Tag Archives: chemistry

Briggs-Rauscher Oscillating Reaction

video showing the Briggs-Rauscher Oscillating Reaction. From Wikipedia:

The first known homogeneous oscillating chemical reaction, reported by W. C. Bray in 1921, was between hydrogen peroxide (H₂O₂) and iodate (IO₃^âˆ’) in acidic solution. Due to experimental difficulty, it attracted little attention and was unsuitable as a demonstration. In 1958 B. P. Belousov in the Soviet Union discovered the Belousov–Zhabotinsky reaction (BZ reaction), is suitable as a demonstration, but it too met with skepticism (largely because such oscillatory behavior was unheard of up to that time) until A. M. Zhabotinsky, also in the USSR, learned of it and in 1964 published his research. In May of 1972 a pair of articles in the Journal of Chemical Education brought it to the attention of two science instructors at Galileo High School in San Francisco. They discovered the Briggs–Rauscher oscillating reaction by replacing bromate (BrO₃^âˆ’) in the BZ reaction by iodate and adding hydrogen peroxide. They produced the striking visual demonstration by adding starch indicator.

The detailed mechanism of this reaction is quite complex. Nevertheless, a good general explanation can be given.
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Zubbles – Get Your Colored Bubbles

photo of blue colored bubble.

I first posted on this in 2005: Colored Bubbles. Now you can order your own via Zubbles. Colored Bubbles Have Landed (and Popped and Vanished)

Having solved the colored bubble dilemma, we spent most of 2006 trying to refine our dyes and the manufacturing process. We had invented several completely new dyes and a few derivatives of existing dyes. But the manufacturing process was long, tedious and expensive. It took three days just to make a few grams of each dye. It quickly became apparent that we needed to radically streamline the production process in order to have a viable product.
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The complexities of the chemistry resembled a pharmaceutical more than a toy. So I enlisted the help of Gary Willingham, and the Belgium development team, at Fisher Scientific. Fisher is a pharmaceutical chemical manufacturer with the equipment and expertise needed to manufacture tons of our dyes.
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Due to the complexities of the chemistry, Jamm decided to stay close to the production process and manufacture Zubbles in the US. The first bottles rolled off the line this week. Jamm presented me with the very first case of Zubbles. And it was a very strange feeling to finally hold the product in my hand—15 years after I mixed my first batch of dishwashing detergent and food coloring.

Being an entrepreneur is a challenge any time. When your product requires complex science and engineering that adds additional challenges. It is great to see this product is now available.

Protein Synthesis: 1971 Video

The above webcast shows protein synthesis, from a 1971 Stanford University video with Paul Berg (Nobel Laureate – 1980 Nobel Prize for Chemistry and National Medal of Science in 1983). The film does not exactly present the traditional scientist stereotype. It does pretty much present the typical California 1970’s hippie stereotype though.

2009 Nobel Prize in Chemistry: the Structure and Function of the Ribosome

graphic image of the components of a cell

Cross section of a cell by the Royal Swedish Academy of Sciences. A ribosome is about 25 nanometters (a millionth of a millimeter) in size. A cell contains tens of thousands of ribosomes.

The Nobel Prize in Chemistry for 2009 awards studies of one of life’s core processes: the ribosome’s translation of DNA information into life. Ribosomes produce proteins, which in turn control the chemistry in all living organisms. As ribosomes are crucial to life, they are also a major target for new antibiotics.

This year’s Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant or a bacterium, looks and functions. But the DNA molecule is passive. If there was nothing else, there would be no life.

The blueprints become transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make proteins: oxygen-transporting haemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar. There are tens of thousands of proteins in the body and they all have different forms and functions. They build and control life at the chemical level.

Details from the Nobel Prize site (which continues to do a great job providing scientific information to the public openly).
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Atomic Force Microscopy Image of a Molecule

The delicate inner structure of a pentacene molecule imaged with an atomic force microscope. For the first time, scientists achieved a resolution that revealed the chemical structure of a molecule. The hexagonal shapes of the five carbon rings in the pentacene molecule are clearly resolved. Even the positions of the hydrogen atoms around the carbon rings can be deduced from the image. (Pixels correspond to actual data points). Image courtesy of IBM Research – Zurich

IBM scientists have been able to image the “anatomy” — or chemical structure — inside a molecule with unprecedented resolution. “Though not an exact comparison, if you think about how a doctor uses an x-ray to image bones and organs inside the human body, we are using the atomic force microscope to image the atomic structures that are the backbones of individual molecules,” said IBM Researcher Gerhard Meyer. “Scanning probe techniques offer amazing potential for prototyping complex functional structures and for tailoring and studying their electronic and chemical properties on the atomic scale.”

The AFM uses a sharp metal tip to measure the tiny forces between the tip and the sample, such as a molecule, to create an image. In the present experiments, the molecule investigated was pentacene. Pentacene is an oblong organic molecule consisting of 22 carbon atoms and 14 hydrogen atoms measuring 1.4 nanometers in length. The spacing between neighboring carbon atoms is only 0.14 nanometers—roughly 1 million times smaller then the diameter of a grain of sand. In the experimental image, the hexagonal shapes of the five carbon rings as well as the carbon atoms in the molecule are clearly resolved. Even the positions of the hydrogen atoms of the molecule can be deduced from the image.

Read full press release: IBM Scientists First to Image the “Anatomy” of a Molecule
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What is a Molecule?

One of the things I keep meaning to do more of with this blog is provide some post on basic science concepts that may help raise scientific literacy. Some of these will be pretty obvious but even reminders on some facts you know can sometimes help.

What is a molecule?

A molecule is the smallest particle of a compound that has all the chemical properties of that compound. Molecules are made up of two or more atoms, either of the same element or of two or more different elements. The example of molecules are water (H₂O) and carbon dioxide (CO₂) and molecular nitrogen (N₂).

Organic molecules contain Carbon, for example, Methane CH₄). The original definition of “organic” chemistry came from the misconception that organic compounds were always related to life processes.

A few types of compounds such as carbonates, simple oxides of carbon and cyanides, as well as the allotropes of carbon, are considered inorganic. The division between “organic” and “inorganic” carbon compounds while “useful in organizing the vast subject of chemistry…is somewhat arbitrary”

Ionic compounds, such as common salt, are made up not of molecules, but of ions arranged in a crystalline structure. Unlike ions, molecules carry no net electrical charge.

Roger Tsien Lecture On Green Florescent Protein

Nobel Laureate Roger Tsien discusses his research on green florescent protein. From the Nobel Prize web site:

n the 1960s, when the Japanese scientist Osamu Shimomura began to study the bioluminescent jelly-fish Aequorea victoria, he had no idea what a scientific revolution it would lead to. Thirty years later, Martin Chalfie used the jellyfish’s green fluorescent protein to help him study life’s smallest building block, the cell.
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when Anton van Leeuwenhoek invented the microscope in the 17th century a new world opened up. Scientists could suddenly see bacteria, sperm and blood cells. Things they previously did not know even existed. This year’s Nobel Prize in Chemistry rewards a similar effect on science. The green fluorescent protein, GFP, has functioned in the past decade as a guiding star for biochemists, biologists, medical scientists and other researchers.
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This is where the third Nobel Prize laureate Roger Tsien makes his entry. His greatest contribution to the GFP revolution was that he extended the researchers’ palette with many new colours that glowed longer and with higher intensity.

To begin with, Tsien charted how the GFP chromophore is formed chemically in the 238-amino-acid-long GFP protein. Researchers had previously shown that three amino acids in position 65–67 react chemically with each other to form the chromosphore. Tsien showed that this chemical reaction requires oxygen and explained how it can happen without the help of other proteins.

With the aid of DNA technology, Tsien took the next step and exchanged various amino acids in different parts of GFP. This led to the protein both absorbing and emitting light in other parts of the spectrum. By experimenting with the amino acid composition, Tsien was able to develop new variants of GFP that shine more strongly and in quite different colours such as cyan, blue and yellow. That is how researchers today can mark different proteins in different colours to see their interactions.

The Amazing Rusting Aluminum

when aluminum rusts, it forms aluminum oxide, an entirely different animal. In crystal form, aluminum oxide is called corundum, sapphire or ruby (depending on the color), and it is among the hardest substances known. If you wanted to design a strong, scratchproof coating to put on a metal, few things other than diamond would be better than aluminum oxide.

By rusting, aluminum is forming a protective coating that’s chemically identical to sapphire—transparent, impervious to air and many chemicals, and able to protect the surface from further rusting: As soon as a microscopically thin layer has formed, the rusting stops. (“Anodized” aluminum has been treated with acid and electricity to force it to grow an extra-thick layer of rust, because the more you have on the surface, the stronger and more scratch-resistant it is.)

This invisible barrier forms so quickly that aluminum seems, even in molten form, to be an inert metal. But this illusion can be shattered with aluminum’s archenemy, mercury. Applied to aluminum’s surface, mercury will infiltrate the metal and disrupt its protective coating, allowing it to “rust” (in the more destructive sense) continuously by preventing a new layer of oxide from forming.

Electrolyzed Water Replacing Toxic Cleaning Substances

Simple elixir called a ‘miracle liquid’

The stuff is a simple mixture of table salt and tap water whose ions have been scrambled with an electric current. Researchers have dubbed it electrolyzed water
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Used as a sanitizer for decades in Russia and Japan, it’s slowly winning acceptance in the United States. A New York poultry processor uses it to kill salmonella on chicken carcasses. Minnesota grocery clerks spray sticky conveyors in the checkout lanes. Michigan jailers mop with electrolyzed water to keep potentially lethal cleaners out of the hands of inmates.

In Santa Monica, the once-skeptical Sheraton housekeeping staff has ditched skin-chapping bleach and pungent ammonia for spray bottles filled with electrolyzed water to clean toilets and sinks. “I didn’t believe in it at first because it didn’t have foam or any scent,” said housekeeper Flor Corona. “But I can tell you it works. My rooms are clean.”
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It turns out that zapping salt water with low-voltage electricity creates a couple of powerful yet nontoxic cleaning agents. Sodium ions are converted into sodium hydroxide, an alkaline liquid that cleans and degreases like detergent, but without the scrubbing bubbles. Chloride ions become hypochlorous acid, a potent disinfectant known as acid water.

“It’s 10 times more effective than bleach in killing bacteria,” said Yen-Con Hung, a professor of food science at the University of Georgia-Griffin, who has been researching electrolyzed water for more than a decade. “And it’s safe.”

There are drawbacks. Electrolyzed water loses its potency fairly quickly, so it can’t be stored long. Machines are pricey and geared mainly for industrial use. The process also needs to be monitored frequently for the right strength.

Very cool use of science: providing a green cleaning agent that is effective.

Engineers and Scientists in Congress

I started maintaining a list of Congressmen with PhDs and graduate degrees in science, engineering and math awhile back.

Please comment with any additions that you know of.

The following were re-elected:
Vernon Ehlers, Michigan, physics PhD; Rush Holt, New Jersey, physics PhD; John Olver, Massachusetts, chemistry PhD; Brian Baird, Washington, psychology PhD; Bill Foster, Illinois, physics PhD.

Other scientists, engineers and mathematicians that were reelected include: Ron Paul, Texas, biology BS, MD; Jerry McNerney, California, mathematics PhD; Dan Lipinski, Illinois, mechanical engineering BS, engineering-economic systems MS; Todd Akin, Mississippi, management engineering BS;Cliff Stearns, Florida, electrical engineering BS; Louise Slaughter, New York, microbiology BS; Joe Barton, Texas, industrial engineering BS, Pete Stark, California, engineering BS, Mike Honda, California.

Lost: Nancy Boyda, Kansas (BS chemistry).

Newly elected: Bill Cassidy, Louisiana (BS Biochemistry, MD); Pete Olson, Texas (BA computer science); Kurt Schrader, Oregon (Doctor of Veterinary Medicine); Martin Heinrich, New Mexico (BS engineering), Gregg Harper, Mississippi (BS chemistry), Joseph Cao, Mississippi (BA physics); Brett Guthrie, Virginia (BS mathematical economics); Erik Paulsen, Minnesota, mathematics BA; Parker Griffith, Alabama (BS chemistry, MD); Cynthia Lummis, Wyoming (BS animal science and biology).

Before you leap to the conclusion that scientists are taking over Congress, remember 2 things: 1) I have probably been missing plenty that were in congress already and 2) this is still a total of less than 10% with even a BS in science, math or engineering. I attempted to determine the status of all those newly elected this year.

Please comment, if you know of others in Congress with science and engineering backgrounds. If we get this list to be relative close to accurate then we can start tracking the total representation in congress and see if it is increasing, decreasing or randomly fluctuating over time.