Chemistry Common Sense

Some Answers to Questions You Didn't Know to Ask

John Engelbrecht Austin, Texas Februay 27, 2017 Chemistry is complex enough. But as a person studies more chemistry, it just seems to get more and more complex.

But this shouldn’t scare off a person from being a chemist, most fields of study have practically unlimited complexity. I found over decades of reading books and seeing TV shows that a small number of ideas helped me understand much better.

These ideas are written out here. I don’t see them in textbooks very much, for some reason. There are three sections: the extreme speeds of molecules, dissociation of water (acid and base), and electron orbitals.

The extreme speeds of molecules

Molecules are always in motion and bounce off each other elastically. Air molecules average around 1000 miles per hour

at room temperature, and any particular molecule will go at different speed after each collision.

(If molecule A overtakes molecule B, A will end up slower as it boosts B to be faster.) Because of the random directions and speeds of the molecules, statistics can be used to study molecule speeds. You would think that air molecules hitting our skin at 1000 miles per hour would hurt, but the molecules of skin

are bonded tightly and there is no tearing. 1000 mph is way above the speed of sound (741 mph) but the air

molecules do not make sonic booms. Even in solids and crystals, the molecules are moving and bouncing off. But they are trapped in fixed

positions so the bonds don't get broken. Melting and vaporizing If you heat any substance, the molecule speeds increase. Think now about a solid. If you heat it to higher and

higher temperature, the speeds become so high that the bonds (or crystal forces) break

and the solid melts. If you heat a liquid, there comes a temperature when molecules at the top surface go so

fast that they whiz off into the air. (It is only the fastest molecules that whiz off, the slower ones stay in the liquid.) Chemical reactions happen faster at higher temperature.

1) When molecules crash into each other faster, they might squash together and stick, making a compound.

2) On the other hand, the atoms in a molecule vibrate faster and might break apart the molecule.

Large organic molecules like proteins break apart or burn (oxidize). This is why you get burned

by hot objects, your proteins and other life molecules are coming apart at high temperature.

3) It never happens that a chemical reaction is caused when three molecules come together at once.

It turns out that this almost never happens, reactions are when two molecules collide. Organic chemistry only works at moderate temperature. Too high a temperature breaks apart the big molecules.

(Scorches them. Burns them with oxygen.) Too low a temperature and there isn’t enough collision force to

produce chemistry. At the extreme temperature of plasma, so many electrons have been stripped off of atoms that everything

is ionized; then you don’t have chemistry, you have ion reactions. Heavy air atoms like argon have the same average kinetic energy (from physics, kinetic energy is ½ m v²) as

lightweight atoms like helium or medium molecules like oxygen or nitrogen. This means that helium atoms travel much faster than argon atoms. If we think about large molecules in the air

like a cyclohexane ring or a cinnamon molecule, they are very heavy and they travel slowly.

It is very surprising that the average kinetic energy is the same no matter how heavy the molecule is.

This is true in gases but I am not sure it is true of liquids. Atoms were proven only about 120 years ago, in association with Brownian motion. Before that,

a few scientists (especially Germans) thought there were no atoms, just energy packets. The size of atoms was determined about 100 years ago, which gave a way to find Avogadro's number.

Einstein found the size of atoms to about 30% accuracy, then others got more precise, like Millikan

and the oil drop experiment. When you listen to an audio system where there is no media being played, you hear a hiss if you

turn up the volume. The hiss is from the vibrations of the molecules in the first stage of the

amplifier. There are three ways of reducing hiss. One is to chill the first amplifier and any

microphone that is attached. Another is to use resistors that are either bulk metal

(like wirewound resistors) or made of metals and oxides evaporated onto very smooth ceramic substrates.

The last is to use semiconductors that are passivated to avoid noise at the surface of the semiconductor.

(Surface states.) By the way, when audiophiles speak highly of old-style carbon resistors, they are being misled.

Carbon resistors are noisy resistors.

When I say that semiconductors can be chilled, I must note that most semiconductors stop amplifying

at low temperature; researchers doing low-noise work at cryogenic temperature have to select their

semiconductors carefully. Small insects and protozoa find that swimming through water is like people swimming through molasses.

Small life is much closer to the size of molecules and that makes the viscosity high for them. Chemical reactions are largely from 1) the high speeds of molecules and 2) electrical polarization

of the atoms and molecules, which is like static electricity. Another reason for reactions is that

covalent bonding helps molecules let each atom get a full complement of eight s & p electrons in the

second shell.

As temperature increases, molecules speed up. Every 7ºC or 10ºF, chemical reactions go about twice

as fast. If the temperature goes up by 21ºC, reactions go 2*2*2 = 8 times as fast. Oxygen atoms are very polar, having a strong + side and a strong - side. If you mix oxygen with

hydrogen and make it explode with a spark, it will cool into liquid water. Two hydrogens join onto an oxygen

at about 100º angle (not 180º!). The hydrogen side of a water molecule is very + and the opposite side

is very minus. If you hear about the "lone pairs" of electrons on oxygen, the lone pairs are toward one

side and make that side negative.

Because of this high polarization of water molecules, they clump together like +-+-+-+- because

opposites attract. (But liquids are really 3D, so the water molecules really don't line up in a line.) This is

where surface tension comes from. The surface tension of water is so extreme that it shapes the

water surface through ten million atoms. That is why there is a meniscus and why rain drops are round. The high polarization of water makes it a great solvent for ionic salts such as table salt, sodium chloride. Polarization of water is why water in clouds makes the tiny droplets that make clouds white.

The molecules clump together, and when their size gets up to be the wavelength of light, they

reflect light. In high-temperature steam, there isn't much clumping, the droplets are quite small,

and high-temperature steam is completely clear, not white. But high-temperature steam is usually at

high pressure so we are not accustomed to seeing it. Cloud droplets that attract enough water molecules get heavy and sink due to gravity. Even heavier

droplets start falling as rain, or as ice crystals up in the cirrus clouds. But carbon dioxide has the two oxygen atoms exactly 180º apart, on either side of the carbon.

So while water is polar, carbon dioxide is non-polar. In fact, hydrocarbons generally are non-polar. So oil and water

don't mix, the polarizations are wrong.

(Disclaimer: the detergent diagram above shows hydrogens as red, but the normal convention

is to show hydrogens as white.)

Detergent can dissolve fat and oil because a detergent molecule has two ends, polar and non-polar.

The polar end on the right attracts water and the non-polar end on the left attracts fat, oil, and

other non-polar molecules. So the action of detergent to clean greasy plates has a basis at the atomic level! Because water is so polar, it is correct to think of water as being a "vicious" molecule.

It is very reactive, chemically, with other polar molecules. This is why water is vital to

life, it is light weight, abundant, and reactive. We don’t think of water as being vicious, but it really is. When water molecules are around a sodium chloride crystal, the water molecules, traveling on

average about 1000 miles per hour at room temperature, strike the sodium and chlorine atoms

of the solid crystal and tend to knock off sodium and chlorine ions. Then the polarized water

molecules clump around the ions. I think of this dissolving action of water as being a violent thing. In ice crystals, dissociating water molecules do not get separated by jostling water molecules,

everything is locked in the crystal. The dissociated ions immediately recombine.

Dissociation of water (acid and base)

K_w is the ionic product for water, http://chemguide.co.uk/physical/acidbaseeqia/kw.html. K_w relates to how much pure water molecules break up spontaneously (dissociate). At 25ºC,

it happens that K_w is a round number, 1.00 x 10^-14 mol² dm^-6. At higher or lower temperature,

K_w is very different. In other words, there is more spontaneous dissociation at high temperature,

more hydrogen ions and hydroxide ions at high temperature. If ions, like from an acid, get into water and make lots more hydrogen ions, the K_w constancy

means there will be fewer hydroxide ions. Promoting H+ depresses OH- so that K_w stays the same.

(This is only sort of true, I suspect it is more complex.) In an acid, there are many hydrogen ions and few hydroxide ions. In a base, there are many

hydroxide and few hydrogen. This is so the product remains the same, K_w.http://www1.lsbu.ac.uk/water/water_dissociation.html talks more about pH and K_w. The pH of 7

for pure water changes for ice and boiling water.The pH of 7 for pure water is from the square root of 1.00 x 10^-14. At room temperature, a given water molecule will spontaneously dissociate about every 11 hours.

Most of the time, the ions immediately recombine. But rarely the polarized water molecules will

hit the ions just right to drive the hydrogen and hydroxide ions apart. These are the water ions

that pH talks about. See (a) and (b) in the following diagram I find on the Web. (In (a), a hydrogen

ion has already been joined to a water molecule, making H₃O.)

Since the ions are electrically charged, the neutral (but polarized) water

molecules cluster around the ions and “hydrate” them, spreading out and diluting the charge

concentration of the water ions.

In (c), three water molecules have clumped around the positive-charged H₃O. In (d), three

water molecules have clumped around the OH.

This hydration of the ions means that, even though a hydrogen dissociating from a water molecule

might be a bare proton, it will immediately have the negative sides of numerous water molecules

cluster around it.

Electron orbitals

Electrons are popularly thought of as spinning around nuclei like planets orbit around the sun,

or like satellites orbit the earth.

But when quantum physicists were doing their work in 1920, they decided that the planet model

is not at all how electrons behave. They started saying that electrons are sort of like clouds,

the electron position is a statistical thing. If you have heard of s, p, d, and f, those are different shapes of electrons in clouds.

The polarization of oxygen is due to s & p electrons in the second shell, namely that there aren’t enough electrons

to complete the p orbital, and the second-shell electrons that are there pair up and make a negative side

to the oxygen atom. Another quantum idea is that electrons are not little hard balls. Electrons are really

wave things that have energy. But it is true that every electron has exactly the same

electrical charge as every other electron. Moving electrons have speed, mass, energy,

inertia, and momentum. In old-style TV picture tubes

and X-ray tubes, 13,000 volts or more “accelerate” electrons to half the speed of light or faster!

This happens because electrons are light weight. If you think of nuclei, that is more like hard balls. But physicists in the 1940s and up to

the present say that neutrons and protons are composed of various sub-atomic particles, like lepton and quark.

A free neutron, which can happen when a radioactive atom emits radiation, might travel at

50 miles per hour if it is in “thermal equilibrium” with the environment. That is only 5% of an atom's speed.

After a neutron has a half life or so, about 90 seconds, it will split into a proton and an electron.

While the neutron is free, it floats around freely, right through any electron orbitals that might

be in its path. Electron Stiffness When we think about electron clouds, that makes it sound like atoms are soft and fuzzy,

like clouds in the sky. But that is not how electrons in atoms are. The orbitals are very stiff.

In fact, when you study organic chemistry, you learn about bond strain when you have a

nitrogen atom in a carbon ring.

There is bond strain and the energy of the molecule is higher

than a 6-carbon ring.

Bond strain is also vital to understanding proteins. Proteins fold up

at lower temperature to minimize bond strain.

The protein folding above is simulated on a supercomputer. A protein is a polymer made from the 20 amino acids. The protein that is

pictured does its folding in just 3 microseconds! The amino acids on the outside of the molecule are chemically active. The amino acids

on the inside are shielded from the outside and are not chemically active, but their acidic or basic natures aid the folding, because the

amino acids get folded close together as the folding happens.

Another way to think about orbital stiffness, or the stiffness of the electrons around an atom,

is to think about hitting a hammer on a nail. What you are really doing is hitting the hammer’s

electron clouds onto the nail’s electron clouds. We know that a hammer striking a nail

is extreme hardness hitting extreme hardness, but it is really the electron clouds hitting each

other. This shows how extremely stiff the electron clouds are.

Astrophysicists think about an even greater stiffness when they think about neutron stars or

white dwarfs. These strange little stars are made of "degenerate matter" where there are no

electron clouds around nuclei, just nuclei jammed together. The surface of such a star is

so much stiffer and harder that you can't imagine it.

Yet another way to think about orbital stiffness if to think about a steel-framed skyscraper.

You might think that the framework is stiff because of the concrete poured around the steel.

But the concrete is to protect the steel from getting soft if there is a fire

(read about the Sept. 11 2001 World Trade Center buildings collapsing in the fire of the jet

fuel and burning paper and carpets). The steel is just as stiff as the concrete. In 1000

feet of a skyscraper height, the steel compresses only about 1/3 inch due to electron clouds

getting deformed from all the pressure. In other words, if you could launch a skyscraper

into orbit and take the load off the steel, the skyscraper would be only 1/3 inch taller.

In ocean water, the oceans would rise about two inches if the water were completely incompressible.

These examples of the stiffness of electrons in orbitals emphasize how amazing the stiffness is. Orbital stiffness reaches its limit when you talk about high explosives imploding

plutonium and uranium in atom bombs. High explosives are like C-4, TNT, RDX, and Semtex.

The 20 pounds to one ton of high explosive, cast into “shaped charges,” creates such an intense,

focused shock wave that the heavy plutonium or uranium actually does compress to about eight

times the density. (In terms of one dimension, the atoms are pushed to about half the normal spacing.)

But in just microseconds, the explosion of the high explosive “lens” is over and

the heavy metal will rebound to normal size (actually, it all gets vaporized), so to get a

chain reaction

going during the maximum compression, the bomb “initiator” (second diagram above) has

to release neutrons during the highest compression. Otherwise, the bomb fizzles.

This is described in Richard Rhodes’ book, The Making of the Atomic Bomb.