Today we talked about LINUX and how to enter in basic data into the computer via a program called PuTTY.

We talked about a program called Gaussian 03 today which is a molecular modeling program. We entered the molecule of water into the program and it gave tons of information regarding the water including stuff like orbital symmetries, charges, and coordinates. I also created this journal page and updated my homepage This is an example of a table generated from Gaussian 03.

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 Center     Atomic     Atomic              Coordinates (Angstroms)
 Number     Number      Type              X           Y           Z
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    1          8             0        0.000000    0.000000    0.000000
    2          1             0        0.000000    0.000000    0.941999
    3          1             0        0.908672    0.000000   -0.251792
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Today in class we talked about the data we generated from yesterday. The reason I didn't post the bondlength table yesterday is because I couldn't find it in all the data generated. But I now know where it is, so here are the bond lengths of water:

Distance Matrix in angstroms also known as Bondlengths

		1	2	3
1	O	0.000000
2	H	0.941999	0.000000
3	H	0.942913	1.500274	0.000000

To find the Bond Angles, we would have to do an Optimization program, wheras here, we just did an energy program. We can still find the Bond Angles by using sine, cosine and tangent rules, but I haven't done so yet. I am going to compare this data to data online, and see if anyone found similar data.

Today we ran the optimization and frequency programs on Gaussian 03 to find better results from what we did yesterday. When we optimize the molecule, we are trying to find the point where the least energy is used. In the optimized version, the Free Energy, or Gibbs Energy, is -75.582475 after 9 cycles, while in the SP, or Energy equation we did yesterday, the Free Energy was -75.5844780197 after 5 cycles. So, the optimized version is not very far off from our original value and only shaved off about .002 Hartrees of energy. The optimized program took 13 seconds to run, while yesterday, it only took 7.2 seconds. Given how much more data we generated today though, this is not a significant time increase.

The table below represents the optimized values of water. The biggest thing to notice is the bond angle of the Hydrogens to the Oxygens, which in this table is 107.6896, whereas yesterday before optimizing it was 105.488.

                        ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
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 ! R1    R(1,2)                  0.9665         -DE/DX =    0.0002              !
 ! R2    R(1,3)                  0.9665         -DE/DX =    0.0002              !
 ! A1    A(2,1,3)              107.6896         -DE/DX =    0.0                 !
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Today in class we discussed our ideas for projects. My topic now is too vague to narrow down, but I think it will involve amphetamines and their receptors in the brain. I also compared my results from my H2O program and the H2O dimer program. Most notable difference is that the RHF, or free energy, of the dimer is about double that of a single H2O molecule. The values being, for the dimer: -152.007633 and for the single H2O: -75.582475. The water dimer has slightly more than double the energy because it has more bond interaction than the monomer. The reason it is slightly more is because in addition to the bonds throughout H2O, there are bonds connecting those two molecules together. In the case of the enthalpies, the situation is similar with the total enthalpy of the dimer being -151.974165 and the total enthalpy of the monomer is at -75.560399. We can use this to find the difference in enthalpies between the two. The way that works is we double the enthalpy of the water monomer, and then subtract that number from the water dimer. We then take that number and convert it from hartrees to kilocalories/mole by the conversion factor of 627 Kcal/mol=1 hartree. Then we can take that number and convert it to kilojoules/mole with the conversion factor of 4.187 KJ/Mol=1 KCal/Mol. After all that math, the answer is supposed to be 44, however, the answer we got is about 332.

This is the equation described in detail above, but in a much easier to read format.

On the technology front, I have now figured out how to add to my website and do programs with Gaussian 03 from the computer in my room. All that needs to be done is to open up a new terminal and type "ssh" and then the name of the drive, such as pandora.gac.edu, and I can then do everything in my room that I can do in the labs. This will hopefully increase my productivity.

Today in class we talked about a new website that we can use to find models of proteins. The website is rcsb.org and has thousands of different proteins and drugs bound to them. We also found that by downloading the file to our harddrive, we can then put images of the models on our website. As of now, I still have not nailed down what I will definitely do for my project. I did some research on Adenosine, and it seems interesting, but as of now I cannot translate that into a project. As for the website I was talking about, here is an example of one type of model you can generate.

Today in class we talked about project ideas and finished up working with the water dimer. Tomorrow we are presenting a rough outline of what our projects will cover. As of now, I think that I will look at serotonin N-acetyltransferase. I don't know specifically what I will do by looking at it, but possibly look at different bond strengths when compared to just serotonin or N-acetylserotonin,which the serotonin N-acetyltransferase helps to create. I am not sure if I understand the process enough yet, so as stated, I am not precisely sure what can be done with serotonin. Another possibility is to look at how it bonds with different proteins, but I have more research to do this afternoon as well as tonight. Aside from that, I have been finding more articles on the ACS website ACS to help spur further ideas. Also looked up serotonin n-acetyltransferase and came up with a few examples that are promising. Also, tonight, I should be updating with a link on the homepage to all of the websites I have been using, as well as some of the HTML stuff I have learned, just so I don't forget. That's all for now. Seacrest. OUT.

Today in class we talked about some different ways to run calculations on Gaussian 03 that will give more accurate results. Also talked about projects and about setting up a page specifically for our project.

In class today we learned about some new modeling tools that should really help a lot with our projects. We also talked about what kind of time costs we can expect with different programs we run in Gaussian or WebMO. On the project front, I am starting to make some more progress especially regarding my understanding of serotonin and its functions, but I will put more of that on my project page, which is right here: Dan's Project Unfortunately, at the moment, Dr. Smith has not set up our accounts to use WebMO, so probably all that will be done today is some more research into serotonin, and working on the webpages.

Today in class we discussed in detail WebAMBER. This is another program usedto do calculations of energy of bigger molecules such as proteins. It does thousands of calculations very quickly to optimize the molecule. I am not entirely sure how I will use this program for my project or if I will. I am still trying to figure out how to get links to other pages to work, but as of yet, I have no idea. Today, I am using WebMO to compare energies within serotonin, and acetylserotonin to find whether the reaction that takes place gives off or takes in energy. Those results will be posted on my project page as soon as they are done and I am able to get them into a good enough format. Also hoping to put more background on serotonin on my project page today or tomorrow.

In class today we discussed yet another set of tools to use. One of which was called VMD. We also went over how to embed Jmol files onto our webpages which will allow the image to be moved around, however as of now I am unable to complete this process. I need to troubleshoot it a bit more and I will get back to you. Today I processed some information I got regarding the formation of acetylserotonin. I will post those calculations on the project website as soon as I have enough information to convey what I am trying to express.

Today in class a couple of people just showed how their progress is going with their web pages and/or projects. Two people are doing some really interestingthings involving carbon capture, but aside from that, we did not do anything with any new tools or calculations.

In class today we just talked about how our projects are going and what we hope to accomplish by the end of the week. On the website front, I did a lot of work on the project page. I now have a working idea of what the final product will look like and all I need to do yet is put calculations as well as some background and just organize the site in general.

Today in class we gave a mini presentation so that we would have an idea of what we need to improve on as well as to introduce us to everone's projects.

On the website front, I spent probably about 2 hours or so getting my jmol figure about how I want it. There is just one thing that I can't get it to do, and it is the thing I wanted it to do most in the first place. Aside from that, there are updates all around getting ready for presentations on Friday.

In class we went over some final questions about our projects and technology problems. Apparently one of the nodes went down yesterday, so there could only be two calculations going at a time. That can be very frustrating when many of the calculations were going upwards of 10 and 15 hours.

The website is now as done as it is going to be for presentations tomorrow. There is always more to do, but at some point you just have to draw a line. So I did. Tomorrow is our last day and we are presenting so this will probably be my last journal entry. It's been great... I laughed, I cried, I lost 15 pounds!But now we must say our heartfelt goodbyes, and move on, maybe our paths will cross some day. I can only hope they do.
Yours Sincerely,
Daniel "Count Braakula" Braak