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I don't get it. Aren't simulations of chemical reactions based on things you already KNOW about those reactions? How are they being used to find out new things

I don't get it. Aren't simulations of chemical reactions based on things you already KNOW about those reactions? How are they being used to find out new things about the reactions?

josephagoss 13y ago
I haven't read anything in the link, but I guess that if the simulation system is of sufficient precision and that it is accurate enough for known chemical reactions, such a simulation system should be able to be pushed further and it may end up simulating events and phenomena that have not been observed in the real world before. Bonus points if they observe real world reactions that agree with the model after the simulation has run.
tlarkworthy 13y ago
Several generic approaches yield results:- 1. You take a lot of empirical observations of known reactions, build a predictive model, then apply it to contexts you don't have empirical observations of. 2. You program in the low level rules of chemistry (e.g. quantum mechanics), and see how the scenario plays out at a higher level (molecular reactions). I think in their work they are more number 1. A predictive model of proteins without having the simulate the (exceedingly expensive) low level details of QM
weland 13y ago
I'm only casually familiar with chemistry, but I used to do research of a similar type (only far worse, of course) related to electromagnetism. You know the main mechanisms at work, but that does not mean you can study all the processes. Sometimes it's just that the sheer size of the mathematical model itself is basically impossible to study without a computer. Oftentimes, though, it's the inadequate formulation of a model that doesn't allow you to simulate it. A good simulation is an immensely useful tool. There are phenomenons which you know and can simulate, but you cannot easily measure their parameters while they are happening (e.g. you risk disrupting the phenomenon because of your measurement installation). I imagine this is even more so for chemists. Real-life example from my own research: we worked on tools that helped engineers who designed really high-frequency ICs (think tens of GHz) study things like cross-talk through the substrate. The mechanism itself is basically well-understood, but save for really, really simple structures that are nothing like those in an IC, you can't solve that by hand. Of course, ours were modest achievements, but the point is that this kind of research can open new gates and shouldn't be considered "second-rate".
blumkvist 13y ago
There are programs which allow you to input desirable qualities (smell, color, density, /non/conductor, molecule mass, stereo orientation to name a few, very basic ones) and it will make computations and it will give you possible compounds. Also software in chemistry can be used to simulate reactions and processes, which can take years to analyze with conventional methods(if at all possible), like folding protein chains.
- varelse 13y ago
  Actually, Vijay Pande's lab has been "folding" proteins in hours to days for years now by massively parallelizing the trajectories: http://en.wikipedia.org/wiki/Markov_chain_Monte_Carlo http://en.wikipedia.org/wiki/Markov_chain_Monte_Carlo Similarly, David Baker's lab has focused on producing the folded conformations of proteins in hours to days using simplified models that are designed for that task: http://boinc.bakerlab.org/rosetta/ http://boinc.bakerlab.org/rosetta/
deleted 13y ago
[deleted]
shiven 13y ago
You are thinking about reactions as written out in a chemistry textbook. Those representations tell you about the reactants, products and maybe a few other details like catalysts, solvents and temperature. However, none of it explains the mechanism at the quantum or atomic level. Simulating the reaction with specialized software enables you to 'calculate' additional data points, such as, free energy, enthalpy and entropy among others, using 'molecular dynamics' (which 'solves' Classical and Quantum Mechanics equations for a given system and is extremely essential to understand movement of different parts of a molecule and their interaction with surrounding atoms to build a more complete picture of 'how' a reaction proceeds). Today is a great day for computational chemistry. It is good to see the detailed Nobel announcement acknowledge other stalwarts of the field like Peter Kollman (who created AMBER, a package similar to CHARMm by Karplus et al). I have no doubt that Kollman would have received this prize had he been alive today.
- raverbashing 13y ago
  Exactly Chemistry is applied physics. Chemistry answers that H2 and O2 can be joined to form water under certain conditions, but doesn't answer the "Whys" Physics answers that. And the answer goes around orbitals, energy states, electrons, etc.
  - aristomc 13y ago
    "Chemistry answers that H2 and O2 can be joined to form water under certain conditions, but doesn't answer the whys". Chemistry does answer the whys beyond product yields, why certain elements react is vastly covered throughout organic, inorganic & physical chemistry . It is the basis of these sub-fields, and how this is determined is looking at orbitals, energy states etc...
    - raverbashing 13y ago
      Yes, there's an overlap of knowledge So, Pauli's exclusion principle is Physics or Chemistry? I'd say it's "both".
sp332 13y ago
You can simulate the reaction at a quantum-mechanical level at sub-nanosecond timesteps. That gives you a lot of information that you couldn't get from a test tube!
- varelse 13y ago
  OTOH you can't get sufficient sampling on anything but the smallest systems to make any sort of dynamic prediction about it. Not to mention the approximations that were made during the choice of basis sets for the atomic orbitals and how one decides to handle the configuration interaction. TLDR: Approximations are everywhere, make sure you work that into your conclusions.
- Xcelerate 13y ago
  I'll clarify that when he says sub-nanosecond timesteps, he means way sub-nanoscale timesteps. Femtosecond timesteps are used at the molecular dynamics level. Even smaller ones are used at the QM level.

I don't get it. Aren't simulations of chemical reactions based on things you already KNOW about those reactions? How are they being used to find out new things about the reactions?

josephagoss 13y ago

I haven't read anything in the link, but I guess that if the simulation system is of sufficient precision and that it is accurate enough for known chemical reactions, such a simulation system should be able to be pushed further and it may end up simulating events and phenomena that have not been observed in the real world before. Bonus points if they observe real world reactions that agree with the model after the simulation has run.

tlarkworthy 13y ago

Several generic approaches yield results:- 1. You take a lot of empirical observations of known reactions, build a predictive model, then apply it to contexts you don't have empirical observations of. 2. You program in the low level rules of chemistry (e.g. quantum mechanics), and see how the scenario plays out at a higher level (molecular reactions). I think in their work they are more number 1. A predictive model of proteins without having the simulate the (exceedingly expensive) low level details of QM

weland 13y ago

I'm only casually familiar with chemistry, but I used to do research of a similar type (only far worse, of course) related to electromagnetism. You know the main mechanisms at work, but that does not mean you can study all the processes. Sometimes it's just that the sheer size of the mathematical model itself is basically impossible to study without a computer. Oftentimes, though, it's the inadequate formulation of a model that doesn't allow you to simulate it. A good simulation is an immensely useful tool. There are phenomenons which you know and can simulate, but you cannot easily measure their parameters while they are happening (e.g. you risk disrupting the phenomenon because of your measurement installation). I imagine this is even more so for chemists. Real-life example from my own research: we worked on tools that helped engineers who designed really high-frequency ICs (think tens of GHz) study things like cross-talk through the substrate. The mechanism itself is basically well-understood, but save for really, really simple structures that are nothing like those in an IC, you can't solve that by hand. Of course, ours were modest achievements, but the point is that this kind of research can open new gates and shouldn't be considered "second-rate".

blumkvist 13y ago

There are programs which allow you to input desirable qualities (smell, color, density, /non/conductor, molecule mass, stereo orientation to name a few, very basic ones) and it will make computations and it will give you possible compounds. Also software in chemistry can be used to simulate reactions and processes, which can take years to analyze with conventional methods(if at all possible), like folding protein chains.

varelse 13y ago
Actually, Vijay Pande's lab has been "folding" proteins in hours to days for years now by massively parallelizing the trajectories: http://en.wikipedia.org/wiki/Markov_chain_Monte_Carlo http://en.wikipedia.org/wiki/Markov_chain_Monte_Carlo Similarly, David Baker's lab has focused on producing the folded conformations of proteins in hours to days using simplified models that are designed for that task: http://boinc.bakerlab.org/rosetta/ http://boinc.bakerlab.org/rosetta/

deleted 13y ago

[deleted]

shiven 13y ago

You are thinking about reactions as written out in a chemistry textbook. Those representations tell you about the reactants, products and maybe a few other details like catalysts, solvents and temperature. However, none of it explains the mechanism at the quantum or atomic level. Simulating the reaction with specialized software enables you to 'calculate' additional data points, such as, free energy, enthalpy and entropy among others, using 'molecular dynamics' (which 'solves' Classical and Quantum Mechanics equations for a given system and is extremely essential to understand movement of different parts of a molecule and their interaction with surrounding atoms to build a more complete picture of 'how' a reaction proceeds). Today is a great day for computational chemistry. It is good to see the detailed Nobel announcement acknowledge other stalwarts of the field like Peter Kollman (who created AMBER, a package similar to CHARMm by Karplus et al). I have no doubt that Kollman would have received this prize had he been alive today.

raverbashing 13y ago
Exactly Chemistry is applied physics. Chemistry answers that H2 and O2 can be joined to form water under certain conditions, but doesn't answer the "Whys" Physics answers that. And the answer goes around orbitals, energy states, electrons, etc.
- aristomc 13y ago
  "Chemistry answers that H2 and O2 can be joined to form water under certain conditions, but doesn't answer the whys". Chemistry does answer the whys beyond product yields, why certain elements react is vastly covered throughout organic, inorganic & physical chemistry . It is the basis of these sub-fields, and how this is determined is looking at orbitals, energy states etc...
  - raverbashing 13y ago
    Yes, there's an overlap of knowledge So, Pauli's exclusion principle is Physics or Chemistry? I'd say it's "both".

sp332 13y ago

You can simulate the reaction at a quantum-mechanical level at sub-nanosecond timesteps. That gives you a lot of information that you couldn't get from a test tube!

varelse 13y ago
OTOH you can't get sufficient sampling on anything but the smallest systems to make any sort of dynamic prediction about it. Not to mention the approximations that were made during the choice of basis sets for the atomic orbitals and how one decides to handle the configuration interaction. TLDR: Approximations are everywhere, make sure you work that into your conclusions.
Xcelerate 13y ago
I'll clarify that when he says sub-nanosecond timesteps, he means way sub-nanoscale timesteps. Femtosecond timesteps are used at the molecular dynamics level. Even smaller ones are used at the QM level.