Molecular Structure Simulation Service

CD ComputaBio can provide services to simulate macromolecule systems, which can be organic compounds or biological macromolecules. CD ComputaBio can perform molecular stratification, calculate path setting, and use the Gaussian program to perform ONIOM calculation of organic compounds.

Method

In actual research, the molecular system may contain a large number of atoms. Due to the limitation of computing resources and computing time, it is often impractical to use a higher-precision model method for simulation for this system. The idea of the ONIOM method is to divide a molecular system into several regions (also called layers, usually divided into 2 layers and 3 layers), and different layers can be calculated with different precision methods, as shown in Figure.

Molecular Structure Simulation Service 1

Overall solutions

In ONIOM calculations, different layers are calculated with different precision methods. Compared with traditional calculations, the steps of the ONIOM are more complicated for the electronic energy of the system. Each circle in Figure 2 corresponds to the calculated electron energy under the layer system. The plus sign means adding this energy term to the ONIOM energy expression, and the minus sign means subtracting this energy term.

Molecular Structure Simulation Service 2 Figure 2. For 2-layer system:

E(ONIOM) = E(Low, Real) + E(High, Model)-E(Low, Model)

or the 3-layer system:

E(ONIOM) = E(Low, Real) + E(Medium, Middle) + E(High, Model)-E(Medium, Model)-E(Low, Middle)

In order to perform an ONIOM calculation, the following three steps are required:

  • Use GaussView to layer the molecular system.
  • Build ONIOM input file.
  • Result analysis.

It should be noted that:

Molecular Structure Simulation Service 3To better simulate the real system, when stratifying the molecular system, several principles need to be considered when using ONIOM calculations:

  • The truncated chemical bond should be a single bond (at the same time it should be a non-polar bond), not a double bond or a triple bond
  • The truncated bond cannot be a ring bond.
  • The conjugated part of the molecule should be divided into the same layer. 
  • In a chemical reaction, the parts involved in bond breaking and bond formation should be divided into the same layer.

Our services

Project name Molecular Structure Simulation Service
Samples requirement Our Molecular Structure Simulation Service requires you to provide specific requirements.
Cycle Decide according to your needs.
Deliverables We provide you with raw data and analysis service.
Price Inquiry

 CD ComputaBio can offer you but not limited to:

CD ComputaBio' Molecular Structure Simulation Service reduces the cost of later experiment. Molecular Structure Simulation Service is a personalized and customized innovative scientific research service. Before determining the corresponding analysis plan and price, each project needs to be evaluated. If you want to know more about service prices or technical details, please feel free to contact us.

* It should be noted that our service is only used for research, not for clinical use.

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