Chemistry for Biologists Part 1

Neutrons

no charge, in nucleus

Protons

Positive charge, in nucleus

Electrons

Negative charge, outside nucleus

Alkali Metals

-Group one

-soft and silvery

-melt at low temp

-produce H2 with water

-single electron

Alkaline Earth Metals

-Group 2

-soft

-in nature as oxides

-2 electrons

Halogens

-Group 17

-very reactive

-F and C are gases

-Br and I are solids

Noble Gases

-Group 18

-colorless, odorless gas

-full outer shell

-unreactive

-low temp crygenics

-absorb and emit electromagnetic radiation

Transition Metals

-Groups 3-12

-Highly colored compound

Lanthanides and Actinides

-Heavy metals

-can form compound in several oxidation states

-actinides are radioactive in nature

Atomic Radii

Size of the atom

Increase left and down table

Ionic Radius

Distance between nucleus and outermost ion

Increase left and down table

Electronegativity

Tendency for an atom to attract electrons toward itself

Increase right and up table

Ionization Energy

Minimum energy to lose outer most ion

Increase right and up table

Octet Rule

-Elements try to attain number of electrons as closest noble gas

-Want to have 8 in outer shell

-Will gain or lose electrons

Electron Configuration

Distance of electrons within the levels

-conttrols chem and physical properties

-N

-I

-M1

-M2

-Principle Energy

-subshell

-orbital

-spin

How many electrons and sub shells?

-n=1

-n=2

-n=8

-holds 8 electrons, two subshells

-holds 18 electrons, three sub shells

How many orbitals and shape?

-s

-p

-d

-f

-3 orbitals, dumbbell

-5 orbitals, clover

-7 orbitals

Hund's Rule

orbitals of equal energy are each occupied by one electron before any orbital is occupied by a second electron, and all electrons in singly occupied orbitals must have the same spin

Ionic Bond

attraction of oppositely charged ions

large difference in electronegativity

Covalent Bond

sharing electrons of uncharged atoms

small difference in electronegativity

Lewis Structure

Diagram of an element showing its valence electrons as dots

Discrete Ions

Hydroxide, Carbonate, Bicarbonate, Sulfate, Sulfite, Nitrate, Nitrite

VSEPR

Valence shell electron pair repulsion theory

Lone Pairs

Treated like bonding pairs and repelled by valence electrons; slightly more repulsive

Order or repulsion

Lone pair-lone pair > lone pair-bond pair > bond pair-bond pair

What direction is the atom?

-line

-dashed

-filled

-in the plane of the paper
-backward into the page
-forward from the page

Mole

the amount of a substance that contains as many units there atoms in an element

Avogadro's number

6.022 x 10^23

State symbols

-s
-l
-g
-aq

-solid
-liquid
-gas
-aqueous

Solubility of ionic substances

-solubility in water varies
-depends on relative attraction of ions for each other and for water molecules

Solubility of non ionic substances

-water dissolves non-ionic substances

-polar substances are only soluble in polar solutions

Concentration

A measurement of how much solute exists within a certain volume of solvent

Molarity (M) = mol/L

Theoretical and Percentage Yields

-amt of product when limiting reagent is completely consumed

-actual yield of a product in % of theoretical (actual/theoretical x 100)

Electrolyte

-strong
-weak
-non

a substance that dissolves to give a solution that contains ion
-mainly ions
-mainly molecules
-doesn't conduct

Oxidation Rules

1. oxidation # of an ion equal the charge on that ion
2 oxidation # of an uncharged element is 0
3. an increase in oxidation # indicates oxidation
4. a decrease in oxidation # indicates reduction
5. -oxidation # of H = -1 in compounds with metals, +1 in compounds with nonmetals
-oxidation # of O = always -2, except peroxide = -1
-oxidation # of F = always -1
-oxidation # of all other halogens = -1 except if bound to oxygen or halogen w/ large atomic weight
6. oxidation # of a compound w/ several atoms is = sum of oxidation # of all atoms

Half Reactions

split reactions into reduction and oxidation to see electron transfer

step 1: reduce ions
step 2: balance half equation; add electrons, water, or H ions
step 3: combine half equations

Isotopes

atoms with the same number of protons but different number of neutrons

Radioactive Decay

1. alpha
2. beta
3. y-emission
4. position emission
5. electron capture

unstable nucleus emits radiation, forms another nucleus
1. helium nucleus ejected
2. neutron converted to proton
3. nucleons reorganize into more stable arrangement, high energy photons released
4. unstable nuclides which are neutron deficient, proton -> neutron + high energy position
5. nucleus captures electron from electron cloud

Radioactive Half-life

Time to reach half of initial value

Carbon Properties

1. can form 4 strong, stable bonds to a lot of elements
2. can form stable double bonds and triple bonds
3. suitable electronegativity for polar bonds
4. abundant

Hybridization

mixing of atomic orbitals to produce equivalent # of hybrid orbitals - energetically favorable

Sigma Bond

single bond between 2 atoms

Hydrocarbon

most simple organic molecule, contains C & H, acyclic or cyclic

Alkanes

Saturated hydrocarbons with one covalent bond between carbon atoms and each have sp3 hybrid orbitals - CnH2(n+2)

Alkenes

unsaturated hydrocarbons with greater than or = 1 double or triple bonds between carbon atoms - CnH2n

Pi-bond

contains electrons for chem reeactios - weaker and broken to two sigma bonds

Naming

1. Parent
2. Suffix
3. Prefix
4. Locants

1. describes main carbon section
2. identifies the principle functional group
3. identifies the substituents on the main chain or ring
4. shows where the substituents are located

Naming Rules

1. identify longest carbon chain containing the most functional groups
2. identify the most important functional group and add suffix
3. name and substituents, if >1 add number (di, triple, tetra)
4. specify substituents location, hyphen to separate # and letters, commas to operate # and #

Nucleophiles

Nucleus loving, electron rich reagent that forms a bond by donating an electron pair -becomes a neg charged anion

Electrophiles

Electron loving, electron deficient reagent that forms a bond by accepting an electron pair - becomes pos charged cation

Organic Reaction Mechanism

Step-by-step account of how a reaction of organic compounds take place
- use curly arrow
1. creating bonds
2. shared pair moves to adjacent binding location
3. breaking bonds