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Organic Catalytic Reaction Mechanism Calculation


The study of organic reaction mechanism, especially the mechanism of catalytic reaction, has become one of the most important and active fields of computational organic chemistry. Computational chemistry has evolved into a powerful tool to study the mechanism and selectivity of catalytic reactions. The calculation of the mechanism of organic catalytic reactions is established based on the principles of theoretical chemistry and physical organic chemistry. It reveals the pathways and ways of the reaction from the molecular level through computational chemistry methods. Scientists study the reaction mechanism by analyzing the calculation results.

Organic Catalytic Reaction Mechanism CalculationFigure 1. DFT calculation and schematic of reaction pathway. (Sun, J.; et al. 2018)

Scope of Application

  • Screen and control the key factors which effect organic reaction activity and selectivity.
  • Design and optimize the organic reaction catalysts, thereby improving the the reaction process.
  • Design new thermochemical energy storage materials through high-throughput calculation simulation and database construction.
  • Design and improve the catalysts for stereoselective organic reactions.
  • Reveal the ways of chemical reactions from the atomic level, explain and predict experimental phenomena and results using density functional theory calculations.

Our Services

Alfa Chemistry offers valuable services including density functional theory, QM/MM method, machine learning and molecular force field approach to calculate the mechanism of catalytic reaction. Our fast and high-quality services include the following:

  • Density functional theory (DFT)

A large number of chemical insights and mechanism understanding of organic catalytic reactions come from density functional theory calculations, which in turn promotes the further development of this field. Based on the DFT calculation method, automatic pathway search and kinetic studies, the mechanism of the organic catalytic reaction is further studied through the obtained data, and more detailed reaction rate equations are derived.

1. At Alfa Chemistry, our scientists determine the speed-determining step, reaction path and activation energy of the reaction through the DFT calculation.

2. Moreover, a more active catalyst structure can be designed using our calculation methods. We help our customers to study the mutual transformation between different intermediates and the exchange process of ligands, and establish a detailed reaction pathway through a comprehensive DFT calculation.

  • QM/MM method

A combined quantum mechanics and molecular mechanics method is widely applied to study the catalytic reaction mechanisms of some novel organometallic catalysts, including the study of the stereoselectivity and regioselectivity of the reaction. Scientists use QM/MM approach to investigate the organic reaction mechanism and design catalysts with higher activity.

1. We have applied QM/MM to calculate various thermodynamic properties in organic reactions with metal catalysts such as C-H, C-C activation reaction, bond dissociation energy, pKa and redox potential, etc.

2. Our teams can also clarify and predict substituent effects, study structure activity relationships, and explore the reaction mechanism and molecular dynamics of this kind of organic reaction.

3. We provide thermodynamic data to support for the following experimental research of organic reaction, and offer further theoretical guidance on the design and screen of the catalyst and substrate in the experiment.

  • Automatic pathway search method

In order to perform systematic calculation and prediction of reaction pathways in complex organic reaction systems by using quantum chemical calculations, a novel automatic pathway search approach has been proposed on the basis of the artificial force induced reaction.

1. We apply automated potential energy surface exploration technique to uncover novel reaction routes and key pathways in reaction mechanisms, and explore more chemical space.

2. Our teams have developed a strategy that enables to determine thermochemistry and kinetics correctly, as well as allows for the construction of accurate reaction mechanisms.

3. We have designed automated transition state finding algorithms based on quantum chemistry to assess which algorithm is most viable for the efficient discovery of new reactions and identification of key pathways.

  • Machine learning

It has demonstrated that the combination of quantum chemistry and machine learning methods plays an essential role in studying the organic catalytic reaction mechanism.

1. We use deep learning to improve the throughput of automated discovery via a combination of quantum chemistry data generation and reactivity prediction.

2. Our machine learning methods can automatically generate a data set which can be used to quickly calculate the organic reaction mechanism.

  • Molecular force field

Molecular force field is a potential energy function that represents the interaction between atoms. Combined with molecular dynamics calculations, molecular force field can be used to predict the reaction mechanism, and assist in the development of new drugs and catalyze reactions.

1. Our molecular force field method is developed based on the first principles and can be applied to accurately describe the intermolecular interaction. We use DFT to fit and optimize the parameters of the interaction between atoms, and dynamically simulates the reaction process through the electronegativity balance method (EEM).

2. We can also use it to predict the lattice parameters, sublimation enthalpy and state function of molecular crystals, predict the phase transition process and study the reaction mechanism.

Key Advantages

1. Our experts can systematically study reaction pathways and reveal the structural characteristics of various intermediates.

2. We also help to understand and analyze the reactivity and selectivity of catalyst in a specific organic reaction.

3. At Alfa Chemistry, the role of some key residues and the binding site are also studied.

Alfa Chemistry provides organic catalytic reaction mechanism calculation services, aiming to deepen the understanding of organic reaction mechanism and help design more catalytic reactions and catalysts. If you have any questions, please feel free to contact us.


  • Sun, J.; et al. Freezing copper as a noble metal-like catalyst for preliminary hydrogenation. Science Advances, 2018, 4.

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