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Molecular Structure Prediction


Introduction to Molecular Structure Prediction

Figure 1. Molecular structure.

Molecular structure (molecular geometry) refers to the three-dimensional arrangement of the constituent atoms. It relates to the position of atoms in space and the type of bonds, including bond lengths, bond angles, dihedral angles, torsional angles, and other geometrical parameters. The molecular structure is determined by the quantum mechanical properties of electrons. As a rule, the main types of chemical bonds in molecules can be divided into ionic bonds, covalent bonds, and metallic bonds. Valence bond theory can be used to understand the effect of types of chemical bonds (such as σ bonds and π bonds) on the molecular structure. Molecular structure prediction is a useful tool to calculate chemical isomers, predict organic compounds structures, study space technology and astrophysics. All possible polymorphisms of given molecules can be calculated by molecular crystal structure prediction methods, and the best structures are able to be generated by the re-ranked process.

Scope of Applications

  • Molecular structure analysis helps us to predict the molecular interactions and understand the biomolecular structure-function relationship.
  • Molecular structure can largely affect multiple molecular properties, we therefore use the information of molecular structure to predict polarity, color, phase state, magnetism, and biological activity.
  • Molecular structure plays an important role in the investigation of physical properties and chemical properties. Studying molecular structure can help to make accurate predictions about reaction sites and the reactivity of chemical compounds.
  • Molecular structure offer crucial information on the molecular energy level structure which can be useful in the prediction of critical impact on the determination of spectroscopic properties of molecules.

Alfa Chemistry provides molecular structure prediction services including,

a) Chemical Isomers Calculation

Chemical Isomers contain structural isomers, enantiomers, diastereoisomers and so on. A molecule often has many conformations and each conformation has different energy, our scientists have rich experience in determining the ratio of different conformations. We are also able to identify the basic structural features of different isomers. At Alfa Chemistry, our teams provide various structural isomers calculation methods including carbon chain isomers calculation, position isomers (substitution isomers) calculation, and functional group isomers calculation.

b) Molecular Volume Calculation

The volume enclosed by the surface of the molecular van der Waals is usually defined as the molecular volume, which is also known as the van der Waals volume of the molecule. At Alfa Chemistry, both small and large molecular volume calculation methods are available for us to predict molecular surface and molecular volume. We use a variety of software to calculate the molecular volume, and our basic process is as follows: 1. Optimize molecular structure 2. Volume calculation 3. Read the calculation result.

Our Capabilities

  • Ab initio methods

Ab initio calculations use the Schrodinger equation to analyze the wave function, and then calculate the energy state distribution of atoms and molecules. We apply ab initio approaches to optimize the ground and excited states of atoms and molecules. Moreover, we can also use ab initio dynamics to analyze the electronic structure and predict the molecular structure.

  • Machine learning

As a widely applied technique, machine learning can predict molecular structure and electronic properties with relatively high accuracy and low cost. At Alfa Chemistry, our experts have trained our system with multiple atom types and bond angles of different molecules. Our machine learning method is developed based on a set of known data to predict the relevant energy of the electronic structure, the interaction between the electrons and other useful values. In addition, we can apply various machine learning approaches to simulate the behavior of molecules and predict molecular structure.

  • Coupled-cluster (CC) theory

CC theory refers to a theoretical method for solving multi-body problems. A coupled cluster method includes single, double, triplet and quadruple excited states, which is calculated by perturbation theory. At Alfa Chemistry, we provide the following coupled-cluster calculation services:

(1)We can offer a collection of coupled-cluster singles and doubles methods to speed up molecular structure calculations through multi-level approximation and DFT embedding technology.

(2)The final calculation result can be connected to the interface of molecular mechanics software to perform the subsequent quantum mechanics/molecular mechanics calculations.

(3)We can also combine the experimental results of Fourier transform microwave spectroscopy with the force field calculations performed in the coupled cluster singles and doubles models, and enhance the perturbation correction at the level of the triple excitation to obtain a semi-experimental data of molecular structure.

Our Features

  • We provide accurate calculation results by reducing the errors to as close to zero as possible in terms of the basis set and the wave function.
  • Our services can overcome pool biases, selection biases, and time-consuming ways, offering our customers accurate prediction.
  • Apart from small molecules, large molecules structure can be predicted as well, such as protein, DNA and RNA structures, two-dimensional and three-dimensional structures.
  • At Alfa Chemistry, high-throughput molecular structure prediction is also available.

Customer Notice

Customers provideWe deliver
Specific requirements of molecular structure prediction servicesSuitable calculation algorithms and methods
Analysis cycleRaw data and Analysis results

Alfa Chemistry provides fast, specialized, high-quality services of molecular structure prediction at competitive prices for global customers. Our molecular structure prediction services involve small and large molecular structure prediction, isomers prediction, and related applications, which will be your good partners in scientific research. Our clients have direct access to our staff and prompt feedback to their inquiries. If you are interested in our services, please feel free to contact us for more details.

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