Category: Chemistry

Well, well, well

On By rolcottIn Chemistry, UncategorizedLeave a comment

<chirp, chirp> “Moire here.”

“Hi, Sy, it’s Susan Kim. I’m at a break point while this experiment runs. Do you want to check the scones at Al’s?”

“I’ve got a bad case of February, feel like just hibernating somewhere. Can’t get started on anything so I might as well head over there.”

“You need Al’s patented Morning Dynamite brew. See you in a couple of minutes.”

“Hi, Al. My usual mocha latte, please, and your special wake-up potion for Sy. He’s got the Februaries.”

“Here you go, Susan. Bottom of the pot coming at ya, Sy. It’ll get ya lively, for sure.”

<We grab a table.> “So, Susan, what’s this experiment that you can just let alone for a while?”

“One of your blog posts inspired it. Do you remember the one about warm water freezing faster than cold?”

“Sometimes it does that, but the point of the post was how it’s only randomly sometimes in some experiments and not at all in others. Are you experimenting with water freezing?”

“No, but I’m working on a related problem. I can’t say much about it other than that there’s an industrial process that depends on recovering a crystalline product from a hot, concentrated solution. The problem is that if the solution is too weak nothing crystallizes when it cools but if it’s too concentrated the whole batch solidifies in one big mass. The industry wants to find the right conditions for making lots of small crystals. I’ve got a grant to research ways to do that.”

“That does sound a little like water freezing. How did my blog post help?”

“I was thinking about how crystals form. We know a lot about how ions or molecules come in from solution to attach to the surface of a growing crystal. Either they’re electrostatically pulled to just the right spot or they bounce on and off the surface until they find a place they fit into. But how does that surface get started in the first place?”

“Well, I imagine it happens when two molecules love each other very mu— OW!”

“Sy Moire, get your mind back on Science! … Sorry, did it really hurt that much?”

“It wouldn’t have but that’s the same spot on the same shoulder that Cathleen got me on.”

“Actually, your flip remark isn’t that far from what we think happens except the correct verb is ‘attract,’ not ‘love.‘ Some researchers even call the initial speck ‘the embryo‘ but most of us say ‘nucleus.’ Nucleation might start with only a few molecules clicking into the right configuration, or it might require a cluster of hundreds being mostly right. The process might even require help from short‑lived solvent structures. So many variables. Nobody has a good predictive theory or even broadly useful models. It’s all by art and rule of thumb.”

“Sounds like a challenge.”

“Oh, it is. Here’s the tip I took from your blog post. You mentioned that some of the freezing studies used hundreds of trials and reported what percent of them froze. Most of the industrial crystallization studies work at pilot plant scale, with liters or gallons of solution going into each trial. I decided to go small instead. Lab supply companies sell culture plates for biological work. Typically they’re polystyrene trays holding up to a hundred one‑milliliter wells. I bought a bunch of those, and I also bought a machine that can automatically load the wells with whatever solutions I like. I’ve positioned it next to a temperature‑controlled cabinet with a camera to photograph a batch of trays at regular intervals.”

“Nice, so you can set up many duplicates at each chemical concentration and keep statistics on how many form crystals at each temperature.”

“At high concentrations I expect all the wells to show crystals. The obvious measurement will be crystal size range at each temperature. But with no change in apparatus I can go to lower and lower concentrations to where crystallization itself is random like the freezing experiments. Some wells will crystallize, some won’t. Statistics on those trays may tell us things about nucleation. It’s gonna be fun.”

“D’ya suppose the planets are culture plate wells for creation’s life experiments?”

~~ Rich Olcott

A Match Game

On By rolcottIn Chemistry, UncategorizedLeave a comment

<chirp chirp> “Lab C-324, Susan Kim speaking.”

<hoarsely> “Hi Susan, it’s Sy. Fair warning. The at‑home test I just ran says I’ve got Covid. I’ve had all four shots but it looks like some new variant dodged in anyway. We had coffee together at Al’s yesterday so I wanted to warn you. Better stock up on cough medicine and such.”

“Ooh. Thanks, Sy, sorry to hear that. If it’s any consolation, you’re not alone. About half the lab’s empty today because of Covid. I’m just waiting for this last extraction to complete and then I’m outta here myself. There’s chicken soup going in the slow‑cooker at home.”

“Ah, yes, a Jewish mother’s universal remedy.”

“Korean mothers, too, Sy, except we use more garlic. Chicken soup’s a standard all over the world — soothing, easy on the stomach and loaded with protein.”

“While you’re in wait mode, maybe you could explain something to me.”

“I can try. What is it?”

“How do these tests work? I swabbed my nose, swirled the yuck with the liquid in the little vial and put three drops into the ‘sample port‘ window. In the next few minutes fluid crept across the display window next to the port and I saw dark bars at the T and C markers. What’s that all about?”

“Miracles of modern immunochemistry, Sy, stuff we wouldn’t have been able to execute fifty years ago. What do you know about antibodies?”

“Not much. I’ve read a little about immunology but I always get the antibodies confused with the antigens and then my understanding goes south.”

“Ignore the ‘anti‘ parts — an antigen is usually a part of something from outside that generates an immune response. As part of the response, cells in your body build antibodies, targeted proteins that stick to specific antigens. Each unique antibody is produced by just a few of your cells. When you’re under a disease attack, your antibodies that match the attacker’s antigens lock onto the attacker to signal your defender cells what needs chewing up. About half‑a‑dozen Nobel Prizes went to researchers who figured out how to get a lab‑grown cell to react to a given antigen and then how to clone enough copies of that cell to make industrial quantities of the corresponding antibody. You follow?”

“So far, so good.”

“One more layer of detail. All antibodies are medium-sized proteins with the same structure like a letter Y. There’s a unique targeting bit at the end of each upper arm. An antigen can be anything — a fragment of protein or carbohydrate, a fatty acid, even some minerals.”

“Wait. If a protein can be an antigen, does that mean that an antibody can be an antigen, too?”

“Indeed, that’s the key for your test kit’s operation. The case holds a strip of porous plastic like filter paper that’s been treated with two narrow colorless stripes and a dot. The T stripe contains immobilized antibody for some fragment of the virus. The C stripe contains immobilized antibody antibody.”

“Hold on — an antibody that targets another antibody like maybe the bottom of the Y?”

“Exactly. That’s the control indicator. The dot holds virus antibodies that can move and they’re linked to tiny particles of gold. Each gold particle is way too small to see, but a bunch of them gathered together looks red‑brown. Okay, you put a few drops of yuckified liquid on top of the dot and the mixture migrates along the porous material. You tell me what happens.”

“Wait, what’s in that liquid?”

“It’s standard pH-buffered saline, keeps the proteins healthy.”

“Hmm. Alright, the dot’s gold‑labeled virus antibody grabs virus in my yuck and swims downstream. The T stripe’s virus antibody snags the virus‑antigen combination particles and I see red‑brown there. Or not, if there’s no virus. Meanwhile, the creeping liquid sweeps other gold‑labeled antibodies, virus‑bound or not, until they hit the C stripe and turn it red‑brown if things are working right. Uhhh, how much gold are we talking about?”

“Colloidal gold particles are typically balls maybe 50 nanometers across. Stripe area’s about 1 mm2, times 50 nanometers, density 19.32 kg/m3, gold’s $55 per gram today … about 5 microcents worth.”

~~ Rich Olcott

The Threshold of Stuffiness

On By rolcottIn Chemistry, Physics: Fundamentals, UncategorizedLeave a comment

<chirp chirp> “Moire here.”

“Hi, Sy, it’s Susan Kim. I read your humidifier piece and I’ve got your answer for you.”

“Answer? I didn’t know I’d asked a question.”

“Sure you did. You worked out that your humidifier mostly keeps your office at 45% relative humidity by moisturizing incoming air that’s a lot drier than that. As a chemist I like how you brought in moles to check your numbers. Anyway, you wondered how to figure the incoming airflow. I’ve got your answer. It’s a scaling problem.”

“Mineral scaling? No, I don’t think so. The unit’s mostly white plastic so I wouldn’t see any scaling, but it seems to be working fine. I’ve been using de-ionized water and following the instructions to rinse the tank with vinegar every week or so.”

“Nope, not that kind of scale, Sy. You’ve got a good estimate from a small sample and you wondered how to scale it up, is all.”

“Sample? How’d I take a sample?”

“You gave us the numbers. Your office is 1200 cubic feet, right, and it took 88 milliliters of water to raise the relative humidity to where you wanted it, right, and the humidifier used a 1000 milliliters of water to keep it there for a day, right? Well, then. If one roomful of air requires 88 milliliters, then a thousand milliliters would humidify (1000/88)=11.4 room changes per day.”

“Is that a good number?”

“I knew you’d ask. According to the ventilation guidelines I looked up, ‘Buildings occupied by people typically need between 5 and 10 cubic feet per minute per person of fresh air ventilation.‘ You’re getting 11.4 roomfuls per day, times your office volume of 1200 cubic feet, divided by 1440 minutes per day. That comes to 9.5 cubic feet per minute. On the button if you’re alone, a little bit shy if you’ve got a client or somebody in there. I’d say your building’s architect did a pretty good job.”

“I like the place, except for when the elevators act up. All that figuring must have you thirsty. Meet me at Al’s and I’ll buy you a mocha latte.”

“Sounds like a plan.”

“Hi, folks. Saw you coming so I drew your usuals, mocha latte for Susan, black mud for Sy. Did I guess right?”

“Al, you make mocha lattes better than anybody.”

“Thanks, Susan, I do my best. Go on, take a table.”

“Susan, I was thinking while I walked over here. My cousin Crystal doesn’t like to wear those N95 virus masks because she says they make her short of breath. Her theory is that they trap her exhaled CO2 and those molecules get in the way of the O2 molecules she wants to breathe in. What does chemistry say to that theory?”

“Hmm. Well, we can make some estimates. N95 filtration is designed to block 95% of all particles larger than 300 nanometers. A couple thousand CO2 molecules could march abreast through a mesh opening that size no problem. An O2 molecule is about the same size. Both kinds are so small they never contact the mesh material so there’s essentially zero likelihood of differential effect.”

“So exhaled CO2 isn’t preferentially concentrated. Good. How about the crowd‑out idea?”

“Give me a second. <tapping on phone> Not supported by the numbers, Sy. There’s one CO2 for every 525 O2‘s in fresh air. Exhaled air is poorer in O2, richer in CO2, but even there oxygen has a 4‑to‑1 dominance.”

“But if the mask traps exhaled air…”

“Right. The key number is the retention ratio, what fraction of an exhaled breath the mask holds back. A typical exhale runs about 500 milliliters, could be half that if you’ve got lung trouble, twice or more if you’re working hard. This mask looks about 300 milliliters just sitting on the table, but there’s probably only 100 milliliters of space when I’m wearing it. It’s just arithmetic to get the O2/CO2 ratio for each breathing mode, see?”

“Looks good.”

“Even a shallow breather still gets 79 times more O2 than CO2. Blocking just doesn’t happen.”

“I’ll tell Crys.”

~ Rich Olcott

It’s The Heat AND The Humidity

On By rolcottIn Chemistry, UncategorizedLeave a comment

<from the casebook of Sy Moire, Consulting Physicist> Monday. Weather sunny, warm for this time of year. Dry, bad effects on nose and throat at wake‑up time. Bought a room humidifier Friday at Big Box — up‑scale, 4‑liter reservoir, ultrasonic but silent, WiFi‑enabled etc. Long way from the jug with boiler tube my folks used to use. WiFi’s a sneaky way to avoid building a remote control — just use the customer’s smart phone. Guess that keeps the price down.

Good news is, phone app does graphs of relative humidity against time. Had it in measure-only mode in office Monday night, baseline wobbled in the 32-36% range. Bad news is, when the device is running on Automatic it works toward a 45% target but had trouble getting near that high on its maiden effort on Saturday. Wondered, how much water would it have to send into the room to hit the target?

Start with the numbers. “45%” is forty‑five percent of what? Surely not some arbitrary maximum. Weather guy talks about relative humidity so, relative to what? Searched a little in the internet. All the sources say RH is a ratio of ratios, something over maximum something. “Something” is water vapor mass per unit volume or else water vapor mass per total gas mass in the same volume. Clouds, fog, raindrops and snowflakes don’t count. Then things get fuzzy. Some sources say the maximum is “saturation” which is just a tautology. The most precise definition says “the partial pressure of water in air over a large flat surface of pure water under laboratory conditions” <shudder>.

Doing engineer stuff here so keep it simple. Found a chart of water vapor content at 100% humidity at different temperatures. Will go with that. No surprise, the warmer the air, the more water mass it can hold before fogging up. I’m comfortable around 68°F which is 20°C. The chart says 100% saturated 20°C air holds 17.3 grams of water per cubic meter. 45% of that is 7.8 and 30% is 5.3. Need to know how many cubic meters in the office.

OK, measured the room as 10’×15′ with an 8′ ceiling. Ignore the space the furniture takes up. Total volume is 1200 cubic feet. Old Reliable says that’s 34 cubic meters. If the room’s at 100% humidity its air holds
  (34 m3)×(17.3 g/m3)
   = 588 grams of water.
At 1000 grams per liter that’s 0.588 liter or about a pint. Suppose humidifier starts when the room’s at 30% humidity. For a 15% bump to 45% the gadget has to vaporize
  (34 m3)×(17.3 g/m3)×(0.45-0.30)
   = 88 g = 88 milliliters.

Wow, that’s only about 6 tablespoons. Does that number even make sense? OK, air is about 80% N2, molecular weight 28. The other 20% is mostly O2, molecular weight 32. The average is near 29. Basic chem class stuff — at Earth‑typical room temp and pressure, a 22.4‑liter chunk of air has a mass near 29 grams, so office’s roomful of air would mass
  (29g/mole)×(1 mole/22.4 liters)
   ×(1000 liters/m3)×(34 m3/room)
    = 44 kilograms
The 588-gram number says that it’d get foggy in here if the moisture content ever got much above (588 g)/(44000 g) = 1.3% by mass, which sounds reasonable.

88 milliliters ain’t much, so how come the unit used up a liter of water in just one day?

Ah-hah. Air’s not sitting still. Ventilation system continually brings in low‑humidity outside air. Plus, clients complain in the wintertime about cold drafts leaking in around the door, transom and windows. If it weren’t for air shuttling in and out, we’d use up all the oxygen in here — that isn’t happening. Wonder how to calculate that flow. Bottom line is, humidifier doesn’t moisten what’s in the room so much as it loads up what comes in dry.

Problem — evaporating water cools air, Old Reliable says 2256 kilojoules per kilogram. 88 grams won’t have much effect, but a liter/day is a kilogram/day. An hour is 1/24 of a day. 1/24 liter means 94 kilojoules per hour of cooling. Air heat capacity is 1 kilojoule/(kilogram oC). (94 kJ/44 kg air)=2.1 degrees per hour. Suddenly I feel chilly.

~~ Rich Olcott

Candle, Candle, Burning Bright

On By rolcottIn Chemistry, Physics: Light and Relativity, UncategorizedLeave a comment

<chirp, chirp> “Moire here.”

“Hi, Sy, it’s Susan Kim. I did a little research after our chat. The whale oil story isn’t quite what we’re told.”

“Funny, I’ve been reading up on whales, too. So what’s your chemical discovery?”

“What do we get from a fire, Sy?”

“Light, heat and leftovers.”

“Mm-hm, and back in 18th Century America, there was plenty of wood and coal for heat. Light was the problem. I can’t imagine young Abe Lincoln reading by the flickering light of his fireplace — he must have had excellent eyesight. If you wanted a mostly steady light you burned some kind of fat, either wax candles or oil lamps.”

“Wait, aren’t fat and wax and oil three different things?”

“Not to a chemist. Fat’s the broadest category, covers molecules and mixtures with chains of ‑CH2‑ groups that don’t dissolve in water. Maybe the chains include a few oxygen atoms but the molecules are basically hydrocarbons. Way before we knew about molecules, though, we started classifying fats by whether or not the material is solid at room temperature. Waxes are solid, oils are liquid. You’re thinking about waxy‑looking coconut oil, aren’t you?”

“Well….”

“Coconuts grow where rooms are warm so we call it an oil, OK? I think it’s fun that you can look at a molecular structure and kind of predict whether the stuff will be waxy or oily.”

“How do you do that?”

“Mmm… It helps to know that a long chain of ‑CH2‑ groups tends to be straight‑ish but if there’s an ‑O‑ link in the chain the molecule can bend and even rotate there. Also, you get a kink in the chain wherever there’s a –CH=CH– double bond. We call that a point of unsaturation.”

“Ah, there’s a word I recognize, from foodie conversations. Saturated, unsaturated, polyunsaturated — that’s about double bonds?”

“Yup. So what does your physicist intuition make of all that?”

“I’d say the linear saturated molecules ought to pack together better than the bendy unsaturated ones. Better packing means lower entropy, probably one of those solid waxes. The more unsaturation or more ‑O‑ links, the more likely something’s an oil. How’d I do?”

“Spot on, Sy. Now carry it a step further. Think of a –CH2– chain as a long methane. How do suppose the waxes and oils compare for burning?”

“Ooo, now that’s interesting. O2 has much better access to fuel molecules if they’re in the gas phase so a good burn would be a two‑step process — first vaporization and then oxidation. Oils are already liquid so they’d go gaseous more readily than an orderly solid wax of the same molecular weight. Unless there’s something about the –O– links that ties molecules together…”

“Some kinds have hydrogen-bond bridging but most of them don’t.”

“OK. Then hmm… Are the double-bond kinks more vulnerable to oxygen attack?”

“They are, indeed, which is why going rancid is a major issue with the polyunsaturated kinds.”

“Oxidized hydrocarbon fragments can be stinky, huh? Then I’d guess that oil flames tend to be smellier than wax flames. And molecules we smell aren’t getting completely oxidized so the flame would probably be smokier, too. And sootier. Under the same conditions, of course.”

“Uh-huh. Would you be surprised if I told you that flames from waxes tend to be hotter than the ones from oils?”

“From my experience, not surprised. Beeswax candlelight is brighter and whiter than the yellow‑orange light I saw when the frying oil caught fire. Heat glow changes red to orange to yellow to white as the source gets hotter. Why would the waxes burn hotter?”

“I haven’t seen any studies on it. I like to visualize those straight chains as candles burning from the ends and staying alight longer than short oil fragments can, but that’s a guess. Ironic that a hydrogen flame is just a faint blue, even though it’s a lot hotter than any hydrocarbon flame. Carbon’s the key to flamelight. Anyway, the slaughter started when we learned a mature sperm whale’s head holds 500 gallons of waxy spermaceti that burns even brighter than beeswax.”

~~ Rich Olcott

  • Whale image adapted from a photo by Gabriel Barathieu CC BY SA 2.0

The Venetian Blind Problem

On By rolcottIn Astronomy: Planetary Science, Chemistry, Physics: Light and Relativity, UncategorizedLeave a comment

Susan Kim gives me the side‑eye. “Sy, I get real suspicious when someone shows me a graph with no axis markings. I’ve seen that ploy used too often by people pushing a bias — you don’t know what happens offstage either side and you don’t know whether an effect was large or small. Your animated chart was very impressive, how that big methane infrared absorption peak just happens to fill in the space between CO2 and H2O peaks. But how wide is the chart compared to the whole spectrum? Did you cherry‑pick a region that just happens to make your point?”

“Susan, how could you accuse me of such underhanded tactics? But I confess — you’re right, sort of. <more tapping on Old Reliable’s keyboard> The animation only covered the near‑IR wavelengths from 1.0 to 5.0 micrometers. Here’s the whole strip from 0.2 micrometers in the near UV, out to 70 micrometers in the far IR. Among other things, it explains the James Webb Space Telescope, right, Al?”

Spectrum of Earth’s atmosphere. Adapted
under the Creative Commons 3.0 license
from Robert Wohde’s work
with the HITRAN2004 spectroscopic database,

“I know the Webb’s set up for IR astronomy from space, Sy. Wait, does this graph say there’s too much water vapor blocking the galaxy’s IR and that’s why they’re putting the scope like millions of miles away out there?”

“Not quite. The mission designers’ problem was the Sun’s heat, not Earth’s water vapor. The solution was to use Earth itself to shield the device from the Sun’s IR emissions. The plan is to orbit the Webb around the Earth‑Sun L2 point, about a million miles further out along the Sun‑Earth line. Earth’s atmosphere being only 60 miles thick, most of it, the Webb will be quite safe from our water molecules. No, our steamy atmosphere’s only a problem for Earth‑based observatories that have to peer through a Venetian blind with a few missing slats at very specific wavelengths.”

“Don’t forget, guys, the water spectrum is a barrier in both directions. Wavelengths the astronomers want to look at can’t get in, but also Earth’s heat radiation at those wavelengths can’t get out. Our heat balance depends on the right amount of IR energy making it out through where those missing slats are. That’s where Sy’s chart comes in — it identifies the wavelengths under threat by trace gases that aren’t so trace any more.”

“And we’re back to your point, Susan. We have to look at the whole spectrum. I heard one pitch by a fossil fuel defender who based his whole argument on the 2.8‑micrometer CO2 peak. ‘It’s totally buried by water’s absorption,‘ he claimed. ‘Can’t possibly do us any further damage.’ True, so far as it goes, but he carefully ignored CO2‘s other absorption wavelengths. Pseudoscience charlatan, ought to be ashamed of himself. Methane’s not as strong an absorber as CO2, but its peaks are mostly in the right places to do us wrong. Worse, both gas concentrations are going up — CO2 is 1½ times what it was in Newton’s day, and methane is 2½ times higher.”

Data from EPA Climate Indicators Explorer

“Funny how they both go up together. I thought the CO2 thing was about humanity burning fossil fuels but you said methane operations came late to that game.”

“Right on both counts, Al. Researchers are still debating why methane’s risen so bad but I think they’re zeroing in on cow gas — belches and farts. By and large, industry has made the world’s population richer over the past two centuries. People who used to subsist on a grain diet can now afford to buy meat so we’ve expanded our herds. Better off is good, but there’s an environmental cost.”

Al gets a far-away look. “Both those gases have carbon in them, right? How about we burn methane without the carbon in, just straight hydrogen?”

Susan gets excited. “Several groups in our lab are working on exactly that possibility, Al. The 2H2+O2→2H2O reaction yields 30% more energy per oxygen atom than burning methane. We just need to figure out how to use hydrogen economically.”

~~ Rich Olcott

Going from Worse to Bad

On By rolcottIn Astronomy: Planetary Science, Chemistry, Uncategorized3 Comments

Al delivers coffees to our table, then pauses. “Why methane?”

Susan Kim looks up from her mocha latte. “Sorry?”

“Why all the fuss about methane all of a sudden? I thought carbon dioxide was the baddie. Everybody’s switching from coal to natural gas which they say is just methane and now that’s a bad thing, too. I’m confused. You’re a chemist, unconfuse me.”

“You’re right, there’s mixed message out there. Here’s the bottom line. Methane’s bad, but coal’s a worse bad.”

“OK, but why?”

“Pass me a paper napkin so I can write down the chemical reactions. When we look at them in detail there’s all kinds of complicated reaction paths, but the overall processes are pretty simple. The burnable part of coal is carbon. In an efficient coal‑fired process what happens is
  C + O2 → CO2 + energy.
The C is carbon, of course and O2 is an oxygen molecule, two atoms linked together. Carbon atoms weigh 12 and each oxygen atoms weighs 16, so 12 grams of carbon produces 12+(2×16)=44 grams of CO2. Scaling up, 12 tons of carbon produces 44 tons of CO2 and so on. The energy scales up, too. and that’s what heats the boilers that make the steam that spins the turbines that make electricity.”

“I heard a couple of weasel words but go on to methane.”

“You caught them, eh? They’re important weasels and we’ll get to them. OK, methane is CH4 and its overall burn equation is
  CH4 + 2O2 → CO2 + 2H2O + energy.
Oxidizing those hydrogens releases about twice as much energy per carbon as the coal reaction does.”

“Already I see one big advantage for methane — more bang per CO2. So about those weasels…”

“Right. Well, coal isn’t just pure burnable carbon. It’s 350‑million‑year‑old trees and ferns and animal carcasses and swamp muck and mineral sediments, all pressure‑baked together. There’s sulfur and nitrogen in there, mixed in with nasty elements like mercury and arsenic.”

“The extras go up the smokestack along with the CO2, huh? Bad, for sure.”

“The good news is that coal-burning power plants are under the gun to clean up those emissions. The bad news is that effective mitigation technologies themselves cost energy. That lowers the net yield. But the inefficiency gets worse. Think coal trains.”

“Yeah, half the time I get held up on the way home by one of those hundred‑car strings, either full-up heading to the power plant or empties going back for another load.”

“Mm-hm. Transporting coal takes energy, and so does mining it and crushing it and pre‑treating to get rid of dirt and then taking care of the ashes. Even less net energy output per ton of smokestack CO2, even worse inefficiency. See why coal’s on its way out?”

“I guess all that didn’t matter when it was cheap to dig up and there wasn’t much competition.”

“You put your finger on it, Al. Coal got its foot in the door with steam engines 300 years ago when about the only other things you could burn were wood and whale oil. Crude oil got big in the mid‑1800s but it had to be refined and that made it expensive. Cheap natural gas wasn’t really a thing until fracking came along 50 years ago, but that brought a different set of issues.”

“Yeah, I’ve seen videos of people lighting their kitchen sink water on fire. And wasn’t there an earthquake thing in Oklahoma?”

“That was an interesting situation. Oklahoma’s in the middle of the continent, not a place you’d expect earthquakes, but they began experiencing flurries of shallow ones in 2011. The fracking process starts with water pumped at high pressure into gas-bearing strata to loosen things up. People suspected fracking was connected to the earthquakes. It was, but only indirectly. When fracked gas comes out of a well, water does, too. The rig operators pump that expelled water down old oil wells. Among other things, the state’s Corporation Commission is in charge of their hydrocarbon production. When the Commission ordered a 60% cut in the waste‑water down‑pumping, the earthquake rate dropped by 90%. Sometimes regulations are good things, huh?”

~~ Rich Olcott

Elementary History

On By rolcottIn Chemistry, UncategorizedLeave a comment

<chirp, chirp> “Moire here.”

“Hi, Sy, it’s Susan.”

“Well, hello. Good to hear from you. What’s up?”

“I’m out here on my back porch, fooling around on my laptop. It’s too nice to work in the lab today.”

“I agree with you. I’m outside, too, enjoying the Springtime. What’s your fooling around?”

“I found a discovery date list for all the chemical elements. Guess which element was the first that humanity worked with in pure form?”

“Mmm, I’d say carbon, in charcoal.”

“Nope, it’s copper.”

“Copper?”

“Mm-hm. Or maybe gold. They both occur as the raw metal but copper’s more common. There was a Copper Age before the Bronze age. The dates are fuzzy because they depend on what the archaeologists find after site scavengers have been there. I’m sending you the first few rows from the list.

Cumulative
Count 		Element
(Symbol)		Atomic
number 		Estimated
years ago
1Copper (Cu)2910000
2Lead (Pb)826000
3Carbon (C)65750
4Silver (Ag)475000
5Tin (Sn)505000
6Antimony (Sb)515000
7Gold (Au)794500
8Iron (Fe)264000
9Mercury (Hg)803500
10Sulfur (S)162500

“You can win most of them from the right ore with relatively simple processing. It makes sense they’re the ones we got to first.”

“Susan, I’m surprised it took a thousand years to realize you can get sulfur from cinnabar ore at the same time you’re cooking the mercury out of it. I wouldn’t want to be downwind from that process or most of the rest.”

“Sure not. I’ll bet there just wasn’t much interest in sulfur until the alchemists started playing with it. Anyhow, I dumped the element data into a spreadsheet and got some fun facts when I graphed it. Look at this. Eight thousand years for 10 elements through sulfur, then 1800 years of nothing. Arsenic doesn’t show up until the Thirteenth Century when I guess royalty started using it to poison each other. And phosphorus — have you read Neal Stephenson’s Baroque Cycle trilogy?”

“Yes, and I know the episode you’re thinking of, where the hero routed a gang at night by coating himself with glowing phosphorus and bursting out of a cave pretending to be a demon. Stephenson put a lot of words into describing how factories obtained mercury and phosphorus back then.”

“Stephenson puts a lot of words into most everything nerdy. That’s why I enjoy reading him. Oh-ho, now I know how you knew about cinnabar being the source for mercury.”

“Hey, Susan, I don’t only do Physics, but yeah, that was from another Baroque Cycle episode. … Looking at your graph here — things certainly took off at the start of the Eighteenth Century.”

“Yes, indeed. Seventy-four elements, everything that’s not radioactive plus a couple that are. I get a chuckle from cobalt being the first element in that wave after phosphorus. You know the story?”

“What story is that?”

“Seventeenth Century miners kept digging up nasty rocks that emitted poisonous gas when smelted along with the desirable copper and nickel ores. They called the bad stuff kobald Oren, German for ‘goblin ores.’ When a Swedish chemist finally purified the material he simply re-spelled the adjective and called the metal cobalt. I love the linkage with Stephenson’s fictional phosphorus-covered demon.”

“Cute. Why the break between rhenium and technitium?”

“That second wave after 1935 is all radioactives. Funny how the timing paralleled Seaborg’s research career even though he never got involved with technitium, the first artificially-produced element. Imagine being the discoverer of ten different elements.”

“Seaborg practically invented that funny bottom row of the Periodic Table, didn’t he?”

“Oh, yes. Not only did he discover or co-discover more than half of those elements, he was the one who proposed setting off the entire group as Actinides, in parallel with the Lanthanides above them. Oh, that reminds me, I meant to show you the other display I built. You’ve probably never seen one like this.”

“Whoa, you’ve colored each element block by how long we’ve known about it. That’s not the kind of thing you can do with crayons.”

“No, I had to do some programming to get the right tints.”

“What’s the little star for in the middle of the scale?”

“That’s when Mendeleev first proposed the Table, smack in the logarithmic center of my timeline. Don’t you love it?”

~~ Rich Olcott

Getting over The Hill

On By rolcottIn Uncategorized, ChemistryLeave a comment

“You guys want refills? You look like you’re gonna be here a while.”

“Yes, thanks, Al. Your lattes are sooo good. And can we have some more paper napkins?”

“Sure, but don’t let ’em blow away or nothin’, OK? I hate havin’ to pick up the place.”

“They’ll stay put. Just a half-cup of mud for me, thanks.”

The Spring breeze has picked up a little so we hitch our chairs closer together. Susan reaches for a paper napkin, draws a curve. “Here’s another pattern you haven’t featured yet, Sy. It’s in every chemist’s mind when they think about reactions.”

“OK, I suppose this is molecules A and B on one side of some sort of wall and molecule C on the other.”

“It’ll be clearer if I label the axes. It’s a reaction between A and B to make C. The horizontal axis isn’t a distance, it’s a measure of the reaction’s progress toward completion. Beginning molecules to the left, completed reaction to the right, transition in the middle, see? The vertical axis is energy. We say the reaction is energetically favored because C is lower than A and B separately.”

“Then what’s the wall?”

“We call it the barrier. It’s some additional dollop of energy that allows the reaction happen. Maybe A or B have to be reconfigured before they can form an A~B transition state. That’s common in carbon chemistry, for instance. Carbon usually has four bonds, but you can get five‑bonded transition states. They usually don’t last very long, though.”

“Right, carbon and its neighbors prefer the tetrahedral shape. Five‑bonded carbon distorts the stable electron clouds. Heat energy shoves things into position, I suppose.”

“Often but hardy always. Especially for large molecules, heat’s more likely to jostle things out of position than put them together. That’d what cooking does.”

“The curve reminds me of particle accelerator physics, except it takes way more energy to overcome nuclear forces when you mash sub‑atomic thingies together.”

“Oh, yes, very similar in terms of that general picture — except that the C side could be multiple emitted particles.”

“So your sketch covers a processes everywhere, not just Chemistry. They all have different barrier profiles, then?”

“Of course. My drawing was just to give you the idea. Some barriers are high, some are low, either side may rise or fall exponentially or by some power of the distance, some are lumpy, it all depends. Some are even flat.”

“Flat, like no resistance at all?”

“Oh, yes. Hypergolic rocket fuel pairs ignite spontaneously when they mix. Water and alkali metals make flames — have you seen that video of metallic sodium dumped into a lake and exploding like mad? Awesome!”

“I can imagine, or maybe not. If heat energy doesn’t get molecules over that barrier, what does?”

“Catalysts, mostly. Some do their thing by capturing the reactants in adjacent sites, maybe doing a little geometry jiggling while they’re at it. Some play games with the electron states of one or both reactants. Anyhow, what they accomplish is speeding up a reaction by replacing the original barrier with one or more lower ones.”

“Wait, reaction speed depends on the barrier height? I’d expect either go or no‑go.”

“No, it’s usually more complicated than that. Umm … visualize tossing a Slinky toy into the air. Your toss gives it energy. Part of the energy goes into lifting it against Earth’s gravity, part into spinning motion and part into crazy wiggles and jangling, right? But if you toss just right, maybe half of the energy goes into just stretching it out. Now suppose there’s a weak spot somewhere along the spring. Most of your tosses won’t mess with the spot, but a pure stretch toss might have enough energy to break it apart.”

“Gotcha, the transition barrier might be a probability thing depending on how the energy’s distributed within A and B. Betcha tunneling can play a part, too.”

“Mm? Oh, of course, you’re a Physics guy so you know quantum. Yes, some reactions depend upon electrons or hydrogen atoms tunneling through a barrier, but hardly ever anything larger than that. Whoops, I’m due back at the lab. See ya.”

<inaudible> “Oh, I hope so.”

~~ Rich Olcott

The Edge of Pinkness

On By rolcottIn Chemistry, Mathematics: Logs and Exponentials, Uncategorized1 Comment

Susan Kim takes a sip of her mocha latte. eyes me over the rim. “That’s quite a set of patterns you’ve gathered together, Sy, but you’ve left out a few important ones.”

“Patterns?”

A log-linear plot

“Regularities we’ve discovered in Nature. You’ve written about linear and exponential growth, the Logistic Curve that describes density‑limited growth, sine waves that wobble up and down, maybe a couple of others down‑stack, but Chemistry has a couple I haven’t seen featured in your blog.”

“Such as?”

“Log-linear relationships are a biggie. We techies use them a lot to handle phenomena with a wide range. Rather than write 1,000,000,000 or 109, we sometimes just write 9, the base‑10 logarithm. The pH scale for acid concentration is my favorite example. It goes from one mole per liter down to ten micro‑nanomoles per liter. That’s 100 to 10-14. We just drop the minus sign and use numbers between 0 and 14. Fifteen powers of ten. Does Physics have any measurements that cover a range like that?”

“A handful, maybe, in theory. The limitation is in confirming the theory across a billion-fold range or wider. Atomic clocks that are good down to the nanosecond are our standards for precision, but they aren’t set up to count years. Mmmm … the Stefan‑Boltzmann Law that links an object’s electromagnetic radiation curve to its temperature — our measurements cover maybe six or seven powers of ten and that’s considered pretty good.”

“Pikers.” <but I like the way she grins when she says it>

“I took those Chemistry labs long ago. All I remember was acids were colorless and bases were pink. Or maybe the other way around.”

“You’ve got it right for the classic phenolphthalein indicator, but there are dozens of other indicators that have different colors at different acidities. I’ll tell you a secret — phenolphthalein doesn’t kick over right at pH 7, the neutral point. It doesn’t turn pink until the solution’s about ten times less acidic, near pH 8.”

Adapted from this file by Damitr, CC BY-SA 4.0

“So all my titrations were off by a factor of ten?”

“Oh, no, that’s not how it works. I’m going to use round numbers here, and I’ll skip a couple of things like the distinction between concentration and activity. Student lab exercises generally use acid and base concentrations on the order of one molar. For most organic acids, that’d give a starting pH near 1 or 2, way over on the sour side. In your titration you’d add base, drop by drop, until the indicator flips color. At that point you conclude the amounts of acid and base are equivalent, not by weight but by moles. If you know the base concentration you can calculate the acid.”

“That’s about what I recall, right.”

“Now consider that last drop. One drop is about 50 microliters. With a one‑molar base solution, that drop holds 50 nanomoles. OK?”

<I scribble on a paper napkin> “Mm-hm, that looks right.”

“Suppose there’s about 50 milliliters of solution in the flask. Because we’re considering the last drop, the solution in the flask must have become nearly neutral, say pH 6. That means the un‑neutralized acid concentration was 10-6 moles per liter, or one micromolar. Fifty milliliters at one micromolar concentration is, guess what, 50 nanomoles. Your final drop neutralizes the last of the acid sample.”

“So the acid concentration goes to zero?”

“Water’s not that cooperative. Water molecules themselves act like acids and bases. An H2O molecule can snag a hydrogen from another H2O giving an H3O+ and an OH–. Doesn’t happen often, but with 55½ moles of water per liter and 6×1023 molecules per mole there’s always a few of those guys hanging around. Neutral water runs 10-7 moles per liter of each, which is why neutral pH is 7. Better yet, the product of H3O+ and OH– concentrations is always 10-14 so if you find one you can calculate the other. Take our titration for example. One additional drop adds 50 nanomoles more base. In 50 milliliters of solution that’s roughly 10-6+10-7 molar OH–. Call it 1.1×10-6, which implies 0.9×10-8 molar H3O+. Log of that and drop the minus sign, you’re a bit beyond pH 8 which sends phenolphthalein into the pink side. Your titration’s good.”

I eye her over my mug of black mud. “A gratifying indication.”

~~ Rich Olcott