Six-membered Cyclic Transition State Research Articles

COMPUTATIONAL MODELLING OF THE ACTIVATION PARAMETERS OF DIELS ALDER REACTION OF QUINOFLAVONOID AND 2, 3 DIMETHYLBUTA-1, 3-DIENE

Kinetics and thermodynamics of Diels alder reaction of quinoflavoniod and 2, 3 dimethylbuta-1,3-diene was studied using ab-initio method with Hartree Fock at 6-311G* basis set in spartan, Conformational search was carried out on the molecules to obtain the structures that has the lowest energy, an indication of the stability of the structure. Reaction path calculation was done on the most stable structure using C26 – C15 and C27 – C14 as reaction coordinate in 20 iterations, this was done to ascertain the reaction mechanism. Geometric calculation was carried out on the structures of the reactant, transition state and products to obtain the bond length, bond angle, dihedral angle and atomic charge distributions. Kinetics and thermodynamic parameters was calculated at 3480C. The reaction proceeded through a concerted asynchronous six-membered cyclic transition state. True saddle point was characterized and verified by the presence of only one imaginary vibrational frequency which smoothly connect the reactant, the transition state and the product. Negative values obtained for ?H* (-66.65kJ/mol shows that the reaction is exothermic and according to literature this may be as a result of conversion of two of the ?-bonds to two new ?-bonds). Values obtained for energy of formation (-1329.974 hatrees, -1329.911 hatrees, and 1330.023 hatrees for GS, TS and PRD respectively) according to Hammond’s postulate, confirms the exothermicity of the reaction. ?Greaction (-60.16kJ/mol, shows that the reaction is favourable, Negative ?S* (-11.29J/mol.K) suggests the spontaneity of the reaction and Ea (-63.76kJ/mol) suggests that the reaction involves transfer of electrons. It was also observed that rate constants decrease with increase in temperature, although very uncommon but suggested a complex reaction mechanism.

Theoretical study on thermal degradation mechanism of polybutylene terephthalate dimer

Thermal degradation mechanism of polybutylene terephthalate (PBT) dimer was studied by density functional theory (DFT) method M06-2X/6-311G(d). Eight possible reaction paths were designed for the thermal decomposition of PBT dimer, and the thermodynamic and kinetic parameters of elementary reaction steps in each reaction path were calculated. Calculation results show that, in the initial pyrolysis process of PBT, the energy barrier of concerted reaction occurring on the main chain is significantly lower than that of the radical reaction, so terephthalic acid, monobutenyl terephthalate, dibutenyl terephthalate and diterephthalate-1,4-butadiester formed by concerted reaction are main products in PBT initial pyrolysis. The energy barrier of the main chain fracture through the six-membered cyclic transition state is lower than that through the four-membered cyclic transition state, and the main chain fracture of PBT is mainly through the concerted reaction with six-membered cyclic transition state. In addition, the secondary degradation reaction of the main products of PBT pyrolysis was also discussed. It is found that the main products such as 1,3-butadiene, tetrahydrofuran, benzene, CO2 and benzoic acid are mainly generated through concerted reaction in the processes of secondary degradation.

Understanding cyclic(alkyl)(amino)carbene-copper complex catalysed N-H and O-H bond addition to electron deficient olefins.

The hydroamination of electron-deficient olefins was carried out using the (CAAC)Cu-Cl (CAAC = cyclic (alkyl)(amino)carbene) catalyst with an excellent yield at room temperature and under an open atmosphere. Furthermore, the catalyst shows excellent efficiency in the hydroaryloxylation and hydroalkoxylation of alkenes under mild conditions. The efficiency of the catalyst was tested for a wide range of substrates with different electronic and steric functionalities. Detailed computational studies have been carried out to understand the mechanism of these Cu(I) catalyzed reactions, which revealed that the reaction proceeds via either a four-membered or a six-membered cyclic transition state containing the copper ion.

Computational studies on thermo-kinetics aspects of pyrolysis of isopropyl acetate and its methyl, bromide and hydroxyl derivatives

The gas-phase decomposition kinetics of isopropyl acetate (IPA) and its methyl, bromide and hydroxyl derivatives into the corresponding acid and propene were investigated using density functional theory (DFT) with the ωB97XD and M06–2x functionals, as well as the benchmark CBS-QB3 composite method. Transition state theory (TST) and RRKM theory calculations of rate constants under atmospheric pressure and in the fall-off regime were used to supplement the measured energy profiles. The results show that the formation of propene and bromoacetic acid is the most dominant pathway at the CBS-QB3 composite method, both kinetically and thermodynamically. There was a good agreement with experimental results. Pressures greater than 0.01 bar, corresponding to larger barrier heights are insufficient to ensure saturation of the measured rate coefficient when compared to the RRKM kinetic rates.Natural bond orbitals (NBO) charges, bond orders, bond indices, and synchronicity parameters all point to the considered pathways taking place via a homogenous, first-order concerted, as well as an asynchronous mechanism involving a non-planar cyclic six-membered transition state. The calculated data exhibit that the elongation of the Cα−O bond length and subsequent polarization of the Cα+δ…O−δ bond is the rate-determining step of the considered reactions in the cyclic transition state, which appears to be involved in this type of reaction.

Theoretical Study on the Selective 1,2-Reduction of α,β-Unsaturated Ketones by Hydrogen Transfer Reaction on MgO(100).

Catalytic reduction of α,β-unsaturated ketones with MgO has been found to improve selectivity to the desired unsaturated alcohol product. Using density functional calculations, we have studied the competitive hydrogenation of C=O and C=C bonds on Mg(100) employing two α,β-unsaturated ketones: mesityl oxide (MO) and 2-cyclohexenone (CH), with isopropanol (IPA) as hydrogen source. For both ketones, MgO promotes the formation of a six-membered cyclic transition state for selective C=O reductions via a Meerwein-Ponndorf-Verley mechanism. Similar concerted mechanism is also possible for the C=C hydrogenation following an Eley-Rideal mechanism, in which the IPA interacts directly with the adsorbed ketone. The activation barriers are smaller for C=O reduction because this bond is activated on MgO(100). The selective C=O reduction is more favorable for CH than for MO due to the tendency of CH to be perpendicularly oriented. The desorption energies of the unsaturated alcohol are lower than the subsequent C=C reductions.

Confronting the Challenging Asymmetric Carbonyl 1,2-Addition Using Vinyl Heteroarene Pronucleophiles: Ligand-Controlled Regiodivergent Processes through a Dearomatized Allyl-Cu Species.

The selective reductive coupling of vinyl heteroarenes with aldehydes and ketones represents a versatile approach for the rapid construction of enantiomerically enriched secondary and tertiary alcohols, respectively. Herein, we demonstrate a CuH-catalyzed regiodivergent coupling of vinyl heteroarenes with carbonyl-containing electrophiles, in which the selectivity is controlled by the ancillary ligand. This approach leverages an in situ generated benzyl- or dearomatized allyl-Cu intermediate, yielding either the dearomatized or exocyclic addition products, respectively. The method exhibits excellent regio-, diastereo-, and enantioselectivity and tolerates a range of common functional groups and heterocycles. The dearomative pathway allows direct access to a variety of functionalized saturated heterocyclic structures. The reaction mechanism was probed using a combination of experimental and computational approach. Density functional theory studies suggest that the ligand-controlled regioselectivity results from the C-H/π interaction and steric repulsion in transition states, leading to the major and minor regioisomers, respectively. Hydrocupration of vinyl heteroarene pronucleophile is the enantiodetermining step, whereas the diastereoselectivity is enforced by steric interactions between the benzylic or allyl-Cu intermediate and carbonyl-containing substrates in a six-membered cyclic transition state.

Insights into the thermal degradation mechanisms of polyethylene terephthalate dimer using DFT method

The thermal degradation mechanisms of polyethylene terephthalate (PET) dimer were studied by the B3P86 density functional theory (DFT) approach at 6–31++G (d, p) base set in this paper. Seven possible reaction paths were designed and analyzed, and the thermodynamic parameters for all reactions were computed. The calculated results indicate that the bond dissociation energy values (BDEs) of C–C bonds on the main-chain are the smallest, followed by those of C–O bonds. The kinetics analysis indicates that the concerted reactions are obviously liable to occur rather than radical reactions in the initial thermal decomposition process. In the processes of initial reactions, all concerted reactions occurred by six-membered cyclic transition states (TSs) are more prone to carry out than those happened by four-membered cyclic transition states. The research results show that the primary products of PET dimer pyrolysis are terephthalic acid, vinyl terephthalate, CH3CHO and divinyl terephthalate. CH3CHO is mainly formed by a concerted reaction in the initial degradation process, and CO2 is mainly produced by the decarboxylation via a concerted reaction and CO is mainly produced by the decarbonylation of a radical in secondary degradation.

Infrared Spectroscopy of Solvation in the TaO2+ Hydrolysis Reaction.

The solvent effect of the TaO2+ reaction with water molecules in the gas phase is examined. Stoichiometric TaO2(H2O)n+ cations are generated by the laser vaporization of a tantalum metal target in the pulsed supersonic expansion of H2O/He mixed gas. The infrared photodissociation spectra of TaO2(H2O)n+ cations are measured using the argon-tagging technology in the 2800-3850 cm-1 region. Density functional theory calculations are carried out to identify the observed infrared bands and elucidate the reaction mechanism. In the TaO2+ reaction with one H2O molecule, both the hydrated adduct H2O-TaO2+ and dihydroxide TaO(OH)2+ are generated. The coexistence of tetrahydroxide Ta(OH)4+ and hydrated dihydroxide H2O-TaO(OH)2+ is seen when the second H2O molecule is involved. However, only the hydrated H2O-Ta(OH)4+ product is obtained in the TaO2 reaction with three H2O molecules. Theoretical calculations indicate that in the reaction, the formation of a six-membered cyclic transition state through the hydrogen bond lowers the energy barrier significantly, which promotes the transfer of the hydrogen of hydrated adducts to generate di- and tetrahydroxides.

Hydration of Aliphatic Nitriles Catalyzed by an Osmium Polyhydride: Evidence for an Alternative Mechanism.

The hexahydride OsH6(PiPr3)2 competently catalyzes the hydration of aliphatic nitriles to amides. The main metal species under the catalytic conditions are the trihydride osmium(IV) amidate derivatives OsH3{κ2-N,O-[HNC(O)R]}(PiPr3)2, which have been isolated and fully characterized for R = iPr and tBu. The rate of hydration is proportional to the concentrations of the catalyst precursor, nitrile, and water. When these experimental findings and density functional theory calculations are combined, the mechanism of catalysis has been established. Complexes OsH3{κ2-N,O-[HNC(O)R]}(PiPr3)2 dissociate the carbonyl group of the chelate to afford κ1-N-amidate derivatives, which coordinate the nitrile. The subsequent attack of an external water molecule to both the C(sp) atom of the nitrile and the N atom of the amidate affords the amide and regenerates the κ1-N-amidate catalysts. The attack is concerted and takes place through a cyclic six-membered transition state, which involves Cnitrile···O–H···Namidate interactions. Before the attack, the free carbonyl group of the κ1-N-amidate ligand fixes the water molecule in the vicinity of the C(sp) atom of the nitrile.

Infrared photodissociation spectroscopic investigation on VO+ and NbO+ hydrolysis catalyzed by water molecules.

We investigate the hydrolysis of vanadium/niobium monoxide cation (VO+/NbO+) with water molecules in the gas phase. Cationic argon-tagged intermediates, TMO(H2O)nArm+ (TM = V, Nb; n = 1-2, m = 1-2), are prepared for examination using infrared photodissociation spectroscopy. The structures of the intermediates are elucidated by comparing them with simulated spectra. VO(H2O)Ar+ or NbO(H2O)Ar+ (for n = 1) is intrinsically a hydrated adduct, represented by H2O-VOAr+ or H2O-NbOAr+, rather than a dihydroxide, V(OH)2Ar+ or Nb(OH)2Ar+. However, when a second H2O molecule is involved (for n = 2), the dihydroxide V(OH)2(H2O)Ar+ and trihydroxide HNb(OH)3Ar+ are formed. In this process, the six-member cyclic transition state formed by two H2O molecules markedly reduces the hydrogen transfer energy barrier based on our calculations. This work provides more precise experimental evidence for the Grotthuss-like mechanism proposed in the studies of hydrolysis and tautomerization reactions.

Mechanistic study of the catalytic transfer hydrogenation of biodiesel catalyzed by Raney-Ni under microwave heating

The use of microwave heating (MH) constitutes a promising way to upgrade biodiesel via catalytic transfer hydrogenation (CTH) catalyzed by Raney-Ni. However, mechanistic reports on this reaction are rare and the mechanisms involved in CTH process remains unclear. Herein, we presented a thorough mechanistic study of CTH of Jatropha oil biodiesel catalyzed by Raney-Ni under MH, using isopropyl alcohol as hydrogen donor and water as solvent. The intensification effect under microwave radiation has been studied from three aspects of catalyst, water, and hydrogen donor. It was found that microwave made an adverse effect on the activity of Raney-Ni. The solvent of water could provide hydrogen to some extent for the CTH of biodiesel, and the influence of Raney-Ni from microwave radiation had a positive role for the water to provide hydrogen during CTH reaction. Under microwave irradiation, the activity of isopropyl alcohol would be enhanced, and the transfer of hydrogen atoms from hydrogen donors to hydrogen acceptors became easy. Based on the characterization of catalyst by SEM, XRD, FTIR and TGA, it was found that the reason for the catalyst deactivation was mainly the carbonaceous deposits of fatty acid methanol esters (FAMEs) on the surface of the catalyst. A schematic representation of mechanism of microwave-assisted CTH has been presented. Furthermore, combining theory of heterogeneous catalytic process with mechanism of six-membered cyclic transition state, the reaction course for the CTH of Jatropha oil biodiesel under microwave heating has been explained successfully. Lastly, the performance improvement of the upgraded Jatropha oil biodiesel was briefly analyzed in view of composition change of biodiesel. Overall, our results provide a systematic understanding of CTH of biodiesel catalyzed by Raney-Ni under microwave heating, and our findings help to develop a green technology for the upgrading of biodiesel in industry.

Design of fluorescent probes with optimized responsiveness and selectivity to GSH

We designed and synthesized a series of BODIPY based probes with fast and distinct ratiometric responsiveness for discriminative detection of GSH from Cys and Hcy. The discriminative detection is based on the different products obtained by the SNAr between probes and thiol-containing amino acids. The amino group of the obtained thioether from the reaction with Cys or Hcy but not GSH would trigger an intramolecular nucleophilic substitution through five- or six-membered cyclic transition state, finally yielding an amino substituted derivative. To achieve highly discriminative detection and fast response, a series of structure modifications and improvements have been made by elongating the π-conjugation and introducing electron withdrawing groups, finally affording probe BOD-DBNPF with optimized responsiveness and selectivity. Importantly, BOD-DBNPF was successfully used for the selective detection of GSH from Cys with distinct fluorescent ratiometric responses in living HeLa cells.

Mechanism of glycerol dehydration and dehydrogenation: an experimental and computational correlation

Experimental formation of hydroxyacetone (HA) from glycerol over La2CuO4 catalyst under mild experimental conditions (533 K, N2 atmosphere) was correlated with molecular modeling results with the aim to propose reaction pathways. Based on these results, a novel mechanism in terms of elementary reactions is proposed for gaseous phase process. The results suggest that there are two main routes that contribute to HA formation. The main and more feasible reaction pathway corresponds to the direct 1,2-dehydration of glycerol. The second pathway involves the dehydrogenation of glycerol to produce glyceraldehyde, which is then dehydrated toward HA through the formation of a six-membered cyclic transition state during the hydrogenation step. Finally, the pyruvaldehyde formation pathway was found to be a parallel reaction to the HA formation which could be displaced by tuning the reaction conditions. HA formation as a result of pyruvaldehyde hydrogenation was also proposed, but it was found to be a less important route.

Unexpected medium effect on the mechanism for aminolysis of aryl phenyl carbonates in acetonitrile and H2O: transition-state structure in the catalytic pathway

Upward curvature in the kinetic plots of pseudo first-order rate constants (kobsd) vs. [amine] for the aminolysis of aryl phenyl carbonates (5a–5j) in MeCN demonstrates that these reactions proceed via a zwitterionic tetrahedral intermediate (T±) that partitions between catalyzed and uncatalyzed routes to give the products. Yukawa–Tsuno plots for the reactions of 5a–5j with piperidine result in excellent linear correlations with ρY = 4.82 and r = 0.47 for the uncatalyzed reaction versus ρY = 2.21 and r = 0.21 for the catalyzed reaction. Brønsted plots for reactions of 4-(ethoxycarbonyl)-phenyl phenyl carbonate (5f) with a series of cyclic secondary amines exhibit excellent linear correlations with βnuc = 0.87 and 0.58 for the uncatalyzed and catalyzed reactions, respectively. The ΔH‡ and ΔS‡ values are 0.92 kcal/mol and –50.1 cal/mol K, respectively, for the catalyzed reaction of 5f with piperidine. Deuterium kinetic isotope effects found for reactions of 5f with piperidine/deuterated piperidine are 0.84 (uncatalyzed) and 1.42 (catalyzed). Multi-parameter analysis supports a concerted catalytic pathway involving a six-membered cyclic transition state rather than a traditionally accepted stepwise pathway with an anionic intermediate. The current unexpected results, where T± is the essential central intermediate in this aminolysis, contrast with previous calculation studies that deemed T± unstable in gas phase or MeCN.

Theoretical study on the elimination kinetics in the gas phase of allyl methyl compounds

The thermal decomposition kinetics of allyl methyl amine, allyl methyl ether, and allyl methyl sulfide in the gas phase has been studied theoretically using the M06-2x/aug-cc-pVTZ quantum chemical approach. The observed activation parameters are consistent with a concerted unimolecular mechanism involving a non-planar cyclic six-membered transition state. Based on the optimized ground state geometries, a natural bond orbital analysis of donor–acceptor interactions reveals that the stabilization energies corresponding to the electronic delocalization from the lone-pair (LP) non-bonding orbitals on the heteroatom to the neighboring $$\sigma_{{{\text{C2}} - {\text{C3}}}}^{*}$$ antibonding orbitals decrease from allyl methyl amine to allyl methyl sulfide. This delocalization fairly explains the increase of occupancies of LP orbitals on the heteroatom from allyl methyl sulfide to allyl methyl amine. The results also suggest that the kinetics of the thermolysis of the studied compounds are dominated by $${\text{LP}}\, \to \,\sigma^{*}$$ electronic delocalization effects. Analysis of bond order, bond indices, and synchronicity parameters demonstrates that these reactions proceed through a concerted and slightly asynchronous mechanism.

One-Pot Reductive Allylation of Amides by Using a Combination of Titanium Hydride and an Allylzinc Reagent: Application to a Total Synthesis of (–)-Castoramine

A one-pot direct reductive allylation protocol has been developed for the synthesis of secondary amines by using titanium ­hydride and an allylzinc reagent. This protocol is applicable to a broad range of substrates, including acyclic amides, benzamides, α,β-unsaturated amides, and lactams. The stereochemical outcome obtained from the reaction with crotylzinc reagent suggested that the allylation reaction proceeds through a six-membered cyclic transition state. A total synthesis of (–)-castoramine was accomplished by following this protocol for the highly stereoselective construction of contiguous stereo­centers.

The ion pair mechanism in the thermal deamination of primary amines catalyzed by HBr in the gas phase: DFT and AIM analysis

The possible reaction mechanisms for the gas-phase thermal deamination of isopropylamine, tert-butylamine, and dextroamphetamine in the presence of hydrogen bromide are investigated by DFT calculations with several functionals. In each case, QTAIM analysis supports the formation of an ion-pair complex, which subsequently decays through a six-membered cyclic transition state (TS). NBO charges and interatomic lengths suggest the polarization of the N1δ−···δ+C2 bond in the TS is rate determining.

Indium(III) Triflate-Catalyzed Reactions of Aza-Michael Adducts of Chalcones with Aromatic Amines: Retro-Michael Addition versus Quinoline Formation.

The indium(III) triflate-catalyzed reaction of aza-Michael adducts of chalcones with aromatic amines has been investigated. The Michael adducts derived from substituted anilines and chalcones underwent retro-Michael addition to give the original starting materials, whereas the adducts derived from 1-naphthylamines and chalcones afforded quinolines. A six-membered cyclic transition state has been proposed to explain the retro-Michael addition, while a Povarov mechanism has been put forward to explain the quinoline formation.

Theoretical calculations of homogeneous catalysis in the gas phase: elimination kinetics of 2,2-dimethoxypropane in the presence of HCl, F3CCOOH and CH3COOH

ABSTRACTThe mechanisms of gas-phase elimination kinetics of 2,2-dimethoxypropane in the presence of hydrogen chloride, trifluoroacetic acid and acetic acid were studied using Moller Plesset, ab initio combined method Complete Basis Set (CBS)-QB3 and various density functional theory methods with 6-311G(d,p) and 6-311++G(d,p) basis sets. The M06-2X/6-311++G(d,p) method provided reasonable agreement with the experimental enthalpy and energy of activation. Formation of 2-methoxypropene and methanol products occurs through six-membered cyclic ring transition state (TS) structure. The TS was characterised by single imaginary frequency, and confirmed through intrinsic reaction coordinate (IRC) calculations. The IRC calculations suggest the development of a van der Waal complex between the 2, 2-dimethoxy propane and the acid catalyst, leading to the TS formation. The process of decomposition in the absence of the acid catalyst requires much higher temperature with an energy of activation above 200 kJ/mol. This fact appears to be a consequence of a four-membered cyclic TS-type of mechanism in the non-catalysed reaction. Structural parameters, analyses of natural bond orbital charges and bond orders of the acid-catalysed elimination reactions in this study suggest that the polarisation of the C–O bond, in the direction Cδ+—Oδ−, is rate-determining in the TS. These reactions are non-synchronous concerted polar in nature.

Medium effect (water versus MeCN) on reactivity and reaction pathways for the SNAr reaction of 1-aryloxy-2,4-dinitrobenzenes with cyclic secondary amines

A kinetic study on SNAr reactions of 1-aryloxy-2,4-dinitrobenzenes (1a–1h) with a series of cyclic secondary amines in 80 mol% water – 20 mol% DMSO at 25.0 ± 0.1 °C is reported. The plots of kobsd versus amine concentration curve upward except for the reactions of substrates possessing a strong electron-withdrawing group in the leaving aryloxide with strongly basic piperidine. The curved plots indicate that the reactions proceed through both uncatalytic and catalytic routes. Linear Brønsted-type plots have been obtained for the uncatalyzed and catalyzed reactions of 1-(4-nitrophenoxy)-2,4-dinitrobenzene (1a) with βnuc = 0.84 and 0.78, respectively. The Yukawa–Tsuno plot for the uncatalyzed reactions of 1a–1h with piperidine results in an excellent linear correlation with ρ = 1.66 and r = 0.31. In contrast, rate constants for catalyzed reactions are independent of the electronic nature of the substituent in the leaving group. The current SNAr reactions have been proposed to proceed via a zwitterionic intermediate (MC±) that partitions to products through uncatalytic and catalytic routes. The catalyzed reaction from MC± has been concluded to proceed through a concerted mechanism with a six-membered cyclic transition state (TScycl) rather than via a stepwise pathway with a discrete anionic intermediate (MC−), the traditionally accepted mechanism. Medium effects on the reactivity and reaction mechanism are discussed. Particularly, hydrogen bonding of the amines to water precludes formation of kinetically significant dimers found in some aprotic solvents; no explicit role for water in the catalytic transition state is required or proposed. The specific stabilization of the leaving aryloxides substituted with strong electron-withdrawing groups accounts for the lack of the catalytic pathway in these systems (1a–1c) with piperidine nucleophile.