ChemNews - Chemistry 111-2

Part of The Alchemist's Lair Web Site
Maintained by Harry E. Pence, Professor of Chemistry, SUNY Oneonta, for the use of his students. Any opinions are totally coincidental and have no official endorsement, including the people who sign my pay checks. Comments and suggestions are welcome (pencehe@oneonta.edu).

Last Revised Mar. 8, 2002

(Chem 111 - Second Examination, Fall, 2002)

2002 Nobel Prize in Chemistry

New Methods for Drug Design

James B. Fenn, Koichi Tanaka, and Kurt Wuthrich, scientists from America, Japan, and Switzerland, received the 2002 Nobel Prize in chemistry for their discoveries on new ways to map large biological molecules. Taken together, their work has played a major role in creating the new science of proteomics, which is concerned with the interactions of the thousands of proteins that make up cells. It is expected that these new discoveries will lead to a better understanding of the relationship between genetics and disease, which will acclerate the development of new drugs and medical treatments.

Fenn and Tanaka worked on the applications of a technique called mass spectrophotometry, which can be used to identify proteins rapidly. Tanaka and Fenn shared half of the prize for developing sampling methods that can vaporize proteins without breaking them apart. This is an essential step in mass spectrphotometic analysis, and was very difficult because the proteins were such large molecules. Wuthrich's research deals with the use of nuclear magnetic resonance to identify the shape of large protein molecules. Protein folding is important, because incorrect structures can produce serious diseases, like mad cow disease.

There are several sources of further information available on the WWW. A good general source is the page on The Science Box or the Nobel e-Museum press release on this year's awards. At a somewhat higher level, but still at moderately readable, is the the Nobel e-Museum page for the general public. Dr. Sharpless works at the the Scripps Research institute, which has created a web page entitled, "K. Barry Sharpless is Awarded the 101st Nobel Prize in Chemistry." You may also wish the go to the home page for Ryoji Noyor's laboratory. but this page will probably be rather difficult for general chemistry students. Dr. William Knowles has been retired for several years, and so there is less information on he web about him. Finally, You may to peruse a list of all the previous Nobel Prize Winners in Chemistry.

(Chem 112 - Third Examination, Spring, 2002)

The First Compounds with Uranium-Noble Gas Bonds!

In the February 28, 2002 issue of Science magazine (Science, Vol. 295, pgs. 2242-2245, March 22, 2002), Dr. Bruce Bursten from Ohio State university reported the synthesis of the first compound with three of the noble gases, argon, krypton, and xenon, with uranium. Until the 1960s, the noble gas elements were considered to be inert, and even when the first compounds were made, they often required extremely reactive reagents, like fluorine. Bursten said that the discovery happened because his research group was following up on some unexpected results obtained by a research group in Virginia.

The two research teams had been studying the reaction of uranium with simple molecules, like carbon monoxide, to attempt to better understand how radioactive elements behave in the environment. They found that uranium combined with carbon monoxide, CO, to form an unusual compound, CUO. They did the reaction at very low temperatures (about 4 K or -270 degrees Celsius) in a neon atmosphere, so that the neon molecules would form a protective cage around the CUO and make it stable long enough to be observed. They were surprised to discover that the spectra looked much different when the reaction was done in argon. This suggested that the "inert atmosphere" wasn't really inert. The Ohio State team then did calculations on a supercomputer and discovered, much to their surprise, that theory predicted that it was possible to form chemical bonds between uranium and an inert gas under these conditions. Bursten says that these experiments may give us a new look at how chemical bonds form.

As early as 1933, Linus Pauling predicted that compounds of what were then called the inert gases should exist, but there were apparently few efforts to follow up on his suggestion. In 1962, Prof. Neil Bartlett announced the first compounds of xenon. He accidentally obtained a reaction between oxygen gas and hexachloroplatinum. Realizing that oxygen gas and xenon had similar ionization, Bartlett decided to attempt to react xenon with the hexachloroplatinum, and he was rewarded with a compound. Since then several more compounds of xenon, argon, and krypton have been discovered, usually with highly electronegative reactants. To gain a better understanding of the excitement of fluorine chemistry, go to the web site of Prof. Gary Schrobilgen, who created the first compound with a bond between xenon and nitrogen, and read about his research. If you read nothing else on this site, page down to the sidebar that reads, "this experience was almost as hazardous as being drafted into the U.S. Army" and read from there. Who says chemists don't have fun!

(Chem 112 - Second Examination, Spring, 2002)

Science Magazine Names Nanoelectronics Molecule of the Year

Just asTime magazine chooses a Man of the year, each year Science magazine, a publication of the American Association for the Advancement of Science, chooses a molecule of the year; some species that has had, or is expected to have, an unusual impact on science. For the year just ended, the molecule of the year was nanoelectronics (Science, 2001, 294, 2442). Although nanoelectronics has been the focus of extensive research for many years, this year for the first time it became possible to create electronic circuits on the moledular scale. The hope is that these small circuits can be combined to produce a major breakthrough in electronis that may have the same impact as the invention of the transisor.

The prefix nano means one billionth, and so nanotechnology is concerned with creating new machines and circuits that are on the scale of a billionth of a meter. By comparison, an atom is about one-third of a nanometer in diameter. The idea of nanotechnology has been around for many years. In 1965, Richard Feynman pointed towards the possibilities for this type of research in a paper entitled "There's Plenty of Room at the Bottom." In the late 1990s, a number of researchers had succeeded in creating the basic components of electronic circuits, including fuses, switches, and diodes, using molecular sized devices, cut they had not been able to string theses pieces together into a circuit. Within the past year, however, anumber of research groups have reported the creation of working circuits, and a group from Bell Labs has designed organic molecules that chemically assemble themselves to form transistors. A recent survey (NY Times, Mar. 11, 2002, pg. C1) extimates that $30 million worth of nanodevices will be sold in the current year and the U.S. National Science Foundation predicts that sales will be over $1 trillion by 2015. nano-sized materials are already in use for a broad range of products, including self-cleaning window glass, sunscreens for cosmetics, antimicrobial dressings, and automobile components (i.e. running boards and dashboards).

Technology Review, a publication of MIT, has an Executive Review of nanotechnology on the WWW, and the Zyvex Corporation hosts a web site with a number of links to nanotechnology pages. The U.S. Government has a National Nanotechnology Initiative which is strongly funded in the 2002 U.S. budget for nanotechnology. If you would like to explore the possible future of this technology, you may wish to check out a site on Nanomedicine, especially the Gallery of nanomedicine, which contains artists ideas of possible new developments. Finally, a search for nanotechnology on Google returned over 350,000 hits. You may wish to follow up at some of these sites.

(Chem 112 - First Examination, Spring, 2002)

A New Way to "Fix" Nitrogen?

A recent article (Science, 1998, 279, 540) reports that Japanese scientists have discovered a new method for producing ammonia from nitrogen and hydrogen gases. The reaction could be a replacement for the process (discussed in class), which has been used to produce ammonia since 1913. In both cases, the goal is to transform atmospheric nitrogen gas into more reactive compounds that can be used for commercial processes.

The main difference between the old and new methods is that while the Haber process is carried out at 200 atmospheres of pressure and 500°C, the new process uses a tungsten catalyst that allows the reaction to occur at 55°C under normal atmospheric pressure . The research team, based at the University of Tokyo, managed to convert 40 to 50% of the nitrogen into ammonia within 24 hours.

There is a crossword puzzle on the net based on the Haber Process. Most of the questions aren't too hard, and there are a couple of ways that you can peek at the answers if you get stuck. If you would like to read more about the Haber Process, the site called gcsechemistry has a brief, but good, discussion. The on-line museum of Nobel Prize has a short biography of Haber. For a more extensive (and grphic) discussion of World War I, you might try the idiot's guide page titled, "Blueprints for a Bloodletting." It has a lot of informaiton about Haber and the result of his process. Raymond Zmaczynski, a secondary school teacher, has a good summary article on the Princeton Univ. History of Science web site entitled, "The Effect of the Haber Process on Fertilizers."

CAUTION! THIS SITE IS MUCH MORE TECHNICAL! Prof. Richard Terry, College of Biology and Agriculture at Brigham Young University, also has a useful treatment of the nitrogen cycle, including nitrogen fixation. Please note that Prof. Terry's material is in a PowerPoint presentation. To move from frame to frame you must click on the little right-handed triangle in the upper right corner of each frame.

(Chem 111 - Third Examination, Fall, 2001)

2001 Nobel Prize in Chemistry

William Knowles, K. Barry Sharpless and Ryoji Noyori, two American scientists and one from Japan, received the 2001 Nobel Prize in chemistry for their discoveries on new ways to control chemical reactions. The new techniques that they have developed have been used to by pharmaceutical chemists to create a number of new drugs, including as antibiotics, beta-blockers (heart medicine), and ulcer treatments. The research honored has been in process for over thirty years, but the success of this approach has been increasingly recognized.

Many important biological molecules, such as proteins, DNA, and carbohydrates, are chiral, that is, they have a special structure which can occur in either a left-handed or a right-handed form. For example, even if your left and right hands were exactly the same size, it would be impossible to superimpose one on top of the other and make all the fingers match. This feature is of critical importance in drug design, since the different chirality causes different behavior, even though the molecular formula is exactly the same. Effective drugs much match the chirality of the biological systems. When this doesn't happen, the drug may be ineffective or even harmful. The Nobel Prize was awarded for the discovery of new methods to insure that molecules have the desired handedness, so that they will function correctly as drugs.

(Chem 111 - Second Examination, Fall, 2001)

Ionic Solvents Create New Chemical Environments

During the past few decades, the increasing emphasis on protecting the environment has forced chemists to rethink many of the processes that have traditionally been used to synthesize chemicals. Often the methods used in the past have created large amounts of byproducts and contaminated solvents, which required disposal. Chemists are now developing alternative methods that use a new type of solvent, called an ionic liquid. These solvents dissolve almost everything from plastics to metals, are relatively inexpensive, do not evaporate or burn, are generally not toxic, and finally and most important, are much easier to recycle than traditional solvents. It is this latter property that is most interesting to those hoping to decrease the amount of environmental pollution. Environmentally friendly changes like are often called Green Chemistry. (This URL has a great deal of information about Green Chemistry in Education, including the 12 Principles of Green Chemistry. Barry Trost has proposed one of the fundamental ideas of Green Chemistry, The Concept of Atom Economy, although General Chemistry students may find the discussion at this URl to be tough going.)

Up until the 19th Century, most chemists used water as a solvent for reactions. At that time, organic liquids, such as alcohol, benzene, and other hydrocarbons, became popular. All of these liquids were molecular solvents; they either were not ionic or else they ionized to a very small extent (like water). The reason that normal ionic solids, commonly called salts, were not used in the past is that they melt at rather high temperatures, for example, LiCl (610 oC), NaCl (803 oC), and KCl (772 oC).

The crucial change has been the development of Room Temperature Ionic Liquids (RTILs). In the late 1940s, researchers at Rice Institute of Technology discovered that if they made ionic salts where the cation was replaced by a large organic group, the resulting materials were liquids from below room temperature to 200 oC or higher. Since the interaction between the solvent and the solute can have important effects of what happens in a chemical reaction, reactions in ionic solvents are often significantly different from those observed in molecular solvents. Several cases are already known where the use of ionic solvents is not only better for the environment but also produces products that were more difficult or even impossible to produce with molecular solvents. Just to give one example, a common industrial reaction that usually requires seven hours and gives a mixture of products can be run in only 30 seconds and gives almost 100% yield in an ionic liquid.

The only road block to widespread use of these liquids is the need for fundamental research that will reveal more information about the properties and possible toxic effects of these compounds. If you wish to lean more about ionic solvents, there are several good sources of information on the WWW. Science News has a very readable discussion, and the review by Kenneth R. Seddon may contain some unfamiliar concepts, but it is also quite informative if you are feeling brave.

(Chem 111 - First Examination, Fall, 2001)

Superheavy Hydrogen is Created

A team of scientists from Russia, Japan, and France, working at the Joint Institute for Nuclear Research near Moscow, Russia, has recently reported that they created a new isotope of the element hydrogen. This isotope, which has a mass of 5, is the heaviest hydrogen isotope known, consisting of one proton and four neutrons. It has been speculated for over 40 years that such an isotope is possible, but this is the first time that reasonable proof has been presented that it actually exists. These scientists used a beam of helium-6 ions (which is an unusual isotope itselt) to bombard hydrogen ions, producing hydrogen-5 and helium-2 ions, both of which rapidly decayed. The determination that hydrogen-6 was one of the products was the result of an analysis of the decay products from this interaction.

Aside from the fact that hydrogen-5 is unusual, there are several other reasons why this observation is interesting. It has been suggested that the conditions in a black hole in space might be appropriate for forming species like hydrogen-5 that would not normally be stable. Thus, the spectrum of hydrogen-5 might be observed by astronomers who study black holes. The behavior of this rare species might also provide a test for the theories that attempt to explain what causes matter to be stable. If the Big Bang Theory is correct, it would appear that after the initial explosion, there was a period of cooling, during which individual protons, neutrons, and electrons began to coalesce. This initial process that formed the elements that are the foundation of our universe is called nucleosynthesis. If, as seems possible, hydrogen-5 played a role in that process, understanding the properties of this species will also help to understand the formation of matter in the universe. The Astronomy Hypertext Book has some good animations of the basic processes involved in nucleosynthesis (although hydrogen-5 is too new to be included in any of these proposed reactions).

(Chem 112 - Third Examination, Spring, 2001)

Observing the Fastest Chemical Reactions with Lasers!

When chemical reactions occur, the individual atoms may shift so rapidly that the making and breaking of chemical bonds.
may occur in only a few femtoseconds (that is, 1E-15 seconds). Traditional methods for observing reaction rates include allowing the system to come to equilibrium, then quickly increasing the temperature and observing how fast the system returns to equilibrium. This is called the relaxation method. Another approach is to prepare two solutions that contain the reactants, then continuiously inject them into a tube at high velocities, where they mix and react. This is called the stopped flow method, because the reaction seems to have stopped in the tube, even though the reactions are moving past at a very high rate. Moving the observation point down the tube makes it possible to observe the reaction as it proceeds. Neither of these methods is fast enough to observe reactions that only require femtoseconds to happen.

Recently new methods have been developed that make it possible to observe the fastest reactions known. The method is similar to using a flash camera to freeze the movement of a hummingbird's wings while it is in flight. The trick was to find a source for a light pulse that would have a short enough duration to make the molecules appear to freeze as they are moving. In femtosecond spectroscopy, an initial laser pulse provided the activation energy for the process so that bonds would begin to break. This is followed a series of weaker laser pulses that are absorbed by the molecules as they react. This latter series of absorptions provides information about how the reaction occurs.

In 1999, Dr. Ahmed H. Zewail won the Nobel Prize in chemistry for developing this method of using lasers to observe ultra-fast chemical reactions. Prof. Zewail, who is a citizen of both the U.S. and Egypt, holds the Linus Pauling Chair of Chemical Physics at the California Institute of Technology.The first reactions he studied were elementary processes, such as the dissociation of iodocyanide (ICN) into iodine (1) and cyanide (CN) or the reaction between a hydrogen atom (H) and carbon dioxide to produce carbon monoxide (CO) and hydroxyl (OH). In the second of these reactions, it was observed that the hydrogen atom combined with the carbon dioxide to form a relatively long-lived intermediate, which then broke down to give the products. The technique is now being used to investigate a wide variety of reactions, ranging from photosynthesis to human night vision.

To learn more about Prof. Zewail, go to his home page at CalTech (including his picture) .

(Chem 112 - Second Examination, Spring, 2001)

The First "Big One"??

It is now generally accepted that the extinction of the dinosaurs was caused by a massive meteorite that struck the earth about 65 million years ago. Geologists identify this change in life forms with the transition from the Cretaceous to the Triassic periods. Now there is evidence that a similar catastrophic event happened 251 million years ago and caused a mass extinction at the end of the Permian geologic period. This event is identified as the transition from the Permian to the Triassic periods. In the Feb. 23, 2001 issue of Science (pgs. 1530-1533), Luann Becker (Univ. of Washington) and Robert Poreda (Univ. of Rochester) report that they have found evidence of a major meteorite strike by studying the sediments from the Permian-Triassic (P-T) transition. These scientists separated and analyzed a special form of carbon, called fullerene, which was present in these samples. Fullerenes have a roughly spherical shape, and the carbon atoms are organized in space so that they resemble a soccer ball. The center is hollow, and gas molecules can be trapped in this central region. In this case, the trapped molecules they studied were helium. Becker and Poreda determined that the ratio of helium-3 to helium-4 was very different from that normally observed in terrestrial samples but was similar that that found for interplanetary dust and meteorites. This indicates that these carbon molecules formed in deep space and were brought to Earth by some large astronomical body, like a meteorite or an asteroid. Other evidence has suggested that some event of this magnitude occurred, but this new data seems to be more convincing.

Fullerenes are unusual molecules that are very interesting and potentially useful. The 1996 Nobel Prize in Chemistry was awarded for the discovery of these molecules. In 1999, fullerenes were found in a meteorite, indicating that they are not uncommon in the universe. Among other areas, there is currently a great deal of research on the use of fullerenes to create very tiny machines, what are the size of individual molecules, a field called nanotechnology. Fullerenes are named after Buckminster Fuller, a famous 20th century architect, who popularized concepts like synergy and spaceship earth. He is also the origin of the alternative name for this class of compounds, namely bucky balls.

(Chem 112 - First Examination, Spring, 2001)

Bioinformatics is a hot new career field in science.

According to a story in the Jan. 1, 2001 issue of C&E News (pgs. 47-55), the field of bioinforematics has suddently become one of the hottest career fields for scientists. Although the combination of computing and biology or biological chemistry has been around since the 1960s, it has acquired a new name, bioinformatics, and new prestige with the work on the human genome by the Celera Corporation and the U.S. Government's Human Genome Project. The goal is to use computers to correlate data from climical studies with genetic data to improve the treatment and prevention of disease. The development of new methods in computational biology has created an explosion of data, but there are relatively few people who have the combinaton of computer and scientific skills that are required to make the most effective use of this information. Most companies are looking for molecular biologists who have a strong background in computer science, but in the absence of candidates who combine these skills, opportunities are also opening up for chemists who have a strong biological background. More information can be found on the DOE Web Page for the Human Genome Project (see above), and from the Primer on Molecular Genetics . as well as some useful print references, such as C&E News, Oct. 19, 1998, pgs. 29-33 and Today's Chemist, Sept. 1998, pgs.42-44 .

To qualify for a job in this field, you must have a good background in BOTH computer science as well as chemistry or biology. There are many sites that deal with bioinformatics, but a good place to start is Bioplanet, a career site that focuses on this field. Here you will find a description of the field, including what training is required, career information, and also a listing of jobs currently available in bioinformatics. For a more extensive, but still very understandable, explanation of the field, see Biocomputing in a Nutshell.

There are very few undergraduate programs in bioinformatics at this time. If you wish to pursue this career direction, be sure that you have a strong background in chemistry and biology, as well as courses in computer programming (experience with common UNIX tools, structured and object-oriented design, Oracle (SQL, PL/SQL), and languages, such as C, C++, Perl, Python, HTML, Java, ,and/or CORBA is desirable.) Since a number of ethical questions have been raised about this type of work, you may well wish to look at some of the sites that attempt to deal with ethical issues in biotechnology. The Bioinformatics and Computational Biology site at The University of Nebraska-Lincoln is another excellent site with many useful links

U.S. graduate programs in bioinformatics (Note: Most of these are in Biology or Medical Depts.)

Bioinformatics at Boston University both M.S. and Ph.D. programs are available
Computational Biology at Carnegie Mellon University - B.S. in computational biology
Computational Biology at Johns Hopkins University - Ph.D. at the Instute for Biophysical Research
Biomedical Informatics at Univ. of California at Irvine, M.S. and Ph.D. degrees
Computational Biology at Univ. of California at Santa Cruz
Computational Science and Informatics - George Mason U (Be sure to page down past the faculty list!)
Institute for Biomedical Computing - Washington Univ. at St. Louis
Keck Center for Computational Biology - Rice Univ
Stanford Medical Informatics at the Stanford University School of Medicine

(Chem 111 - Third Examination, Fall, 2000)

Year 2000 Antarctic Ozone Hole the Deepest Ever.

According to a story on CNN, the World Meteorological Organization (WMO), an agency of the United Nations, announced that the destruction of ozone in the stratosphere over Antarctica began earlier and covers more area that at any time since the problem was first detected in 1985. The ozone in the stratosphere protects the earth from harmful ultraviolet radiation that can cause human skin cancer as well as destroying destroy tiny plants that are a crucial part of the food chain. The size of the ozone hole is so large that health officials in the sourther parts of both Chile and Argentina have warned the population to avoid exposure to the sun during the middle of the day. The WMO also announced that the level of depletion during the last 10 days of September was greater than ever before although the U.S. National Oceanic and Atmospheric Administration (NOAA) said its measurements indicated the ozone was not the lowest on record.

It is now generally accepted that this ozone depletion is caused by a type of compound, called chlorofluorocarbons, that was widely used a decade or so ago in many domestic products. These compounds are normally very unreactive, and were thought to be environmentally safe. After billions of tons had been emitted into the troposphere (the layer of the atmsophere nearest the surface of the earth), these compounds began to diffuse upwards into the next higher layer, the stratosphere. In the stratosphere, these compounds react with ultraviolet light and chlorine atoms are released. It is these chlorine atoms that actually decrese the ozone concentration. For a more extensive description of this process, go to The Ozone Hole Tour - Part III, The science of the ozone hole. This site contains a number of useful resources. Go to The Ozone Hole Tour home page and follow any of the links you find there. You may also be interested in seeing satellite images of the ozone depletion on any date of your choice, which are availble at the TOMS ozone page. In the selection box on the left, click on the South Pole images, then select a date, and finally, hit the request button on the right side of the box. Even though the levels of chlorofluorocarbons in the troposphere have begun to decrease, it may be decades before this has any impact on the stratosphere. CNN reports that NOAA scientists believe that the current ozone levels are as low as they will get and ozone should return to previous levels in 15 to 45 years.

(Chem 111 - Second Examination, Fall, 2000)

Chemistry Nobel Prize Winners Announced for 2000.

It was recently announced that two American chemists, Alan J. Heeger and Alan G. MacDiarmid, and Hideki Shirakawa of Japan won the 2000 Nobel Prize in chemistry for the ''discovery and development of conductive polymers,'' according to the Royal Swedish Academy of Sciences. Normally plastics are insulators, that is, they do not conduct an electric current, but a thin film of polyacetylene is oxidized with iodine vapor, the electrical conductivity can become a billion times greater. The resulting materials have already found many commercial applications, for improved television screens, computer monitors, and photographic film, as well as "smart windows" that can change transparency to sun light. One type of research that appears to be particularly interesting is the use of conducting plastics to conduct electrical impulses through damaged nerves. This type of development could be especially important for those who are paralyzed due to spinal cord injury.

If you wish to read more about this topic, you may find the press release entitled, "American Chemistry Council Congratulates the 2000 Nobel Laureates in Chemistry" to be interesting. It is relatively non-technical. For a more technical discussion, you may wish to look at a paper by C.Bruce Robinson on Conducting Polymers for Electric Switches, from the Proceedings from the 1989 Nano Con (The Northwest Regional Nanotechnology Conference or an article from the May 1996 issue of ChemTech For more information on the nerve cell research, go to NYU/MIT researchers create first "designer" biomaterial for growing mammalian nerve cells or Biological Scaffold Allows Nerve Cells to Grow and Form Connections

You may also page down to read a Chemnews article about last year's Nobel Prize winner in Chemistry or look at a list of all the previous Nobel Prize Winners in Chemistry.

(Chem 111 - First Examination, Fall, 2000)

Scientists move closer to producing artificial muscles

For years scientists have been looking for a better way to directly convert electrical energy into mechanical energy. Of course, the obvious use of such a technology would be to make better valves and motors, but since human muscles also work on a similar principle, there is also the hope that it may be possible to replace diseased or damaged human muscles or even to enhance the effectiveness of healthy muscles. The NASA Jet Propulsion Laboratory at CalTech has been particularly interested in this work, and it has recently been announced that one of the first practical applications of this technology may be the use of two artificial muscles to power miniature wipers to clear dust off the viewing windows of optical and infrared science instruments on the MUSES-CN, a spacecraft that is planned to explore a nearby asteroid in 2002.

NASA is by no means the only organization looking into this technology. Mo Shahinpoor, an engineering professor at the University of New Mexico, makes artificial muscles from polyacrylonitrile (PAN), a common polymer is used for many purposes (including women's stockings) under the trade name Orlon. This material not only has the ability to contract dramatically when its acidity (pH) is changed but can contract about as fast a human muscle. In addition, these fibers are about twice as strong as a typical human biceps muscle. Shahinpoor has actually placed these muscles in a human skeleton and been able to lift and lower the arm.

There is still a long ways to go before these artificial muscles will be used to replace their biological counterparts. Current muscles tend to dry out and become inactive, and electrical activation appears likely to be more effective than pH changes. The first applications will probably be in nanotechnology, very tiny machines, or simple robots, like those developed by JPL. It may soon be possible to create electric motors that are only a few millimeters in size. It is clear that there could be many applications for these inexpensive and efficient replacements for tradition gears and hydraulic systems, and with the current rate of development, they may be coming to commercial markets very soon.

(Chem 112 - Third Examination, Spring, 2000)

New report says that the 1990 clean air amendments have decreased atmospheric levels of sulfur oxide, but had little effect on nitrogen oxide emissions.

According to recent news stories, the U.S. General Accounting Office, the nonpartisan, investigative office of the U.S.Congress, has released a study entitled, "Acid Rain: Emissions Trends and Effects in the Eastern United States." which reports that acid precipitation continues to be a serious problem in the many northeastern states. The primary source of acidic atmospheric pollution is the combustion of fossil fuels. This produces sulfur and nitrogen oxides, which can be transported long distances in the atmosphere. As they move through the atmosphere, these pollutants are transformed into nitric and sulfuric acids and are eventually deposited in the form of sulfate and nitrate particular matter.

The Acid Rain Program, which was part of the 1990 Clean Air Act Amendments, was intended to control this problem. Although these regulations have been successful in decreasing the emissions of sulfur oxides , they have not had any significant effect on nitrogen oxide emissions. These two gases are major sources of acid precipitation. Since 1990, the sulfur dioxide emissions decreased by seventeen percent , but the nitrogen oxide emissions were virtually unchanged. As a result of these emissions controls, the total sulfur deposited in the Northeast decreased by 26 percent, but the total nitrogen deposited increased by two percent. The level of nitrates in the lakes of the Adirondack region of New York State increased by 48 percent.

Many regions of this country, such the Adirondack mountains and the mid-Appalachian highlands, are especially vulnerable to acid precipitation because the local soil has very little buffering capacity, that is, a low resistance to changes in pH when acid or base is added. This is primarily true in regions where there is little carbonate in the bedrock to react with acid. As a result, much of the fish and other forms of life in these lakes has been eliminated in these regions. Acidic precipitation also causes forest degradation, agricultural crop damage, depletion of soil nutrients, decreased visibility, and erosion of many building materials. Acidic waters also increase the mobility of some toxic pollutants, such as metal ions.

There are many sources of further information about the causes and effects of acid precipitation on the WWW. You may simply use the term "acid rain" in your favorite search engine, or, if you wish to simplify the process, visit the Fact Sheet maintained by the U.S. Environmental Protection Agency, or the list of frequently asked questions about acid deposition prepared by Environment Canada, the Canadian equivalent of the EPA.

(Chem 112 - Second Examination, Spring, 2000)

Arsenic Contamination in Bangladesh Groundwater.

During the past year, there has been considerable media attention directed towards the problem of arsenic contamination in much of the drinking water in Bangladesh. Groundwater is the main source of drinking water, and high arsenic levels have been found in the groundwater of most sections of Bangladesh. Estimates of the number of people affected range widely, from 20 to 75 million. Arsenic can cause bleeding sores, respiratory diseases and cancer of the bladder, kidney, liver, skin, and lungs. The exact cause of arsenic contamination is not yet fully determined, but it is probably due to oxidation of naturally occurring minerals (pyrites) that were exposed to air when the ground water level was lowered by pumping drinking water.

Ironically, the arsenic contamination resulted from a program to improve the quality of the drinking water. A major campaign convinced the population to stop using surface water supplies, which could easily be contaminated, and switch to shallow tube wells. Perhaps because of pride in the apparent success of these efforts, local health authorities were slow to respond when the first cases of arsenic poisoning were detected in 1993. The severity of the problem in Bangladesh has attracted attention to the possibility that other countries, such as India, Taiwan, Japan, Mexico, Chile, Argentina, Poland, and even the United States may also be at risk for this type of arsenic pollution.

A map of Bangladesh and the surrounding region is available on the WWW, as well as a report from the U.S. Library of Congress that gives extensive historical, economic, and political information about the country. There are several links that provide further information about this problem. For example, the West Bengal and Bangladesh Arsenic Crisis Information Center links to several media sources that have reported on the arsenic contamination. For more about the human side of this disaster, see Arsenic Poisoning in Bangladesh. The U.S. EPA has proposed decreasing the allowed level of arsenic in drinking water in this country. Click here to read more about this proposal.

(Chem 112 - First Examination, Spring, 2000)

A New Way to "Fix" Nitrogen?

If you would like to read more about the Haber Process, Raymond Zmaczynski, a secondary school teacher, has a good summary article on the Princeton Univ. History of Science web site entitled, "The Effect of the Haber Process on Fertilizers." The Raffles Institution, a school in Singapore ("easily reached by Mass Rapid Transit" according to their description), also has a good series of pages on the Haber Process and a brief biography of Haber. Their main page, has links to the various components.

CAUTION! THESE TWO SITES ARE MUCH MORE TECHNICAL! Dr. Susan Smith, Division of Life Sciences at the Nottingham Trent University in England, has a more biological (and far more technical) discussion of how this process naturally works on her Nitrogen Fixation page. Prof. Richard Terry, College of Biology and Agriculture at Brigham Young University, also has a useful treatment of the nitrogen cycle, including nitrogen fixation. Please note that Prof. Terry's material is in a PowerPoint presentation. To move from frame to frame you must click on the little right-handed triangle in the upper right corner of each frame.

(Chem 111 - Final Examination, Fall 1999)

Wave Properties Observed for Large Molecules!

As noted in class, all physical objects tend to have wave-like properties, but most of the objects that we can directly observe, such as golf balls and baseballs, have such a small wavelength that it is not normally observable. Thus, the main focus of our attention during the classroom discussion of particle waves has been very small particles, like electrons and neutrons.

In the October. 14, 1999 issue of Nature, Anton Zeilinger , a researcher at the University of Vienna, reports that his group has been able to demonstrate that fullerenes, rather large molecules, display wavelike properties. Fullerenes, which are sometimes called Buckyballs, are a class of molecules based on cage of 60 carbon atoms in a structure that resembles the surface markings of a soccer ball.

When Zeilinger passed a beam of C-60 molecules through a pair of slits and a grating, the result was an interference pattern that resembled what we saw in class produced by a beam of light. These fullerene molecules are about ten times bigger than the largest particles which have been observed to have wave properties. This observation continues to support de Broglie's proposal that even particles have wave-like characteristics.

Fullerenes are unusual molecules that are very interesting and potentially useful. The 1996 Nobel Prize in Chemistry was awarded for the discovery of these molecules. Earlier this year, fullerenes were found in a meteorite, indicating that they are not uncommon in the universe. Among other areas, there is currently a great deal of research on the use of fullerenes to create very tiny machines, what are the size of individual molecules, a field called nanotechnology. Fullerenes are named after Buckminster Fuller, a famous 20th century architect, who popularized concepts like synergy and spaceship earth.

(Chem 111 - Hour Test #3, Fall 1999)

New Technique Makes it Possible to Observe the Fastest Chemical Reactions!

On October 12, 1999, it was announced that Dr. Ahmed H. Zewail had won this year's Nobel Prize in chemistry for developing a method of using lasers to observe molecules as they move in ultra-fast chemical reactions. Prof. Zewail, who is a citizen of both the U.S. and Egypt, holds the Linus Pauling Chair of Chemical Physics at the California Institute of Technology.

The method works on the same basic idea as using a flash camera to freeze the movement of a hummingbird's wings while it is in flight. The trick was to find a source for a light pulse that would be short enough to freeze the molecules in motion. In the 1970s, a new type of laser, called a colliding pulsed mode-locked (CPM) laser, was developed at the Bell Labs. It can give a flash as short as 7 femtoseconds, that is, 7E-15 seconds. This speed is necessary, since some chemical reactions require less than 100 femtoseconds to occur.

Zewail used this new laser to pass a closely spaced pair of pulses through a reactant gas. The first laser pulse supplied the activation energy needed for the reaction, and the second pulse, which arrived only a few femtoseconds later, was absorbed by the reacting molecules and allowed Zewail to "see" what was happening. The technique is now being used to investigate a wide variety of reactions, ranging from photosynthesis to human night vision.

In the award citation, The Royal Swedish Academy of Sciences said, "We have reached the end of the road; no chemical reactions take place faster than this."

To learn more about Prof. Zewail, go to his home page at CalTech (including his picture).

To read more about femtochemistry, go to the CNN news story (not too technical) or the web site of the Ultra-Fast Laser and Spectroscopy Lab at the University of Groningen (more technical).

For a list of all the previous Chemistry Nobel Prize winners, go to Nobel Prize Winners in Chemistry.

(Chem 111 - Hour Test #2, Fall 1999)

Faster Computer Chips, with Molecules!

Oct. 11, 1999

It has long been recognized that the present computer technology will reach its theoretical limits within 10 or 15 years because it has become impossible to build smaller and smaller circuits on silicon chips. An article in the latest issue of the journal, Science, indicates that there may be a way around this size barrier. Scientists at UCLA and the Hewlett-Packard Research labs have been able to create one of the basic structures needed for computer chips using molecules.

A computer works by breaking down all tasks into binary code, that is, a combination of zeros and ones (or on and off signals). A molecule can also represent a similar type of coding, but the size is so much smaller that if it were possible it would operate much faster than is possible on a silicon chip . For example, the DNA molecule is a sequence of four bases combined in a definite fashion that also represents a code. If it were possible to systematically change the configuration of the DNA molecule, it would be possible to create the equivalent of an electrical switch, but a switch much smaller and much faster than anything known today. Some scientists have been successful at doing just that. The resulting link between computational science and life science has been called the "first example of true nanotechnology."

This new technology is still in its infancy, and it will probably be more than a decade before you see commercial products that use molecular computers, but if the many technical problems can be overcome, the potential is incredible. The combination of very fast but very small computers may find uses in many different ways, from programmed medical labs that may be injected directly into the blood stream to truly personal computers, so small that they can be hidden as buttons of pins.

If you are curious about this topic and want to learn more beyond what is required for the exam, either do a web search on the keywords "DNA Computer", go to the DNA Microarray Site for background information and many helpful links, or try the DNA computer site at Cornell University. Other fine sites with many excellent links are the Baskin Center for Computer Science and Engineering at the Univ. of California, Santa Cruz and the Biology Workbench Site at Computational Biology Group of the National Center for Supercomputing Applications (NCSA).

(Chem 111 - Hour Test #1, Fall 1999)

Helium: Inert, but not uninteresting

Sept 17, 1999

A recent article in the New York Times reports that a newly discovered technique is making it possible to see the human lung in three dimensions with details that cannot be obtained by traditional X-rays. The patient inhales specially treated helium-3 gas, which makes the lung visible by Magnetic Resonance Imaging (MRI).

In a typical magnetic resonance imaging device, a powerful magnet polarizes the hydrogen nuclei inside water molecules (e.g., in a human body). Then the polarized nuclei are momentarily tipped over by a radio-frequency pulse, and the absorption of the radio energy is detected. MRI is an effective diagnostic tool for many parts of the human body, but normal gases in the lung have low densities and so produce radio signals that are too weak to be very useful.

To prepare the helium-3 gas, it is treated with special laser light to force the nuclear spins to align in the same direction. This gas is now a strong absorber of radio waves, and so when the patient takes a breath of this gas the lung becomes clearly visible on an MRI machine. Because the helium is chemically inert, it is nontoxic, and the technique requires much smaller magnetic fields that are normally used for MRI measurements. Research is currently underway to extend this diagnostic tool to other parts of the human body.

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