Chemistry Thread

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Chemistry Thread

Post by ScholasticSpastic » Wed Mar 04, 2009 7:13 pm

It had to happen eventually. While I am a lowly undergraduate chemistry minor I will attempt to address issues in chemistry and encourage others to do the same within this thread. This thread was inspired by posts in the Ask a geologist thread concerning the origins of water on Earth. Other issues will doubtless be simpler as I can only congecture as to the early Earth environment.
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Re: Chemistry Thread

Post by ScholasticSpastic » Wed Mar 04, 2009 7:17 pm

I have stolen a post from the Ask a geologist thread:
Paco wrote:
Faithfree wrote:
Paco wrote:
Faithfree wrote:
Psi Wavefunction wrote:I'll start with a simple one, before Gawd gets to it:

How did the Earth come to be as it is now? How was it formed? :coffee:
The creationists have it so easy - just turn the Genesis 1 and no further brain exercise is required. :roll:

Ok executive summary of Earth history:
Earth accreted from the condensation of a rotating solar nebular, simultaneously with the other planets, about 4.5 billion years ago. Initially very hot with frequent volcanism and impacts from space and in the final stages of accretion. After a few hundred million years the temperature dropped to the point where liquid oceans formed - a Goldilocks planet rife for the appearance of life. Life probably started before 3.5 billion years ago (controversial) and by 2.5 - 2 billion years ago (plus or minus quit a bit) had changed the Earth to an oxygen bearing planet rather like today. Animals emerged around 600 million years ago and have infested the Earth ever since.
In this post you mention that the Earth eventually cooled to a point where liquid oceans could form, was the water always there or did we aquire it from the snowball effect believed by some astronomers like Lawrance Krauss?
Water, or more correctly the elements to form water, should have been present in the original mix of particles and planetesimals that accreted to form the early Earth, and such elements have continued to be added at a much slower rate, eg by the rare impact of comets. I'm not familiar with the ideas of Lawrance Krauss, but I think most people in this field think that the majority of water derives from the components of the initial accretion. Exactly when the first oceans formed is a matter of some debate.
Krauss mentioned something in his book ATOM about the amount of Oxygen expected in the accretion period of the Earth to be much less than we see today and uses the idea of massive snowballs as a means to compensate for the extra water we have observed.

On another note about planet formation, I understand that our sun is a second or third generation star, during the previous supernovae could magnetism in the initial stages of the explosion and molecular density be responsible for the larger quantity of heavier elements closer to the sun since the forces of magnetism and gravity would work to slow them down more than the lighter / non metallic elements. Also expanding on this is it then possible for the distances of certain planets to be more predictable than we currently believe? like the same predictability we have of different bands of clouds in the atmosphere. Not sure if I've worded that last bit as well as I should have.
http://rationalia.com/forum/viewtopic.p ... 0&start=25

This post will serve as my jumping-off point. Give me a moment to think about some chemistry and I'll post again with a response.
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Re: Chemistry Thread

Post by Mallardz » Wed Mar 04, 2009 7:33 pm

Chemistry seems boring make the physics thread!
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Re: Chemistry Thread

Post by ScholasticSpastic » Wed Mar 04, 2009 8:00 pm

Even Liam wrote:Chemistry seems boring make the physics thread!
We'll see. You have yet to observe my propensity to resort to decidedly un-sciencey language when discussing science- a habit I picked up from tutoring chemistryphobic students.
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Re: Chemistry Thread

Post by Mallardz » Wed Mar 04, 2009 8:12 pm

ScholasticSpastic wrote:
Even Liam wrote:Chemistry seems boring make the physics thread!
We'll see. You have yet to observe my propensity to resort to decidedly un-sciencey language when discussing science- a habit I picked up from tutoring chemistryphobic students.
I science our teachers talk to us about necrophilia.
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Re: Chemistry Thread

Post by ScholasticSpastic » Wed Mar 04, 2009 8:21 pm

Even Liam wrote:
ScholasticSpastic wrote:
Even Liam wrote:Chemistry seems boring make the physics thread!
We'll see. You have yet to observe my propensity to resort to decidedly un-sciencey language when discussing science- a habit I picked up from tutoring chemistryphobic students.
I science our teachers talk to us about necrophilia.
They're probably just trying to keep your attention.
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Re: Chemistry Thread

Post by ScholasticSpastic » Wed Mar 04, 2009 9:16 pm

Right, then. The toughest thing about answering the question of the origins of water on Earth is finding a good place to start. I know very little about Geology or Astronomy, so much of what I'll write will be prone to conjecture and oversimplification.

We'll start with the accretion of the Earth, in which little bits are drawn together by their mutual gravitational attraction to form larger bits, eventually resulting in something roughly the size of (perhaps) the Earth-Moon system. When this happened, their individual kinetic energy would have been transformed to thermal energy as the system accreted- resulting in a highly energetic and very hot initial condition. The important thing about heat is that it tends to facilitate chemistry by providing energy for reactions as illustrated by the Gibbs free energy equation:

G=H-TS

Where G is Gibbs free energy (the energy available for chemical reactions), H is enthalpy (the measure of thermodynamic potential within a system), T is temperature (preferably on the Kelvin scale) and S is entropy.

The upshot is that systems tend to work to minimize G. When T is very large and H is small relative to T, then we can get away with reducing S- or slamming things together to make larger things. (S is larger when the bits are smaller- we can approximate S by thinking about it in terms of degrees of freedom for the components of a system. When we slam bits together to make larger stuff, the components of the larger things will tend to have fewer degrees of freedom and entropy is reduced.) So, basically, hot stuff can often facilitate the formation of larger molecules.

It seems reasonable to suppose, then, that during and shortly after the accretion of the Earth, elements will have reacted with each other quite a bit to result in molecular compounds. So there is no reason to object to the idea that all of the oxygen will have been bound up in things which form more stable products from oxidation than water. The young Earth was a dry place, but it was not devoid of oxygen.

The oldest rocks found contain primarily silicates and oxidized metals, so Earth probably was not dry for lack of oxygen, but rather for lack of free oxygen. I’m not sure how indicative of the pre-aqueous Earth the composition of the oldest rocks we’ve found can be, though, as there may already have been water on Earth at the time of their formation.

Turning our attention to lunar rocks, assuming they have something to do with the young Earth, we find that the moon also has high silicon dioxide content as well as a wealth of metal oxides. Water is much more difficult to find on the moon, so we can reasonably assume that dry, rocky worlds in our neighborhood contain bound oxygen. Or not. Remember, I’m no geologist and I’m certainly no astronomer.

Right, so, remembering that I have no idea what I’m talking about regarding matters geological and astronomical, we’ll start with an Earth with little to no free oxygen and a lot of metal and silicon oxides.

Key concepts:
Oxidation, reduction, and redox reactions
Chemical equilibria and Le Chatelier’s Principle
A novice’s unsupported conjecture about the early Earth
Molecules are dynamic entities

Let’s begin with the last thing on my list- the dynamic nature of molecules. If your idea of molecules is anything like mine was, you’re probably thinking in terms of balls and sticks. The trouble with that mental model is that balls and sticks have an air of finality to them. Ball-and-stick models of molecules, while useful for visualizing a moment in the life of a model, don’t give us any conception of what’s going on, energetically, within molecules.

Molecules are not adamant- they are constantly wiggling and spinning around at any temperature above zero Kelvin. This tendency to store energy in the form of internal movement is the basis for all our spectroscopic technologies. Even the most sedate-seeming molecules are likely more exciting than we suppose and may engage in swapping atoms with adjacent molecules. If the adjacent molecules are the same, then we might not notice this activity because the new molecules formed are the same as the original molecules. In that case, there was by definition no chemical reaction. This does not mean, however, that there was no interaction between the molecules. The take-home message of this paragraph is that molecules are not static- they dance, they whirl and they swap bits with their neighbors. The do all this at speeds which beggar the human imagination. In short, molecules are exciting and excitable.

Redox reactions are reactions in which one element is oxidized and another is reduced. Whenever one element is oxidized, another must be reduced- no exceptions. Combustion is a redox reaction. In the combustion of methane:

CH4 + 2O2 ---> 2H2O + CO2

Carbon is oxidized while oxygen and hydrogen are reduced. Oxidation and reduction refer to changes in oxidation number of an element such that the oxidized element obtains a larger (less negative) oxidation number and the reduced element winds up with a smaller (more negative) oxidation number. For those who don’t want a headache I can simplify this:

Oxidation usually involves the addition of oxygen or an increase in the number of molecular bonds with oxygen. We can think of oxidation as a loss of associated electrons from an element.

Reduction usually involves the loss of oxygen, a decrease in the number of bonds with an oxygen, or the addition of hydrogen atoms to a molecule. We can think of reduction as an increase of electrons associated with an element.

Chemistry is not a unidirectional process. While there are chemical reactions which proceed from reactants to products under standard conditions, this does not mean that there aren’t conditions under which the reaction will proceed in reverse. So it’s helpful to think about chemistry in terms of equilibria in many cases. A chemical system in equilibrium is one in which the relative concentrations of participating molecules are constant. Pure water is a chemical system in equilibrium. At any given moment, and at astonishing speed, protons (hydrogen ions) are dissociating from water molecules to form H+ and OH- and the reverse process is also taking place. We can express it thus:

H2O <---> H+ and OH-

This goes back to my earlier assertion that molecules are dynamic. Even when they don’t appear to be changing, they are. If we’re allowed to deviate from standard conditions, every chemical reaction can be written with a bidirectional arrow rather than a unidirectional arrow.

Le Chatelier’s Principle helps us predict the behaviors of chemical systems in equilibrium or what a chemical system will do to reach equilibrium. Given a system in equilibrium, the addition of molecules which appear on one side of the chemical equation will result in an increase of molecules appearing on the other side of the chemical equation. Let’s revisit the combustion of methane:

CH4 + 2O2 <---> 2H2O + CO2

I’ve rewritten it with a double arrow. This is because, under the right conditions, this seemingly unidirectional reaction can be made to go in reverse or even to obtain an equilibrium in which both the products (the stuff on the right) and the reactants (the stuff on the left) coexist in stable partial pressures (partial pressure is how we work concentration in the gas phase). Running this reaction in reverse is called the Sabatier Reaction, named after its discoverer, Paul Sabatier. In this case, the right conditions could be obtained by eliminating oxygen from the mix, increasing the amount of hydrogen in the mix, and adding a catalyst or increasing the amount of energy in the system (heat the stuff).

The Haber process is another equilibrium reaction following Le Chatelier’s Principle:

N2 + 3H2 < ---- > 2NH3, (Delta)H = -92.4kJ/mol

Nitrogen gas will react with hydrogen gas in an anoxic environment to produce ammonia and heat. In the presence of a hot environment and an excess of ammonia, the reaction will run in reverse. Adding more hydrogen or more nitrogen can push the reaction further to the right. The Haber process is important because it’s where a lot of our fertilizer comes from. The Haber process is how we feed ourselves. The Haber process is also important in terms of the early Earth. Looking at how it works, we can reasonably assume that the early Earth’s atmosphere probably contained a lot more ammonia than it does now due to the presence of unbound hydrogen.

An environment which contains very little (or no) oxygen is called a reducing environment.

I’ll continue this when I get home from work. I’ve laid the groundwork and now I can get around to making my point.

Edit: I've stricken a bit of this out while I go check my facts. I'll have the redox bit right by the time I get around to making my point.

Edit 2: Fixed the oxidation and reduction bits.
Last edited by ScholasticSpastic on Thu Mar 05, 2009 6:32 am, edited 1 time in total.
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Re: Chemistry Thread

Post by Existentialist1844 » Thu Mar 05, 2009 5:08 am

Name all the elements on the periodic table.
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Re: Chemistry Thread

Post by BrettA » Thu Mar 05, 2009 5:21 am

Existentialist1844 wrote:Name all the elements on the periodic table.
Here ya go. :lol:
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Re: Chemistry Thread

Post by Existentialist1844 » Thu Mar 05, 2009 5:25 am

BrettA wrote:
Existentialist1844 wrote:Name all the elements on the periodic table.
Here ya go. :lol:
Obviously, one can easily post a link to the periodic table.

I want SS to write out each one and have them color coded.
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Re: Chemistry Thread

Post by ScholasticSpastic » Thu Mar 05, 2009 6:29 am

BrettA wrote:
Existentialist1844 wrote:Name all the elements on the periodic table.
Here ya go. :lol:
Here's a link to my favorit online periodic table: http://www.dayah.com/periodic/
Existentialist1844 wrote:Name all the elements on the periodic table.
I haven't memorized it, so what would be the point of the exercise? Memorizing the periodic table isn't required in order to do chemistry. All that is required is access to a periodic table and understanding how to read it- recognizing the periodic trends and remembering the shared properties of the groups. Transition metals are funky.
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Re: Chemistry Thread

Post by ScholasticSpastic » Thu Mar 05, 2009 8:49 am

Follows the exciting conclusion of my long-winded commentary on the possible origins of water on Earth:

I've been thinking about the origin of water issue and I've decided that it isn't reasonable to postulate a dry Earth from the time of its formation. There is water in space. There is water in comets. Why should there not have been water in the accretion disk which eventually became Earth? Certainly the newly formed world would have been too hot for liquid water, but this only means that the atmosphere would contain more water vapor than it does now.

Even so, I'll stick with a dry Earth in order to simplify things. We'll pretend it was dry and I'll go from there to demonstrate why it couldn't have stayed that way- or at least to present a very good reason why we should not have expected this to be so.

Young Earth was hot. So, in keeping with Gibbs free energy as we understand it now that I’ve spent a lot of time boring you, we understand that there was a lot of energy around for chemical reactions.

Young Earth was oxygen-poor because all that oxygen was locked into silicate matrices or associated with metal oxides. So we can expect to see reactions taking place which resemble the Haber process or a working smelter (only we tend to use carbon as our reducing agent in smelters) to convert elements with relatively high oxidation states into elements with lower oxidation states just as long as those oxidized elements had access to a reducing agent. Hydrogen gas is a reducing agent.

Because we understand Le Chatelier’s Principle, we now expect that a dry young Earth would favor the formation of water whenever free (or loosely associated) oxygen and hydrogen were proximate to each other. The dynamic nature of molecules ensures that any reaction which is favored will proceed. Even those reactions which require catalysts will proceed without them albeit at a slower rate or will require higher temperatures in order to proceed at a faster rate.

The reducing nature of Earth’s early atmosphere, prior to the loss of free hydrogen due to our relatively shallow gravity well, means we get to write all our favorite and familiar chemical equations in reverse. Ferric oxide (rust) will naturally become Ferrous oxide in a reducing environment with the passage of enough time or the addition of thermal energy and the oxygen liberated would naturally hook up with hydrogen in the atmosphere to form water. Carbon would tend to become methane (a reducing agent). Nitrogen would tend to form ammonia. Ammonia is, itself, a reducing agent and will tend to react with oxygen to form nitrogen gas and water.

So the presence of oxides in a reducing environment rich in hydrogen (or the methane, ammonia, and hydrogen sulfide which would be left over when we’d run out of hydrogen) pretty much guarantees the formation of water over time and water will form faster if the Earth is hot. Water would inevitably form on a young, hot, dry Earth with a reducing environment (an atmosphere high in hydrogen, ammonia and methane).

But there is no reason to suppose that the early Earth was dry at all. Water is the third most common molecule in space (I just found out) and this means we probably began our planet’s history with a sizeable store of it for all that surface temperatures were too high for puddle formation. No comets required. This isn’t to say that we can’t have been hit by a/some comet(s), but why might comets have ended up with all that water while our planet got slighted? It seems terribly un-parsimonious to me that this would be the case.

Finally, comets may not contain as much water as we’ve assumed:
A note on the total mass of comets in the solar system wrote:It is apparent that what we are seeing is not the evaporating surface of a dirty snowball but rather a mantle of dark dust, which may be at least partially consolidated into a crust. The dust and gas seem to emanate largely from cracks in this mantle, which are periodically rotated toward the sun as the comet spins with a period of about 2.2 days. The Vega IR observation which indicates a surface temperature of about 330 +/- 30K (although this measurement may be partially contaminated by the circum-nuclear dust) is consistent with a black body in radiative equilibrium with the sunlight at ~0.8 AU rather than a sublimating surface of H2O clathrate which could never exceed ~190K at that distance (Mendis et al., 1985). The darkness of the surface material itself may indicate a large component of carbon, perhaps left over from the pyrolysis of hydrocarbon polymers which may largely constitute the non-volatile (dust) component of the nucleus (e.g., see Vanysek and Wickramasinghe, 1975).
http://www.springerlink.com/content/q2p26v0521hj7lg3/
NASA wrote: New research by scientists at Lawrence Livermore National Laboratory, Livermore, Calif., and collaborators reveals that, in addition to containing material that formed very close to the young sun, the dust from Wild 2 also is missing ingredients that would be expected in comet dust. Surprisingly, the Wild 2 comet dust samples better resemble a meteorite from the asteroid belt rather than an ancient, unaltered comet.
http://www.nasa.gov/topics/solarsystem/ ... 80125.html

I don’t know enough to say that cometary collision as a source for our terrestrial water is bullshit, but there seem to be enough other sources for our water closer to home that we should require compelling evidence before we accept the hypothesis. The comets themselves seem reticent to provide such evidence.
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Re: Chemistry Thread

Post by JimC » Thu Mar 05, 2009 9:26 am

I have always found it difficult to explain to students why some elements (particularly transition metals) can exist in more that one oxidation state (eg. Fe +2 vs Fe+3), while , for example, Group 1 elements will always just become +1 ions...

Give me a (clever) student level explanation...

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Re: Chemistry Thread

Post by ScholasticSpastic » Thu Mar 05, 2009 10:45 am

JimC wrote:I have always found it difficult to explain to students why some elements (particularly transition metals) can exist in more that one oxidation state (eg. Fe +2 vs Fe+3), while , for example, Group 1 elements will always just become +1 ions...

Give me a (clever) student level explanation...

:cheers:
It's those twice-damned d-orbitals! :lay: (I don't like those d-orbitals. No, I do not.) Are you thinking grade ten? What concepts have you already covered by the time you get to the subject of oxidation states? Do they know about electron shells and their component sub-shells? Because I can only think of an explanation of it in those terms.

The dynamic periodic table: http://www.dayah.com/periodic/ is a fun resource. If you're able to project media from the internet it might be a useful tool for explaining electron shell weirdness and the 'd' subshells. Click on the tab marked orbitals and it shifts the display to show the oxidation states for elements. Mouse-over an element and it displays how the sub-shells are filled. So you can use it as a tool to help them visualize how to remove electrons in order to obtain a more stable ion.
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Re: Chemistry Thread

Post by JimC » Thu Mar 05, 2009 11:05 am

ScholasticSpastic wrote:
JimC wrote:I have always found it difficult to explain to students why some elements (particularly transition metals) can exist in more that one oxidation state (eg. Fe +2 vs Fe+3), while , for example, Group 1 elements will always just become +1 ions...

Give me a (clever) student level explanation...

:cheers:
It's those twice-damned d-orbitals! :lay: (I don't like those d-orbitals. No, I do not.) Are you thinking grade ten? What concepts have you already covered by the time you get to the subject of oxidation states? Do they know about electron shells and their component sub-shells? Because I can only think of an explanation of it in those terms.

The dynamic periodic table: http://www.dayah.com/periodic/ is a fun resource. If you're able to project media from the internet it might be a useful tool for explaining electron shell weirdness and the 'd' subshells. Click on the tab marked orbitals and it shifts the display to show the oxidation states for elements. Mouse-over an element and it displays how the sub-shells are filled. So you can use it as a tool to help them visualize how to remove electrons in order to obtain a more stable ion.
Yr 10 certainly.

They know about electron shells, 2N2, and the octet rule.

Sub-shells are a little beyond them, I think, so I have just said that from Shell 3 onwards, the order of filling gets a little weird, and they will learn more about it later... :mrgreen:

Apreciate the periodic table link, I may be able to put a link to it on the school net, which will be good for the keen ones... :cheers:

Personally, I am a little rusty, since the last chemistry I did was 1st year uni, over 35 years ago!
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