Formation Of Pre-reactive Complex Research Articles

Теоретическое исследование получения диметилкарбоната алкоголизом мочевины

Using the density functional method М06, the mechanisms of non-catalytic reactions of transesterification of urea with methanol with the formation of dimethyl carbonate, as well as in catalysis with zinc oxide and acetate, were studied. The transesterification proceeds stepwise with the intermediate formation of methyl carbamate. The non-catalytic process of transesterification of urea with methanol proceeds by the mechanism of nucleophilic SN2 substitution and is accompanied by the formation of pre-reaction complexes, which through synchronous transition states turn into post-reaction complexes, decomposing into ammonia and methyl carbamate in the first stage and dimethyl carbonate in the second. It has been established that methanol associates can take part in these reactions. Their participation is preferable both kinetically and thermodynamically. An analysis of the equilibrium constants of the reaction of urea with methanol at various temperatures showed that in a wide temperature range their values remain large in the first stage – the formation of methyl carbamate and become significantly reversible in the second – the conversion of methyl carbamate to dimethyl carbonate. Reactions involving acetate and zinc oxide proceed through the same stages as non-catalytic interactions. In the case of zinc acetate catalyzed reactions, if methanol monomer is involved in the reaction, the reaction of formation of methyl carbamate has a lower activation barrier compared to the reaction of conversion of methyl carbamate to dimethyl carbonate. If a methanol dimer is involved in the reaction, both reactions have a practically equal activation barrier. In the case of zinc oxide catalyzed interactions, reactions involving a methanol dimer were not detected. The participation of the catalyst leads to a significant decrease in activation barriers, and a more significant decrease occurs in the case of catalysis with zinc oxide. The reason for the different catalytic activity, in our opinion, is the difference in the charges on the urea carbon atom in the pre-reaction complexes.

Theoretical studies on atmospheric chemistry of (CF3)2C(OH)CH3: Kinetics, mechanism and thermochemistry of gas phase reactions with OH radicals

Abstract The mechanism, kinetics and thermochemistry of the reaction of (CF3)2C(OH)CH3 with OH radicals are theoretically investigated using DFT based M06-2X functional method. Three important H-abstraction channels have been identified for (CF3)2C(OH)CH3 + OH reaction and one transition state has been located for each reaction channel. Formation of pre-reactive complex at the entry of each reaction channel indicates an indirect mechanism for hydrogen-abstraction reaction. The rate coefficients for (CF3)2C(OH)CH3 are evaluated using canonical transition state theory along with Eckart's tunneling correction over a wide range of temperature (270–1000 K). At 298 K, our calculated total rate coefficient for (CF3)2C(OH)CH3 + OH reaction is in good agreement with the experimental result. The results show that H-abstraction from the CH3 group is the predominant channel and has more contribution to the total rate coefficient than that from the OH group of (CF3)2C(OH)CH3. The standard heats of formation for (CF3)2C(OH)CH3 molecule, (CF3)2C(OH)CH2 and (CF3)2C(O)CH3 radicals are estimated by using group-balanced isodesmic reactions and the values are −1599.6, −1369.8 and −1335.6 kJ mol−1, respectively at 298 K. The atmospheric lifetime of (CF3)2C(OH)CH3 is estimated to be around 5.0 years. The 100-year time horizon global warming potentials of (CF3)2C(OH)CH3 with respect to CO2 is 705. Potential atmospheric degradation routes for the resulting (CF3)2C(OH)CH2 radical is also discussed here.

Theoretical investigation on kinetics and thermochemistry of reaction of CHF2CF2OCH2CF3 with OH radicals and global warming potentials

Theoretical investigation has been carried out on the mechanism, kinetics and thermochemistry of the gas-phase reactions between CHF2CF2OCH2CF3 and OH radical using a new hybrid density functional M06-2X/6-31+G(d,p) and G2(MP2)//M06-2X/6-31+G(d,p) methods. The most stable conformer of CHF2CF2OCH2CF3 is considered in our study and the possible H-abstraction reaction channels are identified. Each reaction channel shows an indirect H-abstraction reaction mechanism via the formation of pre-reactive complex. The rate coefficients are determined for the first time over a wide range of temperature 250–1000 K. At 298 K, the calculated total rate coefficient of kOH = 1.01×10−14 cm3 molecule−1 s−1 is in good agreement with the experimental results. The heats of formation for CHF2CF2OCH2CF3 and CF2CF2OCH2CF3 and CHF2CF2OCHCF3 radicals are estimated to be -1739.25, -1512.93 and -1523.94 kJ mol−1, respectively. The bond dissociation energies of the two C-H bonds are C(-H)F2CF2OCH2CF3: 423.34 kJ mol−1 and CHF2CF2OC(-H)HCF3: 411.87 kJ mol−1. The atmospheric lifetime of CHF2CF2OCH2CF3 is estimated to be around 4.5 years and the 100-year time horizon global warming potentials of CHF2CF2OCH2CF3 relative to CO2 is estimated to be 601.

Kinetics, mechanism and thermochemistry of the gas phase reactions of CF3CH2OCH2CF3 with OH radicals: A theoretical study

Theoretical investigations have been carried out on the mechanism, kinetics and thermochemistry of the gas-phase reactions between CF3CH2OCH2CF3 and OH radical using a newly developed DFT based M06-2X functional method. Two important H abstraction channels have been identified according to different orientations of the two H atoms bonded to same carbon atom in CH2 group, and one transition state has been located for each reaction channel. At the entry of each reaction channel, formation of pre-reactive complex indicates an indirect hydrogen-abstraction reaction. The rate coefficients were calculated for the first time over a wide range of temperature (250–1000K) and can be expressed as a model equation: kOH=2.55×10−11exp(−(2883.7−387626/T)/T)cm3molecule−1s−1. At 298K, our calculated rate coefficient for CF3CH2OCH2CF3 with OH radical 1.32×10−13cm3molecule−1s−1 is in very good agreement with the experimental result of kOH=1.30×10−13cm3molecule−1s−1. Using a group-balanced isodesmic reaction, the standard heats of formation for CF3CH2OCH2CF3 and CF3CHOCH2CF3 radical are estimated to be −365.64 and −316.84kcalmol−1, respectively. The calculated bond dissociation energy for the CH bond in CF3CH(H)OCH2CF3 is found to be 95.82kcalmol−1 at 298K. The atmospheric lifetime of CF3CH2OCH2CF3 was estimated to be around 0.272 years. The global warming potential and the main degradation process of alkoxy radical CF3CH(O)OCH2CF3 are also discussed.

Theoretical study on the mechanism and kinetics of addition of hydroxyl radicals to fluorobenzene

Geometries, frequencies, reaction barriers, and reaction rates were calculated for the addition of OH radical to fluorobenzene using Möller-Plesset second-order perturbation (MP2) and G3 methods. Four stationary points were found along each reaction path: reactants, prereaction complex, transition state, and product. A potential for association of OH radical and fluorobenzene into prereaction complex was calculated, and the associated transition state was determined for the first time. G3 calculations give higher reaction barriers than MP2, but also a significantly deeper prereaction complex minimum. The rate constants, calculated with Rice-Ramsperger-Kassel-Marcus (RRKM) theory using G3 energies, are much faster and in much better agreement with the experiment than those calculated with MP2 method, as the deeper well favors the formation of prereaction complex and also increases the final relative populations of adducts. The discrepancies between the experimental and calculated rate constants are attributed to the errors in calculated frequencies as well as to the overestimated G3 reaction barriers and underestimated prereaction complex well depth. It was possible to rectify those errors and to reproduce the experimental reaction rates in the temperature range 230-310 K by treating the relative translation of OH radical and fluorobenzene as a two-dimensional particle-in-the-box approximation and by downshifting the prereaction complex well and reaction barriers by 0.7 kcal mol(-1). The isomeric distribution of fluorohydroxycyclohexadienyl radicals is calculated from the reaction rates to be 30.9% ortho, 22.6% meta, 38.4% para, and 8.3% ipso. These results are in agreement with experiment that also shows dominance of ortho and para channels.

Mechanism and kinetics for the reaction of O(3P) with DMSO: A theoretical study

Mechanism and kinetics for the reaction of DMSO with O(3P) have been investigated by M06-2X/MG3S, CBS-QB3 and G4MP2 methods. Four possible reaction pathways are identified. Among them, the O(3P) addition to S-atom followed by CH3 elimination is almost exclusive. Four pre-reactive complexes have been located. AIM theory is used to determine the nature of interactions in these complexes. Considering the formation of pre-reactive complex, the rate constant for major pathway is calculated using transition state theory applied to a two-step mechanism. Enthalpies of formation at 298.15K (ΔfH°298.15) have been calculated using the composite CBS-QB3, G4MP2 and G3B3 methods.

Solvent Effects on Free Radical Polymerization Reactions: The Influence of Water on the Propagation Rate of Acrylamide and Methacrylamide

The polymerization of acrylamide (AA) and methacrylamide (MAA) was studied by an extensive set of computational methods with a particular focus on the possible influence of water molecules on the propagation reaction. An extensive set of electronic structure methods was tested, consisting of B3LYP, BMK, MPWB1K, MP2, and B2-PLYP of which some include dispersion effects. The effect of water on the transition state is modeled in two different ways. Explicit water molecules are added to the system, showing that replacing the hydrogen bond that dominates the transition state structure by a water-mediated hydrogen bond, results in more stable, more feasible transition states. This effect is the largest for AA polymerization, a monomer that is known to experience a larger solvent effect than MAA. Additionally, a conductor-like polarizable continuum model (C-PCM) is applied on both the transition states in gas phase and the ones bearing explicit water molecules. This model has a dramatic effect on all the propagation rates, raising them by about 3 orders of magnitude. The inclusion of explicit water molecules gives insight into the role of water molecules and the formation of prereactive complexes. The relative rate of polymerization of AA with regard to MAA is well reproduced for a trimeric propagating radical with inclusion of explicit water molecules or by using an implicit solvation model at the BMK and MPWB1K level of theory.

Kinetics and mechanism of triphenylphosphine quarternization with unsaturated carboxylic acids in the medium of acetic acid

Kinetics of reaction of triphenylphosphine with a series of unsaturated carboxylic acids and related esters in the medium of acetic acid as well as in mixtures of acetic acid and acetonitrile was studied by spectrophotometry. The data obtained show that the process of quarternization should be described by kinetic equation of third order, the proton transfer occurs from the solvent. A stepwise mechanism of interaction including formation of prereaction complex on the reaction pathway is proposed.

Thermodynamics of the hydroxyl radical addition to isoprene.

Oxidation of isoprene by the hydroxyl radical leads to tropospheric ozone formation. Consequently, a more complete understanding of this reaction could lead to better models of regional air quality, a better understanding of aerosol formation, and a better understanding of reaction kinetics and dynamics. The most common first step in the oxidation of isoprene is the formation of an adduct, with the hydroxyl radical adding to one of four unsaturated carbon atoms in isoprene. In this paper, we discuss how the initial conformations of isoprene, s-trans and s-gauche, influences the pathways to adduct formation. We explore the formation of pre-reactive complexes at low and high temperatures, which are often invoked to explain the negative temperature dependence of this reaction's kinetics. We show that at higher temperatures the free energy surface indicates that a pre-reactive complex is unlikely, while at low temperatures the complex exists on two reaction pathways. The theoretical results show that at low temperatures all eight pathways possess negative reaction barriers, and reaction energies that range from -36.7 to -23.0 kcal x mol(-1). At temperatures in the lower atmosphere, all eight pathways possess positive reaction barriers that range from 3.8 to 6.0 kcal x mol(-1) and reaction energies that range from -28.8 to -14.4 kcal x mol(-1).

Quantum mechanical approach to isoleucine+OH gas phase reaction. Mechanism and kinetics

The gas phase OH hydrogen abstraction reaction from isoleucine is studied using Unrestricted Density Functional Theory (BHandHLYP) calculations and the 6-311G(d,p) basis sets. The structures of the different stationary points are discussed. Ring-like structures are found for all the transition states. Reaction profiles are modeled including the formation of pre-reactive complexes, and negative net activation energy is obtained for the overall reaction. A complex mechanism is proposed, and the rate coefficients are calculated using Transition State Theory over the temperature range 250–350 K. The rate coefficients are proposed for the first time and it was found that in gas phase the hydrogen abstraction occurs mainly from the beta site. The following expressions, in l mol −1 s −1, are obtained for the alpha and beta H-abstraction channels, and for the overall temperature dependent rate constants, respectively: k α =1.02×10 8 exp(317/T), k β =2.57×10 8 exp(3047/T), and k tot =3.19×10 7 exp(2946/T).

Rate coefficients and mechanism of the gas phase OH hydrogen abstraction reaction from serine: a quantum mechanical approach

Unrestricted density functional theory (B3LYP) calculations have been performed using the 6-311G(d,p) basis sets, to study the hydrogen abstraction from serine by OH in the gas phase. The structures of the different stationary points are discussed. Ring-like structures are found for the transition states. Reaction profiles are modeled including the formation of pre-reactive complexes, and negative net activation energies are obtained, after including basis set superposition error corrections. A complex mechanism involving the formation of a pre-reactive complex is proposed, and the rate coefficients are calculated using conventional transition state theory over the temperature range 250–350 K. The rate coefficients are proposed for the first time. The following expressions, in L mol −1 s −1, are found for the alpha channel, beta channel and the overall temperature-dependent rate coefficients: k α =(2.76±0.08)×10 8 exp[(1389±8)/T], k β =(1.26±0.07)×10 8 exp[(1524±17)/T] and k tot =(3.91±0.17)×10 8 exp[(1446±12)/T], respectively.

Kinetics and mechanism of the gas‐phase OH hydrogen abstraction reaction from methionine: A quantum mechanical approach

AbstractUnrestricted density functional theory (BHandHLYP) calculations have been performed, using the 6‐311G(d,p) basis sets, to study the gas‐phase OH hydrogen abstraction reaction from methionine. The structures of the different stationary points are discussed. Ring‐like structures are found for all the transition states. Reaction profiles are modeled including the formation of prereactive complexes, and negative net activation energy is obtained for the gamma H‐abstraction channel. A complex mechanism is proposed, and the rate coefficients are calculated using transition state theory over the temperature range 250–350 K. The rate coefficients are proposed for the first time and it was found that in gas phase the hydrogen abstraction occurs almost exclusively from the gamma site. The large overall rate coefficient for the methionine + OH reaction compared to other free amino acids could explain the significant role of methionine in the oxidative processes. The following expressions in [L/(mol s)] are obtained for the alpha, beta, and gamma H‐abstraction channels, and for the overall temperature‐dependent rate constants, respectively: kα = (3.42 ± 0.11) × 108 exp[(−1118 ± 9)/T], kβ = (1.13 ± 0.03) × 108 exp[(−1070 ± 8)/T], kγ = (2.11 ± 0.26) × 107 exp[(2049 ± 34)/T], and ktot = (2.12 ± 0.26) × 107 exp[(2047 ± 34)/T]. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 212–221, 2003

Mechanism and rate coefficients of the gas phase OH hydrogen abstraction reaction from asparagine: a quantum mechanical approach

Unrestricted density functional theory (B3LYP) calculations have been performed using the 6-311G(d,p) basis sets, to study the gas phase OH hydrogen abstraction reaction from asparagine. The structures of the different stationary points are discussed. Ring-like structures are found for the transition states. Reaction profiles are modeled including the formation of pre-reactive complexes, and negative net energy barriers are obtained. A complex mechanism involving the formation of a pre-reactive complex is proposed, and the rate coefficients are calculated using Conventional transition state theory over the temperature range 250–350 K. ZPE and thermal corrections to the energy for all the species, and BSSE corrections for the pre-reactive complex stabilization and for the energy barriers are included. The rate coefficients are proposed for the first time and it was found that the hydrogen abstraction occurs almost exclusively from the beta site. The following expressions, in L mol −1 s −1, are obtained for the alpha channel, beta channel and the overall temperature dependent rate constants: k α=(1.46±0.04)×10 8 exp[(−1217±7)/ T], k β=(5.48±0.25)×10 7 exp[(1483±13)/ T], and k=(5.50±0.25)×10 7 exp[(1482±13)/ T], respectively.

OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approach

Density functional theory (B3LYP and BHandHLYP) and unrestricted second-order Møller–Plesset (MP2) calculations have been performed using 3-21G, 6-31G(d,p), and 6-311 G(2d,2p) basis sets, to study the OH hydrogen abstraction reaction from alanine and glycine. The structures of the different stationary points are discussed. Ring-like structures are found for all the transition states. Reaction profiles are modeled including the formation of prereactive complexes, and very low or negative net energy barriers are obtained depending on the method and on the reacting site. ZPE and thermal corrections to the energy for all the species, and BSSE corrections for B3LYP activation energies are included. A complex mechanism involving the formation of a prereactive complex is proposed, and the rate coefficients for the overall reactions are calculated using classical transition state theory. The predicted values of the rate coefficients are 3.54×108 L⋅mol−1⋅s−1 for glycine and 1.38×109 L⋅mol−1⋅s−1 for alanine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1138–1153, 2001

OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approach

AbstractDensity functional theory (B3LYP and BHandHLYP) and unrestricted second‐order Møller–Plesset (MP2) calculations have been performed using 3‐21G, 6‐31G(d,p), and 6‐311 G(2d,2p) basis sets, to study the OH hydrogen abstraction reaction from alanine and glycine. The structures of the different stationary points are discussed. Ring‐like structures are found for all the transition states. Reaction profiles are modeled including the formation of prereactive complexes, and very low or negative net energy barriers are obtained depending on the method and on the reacting site. ZPE and thermal corrections to the energy for all the species, and BSSE corrections for B3LYP activation energies are included. A complex mechanism involving the formation of a prereactive complex is proposed, and the rate coefficients for the overall reactions are calculated using classical transition state theory. The predicted values of the rate coefficients are 3.54×108 L⋅mol−1⋅s−1 for glycine and 1.38×109 L⋅mol−1⋅s−1 for alanine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1138–1153, 2001

Quantum chemical study of reactions of episulfonium ions. 1. Comparative MNDO study of opening of the episulfonium ion ring by neutral nucleophiles and SN2 substitution in protonated methylthiol

1. From MNDO quantum chemical calculations, opening of the episulfonium ion ring by neutral nucleophiles X (X=NH3 and HCN) and related SN2 reactions of protonated methylthiol (PMT) with X proceed through formation of pre-reaction complexes in which X is coordinated either at the reacting C atom or (only in opening of episulfonium ion rings) at the center of the C-C bond. 2. In their electronic structure, the transition states for the reactions are reminiscent of a carbocation simultaneously reacting with the attacking and the leaving nucleophilic fragments (X ⋯\(\mathop C\limits^ + \) ⋯S). 3. Opening of episulfonium ion rings proceeds slightly more easily (Ea ∿ 10–12 kcal/mole) than substitution in PMT (Ea ∿ 22–25 kcal/mole). The ease of ring opening for episulfonium ions is due to the large exothermicity of the reaction and the lower internal activation barrier compared with SN2 reactions in PMT.