Dr. Ellie L. Uzunova

Institute of General and Inorganic Chemistry

Welcome to my Web Site!

What occurs in every chemical reaction is creating bonds between atoms, while other existing bonds may dissociate or not. Still, we are not able to “see” a reaction mechanism, and moreover, if we want to predict chemical reactivity, only theoretical methods can provide a correct answer.

Molecular mechanics and semiempirical methods were largely used till 1990 and are nowadays applied to large systems. After 1990, Density Functional Theory (DFT) methods were successfully introduced in computer software (Gaussian) and soon became very popular, compared to Hartree-Fock ab initio calculations. Molecular and atom-in molecule properties can be derived from the DFT density of the optimised structure: molecular orbital (MO) population, charge and spin density distribution, dipole and multipole momenta, vibrational frequencies, etc.

 

The leading software for scientific computing in quantum chemistry and physics is presently Gaussian, presenting high standards in accuracy of the calculations and excellent performance with contemporary hardware. The list of other software packages is quite extensive; they have different features depending on the basis sets used and the methods included.

Studies in surface science and catalysis, where adsorption and elementary reactions at an active sites are important steps can be performed by the following methods: (i) cluster model  (ii) applying periodic boundary conditions (iii) ONIOM method. In all three methods, DFT can be applied. In studies of active sites in zeolites by the cluster approach a structural fragment which is representative for a selected adsorption site should be selected. Single and double rings have been successfully used to study interactions of N₂ and O₂ with alkali and alkaline-earth cations and for NO adsorption at transition metal cation exchanged Y zeolite (FAU) and SAPO-34, see publications section. The unsaturated bonds arising from cutting the structural fragment from the framework are terminated by hydrogen atoms. Periodic boundary conditions are important for describing the properties of crystal solids, thin layers and surfaces. In the periodic models, unsaturated bonds do not exist; the adsorption site is repeated uniformly throughout the framework with the unit cell replication. Zeolites possess distinct extraframework sites, which are occupied by an adsorbate molecule according to the site energy and the ease of access; the adsorption sites distribution thus does not necessarily follow the periodicity of the unit cell. Therefore, the use of periodic models for the study of such systems does not always produce more representative or accurate results, compared to ONIOM or cluster models, while the computational costs might increase immensely. The two-layer ONIOM approach can be applied successfully in studies of silicate and zeolite frameworks. The high-layer is described by DFT, while for the low-layer the choice is between a semiempirical method and molecular mechanics (MM). For large-size models of more than 50 tetrahedral atoms, MM is the better choice with respect to computational costs.

 

 

MO and MEP maps of a) NO and c) NO₂, derived from the B3LYP density.

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Chemistry: Theoretical Methods in Molecular Modeling

Primary Address:

Institute of General and Inorganic Chemistry

Bulgarian Academy of Sciences

Sofia 1113, BULGARIA

To contact me:

Fax: +(359 2) 870 5024

E-mail: ellie@svr.igic.bas.bg

BULGARIAN ACADEMY OF SCIENCES 1869

The frontier orbitals of the b) CoNO and d) CuNO₂⁺ adsorption complexes.

c)

d)

Chemical reactivity in electrophilic and nucleophilic reactions can be assessed from the molecular electrostatic potential (MEP) maps, which indicate areas of enhanced or depleted electron density.

The cation mobility upon adsorption has been studied for SAPO-34 molecular sieve material with chabazite structure. Divalent cobalt cations shift from the site SI in the center of the double six-member rings (D6R) – a site at which, they are in general more stable – to site SII above the D6R, at which they are more reactive. The occurrence of this effect depends on tetrahedral site ordering: closely spaced Si atoms (Si-O-Al-O-Si). 

Cu

6a₁¹

SOFTWARE

“Ab initio” molecular modeling and density functional theory in studying inorganic materials

The last decades were marked by rapid development in theoretical methods. This has been made possible by the vast increase of computer processor speed and memory capacity, and the creation of efficient programs for ab initio calculations. Thus, semiempirical methods have been replaced by Hartree-Fock (HF) and Density-Functional Theory (DFT) methods. In Hartree-Fock theory, the total energy for a set of atomic coordinates is the expectation value of the exact non-relativistic Hamiltonian of the total wavefunction (Ψ), which is approximated by a Slater deteminant. In DFT, the total energy is expressed as a functional of the electron density (ρ) for a given position of atom nuclei. The energy is formally decomposed in three terms: kinetic T(ρ), electrostatic or Coulomb V(ρ) and a many-body term E_xc(ρ) which accounts for exchange and correlation effects. The condition for a minimum in HF theory reads as ∂E/∂Ψ = 0, while for DFT it is ∂E/∂ρ = 0. If the exchange-correlation potential of a system would be known, the DFT equations would converge to an exact solution. The basic principles of DFT were laid in the 60’s by Hohenberg, Kohn and Sham, but a real breakthrough occurred in the 90’s, when efficient exchange-correlation functionals were developed and included in quantum-chemistry software. The most important features included in the presently used density functionals are the gradient corrections to the density to improve the description of non-local effects; and also the inclusion of parameters, called often semiempirical. The hybrid functionals, which include Hartree-Fock exchange and DFT exchange-correlation in a proportion, defined by one or more parameters, (e.g. B3LYP, B3PW91) have reached great popularity, because of the highly accurate predictions of molecular properties. A further challenge for using hybrid functionals remains the solid state, where periodic boundary conditions are applied for studying three-dimensional (3D) crystals or 2D crystal surfaces.