Well Loved Books

I love it when I get a chemistry book or a cookbook out of the library and it has spots on the page or there are pieces of pages missing.  It is at that point that I know someone has used and loved the book.  Here are three recent examples.

This is one of the pages I printed from a digital book I have.  It is all about sulfur and I have more pictures at a future date of all the fun things I did with it.

This comes from a book entitled "Things A Boy Can Do With Chemistry"  This page is talking about silicate gardens.  I'm guessing that the yellow blotch is iron silicate.

This is from an old chemistry set that my dad had.  

Phenom-enal

Our university has a Phenom scanning electron microscope.  I was recently trained on how to use it and so I took some time after being trained to play around and learn more about the instrument.  Below are some of the pictures that I took.  See if you can guess at what they are before reading the labels.

It is a booger.

These are diatoms on the shell of a crab's claw.

This is earwax.

These three are a piece of woven cotton fabric.

These are of one of my fingernail clippings.

A Kim-wipe and a piece of notebook paper.

Gold wire contacting microelectronic pad.

The leg of a pillbug.

A pin head.

This is some of my blood.  I poked myself with the pin from the previous pictures and looked at it.  I think the regular cracking circles might be red blood cells.

Cotton from a Q-tip.

Some broken wood from the shaft of the Q-tip.

If there is anything that you would like to see under the SEM let me know and I'll see what I can do.

I Am Your Density

I've given away some test tubes and now for some ideas on how to use them. This is the first of those posts.

Density is a measure of the mass of something for a given volume, or in other words how much stuff is smashed into some space. It has a formula of ρ=m/v where:

ρ = density
m = mass
v = volume

Different materials have different densities. Old home chemistry books encouraged you to run to the drug store and get some mercury, carbon tetrachloride, water, oil, iron, a rubber stopper, and a cork. Pour the liquids in in order and then drop in the solids and you have a seven layer density column. This particular column is now very difficult to recreate because both mercury and carbon tetrachloride are no longer sold at the drug store. Steve Spangler has a great description of another 7 layer column that can be created from things found around the house.

Our set up for today is even easier. We are going to make a four layer column using three sugar solutions and plain water. So start by getting five test tubes and a pipette. Three test tubes will have sugar solutions one will have plain water and the last will be used for making the column. In the first tube put two mL of sugar, one drop of red food coloring, and fill it to the 10mL mark with water. In the second tube place four mL of sugar, one drop of green food coloring, and fill it to the 10mL mark with water. In the third tube add six mL of sugar, a drop of blue food coloring , and fill it to the 10mL mark with water. Lastly, in the fourth tube fill it with water. Now shake them until they are all dissolved. One mL of granulated sugar has a mass of about 0.8 g while one mL of water has a mass of 1 g. So your solutions have densities of:

plain water:(10g H₂O+ 0g sugar)/10 mL =1 g/mL
red: (10g H₂O+ 1.6g sugar)/10 mL =1.16 g/mL
green: (10g H₂O+ 3.2g sugar)/10 mL =1.32 g/mL
blue:(10g H₂O+ 6.4g sugar)/10 mL =1.64 g/mL

Now take a pipette full of the blue solution and add it to the empty fifth test tube. Now take a pipette full of the green solution and add it very carefully to the column. To do this you will need to slowly dribble it down the edge of the test tube. It should form a layer on top of the first one. Now do the same with the red layer and the water layer. It should look something like this.


Amazingly it will stay this way for quite a while. The next picture is the column after 12 hours. You can see that the plain water and the weakest concentration have begun mixing.


They will slowly go on mixing and after a week mine looks like this

You can still see separation between the top two and bottom two layers. After another few days in the window some mold started growing on the top so I washed it down the drain.

Now try playing with the solutions. Can you get them to stack in the wrong order? Can you make a solution dense enough to float a raisin in it? If you make alternating solutions of sugar and salt do they last as long as a column made from just sugar? Do they last longer?

I hope you all enjoy making and playing with your own density columns. Let me know how it goes.

Euclid

Geometry has always been my favorite math class. I always wanted to take a college level geometry class but I've never been able to fit it into my schedule. So I decided to read Euclid's Elements and cover the basics again. I really wanted to see the Greek (I don't read Greek but I wanted to see it) while I read the text in English. Marcelle had read and used the Elements as a text book in her days at St. John's in Santa Fe and I asked her if her text had the Greek. She said that it did not and that as far as she knew an inter-columnar version didn't exist or they would have used it.

I searched on Google and found that in 2007 Richard Fitzpatrick published a completely free and wonderful pdf version of the Elements in both Greek and English along with a Greek-English Lexicon. My plan is to print and bind the book along with blank pages in between the text so that I can work the proofs along with the text. Towards this goal Marcelle bought me a great compass so that I can make it look good to.

While I was searching for information on Euclid I decided that I wanted some old manuscripts of the Elements like this one. So I bought a sheet of papyrus from the local art store and while Marcelle and the kids were visiting her parents I acquired some papyri with parts of the Elements on them. These are pictures of them.

These first two are the definitions from the start of Book 1 "1. A point is that of which there is no part." You can see that this item is a composite of two pieces of papyrus "glued" together to make one larger piece.

This is the end of Proposition 11 from Book 4 inscribing a regular pentagon in a given circle. I haven't decided if I'm going to distress these last two like I did the first one.

This, of course, is the famous start of Proposition 47 from Book 1 proving the Pythagorean Theorem.

Liquid Diet

A few days before Christmas 2003 I had my mouth wired shut after having surgery on my jaw. I was on a liquid diet for a week and then I graduated to things like jello. I am here to tell you that you can only drink so much chicken broth before your body starts screaming "Give me a steak!" and I still gag when I think about drinking Ensure. Remembering this episode got me wondering if it is possible to survive solely on pure chemicals? While searching the literature I found out not only that it is possible but what the perfect recipe is. In a paper entitled "Evaluation of Chemical Diets as Nutrition for Man-in-Space¹" Winitz et al inform us that the perfect diet is:

Amino-acids
l-Lysine·HCl 3.58 g
sodium l-aspartate 6.40 g
l-Leucine 3.83 g
l-Threonine 2.42 g
l-Isoleucine 2.42 g
l-Proline 10.33 g
l-Valine 2.67 g
Glycine 1.67 g
l-Phenylalanine 1.75 g
l-Serine 5.33 g
l-Arginine·HCl 2.58 g
l-Tyrosine ethyl ester·HCl 6.83 g
l-Histidine·HCl·H₂O 1.58 g
l-Tryptophan 0.75 g
l-Methionine 1.75 g
l-Glutamine 9.07 g
l-Alanine 2.58 g
l-Cysteine ethyl ester·HCl 0.92 g

Water-soluble vitamins
Thiamine.HCl 1.00 mg
d-Biotin 0.83 mg
Riboflavin 1.50 mg
Folic acid 1.67 mg
Pyridoxine.HCl 1.67 mg
Ascorbic acid 62.50 mg
Niacinamide 10.00 mg
Cyanocobalamin 1.67 mg
Inositol 0.83 mg
p-Aminobenzoic acid 416.56 mg
d-Calcium pantothenate 8.33 mg
Choline bitartrate 231.25 mg

Salts
Potassium iodide 0.25 mg
Potassium hydroxide 0.83 g
Manganous acetate 18.30 mg
Magnesium oxide 0.38 g
Zinc benzoate 2.82 mg
Sodium chloride 4.77 g
Cupric acetate 2.50 mg
Ferrous gluconate 0.83 g
Sodium glycerophosphate 1.67 mg
Calcium Chloride·2H₂O 2.44 g
Ammonium molybdate·4H₂O 5.23 g
Sodium benzoate 1.00 g

Carbohydrates
Glucose 555.0 g
Glucono-δ-lactone 17.2 g

Fats and fat-soluble vitamins
Ethyl linoeate 2.0 g
α-Tocopherol acetate 57.29 mg
Vitamin A 3.64 mg
Menadione 4.58 mg
Vitamin D 0.057 mg

They point out that these diets are unique because " (a) their essential and nonessential nitrogen is provided in the form of highly pure L-amino-acids; (b) the are administered as single, crystal clear solutions which are nutritionally complete in themselves"

The dry ingredients were dissolved in distilled water to give a solution of 50-75% solids by weight which was completely sterile and had about 2-3cal per mL and could be stored almost indefinitely.

24 inmates from the California Medical Facility volunteered to drink/eat nothing but this liquid diet for 19 weeks. They were allowed to drink as much as they wanted and they could have all the water they wanted too. I can understand why they needed to use inmates because if they were on the outside after a week or so a cheeseburger looks really good.

They found that this diet provided well for these inmates and that there were no ill effects on their health. The authors go on to explain that these diets overcome some of the limitations inherent in alternative space-food sources:

"[These diets provide] high nutritive efficacy in ultra-compact form-1 ft³ of the diet as a 75% solution in water, will provide a 154-lb astronaut with all his required essential and nonessential nitrogen, salts, vitamins, and fats, in addition to his estimated requirement of 2,830 calories per day, for a period of a month; (b) complete water solubility- provides advantages in the administration of the diets in liquid form under conditions that will not permit the use of solids; (c) low bulk reduces low faecal residues and mitigates the critical problem of disposal of solid wastes; (d) complete nutrilite accessibility-allows alteration at will of the amino-acid ratios, carbohydrate content, and levels of all other components, thereby making it possible to tailor formulations to specific dietary needs of individual astronauts; (e) complete digestibility- provides dietary components in the most elemental form in the event of disturbances of the digestive system; (f) good storage stability either in the solid state or as aqueous solution."

This might be worth looking at for food storage...
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¹Winitz, M.; Graff, J.; Gallagher, N.; Narkin, A.; Seedman, D. A.; Nature 1965, 205, 741-743

Dutched Chocolate

My sister recently asked me "Why is cocoa processed with alkali in so many chocolate flavored products?"

First what is alkali processing or dutching? A solution of alkali (a base), usually potassium carbonate, is added to the cocoa nib before roasting. It's also possible to dutch cocoa liqueur or powder. Most of the cocoa liqueur used for making cocoa powder is dutched but the majority of liqueur used for making chocolate is not. Alkalising was developed in the 19th century in the Netherlands by Coenraad Johannes van Houten¹. He was trying to develop a chocolate powder that dissolved better in milk or water. Whether or not dutched cocoa dissolves better is still disputed but what the process definitely does do is change both the color and flavor of the cocoa.

The trick is to add just the right amount of base not too much because too much base will cause the triglycerides found in the cocoa butter to saponify thus giving it a soapy flavor. To avoid these off putting flavors small amounts of ethanoic or tartaric acid added to neutralize the high pH.

Some cocoa nibs are very acidic and the alkalising greatly helps flavor of the final chocolate product. Another thing that the base does is promote the formation of Miallard products (see another great article about how bases catalyze the Miallard reaction here.) Miallard products are those great flavors that form when proteins and sugar react.

The color change in the cocoa is due to reactions of the tannins in the cocoa. Tannins are polyhydroxyphenols, which means they are aromatic compounds (as apposed to an aroma compound) with several alcohol (-OH) groups. In the figure you can see a common one in cocoa, epicatechin. Depending on how the nib is fermented, dried, and roasted the tannins can join together, oxidize, and react with other chemicals in the cocoa to form color-giving molecules. This makes the cocoa much darker in color. By varying the pH, moisture content, and processing conditions it is possible to make cocoa of many different colors.

So when should you use alkali unprocessed cocoa? Well that depends on your leavening agent. Baking soda needs an acid to make it form CO₂ and cause your cake to fluff up nicely. Adding acidic unprocessed cocoa will cause it to rise. Further more, baking soda is a base and if added to the already basic dutched cocoa it can cause the cocoa butter to saponify and give soapy flavors to the dish. But because baking powder is a mixture of an acid and baking soda you want to use dutched cocoa so that it doesn't taste too acidic.

______________________
¹Casparus van Houten, Coenraad's dad, figured out how to easily remove cocoa butter from the nibs enabling the creation of cocoa powder. The nib contains about 54% cocoa butter by weight and this butter makes it difficult to mix into water or milk to make a drink. By pressing the beans, either with a hydraulic press or with a screw press, about half of the butter is expelled from the bean and the cocoa mass that is left can be ground into cocoa powder. This then allowed others to combine cocoa powder and sugar together and then remixing it with some of the cocoa butter thus forming something very close to the of chocolate of today.

DB Lavash and dips.

During this challenge Marcelle asked me to take a turn kneading the dough. A little while later, she gave me some constructive criticism on how I knead dough. It turns out that while I thought that I was kneading the dough, I was really just folding the dough in half and smashing it flat time and time again. What I was not doing was pulling and stretching the gluten molecules into a nicely aligned mass.

Harold McGee informed me that wheat flour is special in the grain family because it is the only grain whose endosperm proteins will interact strongly enough to form a gluten (most simply, a combination of gliadin and glutenin) that will support a raised bread. It is true that some other grains (like rye) will form gluten, but the formed gluten is weak and can't support the raising of the bread. To form a good bread the dough must be both plastic and elastic. Able to stretch out of shape when pressure is applied (plastic) and able to pull back to its original shape after the stress is removed (elastic). If the dough were just plastic, all of the carbon dioxide produced by those hard-working, fermenting yeasts would just flow to the surface and escape, making something very like bricks or hockey pucks. On the other hand, if the dough were completely elastic, the CO₂ would be crammed into a few very pressurized pockets and the bread would come out looking like swiss cheese: a very dense mass with a few pressurized pockets of gas.

Unkneaded gluten is a coiled up protein that you can visualize like a Slinky. Unlike a slinky, the reason gluten stays coiled up is that there are chemical bonds (disulfide bonds) holding the spiral layers together. Kneading stretches the "gluten-Slinky" until those disulfide bonds break. Once stretched the disulfide bonds can reform with other broken disulfide bonds in the new stretched position to keep the gluten all aligned. After reading about kneading gluten doughs I realized that the disulfide breaking and forming is a lot like what is happening during a permanent wave, but this explanation will have to wait for another post. So even with my poor kneading technique the lavash was delicious, the dips were delightful (mostly), and best of all I learned some new chemistry.

I didn't find this project very challenging. My cracker experience is not vast, but I did make whole-wheat saltine/"wheat thin" type crackers once a week for our baby for about 8 months after he started eating solid foods and before I wanted to expose him to long-ingredient-list store-bought crackers. I have made a lot of pita bread--with a variety of outcomes and a ton (almost literally) of pizza dough, so flatbreads are not altogether foreign to me. The recent lavash challenge was fun and easy and made for a nice snack when we had some friends over to play games one evening.

I followed the instructions exactly, but I had a few problems; here they are, in no particular order. Despite using an oven thermometer and switching the lavash from top to bottom rack and front to back partway through baking, one pan was much darker brown than the other. The paler pan also made lavash that were puffed and chewy. I'm sure this has reference mostly to the cheap oven in our rental home, but other bakers I conferred with confirmed my experience. I used sea salt on one pan and poppy seeds on the other, but despite spraying water, 70% of them fell off before they were eaten.

For the toppings, we decided to try to the Tahitian almond spread recipe provided and also made a basic pico de gallo (tomatoes from our garden, onion, serrano chile, cilantro, salt). I also served some olivada (see Moosewood Restaurant Cooks at Home) I had made with green olives a few days before. The olivada is a long-time favorite and the pico disappeared quickly; when all the chunks had been dipped out of the bowl, the juices were very nearly drunk by our friend. The almond spread was a little weird. I love almond butter and eat it almost every day on toast for either breakfast or on an apple for a maternity snack, but putting it with garlic, cilantro, honey, orange juice and pine nuts did nothing to further endear me to a food I already enjoy as it is. I'm really looking forward to next month.

Daring Bakers

Marcelle and I have joined a great group called the Daring Bakers. Each month they send out a recipe that everyone is to follow and then on a given day everyone posts their results on the same day. August was our first month with the group and we made éclairs. We made a hazelnut cream filling with a chocolate toping. To quote our toddler son they were "DEElishush."


This, however, is a blog about science, so I want to talk about the science behind éclairs. The dough is very simple to make. First water, butter, and milk are brought to a boil, then flour is stirred in all at once. The dough that forms is stirred and cooked for a few minutes on the stove to swell the starch. Then you transfer the dough to a mixer bowl and eggs are beaten in, one at a time. The dough is piped onto cookie sheets and baked in a hot oven.

You notice that there is no chemical leavening agent included in the dough, such as yeast or baking soda, and yet it forms lots of wonderful air pockets during baking. How does this happen? Steam forms as the puffs bake and the strong gluten structure formed by beating the dough stretches to hold the steam. With the steam trapped, the heat then coagulates the gluten and egg proteins forming a rigid wall that will hold its shape. If done properly, the puffs will be golden brown, with a hollow center crisscrossed by a soft network of dough filaments.

Each ingredient plays a part in making a good puff. First the water, milk, and butter need to be boiling so that when the flour is added it will swell (hydrate) the starch granules and gluten (gluten is made up of two proteins gliadin and glutenin). The more butter you add, the more tender the cream puff will be, but if you have too much it will interfere with the gluten stretching and the cream puff will collapse.

The eggs that are beaten into the dough act as the leavening agent. The yolks add fat and act as an emulsifier for a smooth and even texture in the finished product. Egg proteins add to the structure of the cream puff as it cooks.

Baking any dough is a delicate dance between two processes: the expanding of gas and the coagulation of gluten and gelatinization of starch. If the oven temperature is too low, the trapped air will expand and escape before the gluten and starch have set. The puff will collapse and be a tough mass. Also, the puffs depend on steam production to cause the to rise: if the temperature is too low there won't be enough steam to cause the puff to rise, and if the temperature is too high, the proteins and starch will set and brown before the gas has expanded to its full size. This will again lead to unpuffed puffs.


This recipe was an exciting start to our membership in the Daring Bakers Club. I felt like many of the components were unnecessarily complicated--for example, the best glaze for eclairs I've ever tasted (and had great success with) is a simple 5/4 chocolate/cream ganache. It doesn't get any easier than making it in the microwave. The glaze recipe we were instructed to follow to the letter never set up, not even after time spent in the cool of our freezer for a while. It included silly component recipes (which tasted great as ice cream toppings) but did nothing to further our desire to repeat this recipe experience. The choux recipe chosen for us by this month's host was a good one, although many important instructions were omitted from the instructions--like how wide the puffs should have been in addition to how long, and whether they should cool on racks or on sheets or on parchment paper pulled off the sheets and placed on a counter/table. Dave complained that it seemed like this recipe was intended to dirty as many dishes as possible, and because he is our "dishwasher," he should know. We thought the double chocolate hit from the pastry cream and the glaze would be too much (even for confirmed chocolate lovers), so we opted for a hazelnut pastry cream that we created from our vast store of experience making hazelnut gelato and it turned out really nice. We WILL be making that part again. All in all, this was supposed to get us cooking together in the kitchen, which happened three nights in a row this week for us to get all our components together. So, in that way, despite my quibbling, it was an unqualified success! ---Dave's lab assistant

Chinese Chemistry

I really enjoy looking at the Periodic Table. I love the amount of information that is available in such a condensed form. I like the Table so much that I carry one in my wallet. There is one in the kitchen (in English) and one in the bathroom (in Spanish). As I was thinking about the periodic table I began to wonder what it looks like in Chinese. It just so happens that I work with a couple of Chinese guys so I asked them to show me a Chinese periodic table. I noticed right off that all of the Nobel gases had one shape in common throughout the family. Then I noticed that it wasn't just the Nobel gases but all of the gases had the same character. Then I noticed that the metals had another character and last the non-metal solids another character. My labmate explained that in Chinese the majority if the symbols are made up from two parts. The first part (the radical) tells you what the physical state of the element is at STP. The second part is phonetic and tells you how to pronounce the symbol.

I learned (after installing the East Asian languages on my computer) that there are four radicals used on the periodic table and they were the shapes I had noticed at the beginning. They are 金or 钅(literally "gold" for metal), 石 (literally "stone" for non-metal and metaloid solids), 水 or 氵 (literally "water" for liquids), and 气 (literally "air" for gases). The phonetic part is based on the western name of the element. Below you can see some examples of this radical phonetic symbol pairing.


Here "metal" and the phonetic "bi" combine to form bismuth.


"Metal" plus "nei" form "na" for natrium or sodium in English. I like this one because it shows that they aren't just using the English pronunciations of the elements.

"Stone" and "dian" form iodine.


"Air" combines with "fu" to make fluorine.

There is set class of symbols which are for elements that were known since ancient times. Elements which were known to the Chinese alchemists like gold, iron, sulfur, and mercury. I especially enjoy the symbols for iron and sulfur. Iron can be broken up into several parts.


Which could be interpreted "metal from the mountain for making weapons." Sulfur can be broken apart to show that it is a stone that flows.


Lastly there are some characters that are descriptive of the element that they represent. Examples are phosphorus and bromine. Phosphorous breaks down to "the stone that glows" and bromine is the "stinky liquid."



Some of the websites that I found especially useful are Zhongwen, a website about Chinese characters and their etymology, the Wikipedia entry on the chemical elements in East Asian languages, and an IUPAC article on the Chinese terms for chemical elements.

Chemistry or Star Wars?