How to Deal with the Computational Models
Computational 3D models in this web site are given in xyz file format.
The xyz files can be viewed in 3D space using a variety of viewers.
In the viewers you can select different representations of atoms and chemical bonds between atoms.
The models can zoomed in/out and rotated in 3D space.
Chemistry
Chemistry is a field of science that deals with substances and their chemical transformations. Chemistry started its development thousands years ago when humans learned how to obtain and keep fire, possibly the first chemical reaction (fire is the reaction of oxidation with oxygen of air). Since then, numerous advances in chemistry resulted in creation of the modern civilization. Actually, all the materials and substances around us have been created using chemistry and chemical reactions. Moreover, our own bodies consist of molecules and compounds created in biochemical reactions, and the life itself exists as long as the chemical and biochemical reactions continue in due order in living things.
Chemistry has several general branches:
- General chemistry
- Physical chemistry
- Inorganic chemistry
- Analytical chemistry
- Organic chemistry
- Electrochemistry
- Radiochemistry
- Polymer chemistry
- Biochemistry
- Chemical thermodynamics
- Chemical kinetics
- Computational chemistry
- Quantum chemistry
- Solid state chemistry
- Photochemistry
Each field of chemistry has its own subfields. Some branches and subbranches are considered in this site.
To learn more about photochemistry and photocatalysis proceed to Photocatalysis.
Computational Chemistry and Modeling
Computational chemistry is a branch of chemistry that uses computers and computations for solving problems of chemistry and advancing scientific knowledge. Computational chemistry appeared when computers and computations stared their way into our life. Since computers are best at performing tasks requiring extensive numerical operations, often the most important application of computational chemistry is considered to be modeling of various chemical systems. However, computational chemistry is a much wider subject. All stages in the chain of chemical research - formation of the initial idea, planning, performing research, results processing and analysis - involve computers and software often specially crafted for the purposes of chemistry.
Modeling is a method to describe, explain and predict various real world systems by representing them in a simplified form that is called model. The real world systems are extremely complex, and therefore they usually cannot be described quantitatively. To describe real world systems, one requires to apply various simplifications and approximations. It is important to determine what kinds of interactions in the system are essential. Then one can build a model of a system that adequately represents it.
You can learn more about computational chemistry and its applications in Publication.
Modeling is an effort and time consuming task that requires dedication and experience. You can order modeling of your chemical systems in this site. Click here to return to the home page.
To learn about the computational models available in this web site click here.
To learn about adsorption and adsorption complexes click here.
Quantum Chemistry
Quantum chemistry is a part of computational chemistry that uses quantum mechanics for computing structures of materials and molecules, properties of chemical objects such as atoms, molecules, ions, radicals, and assemblages of them into larger structures. Quantum chemistry is also used for obtaining qualitative and quantitative values describing chemical reactions.
Quantum chemistry relies on quantum mechanics which is mechanics of very small objects that due to their very small size possess properties of both particles and waves. Thus, quantum mechanics uses wavefunction to completely describe the system that contrasts to classical mechanics that deals with exact coordinates and momentum. The wavefunction ψ and energy of the system E are obtained by solving Schrodinger equation (stationary Schrodinger equation):
Ĥψ = Eψ,
where Ĥ is the Hamiltonian operator.
Ĥ = T + U
Chemical objects contain many particles. The simplest chemical object is the hydrogen atom. Hydrogen atom contains nucleus (proton) and only one electron orbiting around the nucleus. Exact analytical equations for chemical objects can be obtained only for hydrogen atom and hydrogen atom-like ions. Any other chemical objects containing more than one electron are not solved in analytical equations and can be solved numerically only.
There are a number of methods in quantum chemistry to perform modeling. They possess different precision and require different computational efforts. Most widely used modern methods are listed below in the order of decreasing precision and reducing time of computations.
- Density Functional Theory (DFT) methods.
- Semiempirical methods.
- Molecular mechanics (MM) methods.
For carrying out modeling using quantum chemistry, it is needed to prepare initial chemical structure that is called initial geometry. For modeling of molecules, the initial geometry is the coordinates of all atoms in the molecule. For modeling of materials, a number of different approaches are used.
- Small nanoparticles of materials can be modelled similar to molecules: the initial geometry contains coordinates of all atoms of the nanoparticle.
- Bulk materials can be modelled using two common approaches. The first approach is to use cluster models of material. The second approach is to use periodic models.
Quantum chemical computations nowadays are a well established field of chemistry and are often used to complement and even guide experimental research. Development of novel materials and introduction of improvements to existing materials is done much cheaper if the suggested improvements and materials are first evaluated using modeling. This is especially true for development of novel pharmaceuticals. The present protocol for creation of new drugs includes the initial stage when a set of lead compounds is selected using computational chemistry methods such as docking and molecular dynamics. The selected leads then need to be checked for toxicity, a task that also is performed first using computational chemistry and then using laboratory experiments.
Quantum chemical computations can be performed using desktop workstations or supercomputers. Modern supercomputers are networks containing hundreds of computing nodes. Each node is a computer with its own processor(s) (CPU), motherboard, memory and can also contain graphical processing units (GPU) and storage drives.
Design and development of initial geometries for modeling often represent a significant challenge since the crystallographic data are often inconsistent, and careful consideration is required for a number of publications . Among our products you can find ready carefully prepared geometries of molecules, nanoparticles and materials. To browse them click here. The initial structures for modeling can also be prepared according to your needs.
To learn about the chemical models present in this web site click here.