This is the homepage for my J-term class and project. It will include daily journals of what happens.
This is the homepage for my J-term class and project. It will include daily journals of what happens.
Today we began work on our website and began to become familiar with lennox and puTTY
Today we were introduced to Gausian 03, a program that will help us look different molecules and their bond lengths, angles, and charges. We began with a simple water molecule to aid us in becoming familar with Gausian 03.
Today we went over and analyzed our results from Gausian 03, I learned that Gausian give results in units that I am not familar with and that I will have to use unit conversions to better understand my results. I also began working on H2O dimer with Gausian.
Today we discussed the articles that we read over the weekend to get an idea for possible projects. I think I might want to do something with a material or something that is somehow related to Geology. My article was about C8, a carbon nanocrystal that is denser than diamond. The article for those with access to the American Chemical Society can be found at http://pubs.acs.org/cgi-bin/abstract.cgi/cgdefu/asap/abs/cg7006777.html. In the computer lab worked on finishing water dimer data and analysis.
Today we were introduced to a website www.rcsb.org which is a Protein database with 1000's of proteins and drugs that bond to them. We also talked a little about x-ray crystallography. One main aspect that struck me was the short comings of this method, such as the fact that it needs to be in crystall form, where as when it is in the body it is not in crystall form. Another short coming is that the Hydrogens are too small to show up so other methods need to be used to make educated guesses as to were they are. But never the less x-ray crystallography is a way in which to gain insight into the 3-D structure. In the afternoon I looked at the protein 1r5p, which is a circadian oscillation regulator.
Today we talked about what we found on the website yesterday. And the expectations for class tomorrow. I will need to come up with a project idea soon.
Today I mainly changed color scemes on my webpages to all be the same, and talked with Professor Smith about possible projects that relate to color of different minerals, more specifically gemstones.
Today we were introduced to the AMBER system and WebMO. I got my project idea cleared and began researching and looking through the books that I got from a Geology Professor.
Today we talked more specifically about the bonds and what happens at the molecular level and the fact that the bonds change and are in different positions. The professor used the word floppy to describe this type of motion in the bonds, but ultimately on the molecular level the bonds just aren't permanently fixed in a given conformation like most pictures or models might lead one to believe.
Today we were introduced to a couple new image sites to visually model our molecules, one site we were introduced to we also have the option of making a movie. This was rather complicated and if I decide to use this option I will most likely need help with that. Did more background research hopefully by tomorrow I will have picked a mineral with two different colors.
Today in class several individuals shared their progress on their projects, and although not neccessarily the intention but we discussed both current and new ways of displaying images. I have decided to do my modeling project on the mineral corundum, also known as Ruby (in it's red form) and Sapphire (when it is any other color). I will assume that it is in it's pure form and see how the UV spectrum changes with the addition of more and more molecules.
Today I spent several hours searching for a corundum that was already built for me after several failed attempts at making my own structure. I would like to have a structure that is large enough so that it has 100 or better yet 200 total atoms, because usually ruby is found to have only 1% chromium and I would also be able to add in one Fe and one Ti. In this manor I could stay consistant with the changes to the structure, eventhough I have not yet found the ratio for blue sapphire.
Late last night I found a structure of corundum in xyz format, but I didn't realize until lab today that it was different than most of the structures that I have seen so far. I also found some Jmol applets, but couldn't get any information off of them. The Professor did notice that I could get them in cif format, but then I would have to reformat them into pdb format to use them on webMO. I set up the calculations for corundum, ruby, and blue sapphire, hopefully they will workout. I will check on them later tonight. Now I just need to put up somemore information that I have and put in new links on my web page to help with my presentation. I also need a better concept of the information that I have found on the causes of color. Note chromium also causes the green color in emeralds.
Today I tried to add the finishing touches on my website, but I also had to wait for my calculations to finish. Ultimately they ended up failing just before 3:00pm central time. I entered in two new calculations for geometry optimization in the hopes of then retrying the UV-vis calculations, but they ended up failing as well. So I added the data I had and found images to put on my project page.
