Small Molecules: Structure and Behavior

Atoms: The Constituents of Matter Matter is composed of atoms with positively charged nuclei of protons and neutrons surrounded by negatively charged electrons.

Classification of Elements

Main Elements Found in Living Organisms

Isotopes of an element differ in numbers of neutrons Some isotopes are unstable and are termed radioactive. These radioisotopes are useful for many purposes.

Electrons are distributed in orbitals Each orbital contains a max of 2 electrons

Orbital Shell Representations

Bonding Occurs Due to Electrons

Ionic bonds Complete gain/loss of electron to form a charged species Oppositely charged ions then interact electrostatically

Covalent Bonds 2 nuclei share one or more pairs of electrons. electrons in orbitals whose spatial orientations give molecules shapes

Covalent Bonds Combining electrons in all the orbitals into a new set of orbitals often occurs. sp3 bonds of carbon are the combination of the 2s orbital and the 3, 2p orbitals to form 4 sp3 orbitals which each have a single electron that is shared with the single electron in H’s 1s orbital

Table 2.2 Table 2.2

Covalent Bonds Nonpolar covalent bonds Polar covalent bonds electronegativities of two atoms are ~ equal. electronegativity difference <1 Polar covalent bonds Between atoms with strong electronegativity & atoms with weaker electronegativity electronegativity difference >1

Polar Covalent Bonds figure 02-08.jpg

Polar & Non-polar Molecules Electronegativity difference: O 3.5, H 2.1 3.5-2.1 = 1.4 Electronegativity difference: C 2.5, H 2.1 2.5-2.1 = 0.4

Polarity of H2O Dissolves Ionic Compounds

Hydrogen Bonds form btwn a d+ H atom in one molc & a d– N or O atom in another molc or region of same molc. H donated by -O-H -N-H H accepted by O= -O- -O-H :N- =N- : : : : : : :

Hydrogen bonds figure 02-09.jpg

H-Bonds in H2O

Van der Waals Forces Weak molecular orbital interactions between non-polar molecules

Chemical Reactions: Substances change their atomic compositions and properties. Energy is either released or added. Matter and energy are not created or destroyed, but change form.

Chemical Reactions

Ionization of H2O – Basis of pH

Acids, Bases, and the pH Scale Substances that donate H ions Bases Substances that accept H ions. The pH of a solution is a result of its [H+] pH= -log[H+] pH < 7 = acidic pH > 7 = basic

pH and Buffers Buffers Systems of weak acids and bases that resist changes in pH Common buffering compounds Phosphate Carbonate Acetate Citrate

The Properties of Molecules Molecules vary in size, shape, reactivity, solubility, and other chemical properties. Functional groups make up part of a larger molecule and have particular chemical properties. The consistent chemical behavior of functional groups helps us understand the properties of the molecules that contain them.