Chemistry: A Very Short Introduction

Origins, Scope, and Organization

• Chemistry exploits quantum mechanics and thermodynamics from physics.
• Biology is merely an elaboration of chemistry.
• Chemistry can be divided into:
  • Physical Chemistry - At the interface between physics and chemistry.
  • Organic Chemistry - Concerned with compounds of carbon. As a result of its mild and unaggressive character, Carbon is able to form chains and rings of startling complexity., which is exactly what organisms need if they are to be regarded as being alive, and thus the compounds of carbon are the structural and reactive infrastructure of life.
  • Inorganic Chemistry - Covers the rest of the elements (including carbon).
• Also can be divided into:
  • Analytical Chemistry - Breaking down substances to understand what is in them.
  • Biochemistry - Concerned with the structures and reactions that constitute living things.
  • Industrial chemistry - Where chemist meets engineer.

Atoms and Molecules

• An atom contains a nucleus at its center which consists of two types of subatomic particles:
  • Protons - Positively charged. The number of protons in the nucleus is called the atomic number of the element.
  • Neutrons - Electrically neutral. About the same number as protons. Isotopes are different versions of the same element with different numbers of neutrons. Hydrogen has three isotopes:
    • Hydrogen itself - one proton, no neutrons
    • Deuterium - One proton, one neutron
    • Tritium - One proton, two neutrons
• Electrons:
  • Has the same magnitude of electric charge as a proton, but is opposite in sign.
  • Are arranged in layers of clouds around the nucleus with a maximum at each successive layer of 2, 8, 18, 32
  • Electrons are about 2,000 times lighter than protons and so their presence barely affects the mass of an atom.
  • All chemical reactions leave nuclei intact and only impact the electrons
  • The layout of the Periodic Table represents the filling out of the cloud layers of electrons, with one electron present in the layer on the left of the table and the layer completed on the right.
• Atoms are electrically neutral, with the total negative charge of all its electrons matching and cancelling the total positive charge of all the protons in the nucleus.
• Ionic bonding - When an atom gains or loses and electron, the balance of charges is upset and the atom becomes an ion (an electrically charged atom):
  • A cation is an atom that has lost one or more electrons and is now positively charged. For example, Sodium (Na) lies on the left of the Periodic Table, and readily releases its single outermost electron to form a sodium cation.
  • An anion is an atom that has gained one or more electrons and is now negatively charged. Chlorine (Cl) lies on the right of the table, and happily accommodates an additional electron to complete its outer layer and thereby become a chloride anion. The ions clump together, and form sodium chloride, table salt, a solid rigid mass of ions held together by their mutual attraction.
  • Ionic bonding typically results in rigid, brittle solids that melt only at high temperatures. Granite and limestone, and our bones are largely ionic.
• Covalent bonding - Is where electrons are shared:
  • Water is made of a covalent bond. Oxygen has six outermost electrons and can accommodate two electrons to complete its outermost cloud layer and so can link to two Hydrogen atoms
  • All gases are covalent, as are just about all substances that are liquid at room temperature.
• The majority of elements are metals, and metal atoms are bound together by metallic bonding. All metals lie towards the left hand side of the Periodic Tables where the atoms of the elements have only a few electrons in their outermost cloud layers and which are readily lost.

Energy and Entropy

• The first law of thermodynamics asserts that the total energy of the universe is constant and cannot be changed.
• Enthalpy is a name for the energy trapped in a compound and available as heat.
• In exothermic reactions, energy is released as heat and the store of enthalpy decreases. Most reactions (and all combustions) are exothermic, with the starting materials collapsing into the lower-enthalpy products of the reaction and thereby achieving lower enthalpy overall.
• Reactions that absorb heat and increase their store of enthalpy are called endothermic reactions.
• The study of reaction rates is called chemical kinetics. Why aren't all reactions over in a flash? If biological reactions were all instantaneous we would all instantly be goo.
• Catalysts help reactions by providing a different sequence of atom migrations and bond formations - for a reaction, a pathway with a lower activation barrier.
• Enzymes are protein molecules that function as catalysts and control with considerable specificity and effectiveness just about all the chemical reactions going on inside u. Life is the embodiment of catalysis.

Reactions

• All the wonders of the world, both natural and synthetic, are spun from a handful of elements and four ways of manipulating them:
  • Proton Transfer - A proton slips from one molecule to another:
    • An acid is any molecule or ion that contians hydrogen atoms that can release their proton nucleus to another molecule or ion, ie, it is a compound with little control over its nucleus and is apt to lose it. What tickles your tastebud in vinegar or soda are protons.
    • If acids are proton donors, proton acceptors are alkalis (or bases). Alkalis turn fats into soaps. They contain hydroxide ions, OH-, which can attract and keep protons, in the course of which becoming water molecules, H20
    • Ionic substances formed by the reaction of an acid and a base are called salts, after sodium chloride.
    • Many enzyme-controlled biochemical reactions, such as the metabolism of food and respiration are proton transfers (acid-base reactions)
    • Water is both an acid and a base.
  • Electron Transfer - An electron passes from one molecule to another:
    • Oxidation is the loss of electrons.
    • Reduction is the reception of electrons.
    • Oxidation and Reduction always happen together.
    • Redox reactions are involved in both the creation of steel and its breakdown through corrosion, and in batteries.
    • Photosynthesis is a chain of electron transfer reactions, which use the hydrogen atoms of water and the carbon and oxygen atoms of carbon dioxide to construct carbohydrates, including starch and cellulose.
  • Radical Reactions:
    • A radical (or free radical) is a molecule with an odd number of electrons. Most radicals are aggressively reactive and do not survive for long in the wild
    • Flames are environments rich in radicals because the stress of high temperatures rips molecules apart, sundering the electron-pair bonds.
    • Other radicals are involved in the formation of many plastics through polymerization.
  • Lewis Acid-Base Reactions:
    • Transition metals are in the skinny central part of the Periodic Table, such as iron (Fe), chromium (Cr), cobalt (Co) and Nickel (Ni).
    • The ions these elements form, such as Fe2+ and Co3+ are commonly found surrounded by and bonded to six small molecules and ions that have an independent existence (such as H2O, NH3 and CN-), called ligands, with the clusters called complexes.
    • A complex is held together by bonds formed by the sharing of a pair of electrons provided by each ligand, so the metal ion is acting as the Lewis acid and each ligand as the Lewis base
    • Breathing is a Lewis acid-base reaction, as is suffocation by carbon monoxide poisoning.