In a recent episode of one of my favorite podcasts, the Skeptic’s Guide to the Universe, they discussed a recent paper from the John Goodenough lab. I figured I’d take a look at this paper and see what’s inside. They propose a type of battery where there’s a lithium-metal reduction on both sides of the cell. Overall, the electrochemical results they show are impressive: very high capacities with good cyclability at a decent cell potential (between 2.5 and 2.7V); though not quite as impressive as the press-release makes them sound. However, I’m not clear on how they think this reaction actually happens. Many of the clarifying details are missing, which makes it hard to properly evaluate. Regardless of the electrochemical mechanism, though, if the results can be reproduced reliably, then great!

## GSAS-II Introduction - Basic Profile Refinement

This document will guide the user through a basic whole-pattern decomposition of a single phase using the Pawley method. This method is simpler than the Rietveld method and will provide a closer fit, however the the refined parameters are not physically meaningful so the amount of information obtained is limited.

In this tutorial, I will refine a corundum scan taken on our Bruker D8 Discover ("Alice"). The diffractogram can be downloaded in .xye format. You may also want to look at the finished GSAS-II project.

## Research Update: Mapping Artifacts

06 Jul 2015 chemistry X-Ray-Diffraction Comments

I'm almost one year into my time here at UIC. I've been making steady progress on my research and have run into a strange issue. My research focus is developing a new technique to make surface maps, like the one on the right, of battery cathode materials using X-ray diffraction. The material studied in this post is $$MgMn_2O_4$$. By creating these maps, I am able to look for areas where the electrochemistry is different from the rest of the material. The map at the right looked promising at first; however as described below this excitement may have been premature.

Map of discharged $$MgMn_2O_4$$ battery cathode based on area of 18° peak.

## Beamtime Galore

My PhD research project involves using X-rays to probe the chemistry of lithium-ion battery electrodes. In order to see something with a high level of detail, you need to look at it in bright light. Analogously, I need access to very high quality X-rays. The last two weekends I traveled to two different synchrotron; particle accelerators whose sole purpose is to generate high intensity X-rays. Each one has 10-30 X-ray beams coming off of it, set up to run a variety of experiments. At Argonne National Lab's Advanced Photon Source (APS), we used diffraction to measure the strain withing a micrometer sized particle. At the Stanford Synchrotron Radiation Lightsource (SSRL) we collected the data to make three-dimensional reconstructions of the micro-structure of some samples using X-ray Transmission Tomography.

Fellow grad-student Brian May at beamline 34-ID-E at Argonne National Lab.

## Image Formats

This post is meant as a resource for helping to decide how best to send images for posting on websites. There are usually three possible options: lossly bitmaps, lossless bitmaps and vector graphics. The right decision is usually a compromise between a high-quality image that gives a clean, sharp presentation to the user, and a small file-size so a user doesn't get bored while waiting for your website to load all of the 2MB images. Using the right image formats will result in a website that loads quickly and has a consistent, sharp layout.

Image type Format Example Extension Min Resolution (pixels)
Photograph Lossy bitmap .jpg .jpeg Landscape: 750×464
Portrait: 350×475
Logos and other flat graphics Vector graphics (preferred) .svg .ai .eps N/A
Lossless bitmap .png .tiff .gif .bmp Context dependent

I've been tasked with finding a new computer for my PhD research here at UIC. I'll be collecting multiple data frames and then processing and combining them into one image; I think it's worth the time to get this right. If you have anything to share on the issue, feel free to leave a comment. I wasn't given many restrictions other than that it must have a monitor, keyboard and mouse (for ergonomic reasons) and that “$1000 is on the high end but reasonable”. I've spent the past few days researching current technologies and have come up with some suggestions. All of the products listed will probably by obsolete by the time I'm done writing this, but hopefully the background will still be valid for a while. If you want to see specifically which parts I'm considering, jump straight to the parts list. ## Entropy of the Universe 17 Dec 2014 chemistry Teaching physics Comments I had the following e-mail exchange with one of my Chem 114 students, Kinza. Usually, the questions I get are specific to what we’re studying in class and they tend to be easier to answer during office hours. These questions, on the other hand, were Kinza trying to understand the concept of entropy. We had covered it briefly earlier in the semester in the chaprter on thermodynamics. It’s definitely a difficult concept, one I don’t understand fully myself. It’s more in the physics realm than chemistry but I still felt it was worth sharing. Published with student’s permission. Hi Mark, If every reaction that occurs increases the entropy of the universe, doesn't that mean that all the reactions going on in the universe are causing the entropy of the universe to keep going up? What's going to happen to the universe as predicted by thermochemistry? -Kinza ## More Sunshine (Vitamin): Doctor's Orders 02 Jul 2014 chemistry health Comments As per my doctor's suggestion, I'm spending the next week on a sailboat. No, it's not a blood pressure or a stress thing. I had a physical exam a while ago and for the most part everything was normal. The one exception was vitamin D deficiency. The solution? Spend more time in the sun. Vitamin D is actually a group of five vitamins: D1 through D5. The most relevant to human health are vitamins D2 and D3 and are usually what people mean when they refer to “vitamin D”. My results listed “Vitamin D, 25-hydroxy” as 18 $$\frac{ng}{mL}$$ and the target range was 30-96 $$\frac{ng}{mL}$$. An article in The American Journal of Clinical Nutrition suggests that levels below 20 $$\frac{ng}{mL}$$ indicates a deficiency. Clearly I need to get those levels up. But why? The sun at 17.1 nm light. Courtesy of SOHO/EIT consortium. SOHO is a project of international cooperation between ESA and NASA. ## Follow-up: I Have a Carbon Monoxide Detector. Now What? 01 Jun 2014 chemistry health Comments This is a follow-up post to “Why Do I Need a Carbon Monoxide Detector?”, which talks about the chemistry of carbon monoxide with oxygen-transporting proteins in your blood. I received a few questions about the relationship between carbon monoxide levels in the air and the levels in your hemoglobin. I also wanted to learn how carbon monoxide alarms respond to carbon monoxide (CO) but not other gases in the air, like carbon dioxide (CO2). ## CO Levels in Air and Blood When I was younger, I was terrified that carbon monoxide binds permanently to hemoglobin and that the damage might never be undone. Real life is a lot more complicated than that. Small amounts of carbon monoxide are produced routinely in your body and may serve a function as a neurotransmitter. But at higher levels, it becomes very toxic. In 1965, a paper was published ("Coburn-Forster-Kane") that provided an equation for estimating levels of hemoglobin bound up with carbon monoxide ("COHb"), based on a variety of factors. In case you're curious, the equation is: $\frac{A[HbCO]_t - (BV_{CO} + PI_{CO})}{A[HbCO]_0 - (BV_{CO} + PI_{CO})} = e^{-tAV_bB}$ It's not terribly important that you understand the whole equation so I'll point out the the interesting parts. We're trying to solve for $$[HbCO]_t$$, the concentration of carboxyhemoglobin in the blood at any given time. First there's the presence of a term $$t$$, which means the duration of exposure to CO, measured in minutes. This means that, in some way, the amount of time you spend exposed to higher levels of carbon monoxide is important. Then there's $$PI_{CO}$$, which represents the concentration of carbon monoxide in the air you're breathing. Lastly there's $$B$$, which tracks how much air enters your lungs every minute. So the effect depends on how fast you're breathing. Basically, exercise and other vigorous activites make the whole process run faster. The rest of the equation takes care of things like total volume of blood and how much carbon monoxide is naturally present in the body. Some smart people who are good at math have made graphs that show how this equation works. The one on the right has been shamelessly borrowed from CO Headquarters. It shows the per cent of hemoglobin that's in the carbon monoxide form as a function of time. Each curve is a different level of CO exposure in the surrounding air. The World Health Organization has published some information that is helpful here. Levels of COHb below 5% have no noticeable impact unless you are a member of an at-risk population (heart-disease, etc). Severe symptoms occur between 30-50% and bad things like coma, convulsions and death occur at levels above 50%. So let's say you're pregnant and are concerned about hitting the 15% COHb threshold at which the WHO reports developmental problems. This means that if you're exposed to 200ppm carbon monoxide in the air, you have about 300 minutes (5 hours) before the level of COHb hits 15%. At 500ppm this drops to 100 minutes (1 hour 40 minutes) and 1000 ppm to 30 minutes. Of course if any number of variables change (breathing rate, etc), so do these numbers. Also, if you get into fresh air, the concentration returns to normal levels over a similar time frame. Solutions to the Coburn-Forster-Kane equation for various air carbon monoxide levels. Each line is a different level of carbon monoxide in the surrounding air. ## How to Detect Carbon Monoxide So how does any of this impact carbon monoxide detectors? A CO level of 35 ppm can be problematic but only for extended periods of time. The need to avoid false alarms is important, especially in places like hospitals where evacuation has its own problems. Cigarette smoke produces lots of carbon monoxide but you wouldn't want your alarm going off every time you light one. Alarms typically have a threshold that's a combination of CO concentration and exposure time (eg "150 ppm, 10-50 minutes"). There are several ways to achieve this but here's my favorite: the biomimetic sensor. It uses a disc of gel that absorbs carbon monoxide over time. The composition of the gel is designed in such a way that it responds to carbon monoxide in a similar way to hemoglobin, hence the term "biomimetic". It's made of an atom of metal (to simulate the iron in hemoglobin) bound to a large organic molecule. Part of the molecule holds the metal and another part, the "chromophore", changes color depending on whether the metal is bound to carbon monoxide. The color of the sensor then follows the curves in the graph above. By putting a light source on one side and a detector on the other, the darkness can be measured and the alarm triggered once it hits a certain level. This type of alarm is the most reliable but also expensive so most consumer products use other methods. ## Why Do I Need a Carbon Monoxide Detector? 25 May 2014 Chemistry Comments What if I told you carbon monoxide detectors are a scam? Well I'd be lying. Carbon monoxide is a poisonous gas that gets into your red blood cells and messes everything up; knowing when it's in your house is worth the investment. It doesn't help that it's colorless and odorless either. We had some furnace troubles last winter and after a night of not being sure if we'd die quietly in our sleep, I decided to buy a CO detector ($20 at my local hardware store). In order to understand why carbon monoxide is so deadly, we first need to learn a little about how the body transports oxygen.

It starts with red blood cells. These are special cells that are really rich in a molecule called hemoglobin. It's a big curled up protein with an iron atom in just the right place. This iron atom wants electrons and holds on to the extra ones that are in a molecule of oxygen. The rest of the protein makes sure there's a space that's just big enough to fit an oxygen molecule (more on this later). Each molecule of hemoglobin has four of these iron centers. When the red blood cells are in a place with lots of oxygen, like your lungs, these four sites fill up quickly. When the cells are in an area with low oxygen, like your muscles during a workout, then hemoglobin rearranges and lets go of the oxygen so your muscle can use it to turn carbs into energy.

An iron atom can bind an oxygen molecule while the rest of the protein makes a nice pocket that keeps other things out of the way.

So what about carbon monoxide? Well it's a similar shape and size to an oxygen molecule. They have some other properties in common too, like sticking to that iron atom. The problem is that carbon monoxide binds to the iron way better than oxygen does. So much so that no matter how much rearrangement it does in your muscles, hemoglobin can't shake any CO molecules that are attached. It gets worse, actually. Once a carbon monoxide is stuck to one of the four oxygen-binding sites, it gums up the other three so they don't work properly either.

Humans (and other animals) have evolved some defenses against this problem, namely in the structure of hemoglobin itself. Remember how I said that the protein has an oxygen-shaped pocket next to the iron? One way in which oxygen and CO are different is in how they stick to the iron atom; carbon monoxide sticks out straight and oxygen at an angle. There's a pentagon-shaped part right next to where the oxygen sits. It doesn't really bother the bent oxygen much but it gets in the way of the straight carbon monoxide. This means that the oxygen can fit into that space a lot better than cabon monoxide can. Carbon monoxide still binds to hemoglobin about 250 times better than oxygen does, but it gives your body the ability to tolerate a low level of the poisonous gas.

Oxygen (left image, light-red) binds in a slightly bent configuration which doesn't get in the way of the distal hystadine (blue-green pentagon). The straight carbon monoxide molecule (right image, light-red) doesn't fit nearly as well.

Levels of naturally occuring carbon monoxide are rarely high enough to overwhelm this defense. However, incomplete burning of fossil-fuels like the natural gas in our furnace, creates artificially high levels in the immediate area and there hasn't been nearly enough time for our species to evolve any sort of response. The symptoms of cabon monoxide poisoning are pretty general (headache, nausea, etc). If you have a CO detector, on the other hand, you can do something about it. Get yourself and loved ones to some fresh air. In regular air it takes about 2-6 hours for half of the carbon monoxide to be replaced with good old oxygen. If you're given pure oxygen at 3 atmospheres, this time goes down to tens of minutes. And if you don't have a CO detector, go get one right now.

This article prompted me to write a follow-up piece: I Have a Carbon Monoxide Detector. Now What?.

## Hello, world!

So I’ve decided to start a blog. I think I’ll make it about chemistry. You know, explaining everyday phenomena in a way that’s both informative and easy to understand. Who knows if I’ll succeed. I’m also planning to throw some stuff in about going to grad school and computer programming.

I’ll probably need a fair amount of content to post so if you have chemistry related questions, I’d love to hear about them. I’ve put up a thread here. Leave a comment with your question and I’ll see what I can dig up. I’m thinking of starting out with a post on how oxygen gets transported from your lungs to your muscles.