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A combined kinetic-quantum mechanical model for assessment of catalytic cycles: application to cross-coupling and Heck reactions.

The efficiency of catalytic cycles is measured by their turnover frequency (TOF). The degree of TOF control determines which states contribute most to the rate of the cycle, and thus indicates the steps that have the highest impact on the cycle. A kinetic model developed by Christiansen (Christiansen, J. A. Adv. Catal. 1953, 5, 311) for catalytic cycles is implemented here in a form that utilizes state energies. This enables one to assess the efficiency of quantum mechanically computed catalytic cycles like the palladium-catalyzed cross-coupling and Heck reactions, to test alternative hypotheses, and to make some predictions. This implementation can also account for effects such as Sabatier's volcano curve for heterogeneous catalysis. The model leads to a dependence of the TOF for any cycle on the "corrected" energy span quantity, deltaE, whose precise expression depends on the location of the summit and trough of the cycle in the step sequence of the cycle. Thus, knowing the highest energy transition state, the most abundant reaction intermediate, and the reaction energy enables one to make quick predictions about relative efficiency of cycles. At the same time, the degree of TOF control determines which states contribute most to the rate of reaction, and thus indicates the values to be included in the calculation of the energetic span and the steps that may be tinkered with to improve the cycle.

Journal Article↗

Hydrogen- and fluorine-bridged disilyl cations and their use in catalytic C-F activation.

The hydrogen-bridged disilyl cation 6 with an 1,8-naphthalenediyl backbone was synthesized and was characterized by NMR spectroscopy and X-ray crystallography, supported by quantum mechanical computations. The SiHSi linkage is symmetrical, corresponding to a single minimum potential, and the structural parameters are in agreement with the presence of a two electron-three center bond in 6. Treatment of disilyl cation 6 with alkyl fluorides yields the disilylfluoronium ion 10. The SiFSi group in the disilyl fluoronium ion 10 is symmetrical with an average SiF bond length of 175.9(8) and a bent angle beta = 130 degrees . Both cations catalyze the hydrodefluorination reaction of alkyl and benzyl fluorides to give alkanes.

Journal Article↗

Optical rotation of achiral pentaerythritol.

The optical rotatory power of achiral crystals of achiral pentaerythritol molecules was measured. The maximum rotations were found to be +/-6 degrees /mm. The quantum mechanically computed rotation of pentaerythritol molecules using linear response theory was 6 times larger although the experimental and theoretical tensors were similarly oriented to within 5 degrees .

Journal Article↗

Substituent effects in cephalosporins as assessed by molecular orbital calculations, nuclear magnetic resonance, and kinetics.

For cephalosporins with different side chains at position 3, the quantum mechanically computed charge distribution in the beta-lactam carbonyl group can be correlated with observables, such as carbon-13 chemical-shift differences at C3 and C4 of the dihydrothiazine ring and alkaline rates of hydrolysis of the beta-lactam. The relationship of these properties and the theoretical transition-state energy (TSE) corroborate the fact that chemical reactivity is one important determinant affecting inhibitory activity of cephalosporins against peptidoglycan-regulating enzymes.

Cephalosporins↗

Periodic DFT study of the structural and electronic properties of bulk CoAl2O4 spinel.

In this study, structural and electronic properties of CoAl2O4 spinel are investigated for the first time by means of quantum chemical computational tools. Coupling supercell periodic calculations under the density functional theory formalism with a nonempirical quasi-harmonic Debye model, we examine the influence of temperature on the relative stability of several cation distributions of Co2+ and Al3+ over tetrahedral and octahedral interstices of the oxygen sublattice. Our simulations are able to reproduce the experimentally observed trend: (i) the normal spinel is calculated to be the stable structure at static and low-temperature conditions, and (ii) as the temperature increases, the preference of structures with Al3+ at tetrahedral sites (and Co2+ at octahedral sites) is found to progress following an asymptotic conduct. The effects of the cation distributions on geometrical variations of electronic and magnetic properties of CoAl2O4 can be interpreted as dominated by the local behavior of Co2+ at octahedral sites.

Journal Article↗

Kinetic and thermodynamic properties of the aminoxyl (NH2O*) radical.

The product of one-electron oxidation of (or H-atom abstraction from) hydroxylamine is the H2NO* radical. H2NO* is a weak acid and deprotonates to form HNO-*; the pKa(H2NO*) value is 12.6+/-0.3. Irrespective of the protonation state, the second-order recombination of the aminoxyl radical yields N2 as the sole nitrogen-containing product. The following rate constants were determined: kr(2H2NO*)=1.4x10(8) M-1 s-1, kr(H2NO*+HNO-*)=2.5x10(9) M-1 s-1, and kr(2HNO-*)=4.5x10(8) M-1 s-1. The HNO-* radical reacts with O2 in an electron-transfer reaction to yield nitroxyl (HNO) and superoxide (O2-*), with a rate constant of ke(HNO-*+O2-->HNO+O2-*)=2.2x10(8) M-1 s-1. Both O2 and O2-* seem to react with deprotonated hydroxylamine (H2NO-) to set up an autoxidative chain reaction. However, closer analysis indicates that these reactions might not occur directly but are probably mediated by transition-metal ions, even in the presence of chelators, such as ethylenediamine tetraacetic acid (EDTA) or diethylenetriamine pentaacetic acid (DTPA). The following standard aqueous reduction potentials were derived: E degrees (H2NO*,2H+/H3NOH+)=1.25+/-0.01 V; E degrees (H2NO*,H+/H2NOH)=0.90+/-0.01 V; and E degrees (H2NO*/H2NO-)=0.09+/-0.01 V. In addition, we estimate the following: E degrees (H2NOH+*/H2NOH)=1.3+/-0.1 V, E degrees (HNO, H+/H2NO*)=0.52+/-0.05 V, and E degrees (HNO/HNO-*)=-0.22+/-0.05 V. From the data, we also estimate the gaseous O-H and N-H bond dissociation enthalpy (BDE) values in H2NOH, with BDE(H2NO-H)=75-77 kcal/mol and BDE(H-NHOH)=81-82 kcal/mol. These values are in good agreement with quantum chemical computations.

Free Radicals↗

Local structure of beta-hairpin isotopomers by FTIR, 2D IR, and ab initio theory.

The 12-residue tryptophan zipper beta-hairpin (SWTWENGKWTWK) and two (13)C-isotopomers were examined in the amide-I region using FTIR and femtosecond two-dimensional infrared (2D IR) spectroscopies. Spectroscopic features of the labeled transitions with (13)C-substituted amide unit present in the terminal or turn region of the hairpin, including their frequency shifts and distributions, line broadenings, orientations, and anharmonicities of diagonal peaks, allow the peptide local structure and local environment to be examined. The results suggest a larger structure fluctuation in the terminal region than in the turn region as a result of the side chain effect and solvent-peptide interaction. The results also suggest that the uncoupled amide-I modes are not degenerate and that this is likely to be a common situation for solvated polypeptides. In addition, the amide-I states in the terminal and turn regions were found to be delocalized over several neighboring amide units. Cross-peaks between the various labeled and unlabeled structural regions were clearly observed in the 2D IR correlation spectra, allowing them to be characterized for monitoring structural changes. These results illustrate the sensitivity of 2D IR to the local environment of solvated peptides. The simulated 1D and 2D IR spectra of the hairpin, obtained by using the vibrational exciton model incorporating coupling constants from quantum chemical computations and semiempirical calculations, were found to reproduce the essential features of the experimental results.

Amides↗

13C NMR relaxation study of molecular motions in tetraphenyltin and tetra(p-tolyl)tin in solution.

The Woessner approach is applied to the 13C relaxation data for tetraphenyltin (1) and tetra(p-tolyl)tin (2) in CDCl3 solution over the temperature range 5-42 degrees C to obtain correlation times for rotational motions and hence the activation barriers. Quantum mechanical computations were carried out to obtain the rotational energy barriers for comparison. For 2 the relaxation data indicate (1) slower ring rotation than in 1, (2) highly hindered internal rotation of the methyl group. IR and chemical shift data support the hypothesis of hyperconjugation of the methyl correlated with interaction between the pi-electrons and the 5d orbitals of tin in the (p-tolyl)Sn moiety to account for the hindrances to the rotations of the ring and the methyl. The activation barrier for the tolyl group rotation is found to be much higher than that for the phenyl rotation. However, the Woessner approach yields an anomalously high barrier for the methyl rotation. An explanation based on correlated rotations of the tolyl ring and the methyl is offered.

Journal Article↗

High-level ab initio studies of hydrogen abstraction from prototype hydrocarbon systems.

Symmetric and nonsymmetric hydrogen abstraction reactions are studied using state-of-the-art ab initio electronic structure methods. Second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] methods with large correlation consistent basis sets (cc-pVXZ, where X = D,T,Q) are used in determining the transition-state geometries, activation barriers, and thermodynamic properties of several representative hydrogen abstraction reactions. The importance of basis set, electron correlation, and choice of zeroth-order reference wave function in the accurate prediction of activation barriers and reaction enthalpies are also investigated. The ethynyl radical (*CCH), which has a very high affinity for hydrogen atoms, is studied as a prototype hydrogen abstraction agent. Our high-level quantum mechanical computations indicate that hydrogen abstraction using the ethynyl radical has an activation energy of less than 3 kcal mol(-1) for hydrogens bonded to an sp(2) or sp(3) carbon. These low activation barriers further corroborate previous studies suggesting that ethynyl-type radicals would make good tooltips for abstracting hydrogens from diamondoid surfaces during mechanosynthesis. Modeling the diamond C(111) surface with isobutane and treating the ethynyl radical as a tooltip, hydrogen abstraction in this reaction is predicted to be barrierless.

Computer Simulation↗

Binding energies of first row diatomics in the light of the interacting quantum atoms approach.

Binding energies of first row diatomics are revisited within the interacting quantum atoms (IQA) approach. This is a formalism in chemical bonding theory based upon the quantum theory of atoms in molecules. It is characterized by the preservation of the energetic identity of atoms within molecules. Quantum mechanically computed binding energies are recovered in IQA as a sum of small atomic deformation energies and large pairwise interaction terms. We show how this partition responds faithfully to chemical intuition, and how the different evolution of deformations and interactions accounts in a unified manner for the subtle variations of the binding energy of these molecules.

Journal Article↗

Arene-cation interactions of positive quadrupole moment aromatics and arene-anion interactions of negative quadrupole moment aromatics.

Intermolecular interactions involving aromatic pi-electron density are widely believed to be governed by the aromatic molecular quadrupole moment, Theta(zz). Arene-cation binding is believed to occur primarily with negative Theta(zz) aromatics, and arene-anion binding is believed to occur largely with positive Theta(zz) aromatics. We have performed quantum mechanical computations that show the cation binding of positive Theta(zz) aromatics and the anion binding of negative Theta(zz) aromatics is quite common in the gas phase. The pi-electron density of hexafluorobenzene, the prototypical positive Theta(zz ) aromatic (experimental Theta(zz) = 9.5 +/- 0.5 DA), has a Li+ binding enthalpy of -4.37 kcal/mol at the MP2(full)/6-311G**level of theory. The RHF/6-311G** calculated Theta(zz) value of 1,4-dicyanobenzene is +11.81 DA, yet it has an MP2(full)/6-311G** Li+ binding enthalpy of -12.65 kcal/mol and a Na+ binding enthalpy of -3.72 kcal/mol. The pi-electron density of benzene, the prototypical negative Theta(zz) aromatic (experimental Theta(zz) = -8.7 +/- 0.5 DA), has a F- binding enthalpy of -5.51 kcal/mol. The RHF/6-311G** calculated Theta(zz) of C6H2I4 is -10.45 DA, yet it has an MP2(full)/6-311++G** calculated F- binding enthalpy of -20.13 kcal/mol. Our results show that as the aromatic Theta(zz) value increases the cation binding enthalpy decreases; a plot of cation binding enthalpies versus aromatic Theta(zz) gives a line of best of fit with R2 = 0.778. No such correlation exists between the aromatic Theta(zz) value and the anion binding enthalpy; the line of best fit has R2 = 0.297. These results are discussed in terms of electrostatic and polarizability contributions to the overall binding enthalpies.

Benzene↗

Adsorption and in situ scanning tunneling microscopy of cysteine on Au(111): Structure, energy, and tunneling contrasts.

The amino acid L-cysteine (Cys) adsorbs in highly ordered (3 square root of 3 x 6) R30 degrees lattices on Au(111) electrodes from 50 mM ammonium acetate, pH 4.6. We provide new high-resolution in situ scanning tunneling microscopy (STM) data for the L-Cys adlayer. The data substantiate previous data with higher resolution, now at the submolecular level, where each L-Cys molecule shows a bilobed feature. The high image resolution has warranted a quantum chemical computational effort. The present work offers a density functional study of the geometry optimized adsorption of four L-Cys forms-the molecule, the anion, the neutral radical, and its zwitterion adsorbed a-top-at the bridge and at the threefold hollow site of a planar Au(111) Au12 cluster. This model is crude but enables the inclusion of other effects, particularly the tungsten tip represented as a single or small cluster of W-atoms, and the solvation of the L-Cys surface cluster. The computational data are recast as constant current-height profiles as the most common in situ STM mode. The computations show that the approximately neutral radical, with the carboxyl group pointing toward and the amino group pointing away from the surface, gives the most stable adsorption, with little difference between the a-top and threefold sites. Attractive dipolar interactions screened by a dielectric medium stabilize around a cluster size of six L-Cys entities, as observed experimentally. The computed STM images are different for the different L-Cys forms. Both lateral and vertical dimensions of the radical accord with the observed dimensions, while those of the molecule and anion are significantly more extended. A-top L-Cys radical adsorption further gives a bilobed height profile resembling the observed images, with comparable contributions from sulfur and the amino group. L-Cys radical a-top adsorption therefore emerges as the best representation of L-Cys adsorption on Au(111).

Adsorption↗

Role of tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase.

The tautomerism of 2-azaadenine and 2-hypoxanthine has been examined in the gas phase and in aqueous solution. The tautomerism in the gas phase has been studied by means of semiempirical and ab initio quantum-mechanical computations, as well as density-functional calculations. The influence of the aqueous solvent on the relative stability between tautomers has been estimated from self-consistent reaction field calculations performed with different high-level continuum models. The results provide a detailed picture of the tautomeric preference for these purine bases. The importance of tautomerism in the substrate recognition by xanthine oxidase is discussed. Finally, the rate of oxidation of 2-azaadenine and 2-hypoxanthine by xanthine oxidase is discussed in terms of the recognition model at the enzyme active site.

Adenine↗

Tunneling in the reaction of acetone with OH.

Based on recent detailed quantum mechanical computations of the mechanism of the title reaction and, this paper presents kinetics analysis of the overall rate constant and its temperature dependence, for which ample experimental data are available for comparison. The analysis confirms that the principal channel is the formation of acetonyl radical + H(2)O, while the channel leading to acetic acid is of negligible importance. It is shown that the unusual temperature dependence of the overall rate constant, as observed experimentally, is well accounted for by standard RRKM treatment that includes tunneling. This treatment is applied at the microcanonical level, with chemically activated distribution of entrance species, i.e. using a stationary rather than a thermal distribution that incorporates collisional energy transfer and competition between the redissociation and exit channel. A similar procedure is applied to the isotopic reaction acetone-d6 + OH with equally satisfying results, so that the experimental temperature dependence of the KIE (kinetic isotope effect) is perfectly reproduced. This very good agreement between calculation and experiment is obtained without any fitting to experimental values and without any adjustment of the parameters of calculation.

Acetone↗

Magnetic interactions in calcium and sodium ladder vanadates.

Magnetic interactions in ladder vanadates are determined with quantum chemical computational schemes using the embedded cluster model approach to represent the material. The available experimental data for calcium vanadate is accurately reproduced and the nature of the interladder interaction is established to be ferromagnetic. An analysis of the main contributions to the magnetic couplings is presented and the role of the covalently bonded apex oxygen is elucidated. In the sodium vanadate, the ground state configuration of the rungs is V-3d1-O-2p5-V-3d1. We show that with this configuration good intrachain coupling constants are obtained for the high-temperature phase. The interchain coupling in NaV2O5 is predicted to be approximately 34 K, ferromagnetic in nature.

Journal Article↗

Theoretical study of the hydrogen atom transfer in the heterodimer indole-ammonia and comparison with experimental results.

Ab initio calculations on the heterodimer C8H6NH...NH3 are carried out for its ground, the excited pisigma*, and the ground cationic electronic states, enabling the description of hydrogen or proton transfer, respectively. Two-dimensional quantum-dynamical computations on the pisigma* potential surface help one to understand the mechanism and the time scale of the hydrogen transfer. Subsequent decay processes are discussed depending on the vibrational excitation of the ammonium constituent. Finally, the theoretical results obtained are used for the interpretation of the time-dependent signals observed in femtosecond pump-probe experiments.

Journal Article↗

Pulsed laser photolysis and quantum chemical-statistical rate study of the reaction of the ethynyl radical with water vapor.

The rate coefficient of the gas-phase reaction C(2)H + H(2)O-->products has been experimentally determined over the temperature range 500-825 K using a pulsed laser photolysis-chemiluminescence (PLP-CL) technique. Ethynyl radicals (C(2)H) were generated by pulsed 193 nm photolysis of C(2)H(2) in the presence of H(2)O vapor and buffer gas N(2) at 15 Torr. The relative concentration of C(2)H radicals was monitored as a function of time using a CH* chemiluminescence method. The rate constant determinations for C(2)H + H(2)O were k(1)(550 K) = (2.3 +/- 1.3) x 10(-13) cm(3) s(-1), k(1)(770 K) =(7.2 +/- 1.4) x 10(-13) cm(3) s(-1), and k(1)(825 K) = (7.7 +/- 1.5) x 10(-13) cm(3) s(-1). The error in the only other measurement of this rate constant is also discussed. We have also characterized the reaction theoretically using quantum chemical computations. The relevant portion of the potential energy surface of C(2)H(3)O in its doublet electronic ground state has been investigated using density functional theory B3LYP6-311 + + G(3df,2p) and molecular orbital computations at the unrestricted coupled-cluster level of theory that incorporates all single and double excitations plus perturbative corrections for the triple excitations, along with the 6-311 + + G(3df,2p) basis set [(U)CCSD(T)6-311 + + G(3df,2p)] and using UCCSD(T)6-31G(d,p) optimized geometries. Five isomers, six dissociation products, and sixteen transition structures were characterized. The results confirm that the hydrogen abstraction producing C(2)H(2)+OH is the most facile reaction channel. For this channel, refined computations using (U)CCSD(T)6-311 + + G(3df,2p)(U)CCSD(T)6-311 + + G(d,p) and complete-active-space second-order perturbation theory/complete-active-space self-consistent-field theory (CASPT2/CASSCF) [B. O. Roos, Adv. Chem. Phys. 69, 399 (1987)] using the contracted atomic natural orbitals basis set (ANO-L) [J. Almlof and P. R. Taylor, J. Chem. Phys.86, 4070 (1987)] were performed, yielding zero-point energy-corrected potential energy barriers of 17 kJ mol(-1) and 15 kJ mol(-1), respectively. Transition-state theory rate constant calculations, based on the UCCSD(T) and CASPT2/CASSCF computations that also include H-atom tunneling and a hindered internal rotation, are in perfect agreement with the experimental values. Considering both our experimental and theoretical determinations, the rate constant can best be expressed, in modified Arrhenius form as k(1)(T) = (2.2 +/- 0.1) x 10(-21)T(3.05) exp[-(376 +/- 100)T] cm(3) s(-1) for the range 300-2000 K. Thus, at temperatures above 1500 K, reaction of C(2)H with H(2)O is predicted to be one of the dominant C(2)H reactions in hydrocarbon combustion.

Journal Article↗