Abstract (Smarra)

Predicting the pK_a’s of isolated molecules and molecules in proteins

Smarra, Vincent; Boesch, Scott; Wheeler, Ralph

Department of Chemistry and Biochemistry

Duquesne University

The determination of theoretical pK_a’s is the main purpose of this research. The pK_a’s will be calculated using quantum chemical methods with different thermodynamic cycles.  We have selected molecules with found experimental pK_a’s to test. While it is relatively easy to find the pK_a’s of isolated molecules, molecules in proteins prove to be difficult for experimental scientists. To find the pKa of a molecule when in a protein is only a matter of time. Once the pK_a’s of the isolated molecules are able to be accurately calculated, this will be applied to more complex molecules, eventually resulting in the accurate pK_a calculations of molecules when in proteins.

Blog Challenge 2

Blog Challenge #2

1- Why is the basis set B3LYP the most optimal for our simulations?
2- Why are theoretical pKa's necessary if the experimental pKa's have already been found?
3- Why are quinones the only molecules we are testing?
4- Why do we only use certain data from our simulations in calculations?
5- Why must we use the lowest energy form of each molecule in our simulations?
6- What applications will our research have in the world of computational chemistry?
7- What makes the Gaussian program the best for our simulations?
8- What exactly are our simulations simulating?
9- Once the theortetical pKa's are found what will they be used for?
10- Besides pKa's, what are the other things we can pull from our data?

Blog Challenge 1

This year I will be working on a continuation of my project from last year, which was predicting pKa of molecules found within the protein Cytochrome bc1. This project is important for the simple fact that Cytochrome is found within every animal on the planet. When the protein malfunctions it can lead to a devastating physical disorder like cardiomyapathy, which is a usually fatal muscle rotting disease.
The reason I am trying to find the pKa (acid dissociation constant) for this particular molecule is the promise it holds for future research. Because Cytochrome has different conformations in mammals than it does in bacteria, finding how to make it dissociate can provide a new anti-biotic. The pKa is the point at which hydrogen atoms start to leave the molecule. The absence of one of those hydrogens would set off a devastating chain reaction, for Cytochrome is essential in the storing of energry for organisms. If something is not able to store energy, then it is not able to live. This fact of the world provides us with all the motivation we need for the project to continue.

  Its that Project SEED time of year again. The time when highschool students like myself say goodbye to their just beginning summers and hello to the enormous workload that is this program. I may sound like I'm complaining, and maybe it is because I am. Only a little. And it is only a little because I am well aware of the benefits that SEED provides me with.
 While this is only the second day of the program, I already feel myself getting swept up in the swing of things; the dedication to the research, the endless tune of fingers tapping against keyboards, heated discussions about subjects so confusing thatthe general public would assume it was in a different language. That is SEED in all of its glory, and I couldn't be happier to be back.
 Without SEED my summer would be pretty standard for a teenage boy; wake up, video games, nap, video games, and repeat. I'm not saying I wouldn't enjoy that, because I'd be lying if I said I wouldn't. But I can honestly say I'm happy that I'm breaking the stereotype and am looking forward to this summer.
Sonny Smarra

Big Blog Challenge

For my interview I chose to do Raj, a grad student from Dr. Pintauer's lab. She's currently studying abroad and had a lot of interesting things to say.

Q: How did you get interested in science?

A: I always wanted to be a part of something sciencey. And the subject where I am now is the ost interesting to me.

Q: Is it everything you expected it to be?

A: Yes, it is very fulfilling.

Q: What is your favorite form of science?

A: Biochemistry or science, definitely. They are both limitless in potential.

Q: What was your biggest fear going into college?

A: I actually had none, I was completely optimistic.

Q: If you have 3 oranges and 2 apples in one hand, and 3 apples in another, what do you have?

A: Not enough oranges! I want more!! Also, really big hands.

Q: How is the study abroad program?

A: It is such a great experience. The culture and people here are so different it's nice to know there is a different world.

Q: If you could change one thing about your academic career what would it be?

A: I think I'd play more sports. FIeld hockey was one fo my favorites.

Q: How do you feel about your project?

A: I feel fantastic, mainly because we are studying coordination polymers at room temperature, which is definitely more green than at 180 degrees celsius.

Q: What was your hardest class in college?

A: Quantum Mechanics for sure.

Q: Are you looking forward to getting your phd?

A: Yes, but at the same time I'll miss it. I feel as though I'm doing the same kind of work now that I will be doing when I get a job, but I definitely will miss the college life. I guess it'll be bittersweet.

Thanks a lot for your time Raj, you were really fun to interview!

So long and thanks for all the fish

So this is it. This is the end of our program, the annihlation of what has consumed our lives for eight weeks. These weeks were tough, some more than others, and more than one time the question arose in my head if this was worth it. Looking back now, reviewing all my experiences, I can answer that question with a yes.

First off, (when I say this it is in the same league as Oscar the Grouch's voice) what else would I have done with my summer? That's a no brainer though, sit at home, get a dungeon tan, and play video games. Is that neccesarily a bad thing? The lazy teenager in my head says no, but my brain tells me yes. Where else would I have gotten this kind of experience with college level work routines and the college students themselves? I'll give you a hint, the place begins with an n and ends in an e. Give up? The answer is nowhere. Anything I could've possibly did this summer pales in comparison to this project. For once in my life, I really feel as if I've taken the best possible course of action.

I know I'm gushing, but hey it's hard not to. The people here at Duquesne were just fantastic, through and through. My personal mentor, Scott Boesch, has the most patience I've ever seen. Personally, if I had to deal with a know-nothing highschool kid through the long hot summer months, I would've pulled my teeth out with pliers. Luckily for me though he's better than that. he coached me through learning about proteins, equilibrium, use of the Linux operating system, and just about everything else. He isn't the only one who helped though, my professor, Dr.Wheeler, helped me realize how to act in a proper manner. I mean I'm not Conan the Barbian or anything, but I was definitely lacking etiquette. He left it up to me to get my work done on my own, and even set up our group meetings. At first I though he was just being mean, but then I started to look past the actions themselves. What did I learn by him not holding my hand? To take responsibilty for myself, and that when I further my education I'm not always going to have a teacher available. Sometimes, I'm going to need to put my nose to the grindstone and do it myself. Right now I found that concept a little daunting, but hey I still have two years left of highschool, cut me some slack. Last but not least, there's my grad student Linh. When I say nice what do you think of? Kittens? Cookies? Unlimited lives on Pac Man? Well I think of Linh. She was one of the most kind and caring people I've met in my whole life. She supplied me with pictures for my paper and presentations, and her knowledge about cytochrome bc1 itself. Once I learned that my research was going to play a supporting role in hers ( which is a Phd project ) I was very meticulous with my work. Double checking everything as I went,making sure that my numbers were as accurate as possible. These are only some of the many amazing people I met here, and I wouldn't be have been successful in this program without any of those people.

On to my SEED overseer and the project manager. During the school year Mr.Lucas was definitely a different person. He was laid back, joking around, but he always pushed us to do our work. If I remember correctly, he's one of the main reasons I did this program. In the beginning of SEED though, I realized something: Duquesne was no place to mess around. This was a place where people take their learning seriously. I learned that almost immediately and I'm glad I did. It actually surprised me at first, realizing how much I would have to grow up to succeed. Mr. Lucas really helped me at the beginning and most likely set me on a path for success. I had one more influential person in my SEED experience and that was Dr. Aitken. She wasn't around as much as the others, but that was because she was on a sabbatical with RJ Lee group. They are a well renowned research company and I was impressed that she could transfer from an academic environment to an industrial one so well. I should've expected it though, the woman radiates adaptivity. That is why she was so helpful when we spoke, she could see both sides of the coin, and helped me realize that some things just can't be split up black and white.

I can honestly say that this experience was an eye opener. I didn' t think college was going to be easy by any means, but I definitely didn't think my work routine would have to be so disciplined. I'm really grateful that I got to partake in this program, if not for the people I met, then for the oppurtunity to expand my horizon. If all goes well I will do this again next year and have even more fun! Byebye everybody!

Apex of our year

So much has happened since my last blog I don't even feel like doing this.

<-----END TRANSMISSION----->


Yeah I wish. Last Friday was the main event for the year, the big shebang. Our research symposium was a huge success. There was a few keynote speakers to lead off the event, people had to give their dissertations. You could tell that they were good by the fact that I saw no one sleeping. I mean, it was 9:30 and it was a room full of college students. After that came the best part of the day....I mean lunch. This was when we got to socialize with even more SEED students, these ones hailing from WVU. It was good to talk to them and learn about their projects. I was so happy that it pretty much negated my anger from my ice cream prematurely melting. Almost.....I was really looking forward to that.

Anyways, after lunch came the poster session. It was pretty amazing to see the varying kind of research that had been done. It went from analyzing characters in Russian fairytales to molecular dynamic simulations of the norepinephrine and serotonin transporters in a lipid bilayer membrane. Can you guess which one I understood?

Once it was my turn to present my poster my nerves were at an all time high. With my luck I'd get Stephen Hawking asking me to explain my poster. However, once my first visitors came, I found that I was readily prepared and even managed to slip in a smooth wink.

After the session was over, I realized that this might be the last time I get to see my group, so we didn't pass up the oppurtunity for some amazing photo ops.



After the dust settled from the symposium, we had the Project SEED alumni lunch. I was very anxious to meet some of my predesscesors. I thought they were going to be very stuck up and judgemental. I also thought the Steelers were going to win the Superbowl. Turns out I was wrong on both counts! Everyone was extremely friendly, and very eager to share their experiences and wisdom with us. There were even a few fellow Sto-Rox students who were in college. It is nice to be reminded evry now and then that you shouldn't let where you come from hinder you. Tim McFadden is just starting his PH.D program, and Chris Siden is in his third year of Duquesne's pharmacy program. If they could go on to do great things like that, who's to say I can't?

So that's about it, the last few days in a nutshell. SEED is almost over now and it is weird to think that I'll actually be able to sleep in soon. That is until school starts, at least.

Bayer field trip

Today our group took a tour of the Bayer campus located not far from Duquesne. This was one of the first tastes of industrial chemistry I've ever gotten. RJ Lee group was nice, but I feel like it was more of a small company. That is definitely not the case with Bayer. I first noticed the big feel when we turned onto Bayer road. That's right, they have their own road.
The surprising thing wasn't how big they were, but how friendly the facility was. I'm not just talking about the people, but mostly everything was aesthically pleasing. I find that a very respectable thing about companies, when they care about their employees to tthat extent.
If I haven't stressed just how big Bayer is (which I think I have) prepare for more. Our tour stretched between two buildings, numbered one and eight. That means that there at least eight full sized R&D facilities on the campus, complete with countless machines. At one point we were even at a place where our tour guide had never been. They don't have all of these buildings just for show either. While on our tour we saw the variety of research they took part in, from developing top of the line bowling balls to their explsion proof glass. To say that they specialize in variety is a bit of an understatement.
While there were many enjoyable instances throughout the trip, my favorite was meeting the other two SEED students. They started a little later than us, so they're still acclimating to their environment. From what they could tell us though it is safe to assume our two work places are noticeably different. They have a lot more independence than us, being given a task for the day then left alone to do it. That isn't neccesarily a good or bad thing though, because I'm sure both methods have very fine advantages.
All in all, the Bayer trip was memorable and I won't soon forget it.

Washington and Jefferson trip

Today we went on a field trip to Washington and Jefferson college. To say that it surpassed my expectations is an understatement. You hear the name of two dead presidents and what comes to mind? Money? Snobbery? Maybe that was just for me, but I'm happy to say that none of those things seemed of prevelance to them. Our tour guide was very informative, and he stressed on giving us information about the college experience itself instead of selling us his school. That gave me a hint of the kind of teacher that they employ: caring first for education, then personal gain. I found that very impressive, because I was under the impression that every college was a ruthless business concerned first and foremost about their capital. Washington and Jefferson proved me wrong, and I couldn't be happier.

Blog Challenge 2

This is my interview of collaborator and fellow SEED studet Chelsea Weidaw.

Q: Hi Chelsea, how're you today?
A: Not bad, you?
Q: If you don't mind I'll be the one asking the questions here. Jeeze. Are you ready?
A: Oh yeah...I guess.
Q: Fantastic. Is SEED everything you expected?
A: Yeah I guess. It's a lot harder than i thought it would be. It's actually just the reading. Originally I didnt'k know what any of the words meant.
Q: I know what you mean. But Google was your messiah right?
A: Messiah...? If you mean did it help, yeah.
Q: Are you excited for the symposium?
A: I don't think excited is a good word to describe it. Anxious maybe.
Q: Anxious about what in particular?
A: Pretty much just the people. I might get some Einstein who knows everything to know about Forensic Analysis. He'd probably tear apart everything I said.
Q: I bet not! And plus you could always just hide under a box. Fool proof plan. Do you actually like what you're doing?
A: Of course! I love all the CSi and all the cop shows so this is really interesting. I know it wont't be anything like the shows but I'm ok with that. I don't think guns suit me anyway.
Q: So is your heart set on forensics for college?
A: I'd say so. Nothing else seems as interesting, at least to me.
Q: So what exactly is your project?
A: I'm analyzing hairs and the products used on them. It's basically using the GC/MS to really look at them.

So there it is, my interview of Chelsea. She has what she wants to do figured out. Which is more than I can say. I'm clueless.

Half way there!!

So i glanced at the calendar today and realized that the research symposium (Our main event) was only sixteen days away. It's amazing how fast the time is flying by. It seems like only yesterday i was scrambling to find my way here. I'm even almost okay with waking up at 6:30 in the morning. Almost.
However, on a better note, we went on a field trip today to tour the RJ Lee group building. What they do there is nothing short of amazing; they've studied from the air at Ground Zero to lead paint in Hasbro toys. That was the first time I think i've actually noticed industrial science. I'm not saying I thought everything happened by magic or anything, I just hadn't put much thought into it. I think that appealed to me most there was the talk we had on the finer points of forensic science. I was shocked to learn that bullet particles on an accused criminal didn't automatically spell guilty. They are apparently easily transferrable, the most common place this happens is actually the police station, which seems kind of counter productive to me.
Lets all give me a standing ovation though!! I'm actually starting to semi kind of sorta understand my project. On a serious note, most of it is starting to come together. When i first started to get it I was so thaknful. It was a breath of fresh air when I figured out how to enter my molecules into the supercomputer. I think it's time for me to go though. I still have work and all, so until next time!!

Starting the grind

It is now the third day of the project, and I'm only starting to grasp the basics of my topic. The slow going progress I'm experiencing is new to me, because I've always been a fast learner. Compared to my usual speed, I'm feeling about as fast as molasses, and thats being generous. Very generous. I guess I'm going have to get used to this. I'd say it has humbled me, but I think I'll save that line for later. After all, it's gonna get a lot harder before it gets easier.

Blog challenge 1

Hello, my name is Sonny Smarra, I attend Sto-Rox high school and I live in McKees Rocks.

I think it's fair to say my hopes for this summer can be boiled down into one word; SURVIVE. As of this moment, the work I'm scheduled to get done is on a seemingly impossible to reach plateau. However, I had hoped for this very situation: I came into this program looking to be pushed to my intellectual limits, and right now it seems like that will be no problem. My main goal for this summer is to to be able to hold my own in a conversation with my professor about my project (which by the way is Predicting the protonation states of amino acid side chains in the protein complex cytochrome bc1.) and to develop work habits that will help me in all facets of my life.


Okay, heres the fun part. My first impressions of this program. When I was first told my project name,(Predicting the protonation states of amino acid side chains in the protein complex cytochrome bc1.) my first thought surprisingly wasn't ,"Whaaaaaa??!!?!". I was too busy marveling at the respiratory strength needed to say that in a sentence. So it's safe to say when I met the staff here I was pleasantly surprised. I expected a bunch of hard nosed scientists who didn't want to be bothered by a meager high school student. Instead, I was greeted with respect and I can sense that all of the professors are very passionate about education and their respective projects. I still have no idea what my project is, but I can say i have faith that everyone will do their part to explain everything to me. Now i just have to worry about understanding it.

First thoughts

Overall science is a pretty intimidating idea. I mean, how can you even grasp that you're dabbling in something that took our race hundreds of years to come up with? That is why initially I was frightened at the idea of SEED. However, as i sat down at the conference table to meet my fellow participanta I couldn't help but also be excited. This seems like it will be a fantastic oppurtunity and something that will help me not only in my future, but the here and now. I can honestly say that I think I'll flourish under these conditions. I find that I'm at my best when I'm hard at work, putting my nose to the grindstone. This in no way should detract from the complexity of what we'll be doing here though. I yawned while Dr.Aitken was explaining something and was lost in the huge void that is my ignorance for the rest of her explanation. I think it will suffice to say that I'm genuinely excited for this program and looking forward to the days ahead. +