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Molecular Orbital Analysis


Molecular orbitals (MO, the linear combination of atomic orbitals) describe the state of electrons in polyatomic molecules, firstly proposed by Mulliken and Hund. MO can be divided into bonding orbitals, antibonding orbitals, and non-bonding orbitals. Symmetry labels of MO show σ, π, δ, φ, and γ. Hückel (HMO), Roothaan, Fukui (FMO), Woodward and Hoffmann, and many other scientists have formed a mature theory.

Application of MO Analysis

  • Qualitatively discusses the molecular configuration of polyatomic molecules and symmetry of polyatomic molecules.
  • Applications in molecular activity, electronic structure and magnetism.
  • Studies the surface properties and morphological structure of materials, such as the adsorption of a certain substance.

Scope of Services

  • Chemistry

MO analysis has become the mainstream of modern chemical bond theory, widely used in molecular properties research, quantum chemistry, molecular chemical reactivity, elemental chemical reaction, and guidance for synthesis. At Alfa Chemistry, we apply MO analysis to solve the problem of molecular structures, such as calculations of the potential energy surface of chemical reactions, analyses of relative chemical reactivity and predictions of chemical reactions mechanism. Our teams have achieved the above analysis services with gratifying results from our knowledgeable staff.

Figure 1. A localization method for molecular orbitalsFigure 1. A localization method for molecular orbitals (Heßelmann, A. 2016)

  • Drug discovery

One of the popular analyses in drug discovery is the fragment molecular orbital (FMO) method. FMO method can be applied to large molecular systems, such as proteins, water clusters, and DNA. Our experts can use FMO approach to obtain accurate and well-rounded data, which clearly presents interactions between drug ligands and their surrounding residue groups. We apply these critical information to structure modification, skeleton transitions, and structure enlargement to improving interactions (stronger interactions, or elimination of rejection) with proteins.

Figure 2. FragmentationsFigure 2. The outline of FMO method (Fedorov, D.G.; et al. 2012)

Features and Advantages

  • Study the the native of molecules by using MO

(1) MO visualization

We can use a variety of quantum chemistry software such as Gaussian to draw molecular orbital graphs and plane diagrams to visualize molecular orbitals, and our general process is:

Construct and optimize to obtain the stable configuration of the molecule.

Use the optimized structure as the initial structure and calculate the single point-energy to obtain the molecular orbital data.

Generate molecular generation spectra and use GaussView to draw molecular orbital diagram.

(2) MO calculation

We perform the calculation of the molecular orbit by calculating the contribution of each component that makes up the orbit, which includes:

Calculate the contribution of the basis function.

Calculate the contribution of the atomic orbital.

Calculate the contribution of the atom.

Calculate the contribution of a certain segment.

(3) Prediction of property affected by MO

We can use the electron density, frontier electron density and superdelocalisability indices which have been calculated for the total molecular structures to predict the surface properties of a wide range of different materials.

The pure-component parameters derived from the results of our molecular orbital calculations are able to help us describe and predict the phase behavior of mixtures containing one associating and one nonassociating compound.

Our scientists have abilities in using the calculated value of bond length, stability of molecules and bond order to predict the reactivity and properties like UV spectra.

  • Diverse theoretical methods available

1. Hartree-Fock methods

Hartree-Fock equation, also known as HF equation, is an equation that applies the variational method to calculate the wave function of a multi-electron system. It is one of the most important equations in quantum physics, condensed matter physics, and quantum chemistry. The HF equation is a single-electron eigen equation in form and the eigenstate obtained is a single-electron wave function, which is also called the molecular orbital.

2. Self-consistent field methods

The basic physical idea of the self-consistent field molecular orbital method is to assume that each electron in a molecule moves in the average potential field generated by each nucleus and other electrons. The method assumes that there are a series of single-electron space wave functions in the molecule which is called a molecular orbital. Each molecular orbital has a certain energy corresponding to it, and the wave function of the entire molecule can be approximately described by the product of the molecular orbital.

3. Ab initio methods

Ab initio calculation refers to directly solving the Schrödinger equation based on the basic principles of quantum mechanics. The main characteristic of the ab initio calculation method is that it has no empirical parameters and does not simplify the system too much. It applies basically the same method for calculations of various chemical systems. At Alfa Chemistry, Various ab initio calculation methods are available which include the Hartree-Fokker method based on the Hartree-Fokker equation, the post-Hartree-Fokker method developed by introducing electronic correlation correction based on the Hartree-Fokker equation, and multireference configuration interaction method (MRCI), etc.

4. FMO methods

HOMO-LUMO energy levels are collectively called frontier orbitals, which respectively refer to the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). The FMO theory emphasizes that both the HOMO and LUMO have important impact on understanding the reactivity of molecules. Our teams use the FMO method to evaluate the interaction between protein and ligand. In addition, we can also calculate the solvent model.

Customer Notice

Customers provide

  • Specific requirements of MO analysis services
  • Analysis cycle

We deliver

  • Calculation algorithms and methods
  • Raw data
  • Analysis results

Alfa Chemistry provides quick and professional services of MO analysis for customers all over the world. Our MO analysis is comprehensive, including molecular structures and properties, chemical reactivity and reaction mechanism, drug discovery. Our services have cost advantages without losing efficiency and accuracy. If you are interested in our services, please feel free to contact us.


  • Heßelmann, A. Local molecular orbitals from a projection onto localized centers. J. Chem. Theory Comput. 2016, 12(6): 2720-2741.
  • Fedorov, D.G.; et al. Exploring chemistry with the fragment molecular orbital method. Phys. Chem. Chem. Phys. 2012, 14(21): 7562-7577.

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