Can we predict a complex molecule's shape?

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Discussion Overview

The discussion revolves around the predictability of the shapes of complex molecules, particularly proteins and other larger structures, in the context of molecular chemistry and biochemistry. Participants explore theoretical approaches, computational methods, and the challenges involved in predicting molecular shapes based on atomic bonding and electron repulsion theories.

Discussion Character

  • Exploratory
  • Technical explanation
  • Debate/contested

Main Points Raised

  • Some participants propose that the shape of complex molecules can be predicted by analyzing lone pairs, bond pairs, and using electron repulsion theory.
  • Others define complex molecules as those with many atomic parts, citing glucose and proteins as examples, and question whether their shapes can be predicted based on bonding and electron interactions.
  • A participant notes that there is extensive research in the field of protein folding, indicating a significant scientific effort dedicated to understanding molecular shapes.
  • It is mentioned that supercomputing resources are heavily utilized for protein folding computations, suggesting the complexity involved in predicting these shapes.
  • One participant discusses the potential of quantum computing to aid in determining molecular structures more efficiently, although they express skepticism about the timeline for its practical application.
  • Another participant highlights that computer modeling is routinely used in molecular chemistry and biochemistry to predict molecular interactions, referencing historical educational practices in the field.

Areas of Agreement / Disagreement

Participants express a range of views on the predictability of complex molecular shapes, with some suggesting it is feasible under certain conditions while others emphasize the challenges and complexities involved. No consensus is reached on the overall predictability of these shapes.

Contextual Notes

The discussion reflects varying levels of complexity in molecular structures and the limitations of current computational methods. There is an acknowledgment of the need for advanced technology, such as quantum computing, to improve predictions.

understand.
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I've recently learned that we can predict the shape of molecules with a small amount of atoms. Can the shape of a complex molecule with many atoms be predicted too?
 
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can you give me an example of what you mean by a complex molecule?

theoretically you can, by analysing the lone pairs present, the number of bond pairs and using the electron repulsion theory.
 
By complex, I mean that there are a lot of atomic parts. Water is a simple molecule. Methane is a simple molecule. A complex molecule would be something like glucose. An amino acid is even more complex. And a simple protein is even more complex. Can we predict a protein's shape by knowing the bonding of atoms and electron repulsion? I know there isn't just one shape to each molecule, but can the possible shapes be predicted?
 
Most of the biggest supercomputing clusters in the world are dedicated to protein folding computations.
 
proteins are very complex molecules. but i think it would not be impossible to predict the molecular shape of glucose or an amino acid. you just have to start systematically, say from one of the Carbon atoms, and proceed then with the other bonds. These molecules do not have too many atoms.
 
like DaleSpam said, most of the supercomputing clusters in the world are dedicated to this field. Also since the PS3 was released, there has been a new program also released that allows anyone who wishes to participate in giving even more power. Basically you install it on your PS3, and then scientists from across the world can use the power to add even more computational solving power.

But as far as my knowledge goes into this topic, it takes a very long time in determining the basic structure of a basic complex protein. Which is why scientists are hoping that with the discovery of quantum computing this will be made easier. But I doubt we will see that anytime soon.
 
understand. said:
I've recently learned that we can predict the shape of molecules with a small amount of atoms. Can the shape of a complex molecule with many atoms be predicted too?

Yes, it's done all the time with computer modelling in Molecular chemistry/Biochemistry and Toxicology to predict molecular interractions with receptors on cells, enzyme active sites etc..

Even at Uni in the 80s, in biochemistry we were watching videos showing the construction of a 3d model of the enzyme Lysozyme and well as Insulin, Haemoglobin and DNA.
 

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