrations at the B3LYP/6-31+G** level are basically in agreement with the experimental values. The methyl substituent on β-position slightly lowers the activation energy, which is consistent with the experimental fact. All the IHT reactions are endothermic. The β-H transferring is the most favorable process in view of both thermodynamics and kinetics. The predicted rate constants indicate that only the β-H and γ-H transfer reactions occur when the temperature is not high enough.

The Photolysis of Disulfide Bonds in IgG1 and IgG2 Leads to Selective Intramolecular Hydrogen Transfer Reactions of Cysteine Thiyl Radicals, Probed by Covalent H/D Exchange and RPLC-MS/MS analysis

The evaluation of photo-instability of biotherapeutic products is mandated by regulatory agencies. Photo-irradiation can induce oxidative modifications in proteins, which may lead to undesired biological and therapeutic consequences. Among the modifications, epimerization of amino acid residues can occur upon photo-irradiation of IgGs. We show here, that UV irradiation (λ = 253.7nm) of IgG1 and IgG2 leads to the formation of intermediary carbon-centered radicals, validated by covalent incorporation of deuterium into the protein primary sequence. By MS/MS analysis we identified the sites of deuterium incorporation, such as the sequence QD [303:304, HC], present in the peptide of VVSVLTVVHQDWLNGK [294:309, HC] in both IgG1 and IgG2, and V [111, LC] and K [116, LC], present in the peptide VTVLGQPK [109:116, LC] in IgG2. Both peptides are in the proximity of intrachain disulfide bonds. The exposure of IgG1 and IgG2 to UV-light (λ = 253.7nm) generates specific carbon-centered radicals. The latter were evidenced by a covalent H-D exchange reaction that likely occurred through a hydrogen atom transfer reaction between cysteine thiyl radical and C-H bond.

Intramolecular Hydrogen Transfer Reactions of Thiyl Radicals from Glutathione: Formation of Carbon-Centered Radical at Glu, Cys, and Gly

Glutathione thiyl radicals (GS(•)) were generated in H(2)O and D(2)O by either exposure of GSH to AAPH, photoirradiation of GSH in the presence of acetone, or photoirradiation of GSSG. Detailed interpretation of the fragmentation pathways of deuterated GSH and GSH derivatives during mass spectrometry analysis allowed us to demonstrate that reversible intramolecular H-atom transfer reactions between GS(•) and C-H bonds at Cys[(α)C], Cys[(β)C], and Gly[(α)C] are possible.