What do I do? 2: Spectroscopy

When people find out that I am doing a PhD in Chemistry, they often ask, somewhat foolishly (by those who aren't really that interested), what it is I do.  I then find myself in a position of trying perform a juggling act to find the balance between a number of things.  How in detail do they want me to go?  Where's the right place between talking over their head, and sounding like a condescending jerk.  Are they actually interested, or are they just being polite.  Based on their background, what parts will they find most interesting?  On top of that, I need to plot a coherent course through my thought process so that if they are interested, they don't get lost in the maze inside my head.

So, I've decided to write it down, and see if I can make a logical series of articles about what I do, starting with the background information that's needed, eventually ending up on what I do day to day. Today I'm going to talk about the basics of spectroscopy.

Spectroscopy an important tool used in interrogating molecules (my favorite way of describing it.  Conjures an image of a Hollywood crime drama, with a molecule cuffed to a table,a detective throwing a chair at the window trying to get answers).  It's used in the food industry as a quality assurance tool, by pharma companies to analyze composition of drugs, in the medical field for many tests looking for symptoms of disease, in forensic science for investigating crimes, and by scientists in many fields to study whatever it is they are interested in.

So what is spectroscopy?  Last week I wrote about the different ways that molecules store energy, and the ladder of states that result from that.  I've updated that post with a visual of what those states might look like.  The goal of spectroscopy is to use light to measure the distances between the rungs on the molecular energy ladder.

So how is light related to energy?  Trick question.  It's not related, it is a form of energy.  Light is more than just the familiar brightness that allows you to see..  Visible light makes up a small portion of the electromagnetic spectrum, only the wavelengths between 400 and 800 nanometers. (if you imagine an infinite field of equally spaced waves, the wavelength is the distance between two consecutive peaks.  1 nanometer = 0.000000001 meters, or 1/1 billion meters).  Different wavelengths correspond to different colors that we see.  I found this cool tool that lets you move a slider around on to find your favorite color's approximate wavelength (I like 469).  Visible light is not the only portion of the spectrum that you have had interactions with.  If you've ever had a sunburn, it's from the interaction of ultraviolet light with the DNA in your skin.  The warmth that you feel from the sun is mostly infrared light.  Doctors use x-ray light to examine bones.  Your car radio receives information through radiowaves.  Your cell phone does the same, but in the microwave region.  Your microwave oven?  Yep.  That's light too.  These are all words used to describe light at different wavelengths.

There is an equation called Planck's equation that allows us to convert the wavelength of light into the energy corresponding to that wavelength.  As the wavelength decreases, energy goes up, so shorter wavelengths, like those of UV and x-ray, have more energy that longer, such as radio or infrared.  And here's why we care, in the context of spectroscopy.  Different wavelengths of light roughly map onto the spacing of the different types of rungs on the molecular energy ladders.  I've included a table showing those relationships.


Ok.  So know we've talked about light, how it's energy, and how the energy of different regions of the spectrum can map on to the spacings between the molecular energy ladders.  Now we just need to put these concepts together to understand spectroscopy.  Lets say we have a molecule that is in the X¹∑⁺ v=0  state in the diagram on the right (that corresponds to the lowest electronic rung (or state), and the lowest vibrational state inside that electronic state. X¹∑⁺ is what's called a term symbol.  They contain a lot of information about a molecules electronic state, but I'm not going to go into that now). If we shine a light on this molecule, with an energy that is equal to the difference in energy between X¹∑⁺ v=0 and V¹∑⁺ v=3 state, the energy from that light can be absorbed by the molecule (for a visual see the red arrow).  This condition of the energy of the light matching the energy difference of the states is called the resonance condition, and is the basis for spectroscopy.  It can also go the other way.  If a molecule is in an excited state, it can drop down to a lower energy state, and emit a flash of light, as shown in the diagram as the green arrow.


So there are two ways we can use this simplified picture of spectroscopy to measure properties about the molecule.  We can hit the molecule with many different wavelengths of light, and see which ones it absorbs, or we can give the molecule an excess of energy, and look at the light that it emits.   Both methods give us the basic information on relative spacing of states in the molecule.  Because the molecular energy ladder spacings are unique to each molecule, we can identify which molecule we're looking at, based on the spectroscopy we perform.  That's how it works in theory.

In practice, we have to build an instrument that allows us to select which light the molecule absorbs/emits.  The basic schematic for an absorption spectrometer can be seen below.  I'll outline some of the critical components. The light source, which is represented by a lightbulb, is the light that is used for measurement.  This light source could be as simple as an actual light bulb, or it could be something like a laser, microwave generator, or particle accelerator.  The type of source used is dependent on what is being studied, and the specifics of the instrument.  It is also necessary to have a way of distinguishing the wavelength of the light, as represented by the vertical black screen with a slit below.  This doesn't have to be before the sample, it could be after, or it could be in the processing of the data later.  How well we can distinguish between wavelengths gives the resolution of the technique.  The box below represents the sample that is being measured.  Light passes through it, and some is absorbed.  What is left passes into the detector, represented by the eye.  By comparing this to the light that would be detected with nothing in the sample cell, the wavelengths the molecule absorbs can be identified, and used to characterize the sample.

Next week, I'm going to talk a little more about the emission types of spectroscopy (not because they reaaally apply to what I do, but because I think they're awesome, and you've seen their effects in real life).  So stay tuned.

What do I do? 1: Using the word Quantum correctly.

When people find out that I am doing a PhD in Chemistry, they often ask, somewhat foolishly (by those who aren't really that interested), what it is I do.  I then find myself in a position of trying perform a juggling act to find the balance between a number of things.  How in detail do they want me to go?  Where's the right place between talking over their head, and sounding like a condescending jerk.  Are they actually interested, or are they just being polite.  Based on their background, what parts will they find most interesting?  On top of that, I need to plot a coherent course through my thought process so that if they are interested, they don't get lost in the maze inside my head.

So, I've decided to write it down, and see if I can make a logical series of articles about what I do, starting with the background information that's needed, eventually ending up on what I do day to day.  Today I'm going to talk quantum mechanics.

In Ant-Man and the Wasp, there is a moment where Scott is sitting confused in a room with a bunch of "physicists" who are talking about the quantum realm.  Eventually, he asks them , "Do you guys just put the word quantum in front of everything?"  I wanted to cheer.  Thanks to Hollywood, some people might not realize that quantum is a word that actually means something; it's not just a way of adding the sound of legitimacy to the science that you're talking about.

When I talk about something being "quantum," what I mean is that it can be described by discrete values (whole numbers, none of that fraction or decimal crap).  To illustrate the difference, start with the speed of a car measured by classical physics.  When we talk about the speed, it's a continuum of speeds.  You can be going 90 mph, or 90.1 mph, or 90.000000000000009 mph, etc.  The jumps in speed (or energy) of large objects are infinitesimally small.  The playground analogy to this difference is a slide.  Smooth transitions between each measurement, or smooth enough that it doesn't make a difference at the level we can measure it. In quantum mechanics (physics) the transitions between energy levels are not so smooth.  This happens as the object you're looking at gets smaller and smaller. (This can be explained with the particle-in-a-box model, which I may write a post about at some point in the future).  When you enter this realm the steps between different energies become less smooth, and you end up with discrete energy levels that have gaps between them.  The playground analogy to this type of energy spacing is a ladder, with the rungs on the ladder representing discrete energy levels.  A cool point here is to remember that these two theories aren't actually separate.  As something gets bigger, the spacing between the energy levels gets smaller and smaller, and eventually becomes close enough to a continuum that it doesn't make a difference.

So now that we've talked about what the energy levels look like, we need to talk about how molecules store their energy.  There are 4 main ways that molecules store energy (ignoring a bunch of the other ways they can store energy).  The first 3 are related to the classical physics description of kinetic energy.  Imagine a baseball screaming it's way into the stands after a homerun.  Its energy is manifest through the speed it is moving.  This is the first way a molecule can store energy, through translational movement.  Next, imagine a tennis serve with a lot of topspin.  Some of the power from the serve goes into the translational movement of the ball, but some of it goes into the rotational spin of the ball.  The second way molecules store energy is through rotation (there are several types of "spin" a molecule can have, but for my work, only the overall molecular spin matters for this explanation).  Next, imagine some curly hair, that you stretch downwards, then let go of, and it springs back and forth (maybe a spring is a better analogy, but I like the curly hair one, so I'm sticking with it).  You've put energy into it when you pull it down, then the springing motion is how the hair stores that energy. If you've got two atoms in a molecule, bonded together, the bond acts like a spring, it can store energy in these vibrations.  The last way a molecule stores energy is related to potential energy in classical physics. Potential energy can be thought of a child sitting at the top of the slide.  Before they go down the slide, they have a lot of potential energy.  When they're going down the slide, some of that potential energy is transformed into kinetic energy.  At the bottom of the slide, they have less potential energy than before (although, if they're a typical toddler, not that much less energy (too be clear, that's a joke, unrelated to the analogy...)).  The last way that molecules can store energy is as potential energy, with the energy stored in the orbitals of the electrons.  These are called electronic energy levels.

The spacing between these energy levels varies, but in general, it can be thought that electronic

This is a visual diagram showing relative energies between states. 

Here, we're zoomed in on 2 of the electronic energy rungs, and we show

a few of the vibrational energy rungs  It is not to scale, but the values show

what the spacing is for these states.  EE stansd for Electronic Energy which

is the amount of energy each state has, relative to the lowest energy state. 

ve gives the distance between the vibrational "rungs" of the energy ladder.

energy spacing is bigger than vibrational energy spacing which is bigger than rotational energy spacing, which is bigger than translational energy spacing. 
So imagine the electronic energies as the rungs on that playground ladder.  If you zoom into a close up of 1 rung, you'll be able to see that rung is actually made up of a ladder with many vibrational energy rungs.  Then if you zoom in on one of those rungs, you'll be able to see each of those are made of an even smaller ladder of rotational energy rungs.  And if you do it again, you will be able to see the translational energy rungs. 

Now, this is all a simplification.  The truth is always more complicated.  But this is a basic idea of what "quantum" actually means, and it gives us a framework to understand what my next post will be, which is spectroscopy.

One Year

One year ago today, I posted the following status on Facebook:

"Either time travel never gets invented or what's happening now leads to some good things, and I'm not willing to believe that time travel never happens. #UCBuchanan"

The status, while somewhat lighthearted, was in response to what I worried would be the 2+ years of my PhD coming crashing down around me.  My QE, which was scheduled for 2 days later had just been canceled, because of a poor decision I'd made.  After what was arguably the worst 3 months of my life, followed by the worst week, March 12 last year was probably the worst day I've had.  I remember walking out of the office in shock, walking through the arboretum on campus, glad my sunglasses hid my tears.

At some point, I found myself on a bench thinking about what I was going to do.  Three days before, I'd had a conversation with my friend Sommer, where I was whining and wondering if I should just quit.  She was probably sick of me complaining to her, but her response was: 

"Zach. If you make that decision now, really decide that you are done, then that's it. You should talk to Kyle about getting a Master's. But the other option is at least to try as hard as you can to finish and get to your QE on Tuesday. I can almost promise that you will be more mad at past Zach if just give up now."

Sitting on that bench, thinking about that conversation, I decided I wanted to be optimistic, and I wanted to keep trying as hard as I could, and I posted that Facebook status.  Then I followed Sommer's other advice, went home, strung up my hammock and read a book for the first time in weeks.  The next day, I was back at it, trying to get to the point where I could pass my exam, which I eventually did, a couple months later.

It was still a hard few months.  I had to work to not be jealous as we celebrated the other 2 people in my group passing their exams on their first try.  I had to deal with my boss not being very happy that I hadn't finished mine when I should have.  I still had to go through about 15 iterations of revisions for the report that was required for my exam.  But I did pass, and I did it on the first try.  

My QE experience sucked.  Here are few things that happened in the 6 month stretch leading up to it. I'd experienced feelings of real anxiety for the first time. I'd woken up many times in the middle of the night, realizing that I'd been muttering chemistry explanations under my breath. I'd wake up tired regardless of how much I slept.  I'd put aside my hobbies, ignored my friendships, and had 2 potential relationships fall apart.

I'm extremely grateful to the people who supported me and put up with my crap during that time.  I learned a lot from my QE experience, both in terms of science, and about myself.  Here are some examples:

• It currently takes me about 200 hours to write a good paper.  So start writing early
• Decide what you want, and work hard to get it.
• Having good friends can make a huge impact on your mental health
• I learned what coherence is (I've since mostly forgotten...)
• Making time for hobbies has a huge impact on my mental health
• Getting enough sleep has a huge impact on my mental health
• I'm an optimist

So here's the moral of my post.  I still think time travel can be a thing.  While I came away with some scars, good things have come from that terrible experience for me.  I'm stronger, more grown up, and a better scientist.  I feel a little less like an impostor.  And I think more good things are coming.  

Welcome to the Blog

I get really excited about the nerdiest things.  Most of my friends just roll their eyes, and accept it as one of my quirks.  For example, a while back when I had a canker sore, I was looking up treatments for them.  One of the treatments I found was the use of dental lasers.  I spent the next hour looking for more information on the lasers than "the painless laser energy penetrates the lesion in order to heal the canker sore." I wanted to know about the laser.  What wavelength (color) was it?  How powerful was it?  How is the laser healing the canker sore?  I think I ended that particular search by reading through the user manual for one.  Anyone who has spent any amount of time with a toddler has likely experienced a seemingly never ending stream of questions as they explore the world around them.  People like me never lose that trait, and some of them go on to be scientists.

One reason I love science is because it can provide a lot of the answers to questions that start with "how?" Once you know just a few of the basics of science, you can start to apply them to things around you, and get a better idea of what's going on. The more you know, the more it starts the creep into your thinking, and color the way you see the world.

Most of the people I know outside of my colleagues are not scientists. Most of them roll their eyes at me anytime I get upset about the too liberal (or maybe it's not liberal enough) use of the word "organic."  But I also get to be the person people ask questions to when they want to know how something works, which is both satisfying and nerve wracking.  I take the responsibility to help people understand science seriously, because I don't want to be the cause of them believing Lies (I capitalized it on purpose, because there are Lies, which are completely untrue, and lies, which we tell novices to help them build a foundation in a topic).

The idea for this blog came from that sense of responsibility to help my friends understand science. I remember a conversation I had with an adviser when I was an undergraduate.  There was a professor at the school who was extremely intelligent, but was not very effective at explaining concepts.  My adviser commented that they should have a class where the professor taught concepts, then my adviser translated them so that everyone in the class could understand.  This idea stuck with me.

 I want take awesome things about science that are hard to understand, and write them up in a way that all my friends can read it and get excited.  I'm still solidifying my plan for the blog.  I think I'll write some posts that talk about what I do in my science career (the things I'm excited about at the time).  I think I'll end up writing some posts that read like Science 090 lessons, posts dedicated to a core concept that I can then use in a later post. If I come across an article that makes some outrageous claim based on a "scientific paper," I'll find the paper, read it, and translate it into normal language.  I also think it would be cool to learn about how things work (like phones, or microwave ovens, or airplane wings) and write them up in a way that makes sense. We'll see how that goes though.  There are already quite a few resources out there for that.  But if you have an idea for me, feel free to leave a comment, or contact me and let me know what your thought is.  While this is something fun for me to do, and a chance to learn myself, the reason I'm making this blog is for you.