In your model kits, multiple bonds are modeled by the long, flexible bonds. Often the central atom will have four electron pairs and will have a tetrahedral bonding center. Most of the structures will obey the octet rule. As you build the models also draw the three dimensional structures on paper, so that you can develop skills at representing these three dimensional structures on paper. The tubes represent the bonding electron pairs or valence bonds. The bonding centers represent the hybrid valence electron distribution about the atom. The models consist of plastic bonding centers and bonding tubes. In this exercise you will assemble models for a number of common chemicals and interpret them in the ways we have discussed. When you come to the laboratory use the molecular models to check and refine your Lewis structures. You may want to initially generate your Lewis structures before you come to the laboratory. With models, it is relatively easy to see both geometry and polarity, as well as to deduce Lewis structures. To illustrate how molecular geometry can be obtained from Lewis structures and valence shell electron pair repulsion, we will use molecular models. ChemDraw is a computer “modeling kit” which we use to augment our visualization of the molecule with quantitative information. The ball and stick model kits you use in this chemistry laboratory are very useful for visualizing chemical structures but they do not give quantitative information needed to design and build new molecules with specific properties. Modeling of molecular structures allows us to make predictions about the behavior of these invisible molecules so that we can design new chemicals with beneficial properties such as these inhibitors. We need models like this because actual molecules are too small to see. The figure above is a ball and stick model for an early precursor to one of the anti-HIV drugs known as Protease inhibitors developed at Abbott Laboratories, Inc. These include Lewis structures (including formal charges) based on a simple counting rule valence bond models (including hybridization, and resonance) based on orbital overlap valence shell electron pair repulsion theory (VESPR theory) based on electron repulsion, to predict overall shapes of molecules/ions and molecular orbits to predict certain electrical and magnetic properties. As you learned in class, there are several types of structure representations used by the chemist at different times to explain chemical phenomena. Models provide a useful way of visualizing the arrangement of electrons in a molecule. Theories of chemical bonding allow us to understand the electronic structure and geometrical arrangement of atoms in a molecule or ion.
Here's a picture of the code and the resulting image.Adapted by M. Penicillin_g_smiles = Chem.MolFromSmiles(penicillin_g_smiles)ĭraw.MolToMPL(penicillin_g, size=(200, 200)) Here is one way to convert a SMILES to a structure in rdkit. It does a whole lot more than convert SMILES to structures see some examples here.If you happen to be fluent in C++, a C++ API is available.
The Python API provides access to these functions in Python, making it flexible and easy to learn. The Python API makes using rdkit easy, but all the core functions are written C++, making it fast and efficient.
The license is quite permissive you don't need to worry about what type of work (commercial, personal, or academic) you are doing.The code base is available in GitHub, here.Most people use rdkit via its Python interface.
In addition to the other good answers, I'd recommend rdkit, an open-source, freely available software for chemoinformatics.