Chemistry, atoms and molecules

Atoms are the basic units of chemical matter. Each atom consists of a dense central nucleus, containing positively charged protons and uncharged neutrons, surrounded by negatively charged electrons. The number of protons defines the chemical element, and there are about a hundred naturally occurring or synthesised elements, organised by their properties in the periodic table. The arrangement of an atom's electrons largely determines how it bonds and reacts with other atoms.

A molecule is formed when two or more atoms join through chemical bonds. In a covalent bond, atoms share electrons; ionic bonding, by contrast, involves the transfer of electrons and the attraction between resulting charged ions. Molecules range from the simple, such as the two-atom molecules of hydrogen or oxygen and the three-atom molecule of water, to the very large and complex, such as proteins and synthetic polymers. The way atoms are connected, and the three-dimensional shape this produces, govern a substance's physical and chemical behaviour.

Modern understanding of atomic structure rests on orbital theory, which describes electrons not as particles on fixed paths but as occupying regions of space called orbitals, each with a characteristic shape and energy. This model explains why elements in the same column of the periodic table behave alike and why atoms combine in particular ratios. Molecular models, whether physical kits or interactive computer displays, help make these invisible structures and their geometry tangible to learners.

Frequently asked questions

What is the difference between an atom and a molecule?: An atom is the smallest unit of an element, while a molecule is two or more atoms joined by chemical bonds, such as the two hydrogen atoms and one oxygen atom in water.
What determines which element an atom is?: The number of protons in the nucleus defines the element; for example, every atom with six protons is carbon.
What is an orbital?: An orbital is a region around the nucleus where an electron is likely to be found, each with a particular shape and energy level rather than a fixed orbit.

Chemistry:
Acids and bases	Distillation	Inorganic chemistry
Atoms	Electrochemistry	Miscellaneous	Organic chemistry
Biochemistry	Food chemistry	Molecules	Spectroscopy
Crystals	General	Nomenclature	Stoichiometry

Molecules

3-D virtual chemistry library structure in several formats, physical data, history and reactivity of the molecules

Amino acids linear structure formulas of amino acids and molecular models, Alanin, Arginin, Asparagin, Asparaginsäure, Cystein, Glutamin, Glutaminsäure, Glycin, Isoleucin, Leucin leu, Lysin, Methionin, Phenylalanin, Prolin, Serin, Threonin, Tryptophan, Tyrosin, Valin

Animated molecules rotating molecules

Aspirin One of the best known aromatic acetates is acetylsalicylic acid, or aspirin, which is prepared by the esterification of the phenolic hydroxyl group of salicylic acid

Bonding

Chemical bonding

Chemical bonding A chemical bond is a force that causes a group of atoms to behave as a unit

Chemical bonding

Common molecules molecules are the smallest collection of atoms of a compound which retains the properties of that material, structures of a variety of interesting molecules, java demonstrtions

Gas Laws Kinetic Molecular Theory and Gas Laws

Ionic and Covalent Bonding Ionic and Covalent Bonding

Jena Image Library of Biological Molecules 3-D molecular structures, The Amino Acid Repository, Structural Elements: Helix, Beta Strand, Extended Conformation, Cis-peptide Bonds, Nucleic Acid Nomenclature and Structure, Strand Direction and Torsional Angles, The Base Pair Directory, Nucleic Acid Model Conformations, Double Helix / Bending Analysis, Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

Large molecules learn about structures and properties of sugars, lipids, amino acids, and nucleotides, as well as macro molecules including proteins, nucleic acids and polysaccharides, protein, sequence of a polypeptide

Mathmol (Mathematics and molecules). The mathmol Library of molecular structures contains GIF, PDB and 3-D (VRML) files of molecules that are found in most introductory biology and chemistry textbooks (e.g., water and ice, carbon, hydrocarbons, amino acids, nucleotides, lipids, sugars, photosynthetic pigments and drugs), Water module

Molecular chemistry

Molecular expressions photo galleries that explore the fascinating world of optical microscopy

Molecular geometry and chemical bonding theory pdf file

Molecular models Many small organic molecules, complete with indexes: functional group, molecular type, alphabetical, and formula, Molecular Fragments, Short, informative essays using molecular models and illustrating an aspect of chemistry

Molecular models hypermedia based tutorial on chemical bonds, molecular shapes, and molecular models

Molecular models in .pdb format you need chime (a chemical structure visualization plug in for internet explorer and netscape communicator)

Molecular Orbitals Chemical Accounting, Accounting with Orbitals, Heteronuclear Bonding, Hybridization and Molecular Orbitals, Benzene: An Example of Delocalized Pi Bonding, Molecular Orbitals in Larger Molecules

Molecular orbitals the electronic structure of atoms and molecules

Molecular visualization freeware software for looking at macromolecular structure and its relation to function

Molecule of the month page

Molecules and ions a molecule is comprised of two or more chemically bonded atoms, If electrons are lost or gained by a neutral atom, then the result is that a charged particle is formed - called an ion

Molecules in four dimensions you need chime

Molecules of life

Molecules of the month you need chime (a chemical structure visualization plug in for internet explorer and netscape communicator)

Molecules with silly or unusual names

Moles: Mole Concept Mole Concept, pdf file

Moles: Mole Concept the Mole Concept

Moles The Mass Formula, atomic mass formula, Avagadro's constant

Moles: what is a Mole?

Ozone Ozone

Rasmol a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules

Ruimtelijke bouw van moleculen in Dutch

Simple, common, and interesting molecules molecules are the smallest collection of atoms of a compound which retains the properties of that material

Smell Database Diacetyl, Ethyl butyrate, Ethyl methyl ketone, Eucalyptol, Putrescine, Geranial, Citral A, Geraniol, p-Ethylphenol, Caproic acid, Hydrogen cyanide, Hydrogen sulfide, Vanillin, 3-(para-Hydroxyphenyl)-2-butanone, Isoamyl acetate, Eugenol, Isoamyl alcohol, Skatole, ...

Structure of metals

Structure of solids Categories of Solids Based on the Solid Pack, Categories of Solids Based on Bonds that Hold the Solid Together

Water and organic molecules structure of water and organic molecules

Water molecule structure

Water Structure and Science

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