[xlovenuggetx]

I am going to begin organic chemistry this coming fall. I wanted to ask you all about programs that could help me understand and visualize reactions (i'm a big visual learner). I have used Spartan, which i prefer to any other program i've found, but i haven't learned how to use it extensively, and it seems geared more toward chemical engineers. I thought maybe someone here could direct me to a program that they have used with great success. I want to be able to build molecules, quickly identify the functional parts of the molecule, see orbital configurations and 'react' the molecule with another and see it form. I realize there is a chance that such a program does not exist, but I wanted to check anyways. thanks for any input.

[Honclbrif]

For the calculations end of things there's also Gaussian. Never used it personally but I know some p chemists who spend a lot of time with it.

As for structures and naming, I like ChemSketch and MarvinSketch. They're both pretty intuitive and fairly user friendly. Also, available as freeware .

[xlovenuggetx]

For the calculations end of things there's also Gaussian. Never used it personally but I know some p chemists who spend a lot of time with it.

I'm at work so time is limited at the moment but i did a quick search on Gaussian and looked up a tutorial to browse some of its features and it looks promising. you can view orbitals and reaction pathways. on the downside it costs >$1000 at least. thanks for the suggestion! maybe i can demo the software someplace...

[Honclbrif]

If you're at a school, see which programs you have licenses for. Also worth it to check out student discounts.

However, I'd recommend trying to learn organic on paper rather than Spartan-ing your way through everything. Its cheaper and for ~99% of cases (and 100% of those you'll see in sophomore organic) its just as good. Furthermore, you're not allowed to use Spartan during tests...

I'm a visual learner too and the best way to learn organic IMHO is to get yourself a legal pad, a pack of pens, a model kit, and do every problem in the book. Its how I did it, and with a little time you will really start to learn to visualize what's happening.

[Sepelio]

See if your university has anything on an academic software license that you can use. Personally I recommend Chemdraw for... chemistry and auch damn. There was a good good program for protein/molecule 3d visualisation but I've forgotten the name of it. I'll be sure to come back and edit this post if I remember.

[Honclbrif]

I haven't found anything that Chemdraw does that Chemsketch or Marvinsketch won't do just as well, except the MS isotope distribution thing (which while pretty neat has honestly only been useful to me once or twice because I'm an idiot who can't remember what happens when there's two bromines in a molecule) and the NMR predictor (which honestly isn't that great in the version I used). If you're just using it to draw structures and determine the occasional MW and formula, the freeware programs are just as good.

[nox]

I like ChemSketch's shortcuts, you could pretty much draw anything organic with just left/right clicks. That said, it is HORRIBLE for drawing complexes or anything inorganic. It tries too hard with the charge balancing and in the end you have to go in and fix everything manually. I do wish Chemdraw had as extensive a template library though.

[xlovenuggetx]

I'm uncertain as to whether my school incentivizes the purchase of chemistry software by giving free access to molecular databases or discounts. I will definiately check it out though.

I really wish they would just make a chemistry videogame already.

honclbrif I found that in general chem I and II the volume of problems was overwhelming, and so I never hoped to complete all of the problems in my book, but i'd imagine that your advice is fully legitimate for organic courses. I know it worked in calculus

I own a molymod model set which i used most often when covering VSPR geometry and others. Now I just build molecules I think I should remember and leave them next to my computer to familiarize myself with them. 

Thanks for the input fellow humans. I'll keep looking.

[johnuk]

The piece of software I use the most is the popup nomograph on Sigma's page; google for "nomograph" and it'll come up as the first or second link.

If you click the pull out tabs on the right, those can be really useful; particularly the "physical properties" one.

However, this is more related to the actual practical chemistry. Unless you have a semi-decent lab at home and are doing practical chemistry involving pressure differences and so on, you will be told precisely what to do at university and won't be allowed to run things your own way.

{edit}

Oh, there's another interesting bit of software available from James Hendrickson.

His group has produced two versions. The first, and more basic, version is free. You draw what you're starting with, what you want, define the changes you'll allow to the carbons and it'll come back with a list of ideas from journals that you can then have a look at (provided you want to pay for the articles or can otherwise access them).

The second you pay for and I think it instead works using mechanisms to suggest new routes. Since these are unreferenced, potentially never attempted, suggestions, it is not guaranteed that they will all function, or be nice or economical to do. But it is a good way of looking for new ideas.

You can find them both on his groups website, which seems quite temperamental; sometimes it'll be up, other times it won't respond (so there must be a wonky server or something in the way).

Here's a link to his profile at Brandeis and there's a link on there to his own site with the software on it. You may have to check back as his page isn't working at the moment. I'll send him an email and let him know.

James B Hendrickson - Professor Emeritus of Chemistry - Synthesis of natural products. Computerization of synthesis design and development of new synthetic reactions.

[xlovenuggetx]

The piece of software I use the most is the popup nomograph on Sigma's page; google for "nomograph" and it'll come up as the first or second link.

If you click the pull out tabs on the right, those can be really useful; particularly the "physical properties" one.

However, this is more related to the actual practical chemistry. Unless you have a semi-decent lab at home and are doing practical chemistry involving pressure differences and so on, you will be told precisely what to do at university and won't be allowed to run things your own way.

{edit}

Oh, there's another interesting bit of software available from James Hendrickson.

His group has produced two versions. The first, and more basic, version is free. You draw what you're starting with, what you want, define the changes you'll allow to the carbons and it'll come back with a list of ideas from journals that you can then have a look at (provided you want to pay for the articles or can otherwise access them).

The second you pay for and I think it instead works using mechanisms to suggest new routes. Since these are unreferenced, potentially never attempted, suggestions, it is not guaranteed that they will all function, or be nice or economical to do. But it is a good way of looking for new ideas.

You can find them both on his groups website, which seems quite temperamental; sometimes it'll be up, other times it won't respond (so there must be a wonky server or something in the way).

Yeah the website is down at the moment, but i really appreciate the suggestion. I could see the nomograph being extremely useful in the right line of work. If i have the time and can muster the willpower, i want to create a sticky thread for chemistry software with links and pictures in the near future, rather than add to the growing number of software threads that are now dead. Thanks again everyone.

[BluePill]

ArgusLab is a good freeware for calculations.