Exploration of Reaction Pathways and Chemical Transformation Networks.

@article{Simm2019ExplorationOR,
  title={Exploration of Reaction Pathways and Chemical Transformation Networks.},
  author={G. Simm and A. Vaucher and M. Reiher},
  journal={The journal of physical chemistry. A},
  year={2019},
  volume={123 2},
  pages={
          385-399
        }
}
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 in an automated fashion. These approaches differ in their application range, the level of completeness of the exploration, and the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions… Expand
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References

SHOWING 1-10 OF 261 REFERENCES
Heuristics-Guided Exploration of Reaction Mechanisms.
TLDR
A computational protocol is presented that constructs chemical reaction networks in a parallelized and automated manner and applies it to the Schrock dinitrogen-fixation catalyst to study alternative pathways of catalytic ammonia production. Expand
Methods for exploring reaction space in molecular systems
The area of reaction mechanism discovery simulation has taken considerable strides in recent years. Novel methods that make hypotheses for elementary steps and complementary means for reaction pathExpand
Context-Driven Exploration of Complex Chemical Reaction Networks.
  • G. Simm, M. Reiher
  • Chemistry, Medicine
  • Journal of chemical theory and computation
  • 2017
TLDR
A computational protocol is presented that constructs reaction networks in a fully automated fashion steered in an intuitive, graph-based fashion through a single graphical user interface to study different pathways of sugar formation and to rationalize its autocatalytic nature. Expand
A Networks Approach to Modeling Enzymatic Reactions.
  • P. Imhof
  • Chemistry, Medicine
  • Methods in enzymology
  • 2016
Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated withExpand
Finding reaction mechanisms, intuitive or otherwise.
TLDR
New methods developed by the Zimmerman group are introduced that are designed to uncover sequences of elementary steps, from first principles and without substantial human guidance, to determine reaction mechanisms that were not already preconceived by chemists. Expand
Efficient prediction of reaction paths through molecular graph and reaction network analysis† †Electronic supplementary information (ESI) available: Detailed information on reaction networks and pathways for two example reactions, Cartesian coordinates of molecules in the reaction networks obtained
A minimal subnetwork is extracted from a very complex full network upon exploring the reaction pathways connecting reactants and products with minimum dissociation and formation of chemical bonds.Expand
Automated discovery of chemically reasonable elementary reaction steps
TLDR
A systematic approach is proposed for locating reaction paths that bypasses the required human effort and expands the reactive search space, all while maintaining low computational cost. Expand
Navigating molecular space for reaction mechanisms: an efficient, automated procedure
Mechanism is a core chemical concept that has vital implications for reaction rate, efficiency and selectivity. The discovery of mechanism is not easy due to the great diversity of possible chemicalExpand
Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.
TLDR
Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles. Expand
Automated discovery of reaction pathways, rate constants, and transition states using reactive molecular dynamics simulations.
TLDR
Simulations of the inception stage of methane oxidation are used to demonstrate the agreement of pathways and rates with available literature data that reveals the potential of reactive molecular dynamics studies for developing quantitative reaction models. Expand
...
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2
3
4
5
...