San Diego Community News Group - Scripps researchers mine ocean floor for solution to antibiotic resistance

San Diego Community News Group - Scripps researchers mine ocean floor for solution to antibiotic resistance

Long hours of labor and the frustration of budget cuts and limited space are over!

Why is water a liquid at room temperature?

Have you ever wondered why there is nothing else like water on the planet? Many compounds have similar molecular masses: oxygen, nitrogen, sulfur, etc, etc, etc. Water is the only compound in its molecular weight class that is a liquid at room temperature. Why is it so unique?

It is because of forces between molecules called hydrogen bonds. The hydrogen atoms of one water molecule are attracted to the lone pairs of electrons on the oxygen atoms of adjoining water molecules. This attractive force between molecules is very, very weak on one hand; compared to the attractive forces of a chemical bond, the hydrogen bond attractive forces are really small. Over large distances, however, these small attractive forces add into something very, very powerful. An overall sticky effect is created. "Sticky" in that the water molecules are more attracted to each other than molecules of that molecular mass would normally be. Molecules like oxygen gas and nitrogen gas are gases at room temperature. Because of the hydrogen bonding between water molecules, water is a liquid at room temperature.

Because of hydrogen bonds we have lakes and streams. We have capillary action that allows water to climb the trunks of trees to the branches, we have snowflakes, icicles, and icebergs that float on the top of oceans.

Water is amazing.

PV= nRT

This ubiquitous equation is known throughout the world.
People use it as a password to their website, and as a button slogan. I think my high school chemistry teacher made us write it on stickers and put them on our foreheads..... (oh dear)

The ideal gas equation summarizes the discoveries about the behavior of gases into one neat and tiny equation. Let's start with the left side:

This is Boyle. Boyle's law states that the pressure increases as the volume decreases. This is known in science as an inverse relationship: P ~ 1/V.  The best illustration of this is scuba diving. When a scuba diver goes down into the depths of the ocean the pressure increases. (Makes sense when you think of tons and tons of water weighing down on the ocean floor). As the pressure increases, the volume of the diver's lungs decreases. As the scuba diver rises to the surface, the pressure slowly decreases and the lungs can expand again. When a diver gets "the bends" the person swam upward too quickly and did not allow  pressure/volume equilibration to relieve excess pressure. A scuba diver's lungs can actually explode in such a situation. (Like removing the lid on something tightly compressed in a jar- it springs out)

The left side is equal to nRT. Charles's law told us that volume and temperature are directly proportional: as temperature increases, volume increases. Think about the amount of space something takes up when it is moving slowly versus the amount of space it would take moving quickly. This is why you can get a half-filled balloon to perk up by warming it with a hair dryer. The partially filled balloon seems to suddenly have more air (even though it doesn't) when the particles start moving faster.

We also know P ~ T (direct proportionality). Think about the pressure exerted by air in a balloon. Does it exert more or less pressure at room temperature or when heated with a hair dryer? As the hair dryer heats up the molecules inside they move faster and increase their volume. In the process they exert a higher and higher pressure on the walls of the balloon.

The joys of lecturing.....Today is PV=nRT

Why we can survive carbon monoxide poisoning..... ( read to the end)

My students have been drawing Lewis dot diagrams and predicting shapes of molecules based on their Lewis dot structures. This is a very detailed process and requires them to be familiar with the concepts of valence electrons, types of bonds and bond orders. It is so easy to get lost in all the details. This is why I wanted to stress the importance of WHY. Why does anybody really care about the shapes of molecules. Does it really matter?

Ionic and Covalent Bonding

This week my students did the molecular model lab which is a bummer for them because we are one class period behind in lecture. So- if they didn't take the time to really read chapter 8 thoroughly before lab (most of them probably didn't) then the lab probably went in one ear and out the other.

I'm not sure if it makes more sense to try to explain ionic vs covalent bonding before or after Lewis structures/VSEPR shapes. By learning to use the Lewis Dot model students can predict shapes which influence the overall bonding characteristics of molecules. The larger concepts of ionic vs covalent bonding can be explained without knowledge of Lewis structures, however, the details seem much clearer once the model is explained.

Stay tuned for my upcoming post on ionic vs covalent bonding...

Can't wait!

Friends of the Library

If you have never gone to your local library to look at the paperback books donated to Friends of the Library charity you are missing so, so much. Since I discovered this gold mine of entertainment I have ransacked its shelves with my eyeballs. I have enough restraint not to ransack it with my hands. My most recent comparison to my love of books is my love of food. I eat books like I eat food. It is a hunger to be fed daily.

Today I found Middlesex (Pulitzer Prize winner), The Spirit Catches You and You Fall Down, and The Castle by Kafka. I think perhaps the Kafka and Middlesex usurp the ranking of books on my list. Middlesex is next after I finish The Wednesday Sisters.

I intended to buy Middlemarch (as opposed to Middlesex) because The Wednesday Sisters recommended it but I have too many books in line.

Each paperback is 50 cents. Sure beats spending $15 on amazon.com.

Periodic Trends on the Periodic Table

In class yesterday we covered the electronic structure of an atom. We Primarily focused on electron configurations and orbital diagrams (and many did very well on the simple quiz I gave midway through the period). Near the end of class I briefly talked about periodic trends, the topic I want to focus on in this blog post.

In our discussion about the periodic table we talked about how each period represents a primary energy level within an atom. Period one is the energy level closest to the nucleus while period 2,3,4, etc are further and further from the nucleus. We also talked about how each period represents a fixed energy level. This returns us back to the concepts of electromagnetic radiation we covered earlier in the chapter. Fixed energy levels were first observed in heat radiating from everyday objects. The energy levels of the measured heat were discontinuous. This same observation holds true for electrons surrounding the nucleus of an atom.

Quotation from JD Salinger in Short Story

A break from science for a minute......

My other love in life is literature. I'm reading Nine Short Stories by JD Salinger. Here is a quotation I'd like to share:

"This is the squalid, or moving part of the story, and the scene changes. The people change, too. I'm still around, but from here on in, for reasons I'm not at liberty to disclose, I've disguised myself so cunningly that even the cleverest reader will fail to recognize me."

He turns out to be the main character of the second half. But you don't figure it out until near the end. Genius.

chemicals in everyday items (potentially harmful)

There is an article in the Wall Street Journal on Monday that caught my eye. Actually the entire Personal Journal section caught my interest: emphasis on green energy. Since I teach alternative energy sources in my class this section was an opportunity for me to update my knowledge on the subject.

The article (click on link for article) has a list of chemicals in a table with the corresponding product in which they are found. I'm going to go check out my personal food containers after reading this article because apparently I have to watch out for dibutyl phthalate.

This brings me full circle to my concerns about sulfuryl fluoride (not mentioned in the article) that is used for termite tenting. As a chemist I know that both sulfur and fluorine have some nasty properties as individual elements. And- the fact that the compound is used to kill termites means it is toxic on some level. Will it end up on a list like this one twenty years from now? In the future will we talk about termite tenting and the harm it caused like we talk about the babies harmed by Thalidomide in the 70s? Or even asbestos? It's really scary to me.


I'm getting tented in December and I'm worried about it.

Understanding as "acceptance" rather than related on a deep level

I touched on this below but I wanted to revisit this idea. Often learning the crux of a subject is more about acceptance rather than true understanding. How can you really understand something if you are new? On the level of an introductory course I think this concept applies to other subjects: art, religion, English and even History (to some extent).

I like to think of my students (that may be you if you are my student) as doing practice problems and reading the material in the textbook so that they grasp enough of the details to accept what the experimental evidence tells us about the way chemical elements behave. None of it is intuitive and none of it is something I would expect anybody to figure out without explicit information from the text.

I hope everybody out there who is currently studying chemistry can grow in their acceptance of experimental data. It is only through this acceptance that you can understand more about how the experimental evidence may affect medicine, physics and the everyday way we live our lives.

I'm sure the founders of quantum mechanics had no idea that they had just unleashed the beginning of the information age. The internet and all the small gadgets we take for granted resulted from the acceptance and further creativity of those who observed quantum mechanics in nature.

It is my hope you will be enthusiastic to do the same. Let me be the proud teacher of the next United States inventor. Good luck.

feedback

An old friend of mine from childhood recently visited this blog and told me that he needed to take my class to understand my blog posts.

Agggghhhhhh! Bad. This is exactly what he should NOT say. Poor guy- he probably had no idea how badly I felt about this comment. I think he meant to compliment me.

The idea is to make science understandable to any soul who happens to find themself on my blog. I want people to find the posts generally interesting and students to find them a good introduction to the meatier and drier textbook.

preparing to teach the structure of the atom....

I'm preparing to meet with some students at SDSU who are enrolled in chem 200. I taught the lab for this class back in 2000-2002 so I'm familiar with the textbook and general setup of the class. Actually, I'm using the old text I used as a TA! They are now on the 5th or 6th edition of the book and I'm using the 2nd. (Hint for those of you wondering if you need to buy the next edition every time it comes out)

The concepts I'm preparing for my 200 students are very similar to those I'm preparing for my chem 3 students up in Irvine. We're beginning our study of atomic structure mostly focused around how electrons move in orbitals around the nucleus of an atom. It is these trends that determine most of the trends in how elements behave on the periodic table. If a student understands electronic structure, that student will make more accurate predictions about chemical behavior of different elements.

The first step to really understanding atomic structure is to realize that nothing that is observed in intuitive. To that end I would like to describe the study of atomic structure less as "understanding" and more as "acceptance" about what is observed by experiment. It is too bad we cannot invest in laboratory equipment to demonstrate atomic structure by experiment to all students. Unfortunately, the cost and convenience of doing such is entirely unrealistic and we must resort to explaining what scientists observe when they run these types of experiments. After reading several different ways that atomic structure affects trends in the PT, students will begin to see patterns, learn vocabulary and grow to accept experimental observations. Ideally, they will be able to use this acceptance (rather than "understanding") to make educated guesses about how other trends might function.

But- it's all tied into an understanding of electromagnetic radiation as well. The energy of electrons and how energy is distributed in chemical reactions is done through electromagnetic radiation. This is why there is an entire section about how our understanding of light and energy has changed over the years.

This is a fascinating subject to learn but I must admit, there is a certain amount of drilling and memorization that must accompany your first attempt to learn it. You will encounter concepts, observations and ideas that are completely foreign to you. I recommend whipping out those flashcards that you used to learn the polyatomic ions and using them to drill yourself about the basics of atomic structure.

electromagnetic radiation and chemistry education

The concept of electromagnetic radiation introduces us to the idea that things are not the way we perceive them. This concept applies to more than just e-radiation in life. It is an excellent example of how we should think about other things in life that seem so, so clear. Maybe they really aren't so clear after all.

We see sunlight as white light that allows us to use our eyes during the day and forces us to turn on a floorlamp or flashlight at night. From the gorgeous rainbows left after a storm we know that sunlight can be broken up into different colors.

The makeup of sunlight seems fairly straightforward-logically it would be a wavelength travelling super, duper fast from the sun. If you extend this idea behind what we can see with our eyes, there is an entire spectrum of wavelengths emitted from varying sources (other than just the sun) that serve different purposes. From radio waves (extremely low energy) to cancer-treating gamma rays (extremely high energy) the electromagnetic spectrum has propelled technology in our lives to a level previous thought unattainable.

The seemingly straightforward makeup of white light and other electromagnetic radiation is not so straightforward. The study of this medium led to Einstein's Nobel Prize for the photoelectric effect (light as a wavelength and a particle) and to other phenomena of quantum mechanics. The subatomic processes of light are so different from what we experience in the macroscopic world that it would take an entire degree of classes to really wrap your mind around it. 

If you haven't ever goggled the electromagnetic spectrum, I suggest you google it. Do some background reading on a basic science concept that has revolutionized our lives.

Review for Chapters 4-6

The Exam is a week from Thursday and I suggest you start reviewing now. I am in the process of checking with some other faculty about posting the pdf of complete solutions for the problems in the back of each chapter. Someone brought it to my attention that the solutions manual in the library only works out the solutions to the odd numbered problems. I would like to post a solutions manual (as pdf) that works out both even and odd numbered problems. Please be patient as I verify that I am allowed to do this.

Quotation from the Periodic Table by Primo Levi

I just finished The Periodic Table by Primo Levi. Here is a quotation that jumped right off the page at me.

"Our atom of carbon enters the leaf, colliding with other innumerable (but here useless) molecules of nitrogen and oxygen. It adheres to a large and complicated molecule that activates it, and simultaneously receives the decisive message from the sky, in the flashing form of a packet of solar light; in an instant, like an insect caught by a spider, it is separated from its oxygen, combined with hydrogen and (one thinks) phosphous, and finally inserted in a chain, whether long or short does not matter, but it is the chain of life. All this happens swiftly, in silence, at the temperature and pressure of the atmosphere, and gratis: dear colleagues, when we learn to do likewise we will be sicut Deus, and we will have also solved the problem of hunger in the world."

Photosynthesis made beautiful- don't you think? Primo Levi is a genius of a science writer. I'll have to go back and read his accounts of his days at Auschwitz and other experiences.

Chapter 6 Preview

As I read and prepare chapter 6 (the students are the not the only people responsible for preparing the material) I am reminded that this chapter is really critical to a fundamental understanding of beginning chemistry. Here is why:

You learn how to balance equations in chapter 5. Fair enough. You learn that the relationship between number of molecules on each side of an equation is also equal to the number of moles of each compound on each side of the equation. Let's review a simple example:  O2(g)  +  2H2(g)  = 2H2O
Let's add atoms on each side of the reaction: 2 atoms O and 4 atoms H on the left while there are 2 atoms O and 4 atoms H on the right side of the equation. It is balanced. What does this mean exactly?
For every one molecule of oxygen gas you must have 2 molecules of hydrogen gas to get 2 molecules of water. Can you get less than two molecules of water? No- because you can't cut a molecule in half. Likewise, you must have one mole of oxygen gas for two moles of hydrogen gas to get two moles of water. The relationships, as you can see, between molecules of compounds and moles of compounds are equal.

This is what enables us to use these relationships in the laboratory in a practical way. From these molecule/molar relationships we can calculate the amount of product we should get in a chemical reaction. Returning to our synthesis of water example:  If we start with two moles of oxygen gas and unlimited hydrogen gas how much water should we get? The mole relationship between oxygen gas and water is needed to figure this out:( 2 moles O2) X( 2 moles H2O/1 moles O2 )= 4 moles H2O. This is the maximum yield. What if you go into the lab and determine that this reaction only yields 3 moles of H2O? Then we get into a calculation of percent yield. The percent yield is the comparison of the actual yield you obtain in the lab with the theoretical yield you calculate based on molar ratios of a balanced equation. Percent yield is as follows: actual/theoretical X 100. In this case it is 3/4 X 100 or 75%. You obtained 75% of the maximum amount of material you could get from this reaction with these amounts of reactants.

This chapter also introduces energy transformations. Just as mass is conserved (atomic theory), energy is conserved in nature. This means that energy is transformed from one form to another. This applies to chemical reactions as well as everyday objects like a ball bouncing on the ground. There are a few key terms here you should really learn well: exothermic vs endothermic.
Exothermic: This means a reaction (or process) gives off energy
Endothermic: This means a reaction (or process) absorbs energy
The diagrams for each of these are in Chapter 6. Familiarize yourself with the energy levels of products and reactants for each case.

And...... my favorite thing in chemistry is introduced. That is Calorimetry. What is calorimetry? It is the measure of the transfer of heat.
There is a very simple demonstration you can do in the classroom to show calorimetry. I haven't figured out how to incorporate it into our class- the ice would melt by the time I get to the topic in class.
You take a styrofoam cup, thermometer, and ice/water. You measure the temperature of the water initially. Then, put a  piece of ice into the water. Let the system come to equilibrium (even temp) and measure the temperature again. This is the temperature change you plug into the equation q= mC(Tf-Ti). This measures the transfer of heat from the surrounding water to the melting ice. In this case, the ice is the system and the water is the surroundings. You are measuring the heat that is being transferred from the water to melt the ice.
In the equation: q (heat transferred) = (mass of ice+cup+water)(C-specific heat of water)(Tf-Ti)
Heat transferred is equal to the mass of the entire system  X 4.184 (constant value) X change in temp.

If you understand this basic experiment it will help you understand the concept of heat transfer.

See you Tuesday.

Exam I Feedback for Students

I just completed the grading for exam I and I wanted to summarize my feedback here on the blog. Hopefully this will allow you to look at these issues with your textbook in hand. I will also mention them during class- we can do some examples as a class.

Overall the average was in the mid 60s but this is because there were a few really low scores that really pulled it down. There were 6 people who scored above 90%. One person got a 98%. So- it was a manageable test. I had a good number of people in the 80 range and a few in the 70s. There were also a good chunk below 70 and this concerns me. My goal is to work hard with each of you that scored in this range so you can bring up your scores. Your homework/quiz/activity grade will help you bring your score up somewhat but you need to concentrate on performance on the tests to really do well in the class (A or B grade).

Several of you still struggle with the concepts of conversion, units and volume/density. There are a few of you that only struggled with this concept- if you had answered these questions correctly you would have been above 90% on the test. So..... keep these things in mind: Zeroes that occur before the decimal place or after the decimal place but do not follow a digit that is 1-9 are not considered significant. Therefore the number 0.00347 has only 3 significant digits. The three digits preceding the "347" are not considered significant. The number 0.03470 has 4 significant digits. The last zero is considered significant because although it falls on the right of the decimal, it follows a digit that is 1-9 and is therefore considered significant. Everybody needs to keep in mind that I consider it crucial for you to show your calculations and logic in the short answer section. I CANNOT award partial credit for an incorrect answer if you do not carefully show me your mathematics progression. I wanted problem 44 and 45 to be an easy 20 points for everyone. These were the density/mass/volume conversions and the volume conversion problems. Several of you got an answer that was on the right track but you did not receive partial credit because you did not show your calculations.
Keep in mind that while a cm3 (superscript 3) is equal to a mL, it is a dm3 (superscript 3) that is equal to a Liter. There are two ways to solve this problem (convert to dm3 or just convert from mL to Liter with the conversion 1000 mL/L) Several of you need to review your basic conversion factors- I gave you a table of all of the factors but people did not use this information correctly. I had people converting cm into meters with the conversion factor 0.01cm/m. It is opposite: 100 cm/meter. Review how these are used in word problems.
I wanted people to notice how I put a problem on the test that was an example we worked in class. Actually- this problem was in both the multiple choice section and the calculation section: You were supposed to figure out the relative atomic mass of an element based on two isotopes found in nature. There were too many people who missed this problem. I was hoping you review lecture notes and examples from class so you can get these types of problems correct.

I was very pleased with the knowledge of the class about atomic theory. The last problem was supposed to be an easy 5 points for everyone. Most people got 4/5. The two modifications to Dalton in Modern Atomic Theory are as follows:  1. Discovery of neutrons allows atoms of the same element to have different masses 2. Atoms are not the smallest building blocks of nature due to the discovery of subatomic particles. (Some of you stated that H2O and H2O2 prove that the law of definite proportions is not true and this is false. The law of definite proportions just states that compounds always contain the same ratio of elements. It doesn't mean that the ratios can't vary between compounds  (which they do only in whole number values))

Problem number 10 was a commonly missed question dealing with the law of definite proportions. The ratio of sulfur to oxygen in SO3 is 32:48.  This is obtained by multiplying the atomic mass of sulfur ( 32) by 1 (for one atom of sulfur)  (from the PT) and the atomic mass of oxygen (16) by 3 (from the PT). The mass ratio of sulfur to oxygen in any sample of SO3 will always be 32:48 by the law of definite proportions.

I'll post the key and talk more about it in class.

The Statue of Liberty, Stoichiometry and introductory chemistry.....

(Photo taken from the Introduction to Chemistry text by Bauer, 2010)



What does the statue of liberty in New York have to do with introductory chemistry? Actually, a lot. On the most basic level, the reason it was renovated in the 80s is very related to introductory chemistry. If we want to present the reactions of the statue of liberty accurately then we must consider stoichiometry and balanced equations.

The statue had copper panels on the outside and iron used in the inner framework. Over time, the copper oxidized in air to form copper (II) hydroxide, copper (II) carbonate, and copper (II) oxide while the iron formed iron (III) oxide. This created a displacement reaction situation. Copper metal was in contact with iron (III) ions and iron in contact with copper (II) ions.  Here is where the problem got really messy:

Fe (s)  +   CuO(s)   gives  Cu(s)  +   FeO(s)  (oh how I wish I could figure out subscripts and arrows in blogger.com)

According to the metal activity chart is Fe more active than copper? Yes, therefore it will displace copper's position within the copper (II) oxide compound and create an iron oxide.

This displacement further exacerbated the oxidation problem. In fact it accelerated the problem by a factor of 1000 and the statue needed to be rebuilt.

See page 179 of your text for more information.

Most aspects of e-waste not regulated in U.S., Va. | Richmond Times-Dispatch

Most aspects of e-waste not regulated in U.S., Va. | Richmond Times-Dispatch

This is exactly why we need excellent chemistry education. Many of the hazards of chemicals in this waste dump are not understood. The long term decay and byproducts of waste are often not understood. It makes sense that as technology and materials change, our knowledge about them should increase. This includes not only how they function to improve our lives but how they function in their return to the ashes of the earth. "Ashes to ashes and dust to dust."  Unfortunately, in this context the route to ashes could be a problem.