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

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.

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:

To 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

 CD ComputaBio can offer you but not limited to:

• QM/MM Computing Service
• Molecular Electrostatic Potential (MEP) calculation
• Natural Bond Orbit Analysis (NBO) Service
• Calculation Service of Chemical Isomers

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.

• Thermodynamic Properties Analysis Service
• AMES Test Service
• Molecular Volume Calculation Service
• Wavefunction Stability Testing Service
• Electrostatic Potential Mapping Service on Molecular Surface
• Global Simulations of Enzymatic Catalysis