Stat therm

Last night my boyfriend asked me (he's a chemistry major, although a sophomore taking organic right now) what the reagent NBS did. I could answer him immediately and even describe the structure of the molecule and that NBS stood for "n-bromo succinamide".

Organic reagents, pKas, structures of the amino acids, NMR shifts and typical J-values, IR shifts, even some boiling points, this is all at the tip of my fingers. It's just stored in my head--anything organic or bioorganic is just there. I haven't forgotten it.

There's an incredible amount of information pertaining to organic chemistry and biochemistry that is just completely accessible in my head. I do not understand then, why it is so difficult to download thermodynamics equations in there. It's not like I enjoy memorizing pKas anymore than I enjoy memorizing thermodynamic definitions.

I realized earlier today that I have been approaching physical chemistry all wrong. I have a really shitty memory for information without context and so while some people can just cram equations into their head for tests that tends to not work for me. Organic rarely required memorization beyond a few weirdo reagents whose mechanisms were beyond the scope of the class; it was just mastering a few trends and then applying problem solving. Math is like this too, and physical chemistry is math. I need to learn the definitions and work from there and apply problem solving to derive everything I need.

Since I am uncomfortable with math as a language given my poor schooling in calculus, I have generally considered myself not mathematically facile enough to apply this approach to stat therm. I realized today, though, that the memorize special situations equations approach and memorizing derivations approach isn't going to work either, because there is just too much goddamn material for that. And I am facile enough with algebra and calculus...I just need to be confident that is the case. I need to work with the language and do the problem solving.

Why won't the algebra work out?

Fugacity is currently the bane of my existence.

There's so much to chemistry

Basically what this semester seems to be boiling down to is physical and inorganic chemistry are waaaaayyyy different from organic. Jesus christ.

I've been fussing around trying to calculate the numerical radii for the radial nodes of a 3s and 3p orbital for frickin' ever.

I feel like my rather shitty math background has been a constant handicap. Due to the fact that the math department at Reed only teaches theoretical math geared towards math majors, and due to the fact that Rao (the math head) determined my semester of calc I at UIC as equivalent to Reed math 111 (calculus), I have managed to skate through Reed college only taking probability & statistics. Because of this wacky math system, math 112 is more introduction to proof writing than a calc II course, and I was told that unless I was really into theoretical math it wasn't going to be fun and it certainly wasn't going to be useful. I never took calculus in high school and I didn't want to push physics to my junior year (thank god I didn't).

Due to this situation the chemistry and (especially) the physics department pick up some of the slack. Yesterday I learned how to take a second partial derivative with respect to two different variables. Having never taken a multi class, I picked up the concept of a partial derivative and how to do it in intro physics when learning about the wave equation. I had never seen the notation for a double partial derivative before. I'm a little shake on integral tricks too.

I'm usually ok with this fact, and I've kind of accepted that I'm more prone to think about the world in descriptive terms. This doesn't mean that I'm not down for a few computations, but I'd rather plug it into a modelling program or mathematica. I'm good with scooting around arrows, stability rationalizations in the style that organic chemists do it, and basically things that operate in pictures and words with small amounts of algebra and maybe a derivative or two. I love to learn about biophysics and I think the techniques that are out there are quite fantastic, but my understanding of them is all in pictures and words. Same goes with NMR. My feeling for the physical world is one where math is a tool, but I'm not interpreting it through it. I see math is a way to get better pictures in my head. This is at a stark contrast to the way physicists--and for that matter, even physical chemists--seem to view it--as if they interpret physical phenomena through math.

I'm re-learning about the quantum numbers for inorganic (I learned it in intro chem once but forgot) and there's always something in the book like "you can solve the Schrodinger equation for hydrogen and hydrogen-like nuclei, but we're not going to go into it in here" and sometimes it makes me feel bad about not taking quantum. It's like, even though I did quite well in my synth class, I feel like I don't have quite the feeling for what is all behind it as some people. I know that what I learned in intro physics I generally rarely use beyond bits and pieces here and there, but it was good for backing up my general physical intuition and understanding for how things work. Conservation of energy, waves, momentum, acceleration, electric and magnetic fields, these are all fundamental things that I need to understand as any sort of scientist--and are even helpful conceptually for biology. Ploughing through it all, I can't really do those problems anymore but I left with a better conceptual understanding of the physical world. Dan reminded me the other day that physical chemistry does this for other types of chemistry, i.e. the pictorial representations of stability rationalizations are quantifiable (well, sometimes) and that's where the theoretical basis for these qualitative observations come from even if we don't always have the computational power and models to find them quantitatively. It doesn't mean I have to want to be a physical chemist, but I do realize the power in other chemical approaches and understand why I need to learn about them.

I think a lot of my issue with math is a lack of confidence from being "bad" at it for so long. I mean, calculus is a tool like algebra and not like WHOA COMPLICATED OMG MAGIC!

On the up side, speaking of nice, fuzzy picture-based synthetic organic chemistry, Pat gave me a little project to mess around in the lab with. He gave me a couple compounds he'd like to make and test the pKas. I need to go play with Sci-Finder to see if they have been made before. This is good; they're small molecules and models for the types of compounds the lab as a whole works with, but in the past the research I did with him was more guided like "here's this idea I got, I'd like you to try it out" instead of asking me to find preps that I might be able to run. I also know more chemistry and know how to use Sci-Finder better than I did when I worked for him last summer, though.