Benchmark database of barrier heights for heavy atom transfer, nucleophilic substitution, association, and unimolecular reactions and its use to test theoretical methods

A benchmark database of forward and reverse barrier heights for 19 non-hydrogen-transfer reactions has been developed by using Weizmann 1 calculations, and 29 DFT methods and 6 ab initio wave-function theory (WFT) methods have been tested against the new database as well as against an older database for hydrogen atom transfer reactions. Among the tested hybrid DFT methods without kinetic energy density, MPW1K is the most accurate model for calculations of barrier heights. Among the tested hybrid meta DFT methods, BB1K and MPWB1K are the two most accurate models for the calculations of barrier heights. Overall, the results show that BB1K and MPWB1K are the two best DFT methods for calculating barrier heights, followed in order by MPW1K, MPWKCIS1K, B1B95, MPW1B95, BH and HLYP, B97-2, mPW1PW91, and B98. The popular B3LYP method has a mean unsigned error four times larger than that of BB1K. Of the methods tested, QCISD(T) is the best ab initio WFT method for barrier height calculations, and QCISD is second best, but QCISD is outperformed by the BB1K, MPWB1K, MPWKCIS1K, and MPW1K methods.     

DFT studies of the phosphinidene derivative HPNaF and its insertion reaction with R–H(R=F,OH, NH<Subscript>2</Subscript>, CH<Subscript>3</Subscript>)

The formations of the phosphinidene derivative HPNaF and its insertion reactions with R–H (R=F, OH, NH₂, CH₃) have been systematically investigated employing the density functional theory (DFT), such as the B3LYP and MPW1PW91 methods. A comparison with the results of MP2 calculations shows that MPW1PW91 underestimates the barrier heights for the four reactions considered. Similarly, the same is also true for the B3LYP method depending on the selected reactions, but by much less than MPW1PW91, where the barrier heights of the four reactions are 25.2, 85.7, 119.0, and 142.4 kJ/mol at the B3LYP/6-311+G* level of theory, respectively. All the mechanisms of the four reactions are identical to each other, i.e., an intermediate has been located during the insertion reaction. Then, the intermediate could dissociate to substituted phosphinidane(H₂RP) and NaF with a barrier corresponding to their respective dissociation energies. Correspondingly, the reaction energies for the four reactions are −92.2, −68.1, −57.2, and −44.3 kJ/mol at the B3LYP/6-311+G* level of theory, respectively, where both the B3LYP and MPW1PW91 methods underestimate the reaction energies compared with the MP2 results. The linear correlations between the calculated barrier heights and the reaction energies have also been observed. As a result, the relative reactivity among the four insertion reactions should be as follows: H–F > H–OH > H–NH₂ > H–CH₃.     

Model compound studies of the beta-O-4 linkage in lignin: absolute rate expressions for beta-scission of phenoxyl radical from 1-phenyl-2-phenoxyethanol-1-yl radical

Arrhenius rate expressions were determined for beta-scission of phenoxyl radical from 1-phenyl-2-phenoxyethanol-1-yl, PhC*(OH)CH2OPh (V). Ketyl radical V was competitively trapped by thiophenol to yield PhCH(OH)CH2OPh in competition with beta-scission to yield phenoxyl radical and acetophenone. A basis rate expression for hydrogen atom abstraction by sec-phenethyl alcohol, PhC*(OH)CH3, from thiophenol, log(k(abs)/M(-1) s(-1)) = (8.88 +/- 0.24) - (6.07 +/- 0.34)/theta, theta = 2.303RT, was determined by competing hydrogen atom abstraction with radical self-termination. Self-termination rates for PhC*(OH)CH3 were calculated using the Smoluchowski equation employing experimental diffusion coefficients of the parent alcohol, PhCH(OH)CH3, as a model for the radical. The hydrogen abstraction basis reaction was employed to determine the activation barrier for the beta-scission of phenoxyl from 1-phenyl-2-phenoxyethanol-1-yl (V): log(k beta)/s(-1)) = (12.85 +/- 0.22) - (15.06 +/- 0.38)/theta, k beta (298 K) ca. (64.0 s(-1) in benzene), and log(k beta /s(-1)) = (12.50 +/- 0.18) - (14.46 +/- 0.30)/theta, k beta (298 K) = 78.7 s(-1) in benzene containing 0.8 M 2-propanol. B3LYP/cc-PVTZ electronic structure calculations predict that intramolecular hydrogen bonding between the alpha-OH and the -OPh leaving group of ketyl radical (V) stabilizes both ground- and transition-state structures. The computed activation barrier, 14.9 kcal/mol, is in good agreement with the experimental activation barrier.     

Proton-coupled electron transfer versus hydrogen atom transfer in benzyl/toluene,methoxyl/methanol,and phenoxyl/phenol self-exchange reactions

Degenerate hydrogen atom exchange reactions have been studied using calculations, based on density functional theory (DFT), for (i) benzyl radical plus toluene, (ii) phenoxyl radical plus phenol, and (iii) methoxyl radical plus methanol. The first and third reactions occur via hydrogen atom transfer (HAT) mechanisms. The transition structure (TS) for benzyl/toluene hydrogen exchange has C(2)(h)() symmetry and corresponds to the approach of the 2p-pi orbital on the benzylic carbon of the radical to a benzylic hydrogen of toluene. In this TS, and in the similar C(2) TS for methoxyl/methanol hydrogen exchange, the SOMO has significant density in atomic orbitals that lie along the C-H vectors in the former reaction and nearly along the O-H vectors in the latter. In contrast, the SOMO at the phenoxyl/phenol TS is a pi symmetry orbital within each of the C(6)H(5)O units, involving 2p atomic orbitals on the oxygen atoms that are essentially orthogonal to the O.H.O vector. The transferring hydrogen in this reaction is a proton that is part of a typical hydrogen bond, involving a sigma lone pair on the oxygen of the phenoxyl radical and the O-H bond of phenol. Because the proton is transferred between oxygen sigma orbitals, and the electron is transferred between oxygen pi orbitals, this reaction should be described as a proton-coupled electron transfer (PCET). The PCET mechanism requires the formation of a hydrogen bond, and so is not available for benzyl/toluene exchange. The preference for phenoxyl/phenol to occur by PCET while methoxyl/methanol exchange occurs by HAT is traced to the greater pi donating ability of phenyl over methyl. This results in greater electron density on the oxygens in the PCET transition structure for phenoxyl/phenol, as compared to the PCET hilltop for methoxyl/methanol, and the greater electron density on the oxygens selectively stabilizes the phenoxyl/phenol TS by providing a larger binding energy of the transferring proton.     

Influence of hydrogen bonding on hydrogen-atom abstraction reactions of dehydropyridinium cations in the gas phase

The reactions of several substituted, positively charged dehydropyridinium cations with cyclohexane, methanol, and tetrahydrofuran have been examined in a Fourier-transform ion cyclotron resonance mass spectrometer. All of the charged monoradicals react with the neutral reagents exclusively via hydrogen atom abstraction. For cyclohexane, there is a good correlation between the reaction efficiencies and the calculated electron affinities at the radical sites; that is, the greater the electron affinity of the charged monoradical at the radical site, the faster the reaction. The reaction efficiencies with methanol and tetrahydrofuran, however, do not correlate with the calculated electron affinities. Density functional theory (DFT) calculations indicate that for these reagents a stabilizing hydrogen bonding interaction exists in the hydrogen atom abstraction transition states for some of the charged monoradicals but not for others. At both the MPW1K and G3MP2B3 levels of theory, there is a good correlation between the calculated activation enthalpies and the observed reaction efficiencies, although the G3MP2B3 method provides a slightly better correlation than the MPW1K method. The extent of enhancement in the reaction efficiencies caused by the hydrogen bonding interactions parallels the calculated hydrogen bond lengths in the transition states.     

Computational studies of intramolecular hydrogen atom transfers in the beta-hydroxyethylperoxy and beta-hydroxyethoxy radicals

The beta-hydroxyethylperoxy (I) and beta-hydroxyethoxy (III) radicals are prototypes of species that can undergo hydrogen atom transfer across their intramolecular hydrogen bonds. These reactions may play an important role in both the atmosphere and in combustion systems. We have used density functional theory and composite electronic structure methods to predict the energetics of these reactions, RRKM/master equation simulations to model the kinetics of chemically activated I, and variational transition state theory (TST) to predict thermal rate constants for the 1,5-hydrogen shift in I (Reaction 1) and the 1,4-hydrogen shift in III (Reaction 2). Our multi-coefficient Gaussian-3 calculations predict that Reaction 1 has a barrier of 23.59 kcal/mol, and that Reaction 2 has a barrier of 22.71 kcal/mol. These predictions agree rather well with the MPW1K and BB1K density functional theory predictions but disagree with predictions based on B3LYP energies or geometries. Our RRKM/master equation simulations suggest that almost 50% of I undergoes a prompt hydrogen shift reaction at pressures up to 10 Torr, but the extent to which I is chemically activated is uncertain. For Reaction 1 at 298 K, the variational TST rate constant is approximately 30% lower than the conventional TST result, and the microcanonical optimized multidimensional tunneling (muOMT) method predicts that tunneling accelerates the reaction by a factor of 3. TST calculations on Reaction 2 reveal no variational effect and a 298 K muOMT transmission coefficient of 10(5). The Eckart method overestimates transmission coefficients for both reactions.     

Barrier heights for H‐atom abstraction by HȮ2 from n‐butanol—A simple yet exacting test for model chemistries?

The barrier heights involved in the abstraction of a hydrogen atom from n‐butanol by the hydroperoxyl radical have been computed with both compound (CBS‐QB3, CBS‐APNO, G3) and coupled cluster methods. In particular, the benchmark computations CCSD(T)/cc‐pVTZ//MP2/6‐311G(d,p) were used to determine that the barrier heights increase in the order α <γ < β < δ < OH. Two prereaction hydrogen‐bonded complexes are formed, one of which connects the TGt conformer of n‐butanol to the α and β transition states and the other connects to the γ and OH channels from the TGg conformer. Four postreaction complexes were also found which link the transition states to the products, hydrogen peroxide + C₄H₉O radical. Abstraction from the terminal δ carbon atom does not involve either a pre or postreaction complex. A number of DFT functionals—B3LYP, BMK, MPWB1K, BB1K, MPW1K, and M05‐2X—were tested to see whether the correct ranking could be obtained with computationally less expensive methods. Only the later functional predicts the correct order but requires a basis set of 6‐311++G(df,pd) to achieve this. However, the absolute values obtained do not agree that well with the benchmarks; the composite G3 method predicts the correct order and comes closest (≤ 2 kJ, mol ^?1) in absolute numerical terms for H‐abstraction from carbon. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Testing the performance of density functionals for the calculation of energetic properties of complex-forming radical-molecule reactions

The performance of some popular and some more recent density functional methods for the calculation of energies of stationary points on the potential surfaces of radical-molecule reactions was examined. The functionals studied are B3-LYP, BH&H, BH&H-LYP, MPW1K, MPWB1K, TPSS, TPSSh, BB1K, M05 and M05-2X, in conjunction with nine different AO basis sets. The reaction energies, barrier heights and the relative energies of the pre-and post-reaction complexes were compared with those obtained at the CCSD(T)/CBS limit for the reactions of OH radicals with HOOH and CH₃OOH. Very poor barrier heights are provided by the B3-LYP, TPSS and TPSSh functionals. The best overall performance was obtained with the BB1K, MPW1K and MPWB1K functionals. In these reactions all of the studied functionals provide converged results only if they are used with large basis sets like aug-cc-pVTZ and def2-TZVP. The data show that before relying on a functional for a specific reaction, it is desirable to make some test calculations on the performance. The same functional can predict some relative energies very well and some others very poorly even in systems including chemically similar reactants.     

Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study

The mechanism of the unusual epimerization and desaturation reactions catalyzed by carbapenem synthase was investigated using the hybrid density functional method B3LYP. Several different models have been used in the calculations to study five component reactions. Both protonated and deprotonated models for the substrate have been explored so that the effects of hydrogen bonds could be characterized. Besides the iron site, it is proposed that a some tyrosine residue, possibly Tyr67, is involved in the hydrogen abstraction step. The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases.     

Theoretical study of the addition and abstraction reactions of hydroxyl radical with uracil

The addition as well as abstraction reactions of hydroxyl radical (OH) with the nucleic acid base, uracil (U), in the gas phase has been explored at the B3LYP/6-31+G(d,p) level of density functional theory (DFT). The energy barrier of the OH addition to both the C5 and C6 positions of the uracil is less than 1 kcal/mol while the hydrogen abstractions (H-abstractions) from either the N1 or the N3 positions are ∼9.5 kcal/mol. Further the energetics of these reactions are assessed by applying the effect of aqueous medium through the polarizable continuum model (PCM). Both the gas and the solution phase data established that the thermodynamic and kinetic factors are more favorable for the OH addition to either C5 or C6 positions of the uracil than the H-abstraction reactions. Moreover, calculations at the MPW1K/6-31+G(d,p), CCSD(T)/6-31+G(d,p)//B3LYP/6-31+G(d,p) and CCSD(T)/6-31+G(d,p)//MPW1K/6-31+G(d,p) levels of theoretical methods qualitatively supported the B3LYP/6-31+G(d,p) results.     

Proton-coupled electron transfer of the phenoxyl/phenol couple: effect of Hartree-Fock exchange on transition structures

Proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) reactions of the phenoxyl/phenol couple are studied theoretically by using wave function theory (WFT) as well as DFT methods. At the complete active space self-consistent field (CASSCF) level, geometry optimization is found to give two transition states (TSs); one is the PCET type with two benzene rings being nearly coplanar, and the other is the HAT type with two benzene rings taking a stacking structure. Geometry optimization at the (semilocal) DFT level, on the other hand, is found to give only one transition state (i.e., the PCET-type one) and fail to obtain the stacking TS structure. By comparing various levels of theories (including long-range corrected DFT functionals), we demonstrate that the Hartree-Fock exchange at long range plays a critical role in obtaining the sufficient stacking stabilization of the present open-shell system, and that the sole addition of empirical dispersion correction to semilocal DFT functionals may not be adequate for describing such a stacking interaction. Next, we investigate the solvent effect on the PCET and HAT TS thus obtained using the reference interaction site model self-consistent field (RISM-SCF) method. The results suggest that the free energy barrier increases with increasing polarity of the solvent, and that the solvent effects are stronger for the PCET TS than the stacking HAT TS pathway. The reason for this is discussed based on the dipole moment of different TS structures in solution.     

Theoretical study of the thermodynamics and kinetics of hydrogen abstractions from hydrocarbons

Thermochemical and kinetic data were calculated at four cost-effective levels of theory for a set consisting of five hydrogen abstraction reactions between hydrocarbons for which experimental data are available. The selection of a reliable, yet cost-effective method to study this type of reactions for a broad range of applications was done on the basis of comparison with experimental data or with results obtained from computationally demanding high level of theory calculations. For this benchmark study two composite methods (CBS-QB3 and G3B3) and two density functional theory (DFT) methods, MPW1PW91/6-311G(2d,d,p) and BMK/6-311G(2d,d,p), were selected. All four methods succeeded well in describing the thermochemical properties of the five studied hydrogen abstraction reactions. High-level Weizmann-1 (W1) calculations indicated that CBS-QB3 succeeds in predicting the most accurate reaction barrier for the hydrogen abstraction of methane by methyl but tends to underestimate the reaction barriers for reactions where spin contamination is observed in the transition state. Experimental rate coefficients were most accurately predicted with CBS-QB3. Therefore, CBS-QB3 was selected to investigate the influence of both the 1D hindered internal rotor treatment about the forming bond (1D-HR) and tunneling on the rate coefficients for a set of 21 hydrogen abstraction reactions. Three zero curvature tunneling (ZCT) methods were evaluated (Wigner, Skodje & Truhlar, Eckart). As the computationally more demanding centrifugal dominant small curvature semiclassical (CD-SCS) tunneling method did not yield significantly better agreement with experiment compared to the ZCT methods, CD-SCS tunneling contributions were only assessed for the hydrogen abstractions by methyl from methane and ethane. The best agreement with experimental rate coefficients was found when Eckart tunneling and 1D-HR corrections were applied. A mean deviation of a factor 6 on the rate coefficients is found for the complete set of 21 reactions at temperatures ranging from 298 to 1000 K. Tunneling corrections play a critical role in obtaining accurate rate coefficients, especially at lower temperatures, whereas the hindered rotor treatment only improves the agreement with experiment in the high-temperature range.     

Efficient protocol for quantum Monte Carlo calculations of hydrogen abstraction barriers: Application to methanol

Accurate calculation of hydrogen abstraction reaction barriers is a challenging problem, often requiring high level quantum chemistry methods that scale poorly with system size. Quantum Monte Carlo (QMC) methods provide an alternative approach that exhibit much better scaling, but these methods are still computationally expensive. We describe approaches that can significantly reduce the cost of QMC calculations of barrier heights, using the hydrogen abstraction of methanol by a hydrogen atom as an illustrative example. By analysing the combined influence of trial wavefunctions and pseudopotential quadrature settings on the barrier heights, variance, and time‐step errors, we devise a simple protocol that minimizes the cost of the QMC calculations while retaining accuracy comparable to large‐basis coupled cluster theory. We demonstrate that this protocol is transferable to other hydrogen abstraction reactions.     

Theoretical studies on the intramolecular hydrogen bond and tautomerism of 8-mercaptoquinoline in the gaseous phase and in solution using modern DFT methods

A theoretical quantum chemical study of the intramolecular hydrogen bonding interactions in 8-mercaptoquinoline has been carried out. Special attention has been paid to the rotation of S-H bond and intramolecular proton-transfer reactions. Therewith, the B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p), MPW1K/6-311++G(d,p), MPW1K/6-31+G(2d,2p), BH&HLYP/6-311++G(d,p), and G96LYP/6-311++G(d,p) methods have been used. By means of the Onsager and PCM reaction field methods, the effects of solvent on hydrogen-bond energies, conformational equilibria, rotational barriers, and tautomerism in aqueous solution have been studied. These simulations were done at the MPW1K/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels. Natural-bond orbital analysis has been performed to study the intramolecular hydrogen bond (IHB) in the gaseous phase and in aqueous medium. The stability of forms under consideration in solution does not coincide with that in the gaseous phase, underlining a great importance of the electrostatic influence of solvent. Double-proton transfer in the prototropic tautomerization of 8-mercaptoquinoline, one water molecule complex in the gaseous phase and in solution, has been systematically studied. The double-proton transfer occurs concertedly and synchronously. The water-assisted tautomerization is kinetically less, but thermodynamically more favorable, compared to that of the single-proton transfer. As in the case with single-proton transfer, for water-assisted reaction, the tautomerization energies and barrier heights decrease with the increase in dielectric constant, which implies faster and more complete tautomerization of 8-mercaptoquinoline in a polar solvent.     

DFT and ab initio calculations on two reactions between hydrogen atoms and the fire suppressants 2-H heptafluoropropane and CF3Br

Reaction enthalpies and barrier heights of the reactions CF3Br+H-->CF3+HBr {reaction (1)} and CF3CHFCF3+H-->CF3CFCF3+H2 {reaction (2)} have been calculated at the near state-of-the-art ab initio level, and also by employing the B3LYP, BH&HLYP, BB1K, MPW1K, MPWB1K and TPSS1KCIS functionals. In addition, the integrated molecular orbital+molecular orbital (IMOMO) method has been used to study reaction (2). The ab initio benchmark values of the reaction enthalpy (298 K) and barrier height (0 K) of reaction (2) are reported for the first time {-(0.7+/-0.7) and 13.3+/-0.5 kcal/mole respectively}. When density functional theory (DFT) results are compared with ab initio benchmarks for both reactions (1) and (2), the MPWB1K functional is found to have the best performance of the six functionals used. The IMOMO method with the RCCSD/aug-cc-pVTZ and/or RCCSD(T)/aug-cc-pVTZ levels, as the high levels of calculation on the model system, gives reaction enthalpies and barrier heights of reaction (2), which agree with ab initio benchmark values to within 1 kcal/mole. Computed key geometrical parameters and imaginary vibrational frequencies of the transition state structures of reactions (1) and (2) obtained at different levels of calculation are compared. The magnitudes of the computed imaginary vibrational frequencies of the transition states of both reactions considered are found to be very sensitive to the levels of calculation used to obtain them. The heat of formation (298 K) of CF3CFCF3 calculated at the near state-of-the-art level has a value of -(318+/-3) kcal/mole.     

Regioselectivity of aliphatic versus aromatic hydroxylation by a nonheme iron(II)-superoxo complex

Many enzymes in nature utilize molecular oxygen on an iron center for the catalysis of substrate hydroxylation. In recent years, great progress has been made in understanding the function and properties of iron(IV)-oxo complexes; however, little is known about the reactivity of iron(II)-superoxo intermediates in substrate activation. It has been proposed recently that iron(II)-superoxo intermediates take part as hydrogen abstraction species in the catalytic cycles of nonheme iron enzymes. To gain insight into oxygen atom transfer reactions by the nonheme iron(II)-superoxo species, we performed a density functional theory study on the aliphatic and aromatic hydroxylation reactions using a biomimetic model complex. The calculations show that nonheme iron(II)-superoxo complexes can be considered as effective oxidants in hydrogen atom abstraction reactions, for which we find a low barrier of 14.7 kcal mol(-1) on the sextet spin state surface. On the other hand, electrophilic reactions, such as aromatic hydroxylation, encounter much higher (>20 kcal mol(-1)) barrier heights and therefore are unlikely to proceed. A thermodynamic analysis puts our barrier heights into a larger context of previous studies using nonheme iron(IV)-oxo oxidants and predicts the activity of enzymatic iron(II)-superoxo intermediates.     

DFT computational studies on rotation barriers,tautomerism, intramolecular hydrogen bond,and solvent effects in 8‐hydroxyquinoline

Intramolecular hydrogen binding interactions in 8‐hydroxyquinoline, both in its zwitterionic tautomer and in the rotamer without the intramolecular hydrogen bond (IHB), have been computed using the B3LYP and MPW1K density functionals. The rotation of the O? H bond and intramolecular proton transfer reactions were studied theoretically. The following theory levels have been applied: B3LYP/6‐31G(d,p), B3LYP/6‐311++G(d,p), MPW1K/6‐311++G(d,p), and MPW1K/6‐311++G(2d,3p)//MPW1K/6‐311++G(d,p). Natural bond orbital (NBO) analysis has also been carried out. The effect of medium (benzene, chloroform, tetrahydrofuran, 1,2‐dichloroethane, acetone, water) was simulated using the self‐consistent reaction field (SCRF) method within the framework of the polarizable continuum model (PCM), at the MPW1K/6‐311++G(d,p) level. The evolution of geometry, relative energies, heights of rotation (around the O? H bond) and tautomerization barriers, IHB energies, and ΔG(solv) have been systematically investigated. The results obtained have shown the failure to neglect some changes of the above characteristics in polar media with respect to the gaseous phase. The series of stability of the forms under study in the gaseous phase remains the same in solution. Thus, in spite of the important role of the solvent electrostatic effects, the intrinsic stability of those species overcomes the solvent effects. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Activation energies of pericyclic reactions: performance of DFT, MP2, and CBS-QB3 methods for the prediction of activation barriers and reaction energetics of 1,3-dipolar cycloadditions, and revised activation enthalpies for a standard set of hydrocarbon pericyclic reactions

Activation barriers and reaction energetics for the three main classes of 1,3-dipolar cycloadditions, including nine different reactions, were evaluated with the MPW1K and B3LYP density functional methods, MP2, and the multicomponent CBS-QB3 method. The CBS-QB3 values were used as standards for 1,3-dipolar cycloaddition activation barriers and reaction energetics, and the density functional theory (DFT) and MP2 methods were benchmarked against these values. The MPW1K/6-31G* method and basis set performs best for activation barriers, with a mean absolute deviation (MAD) value of 1.1 kcal/mol. The B3LYP/6-31G* method and basis set performs best for reaction enthalpies, with a MAD value of 2.4 kcal/mol, while the MPW1K method shows large errors for reaction energetics. The MP2 method gives the expected systematic underestimation of barriers. Concerted and nearly synchronous transition structures are predicted by all DFT and MP2 methods. Also reported are revised estimated 0 K experimental activation enthalpies for a standard set of hydrocarbon pericyclic reactions and updated comparisons to experiment for DFT, ab initio, and multicomponent methods. B3LYP and MPW1K methods with MAD values of 1.5 and 2.1 kcal/mol, respectively, fortuitously outperform the multicomponent CBS-QB3 method, which has a MAD value of 2.3. The MAD value of the O3LYP functional improves to 2.4 kcal/mol from the previously reported 3.0 kcal/mol.     

*H atom and *OH radical reactions with 5-methylcytosine

The reactions between either a hydrogen atom or a hydroxyl radical and 5-methylcytosine (5-MeCyt) are studied by using the hybrid kinetic energy meta-GGA functional MPW1B95. *H atom and *OH radical addition to positions C5 and C6 of 5-MeCyt, or *OH radical induced H-abstraction from the C5 methyl group, are explored. All systems are optimized in bulk solvent. The data presented show that the barriers to reaction are very low: ca. 7 kcal/mol for the *H atom additions and 1 kcal/mol for the reactions involving the *OH radical. Thermodynamically, the two C6 radical adducts and the *H-abstraction product are the most stable ones. The proton hyperfine coupling constants (HFCC), computed at the IEFPCM/MPW1B95/6-311++G(2d,2p) level, agree well with B3LYP results and available experimental and theoretical data on related thymine and cytosine radicals.     

Proton-coupled electron transfer in solution, proteins, and electrochemistry

Recent advances in the theoretical treatment of proton-coupled electron transfer (PCET) reactions are reviewed. These reactions play an important role in a wide range of biological processes, as well as in fuel cells, solar cells, chemical sensors, and electrochemical devices. A unified theoretical framework has been developed to describe both sequential and concerted PCET, as well as hydrogen atom transfer (HAT). A quantitative diagnostic has been proposed to differentiate between HAT and PCET in terms of the degree of electronic nonadiabaticity, where HAT corresponds to electronically adiabatic proton transfer and PCET corresponds to electronically nonadiabatic proton transfer. In both cases, the overall reaction is typically vibronically nonadiabatic. A series of rate constant expressions have been derived in various limits by describing the PCET reactions in terms of nonadiabatic transitions between electron-proton vibronic states. These expressions account for the solvent response to both electron and proton transfer and the effects of the proton donor-acceptor vibrational motion. The solvent and protein environment can be represented by a dielectric continuum or described with explicit molecular dynamics. These theoretical treatments have been applied to numerous PCET reactions in solution and proteins. Expressions for heterogeneous rate constants and current densities for electrochemical PCET have also been derived and applied to model systems.