Elements & Compounds

Atoms (Elements)

Molecules (Compounds)

Cells

Elements & Compounds

Nucleus

Electrons Cloud of negative charge (2 electrons)

Fig. 2.5: Simplified model of a Helium (He) Atom

He 4.002602

2

Helium Mass Number (~atomic mass)

= number of Neutrons + Protons = 4 for Helium

Atomic number = number of protons

Atomic Mass

The Periodic Table of the Elements

Properties of Elements Depends Upon Atomic Structure

Atoms of different elements differ in their number of subatomic particles:

H 1 1 C 6

12 N 14 7

O 16 8 Na 11

23

C 6 12 C 6

13 Stable isotopes

C 6 14

Unstable (radioactive)

P 15 31

First shell

Second shell

Third shell

Hydrogen 1H

Lithium 3Li

Sodium 11Na

Beryllium 4Be

Magnesium 12Mg

Boron 5B

Aluminum 13Al

Carbon 6C

Silicon 14Si

Nitrogen 7N

Phosphorus 15P

Oxygen 8O

Sulfur 16S

Fluorine 9F

Chlorine 17Cl

Neon 10Ne

Argon 18Ar

Helium 2He

2 He

4.00 Mass number

Atomic number

Element symbol Electron distribution diagram

Fig. 2.9: Electrons are distributed in shells of orbitals. Each orbital contains a maximum of two electrons.

Chemical behavior of an atom depends mostly on number of electrons in outermost shell called Valence Electrons

Fig. 2.8: Energy Levels of Electrons / Electron Shells

Electrons in an atom vary in the amount of potential energy they possess (fixed, discrete amounts)

Different discrete energy levels correlate with average distance of electron from nucleus (electron shells)

Lower energy

Higher energy

(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons

We Are Carbon-Based Lifeforms

Trace elements (< 0.01%): B, Cr, Co, Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V, Zn

~4 %: Ca, P, K, S, Na, Cl, Mg

Composition of other organisms on Earth is similar

~96 % of the Human Body is: Oxygen (O) Carbon (C)

Nitrogen (N) Hydrogen (H)

Fig. 2.10: Electrons are arranged in orbitals that have characteristic shapes and energies

Neon, with two filled Shells (10 electrons)

First shell

Second shell

First shell Second shell

1s orbital 2s orbital Three 2p orbitals

(a) Electron distribution diagram

(b) Separate electron orbitals

(c) Superimposed electron orbitals

1s, 2s, and 2p orbitals

x y

z

Fig. 2.11: Chemical Bonds Link Atoms Together 1H1

1H1

H2

Bonding properties of the most common elements in biological molecules

H: Atomic No. 1 1 electron: 1s1

1st shell needs 1 electron Forms 1 covalent bond

C: Atomic No. 6 6 electrons: 1s2 2s2 2px1 2py

1 2pz0

2nd shell needs 4 electrons Forms 4 covalent bonds

N: Atomic No. 7 7 electrons: 1s2 2s2 2px1 2py

1 2pz1

2nd shell needs 3 electrons Forms 3 covalent bonds

O: Atomic No. 8 8 electrons: 1s2 2s2 2px2 2py

1 2pz1

2nd shell needs 2 electrons Forms 2 covalent bonds

Fig. 2.17a: Hybrid Atomic Orbitals

s orbital z

x

y

Three p orbitals

Hybridization of orbitals Tetrahedron

(a)

Space-Filling Model

Ball-and-Stick Model

Hybrid-Orbital Model (with ball-and-stick

model superimposed) Unbonded Electron pair

Water (H2O)

Methane (CH4)

(b) Molecular-shape models

Fig. 2.17b: Molecular Shape Models

LE 2-11 Fig. 2.12: Covalent Bonding in Four Molecules

(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

Name and Molecular Formula

Electron Distribution

Diagram

Lewis Dot Structure and

Structural Formula

Space- Filling Model

(d) Methane (CH4)

• The two C atoms in Ethene form a second or double bond between themselves using their third unhybridized 2p orbitals.

• The second bond is called a π bond and prevents the C atoms from rotating around the bonds connecting them. • Note: the π bond does not place electron density between the atoms.

π bond

Element Symbol Electronegativity

Oxygen O 3.5

Chlorine Cl 3.1

Nitrogen N 3.0

Carbon C 2.5

Phosphorous P 2.1

Hydrogen H 2.1

Sodium Na 0.9

Potassium K 0.9

Chemical Bonds: Linking Atoms Together

High

High

O H H

δ-

δ+ δ+

Partial negative charge on oxygen

δ-

δ+ Partial positive charge on each hydrogen δ+ H2O

H H

O

Fig. 2.13: Polar Covalent Bonds Are Formed Between Atoms With Unequal Electronegativity

δ-

δ-

δ+ δ+ 104.5°

Fig. 2.17b: sp3 Hybrid Orbitals in Water, H2O

Fig. 3-2

Hydrogen bond

δ – H

δ + H

O —

—

δ + δ +

δ +

δ –

δ –

δ – • Hydrogen Bonds are attractions between the partial negative charge on the Oxygen atoms and the partial positive charges on the Hydrogen Atoms.

• This gives water special properties that we will discuss next time.

LE 2-15

δ–

Water (H2O)

Ammonia (NH3)

δ+

δ+

δ–

δ+

δ+

δ+

Fig. 2.16: Hydrogen Bonds can form between water and other polar molecules.

Hydrogen bond

Na Sodium atom (an uncharged

atom)

Cl Chlorine atom (an uncharged

atom)

Na+ Sodium ion (a cation)

Cl– Chlorine ion (an anion)

Sodium chloride (NaCl)

Fig. 2.14: Ionic Bonds

+ -

Solvation: Water molecules surround ions and neutralize their charge.

Sodium (Na) Chlorine (Cl)

Weak Chemical Bonds: van der Waals Interactions

δ- δ+

δ- δ+ δ- δ+ δ- δ+

δ- δ+ δ- δ+

Weak attraction of atoms due to constant motion of electrons:

High Energy Very Low Energy Low Energy

Weak attraction of atoms due to the constant motion of electrons

Chemical Bonds and Interactions