Fueled by advances in hardware and algorithm design,
large-scale
automated explorations of chemical reaction space have become possible.
Here, we present our approach to an open-source, extensible framework
for explorations of chemical reaction mechanisms based on the first-principles
of quantum mechanics. It is intended to facilitate reaction network
explorations for diverse chemical problems with a wide range of goals
such as mechanism elucidation, reaction path optimization, retrosynthetic
path validation, reagent design, and microkinetic modeling. The stringent
first-principles basis of all algorithms in our framework is key for
the general applicability that avoids any restrictions to specific
chemical systems. Such an agile framework requires multiple specialized
software components of which we present three modules in this work.
The key module, Chemoton, drives the exploration of reaction
networks. For the exploration itself, we introduce two new algorithms
for elementary-step searches that are based on Newton trajectories.
The performance of these algorithms is assessed for a variety of reactions
characterized by a broad chemical diversity in terms of bonding patterns
and chemical elements. Chemoton successfully recovers the
vast majority of these. We provide the resulting data, including large
numbers of reactions that were not included in our reference set,
to be used as a starting point for further explorations and for future
reference.
Several density functional approaches have been considered for their ability to predict enthalpies of formation and bond dissociation energies for lanthanide-containing molecules. To enable comparison with experiment, the Ln54 set, introduced here, is compiled to include lanthanides both in the common 3+ oxidation state as well as in more exotic oxidation states. Due to the magnitude of the experimental uncertainties a "lanthanide chemical accuracy" of 5.0 kcal mol(-1) is proposed. The density functionals considered span the full range of complexity from LDA through double hybrids. The performance of the density functionals is assessed for each class of lanthanide-containing molecules and for the Ln54 molecule set overall. In general, hybrid functionals perform worse than functionals without exact exchange, and TPSS performs the best overall for the Ln54 set with a MAD of 19.2 kcal mol(-1) and MSD of -1.9 kcal mol(-1).
We discuss the possibility of exploiting local minima of the molecular electrostatic potential for locating protonation sites in molecules in a fully automated manner.
Many chemical concepts can be well defined in the context of quantum chemical theories. Examples are the electronegativity scale of Mulliken and Jaffé and the hard and soft acids and bases concept of Pearson. The sound theoretical basis allows for a systematic definition of such
concepts. However, while they are often used to describe and compare chemical processes in terms of reactivity, their predictive power remains unclear. In this work, we elaborate on the predictive potential of chemical reactivity concepts, which can be crucial for autonomous reaction exploration
protocols to guide them by first-principles heuristics that exploit these concepts.
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