Lecture 2

• Groups with Names• Student leadership stuff• Seating Chart• Attendance sheet• Finish up from last time• The Genus Homo• Chemistry

– Part 1: Atomic Structure– Part 2: Water– Part 2: Acids & Bases

• 1.5-2.5 million years old.• Homo neanderthalensis died out 24,000 years ago• Homo fluoresiensis died out ~12,000 years ago.

– Assuming it’s not just a microcephalic human

• Example disagreement between taxonomy and phylogenetics:– A minority of zoologists consider that the two species of

chimpanzees (usually treated in the genus Pan), and maybe the gorillas (usually treated in the genus Gorilla) should also be included in the genus based on genetic similarities. Most scientists argue that chimpanzees and gorillas have too many anatomical differences between themselves and humans to be part of Homo.

Chemistry

• Keme, Egyptian word for “earth”– Concerns itself with the static and dynamic properties

and phenomenon of matter, as well as those forces that directly impact these properties and phenomena (such as energy and entropy).

• Metallurgy Alchemy Chemistry• Original gold work was thought to be a

transformation, not a purification.– (kind of ironic the original scientists thought that

elements could change, but biological species were fixed.)

Oops

• Physics: “The sun travels around the earth”

• Chemistry: “Elements can be transformed from one into another”

• Biology: “Species are fixed, and do not change”

Matter4 states of matter, not 3! (Solid, Liquid, Gas,

Plasma)Made of atoms.

Atoms are the smallest unit of matter that still retains the properties of an element (theme: emergent properties)

Atoms as systems of particlesvary the amounts and ratios, vary the physical properties.

Underlying math structure is what counts.

Molecules are systems of atomsCompounds are molecules that contain atoms of more

than one kind of atom (e.g. CH4).Compounds are therefore always heterogeneous.

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

ElementsAtoms can be very different from each other. We name (not

classify!) atoms based on the fact that they have different numbers of protons in the nucleus.

Elements are therefore the most fundamental unit of matter that is imbued with specific properties. (a proton is a proton, electron is an electron, etc.)

Some properties of elementsdensitysolubilitymelting pointreactivity

Look at each element’s properties as the emergent properties of the subatomic system that makes up the element!

Only 92 naturally occurring elements.Concept of “islands of stability”6 elements make up more than 95% of all biomass (define

biomass), and 5 others are also vital (but make up less): Carbon, Hydrogen, Oxygen, Phosphorus, Sulfur (NOT potassium and

sodium!) (CHNOPS)sodium, potassium, calcium, iron, magnesium.Show figure 2.1

Atomsfrom atomos, uncut, indivisible.

Dalton’s atomic theory (early 1800s)• Elements are made of tiny particles called atoms • All atoms of a given element are identical • The atoms of a given element are different from those of

any other element • Atoms of one element can combine with atoms of other

elements to form compounds. A given compound always has the same relative numbers of types of atoms.

• Atoms cannot be created, divided into smaller particles, nor destroyed in the chemical process. A chemical reaction simply changes the way atoms are grouped together

Dalton 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

• 1808: dalton’s atomic theory• 1913: Bohr’s Atom• 1926: Schrodinger: electrons as 3D

waveforms.– Standing waves.

• Demonstration• Video: Standing waves on youtube

• 1977: quantum chromodynamics (QCD)– Research institute:

http://www.physics.adelaide.edu.au/cssm/index.html

link

Various atoms and molecules as depicted in John Dalton's A New System of Chemical Philosophy (1808).

1808

Bohr Models of Atoms

1913

Problem: could only predict spectral lines of H

The animations to the right and above illustrate the typical four-dimensional structure of gluon-field configurations averaged over in describing the vacuum properties of QCD. The volume of the box is 2.4 by 2.4 by 3.6 fm, big enough to hold a couple of protons. Contrary to the concept of an empty vacuum, QCD induces chromo-electric and chromo-magnetic fields throughout space-time in its lowest energy state. After a few sweeps of smoothing the gluon field (50 sweeps of APE smearing), a lumpy structure reminiscent of a lava lamp is revealed. This is the QCD Lava Lamp. The action density (top) and the topological charge density (right) are displayed. The former is similar to an energy density while the latter is a measure of the winding of the gluon field lines in the QCD vacuum.

2.4X2.6femtometers

Within the proton Scale: 10-15 meters = 1 fm = 1 femtometer

• Modern atomic theory is based on the Standard Model– Protons & Neutrons (called hadrons) are made out of

Quarks– “Electrons” as we know them are actually paired to a

neutrino. This doublet is one of several types of subatomic particles called leptons

– SO: fundamental particles are quarks and leptons. Not protons, neutrons, and electrons.

Element AElement A Element BElement B Element CElement 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

metallicdusty

heavyLighter than air

This movie illustrates the action inside the nucleus of a deuterium atom containing a proton and a neutron, each with three quarks. An electron strikes a quark inside a proton, passing energy to the quark before the electron bounces back. The quark now has so much energy "stuffed" into it, it creates a cascade of new particles as it flies out of the proton. The result is two new, two-quark particles.

http://www.jlab.org/news/articles/2004/nucleus.html

one of the first full-energy collisions between gold ions at Brookhaven Lab's Relativistic Heavy Ion Collider, as captured by the Solenoidal Tracker At RHIC (STAR) detector. The tracks indicate the paths taken by thousands of subatomic particles produced in the collisions as they pass through the STAR Time Projection Chamber, a large, 3-D digitial camera

The Periodic Table, “how humans have figured out a way to divide the

elements into chunks of knowledge that make sense to us”.

humans classify things

The Periodic Table is to chemists what Taxonomy is to biologists

The difference: chemical elements are easier to investigate, and so we know a great deal more about them than we do about the various organisms that make up the biosphere.

Cmass

number

12

6The ultimate factor in an elements properties. Change this number and you change the element (transmutation)

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)

This number also gives you the number of electrons an atom of this element will have when it is electrically neutral.

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

• 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.

Periodic Table• Elements grouped in periodic table based on

characteristics

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

II

IIII IIIIII IVIV VV VIVI VIIVII

VIIIVIII

11

22

33

44

Groups

Periods

Periodic Table (Revisited)

Vertical columns indicatenumber of electronsin outermost shell

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 number

of electron shells

I

II III IV V VI VII

VIII

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

– Why “periodic”? • As more elements were discovered, realized themes

emerged were common different groups. • For example, copper, silver, and gold, have characteristics

VERY different from helium, neon, and argon!

– What was the rationale for arranging it?• It is arranged by increasing atomic number.

– What is atomic number?

• Columns = “Groups”– # of electrons the element has in its outer shell (valence #)

• Rows = “Periods”– How many electron shells (energy levels)

– Isotopes• Same element, but bigger.• same physical properties, but will react a slight bit more

slowly due to the increased mass. (kinetic isotope effect) • Iso, same; topos, place. Named due to the early

observation that some elements ended up taking up the same place in the periodic table. Turns out they are the same element, with additional neutrons.

• IUPAC Nomenclature: name of element (which gives those in-the-know the atomic number), a hyphen, and the atomic mass.– Carbon-12, Carbon-14.

– Electrons, Energy• Electrons & energy

– Electrons are -, protons are +. Why not fall into nucleus?» electrons also have the properties of waves.

– Electrons need to have a very particular amount of energy in order to be in orbit around a nucleus.

– These orbits can be thought of as standing waves.– Standing waves on youtube – http://daugerresearch.com/orbitals/index.shtml

Orbital: volume of space occupied by an electronOnly two electrons can exist at any given time within an

orbital.The amount of energy the electron is carrying

determines how far away from the positively charged nucleus it will ‘fall’ into a particular orbital.

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.

Quantized data vs. continuous data

Continuous data: any value within a range.

1 2 3 4

Quantized Data: Discrete Steps

(1.623425)

Example data: height; weight; salt concentration; temperature

People; planets; fingers; electron energy levels

– different energy levels are called “shells”, – This space is organized by a series of orbitals (sometimes

called “subshells”). » The shape of an orbital is directly dependent upon the

amount of energy contained within an electron.– Atoms that are electrically neutral are this way because the

number of + charged protons in the nucleus match the number of – charged electrons in orbit.

» Why is it so important to be neutral?» It’s the most energetically favorable system under most

circumstances.» Atoms with many protons must have many electrons to be

electrically neutral.» The complexity of the system will increase as you increase

the number of system members. (think of the standing waves)

• Atoms that contain many electrons have very complicated electron orbitals (and overall shells). Some examples – animated gifs.

– We can reduce the amount of complexity we must deal with: The only electrons that we need concern ourselves with are the electrons on the very outside of the atom.

– These are called the valence electrons. Valence comes from the greek word meaning “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”.

• Rules for the system:– orbitals can contain only 2 electrons.– recall shells. Shells represent the different volumes of space

corresponding with different energy levels of electrons.– An electron that has just the right amount of energy to keep it

from falling into the positively charged nucleus (so it’s not very energetic, only a little bit) is considered to be in the first “shell” of energy. Within this shell is only a single orbital, which is spherical in shape. Because of the physical and mathematical properties of THIS particular system, no more electrons can be at that exact energy at the same time. Therefore, only 2 electrons can be found in this electron shell, within a single orbital.

• the next precise amount of energy that lets an electron orbit a nucleus describes the next shell.

• This energy shell is much larger than the first, and so there is plenty of room in it for many electron orbitals. It can hold four orbitals, for a total of eight electrons. All elements up to #20 (Ca) follow a general rule due to the commonalities of their subatomic systems.

• The next several (precise) energy levels are also of similar size to fit 4 orbitals.

• Because of this kind of regularity, there is a rule of thumb that can be followed for the first 20 elements, called the octet rule.

• Why?– The most stable electron configuration is one in which

all electrons orbiting the nucleus are paired with a partner. What elements already have this configuration? Noble gases.

• Therefore, all elements are most stable when their outermost electrons are in a stable configuration – or “completely filled”.

• So, For these first 20 elements, this stable configuration means that the valence shell (which is always the outermost one) contains a total of 8 electrons.

• the periodic table is arranged such that the horizontal row indicates the number of electron shells that element has, while the vertical row indicates how many electrons occupy the valence shell.– Examples: – sulfur is #16. It’s in row 3, group 6. Therefore, 3 shells, 6

electrons floating around its valence shell. It needs 2 more to be stable.

– Carbon is #6. It’s in row 2, group 4. It has 2 electrons sitting in the lowest shell, and 4 sitting in its valence shell. It needs 4 to be more stable.

• So how do these unstable systems become stable?

• Chemical Bonds– Let’s keep this simple: Atoms like having their valence shell full of

electrons. – To do this, they can steal an electron from someplace else, or share

one.– If they steal an electron, they will change their electric charge, making it

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

positive.– Atoms that are electrically charged are called ions. (greek, ion, to walk).

• An ion is an atom or group of bonded atoms which have lost or gained one or more electrons, making them negatively or positively charged.

– What happens when negative and positive get together?– They attract.

• This kind of bond is therefore called an “ionic” bond.– This is the sort of bond found in salt.– halogens form ionic bonds. Halogen = “salt maker”

Find animation on CD?

– 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.

• Shape of molecules – to summarize: atoms are most stable when their

valence shell is filled with electrons.– they can fill this shell by either stealing or sharing.– Elements differ from each other by having different

amounts of valence electrons.• Hydrogen has 1• Oxygen has 6• Carbon has 4• Therefore, hydrogen needs 1 more electron. Oxygen needs

2 (8-6); carbon needs 4 (8-4 = 4).

• Why are atoms shaped the way they are?– Lowest possible energy conformation.– The same reason a ball rolls down a hill and

stays there.

• Models: ball & stick vs. space-filling

• Define: Electronegativity

• 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…

• The shape of a molecule depends upon the electron configuration of the system.– Show some pictures

• 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

• Covalent bonds (more complex version)– 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.• 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.

• Water– One of the most fascinating compounds known.– Explain 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– Acid solutions– Basic solutions– pH scale

Trends in electronegativity

O>N>C