Harald Oberhofer

Report on the sixth blind test of organic crystal structure prediction methods

The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.

Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

We introduce a database (HAB11) of electronic coupling matrix elements (H(ab)) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute H(ab) values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q(-)) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, (<|H(ab)|(2)>)(1/2)=6.7 mH, is significantly higher than the value obtained for the minimum energy structure, |H(ab)|=3.8 mH. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q(-) in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

Charge constrained density functional molecular dynamics for simulation of condensed phase electron transfer reactions

We present a plane-wave basis set implementation of charge constrained density functional molecular dynamics (CDFT-MD) for simulation of electron transfer reactions in condensed phase systems. Following the earlier work of Wu and Van Voorhis [Phys. Rev. A 72, 024502 (2005)], the density functional is minimized under the constraint that the charge difference between donor and acceptor is equal to a given value. The classical ion dynamics is propagated on the Born-Oppenheimer surface of the charge constrained state. We investigate the dependence of the constrained energy and of the energy gap on the definition of the charge and present expressions for the constraint forces. The method is applied to the Ru2+-Ru3+ electron self-exchange reaction in aqueous solution. Sampling the vertical energy gap along CDFT-MD trajectories and correcting for finite size effects, a reorganization free energy of 1.6 eV is obtained. This is 0.1-0.2 eV lower than a previous estimate based on a continuum model for solvation. The smaller value for the reorganization free energy can be explained by the fact that the Ru-O distances of the divalent and trivalent Ru hexahydrates are predicted to be more similar in the electron transfer complex than for the separated aqua ions.

Prediction of reorganization free energies for biological electron transfer: a comparative study of Ru-modified cytochromes and a 4-helix bundle protein.

The acceleration of electron transfer (ET) rates in redox proteins relative to aqueous solutes can be attributed to the proteins ability to reduce the nuclear response or reorganization upon ET, while maintaining sufficiently high electronic coupling. Quantitative predictions of reorganization free energy remain a challenge, both experimentally and computationally. Using density functional calculations and molecular dynamics simulation with an electronically polarizable force field, we report reorganization free energies for intraprotein ET in four heme-containing ET proteins that differ in their protein fold, hydrophilicity, and solvent accessibility of the electron-accepting group. The reorganization free energies for ET from the heme cofactors of cytochrome c and b(5) to solvent exposed Ru-complexes docked to histidine residues at the surface of these proteins fall within a narrow range of 1.2-1.3 eV. Reorganization free energy is significantly lowered in a designed 4-helix bundle protein where both redox active cofactors are protected from the solvent. For all ET reactions investigated, the major components of reorganization are the solvent and the protein, with the solvent contributing close to or more than 50% of the total. In three out of four proteins, the protein reorganization free energy can be viewed as a collective effect including many residues, each of which contributing a small fraction. These results have important implications for the design of artificial electron transport proteins. They suggest that reorganization free energy may in general not be effectively controlled by single point mutations, but to a large extent by the degree of solvent exposure of the ionizable cofactors.

Chemical Activity of Thin Oxide Layers: Strong Interactions with the Support Yield a New Thin‐Film Phase of ZnO

Small Cu particles supported on and most likely activated by a ZnO substrate are the active component in the industrial catalyst used to convert syngas (H2, CO, CO2) into methanol, the third most important chemical product worldwide. Although a topic of intense research, the nature of the active site is still under debate. Recently, it has been pointed out that Zn atoms present at the surfaces of the Cu particles exhibit pronounced chemical activity and could explain some of the experimental findings. Another interesting suggestion is the presence of a thin layer of ZnOx species which forms on the surface of the Cu particles under reaction conditions. The importance of such thin oxide layers on the surface of metals under reaction conditions has already been pointed out in other contexts, where it was found that their chemical properties may differ substantially from those of the corresponding bulk oxides. In the case of ZnO this question is particularly interesting, since strong interactions between ZnO and the supporting metal have been reported for ZnO/ Cu and in recent work thin layers of ZnO have been shown to adopt a depolarized, graphitic structure, ZnO(gr), different from the wurtzite-type bulk. The properties of oxide thin films supported on metal substrates have been successfully studied in a number of cases, for example, for thin aluminum oxide films grown by oxidation of Ni/Al alloys. In contrast, the chemical activity of ZnO thin films supported on Cu single crystals has been investigated in a few cases only. Maroie et al. have investigated the adsorption and oxidation processes for single-crystal brass(110), brass(100), and brass(111) surfaces by X-ray photoelectron spectroscopy (XPS). Brass(110) and brass(111) show the same behavior with regard to the interaction with oxygen: the dissociative adsorption of oxygen on the surface is followed by the growth of thin ZnO layers. Wiame et al. reported that after oxidation of (111)-oriented Cu0.7Zn0.3 samples at room temperature the surface is covered by ZnO islands; it was suggested that these islands have (0001) and (0001) surface terminations. A more detailed characterization of the chemical properties of the thin ZnO layers was not carried out in this early work. In the present paper we report a detailed multitechnique investigation of a brass(111) single-crystal substrate (Cu/Zn ratio 9:1) subjected to different oxidation procedures using scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectroscopy (FTIR) under ultrahigh vacuum (UHV) conditions. The experimental findings are then interpreted by comparison with the results of a rather extensive set of density functional theory (DFT) calculations. Our results reveal the growth of thin ZnO adlayers with chemical properties that are markedly different from those of normal, wurtzite-type ZnO substrates. XPS data recorded for the brass(111) surface before and after different oxidation procedures for two different exit angles of the photoelectrons are shown in Figure 1. Since it is difficult to discriminate between Cu and Cu on the basis of XPS data, also the corresponding results from Auger electron spectroscopy (AES) are shown. For the clean brass(111) substrate the data indicate a Zn atom concentration of 5%, clearly lower than the 10% expected based on the bulk Cu/Zn ratio. Upon oxidation, the XPS data reveal an increase of the surface Zn concentration. Since it is a crucial question whether, in addition to Zn, also Cu or Cu is present, we have carefully analyzed the XPS and AES data. Neither in the Cu2p XPS data nor in the Cu L3M45M45 Auger data were the characteristic signatures of Cu or Cu species resulting from an oxidation of copper atoms detected. Cu exhibits a L3M45M45 peak at electron kinetic energies of 915 eV– 917 eV, which is clearly absent in the present data (see Figure 1). This observation, which agrees with the conclusions presented in a previous study by Rameshan et al., is expected, since in the presence of the less noble Zn one would expect the formation of ZnO to precede that of CuxO. Oxidation at elevated temperatures results in a substantial increase of the Zn signal, revealing the formation of thicker ZnO adlayers. The thickness of these thin ZnO layers was determined from the intensity of the Zn2p3/2 and Cu2p3/2 XPS signals. Exposure of the samples to 500 L of O2 at room temperature yields a ZnO adlayer with an average thickness of about 1.7 , consistent with the presence of a monolayer. More extended exposures to oxygen at room temperature did not result in a significant further increase of the thickness of the ZnO layer. Even the oxidation of the brass substrate at [*] Dr. V. Schott, Dr. A. Birkner, Dr. M. Xu, Dr. Y. Wang Chair of Physical Chemistry Ruhr-University Bochum (Germany)

Equilibrium free energies from fast-switching trajectories with large time steps

Jarzynskis [Phys. Rev. Lett. 78, 2690 (1997)] identity for the free-energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase-space mappings. Solving a systems equation of motion by approximate means generates a mapping that is perfectly valid for this purpose, regardless of how closely the solution mimics true time evolution. We exploit this fact, using crudely dynamical trajectories to compute free-energy differences that are in principle exact. Numerical simulations show that Newtons equation can be discretized to low order over very large time steps (limited only by the computers ability to represent resulting values of dynamical variables) without sacrificing thermodynamic accuracy. For computing the reversible work required to move a particle through a dense liquid, these calculations are more efficient than conventional fast-switching simulations by more than an order of magnitude. We also explore consequences of the phase-space mapping perspective for systems at equilibrium, deriving an exact expression for the statistics of energy fluctuations in simulated conservative systems.

On the inapplicability of electron-hopping models for the organic semiconductor Phenyl-C61-butyric Acid Methyl Ester (PCBM)

Phenyl-C61-butyric acid methyl ester (PCBM) is one of the most popular semiconductors in organic photovoltaic cells, but the electron-transport mechanism in the microcrystalline domains of this material as well as its preferred packing structure remain unclear. Here we use density functional theory to calculate electronic-coupling matrix elements, reorganization energies, and activation energies for available experimental and model crystal structures. We find that the picture of an excess electron hopping from one fullerene to another does not apply for any of the crystalline phases, rendering traditional rate equations inappropriate. We also find that the cohesive energy increases in the order body-centered-cubic < hexagonal < simple cubic < monoclinic < triclinic, independently of the type of dispersion correction used. Our results indicate that the coupled electron-ion dynamics needs to be solved explicitly to obtain a realistic description of charge transfer in this material.

Proton transfer drives protein radical formation in Helicobacter pylori catalase but not in Penicillium vitale catalase.

Heme catalases prevent cells from oxidative damage by decomposing hydrogen peroxide into water and molecular oxygen. Here we investigate the factors that give rise to an undesirable side reaction competing with normal catalase activity, the migration of a radical from the heme active site to the protein in the principal reaction intermediate compound I (Cpd I). Recently, it has been proposed that this electron transfer reaction takes place in Cpd I of Helicobacter pylori catalase (HPC), but not in Cpd I of Penicillium vitale catalase (PVC), where the oxidation equivalent remains located on the heme active site. Unraveling the factors determining the different radical locations could help engineer enzymes with enhanced catalase activity for detection or removal of hydrogen peroxide. Using quantum mechanics/molecular mechanics metadynamics simulations, we show that radical migration in HPC is facilitated by the large driving force (-0.65 eV) of the subsequent proton transfer from a histidine residue to the ferryl oxygen atom of reduced Cpd I. The corresponding free energy in PVC is significantly smaller (-0.19 eV) and, as we argue, not sufficiently high to support radical migration. Our results suggest that the energetics of oxoferryl protonation is a key factor regulating radical migration in catalases and possibly also in hydroperoxidases.

Charge Transport in Molecular Materials: An Assessment of Computational Methods

The booming field of molecular electronics has fostered a surge of computational research on electronic properties of organic molecular solids. In particular, with respect to a microscopic understanding of transport and loss mechanisms, theoretical studies assume an ever-increasing role. Owing to the tremendous diversity of organic molecular materials, a great number of computational methods have been put forward to suit every possible charge transport regime, material, and need for accuracy. With this review article we aim at providing a compendium of the available methods, their theoretical foundations, and their ranges of validity. We illustrate these through applications found in the literature. The focus is on methods available for organic molecular crystals, but mention is made wherever techniques are suitable for use in other related materials such as disordered or polymeric systems.