Chemistry

Atoms

Atom is greek for uncuttable.

Atoms are made of protons, neutrons and electrons.

The element is defined by the number of protons. e.g. carbon has 6 protons, and 6 is the atomic number of carbon.

12C (Carbon 12) has 6 protons and 6 neutrons in the nucleus. The mass number, or atomic mass units, is 12.

14C (Carbon 14) has 6 protons and 8 neutrons in the nucleus.

Electrons are bounce around the nucleus in an orbital.

Periodic table also has atomic weight. Carbon atomic weight is 12.0107, the weighted average of all isotopes. Isotopes have a different number of neutrons, but protons remain the same.

Elements and atoms at Khan Academy.

Intro to the atom at Khan Academy.

Orbitals

There is a probability density function for the location of the electron around the nucleus. The path is NOT as well defined as a comet or planet's orbit.

Orbitals can hold 2 electrons, any more electrons will go to the next energy state, which is further from the nucleus. Electrons will fill the orbitals in order from low energy state to high energy state. Each shell can fit 2 electrons.

1s is the first energy shell or orbital. It is the lowest energy state an electron can be in.

2s is the next shell, it is around the 1s orbital.

2pz, 2py, 2px

A period is a row in the periodic table, corresponds to the number of electrons in the orbitals.

Electron configuration describes the orbitals the electrons are in.

H is 1s1

He is 1s2

C is 1s22s22p2

N is 1s22s22p3

O is 1s22s22p4

Si (14) is 1s22s22p63s23p2

Fe (26) is 1s22s22p63s23p64s23d6

Xe (54) is 1s22s22p63s23p64s23d104p65s24d105p6

Nd (60) is 1s22s22p63s23p64s23d104p65s24d105p66s24f4

d orbitals begin at 3, and are filled after the 4s shell is filled, but before the 4p shell.

f orbitals begin at 4, and are filled after the 6s shell is filled.

The highest energy state is filled last, but may not be in the highest shell.

You can use a table with diagonalsto help remember the order.

Orbitals and more at Khan Academy.

d and f configuration at Khan Academy.

Valence Electrons

Valence electrons are usually furthest out with the highest energy.

Lewis notation uses dots to represent electrons.

Na (11) ends with 3s1, so it has 1 valence electron that is in a shell that hasn't been stabilised.

He 1s2 has 2 valence electrons.

C electron configuration is 1s22s22p2 has a total of 4 electrons in shell 2. So it has 4 dots in the Lewis notation.

Valence electrons can be shared, e.g. CH4 methane. So now each H has 2 electrons, filling the 1st shell, and C now has 8 electrons, filling the 2nd shell.

Valence electrons at Khan Academy.

Dot Structure example at Khan Academy.

The octet rule states that a stable valence shell has 8 electrons.

Formal Charge

Each atom can have a different formal charge. It is a whole number, and depends on how many valence electrons it usually has, and how many bonds it has. This can be used to determine whether a double bond should be used.

Formal charge at Khan Academy.

Resonance structures show different variations of the same molecule, e.g. the double bond moving between atoms. This shows electrons moving around, or being delocalised.

Resonance structures at Khan Academy.

Atomic Radius

As you go across a period, the more electrons an atom has in their outermost shell, the more Coulomb attractions towards the centre, so their electrons are closer to the centre, so the radius is smaller. He (2) is larger than H(1).

Bonds

Atoms stick together.

bonds at Khan Academy.

Ionic bonds

Atoms may want to lose or gain an electron to complete their outer shell.

Take Na Cl, Na has 1 valence electron, Cl has 7 valence electron.

Na loses the valence electron, so now it has a positive charge. Na+. It is now a cation, a positive ion.

Cl would like to gain an electron, so now it has a negative charge. Cl-. An anion.

So now the 2 ions are attracted due to Coulomb's law. This is an ionic bond.

Covalent bonds

O2

Oxygen has 6 valence electrons. Ideally they want 2 more electrons, so 2 Oyxgen atoms are 2 electrons between them, and both now have 8 electrons in their outer shell. This a covalent bond.

H2O is covalent, but it is polar covalent bond, as O is more electronegative than H. Electrons will spend more time around O than H.

Metallic Bonds

Metals are very good at sharing electrons. An electron pool is shared between all the atoms. They come conductors or electricity.

Electronegativity

Electronegativity is the power of an atom in a molecule to attract electrons to itself. (from Linux Pauling, The Nature of the Chemical Bond). In the case of a covalently bonded H2O molecule, oxygen is more electronegative than hydrogen, so electrons spend more time around the oxygen atom. You can indicate this by writing δ- near the O atom, and δ+ next to each of the two hydrogen atoms. This shows that the molecule is polar, and the bond is a polar covalent bond.

On the period table, as you move towards the right, atoms become more electronegative.

As you move down the periodic table, in the same vertical group, atoms become less electronegative.

The Pauling Scale gives values to each atom in the periodic table. Fluorine is the most powerful.

For each bond, consider the difference between electronegativity values between the two atoms. If it is greater than 0.5 then it is a polar covalent bond, if it less than 0.5 then it is non-polar as the electronegativity difference is weak.

Electronegativeity at Khan Academy.

Electronegativity and bonding at Khan Academy.

Hydride

An hydrogen with 2 electrons, H-.

Functional Group

Group of atom or bonds that have predictable chemical behaviour.

Functional groups I at Khan Academy.

Phosphoryl group

A phosphoryl group is a phosphate (P) attached to three oxygens (O).

Halogen

Group 7 on the periodic table. Halogen elements include fluorine (F), chlorine (Cl), Br, I and At.

Chemical reactions

aq subscript denotes aqueous molecules.

g subscript denotes gaseous form.

If the reaction is one-way, use a one-way arrow. e.g. HCl -> H+ + Cl-

Otherwise use equilibrium arrow ⇌

Reactants

Reactants undergo changes in a chemical reaction, they are on the left of the equation.

Products

Products are made from the reactants.

Mole

Avogadro's constant is 6.02 x 10^23

Moles can be used to define how many molecules of a substance there are.

The unit symbol is mol.

Molarity

Molar concentration, or molarity is the number of moles of something in 1 litre of solution.

The units are mol/L.

If the concentration is 1 mol/L, it can be written as 1 molar, or 1M.

Molality

Molality is moles of something in 1 kilogram of solvent.

Concentrations of Solutions.

Protonation

The addition of a H+ (proton) to a molecule.

Hydronium

Water with an extra H+, or proton. It is produced by the protonation of water.

H3O+

Stereochemistry

Stereochemistry is a branch of chemistry that studies arrangement of atoms that forms their structure. It is 3D chemistry.

Chirality

chiral is greek of hand.

A molecule is chiral if it can't be superimposed on its mirror image.

Chiral carbon

Chiral carbon are carbons bonded to 4 different groups, these are the chiral centres of the molecule.

Introduction to chirality at Khan Academy.

Isomers

In Greek, iso means same, meros means parts.

Structural isomers, or constitutional isomers of a molecule are molecules where the molecular formula, e.g. C5H12, is the same, but their bonds are different.

Stereoisomer

Bond connections are the same, but some elements are oriented differently. e.g. forward vs. back

Enantiomer

A type of stereoisomer where where a mirror image matches the original molecule. In carbohydrates each chiral carbon will be flipped.

Diasteromer

Type of stereoisomer that is not an enatiomer.

Epimer

Epimers differ by just 1 chiral carbon. The other chiral carbons are the same.

Carbohydrates - Epimers, common names at Khan Academy.

Meso compound

Has 2 or more chiral carbons, but is achiral.

Stereoisomers, Enantiomers, Diastereomers, Constitutional Isomers and Meso Compounds at Khan Academy.

Carbohydrates

-ose is a suffix for sugar.

Instead of a chain, some carbohydrates can form cyclic structures instead.

Pyranose is a 6 carbon ring. In a Haworth diagram it is a hexagon, but in reality it is more of a chair shape.

Furanose is a 5 carbon ring.

One of the carbons is designated as anomeric.. it is the one that was double bonded to O. It is also C1.

The hydroxyl (OH) group on the anomeric C is either above (β) or below (α).

In water, the bond between the anomeric Carbon and Oxygen will reopen, and C1 and C2 bond may rotate. WHen it closes again the α or β product may change. This is mutarotation. There is a equilibrium ratio of these. These 2 forms are anomers, a special type of epimer

If the chemical name is something like α-D-galactose then it will be in cyclic formation.

Carbohydrates - Cyclic structures and anomers at Khan Academy.

Sugars at rpi.edu

Galactose

Galactose is a C-4 (4th carbon is flipped) epimer of glucose.

Ligate

Ligate means join two fragments together. The fragments may be nucleotides or peptides.

Dalton

A carbon 12 is 12 Da. It is a measure of mass.

Deuterium

Deuterium is heavy hydrogen, an isotope of hydrogen. It contains a neutron. Usually hydrogen doesn't have a neutron.