DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations

Kästner, Johannes; Carr, Joanne M.; Keal, Thomas W.; Thiel, Walter; Wander, A.; Sherwood, Paul

doi:10.1021/jp9028968

Cited by 571 publications

(559 citation statements)

References 56 publications

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“…The systems are simulated in an NVT ensemble (the ensemble with constant number of particles, constant volume and constant temperature), where the particle mesh Ewald summation 32 is used to describe a long-range Coulombic coupling. In each classical simulation, we first minimize the system energy and then equilibrate the system for B10 ns at T ¼ 300 K. In the quantum MD simulations, we use TeraChem [33][34][35] with energies and forces evaluated using the Becke, Lee, Yang and Parr exchange-correlation functional with a 3-21-g basis set and charges calculated within the Mulliken scheme ( Supplementary Fig. 9).…”

Section: Methodsmentioning

confidence: 99%

Chemical sensing with switchable transport channels in graphene grain boundaries

et al. 2014

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Grain boundaries can markedly affect the electronic, thermal, mechanical and optical properties of a polycrystalline graphene. While in many applications the presence of grain boundaries in graphene is undesired, here we show that they have an ideal structure for the detection of chemical analytes. We observe that an isolated graphene grain boundary has B300 times higher sensitivity to the adsorbed gas molecules than a single-crystalline graphene grain. Our electronic structure and transport modelling reveal that the ultrasensitivity in grain boundaries is caused by a synergetic combination of gas molecules accumulation at the grain boundary, together with the existence of a sharp onset energy in the transmission spectrum of its conduction channels. The discovered sensing platform opens up new pathways for the design of nanometre-scale highly sensitive chemical detectors.

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Section: Methodsmentioning

confidence: 99%

Chemical sensing with switchable transport channels in graphene grain boundaries

et al. 2014

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“…Geometry optimizations in the gas phase on molSimplify-generated 86 structures were carried out using the L-BFGS algorithm in Cartesian coordinates as implemented in DL-FIND 87 .…”

Section: Computational Detailsmentioning

confidence: 99%

Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation

2016

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Selective ion separation is a major challenge with far-ranging impact from water desalination to product separation in catalysis. Recently introduced ferrocenium(Fc + )/ferrocene(Fc) polymer electrode materials have been demonstrated experimentally and theoretically to selectively bind carboxylates over perchlorate through weak C-H … O hydrogen bond (HB) interactions that favor carboxylates, despite the comparable size and charge of the two species. However, practical application of this technology in aqueous environments requires further selectivity enhancement. Using a first-principles discovery approach, we investigate the effect of Fc/Fc + functional groups (FGs) on the selectivity and reversibility of formate-Fc + adsorption with respect to perchlorate in aqueous solution. Our wide design space of 44 FGs enables identification of FGs with higher selectivity and rationalization of trends through electronic energy decomposition analysis or geometric hydrogen bonding analysis. Overall, we observe weaker, longer HBs for perchlorate as compared to formate with Fc + . We further identify Fc + functionalizations that simultaneously increase selectivity for formate in aqueous environments but permit rapid release from neutral Fc. We introduce the materiaphore, a 3D abstraction of these design rules, to help guide nextgeneration material optimization for selective ion sorption. This approach is expected to have broad relevance in computational discovery for molecular recognition, sensing, separations, and catalysis.2

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“…Instanton theory as implemented in DL-FIND (Kästner et al 2009;Rommel et al 2011) is used in this study on the potential energy surface (PES) of Li & Guo (2015) which is fitted to CCSD(T)-F12/AVTZ data. The Feynman paths of the instantons are discretized to 200 images.…”

Section: Computational Detailsmentioning

confidence: 99%

Importance of tunneling in H-abstraction reactions by OH radicals

Lamberts

Fedoseev

Kästner

et al. 2017

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We present a combined experimental and theoretical study focussing on the quantum tunneling of atoms in the reaction between CH 4 and OH. The importance of this reaction pathway is derived by investigating isotope substituted analogs. Quantitative reaction rates needed for astrochemical models at low temperature are currently unavailable both in the solid state and in the gas phase. Here, we study tunneling effects upon hydrogen abstraction in CH 4 + OH by focusing on two reactions: CH 4 + OD − − → CH 3 + HDO and CD 4 + OH − − → CD 3 + HDO. The experimental study shows that the solid-state reaction rate R CH 4 +OD is higher than R CD 4 +OH at 15 K. Experimental results are accompanied by calculations of the corresponding unimolecular and bimolecular reaction rate constants using instanton theory taking into account surface effects. For the work presented here, the unimolecular reactions are particularly interesting as these provide insight into reactions following a Langmuir-Hinshelwood process. The resulting ratio of the rate constants shows that the H abstraction (k CH 4 +OD ) is approximately ten times faster than D-abstraction (k CD 4 +OH ) at 65 K. We conclude that tunneling is involved at low temperatures in the abstraction reactions studied here. The unimolecular rate constants can be used by the modeling community as a first approach to describe OH-mediated abstraction reactions in the solid phase. For this reason we provide fits of our calculated rate constants that allow the inclusion of these reactions in models in a straightforward fashion.

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DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations

Cited by 571 publications

References 56 publications

Chemical sensing with switchable transport channels in graphene grain boundaries

Chemical sensing with switchable transport channels in graphene grain boundaries

Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation

Importance of tunneling in H-abstraction reactions by OH radicals

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