The Nature of Molecules

Structure of the Atoms

All matter is composed of atoms. Protons (+) and neutrons (neutral) are found on the atoms nucleus, while electrons (-) circle the nucleus.  Atomic number - number of protons  Atoms with the same atomic number belong to the same element, and thus have the same inherent properties.

Elementary chemistry
The particles which make up atoms are protons, neutrons, and electrons.

Particle

mass(a.m.u.) 0.00055 electrons protons neutrons 1.00728 1.00866

charge -1e +1e 0

e.g. Boron Atomic number: the number of protons in the nucleus; it also equals the number of electrons Mass number: The number of protons + the number of neutrons

Atoms

Atomic Weight

Mass refers to the amount of a substance. Weight refers to the force exerted on a substance by gravity. Atomic mass of an atom refers to the sum of the masses of protons and neutrons. measured in Daltons

Isotopes

Isotopes - Atoms of an element that possess a different number of neutrons. Radioactive isotopes - Spontaneously decay into elements of lower atomic number.  emit energy and/or subatomic particles  Half-life refers to the amount of time necessary to decay half the atoms of a given sample.
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Electrons = Protons Neutrons

Isotope, one of two or more species of atom having the same atomic number, hence constituting the same element, but differing in mass number. As atomic number is equivalent to the number of protons in the nucleus, and mass number is the sum total of the protons plus the neutrons in the nucleus, isotopes of the same element differ from one another only in the number of neutrons in their nuclei
Microsoft Encarta 2007. 1993-2006 Microsoft Corporation. All rights reserved.

Electrons

Atoms with the same number of protons as electrons are electrically neutral. Ions - Atoms in which the number of protons and electrons differ.  Cation - Contains more protons than electrons, and carries a positive charge.  Anion - Contains fewer protons than electrons, and carries a negative charge.

Electrons and Atomic Behavior

Orbital refers to the area around a nucleus where an electron is most likely found. Chemical behavior of an atom is determined by the number and arrangement of its orbitals.  Electrons are attracted to the positively charged nucleus, thus it takes energy to hold electrons in place.  potential energy of position
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Atomic Energy Levels

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Electrons and Atomic Behavior

During some chemical reactions, electrons are transferred between atoms, while still retaining their energy of position. Oxidation - loss of an electron Reduction - gain of an electron

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Kinds of Atoms

Ninety-two naturally occurring elements Periodic table arranged by grouping atoms based on valence electrons (electrons in the outer energy levels).  Octet rule  Inert atoms have outer level filled.  Reactive atoms do not have outer level filled.

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Periodic Table of the Elements

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Chemical Bonds

A molecule refers to a group of atoms held together by energy in a stable association. Compound is composed of two or more different types of atoms.  Atoms in a molecule are joined by chemical bonds.

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Chemical Bonds

Ionic bonds are formed because ions of opposite charge attract one another. table salt Covalent bonds are formed when two or more atoms share pairs of valence electrons. Strength depends on number of shared electrons.

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Ionic Bonding: a process in which electrons are transferred from one atom to another Second shell Outermost shell

Innermost shell Sodium atom (Na)

Chlorine atom (Cl) electrons protons neutrons

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Ionic Bonding: a process in which electrons are transferred from one atom to another

Sodium cation (Na+)

Valency: number of electrons lost or gained

Chlorine anion (Cl-) electrons protons neutrons

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CARBON
The important chemical properties of carbon are  It is a relatively small atom with a low mass  It has the abilityto form four strong, stable covalent bonds,  It has the ability to form carbon-carbon bonds, thus  Building up large carbon skeletons with ring and/or chain structure,  It has the ability to form multiple covalent bonds with other carbon atoms, oxygen and nitrogen

This unique combination of features is responsible for the enormous variety of organic molecules.  Size, determined by the number of carbon atoms in the skeleton,  Chemistry, determined by the elements and chemical groups attached to the carbon atoms, and how saturated the carbon skeleton is,  Shape, determined by geometry, that is angles of the bonds.

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Alkanes names: The naming sytem used is a rational one. With the exception of the first four compounds methane, ethane, propane, and butane whose names have historical roots, the alkanes are named after Greek numbers according to how many carbons are present. The suffix ane is added to the end of each name to indicate that the molecule identified is an alkane.
Alkane Names
Number of carbon (n)
1 2 3 4 5 6 7 8 9 10 11 12 13

Name

Formula (CnH2n+2)
CH4 C2H6 C3H8 C4H10 C5H12 C6H14 C7H16 C8H18 C9H20 C10H22 C11H24 C12H26 C13H28

Number of carbon (n)

14 15 20 21 22 23 24 30 31 32 40 50 60

Name

Formula (CnH2n+2)
C14H30 C15H32 C20H42 C21H44 C22H46 C23H48 C24H50 C30H62 C31H64 C32H66 C40H82 C50H102 C60H122

Methane Ethane Propane Butane Pentane Hexane Heptane Octane Nonane Decane Undecane Dodecane Tridecane

Tetradecane Pentadecane Eicosane Heneicosane Docosane Tricosane Pentacosane Tricontane Hentricontane Dotricontane Tetracontane Pentacontane Hexacontane

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20

Covalent bonding: electrons are shared +

2 + Water (H2O)
Element atomic # mass # Carbon 6 12 Oxygen 8 16 Hydrogen 1 1

Methane (CH4)

In a polar covalent bond, atoms share electrons unequally, hence there is a slight difference in charge between the two poles of the bond. eg. water

In a nonpolar covalent bond, atoms share electrons equally, hence there is no difference in charge between the two poles of the bond. eg. methane
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Covalent bonding: electrons are shared

H H

c
H

Methane (CH4)

Electrons fro car on Electrons fro Hydrogen proton e tron

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Covalent bonding: electrons are shared

Ethane (C2H6)

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Chemical Reactions

A chemical reaction occurs during the formation or breaking of chemical bonds. Reactants refer to original molecules. Products refer to resultant molecules. Chemical reactions can be influenced by: temperature concentration of reactants and products catalysts
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IUPAC Rules for Naming Hydrocarbons

1. 2.

3.

4.

Choose the correct ending: -ane, -ene, or -yne Determine the longest carbon chain. Where a double or triple bond is present, choose the longest chain that includes this bond. If there is a cyclic structure present, the longest chain starts and stops within the cyclic structure. Assign numbers to each C of the parent chain. For alkenes and alkynes the first carbon of the multiple bond should have the smallest number. For alkanes the first branch (or first point of difference) should have the lowest #. Carbons in a multiple bond must be numbered consecutively. Attach a prefix that corresponds to the number of carbons in the parent chain. Add cyclo- to the 25 prefix if it is a cyclic structure.

Naming Side Chains

Example: use the rules on this handout to name the following structure
CH2 CH3 CH2 C CH2 CH3 CH2 C CH3 CH3

Rule 1: choose the correct ending ene

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Naming Side Chains

CH2 CH3 CH2 C

CH2 CH3 CH2 C CH3 CH3

Rule 2: determine the longest carbon chain ene

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Naming Side Chains

CH2 CH3 CH2 C

CH2 CH3 CH2 C CH3 CH3

Rule 3: Assign numbers to each carbon ene

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Naming Side Chains

CH2
1

CH2 CH3
5 6

CH3 CH2 C
2

CH2 C
3 4

CH3

CH3

Rule 3: Assign numbers to each carbon ene

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Naming Side Chains

CH2
1

CH2 CH3
5 6

CH3 CH2 C
2

CH2 C
3 4

CH3

CH3

Rule 4: attach prefix (according to # of Cs) 1-hexene ene

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Naming Side Chains

CH2

CH2 CH3
5 6

ethyl

1 2 3

CH3 CH2 C

CH2 C
4

CH3

methyl methyl

CH3

Rule 5: Determine name for side chains 1-hexene

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Naming Side Chains

CH2

CH2 CH3
5 6

ethyl

1 2 3

CH3 CH2 C

CH2 C
4

CH3

methyl methyl

CH3

Rule 6: attach name of branches alphabetically

2-ethyl-4-methyl-4-methyl-1-hexene 1-hexene
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Naming Side Chains

CH2

CH2 CH3
5 6

ethyl

1 2 3

CH3 CH2 C

CH2 C
4

CH3

methyl methyl

CH3

Rule 7,8: group similar branches 2-ethyl-4-methyl-4-methyl-1-hexene 1-hexene

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Naming Side Chains

CH2

CH2 CH3
5 6

ethyl

1 2 3

CH3 CH2 C

CH2 C
4

CH3

methyl methyl

CH3

Rule 7,8: group similar branches 2-ethyl-4,4-dimethyl-1-hexene Page 547-8 Questions 3, 5

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CH3 CH
propene

CH2
CH3

CH3 CH CH

CH3 C CH3

CH3 CH

CH CH3
2,4-dimethyl-2-pentene

2-butene

CH

CH2 CH3
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1-butyne

CH3 CH2 CH C CH3 CH2 CH3 CH3

CH3 C CH2 CH CH2

CH3

a) 3,3-dimethyl-1-pentene
CH3 CH3 C C CH CH

b) same
CH3 CH2

CH2 CH3

c) 5-ethyl-4-methyl-2-heptyne

For more lessons, visit 36 www.chalkbored.com

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Water (H2O)
Water has distinctive properties that make it essential for life, water affects life at all levels, from the biological to the ecological. The properties of water profoundly influence the organization and behaviour of substances that make up cells and the cellular environment.

+ 2 -

+
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Fig. 2.11a

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Fig. 2.11b

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Fig. 2.11c

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Hydrogen Bonding

In a water molecule, both the oxygen and hydrogen atoms attract the shared electrons in the covalent bond (electronegativity). Oxygen atom is more electronegative than the hydrogen atoms.  distinct ends with partial charge (polar)  hydrogen bonds

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Water Chemistry

Water consists of an oxygen atom bound to two hydrogen atoms by two single covalent bonds. stable atom with no electrical charge  most outstanding property is its ability to form weak chemical associations

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Polarity is an uneven charge distribution within a molecule. In water, one part, or pole, is slightly positive and the other slightly negative. This is know as dipole. + + 2 + + Hydrogen bond 2 -

Two water molecules attracted by each other by hydrogen bonding

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Covalent bonding: electrons are shared +

2 + Water (H2O) Methane (CH4)

Element atomic # mass # Carbon 6 12 Oxygen 8 16 Hydrogen 1 1 In a polar covalent bond, In a nonpolar covalent bond, atoms share electrons unequally, atoms share electrons equally, hence there is a slight difference hence there is no difference in in charge between the two poles charge between the two poles of of the bond. eg. water 45 the bond. eg. methane

Water Chemistry

Water clings to polar molecules. Cohesion refers to attraction to other water molecules.  responsible for surface tension Adhesion refers to attraction to other substances.  Water is adhesive to any substance with which it can form hydrogen bonds.

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Surface Tension

A number of specialize organisms, the pleuston, are adapted to the interface habitat between air and water. The microscopic component of the pleuston are collectively termed neuston.

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Surface Tension

The quasi-polymeric bonding properties of water are disturbed at the interface with air. At the interface plane, the molecular attraction are unbalanced and exert an inward adhesion to the liguid phase. The surface tenion of water is reduced markedly by the addition of dissolved organic compounds.
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High heat capacity

The heat capacity of water is the amount of heat required to raise the temperature of 1 Kg of water by 1 C. Water has a high water heat capacity. This means that a large increase in heat energy results in a relatively small rise in temperature. This is because much of the energy is used in breaking the hydrogen bonds which holds the water molecules together. Biological processes operate over a small temperature range. Water provides a constant external environment for many cells and organisms

Water

Heat

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High heat of vaporization

Hydrogen bonds attract molecules of liquid water to one another and make it difficult for the molecules to escape as vapour: thus a relatively high energy input is necessary to vaporize water and water has a much higher boiling poin than other molecules of the same size.

Water

Heat
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High heat of fusion

Latent heat of fusion is a measure of the heat energy required to melt a solid, in this case ice. With a high heat capacity, water requires relatively large amounts of heat energy to thaw it. Conversely, liquid water must lose a relatively large amount of heat energy to freeze.

Contents of cells and their environment are therefore less likely to freeze. Ice crystal are particularly damaging if they develop inside cells.

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Unstable hydrogen bonds

Water molecules

Stable hydrogen bonds

Liquid water

Ice

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Water is an excellent solvent for polar substances. A solvent is any fluid in which one or more substance can be disolved.

Cl
-

Na
+

This include ionic substance like salts, which contain charged particles (ions), and some nonionic substances like sugars that contain polar groups (slighly charged) such as the slightly negative highdroxyl group (-OH).

On contact with water, the ions and the polar groups are surrounded by water molecules which separates (dissociates) the ions or molecules from each other. 53

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Hydration shells Cl Na+ Cl

Na+ Cl Na+ Cl Na+

Salt crystal

Water molecules
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Water as a Solvent

Water is an effective solvent as it can form hydrogen bonds. Water clings to polar molecules causing them to be soluble in water.  Hydrophilic - attracted to water Water tends to exclude nonpolar molecules.  Hydrophobic - repelled by water

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Many lipids have hydrophobic tails (which repel water/water hating) attached to hydrophilic head (which being polar, attracts water). In the presence of water, these lipid molecules tend to cluster, with all of the hydrophilic heads facing the water and all the hydrophobic tails packed in a sheetlike array that excludes water. Imagine two such sheets arranged into a sphere that has water on the inside and out. This lipid bilayer arrangement is the framework for all cell membranes.
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pH

pH scale expresses hydrogen ion (H+) concentration in a solution. logarithmic scale ranging from 0-14  neutral = 7

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pH

Acids dissociate in water to increase the concentration of H+. pH values lower than 7 Bases combine with H+ ions when dissolved in water, thus decreasing H+ concentration. pH values above 7 Buffers act as a reservoir for hydrogen ions, donating or removing them from solution as necessary.
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H2O Water

CO2 Carbon dioxide

H2CO3 Carbonic acid

HCO3 H+ Bicarbonate Hydrogen ion ion +

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pH

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