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Chemical Reaction Mechanism Calculation


Introduction of Chemical Reaction Mechanism Calculation

Chemical reaction mechanism, especially catalysis, has been an active, challenging, and momentous area of chemistry. Experimental research of reaction mechanisms has inherent limitations, such as preparation and purification of key intermediates, a large amount of manpower and time, possibly discouraging results and persistent trials. With the boom of computational chemistry, there is a new approach to deeply understanding the mechanism.

Great achievements have taken place in theoretical and computational chemistry. Utilizing computers' progressive capacities and speed, our computational chemists have mastered more and more accurate approximate solutions of the Schrödinger equation. Just as nuclear magnetic resonance (NMR) spectroscopy in organic chemistry, computational chemistry in reaction mechanisms has become an essential technique. Taking full advantage of computational chemistry in applications of chemical reaction mechanism calculation, Alfa Chemistry provides valuable services such as ab initio calculation of mechanism, close collaborations between calculation and experiments to exactly elucidate the mechanism, density functional theory (DFT) calculation of mechanism.

Figure 1. Collaborations between experiments and calculationFigure 1. Collaborations between experiments and calculation (Cheng, G.-J.; et al. 2015)

Scope of Services

  • Catalyst effect

With respect to catalytic reaction mechanisms, catalysts play significant roles in the success of reactions. Thus, we give sufficient consideration to the catalyst effect for mechanism calculation. Our scientists have rich experience in learning various catalyst effect such as size effect, synergy effect, geometric effect and electronic effect.

  • Ligand effect

For metal-ligand cooperative catalysis, ligands often finely tune the reactivity and selectivity. How to understand the interaction and effect normally confuse researchers. Our careful calculation of the ligand effect can solve it. At CD BioSciences, we fully consider the influence of the steric effect of the ligand on the chemical reaction. Moreover, we are capable of providing help in studying the dipole moment between the ligand and the ligand.

  • Additive effect

The choice of additives sometimes is crucial to the yield and selectivity of reaction products. Additive effects can be calculated by our professional staff. We also use density functional theory and ab initio methods to calculate the geometric configuration, electronic structure, molecular orbital index and interaction with reactants of different organic additive molecules. The active atoms and active bonds of the reaction are analyzed using the frontier molecular orbital theory, and the role of additives is also discussed using the principle of orbital energy approximation.

  • Solvent effect

We fully consider the influence of the solvent on the system when studying the chemical system in the solution. Accurate solvent models are critical for simulation, and our teams provide various solvent models to account for the solvent effects. Multiple models such as self-consistent reaction field, quantum-onsager SCRF method, polarizable-continuum model, conductor-like solvation model, etc., are available.

  • Base effect and acid effect.

A small quantity of special bases or (strong/weak) acids can make major impacts on reactivity. Our experts can perform the calculation coefficient of acid effect, coefficient of alkali effect and coefficient of complexation. We also calculate the charge distribution under acidic or alkaline conditions, providing a deeper insight into these effects.

  • Calculations with experimental results

Collaborations between experiments and calculation have been a new trend to understand the mechanism. We have skills in the combination of calculation and mass spectrometry, in situ infrared spectroscopy, NMR spectroscopy and so on.

Our Features and Experience

  • An automated pathway search in the calculation of multi-component reactions mechanism

We use a string-based calculation method to search for the minimum energy path on the two-dimensional global discrete potential energy surface to reveal the multi-component reactions mechanism. Our automated pathway search can be used to study the mechanism of protein folding, chemical reactions, phase transitions and other processes. In addition, information such as transition state and activation energy can also be obtained.

  • Grasp of correlations and informatics between experiments and calculations

The transition state structure in the chemical reaction process exists for a very short time and is difficult to obtain through experimental methods. Our computational chemistry method can accurately and quickly predict the transition state, so as to study the reaction mechanism and reaction dynamics, including Gibbs free energy, changes in enthalpy and entropy. We therefore can identify the correlation between the calculated results and experimental data.

  • Radical and single electron transfer mechanisms

Studying radical and single electron transfer mechanisms is of vital importance in electrochemical reactions. At CD BioSciences, we use DFT functions to simulate and calculate the single electron transfer process by setting the structure, charge and pin multiplicity. We can also study the reaction mechanisms of many radicals such as hydrogen and superoxide anions from the electronic structure level, and in-depth study of the molecular mechanism in chemical reactions.

  • C-H activation mechanism

The plausible C-H activation mechanism is identified as the undirected mechanism rather than the coordination-directed mechanism since the former has lower free-energy barriers than the latter. The kinetic and thermodynamic parameters of different C-H activation reactions have been calculated with the use of quantum mechanics (density functional theory). We are also capable of performing reaction progress kinetic analysis (RPKA) to provide mechanistic insights into both simple and complex catalytic networks.

Our teams have developed ab initio quantum mechanical/molecular mechanical (QM/MM) methods to perform various organocatalysis mechanism analysis. We study a series of chemical steps including the chemical role of the substrate in the formation step and a proton-relaying mechanism. In addition, our scientific experts have made use of efficient semiempirical models and pathway optimization techniques to investigate the mechanism and stereoselectivity of annulation reaction.

We use multiple quantum chemistry calculation methods to study several important organic reactions including asymmetric cyclization reactions and solvent effects, which are catalyzed by transition metal complexes such as Fe, Au, Pt, W, etc. Our teams apply density functional theory to clarify the elementary reaction mechanism at the molecular level, providing help for the development of new organic reactions and the design of new catalysts.

Our Advantages

  • Productive collaborations between experiments and calculation.
  • High quality to meet the demand of emerging reactions
  • Experienced calculation algorithms and methods
  • Accurate analysis of reaction mechanism
  • Cost-effective and time-saving

CD BioSciences provides a wide variety of services for chemical reaction mechanism calculation. We embrace the heterogeneous needs of scientific researchers with advanced methods and flexible ways. More than calculation, our services include further analysis of mechanism to make sure the accuracy. If you need consultation on the calculation of chemical reactions mechanisms, please feel free to contact us so we can discuss your chemical reactions and calculation needs.


  • Cheng, G.-J.; et al. Computational organic chemistry: Bridging theory and experiment in establishing the mechanisms of chemical reactions. J. Am. Chem. Soc. 2015, 137(5): 1706-1725.

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