Cluster structures influenced by interaction with a surface.

Clusters on surfaces are vitally important for nanotechnological applications. Clearly, cluster-surface interactions heavily influence the preferred cluster structures, compared to clusters in vacuum. Nevertheless, systematic explorations and an in-depth understanding of these interactions and how they determine the cluster structures are still lacking. Here we present an extension of our well-established non-deterministic global optimization package OGOLEM from isolated clusters to clusters on surfaces. Applying this approach to intentionally simple Lennard-Jones test systems, we produce a first systematic exploration that relates changes in cluster-surface interactions to resulting changes in adsorbed cluster structures.

Globally-Optimized Local Pseudopotentials for (Orbital-Free) Density Functional Theory Simulations of Liquids and Solids.

The accuracy of local pseudopotentials (LPSs) is one of two major determinants of the fidelity of orbital-free density functional theory (OFDFT) simulations. We present a global optimization strategy for LPSs that enables OFDFT to reproduce solid and liquid properties obtained from Kohn-Sham DFT. Our optimization strategy can fit arbitrary properties from both solid and liquid phases, so the resulting globally optimized local pseudopotentials (goLPSs) can be used in solid and/or liquid-phase simulations depending on the fitting process. We show three test cases proving that we can (1) improve solid properties compared to our previous bulk-derived local pseudopotential generation scheme; (2) refine predicted liquid and solid properties by adding force matching data; and (3) generate a from-scratch, accurate goLPS from the local channel of a non-local pseudopotential. The proposed scheme therefore serves as a full and improved LPS construction protocol.

libKEDF: An accelerated library of kinetic energy density functionals.

Kinetic energy density functionals (KEDFs) approximate the kinetic energy of a system of electrons directly from its electron density. They are used in electronic structure methods that lack direct access to orbitals, for example, orbital-free density functional theory (OFDFT) and certain embedding schemes. In this contribution, we introduce libKEDF, an accelerated library of modern KEDF implementations that emphasizes nonlocal KEDFs. We discuss implementation details and assess the performance of the KEDF implementations for large numbers of atoms. We show that using libKEDF, a single computing node or (GPU) accelerator can provide easy computational access to mesoscale chemical and materials science phenomena using OFDFT algorithms. © 2017 Wiley Periodicals, Inc.

Potential Functional Embedding Theory at the Correlated Wave Function Level. 2. Error Sources and Performance Tests.

Quantum mechanical embedding theories partition a complex system into multiple spatial regions that can use different electronic structure methods within each, to optimize trade-offs between accuracy and cost. The present work incorporates accurate but expensive correlated wave function (CW) methods for a subsystem containing the phenomenon or feature of greatest interest, while self-consistently capturing quantum effects of the surroundings using fast but less accurate density functional theory (DFT) approximations. We recently proposed two embedding methods [for a review, see: Acc. Chem. Res. 2014 , 47 , 2768 ]: density functional embedding theory (DFET) and potential functional embedding theory (PFET). DFET provides a fast but non-self-consistent density-based embedding scheme, whereas PFET offers a more rigorous theoretical framework to perform fully self-consistent, variational CW/DFT calculations [as defined in part 1, CW/DFT means subsystem 1(2) is treated with CW(DFT) methods]. When originally presented, PFET was only tested at the DFT/DFT level of theory as a proof of principle within a planewave (PW) basis. Part 1 of this two-part series demonstrated that PFET can be made to work well with mixed Gaussian type orbital (GTO)/PW bases, as long as optimized GTO bases and consistent electron-ion potentials are employed throughout. Here in part 2 we conduct the first PFET calculations at the CW/DFT level and compare them to DFET and full CW benchmarks. We test the performance of PFET at the CW/DFT level for a variety of types of interactions (hydrogen bonding, metallic, and ionic). By introducing an intermediate CW/DFT embedding scheme denoted DFET/PFET, we show how PFET remedies different types of errors in DFET, serving as a more robust type of embedding theory.

Potential Functional Embedding Theory at the Correlated Wave Function Level. 1. Mixed Basis Set Embedding.

Embedding theories offer an elegant solution to overcome intrinsic algorithmic scaling and accuracy limitations of simulation methods. These theories also promise to achieve the accuracy of high-level electronic structure techniques at near the computational cost of much less accurate levels of theory by exploiting positive traits of multiple methods. Of crucial importance to fulfilling this promise is the ability to combine diverse theories in an embedding simulation. However, these methods may utilize different basis set and electron-ion potential representations. In this first part of a two-part account of implementing potential functional embedding theory (PFET) at a correlated wave function level, we discuss remedies to basis set and electron-ion potential discrepancies and assess the performance of the PFET scheme with mixed basis sets.

Error-Safe, Portable, and Efficient Evolutionary Algorithms Implementation with High Scalability.

We present an efficient massively parallel implementation of genetic algorithms for chemical and materials science problems, solely based on Java virtual machine (JVM) technologies and standard networking protocols. The lack of complicated dependencies allows for a highly portable solution exploiting strongly heterogeneous components within a single computational context. At runtime, our implementation is almost completely immune to hardware failure, and additional computational resources can be added or subtracted dynamically, if needed. With extensive testing, we show that despite all these benefits, parallel scalability is excellent.

Density functional theory + U analysis of the electronic structure and defect chemistry of LSCF (La0.5Sr0.5Co0.25Fe0.75O3-δ).

Reducing operating temperatures is a key step in making solid oxide fuel cell (SOFC) technology viable. A promising strategy for accomplishing this goal is employing mixed ion-electron conducting (MIEC) cathodes. La1-xSrxCo1-yFeyO3-δ (LSCF) is the most widely employed MIEC cathode material; however, rational optimization of the composition of LSCF requires fundamental insight linking its electronic structure to its defect chemistry. To provide the necessary insight, density functional theory plus U (DFT+U) calculations are used to investigate the electronic structure of LSCF (xSr = 0.50, yCo = 0.25). The DFT+U calculations show that LSCF has a significantly different electronic structure than La1-xSrxFeO3 because of the addition of cobalt, but that minimal electronic structure differences exist between La0.5Sr0.5Co0.25Fe0.75O3 and La0.5Sr0.5Co0.5Fe0.5O3. The oxygen vacancy formation energy (ΔEf,vac) is calculated for residing in different local environments within La0.5Sr0.5Co0.25Fe0.75O3. These results show that configurations have the highest ΔEf,vac, while have the lowest ΔEf,vac and may act as traps for . We conclude that compositions with more Fe than Co are preferred because the additional sites would lead to higher overall ΔEf,vac (and lower concentrations), while the trapping strength of the sites is relatively weak (∼0.3 eV).

Observable-targeting global cluster structure optimization.

Traditionally, global cluster structure optimization is done by minimizing energy. As an alternative, we propose minimizing the difference between actual experimental observables and their simulated counterparts. To validate and explain this approach, test cases for small clusters are shown. Additionally, an application to real-life data for a larger cluster illustrates the advantages of this method: it provides direct links between properties and structure, and avoids problems both with insufficient accuracy in theoretical energy-ordering and with non-equilibrium conditions in experiment.

Bond dissociation energies of C10 and C18 methyl esters from local multireference averaged-coupled pair functional theory.

We previously developed a fast, local, reduced scaling Cholesky-decomposed multireference averaged-coupled pair functional (CD-LMRACPF2) method, which takes advantage of the locality of dynamic correlation and numerical approximations such as Cholesky decomposition and integral screening. Motivated by the desire to study large biodiesel methyl ester molecules, here we validate CD-LMRACPF2 for the computation of bond dissociation energies (BDEs) in a suite of oxygenated molecules, and show that the low-cost method is very accurate compared to the conventional variant. We then demonstrate the power of CD-LMRACPF2 for fast and accurate computation of energies of molecules containing up to 13 second-row atoms within a polarized triple-ζ (cc-pVTZ) basis set. We use biodiesel methyl esters as a chemically interesting model system and furnish BDEs of C10 and C18 methyl esters, with the latter performed within a cc-pVDZ basis set. We describe trends in the BDEs and explain how structural (isomeric) differences affect BDEs, as well as discuss implications of BDE trends for biodiesel physical and chemical properties.

A graph-based short-cut to low-energy structures.

A new graph-based move class for global optimization of cluster structures is presented. Its performance and efficiency is analyzed for water clusters (H2O)n, n = 24, 61. This analysis indicates superior basin exploitation capabilities of the new move class for large clusters, compared to traditional moves.

A size resolved investigation of large water clusters.

Size selected water clusters are generated by photoionizing sodium doped clusters close to the ionization threshold. This procedure is free of fragmentation. Upon infrared excitation, size- and isomer-specific OH-stretch spectra are obtained over a large range of cluster sizes. In one application of this method the infrared spectra of single water cluster sizes are investigated. A comparison with calculations, based on structures optimized by genetic algorithms, has been made to tentatively derive cluster structures which reproduce the experimental spectra. We identified a single all-surface structure for n = 25 and mixtures with one or two interior molecules for n = 24 and 32. In another application the sizes are determined at which the crystallization sets in. Surprisingly, this process strongly depends on the cluster temperature. The crystallization starts at sizes below n = 200 at higher temperatures and the onset is shifted to sizes above n = 400 at lower temperatures.

Heteroaromaticity approached by charge density investigations and electronic structure calculations.

In this paper we present the results of a high-resolution single crystal X-ray diffraction experiment at 15 K on a benzothiazol-substituted phosphane and a subsequent charge density study based on multipole refinement and a topological analysis according to Bader's quantum theory of atoms in molecules. Although two valence shell charge concentrations (VSCCs) in the non-bonding region of each phosphorus and sulfur atom were found, the integration of both heteroatomic basins emphasizes charge depletion. Nevertheless they are attractive for C-H···P and C-H···S hydrogen bonding in the solid state. The nature of the P-C bonds and the question of aromaticity in the heterocycles were subject to our investigations. The ellipticities along the bonds were analysed to approach delocalization. The source function is employed to visualise atomic contributions to aromaticity. Theoretical calculations have been carried out to compute nuclear chemical shifts, induced ring currents and a variety of delocalization indices. All applied measures for delocalization point in the same direction: while heteroaromaticity is present in the benzothiazolyl substituents, the bridging P-C bonds are only involved marginally, almost preventing total conjugation of the phosphane. The charge density distributions around the phosphorus and the sulfur atoms have very similar features but turn out to be chemically very different from each other. Commonly used simplifying concepts have difficulties in providing a comprehensive view on the electronic situation in the molecule. Our results raise doubts on the validity of the common interpretation of VSCCs as one-to-one representations of Lewis lone pairs.

Relative anion binding affinity in a series of interpenetrated coordination cages.

Previously, we have reported on the quantitative self-assembly of a series of interpenetrated double-cages [Pd4Ligand8] with ligands based on various organic backbones. For dibenzosuberone-based cages it was shown that anion binding in the outer two pockets follows an allosteric mechanism. Herein we wish to report the anion binding capabilities of three related phenothiazine cages. We present a systematic comparison of the relative halide (Cl(-) and Br(-)) binding affinities and the structural rearrangements of four double-cages based on NMR titrations, NOESY experiments and electronic structure calculations.

The layered structure of [Na(NH3)4][Indenide] containing a square-planar Na(NH3)4(+) cation.

It's hip to be a square! The ammines [Li(NH(3))(4)][Ind] and [Na(NH(3))(4)][Ind] both contain a cation coordinated by four ammonia molecules. Whereas the first shows the anticipated tetrahedral coordination, in the second the metal coordination is unexpectedly square-planar. The solvent-separated ion pair forms a rippled layer structure of alternating planar Na(NH(3))(4)(+) cations and indenyl carbanions that is attributed to NH(3) ⋅⋅⋅π hydrogen bonds.

A push-and-pull model for allosteric anion binding in cage complexes.

A series of electronic structure calculations has been carried out on an artificial anion binding host. The compound with four Pd(II) cations and a total of eight bis-monodentate pyridyl ligands forms by self-assembly an interpenetrated double cage with three binding pockets. Through the use of a simple push-and-pull model connecting the potentials of the different sites, we are able to explain the allosteric effect observed in anion binding. Two factors seem to be particularly significant in the latter, namely the flatness of the potential in each binding pocket as well as the length of the ligand. Our results are found to be in excellent agreement with the experimentally observed structures.

Structural diversity in sodium doped water trimers.

The structures of sodium doped water trimers are characterized on the basis of their infrared action spectra in the OH-stretching region and a global optimization approach to identify the lowest energy minima. The most stable structure is an open ring with two contacts of terminal water molecules to the Na atom. This structure explains the dominating feature in the IR depletion spectrum around 3410 cm(-1). Three additional isomer classes were found in an energy window of 12 kJ mol(-1) with vertical ionization energies ranging from ∼3.83 eV to ∼4.36 eV. These structures show different hydrogen bonding and sodium coordination patterns and are identified by specific spectral features in the IR spectra. The significant abundance of closed rings with an external Na atom, resembling the undoped water trimer, suggests that for larger clusters the picture of the sodium atom being situated on the cluster surface seems adequate.

Computation of induced dipoles in molecular mechanics simulations using graphics processors.

In this work, we present a tentative step toward the efficient implementation of polarizable molecular mechanics force fields with GPU acceleration. The computational bottleneck of such applications is found in the treatment of electrostatics, where higher-order multipoles and a self-consistent treatment of polarization effects are needed. We have implemented a GPU accelerated code, based on the Tinker program suite, for the computation of induced dipoles. The largest test system used shows a speedup factor of over 20 for a single precision GPU implementation, when comparing to the serial CPU version. A discussion of the optimization and parametrization steps is included. Comparison between different graphic cards and CPU-GPU embedding is also given. The current work demonstrates the potential usefulness of GPU programming in accelerating this field of applications.

Monomeric Sn(II) and Ge(II) hydrides supported by a tridentate pincer-based ligand.

Herein we report the syntheses of terminal Sn(II) (3) and Ge(II) (4) hydrides from the corresponding chloride precursors [{2,6-iPr(2)C(6)H(3)NCMe}(2)C(6)H(3)MCl] (M = Sn (1), Ge (2)) using [K{B(sec-Bu)(3)}H] as a hydrogenating agent. Combination of steric shielding and intramolecular N → M interactions resulted in the protection of M(II)-H bonds.

Atomdroid: a computational chemistry tool for mobile platforms.

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.