PluginPlay: Enabling exascale scientific software one module at a time.

For many computational chemistry packages, being able to efficiently and effectively scale across an exascale cluster is a heroic feat. Collective experience from the Department of Energy's Exascale Computing Project suggests that achieving exascale performance requires far more planning, design, and optimization than scaling to petascale. In many cases, entire rewrites of software are necessary to address fundamental algorithmic bottlenecks. This in turn requires a tremendous amount of resources and development time, resources that cannot reasonably be afforded by every computational science project. It thus becomes imperative that computational science transition to a more sustainable paradigm. Key to such a paradigm is modular software. While the importance of modular software is widely recognized, what is perhaps not so widely appreciated is the effort still required to leverage modular software in a sustainable manner. The present manuscript introduces PluginPlay, https://github.com/NWChemEx-Project/PluginPlay, an inversion-of-control framework designed to facilitate developing, maintaining, and sustaining modular scientific software packages. This manuscript focuses on the design aspects of PluginPlay and how they specifically influence the performance of the resulting package. Although, PluginPlay serves as the framework for the NWChemEx package, PluginPlay is not tied to NWChemEx or even computational chemistry. We thus anticipate PluginPlay to prove to be a generally useful tool for a number of computational science packages looking to transition to the exascale.

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape.

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

Correction: Escape of anions from geminate recombination in THF due to charge delocalization.

Correction for 'Escape of anions from geminate recombination in THF due to charge delocalization' by Hung-Cheng Chen et al., Phys. Chem. Chem. Phys., 2017, 19, 32272-32285.

Escape of anions from geminate recombination in THF due to charge delocalization.

Geminate recombination of 24 radical anions (M˙-) with solvated protons (RH2+) was studied in tetrahydrofuran (THF) with pulse radiolysis. The recombination has two steps: (1) diffusion of M˙- and RH2+ together to form intimate (contact and solvent separated) ion pairs, driven by Coulomb attraction; (2) annihilation of anions due to proton transfer (PT) from RH2+ to M˙-. The non-exponential time-dependence of the geminate diffusion was determined. For all molecules protonated on O or N atoms the subsequent PT step is too fast (<0.2 ns) to measure, except for the anion of TCNE which did not undergo proton transfer. PT to C atoms was as slow as 70 ns and was always slow enough to be observable. A possible effect of charge delocalization on the PT rates could not be clearly separated from other factors. For 21 of the 24 molecules studied here, a free ion yield (71.6 ± 6.2 nmol J-1) comprising ∼29% of the total, was formed. This yield of "Type I" free ions is independent of the PT rate because it arises entirely by escape from the initial distribution of ion pair distances without forming intimate ion pairs. Three anions of oligo(9,9-dihexyl)fluorenes, Fn˙- (n = 2-4) were able to escape from intimate ion-pairs to form additional yields of "Type II" free ions with escape rate constants near 3 × 106 s-1. These experiments find no evidence for an inverted region for proton transfer.

Correlation Energy Extrapolation by Many-Body Expansion.

Accounting for electron correlation is required for high accuracy calculations of molecular energies. The full configuration interaction (CI) approach can fully capture the electron correlation within a given basis, but it does so at a computational expense that is impractical for all but the smallest chemical systems. In this work, a new methodology is presented to approximate configuration interaction calculations at a reduced computational expense and memory requirement, namely, the correlation energy extrapolation by many-body expansion (CEEMBE). This method combines a MBE approximation of the CI energy with an extrapolated correction obtained from CI calculations using subsets of the virtual orbitals. The extrapolation approach is inspired by, and analogous to, the method of correlation energy extrapolation by intrinsic scaling. Benchmark calculations of the new method are performed on diatomic fluorine and ozone. The method consistently achieves agreement with CI calculations to within a few mhartree and often achieves agreement to within ∼1 millihartree or less, while requiring significantly less computational resources.

Comparison of S-adsorption on (111) and (100) facets of Cu nanoclusters.

In order to gain insight into the nature of chemical bonding of sulfur atoms on coinage metal surfaces, we compare the adsorption energy and structural parameters for sulfur at four-fold hollow (4fh) sites on (100) facets and at three-fold hollow (3fh) sites on (111) facets of Cu nanoclusters. Consistent results are obtained from localized atomic orbital and plane-wave based density functional theory using the same functionals. PBE and its hybrid counterpart (PBE0 or HSE06) also give similar results. 4fh sites are preferred over 3fh sites with stronger bonding by ∼0.6 eV for nanocluster sizes above ∼280 atoms. However, for smaller sizes there are strong variations in the binding strength and the extent of the binding site preference. We show that suitable averaging over clusters of different sizes, or smearing the occupancy of orbitals, provide useful strategies to aid assessment of the behavior in extended surface systems. From site-projected density of states analysis using the smearing technique, we show that S adsorbed on a 4fh site has similar bonding interactions with the substrate as that on a 3fh site, but with much weaker antibonding interactions.

Mild partial deoxygenation of esters catalyzed by an oxazolinylborate-coordinated rhodium silylene.

An electrophilic, coordinatively unsaturated rhodium complex supported by borate-linked oxazoline, oxazoline-coordinated silylene, and N-heterocyclic carbene donors [{κ(3)-N,Si,C-PhB(Ox(Me2))(Ox(Me2)SiHPh)Im(Mes)}Rh(H)CO][HB(C6F5)3] (, Ox(Me2) = 4,4-dimethyl-2-oxazoline; Im(Mes) = 1-mesitylimidazole) is synthesized from the neutral rhodium silyl {PhB(Ox(Me2))2Im(Mes)}RhH(SiH2Ph)CO () and B(C6F5)3. The unusual oxazoline-coordinated silylene structure in is proposed to form by rearrangement of an unobserved isomeric cationic rhodium silylene species [{PhB(Ox(Me2))2Im(Mes)}RhH(SiHPh)CO][HB(C6F5)3] generated by H abstraction. Complex catalyzes reductions of organic carbonyl compounds with silanes to give hydrosilylation products or deoxygenation products. The pathway to these reactions is primarily influenced by the degree of substitution of the organosilane. Reactions with primary silanes give deoxygenation of esters to ethers, amides to amines, and ketones and aldehydes to hydrocarbons, whereas tertiary silanes react to give 1,2-hydrosilylation of the carbonyl functionality. In contrast, the strong Lewis acid B(C6F5)3 catalyzes the complete deoxygenation of carbonyl compounds to hydrocarbons with PhSiH3 as the reducing agent.