Gradient type optimization methods for electronic structure calculations

The density functional theory (DFT) in electronic structure calculations can be formulated as either a nonlinear eigenvalue or direct minimization problem. The most widely used approach for solving the former is the so-called self-consistent field (SCF) iteration. A common observation is that the convergence of SCF is not clear theoretically while approaches with convergence guarantee for solving the latter are often not competitive to SCF numerically. In this paper, we study gradient type methods for solving the direct minimization problem by constructing new iterations along the gradient on the Stiefel manifold. Global convergence (i.e., convergence to a stationary point from any initial solution) as well as local convergence rate follows from the standard theory for optimization on manifold directly. A major computational advantage is that the computation of linear eigenvalue problems is no longer needed. The main costs of our approaches arise from the assembling of the total energy functional and its gradient and the projection onto the manifold. These tasks are cheaper than eigenvalue computation and they are often more suitable for parallelization as long as the evaluation of the total energy functional and its gradient is efficient. Numerical results show that they can outperform SCF consistently on many practically large systems.Comment: 24 pages, 11 figures, 59 references, and 1 acknowledgement

Gradient-Driven Molecule Construction: An Inverse Approach Applied to the Design of Small-Molecule Fixating Catalysts

Rational design of molecules and materials usually requires extensive screening of molecular structures for the desired property. The inverse approach to deduce a structure for a predefined property would be highly desirable, but is, unfortunately, not well-defined. However, feasible strategies for such an inverse design process may be successfully developed for specific purposes. We discuss options for calculating 'jacket' potentials that fulfill a predefined target requirement - a concept that we recently introduced [T. Weymuth, M. Reiher, MRS Proceediungs, 2013, 1524, DOI:10.1557/opl.2012.1764]. We consider the case of small-molecule activating transition metal catalysts. As a target requirement we choose the vanishing geometry gradients on all atoms of a subsystem consisting of a metal center binding the small molecule to be activated. The jacket potential can be represented within a full quantum model or by a sequence of approximations of which a field of electrostatic point charges is the simplest. In a second step, the jacket potential needs to be replaced by a chemically viable chelate-ligand structure for which the geometry gradients on all of its atoms are also required to vanish. In order to analyze the feasibility of this approach, we dissect a known dinitrogen-fixating catalyst to study possible design strategies that must eventually produce the known catalyst.Comment: 40 pages, 6 tables, 5 figure

A Computational Methodology to Screen Activities of Enzyme Variants

We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction can be computed within 24 hours on roughly 10 processors. The methodology is based on the PM6 and MOZYME methods as implemented in MOPAC2009, and is tested on the first step of the amide hydrolysis reaction catalyzed by Candida Antarctica lipase B (CalB) enzyme. The barrier heights are estimated using adiabatic mapping and are shown to give barrier heights to within 3kcal/mol of B3LYP/6-31G(d)//RHF/3-21G results for a small model system. Relatively strict convergence criteria (0.5kcal/(mol{\AA})), long NDDO cutoff distances within the MOZYME method (15{\AA}) and single point evaluations using conventional PM6 are needed for reliable results. The generation of mutant structure and subsequent setup of the semiempirical calculations are automated so that the effect on barrier heights can be estimated for hundreds of mutants in a matter of weeks using high performance computing

Doping of graphene by a Au(111) substrate: Calculation strategy within the local density approximation and a semiempirical van der Waals approach

We have performed a density functional study of graphene adsorbed on Au(111) surface using both a local density approximation and a semiempirical van der Waals approach proposed by Grimme, known as the DFT-D2 method. Graphene physisorbed on metal has the linear dispersion preserved in the band-structure, but the Fermi level of the system is shifted with respect to the conical points which results in a doping effect. We show that the type and amount of doping depends not only on the choice of the exchange-correlation functional used in the calculations, but also on the supercell geometry that models the physical system. We analyzed how the factors such as the in-plane cell parameter and interlayer spacing in gold influence the Fermi level shift and we found that even a small variation in these parameters may cause a transition from p-type to n-type doping. We have selected a reasonable set of model parameters and obtained that graphene is either undoped or at most slightly p-type doped on the clean Au(111) surface, which seems to be in line with experimental findings. On the other hand, modifications of the substrate lattice may induce larger doping up to 0.30-0.40 eV depending on the graphene-metal adsorption distance. The sensitivity of the graphene-gold interface to the structural parameters may allow to tune doping across the samples which could lead to possible applications in graphene-based electronic devices. We believe that the present remarks can be also useful for other studies based on the periodic DFT

Evolution of electronic and ionic structure of Mg-clusters with the growth cluster size

The optimized structure and electronic properties of neutral and singly charged magnesium clusters have been investigated using ab initio theoretical methods based on density-functional theory and systematic post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. We have systematically calculated the optimized geometries of neutral and singly charged magnesium clusters consisting of up to 21 atoms, electronic shell closures, binding energies per atom, ionization potentials and the gap between the highest occupied and the lowest unoccupied molecular orbitals. We have investigated the transition to the hcp structure and metallic evolution of the magnesium clusters, as well as the stability of linear chains and rings of magnesium atoms. The results obtained are compared with the available experimental data and the results of other theoretical works.Comment: 30 pages, 10 figures, 3 table

New Approaches for ab initio Calculations of Molecules with Strong Electron Correlation

Reliable quantum chemical methods for the description of molecules with dense-lying frontier orbitals are needed in the context of many chemical compounds and reactions. Here, we review developments that led to our newcomputational toolbo x which implements the quantum chemical density matrix renormalization group in a second-generation algorithm. We present an overview of the different components of this toolbox.Comment: 19 pages, 1 tabl