Accurate adsorption energies of small molecules on oxide surfaces: CO-MgO(001)

A hybrid MP2:DFT + D optimization method is applied using a 3 × 3 × 2 cluster model (Mg9O9) embedded in a 4 × 4 × 4 slab model. The calculated CO-Mg(2+) distance is 248 pm, and the calculated CO frequency (blue) shift is 20 cm(-1), 6 cm(-1) larger than the experimental value. For the structure obtained, MP2 calculations with basis set extrapolation on a series of cluster models of increasing size are performed. Taking into account the difference in the periodic limit at the DFT + D level, 20.9 ± 0.7 kJ mol(-1) is obtained as the estimate for the full periodic MP2 limit for the energy of CO desorption from the MgO(001) surface. CCSD(T) corrections are evaluated for the Mg9O9 cluster model using an augmented double-zeta basis set. Basis set extension effects are examined for smaller models. For a loading of Θ = 1/8, the estimated CCSD(T) value is 21.0 ± 1.0 kJ mol(-1), which is 0.4 ± 1.0 kJ mol(-1) larger than the (electronic) desorption energy derived in this study from TPD desorption barriers reported in the literature.

The hemibond as an alternative condensed phase structure for the hydroxyl radical

Despite the critical importance of the hydroxyl radical in major scientific fields, there are still open questions on the behavior of this species in the aqueous phase. In particular, there has been much debate on the existence of a hemibonded interaction between the hydroxyl radical and water molecules. While some reports indicate that the hemibonded radical might explain some experimental data, others have claimed that this interaction is simply a density functional theory (DFT) artifact. Here, we provide results from high level (basis set limit of coupled-cluster levels up to single, double, triple excitations (CCSD(T)) and beyond) ab initio calculations of different OH•(H2O)n clusters in the gas phase to accurately explore the existence of the hemibonded interaction and its energy difference with respect to other well-defined hydrogen bond interactions. Additional comparisons with second order perturbation theory (MP2) and DFT are also presented. Constrained molecular dynamics was applied to determine the free energy for the formation/disruption and ice systems. Overall, our findings confirm that the hemibond can be an alternative structure for the hydroxyl radical in the condensed phase when the formation of hydrogen bonds is impeded. These results will aid the understanding of theoretical and experimental data and help future experimental designs for the detection of this important species.

Cross-talk between amino acid residues and flavonoid derivatives: insights into their chemical recognition

Currently, there is a general consensus that flavonoids exert their antioxidant activity through their ability to interact with a broad range of proteins, enzymes and transcription factors rather than acting as conventional hydrogen-donating antioxidants. For this, the effect of different chemical groups of the conjugated flavonoid metabolites is apparently playing a pivotal role. Yet, many questions concerning the relevant molecular mechanisms still remain open. It is therefore crucial to gain a deeper insight into the amino acid residue-flavonoid interaction. Here we show extensive theoretical thermodynamic data and structural characteristics of the interaction of chalcone, genistein, epigallocatechin gallate, and quercetin and some of its metabolites with amino acid residues. By correlating (a) the binding energies of flavonoids-amino acid residues, (b) the hydrophobicity of amino acids, and (c) the abundance of amino acid residues in the binding sites of proteins, we can conclude that flavonoids appear to be strongly bonded to only few charged hydrophilic amino acids in the protein pockets, and rather weakly bonded to the majority of amino acid residues in the binding sites. This finding strongly impacts the understanding of the chemical recognition of flavonoids and their metabolites in their interaction with proteins and would contribute to a better design of further experimental studies. Particularly, the amino acids Phe, Leu, Ile and Trp seem to play a crucial role in the dynamics of flavonoid ligands in the binding sites of proteins.

Benchmark study of DFT functionals for late-transition-metal reactions

The performance of a wide variety of DFT exchange-correlation functionals for a number of late-transition-metal reaction profiles has been considered. Benchmark ab-initio reference data for the prototype reactions Pd + H2, Pd + CH4, Pd + C2H6 (both C-C and C-H activation), and Pd + CH3Cl are presented, while ab-initio data of lesser quality were obtained for the catalytic hydrogenation of acetone and for the low-oxidation-state and high-oxidation-state mechanisms of the Heck reaction. "Kinetics" functionals such as mPW1K, PWB6K, BB1K, and BMK clearly perform more poorly for late-transition-metal reactions than for main-group reactions, as well as compared to general-purpose functionals. There is no single "best functional" for late-transition-metal reactions, but rather a cluster of several functionals (PBE0, B1B95, PW6B95, and TPSS25B95) that perform about equally well; if main-group thermochemical performance is additionally considered, then B1B95 and PW6B95 emerge as the best performers. TPSS25B95 and TPSS33B95 offer attractive performance compromises if weak interactions and main-group barrier heights, respectively, are also important. In the ab-initio calculations, basis set superposition errors (BSSE) can be greatly reduced by ensuring that the metal spd shell has sufficient radial flexibility in the high-exponent range. Optimal HF percentages in hybrid functionals depend on the class of systems considered, increasing from anions to neutrals to cations to main-group barrier heights; transition-metal barrier heights represent an intermediate situation. The use of meta-GGA correlation functionals appears to be quite beneficial.

Rozen's Epoxidation Reagent, CH3CN·HOF: A Theoretical Study of Its Structure, Vibrational Spectroscopy, and Reaction Mechanism

Rozen's epoxidation reagent, CH(3)CN.HOF, and a prototype epoxidation reaction employing it, have been subjected to an extensive ab initio and density functional study. Its anharmonic force field reveals a very strong red shift for the OH stretch and a strong blue shift for the HOF bend, in semiquantitative agreement with experiment. The very strong hydrogen bond (8.20 kcal/mol at the W1 level) not only serves to stabilize the reactant but also considerably lowers the barrier height for epoxidation of ethylene. Moreover, the reaction byproduct HF is found to act autocatalytically. The OH moiety acquires HO(+) character in the transition state. Our W1 benchmark data for the reaction profile allow the performance of various DFT functionals to be assessed. In general, "kinetics" functionals overestimate barrier heights, the BMK functional less so than the others. The B1B95 and TPSS33B95 meta-GGA functionals both perform very well, whereas general-purpose hybrid GGAs underestimate barrier heights. The simple PBE0 functional does reasonably well.

Unusual hydrogen bonding behavior in binary complexes of coinage metal anions with water

We have studied the interaction of atomic coinage metal anions with water molecules by infrared photodissociation spectroscopy of M-.H2O.Ar(n) clusters (M=Cu, Ag, Au; n=1, 2). We compare our observations with calculations on density-functional and coupled cluster levels of theory. The gold anion is bound to the water molecule by a single ionic hydrogen bond, similar to the halide-water complexes. In contrast, zero-point motion in the silver and copper complexes leads to a deviation from this motif.

Infrared spectra of O2- x (CO2)n clusters (n=1-6): asymmetric docking at the pi* orbital

Isolated superoxide ions solvated by CO2 have been studied by infrared photodissociation spectroscopy and density-functional theory, using CO2 evaporation upon infrared excitation of the O2- x (CO2)n (n=1-6) parent ions. We can assign the observed frequencies to the asymmetric stretch vibration and its combination bands with the symmetric stretch and the overtone of the bending vibration of CO2 in various binding situations. We interpret our findings with the help of density-functional theory. Our data suggest that only one CO2 moiety binds strongly to the O2-, whereas the rest of the CO2 molecules are weakly bound, which is consistent with the experimental spectra. The lobes of the pi* orbital of O2- provide a template for the structure of the microsolvation environment.

The infrared spectrum of Au−∙CO2

The Au-.CO2 ion-molecule complex has been studied by gas phase infrared photodissociation spectroscopy. Several sharp transitions can be identified as combination bands involving the asymmetric stretch vibrational mode of the CO2 ligand. Their frequencies are redshifted by several hundred cm(-1) from the frequencies of free CO2. We discuss our findings in the framework of ab initio and density-functional theory calculations, using anharmonic corrections to predict vibrational transition energies. The infrared spectrum is consistent with the formation of an aurylcarboxylate anion with a strongly bent CO2 subunit.

Development of density functionals for thermochemical kinetics

A density functional theory exchange-correlation functional for the exploration of reaction mechanisms is proposed. This functional, denoted BMK (Boese-Martin for Kinetics), has an accuracy in the 2 kcal/mol range for transition state barriers but, unlike previous attempts at such a functional, this improved accuracy does not come at the expense of equilibrium properties. This makes it a general-purpose functional whose domain of applicability has been extended to transition states, rather than a specialized functional for kinetics. The improvement in BMK rests on the inclusion of the kinetic energy density together with a large value of the exact exchange mixing coefficient. For this functional, the kinetic energy density appears to correct "back" the excess exact exchange mixing for ground-state properties, possibly simulating variable exchange.

W3 theory: Robust computational thermochemistry in the kJ/mol accuracy range

We are proposing a new computational thermochemistry protocol denoted W3 theory, as a successor to W1 and W2 theory proposed earlier [Martin and De Oliveira, J. Chem. Phys. 111, 1843 (1999)]. The new method is both more accurate overall (error statistics for total atomization energies approximately cut in half) and more robust (particularly towards systems exhibiting significant nondynamical correlation) than W2 theory. The cardinal improvement rests in an approximate account for post-CCSD(T) correlation effects. Iterative T3 (connected triple excitations) effects exhibit a basis set convergence behavior similar to the T3 contribution overall. They almost universally decrease molecular binding energies. Their inclusion in isolation yields less accurate results than CCSD(T) nearly across the board: It is only when T4 (connected quadruple excitations) effects are included that superior performance is achieved. T4 effects systematically increase molecular binding energies. Their basis set convergence is quite rapid, and even CCSDTQ/cc-pVDZ scaled by an empirical factor of 1.2532 will yield a quite passable quadruples contribution. The effect of still higher-order excitations was gauged for a subset of molecules (notably the eight-valence electron systems): T5 (connected quintuple excitations) contributions reach 0.3 kcal/mol for the pathologically multireference X 1Sigmag+ state of C2 but are quite small for other systems. A variety of avenues for achieving accuracy beyond that of W3 theory were explored, to no significant avail. W3 thus appears to represent a good compromise between accuracy and computational cost for those seeking a robust method for computational thermochemistry in the kJ/mol accuracy range on small systems.