Many natural compound molecules in nature have optical chirality. Correctly, confirming the three-dimensional configuration of an organic compound molecule is of vital importance for organic chemists, especially drug researchers. Determining the absolute configuration (AC) of natural products is a challenging issue in structural analysis. There are various methods to solve the problem, such as X-ray crystallography and NMR anisotropy method, each of which has its own limitations. Electronic circular dichroism is very sensitive to the spatial orientation of molecular groups and can provide critical information on the three-dimensional structure of chiral molecules. ECD therefore has become a powerful tool for exploring the AC of chiral molecules.
Figure 1. A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: TD-DFT. (Loco, D.; et al. 2015)
Our ECD Simulation Prediction Workflow
Our efficient time-dependent density functional theory (TD-DFT) method can simulate the ECD spectrum of medium-sized molecules in a short time. Our reliable ECD simulation prediction workflow is as follows:
1. Prepare the initial 3D structure
We create 3D structure using Chem3D or GaussView 6, then the structure is optimized with MMFF94.
2. Conformation search
We perform conformational analysis of the compound to obtain all possible conformational isomers.
Molecular mechanics or semi-empirical Monte Carlo methods are applied to conduct conformational analysis and evaluate the relative energy of conformational isomers.
3. DFT structure optimization and TD-DFT excited state calculation
Solvent, calculation method and basis set are determined for DFT calculation.
Further optimization of conformations is carried out using TD-DFT.
4. ECD spectrum of a single conformation
We calculate the ECD of each conformer to obtain the calculated ECD spectrum of the isomer
5. Weight calculation using Boltzmann distribution
The weight is calculated according to the values of thermal free energies.
6. Draw the ECD spectrum after weighted average.
A ECD spectrum of the conformer is obtained after mixing multiple spectrum according to their weights.
At Alfa Chemistry, we provide TD-DFT to predict the ECD spectrum to confirm the absolute configuration of organic compounds. Our fast and high-quality services include the following:
We use molecular force fields such as MMFF (Merck Molecular FF) to perform a thorough conformation search, in which all rotatable bonds and bonds on the ring can be searched so as not to miss any possible conformations.
In order to screen the molecular mechanics-structure and obtain a limited number of conformations with low-energy. We perform the optimization at the level of B3LYP/6-31G(d). Moreover, we fully consider dispersion correction and double ζ basis sets to obtain high-quality geometric shapes of macromolecules.
We also perform further optimization for the conformation including: (i) use larger basis sets, such as triple ζ or polarization and even dispersion functions such as Ahlrichs basis sets inculuding def2-SVP or def2-TZVP. (ii) use solvent models, such as the polarizable continuum model (PCM), COSMO or SMD.
Our scientists calculate the single-point energy of the conformation set with low-energy at a higher theoretical level (use a larger basis set), and perform frequency calculations for verification. Gibbs free energy or zero point corrected (ZPC) energy are also obtained.
We evaluate the consistency between the calculated conformation set and conformation-dependent NMR data (J-coupling, NOE contact, ring current displacement).
Hybrid and range separated (RS) functionals such as CAM-B3LYP and ωB97X, and Ahlrichs' def2-SVP or def2-TZVP basis sets are applied to calculate the absorption spectra and ECD spectra of all conformations.
Alfa Chemistry's Advantages
- We are capable of selecting TD-DFT method and basis set to calculate, and predict the absorption spectra and ECD spectra of all conformations.
- Our experts have a wealth of experience in ensuring the correctness of structure, charge and polymorphism in spin-crossover systems during the DTF structure optimization.
Electronic circular dichroism simulation prediction provides an effective way to identify absolute configuration. Our electronic circular dichroism simulation prediction services remarkably reduce the cost, promote further experiments, and enhance the understanding of chemical process for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!
- Loco, D.; et al. A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved. Physical Chemistry Chemical Physics Pccp. 2015, 18(2): 866-877.