Competing Reaction Pathways Research Articles

Experimental and theoretical studies on the oxidative addition of palladium(0) to β-chlorovinamidinium salts

Abstract Boronic acids, esters and borinic anhydrides are partners in Suzuki–Miyaura cross-coupling reactions with a variety of β-chlorovinamidinium salts to give the desired β-arylvinamidinium salts in up to 88% yield. Reduction is a competing reaction pathway. DFT calculations on the intermediate palladium complex reveal that the Pd–C interaction is predominantly of σ-symmetry and the metal based LUMO is mainly dz2 in character.

The Wittig reaction of fluorinated amides: formation of enamine and imine tautomers

Amides 1a–f reacted with phosphorane 3 at room temperature giving a mixture of enamine 4a–f and imine 6a–f tautomers in excellent yields. These tautomers were formed in competing reaction pathways. Silica gel promoted the conversion of 4d into 6d. Amides 1d and 1f reacted with the methyl analogue of phosphorane 3 giving tautomers 11a,b/12a,b. The β-amino acid derivatives, 13a,b, were formed from sodium borohydride reduction of imines 12a,b.

Theoretical Studies of Competing Reaction Pathways and Energy Barriers for Alkaline Ester Hydrolysis of Cocaine

Reaction pathways, solvent effects, and energy barriers have been determined for the base-catalyzed hydrolysis of the benzoyl-ester and methyl-ester groups of neutral cocaine and three smaller alkyl esters in aqueous solution by performing a series of ab initio molecular orbital and density functional theory calculations. The reaction coordinate calculations indicate that both the benzoyl-ester hydrolysis and the methyl-ester hydrolysis occur through a two-step process known for the majority of alkyl esters, i.e., the formation of a tetrahedral intermediate by the attack of hydroxide oxygen at the carbonyl carbon (first step) followed by the decomposition of the tetrahedral intermediate to products (second step). This is the first first-principles study of the whole reaction pathway for cocaine benzoyl- and methyl-ester hydrolyses. The decomposition of the tetrahedral intermediate requires a proton transfer from the hydroxide/hydroxyl oxygen to the ester oxygen, as the C−O bond between carbonyl carbon and...

Theoretical studies of nonenzymatic reaction pathways for the three reaction stages of the carboxylation of ribulose-1,5-bisphosphate

Alternative reaction pathways of the nonenzymatic carboxylation of D-ribulose-1,5-bisphosphate (RuBP) have been theoretically deduced by carrying out a series of first-principle calculations on two model systems. Several favorable competing reaction pathways have been found. The optimized geometries of the transition states and intermediates and the calculated relative energies are employed to explore the nature of transition-state stabilizing factors. It has been shown that hydrogen bonding plays a key role in the transition state stabilization in the competing reaction pathways for addition of CO2 and H2O. Substituent effects on the calculated energy barriers are also very large for the addition of CO2, but less important for the subsequent reaction stages. Including solvent effects, the energy barriers calculated for the addition of CO2 become significantly lower, while the energy barriers calculated for the addition of H2O and for the C–C bond cleavage step become significantly and slightly higher, respectively.

Reaction Pathways and Energy Barriers for Alkaline Hydrolysis of Carboxylic Acid Esters in Water Studied by a Hybrid Supermolecule-Polarizable Continuum Approach

Reaction pathways, solvent effects, and energy barriers have been determined for the base-catalyzed hydrolysis of two representative alkyl esters in aqueous solution, using a hybrid supermolecule-polarizable continuum approach. Four solvent water molecules were explicitly included in the supermolecular reaction coordinate calculations; the remaining solvent water was modeled as a polarizable dielectric continuum surrounding the supermolecular reaction system. Two competing reaction pathways were observed, sharing a common first step, i.e. the formation of the tetrahedral intermediate. One pathway involves a direct proton transfer in the second step, i.e. the decomposition of the tetrahedral intermediate. A second pathway involves a water-assisted proton transfer during the decomposition of the tetrahedral intermediate. The direct participation of the solvent water molecule in the proton-transfer process significantly drops the energy barrier for the decomposition of the tetrahedral intermediate. Thus, the...

Self-Organization and Irreducibly Complex Systems: A Reply to Shanks and Joplin

Some biochemical systems require multiple, well-matched parts in order to function, and the removal of any of the parts eliminates the function. I have previously labeled such systems “irreducibly complex,” and argued that they are stumbling blocks for Darwinian theory. Instead I proposed that they are best explained as the result of deliberate intelligent design. In a recent article Shanks and Joplin analyze and find wanting the use of irreducible complexity as a marker for intelligent design. Their primary counterexample is the Belousov-Zhabotinsky reaction, a self-organizing system in which competing reaction pathways result in a chemical oscillator. In place of irreducible complexity they offer the idea of “redundant complexity,” meaning that biochemical pathways overlap so that a loss of one or even several components can be accommodated without complete loss of function. Here I note that complexity is a quantitative property, so that conclusions we draw will be affected by how well-matched the components of a system are. I also show that not all biochemical systems are redundant. The origin of non-redundant systems requires a different explanation than redundant ones.

Theoretical Studies of Fundamental Pathways for Alkaline Hydrolysis of Carboxylic Acid Esters in Gas Phase

Fundamental reaction pathways for the alkaline hydrolysis of carboxylic acid esters, RCOOR‘, were examined through a series of first-principle calculations. The reactions of six representative esters with hydroxide ion were studied in the gas phase. A total of three competing reaction pathways were found and theoretically confirmed for each of the esters examined: bimolecular base-catalyzed acyl-oxygen cleavage (BAC2), bimolecular base-catalyzed alkyl-oxygen cleavage (BAL2), and carbonyl oxygen exchange with hydroxide. For the two-step BAC2 process, this is the first theoretical study to consider the individual sub-steps of the reaction process and to consider substituent effects. For the carbonyl oxygen exchange with hydroxide and for the one-step BAL2 process, we report here the first quantitative theoretical results for the reaction pathways and for the energy barriers. The energy barrier calculated for the second step of the BAC2 process, that is, the decomposition of the tetrahedral intermediate, is larger in the gas phase than that of the first step, that is, the formation of the tetrahedral intermediate, for all but one of the esters examined. The exception, CH3COOC(CH3)3, does not have an α hydrogen in the leaving group. The highest energy barrier calculated for the BAC2 process is always lower than the barriers for the oxygen exchange and for the BAL2 process. The difference between the barrier for the BAL2 process and the highest barrier for the BAC2 process is only ∼1−3 kcal/mol for the methyl esters, but becomes much larger for the others. Substitution of an α hydrogen in R‘ with a methyl group considerably increases the energy barrier for the BAL2 process, and significantly decreases the energy barrier for the second step of the BAC2 process. The calculated substituent shifts of the energy barrier for the first step of the BAC2 process in gas phase are in good agreement with the observed substituent shifts for the base-catalyzed hydrolysis of alkyl acetates in aqueous solution. All of the calculated results are consistent with the available experimental results and lead to a deeper understanding of previously reported gas-phase experimental observations.

Bicyclobutonium ion versus cyclopropylcarbinyl cation chemistry: the cycloaddition reaction with ethene in the dilute gas phase

The C4H7+ cations were formed from cyclopropylcarbinyl, cyclobutyl and homoallyl chlorides via chloride atom loss from the radical cations in a chemical ionization source. Their structures were probed on a short time-scale (of the order of 10−6 s) as a function of internal energy by utilizing collisionally activated dissociation with tandem mass spectrometric methods. The results show that the radical cations of cyclopropylcarbinyl and homoallyl chlorides generate primarily the cyclopropylcarbinyl cation, 3, whereas the radical cation of cyclobutyl chloride generates a substantial amount of bicyclobutonium ion, 4. Ion 4 reacts with nucleophiles via multiple competing reaction pathways, unlike 3. Ion 3 undergoes a cycloaddition reaction with ethene to generate the cyclopentylcarbinyl cation. Ion 4, although reactive with ethene, does not generate, to any appreciable degree, the cyclopentylcarbinyl cation. Copyright © 2000 John Wiley & Sons, Ltd.

Uncovering Reaction Pathways of 1-Aminocyclohexenes with [(1-Alkynyl)carbene]tungsten Complexes Leading to Cyclopentadienes and Dihydropyrroles

Reactions of the [(1-alkynyl)carbene]tungsten complex (CO)5WC(OEt)C≡CPh (1) with 1-aminocyclohexenes 2a-c and 7a-c afford different types of products depending on the amino substituents and the reaction conditions. (4-Aminocyclobutenyl)carbene complexes B have been shown to be generated in the first reaction step through a [2+2] cycloaddition. These are key intermediates and afford cross-conjugated tungstatrienes E, (conjugated) 1-tungsta-1,3,5-hexatrienes G, or (non-conjugated) 1-tungsta-1,3,6-heptatrienes F by following competing reaction pathways. Cross-conjugated 1-tungstatrienes 3 have been isolated in 52-74% yield by performing the reactions of 1-aminobenzocyclohexenes 2a-c with compound 1 in pentane. In dichloromethane instead of pentane, (conjugated) 1-tungsta-1,3,5-hexatrienes 4 are obtained, which subse-quently undergo fragmentation to give cyclopentadienes 6 (by π-cyclization) and dihydropyrroles (by α-cyclization) in a molar ratio dependent on the nature of the amino substituents. (Non-conjugated) 1-tungsta-1,3,6-heptatrienes 10 are generated upon reaction of 1-aminocyclohexenes 7a-c with compounds 1, which are transformed into cyclopentadienes 12 via conjugated 1-tungsta-1,3,5-hexatrienes 9 as intermediates. Reactions of 1-tungsta-1,3,6-heptatrienes 10 with the (1-alkynyl)carbene complex 1 afford dinuclear compounds 14, which subsequently yield indenes 15 (by two successive π-cyclization steps) and spiro-tetrahydropyrroles 16 (by both a π-cyclization and an α-cyclization step), depending on the steric bulk of the amino substituent.

Competing reaction pathways from Y+C2H2 collisions

The crossed molecular beams method with 193 and 157 nm photoionization detection was used to study the competing reaction pathways resulting from collisions of ground state Y atoms with acetylene (C2H2). Three channels, corresponding to nonreactive decay of collision complexes, H2 elimination, and H atom elimination, were studied as a function of collision energy (〈Ecoll〉=6–25 kcal/mol). Production of YC2+H2 and decay of long-lived complexes back to reactants were observed at all collision energies studied. Product translational energy distributions for the H2 elimination channel demonstrate that a substantial fraction of excess energy available to the YC2+H2 products is channeled into relative translational energy. Analogous H2 elimination channels were studied in reactions of Zr and Nb with C2H2 at 〈Ecoll〉=6.0 kcal/mol. For these reactions, the H2 elimination product translational energy distributions were found to peak near zero kinetic energy, in contrast to the behavior observed for the YC2+H2 products. This suggests that a significant potential energy barrier exists in the exit channel of the YC2+H2 elimination step, whereas no exit channel barrier exists in forming ZrC2+H2 and NbC2+H2. The reformation of Y + C2H2 reactants following decay of long-lived collision complexes was found to transfer 40%–50% of the initial relative translational energy into C2H2 internal excitation. The YC2H+H product channel was only observed to occur above a collision energy threshold of 21.5±2.0 kcal/mol. Since YC2H+H production is fully spin-allowed and involves simple Y–H bond fission in the intermediate HYC2H complex, it is unlikely that any significant potential energy barrier is present in excess of the reaction endoergicity. Additional studies of Y+C2D2 reactions confirm that the observed collision energy threshold for the H or D atom loss channel corresponds to the energetic threshold for reaction, allowing determination of D0(Y–CCH)=110.2±2.0 kcal/mol.

Change of the Hydrolytic Mechanism of 2-Hydroxy H-Phosphonodiesters in Aprotic Organic Media. cis-1,2-Diol Monoanions as Leaving Groups

The hydrolysis of H-phosphonodiesters bearing a vicinal hydroxyl group is found to be subject to two competing reaction pathways in aprotic organic media. An observation of the increased proportion of cis-1,2-diol leaving with decrease of the water content is interpreted in terms of a change of the hydrolytic mechanism on changing the reaction medium from aqueous to nonaqueous. The hydroxyl group in cis-1,2-diol monoanions hydrogen bonds strongly to the adjacent oxyanion, implying a low-energy route closely related to reactions, catalyzed by large ribozymes.

Fluorescence probes for chemical reactivity at the interface of a self-assembled monolayer

New methods for reversible photoimaging of spatially defined surfaces represent attractive technological applications of thin organized films. Surface immobilization of photoresponsive derivatives of alkanethiols on gold can influence attainable excited state partitioning among competing reaction pathways. Surface fluorescence measurements on such reflective metal surfaces can be used to monitor surface composition when highly emissive molecules are attached to a self-assembled monolayer. These measurements can also be used as a probe for in situ chemical modification of a self-assembled monolayer and for photoreactivity of coumarin- and anthracene-derivatives attached at the end of a variable length tether anchored through an alkyl sulfide onto a smooth polycrystalline gold surface. The observed changes in the fluorescence can be related to local structure and to the unusual environment encountered by the probe molecule within the self-assembled monolayer.

Modifying Surface Reactivities by a Carbide Overlayer: A Vibrational Study of the Reaction Mechanisms of Cyclohexene and 1,3-Cyclohexadiene on Mo(110) and (4×4)-C/Mo(110) Surfaces

The dehydrogenation and thermal decomposition mechanisms of cyclohexene and 1,3-cyclohexadiene on clean Mo(110) and carbide-modified (4×4)-C/Mo(110) surfaces have been studied using temperature-programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS). On the clean Mo(110) surface, partial dehydrogenation of a fraction of the cyclohexene molecules occurs at temperatures as low as 80 K. When the surface is heated to 150 K, the HREEL spectra obtained are characteristic of a C6H9 intermediate, as seen by a comparison with HREEL spectra reported for C6H9 on Pt(111).1,2 At higher temperatures, competing C−C and C−H bond cleavage reactions lead to the formation of surface carbon and the evolution of hydrogen. In contrast, on the carbide-modified surface, the primary reaction pathway for cyclohexene is selective dehydrogenation to form benzene and hydrogen. In the case of 1,3-cyclohexadiene, the HREEL results suggest that dehydrogenation to form benzene occurs at 80 K on the clean Mo(110) surface, based on a comparison with the HREEL spectrum for benzene directly dosed onto Mo(110) at 80 K. However, upon heating, most of the benzene decomposes to form surface carbon and hydrogen, as shown by TPD studies. On the carbide-modified surface, the primary reaction pathway for 1,3-cyclohexadiene is selective dehydrogenation to form benzene, which desorbs at 313 K. Furthermore, the HREEL results also indicate that a competing reaction pathway occurs to form a surface intermediate which most likely has an tilted aromatic c-C6 ring, such as a surface phenyl species.

Quantitative Measurements of CpRh(CO)2 (Cp = η5-C5H5) Photochemistry in Various Hydrocarbon Solutions: Mechanisms for Ligand Photosubstitution and Intermolecular C−H and Si−H Bond Activation Reactions

The quantitative solution photochemistry of CpRh(CO)2 (Cp = η5-C5H5) involving ligand substitution and intermolecular C−H and Si−H bond activation processes has been investigated in several hydrocarbon solvents at room temperature following excitation in the region 313−458 nm. These photoreactions have been monitored by UV−vis and FTIR spectroscopy, and the absolute quantum efficiencies (φcr), determined to be in the 0.0007−0.31 range, are dependent on the entering ligand concentration, excitation wavelength, and solvent. The observed wavelength dependence is consistent with distinct reaction pathways occurring from two rapidly dissociating ligand-field (LF) excited states. Analysis of the quantitative photochemical results has led to a comprehensive mechanistic description for all of the various competing reaction pathways in the photochemistry of CpRh(CO)2. In the absence of an entering ligand, a carbonyl-bridged trans-Cp2Rh2(CO)3 complex is identified as the major photochemical reaction product; this s...

Wet oxidation of AlAs films under ultrahigh vacuum conditions

The initial stages of oxidation of AlAs(001) (using D2O as the oxidant) have been investigated using Auger electron spectroscopy and temperature-programmed desorption. We have found that molecularly adsorbed water on AlAs(001) has two competing reaction pathways available: either desorption back into the gas phase, or dissociation resulting in aluminum oxide, aluminum hydroxide, and arsenic hydride. Recombination of the arsenic hydride produces arsine, which desorbs and depletes arsenic within the oxide film, a process which is shown to enhance the oxide growth. By identifying the various reaction steps that occur (with annealing) after the low-temperature adsorption of water on AlAs(001), we are able to propose a mechanism for the initial stages of wet AlAs oxidation.

Hydroconversion of n-heptane over [formula omitted] containing HZSM5

Ni and Co containing HZSM5 zeolites were compared in the hydroconversion of n-heptane at 460–710 K and a pressure of up to 2 bar. Hydrocracking and hydrogenolysis were observed to be competing reaction pathways over CoHZSM5 and NiHZSM5. n-Heptane reacted directly to methane and small amounts of ethane over CoHZSM5, i.e., hydrogenolysis prevailed, over NiHZSM5 the main reaction products were propane and i-butane i.e., hydrocracking was dominant. With increasing hydrogen partial pressure hydrogenolysis decreased while hydrocracking increased over both metal containing ZSM5 zeolites.

Aqueous High-Temperature Chemistry of Carbo- and Heterocycles. 30.1Aquathermolysis of Phenyl-Substituted Hydroxyquinolines

A range of phenylquinolones and hydroxy-substituted phenylquinolines was synthesized and subjected to aquathermolysis in water alone, in 15% aqueous formic acid, and in 15% aqueous sodium formate at 315 and 460 °C. Thermal controls were obtained using cyclohexane as solvent. It was thought that the hydroxy substituent might provide a “handle” of activation for subsequent ring opening, denitrogenation, and possible biaryl cleavage pathways. At 350 °C all substrates tended to give mainly quinolines via deoxygenation as the main pathway. At 460 °C all substrates gave complex product slates with some ring opening to lower molecular weight products. Some denitrogenation was observed via ring opening and further reaction. Decarbonylation to yield indoles was also noted as a competing reaction pathway to quinoline ring opening. The indoles subsequently underwent ring opening reactions.

Differential cross sections, measured with guided ion beams: applications to N+ + N2 and C2H2+ + C2D4 collisions

Abstract In gas phase ion chemistry, the guided-ion-beam (GIB) technique is well established for measuring reliable absolute integral cross sections over a wide range of collision energies. It is less known that the method is also well suited for recoil velocity distributions of product ions (the axial component is determined by using the time-off-flight method (GIB-TOF), the transverse component by guiding field variation (GIB-VAR)). This additional information can be used as a diagnostic tool and helps to unravel the energetics of competing reaction pathways. In general, it allows determination of absolute doubly differential cross sections with very high sensitivity and in an energy and scattering angular range inaccessible to standard ion-beam methods. The experimental part of this paper describes the technique in detail, its difficulties and advantages and the required experimental test procedures. Numerical simulations aid the understanding of the kinematics and the shortfalls of the technique, mainly caused by the random motion of the gas in the scattering cell. The results section briefly summarizes already published product velocity distributions obtained for simple systems. New measurements will be presented for two collision systems, N + + N 2 and C 2 H 2 + C 2 D 4 . For the first one, product velocity distributions provide information on the role of excited states of both reactants and products. In combination with new ab initio calculations of the N 3 + potential surface [F.R. Bennett et al., Chem. Phys., this issue] the role of barriers and nonadiabatic interactions is elucidated. In the case of the more complicated hydrocarbon system, the method allows us to distinguish between products of same mass but different isotopic compositions. In addition, different reaction pathways are identified and hints to barrier heights are extracted from the product velocity distributions.

Reaction pathways in the photodetachment of an electron from aqueous chloride: A quantum molecular dynamics study

Reaction and relaxation processes induced by photoexcitation of an aqueous chloride ion are studied with quantum molecular dynamics simulations. A predominant channel leading to a metastable hydrated electron-chlorine pair is found. By means of theoretical transient and stationary absorption spectra, the solvent reorganization involved in the charge repartitioning is discussed. The dissipation of excess electron kinetic energy by surrounding water molecules plays an essential role in the equilibration of an electron-atom pair. For this intermediate species, two competing reaction pathways are identified. One is the barrier-impeded dissociation yielding a hydrated electron. Shape and height of the free energy barrier determined by quantum umbrella sampling point to a diffusion controlled electron photodetachment. The other channel is the geminate recombination via a nonadiabatic transition for which a self-consistent and fully dynamical treatment of the solvent electronic polarization is found to be important. From the rate constants computed for the individual channels, a kinetic model is derived to explain time-dependent spectral signatures and electron escape yields recently observed in photodetachment experiments on aqueous halides.

Reduction of Viologen Bisphosphonate Dihalide with Aluminum Foil

An elegant undergraduate experiment similar to the popular Iodine Clock Reaction employs the reduction of methyl viologen by hydroxide ion. A major problem with the hydroxide reduction demonstration is that the mechanism is complicated by the existence of competing reaction pathways. It has been suggested that layered metal viologen phosphonates could be used in the design and construction of molecular materials. The active unit in the reversible photocoloration of these layered materials is the viologen bisphosphonate dihalide (VPX).During our study of these phoshponate systems, we discovered the reduction of viologen bisphosphonate dihalide by aluminum foil, mossy zinc, or magnesium turnings in dilute aqueous hydrofluoric acid solution. When we demonstrated this phenomenon with aluminum foil and VPBr in the classroom, the response of our students was enthusiastic. This demonstration can be used as prelaboratory discussion for an undergraduate kinetic experiment based on the same phenomenon.