An abiotic analogue of the diiron(IV)oxo "diamond core" of soluble methane monooxygenase generated by direct activation of O2 in aqueous Fe(II)/EDTA solutions: thermodynamics and electronic structure

We study the generation of a dinuclear Fe(IV)oxo species, [EDTAH·FeO·OFe·EDTAH](2-), in aqueous solution at room temperature using Density Functional Theory (DFT) and Ab Initio Molecular Dynamics (AIMD). This species has been postulated as an intermediate in the multi-step mechanism of autoxidation of Fe(II) to Fe(III) in the presence of atmospheric O(2) and EDTA ligand in water. We examine the formation of [EDTAH·FeO·OFe·EDTAH](2-) by direct cleavage of O(2), and the effects of solvation on the spin state and O-O cleavage barrier. We also study the reactivity of the resulting dinuclear Fe(IV)oxo system in CH(4) hydroxylation, and its tendency to decompose to mononuclear Fe(IV)oxo species. The presence of the solvent is shown to play a crucial role, determining important changes in all these processes compared to the gas phase. We show that, in water solution, [EDTAH·FeO·OFe·EDTAH](2-) (as well as its precursor [EDTAH·Fe·O(2)·Fe·EDTAH](2-)) exists as stable species in a S = 4 ground spin state when hydrogen-bonded to a single water molecule. Its structure comprises two facing Fe(IV)oxo groups, in an arrangement similar to the one evinced for the active centre of intermediate Q of soluble Methane Monooxygenase (sMMO). The inclusion of the water molecule in the complex decreases the overall symmetry of the system, and brings about important changes in the energy and spatial distribution of orbitals of the Fe(IV)oxo groups relative to the gas phase. In particular, the virtual 3σ* orbital of one of the Fe(IV)oxo groups experiences much reduced repulsive orbital interactions from ligand orbitals, and its consequent stabilisation dramatically enhances the electrophilic character of the complex, compared to the symmetrical non-hydrated species, and its ability to act as an acceptor of a H atom from the CH(4) substrate. The computed free energy barrier for H abstraction is 28.2 kJ mol(-1) (at the BLYP level of DFT), considerably below the gas phase value for monomeric [FeO·EDTAH](-), and much below the solution value for the prototype hydrated ferryl ion [FeO(H(2)O)(5)](2+).     

Modeling solvent effects on electron-spin-resonance hyperfine couplings by frozen-density embedding

In this study, we investigate the performance of the frozen-density embedding scheme within density-functional theory [J. Phys. Chem. 97, 8050 (1993)] to model the solvent effects on the electron-spin-resonance hyperfine coupling constants (hfcc's) of the H2NO molecule. The hfcc's for this molecule depend critically on the out-of-plane bending angle of the NO bond from the molecular plane. Therefore, solvent effects can have an influence on both the electronic structure for a given configuration of solute and solvent molecules and on the probability for different solute (plus solvent) structures compared to the gas phase. For an accurate modeling of dynamic effects in solution, we employ the Car-Parrinello molecular-dynamics (CPMD) approach. A first-principles-based Monte Carlo scheme is used for the gas-phase simulation, in order to avoid problems in the thermal equilibration for this small molecule. Calculations of small H2NO-water clusters show that microsolvation effects of water molecules due to hydrogen bonding can be reproduced by frozen-density embedding calculations. Even simple sum-of-molecular-densities approaches for the frozen density lead to good results. This allows us to include also bulk solvent effects by performing frozen-density calculations with many explicit water molecules for snapshots from the CPMD simulation. The electronic effect of the solvent at a given structure is reproduced by the frozen-density embedding. Dynamic structural effects in solution are found to be similar to the gas phase. But the small differences in the average structures still induce significant changes in the computed shifts due to the strong dependence of the hyperfine coupling constants on the out-of-plane bending angle.     

Step structure in the atomic Kohn-Sham potential

In this work we analyze the exchange-correlation potentialv _xc within the Kohn-Sham approach to density functional theory for the case of atomic systems. The exchange-correlation potential is written as the sum of two potentials. One of these potentialsv _xc,scr is the long-range. Coulombic potential of the coupling constant integrated exchange-correlation hole which represents the screening of the two-particle interactions due to exchange-correlation effects. The other potentialv _xc,scr ^resp contains the functional derivative with respect to the electron density of the coupling constant integrated pair-correlation function representing the sensitivity of this exchange-correlation screening to density variations. As explicit expression of the exchange-part of this functional derivative is derived using an approximation for the Greens function of the Kohn-Sham system and is shown to display a distinct atomic shell structure. The corresponding potentialv _xc,scr ^resp has a clear step structure and is constant within the atomic shells and changes rapidly at the atomic shell boundaries. Numerical examples are presented for the Be and Kr atoms using the Optimized Potential Model (OPM).     

Natural energy orbitals and the one-particle Green's function

It is shown how the properties of the one-particle Green's function lead naturally to the definition of the so-called natural energy orbitals. These orbitals allow the fully correlated total energy of a system to be written in Hartree–Fock-like fashion and might therefore provide a bridge between sophisticated correlated wave functions and approximate theories of chemical structure and reactivity based on a Hartree–Fock-like energy expression. Moreover these orbitals form the basis for a self-consistent scheme to calculate the one-particle Green's function. The relation between these natural energy orbitals and the extended Koopmans' theorem is considered. Finally it is shown that the exactness of the lowest extended Koopmans' ionization potential implies the linear independence of the corresponding Dyson orbital from all other Dyson orbitals.     

Predicting catalysis: understanding ammonia synthesis from first-principles calculations

Here, we give a full account of a large collaborative effort toward an atomic-scale understanding of modern industrial ammonia production over ruthenium catalysts. We show that overall rates of ammonia production can be determined by applying various levels of theory (including transition state theory with or without tunneling corrections, and quantum dynamics) to a range of relevant elementary reaction steps, such as N(2) dissociation, H(2) dissociation, and hydrogenation of the intermediate reactants. A complete kinetic model based on the most relevant elementary steps can be established for any given point along an industrial reactor, and the kinetic results can be integrated over the catalyst bed to determine the industrial reactor yield. We find that, given the present uncertainties, the rate of ammonia production is well-determined directly from our atomic-scale calculations. Furthermore, our studies provide new insight into several related fields, for instance, gas-phase and electrochemical ammonia synthesis. The success of predicting the outcome of a catalytic reaction from first-principles calculations supports our point of view that, in the future, theory will be a fully integrated tool in the search for the next generation of catalysts.     

H-bond contribution to the Compton profile of water

Self-consistent wavefunctions are obtained in the HFX Xα model for a free water molecule as well as dimers and trimers. The dimer and trimer results are synthesized to deduce the contribution of the hydrogen bond to the Compton profile of water. This offers a very reasonable explanation for a substantial part of the difference between theoretical calculation on a free water molecule and experiment.     

Charge transfer, double and bond-breaking excitations with time-dependent density matrix functional theory

Time-dependent density functional theory (TDDFT) in its current adiabatic implementations exhibits three remarkable failures: (a) completely wrong behavior of the excited state surface along a bond-breaking coordinate; (b) lack of doubly excited configurations; (c) much too low charge transfer excitation energies. These TDDFT failure cases are all strikingly exhibited by prototype two-electron systems such as dissociating H2 and HeH+. We find for these systems with time-dependent density matrix functional theory that: (a) Within previously formulated simple adiabatic approximations, the bonding-to-antibonding excited state surface as well as charge transfer excitations are described without problems, but not the double excitations; (b) An adiabatic approximation is formulated in which also the double excitations are fully accounted for.     

Signatures of counter-ion association and hydrogen bonding in vibrational circular dichroism spectra

We study the effect of counter-ion complexation on the example of Cl(-) ions interacting with the [Co(en)(3)](3+) complex. The H-bonding of the N-H groups of the ethylenediamine (en) ligands with the Cl(-) ions may lead to giant enhancement of the VCD intensity for the N-H stretches, but may also lead to VCD sign changes in the finger print region of N-H wagging, twisting and scissoring motions. Such sign changes should not be mistaken for signatures of the presence of the other enantiomer. We elucidate the mechanism for the sign changes and give a recommendation on how to deal with this problem. We also show that the experimental spectrum is only in good accord with the calculations if complexation of 5 Cl(-) ions (two axial, three equatorial) is assumed, but not with two (axial) or three (equatorial) Cl(-) ions, thus showing the potential of VCD to be used as an experimental probe for complexation.