Reddit reviews Essentials of Computational Chemistry: Theories and Models

Don't know about skills you want, but there's quite a bit of free chemical software that it'd be good to be familiar with (Avogadro for building ligands/small molecules, Chimera for supramolecular and docking, etc.). Likewise, if you have access to WebMO, play around with it. The questions you develop while just trying different theories/basis sets with the same compound will lead you into a better understanding of what computational can (or can't) do. Molecular dynamics is a popular approach to protein (and thus biological) simulations. If you've never operated a computer from the command line before, there's a Codecademy course that has a good overview on that.

Google and Wikipedia can be your best friends. Most of my understanding came from seeing something discussed in a paper and researching what it was and why it was useful. This presentation gives a lot of background for theories and where they came from. This site has a nice introduction to semiempirical quantum calculations. I found this site when trying to understand what basis sets were, and it was very informative.

If you want a book, Essentials of Computational Chemistry is pretty widely used in computational courses.

Hope this helped a little bit!

I think more than just an issue with simplicity or difficulty this is a matter or feasibility. A grad student could easily get their dissertation doing this project for just one molecule. However if you're serious about this let me give you some advice.

• When I say decomposition pathway, I mean physically what are the molecules in your battery doing in order to produce a current or energy? This will require a large understanding of electrochem and physics as well as an exceedingly up to date understanding of material sciences in the physical chemistry field. I recommend start by reading publications on current "next gen batteries" and see where that takes you. If you go to the UO science library you can use their computers to go through the literature. I'd recommend reading Journal of Chemical Physics, Physical Chemistry Chemical Physics, American Chemical Society, American Physical Society, and/or Physical Review Letters
  
  
• Drop this notion of a permutation set, or at least limit it to a molecule class (with specific allowed elements or lengths). Unless you set up exceedingly smart parameters all you will get is 99% of your data being for molecules that absolutely can't be used for batteries. For starters, do you want to find organic compounds that combust like gasoline as a source for fuel? I think you more likely want something like a Lithium ion cell which would require you to look at transition metals. Be less concerned about being able to make a set of 10^50 molecules and instead focus on how (from a general molecule motif) would you generate energy in current form. How much energy do you get from a redox reaction of Li in acid versus a complex of (Li)_n. An added complexity is that the order in which you arrange them will also change the bonding. This isn't just, will it make a linear chain or will it fork, or will it be circular; this is going to involve analyzing how the electrons interact on an orbital level. This work is basically probing the question of how catalyst work (an answer to which would undoubtedly get you a Nobel prize).
  
  
• Being that you will most likely need to do some type of oxidation reduction reaction (you'll see a lot of excitonic processes currently being used for energy) to generate free electrons this guarantees that you will need to do ab initio quantum calculations. In order to do that you have to basically derive the energy of losing however many electrons in a specific manner in a vacuum at 0 K. HF will NOT cut it. You will need to use several high leveled theory basis sets and compare the results. This means you will not only need to understand mathematically how these calculations are done, but also understand quantum mechanically how best to represent poorly defined things such as single charge states, ionization, and far more complicated advanced topics.
  
  
• Look into Density Functional Theory (DFT). For reactions that mix between classical and quantum (semi-empirical) it's the current standard way to go. That being said, this is not a technique that can be generalized to any molecule. Every simulation is exceedingly specific to every case.
  
  
• You will need computers. Lots of computers. Either you build your own super computer and drain your bank account funding the electricity (you will need to be a billionaire to do this) or you do what any sane theoretical chemist would do and apply for grants to some of the XSEDE super computers. Keep in mind the grant cycle just ended so you'll have to wait until next year to even begin applying and you'll need to convince way tougher scientists than me. If you're planning on doing semi-empirical and especially if you plan to do any ab initio calculations you will need a lot of computational resources. Try playing around with Gaussian (g09) available for free on most linux machines to get an idea of how long these calculations take and how much more processing power and memory you'll need.
  
  Here are some books and resources that will catch you up McQuarrie, Cramer, Marcus Theory, and all things Mukamel for electron transfer.
  
  Good luck!
  
  [EDIT]: As far as temperature goes, that's a concern more so for the effects on a classical level, so you need a MD or semi-empirical system with a good forcefield defined.

Whatever software you are using will have documentation on how to run calculations and interpret the output. That will be the most practical source for what you are doing. For more info on the DFT method, any computation chemistry book will do. Cramer and Jensen are popular, but I've heard this monograph is great too.

Nice.

I also highly recommend Christopher Cramer's book for applications.

For computational chemistry:

You will need to have a solid understanding of Quantum Chemistry. The two commonly used books for this is the following...

Quantum Chemistry: 6th ed. by Levine

Modern Quantum Chemistry by Szabo.

Honestly don't worry too much about the newest edition of Levine. I've been using the 5th edition and not much has changed. Szabo is published by Dover so its dirt cheap.

For actual computational chemistry, Cramer does a decent job.

There’s a really good one published by Wiley called Essentials of Computational Chemistry. I work in a comp chem lab and this book is still extremely relevant and serves as a great reference imo. If you really really want to get into the theory of MD check out this set of lecture notes. http://fy.chalmers.se/~tfsgw/CompPhys/lectures/MD_LectureNotes_181111.pdf https://www.amazon.com/Essentials-Computational-Chemistry-Theories-Models/dp/0470091827