36 research outputs found
Molecular propensity as a driver for explorative reactivity studies
Quantum chemical studies of reactivity involve calculations on a large number
of molecular structures and comparison of their energies. Already the set-up of
these calculations limits the scope of the results that one will obtain,
because several system-specific variables such as the charge and spin need to
be set prior to the calculation. For a reliable exploration of reaction
mechanisms, a considerable number of calculations with varying global
parameters must be taken into account, or important facts about the reactivity
of the system under consideration can go undetected. For example, one could
miss crossings of potential energy surfaces for different spin states or might
not note that a molecule is prone to oxidation. Here, we introduce the concept
of molecular propensity to account for the predisposition of a molecular system
to react across different electronic states in certain nuclear configurations.
Within our real-time quantum chemistry framework, we developed an algorithm
that allows us to be alerted to such a propensity of a system under
consideration.Comment: 10 pages, 7 figure
Exploration of Reaction Pathways and Chemical Transformation Networks
For the investigation of chemical reaction networks, the identification of
all relevant intermediates and elementary reactions is mandatory. Many
algorithmic approaches exist that perform explorations efficiently and
automatedly. These approaches differ in their application range, the level of
completeness of the exploration, as well as the amount of heuristics and human
intervention required. Here, we describe and compare the different approaches
based on these criteria. Future directions leveraging the strengths of chemical
heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure
Interactive Chemical Reactivity Exploration
Elucidating chemical reactivity in complex molecular assemblies of a few
hundred atoms is, despite the remarkable progress in quantum chemistry, still a
major challenge. Black-box search methods to find intermediates and
transition-state structures might fail in such situations because of the
high-dimensionality of the potential energy surface. Here, we propose the
concept of interactive chemical reactivity exploration to effectively introduce
the chemist's intuition into the search process. We employ a haptic pointer
device with force-feedback to allow the operator the direct manipulation of
structures in three dimensions along with simultaneous perception of the
quantum mechanical response upon structure modification as forces. We elaborate
on the details of how such an interactive exploration should proceed and which
technical difficulties need to be overcome. All reactivity-exploration concepts
developed for this purpose have been implemented in the Samson programming
environment.Comment: 36 pages, 14 figure
Mapping the Space of Chemical Reactions Using Attention-Based Neural Networks
Organic reactions are usually assigned to classes containing reactions with
similar reagents and mechanisms. Reaction classes facilitate the communication
of complex concepts and efficient navigation through chemical reaction space.
However, the classification process is a tedious task. It requires the
identification of the corresponding reaction class template via annotation of
the number of molecules in the reactions, the reaction center, and the
distinction between reactants and reagents. This work shows that
transformer-based models can infer reaction classes from non-annotated, simple
text-based representations of chemical reactions. Our best model reaches a
classification accuracy of 98.2%. We also show that the learned representations
can be used as reaction fingerprints that capture fine-grained differences
between reaction classes better than traditional reaction fingerprints. The
insights into chemical reaction space enabled by our learned fingerprints are
illustrated by an interactive reaction atlas providing visual clustering and
similarity searching.Comment: https://rxn4chemistry.github.io/rxnfp
One Bronze Medal for Switzerland at the 48th International Chemistry Olympiad in Tbilisi, Georgia: 48th International Chemistry Olympiad
Four Swiss high school students participated in the 48th International Chemistry Olympiad (IChO), which took place from July 23 to August 1 in Tbilisi, Georgia. Dominic Egger, Nicolà Gantenbein, Simone Heimgartner and Diego Zenhäusern competed against 260 other
students from 71 countries. Dominic Egger brought home a well-deserved bronze medal