One-Pot Graphene Supported Pt3Cu Nanoparticles-From Theory towards an Effective Molecular Oxygen Reduction Reaction Catalyst.

In this work, recent research progresses in the formation of Pt3Cu nanoparticles onto the surface of graphene are described, and the obtained results are contrasted with previously published theoretical studies. To form these nanoparticles, tetrabutylammonium hexachloroplatinate, and copper acetylacetonate are used as platinum and copper precursors, respectively. Oleylamine is used as a reductor and a solvent. The obtained catalyst is characterized via X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and energy dispersive spectroscopy X-ray (EDS). To assess the catalytic activity, the graphene-supported Pt3Cu material is tested with cyclic voltammetry, "CO stripping", and oxygen reduction reaction potentiodynamic curves to find the nature and the intrinsic electrochemical activity of the material. It can be observed that the tetrabutylammonium cation plays a critical role in anchoring and supporting nanoparticles over graphene, from which a broad discussion about the true nature of the anchoring mechanism was derived. The growth mechanism of the nanoparticles on the surface of graphene was observed, supporting the conducted theoretical models. With this study, a reliable, versatile, and efficient synthesis of nanocatalysts is presented, demonstrating the potentiality of Pt3Cu/graphene as an effective cathode catalyst. This study demonstrates the importance of reliable ab inito theoretical results as a useful source of information for the synthesis of the Pt3Cu alloy system.

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review.

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.

Transition-state searches in metal clusters by first-principle methods.

Elucidation of the chemical reactivity of metal clusters is often cumbersome due to the nonintuitive structures of the corresponding transition states. In this work, a hierarchical transition-state algorithm as implemented in the deMon2k code has been applied to locate transition states of small sodium clusters with 6-10 atoms. This algorithm combines the so-called double-ended interpolation method with the uphill trust region method. The minimum structures needed as input were obtained from Born-Oppenheimer molecular dynamics simulations. To connect the found transition states with the corresponding minimum structures, the intrinsic reaction coordinates were calculated. This work demonstrates how nonintuitive rearrangement mechanisms can be studied in metal clusters.

Magnetizability tensors from auxiliary density functional theory.

The working equations for the calculation of the magnetizability tensor in the framework of auxiliary density functional theory with gauge including atomic orbitals (ADFT-GIAO) are derived. Unlike in the corresponding conventional density functional theory implementations the numerical integration of the GIAOs is avoided in ADFT-GIAO. Our validation shows that this simplification has no effect on the accuracy of the methodology. As a result, a reliable and efficient implementation for the calculation of magnetizabilities of systems with more than 1000 atoms and 14,000 basis functions is presented.

NMR shielding tensors from auxiliary density functional theory.

The working equations for the calculation of NMR shielding tensors in the framework of auxiliary density functional theory are derived. It is shown that in this approach the numerical integration over gauge-including atomic orbitals can be avoided without the loss of accuracy. New integral recurrence relations for the required analytic electric-field-type integrals are derived. The computational performance of the resulting formalism permits shielding tensor calculations of systems with more than 1000 atoms and 15,000 basis functions.

Variational Density Fitting with a Krylov Subspace Method.

In this work, we present the implementation of a variational density fitting methodology that uses iterative linear algebra for solving the associated system of linear equations. It is well known that most difficulties with this system arise from the fact that the coefficient matrix is in general ill-conditioned and, due to finite precision round-off errors, it may not be positive definite. The dimensionality, given by the number of auxiliary functions, also poses a challenge in terms of memory and time demand since the coefficient matrix is dense. The methodology presented is based on a preconditioned Krylov subspace method able to deal with indefinite ill-conditioned equation systems. To assess its potential, it has been combined with double asymptotic electron repulsion integral expansions as implemented in the deMon2k package. A numerical study on a set of problems with up to 130,000 auxiliary functions shows its effectiveness to alleviate the abovementioned problematic. A comparison with the default methodology used in deMon2k based on a truncated eigenvalue decomposition of the coefficient matrix indicates that the proposed method exhibits excellent robustness and scalability when implemented in a parallel setting.

Robust and efficient density fitting.

In this paper we propose an iterative method for solving the inhomogeneous systems of linear equations associated with density fitting. The proposed method is based on a version of the conjugate gradient method that makes use of automatically built quasi-Newton preconditioners. The paper gives a detailed description of a parallel implementation of the new method. The computational performance of the new algorithms is analyzed by benchmark calculations on systems with up to about 35,000 auxiliary functions. Comparisons with the standard, direct approach show no significant differences in the computed solutions.

Boron-doped diamond: Investigation of the stability of surface-doping versus bulk-doping using cyclic cluster model calculations.

Boron-doped bulk diamond and the boron-doped hydrogen terminated (001) surface of diamond were investigated using the cyclic cluster model. Structure and stability of the hydrogen-terminated (001) surface were calculated and compared with experimental and other theoretical results from the literature. Boron-doping was modeled by substitution of a carbon atom by a boron atom in different positions with increasing distance from the surface up to boron-doped bulk diamond. In agreement with experiments on nanoclusters, boron is most stable in the first surface layers. (c) 2008 Wiley Periodicals, Inc. J Comput Chem, 2008.

How important are temperature effects for cluster polarizabilities?

State-of-the-art first-principle all-electron density functional theory calculations on small sodium clusters are performed to study the temperature dependency of their polarizabilities. For this purpose Born-Oppenheimer molecular dynamics simulations with more than 100,000 time steps (>200 ps) are recorded employing gradient corrected functionals in combination with a double-zeta valence polarization basis set. For each cluster 18 trajectories between 50 and 900 K are collected. The cluster polarizabilities are then calculated along these trajectories employing a triple-zeta valence polarization basis set augmented with field-induced polarization functions. The analysis of these calculations shows that the temperature dependency of the sodium cluster polarizabilities varies strongly with cluster size. For several clusters characteristic changes in the polarizability per atom as a function of temperature are observed. It is shown that the inclusion of finite temperature effects resolves the long-standing mismatch between calculated and measured sodium cluster polarizabilities.

Range-Separated Hybrid Functionals with Variational Fitted Exact Exchange.

This work presents a variationally fitted long-range exact exchange algorithm that can be used for the computation of range-separated hybrid density functionals in the linear combination of Gaussian type orbital (LCGTO) approximation. The obtained LCGTO energy and gradient expressions are free of four-center integrals and employ modified three-center integral recurrence relations to obtain optimal computational performance. The accuracy and performance of selected range-separated hybrid functionals with variational fitted long-range exact exchange are analyzed and discussed. A parallel implementation is presented and benchmarked.

First-Principle Calculations of Large Fullerenes.

State of-the-art density functional theory calculations have been performed for the large fullerenes C180, C240, C320, and C540 using the linear combination of Gaussian-type orbitals density functional theory (LCGTO-DFT) approach. For the calculations all-electron basis sets were employed. All fullerene structures were fully optimized without symmetry constrains. The analysis of the obtained structures as well as a study on the evolution of the bond lengths and calculated binding energies are presented. The fullerene results are compared to diamond and graphene which were calculated at the same level of theory. This represents the first systematic study on these large fullerenes based on nonsymmetry adapted first-principle calculations, and it demonstrates the capability of DFT calculations for energy and structure computations of large scale structures without any symmetry constraint.

Parallelization of the deMon2k code.

The parallelization of the LCGTO-KS-DFT code deMon2k is presented. The parallelization of the three-center electron repulsion integrals, the numerical integration using a direct grid algorithm and the matrix multiplication and diagonalization are described. The efficiency of the parallelization is analyzed by selected benchmark calculations. It is shown that geometry optimizations of systems with more than 8,000 basis functions are feasible on cluster architectures.

Separation of sigma and pi energies.

This work presents an all-electron density functional theory implementation of the separation of sigma and pi energies. On the basis of the separation of the electronic density, rho, into sigma and pi parts, an ansatz for the separation of the exchange-correlation energy is proposed. The behavior of the sigma and pi energy parts in benzene is investigated under different distortions. The effect of local and nonlocal functionals on the separation of the exchange-correlation energy is studied, too.

Bond energies for molecules, clusters, and deposit systems.

A new approach is suggested to the assignment of bond energies in molecules and clusters. It uses a shareholder principle for the redistribution of the shifts in atomic energies, which arise in a molecule, on the bonds. The scheme is directly suitable for semiempirical methods, where only one- and two-center terms occur. MSINDO calculations are performed to demonstrate the suitability of the approach for molecules and clusters. As an application the bonding in a deposit system is analyzed for the case of copper on magnesium oxide. It is found that copper atoms do not only bind to the preferred oxygen sites but also substantially to the magnesium sites. The copper-copper bonds are the strongest and will determine the structure of copper clusters on magnesium oxide surfaces.