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Molecular Shapes: Molecules with Lone Pair(s) on Central Atom

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Molecules by Design
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Molecules by Design

Credit: Morton Schamberg (1881?1918)
Source: https://commons.wikimedia.org/wiki/File:Morton_Livingston_Schamberg_Figure_1913_Amon_Carter_Museum.jpg
License: CC BY-NC 3.0

In abstract art, almost anything goes. The painting does not need to represent anything tangible or real. A painting of a face may have the nose above the eyes or both ears under the mouth. The work shown above goes even further. It is extremely difficult to discern any recognizable part of a body. There is little resemblance to reality.

Amazing But True

  • A major challenge to the production of new drugs is finding one that works, preferably better and with fewer side effects than the drugs currently available. Two approaches can be taken. A new drug can be designed to interact with the target molecule if the structure of that molecule is known. Alternatively, modifications of drugs with known effectiveness can be studied to see if they work any better than the present drugs.
  • In designing molecules for pharmaceutical purposes, it’s not enough to draw a structure on paper and play with it. Drugs used for treatment often have specific three-dimensional constraints. The conformation must be such that the drug will attach properly to the target organism or molecule, both in terms of shape and tightness of binding.
  • Credit: Rosenfield Media
    Source: http://www.flickr.com/photos/rosenfeldmedia/6949089342/
    License: CC BY-NC 3.0

    Foldit is an online game that allows regular people to help scientists discover the 3D structure of complex proteins [Figure2]

     

  • The basic rules of chemistry with regard to structure need to be incorporated into any computer program used for drug design. The program must apply fundamental principles to predict the three-dimensional configuration. Bond angles and bond lengths must be accurate. Knowledge of the effects of lone pair electrons, sigma bonds, and pi bonds need to be a part of the computer computations in order for drug design to be successful.
  • Watch a video on computer modeling of a drug at the site below:

https://www.youtube.com/watch?v=dWf5Gj7tfYI

Show What You Know

Use the links below to learn more about the role of computers in chemical synthesis. Then answer the following questions.

  1. How did the University of Washington research team know that the molecule they designed by computer actually had that structure?
  2. What is one possible environmental application of the UW research?
  3. What is one problem with active proteins?
  4. What is chemoselectivity?
  5. What is one advantage of the software developed by ETH Zurich?

Image Attributions

  1. [1]^ Credit: Morton Schamberg (1881?1918); Source: https://commons.wikimedia.org/wiki/File:Morton_Livingston_Schamberg_Figure_1913_Amon_Carter_Museum.jpg; License: CC BY-NC 3.0
  2. [2]^ Credit: Rosenfield Media; Source: http://www.flickr.com/photos/rosenfeldmedia/6949089342/; License: CC BY-NC 3.0

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