CHAPTER 2Basic ChemistryAtomic Theory

Elements & BondingProperties of Water

pH

CHEMISTRY

Chemistry has its roots in ancient Egypt, thousands of years ago.

The word itself has its roots in ancient Egypt; “Keme” is Egyptian for “Earth”.

“Keme” (earth) “Khemia” (trasmutation) “al-khemia” (Arabic) “alchemy” (Europe’s Dark Age) “chymistry” (Boyle’s 1661 publication) “Chemistry” (modern usage).

Modern Definition: The study of matter, its properties and associated phenomena, including the forces that directly impact these (such as energy & entropy).

THE PROGRESS OF KNOWLEDGE

Then

Authority, Experience, Intuition

“The sun travels around the earth”

“Elements can be transmuted (changed) from one type to another”

“The Earth is young; species are fixed and do not change.”

Now

+Science

Quantum Theory, Relativity Theory

Atomic Theory; the Standard Model

Cell Theory; Evolution Theory

MATTER3 states of matter are

normally consideredSolid, Liquid, GasPlasma, the 4th state,

occurs only at very high energy levels

MATTER MULTIMEDIA

Superfluid Drip

Journey Into Steel

Journey Into Concrete

Journey Into Skin

MATTERMatter is composed of atoms.

Atoms are composed of a dense nucleus, which is positively charged.

The nucleus is made out of protons and neutrons. Protons are positively charged (+).

Neutrons aren’t charged. Think of them as bouncers that hold protons apart.

The positively charged nucleus attracts a cloud of electrons, which are negatively charged.

Remember Pig Pen from Charlie Brown? Like that.

MATTERAtoms differ in the number of protons they have. This is

called the… atomic number of an atom.

This is the MOST fundamental difference between atoms. It’s what makes atoms different from each other.

It’s such an important difference, we use this SINGLE characteristic to classify atoms.

Look up at the periodic table. That’s in numerical order, (even if it looks a bit jumbled).

Remember the difference between naming and classifying!

MATTER

An “element” is simply the name we use to distinguish atoms with differing amounts of protons.

Hydrogen has 1 proton. Carbon has 6. Oxygen has 8.

The more protons an atom has the stronger it’s positive charge – and therefore, the more electrons it can attract!

MATTER

Electrons don’t like each other, but they love protons.

So if there’s more than one electron in the cloud around a nucleus, they need to balance their love and hate.

They stay as far away from each other as they can. The more crowded it gets, the weirder the shape of the cloud gets.

Electron clouds can take on beautiful shapes.

MATTERWhile electrons are technically little “dots”, they also

behave like waves.

They vibrate. They have a frequency. They could almost be thought of as a musical note.

Solids that vibrate take on weird shapes.

Simple water does the same thing.

The more energy you put into it, the more complex it gets… Standing waves on

youtube

ELEMENTSAnything smaller than an atom is no longer considered an “element” – it is

now a “subatomic particle” – a proton, neutron, or electron. All protons have the same properties, as do all electrons.

It’s the way these 2 things interact that gives us the diversity of chemistry.

Some example properties of elementsDensity

SolubilityMelting Point (and Boiling Point)

Reactivity

You can think of each element’s properties as the emergent properties of the subatomic system that makes up the element.

ELEMENTSThere are 92 naturally occurring elements, although

scientists can make “artificial” ones by pushing more protons and neutrons into a nucleus.

6 elements make up more than 95% of all biomass (define biomass), and 5 others are also vital (but are less abundant)

ELEMENTS ESSENTIAL TO BIOLOGYCarbon (C)Hydrogen (H)Nitrogen (N)Oxygen (O)Phosphorus (P)Sulfur (S)

Sodium (Na)Potassium (K)Calcium (Ca)Iron (Fe) (latin for iron is ferrum)Magnesium (Mg)

NOT Potassium! Potassium = K(the latin word for “alkali” is “Kalium”)

NOT Sodium!! Sodium = Na(in latin, the name of sodium carbonateis “natrium”)

HISTORIC ATOMIC WORK

Democritus: Atoms (from atomos, uncut, indivisible.) make up matter.

Dalton’s Atomic Theory (early 1800s)1. All matter is made of atoms.

He said they were indivisible. This part of his model was proven wrong…

2. All atoms of an element have the same properties3. Compounds are combinations of different atoms

4. Chemical reactions are just the rearrangement of atoms.

5. Atoms cannot be created, divided into smaller particles, nor destroyed in the chemical process.

(we can do this with high energy physics though!)

FUN FACTDalton had requested that his eyes be examined after

his death, in an attempt to discover the cause of his colour-blindness; he had hypothesised that his aqueous humour might be coloured blue. Postmortem examination showed that the humours of the eye were perfectly normal. However, an eye was preserved at the Royal Institution, and a 1990s study on DNA extracted from the eye showed that he had lacked the pigment that gives sensitivity to green; the classic condition known as a deuteranope

HISTORIC ATOMIC WORK

1913: Bohr’s Atom (pre-quantum mechanics) – atoms are made of still smaller things…Protons and Neutrons make up a nucleus, and electrons orbit the nucleus like planets do the sun (almost there…)

BOHR MODELS OF ATOMS

1913

The Good: Easy to understand

The Ugly: Bohr

The Bad: Not really true

1926: Schrodinger: Learned about quantum physics, and showed that electrons don’t orbit the nucleus the way planets orbit stars, but are actually 3D waves.

Electrons are wavelike particles that form standing waves around the nucleus

HISTORIC ATOMIC WORK

1977: quantum chromodynamics (QCD)Protons, Neutrons, and Electrons are actually comprised of the more

fundamental particles quarks and leptons.

HISTORIC ATOMIC WORK

MOLECULES & COMPOUNDSMolecules are systems of atoms.

Compounds are molecules made of different kinds of atoms. (CH4 is a compound, whereas O2 is not.)

• Like different elements, different compounds have different properties (think of the difference between ethanol (C2H6O) and glucose (C6H12O6)

Molecules are the smallest unit of matter that still retain the properties of a compound

Discussion: What is the difference between using the phrase “Compound” and “Molecule”?

atoms molecules compounds

Life mammals dogs

Atoms

Molecules

Compounds

THE STANDARD MODEL

• Modern atomic theory as we now understand it, is called the Standard Model– Protons & Neutrons are made out of Quarks– Electrons are a type of Lepton.– Quarks and leptons may have underlying structure as well

– we just can’t detect any (yet)

• The Bohr model is still useful as a schematic, because it is useful. Just not accurate.

Element A Element B Element C

Why are they different?The same reason any systemMade up of different things is DifferentCompare an eye to the stock market.Very different? So are carbon and uranium.

How we perceive atomswet metallic

dusty

heavy Lighter than air

CLASSIFICATION OF ELEMENTS• In Biology:

– We name life with Binomial Nomenclature – We classify life according to the rules of

Taxonomy (which is enriched by phylogenetics)

• In Chemistry:– We name elements with 1-2 letter abbreviations,

and molecules and compounds (which can be extremely complex!) according to IUPAC Nomenclature

– We classify elements by • The number of Protons in their nucleus (atomic

number)• Physical and chemical properties that occur over and

over again as atomic number increases (the “periodic” manifestation of various properties).

• They are highly organized within a table called the Periodic Table of Elements

CAtomic mass

12

Atomic Mass: This is how much total “stuff” is in the nucleus. Change this number and you change the mass of the element – but not its physical or chemical properties. (Isotopes of an element differ in their atomic mass, not atomic number; they have different amounts of neutrons.)

Atomic number

6Atomic Number: The ultimate factor in an elements properties. Change this number and you change the element (transmutation) This number also gives you the number of electrons an atom of this element will have when it is electrically neutral.

ATOMIC NUMBER VS. ATOMIC MASS

• You can determine how many neutrons an atom has by subtracting the atomic number from the atomic mass (taking the whole number).– Why not a whole number?

• This number is actually the average mass of the given elements series of isotopes (more later).

PERIODIC TABLE

1

H1.008

3

Li6.941

11

Na22.99

19

K39.10

4

Be9.012

12

Mg24.31

20

Ca40.08

5

B10.81

13

Al26.98

21

Ga69.72

6

C12.01

14

Si28.09

22

Ge72.59

7

N14.01

15

P30.97

23

As74.92

8

O16.00

16

S32.07

24

Se78.96

9

F19.00

17

Cl35.45

25

Br79.90

10

Ne20.18

18

Ar39.95

26

Kr83.60

2

He4.003

1

2

3

4

Horizontal periods indicate

total numberof electron

shells

Vertical columns indicatenumber of valence electrons

I

II IIIIV

VVI

VII

VIII

Vertical columns = groups; chemically similarHorizontal rows = periods; larger and larger

PERIOD TABLE REFERENCE

Great Reference for studying the periodic table:

http://education.jlab.org/itselemental/index.html

ISOTOPES

Isotopes– Same element, but bigger (more massive)– same physical properties (for the most part)– IUPAC Nomenclature: name of element (which

gives those in-the-know the atomic number), a hyphen, and the atomic mass.

• Carbon-12, Carbon-14.

http://en.wikipedia.org/wiki/Isotope

RADIATION

• What is radiation?– A nucleus “radiates”, emits, or “shoots out” bits of itself when it is

unstable.– There is weakly radiating nuclei and strongly radiating.– Weakly radiating nuclei are generally not harmful to cells, because the

energy is absorbed long before the energy can penetrate deep enough to reach DNA

– Strong Radiation blasts right through cells (picture a bullet cutting through water), and can shred DNA.

– Why does hair fall out, the stomach give trouble after chemotherapy?– Strong Radiation can also be good – we use it to sterilize things, like

the mail, or some kinds of food.

ELECTRONS AND ENERGY• Electrons, Energy

Electrons are negatively charged particles that are many orders of magnitude smaller than protons and neutrons.

They can absorb electromagnetic energy (photons).• Thus we can make statements such as “this electron

has more energy than that electron”The more energetic the photon (think wavelength –

x-rays to thermal radiation (heat)) the more energetic the electron.

ELECTRONS AND ENERGY

Electrons are negative, so why don’t they get attracted to the positive proton?– They do! That is why the only electrons you find in orbit

are those with enough kinetic energy (due to their photons) to not fall in.

– If they have TOO much energy, they’ll fly right past (ever get electrocuted before?)

– At just the right amount of energy, they fall into an orbit around the atom at a particular distance from the center. The volume of spherical space with a diameter of this particular distance can be thought of as a big, hollow shell…

SHELLS & ORBITALSShell: The overall volume of space around a nucleus where electrons carrying

similar amounts of energy (from photons) can be found.

When multiple electrons of the same energy level come at the nucleus at the same time, they can’t exactly take up the same space, right? You can’t stand in the same place, at the same time, as another person. Neither can electrons. So they need to crowd into this small volume of space.

The way they do this is by falling into particularly shaped orbits called orbitals

Orbital (or “sub-shell): the (sometimes complex) shape given to the volume of space an electron of a given energy level can be most probably found.

SHELLS & ORBITALSOnly two electrons can exist at any given time within an orbital;

more than that and they feel too crowded. (How many planets do you think you could stick in the same orbit as earth before they start colliding?)

Therefore, Shells have one or more orbitals, and therefore shells can have more than 2 electrons.

How does an electron know where to go? The amount of energy the electron is carrying determines how far away from the positively charged nucleus it will be (and therefore, what shell it will fall into)

ANOTHER ANALOGYFor valentine’s day, there is a special performance going

on. It’s Barry White, in Concert, in a big amphitheater.

Barry

The seats hold 1 male and 1 female

The “section” represents the shell

The “seat” represents the orbital

The farther away, the more seats fit

ADVANCED ELECTRONS & ENERGY• How far an electron is away from the nucleus is dictated by TWO forces

acting on it• The pull from the proton’s + charge, • The kinetic energy inside the proton.

– Think of the gravity “slingshot” of a large planet that space probes use to accelerate; or how we put things in Martian orbit.

• The more energy the farther away; the less energy, the closer to the nucleus.

• Orbital’s shapes start easy and get complicated. The shape depends on several factors, including the number and energy level of the electrons present.

• Here is a great website for showing the shape of electron orbitals: http://winter.group.shef.ac.uk/orbitron/

I II III IV V VI VII VIII

1

2

3

1

H1.008

3

Li6.941

11

Na22.99

4

Be9.012

12

Mg24.31

5

B10.81

13

Al26.98

6

C12.01

14

Si28.09

7

N14.01

15

P30.97

8

O16.00

16

S32.07

9

F19.00

17

Cl35.45

10

Ne20.18

18

Ar39.95

2

He4.003

Shells

Valence Electrons

I II III IV V VI VII VIII1

2

3

What Atoms of Hydrogen Through Xenon Really "Look Like"What Atoms of the Heavy Elements Really "Look Like"Scale Drawings of Atoms and Orbitals: Hydrogen Through KryptonScale Drawings of Atoms and Orbitals: Rubidium Through XenonScale Drawings of Atoms and Orbitals: Cesium Through RadonScale Drawings of Atoms and Orbitals: Francium Through Lawrencium

SHELLS & ORBITALS

This amount of energy, as we said, must be a very precise amount of energy. It’s not a spectrum of continuous values, but a stepped region.analogy: analogue vs. digital. See slide on

continuous vs. quantized data.

Continuous data: any value within a range.

1 2 3 4(1.623425)

Example data: height; weight; salt concentration; temperature

Quantized Data: Discrete Steps

People; planets; fingers; electron energy levels

Quantized data vs. Continuous Data

STANDARD MODELSo, Bohr was wrong: electrons don’t orbit around the

nucleus They behave like waves (which is why they aren’t called orbits, but orbitals!)

Electrons in orbitals are 3D standing waves.Standing waves on youtubeRecall from the video: the more energy input into a wave,

the more complex the pattern will be!

Therefore, electrons form more and more complex patterns (orbitals!) as they gain more and more energy.

A quick trip from Hydrogen through Xenon

Sometimes, electrons in different orbitals are so similar in energy that the distinction between the orbitals

disappears and the orbitals blur together or hybridize. Electrostatic repulsion pushes the orbitals apart into a

tetrahedral arrangement. This accounts for the well known tetrahedral bonding of carbon.

BONDING

• The only electrons that we care about are the electrons on the very outside of the atom.– These are called the valence electrons.

• Valence: Greek for “strength”. • Why this word? Before we knew about the subatomic

world, we referred to the “binding strength” of an element as its “valence”. Once we learned about these important outermost electrons, we called them “valence electrons”.

BONDING– Elements differ from each other by having different amounts of valence

electrons.• Hydrogen has 1 valence electron• Oxygen has 6 valence electrons• Carbon has 4 valence electrons

– Atoms are most stable when their valence shell is full (even if it means changing their electric charge from neutral to plus or minus!)

• The energy need to have full orbitals is greater than the energy need to stay neutral. This is the fundamental reason why elements are reactive or not reactive.

– Nobel gases don’t react, because their valence is full – not because they are electrically neutral!

• Therefore, Since hydrogen is only 1 proton and 1 electron, and the very first shell (which only has enough room for 1 orbital) needs TWO electrons total. How does it get this electron?

• How DO atoms fill their valence?

• They lie, cheat or steal to get their electron fix.

CHEMICAL BONDING• If they steal an electron, they will change their electric charge, making

it go from neutral to negative.• whatever atom they stole from is now missing a negative charge, and is

now positive.• Atoms that are electrically charged are called ions. (Greek for “to

walk”).• Therefore, An ion is an atom or molecules(!) that have a lost or gained

electrons, giving them a net electric charge. • What happens when negative and positive get together?• They attract.• This kind of bond is called an ionic bond.• This is the sort of bond found in salt.

– halogens form ionic bonds. Halogen = “salt maker”

COVALENT BONDING

Covalent bonds (the simple version)– If a nucleus isn’t strong enough to steal an electron, it will

tug on it enough to pull it closer. – The rest of the atom comes along with it – it’s strong

enough to keep its electron.– As they get closer, the electron starts moving around both

nuclei. They begin to share the electron.– This kind of bond is therefore called a “covalent” bond.

A Bohr (incorrect but easy to visualize) model of the formation of a covalent bond

A more realistic View (halfway down the page)

Chemical Bonding

POLAR COVALENT BOND• What happens when one atom wants an electron more badly than

another? (general trend: more protons, more pulling power)• When two different nuclei come together, one will most likely have a

slightly stronger pull on the electron than the other.• Large nuclei that have a lot of positive charge attract electrons more

strongly than small nuclei with less charge.– The property of an atomic nucleus that describes how strongly it attracts

electrons is called electronegativity.– Oxygen is strongest– Then Nitrogen– Then Carbon.

• When this happens, the sharing between the two nuclei is not even. The electron is pulled a little closer to one.

• The opposite of “symmetric” is “polar”. When something is “polar”, it means something is uneven.

• Therefore, this kind of bond is called a polar, covalent one.

HYDROGEN BONDS

• When the nuclei share evenly (e.g. O2), this is called a non-polar covalent bond.

• Back to polar covalent bonds. If there is a slightly uneven shape to the bond, one nucleus is slightly more positive than the other (and vice versa).

• This creates a very small charge. These very small charges can also participate in interactions (bonds) that are very weak. Because hydrogen is element the most commonly associated with these weak bonds, they are called hydrogen bonds.

• In very large numbers, hydrogen bonds can be strong.– DNA double helix– The properties of water.

MOLECULAR SHAPEShapes of molecules (your book writes itself in circles here)• when two atoms share a bond, that molecule forms a straight line (it’s a linear

molecule)• When more than two atoms come together in a molecule (such as CH4), we have

to concern ourselves with 3D space…

• To truly understand why molecules are shaped the way they are requires an advanced understaning of electron configurations around both atoms AND molecules.

• Complex molecules such as DNA and proteins are just a bunch of atoms each sharing electrons with each other. The orbitals overlap and merge – sometimes, a single orbital could be the entire length of the molecule! Give an example:

• Short answer: The shape of a molecule is directly determined by how the electrons around each atom interact.

• Something else the book doesn’t teach you yet: orbitals can hybridize, or combine together to form new, more complicated orbitals.

MOLECULAR SHAPE

• The shape of a molecule depends upon the electron configuration of the system.

• Another way of saying this is the spatial orientation of the bonds between atoms.

• Double & Triple Bonds: Atoms can either share single electrons (and therefore share with more atoms) or share more than one electron with a single atom (double bonds, triple bonds).– O—O, N---N

The real reason molecules adapt particular shapes. The loopy shapes hereRepresent the orbits of electrons in bonds between carbon and hydrogen atoms

In this flat plan of carbon atoms.

A lattice of graphite might look something like this.

MOLECULAR SHAPE

REACTIVITYAtoms are constantly moving around due to the internal energy of their electrons (this is

called “thermal energy”, by the way, and temperature is a measure of how much “bopping around” atoms are doing).

Unpaired electrons are the most reactive kind. If an atom has an unpaired electron in its valence shell, it will either:

lose it (if there are very few electrons in here, like sodium)…o Becoming a positive ion (a cation, pronounced “cat ion”) in the process…

Steal one from another atom (if it is electronegative enough)…o Becoming a negative ion (an anion) in the process…

Atoms that lose an electron will be attracted to the atom that gained the electron (+ attracts -, right?) And as a result, an ionic bond is formed.

Share one with another atom (if it isn’t electronegative enough)o If a pair of atoms has similar electronegativities, the will share the electrons evenly (a

nonpolar covalent bond)o If one atom has more electronegativity than another, the shared electrons will tend to stay

around this atom more than the other (a polar covalent bond)

REACTIVITYAtoms that have an even number of electrons in their valence shell

(pairs of electrons) will generally be less reactive than atoms with an odd number (because electrons tend to pair).

However, as long as there is still space in the valence shell (recall the Octet Rule of 8 electrons filling valence shells of atoms with atomic # up to 20), the atom will still tend to react with other atoms. They are simply not AS reactive.

Think of the difference between Cl and C. Chlorine has an unpaired electron in its valence shell (3 pairs and a single electron for a total of 7), while carbon has 4 (2 pairs of 2). We intuitively know that Chlorine gas is ‘bad’ (highly reactive), while carbon is generally stable (the graphite in your pencil isn’t toxic).

WATER• Let’s apply some of this chemistry knowledge to the most abundant compound on the

planet, Water.• The polar covalent interactions (hydrogen bonds) are what give water its unique

properties– without the extra “cling”, ice wouldn’t freeze until -100 C, and liquid water would boil at -91 C….

most water would be in the form of vapor on earth.• High heat capacity• High heat of vaporization• Water as a solvent “universal” solvent

– solvent vs. solute– touch briefly on solutions and solutes– fall back into ionic bonds of NaCl and why they dissolve and become solutes– hydrophilic vs. hydrophobic– cohesion– adhesion

• high surface tension• solid state is less dense than liquid state (highly unusual for compounds!)

– figure 2.12

WATER MOLECULE

• Acids & bases– Dissociation vs. Dissolving– Water dissociates; salt dissolves– pH scale– Acidic solutions– Basic solutions– Wikipedia has some great stuff on this.

PH

• It’s all about H+ and OH-

H2 O

H+

OH-

OH-

H+ +

PH SCALE

• pH is simply the negative log (-log base 10) of the concentration of hydrogen ions.

• Concentration of [H+] = 10e-6 = 1x10^-6 = 1x10-6

-log(10e-6) = 6

ACIDIC SOLUTIONS

• Dissociate in water, give off H+• HCl H+, Cl-

– Complete dissociation = STRONG ACID• H2CO3 H+ and HCO3-

– Incomplete dissociation = WEAK ACID

BASIC SOLUTIONS

• Bases absorb H+. If there are no H+ to absorb, than they will start releasing hydroxide ions, OH-

• NaOH Na+ and OH-– Complete dissociation = STRONG BASE

• NH3 + H2O NH4+ + OH-– Incomplete dissociation = WEAK BASE

BUFFERS & PH

A buffer keeps the pH of a solution within a limited range.

They are compounds that either absorb or release H+or OH-.

Example: Carbonic Acid: H2CO3 H+ + HCO3-

-

+

There’s roughly equal amounts of each side at a neutral pH

-

+(an easier way of looking at it)

H+ + HCO3- H2CO3 OH- + H2CO3 HCO3

- + H2O

-

+

The H+ will “attack” the negative charge.

++

+

++

Too much OH-

---

-

Too much H+

The OH- will “attack” the uncharged compound