Atoms, molecules, and ions
An atom is the basic unit of chemistry. It consists of a positively charged core (the atomic nucleus) which contains protons and neutrons surrounded by a number of electrons that balance the positive charge in the nucleus. The atom is also the smallest entity that can be envisaged to retain some of the chemical properties of the element, such as electronegativity, ionization potential, preferred oxidation state(s), coordination number, and preferred types of bonds to form (e.g., metallic, ionic, covalent).
A molecule is the smallest indivisible portion of a pure chemical substance that has its unique set of chemical properties, that is, its potential to undergo a certain set of chemical reactions with other substances. Molecules can exist as electrically neutral units unlike ions. Molecules are typically a set of atoms bound together by covalent bonds, such that the structure is electrically neutral and all valence electrons are paired with other electrons either in bonds or in lone pairs.
. One of the main characteristic of a molecule is its geometry, often called its structure. While the structure of diatomic, triatomic or tetra atomic molecules may be trivial, (linear, angular pyramidal etc.) the structure of polyatomic molecules, that are constituted of more than six atoms (of several elements) can be crucial for its chemical nature.
An ion is a charged species, an atom or a molecule, that has lost or gained one or more electrons. Positively charged cations (e.g. sodium cation Na+) and negatively charged anions (e.g. chloride Cl−) can form a crystalline lattice of neutral salts (e.g. sodium chloride NaCl). Examples of polyatomic ions that do not split up during acid-base reactions are hydroxide (OH−) and phosphate (PO43−). Ions in the gaseous phase are often known as plasma.
Atoms sticking together in molecules or crystals are said to be bonded with one another. A chemical bond may be visualized as the multipole balance between the positive charges in the nuclei and the negative charges oscillating about them. More than simple attraction and repulsion, the energies and distributions characterize the availability of an electron to bond to another atom.
A chemical bond can be a covalent bond, an ionic bond, a hydrogen bond or just because of Van der Waals force. Each of these kind of bond is ascribed to some potential. These potentials create the interactions which hold atoms together in molecules or crystals. In many simple compounds, Valence Bond Theory, the Valence Shell Electron Pair Repulsion model (VSEPR), and the concept of oxidation number can be used to explain molecular structure and composition. Similarly, theories from classical physics can be used to predict many ionic structures. With more complicated compounds, such as metal complexes, valence bond theory is less applicable and alternative approaches, such as the molecular orbital theory, are generally used. See diagram on electronic orbitals.
Mole and amount of substance
Mole is a unit to measure amount of substance (also called chemical amount). A mole is the amount of a substance that contains as many elementary entities (atoms, molecules or ions) as there are atoms in 0.012 kilogram (or 12 grams) of carbon-12, where the carbon-12 atoms are unbound, at rest and in their ground state. The number of entities per mole is known as the Avogadro constant, and is determined empirically. The currently accepted value is 6.02214179(30)×1023 mol−1 (2007 CODATA). One way to understand the meaning of the term "mole" is to compare and contrast it to terms such as dozen. Just as one dozen eggs contains 12 individual eggs, one mole contains 6.02214179(30)×1023 atoms, molecules or other particles. The term is used because it is much easier to say, for example, 1 mole of carbon, than it is to say 6.02214179(30)×1023 carbon atoms, and because moles of chemicals represent a scale that is easy to experience.
The amount of substance of a solute per volume of solution is known as amount of substance concentration, or molarity for short. Molarity is the quantity most commonly used to express the concentration of a solution in the chemical laboratory. The most commonly used units for molarity are mol/L (the official SI units are mol/m3).
Chemical substances: elements and compounds
A chemical substance is a kind of matter with a definite composition and set of properties. Strictly speaking, a mixture of compounds, elements or compounds and elements is not a chemical substance, but it may be called a chemical. Most of the substances we encounter in our daily life are some kind of mixture; for example: air, alloys, biomass, etc.
The concept of chemical element is related to that of chemical substance. A chemical element is specifically a substance which is composed of a single type of atom. A chemical element is characterized by a particular number of protons in the nuclei of its atoms. This number is known as the atomic number of the element. For example, all atoms with 6 protons in their nuclei are atoms of the chemical element carbon, and all atoms with 92 protons in their nuclei are atoms of the element uranium. 94 different chemical elements or types of atoms based on the number of protons exist naturally. A further 18 have been recognised by IUPAC as existing artificially only. Although all the nuclei of all atoms belonging to one element will have the same number of protons, they may not necessarily have the same number of neutrons; such atoms are termed isotopes. In fact several isotopes of an element may exist. All chemical elements are listed in the periodic table of the chemical elements, which list elements by atomic number and groups them by the number of valence electrons. Due to its ingenious arrangement, groups, or columns, and periods, or rows, of elements in the table either share several chemical properties, or follow a certain trend in characteristics such as atomic radius, electronegativity, etc. Lists of the elements by name, by symbol, and by atomic number are also available.
A compound is a substance with a particular ratio of atoms of particular chemical elements which determines its composition, and a particular organization which determines chemical properties. For example, water is a compound containing hydrogen and oxygen in the ratio of two to one, with the oxygen atom between the two hydrogen atoms, and an angle of 104.5° between them. Compounds are formed and interconverted by chemical reactions.
Nomenclature of substances is a critical part of the language of chemistry. Generally it refers to a system for naming chemical compounds. Earlier in the history of chemistry substances were given name by their discoverer, which often led to some confusion and difficulty. However, today the IUPAC system of chemical nomenclature allows chemists to specify by name specific compounds amongst the vast variety of possible chemicals. The standard nomenclature of chemical substances is set by the International Union of Pure and Applied Chemistry (IUPAC). There are well-defined systems in place for naming chemical species. Organic compounds are named according to the organic nomenclature system. Inorganic compounds are named according to the inorganic nomenclature system. In addition the Chemical Abstracts Service has devised a method to index chemical substance. In this scheme each chemical substance is identifiable by a number known as CAS registry number.
Molecular, ionic, metallic and network solids
Molecular compounds consist of discrete molecules, i.e. a set of atoms connected by covalent bonds. If a molecular compound is present in the liquid or solid phase, intermolecular interactions are observed between molecules.
Not all solid and liquid substances consist of discrete molecules. Most chemical elements are metallic solids, and some non-metals are network solids. Some compounds are not molecular, but rather are ionic solids and network solids. These substances lack grouping of atoms into molecules, and their chemical formula represent formula units or unit cells as the smallest repeating structure within the substance.
Acidity and basicity
A substance can often be classified as an acid or a base. There are several different theories which explain acid-base behavior. The simplest is Arrhenius theory, which states than an acid is a substance that produces hydronium ions when it is dissolved in water, and a base is one that produces hydroxide ions when dissolved in water. According to Brønsted–Lowry acid-base theory, acids are substances that donate a positive hydrogen ion to another substance in a chemical reaction; by extension, a base is the substance which receives that hydrogen ion. A third common theory is Lewis acid-base theory, which is based on the formation of new chemical bonds. Lewis theory explains that an acid is a substance which is capable of accepting a pair of electrons from another substance during the process of bond formation, while a base is a substance which can provide a pair of electrons to form a new bond. According to concept as per Lewis, the crucial things being exchanged are charges.[unreliable source?] There are several other ways in which a substance may be classified as an acid or a base, as is evident in the history of this concept 
Acid strength is commonly measured by two methods. One measurement, based on the Arrhenius definition of acidity, is pH, which is a measurement of the hydronium ion concentration in a solution, as expressed on a negative logarithmic scale. Thus, solutions that have a low pH have a high hydronium ion concentration, and can be said to be more acidic. The other measurement, based on the Brønsted–Lowry definition, is the acid dissociation constant (Ka), which measure the relative ability of a substance to act as an acid under the Brønsted–Lowry definition of an acid. That is, substances with a higher Ka are more likely to donate hydrogen ions in chemical reactions than those with lower Ka values.
In addition to the specific chemical properties that distinguish different chemical classifications, matter can exist in several phases. The most familiar examples of phases are solids, liquids, and gases. For the most part, the chemical classifications are independent of these bulk phase classifications; however, some more exotic phases are incompatible with certain chemical properties. A phase is a set of states of a chemical system that have similar bulk structural properties, over a range of conditions, such as pressure or temperature. Physical properties, such as density and refractive index tend to fall within values characteristic of the phase. The phase of matter is defined by the phase transition, which is when energy put into or taken out of the system goes into rearranging the structure of the system, instead of changing the bulk conditions.
Sometimes the distinction between phases can be continuous instead of having a discrete boundary, in this case the matter is considered to be in a supercritical state. When three states meet based on the conditions, it is known as a triple point and since this is invariant, it is a convenient way to define a set of conditions.
Many substances exhibit multiple solid phases. For example, there are three phases of solid iron (alpha, gamma, and delta) that vary based on temperature and pressure. A principal difference between solid phases is the crystal structure, or arrangement, of the atoms. Another phase commonly encountered in the study of chemistry is the aqueous phase, which is the state of substances dissolved in aqueous solution (that is, in water). Less familiar phases include plasmas, Bose-Einstein condensates and fermionic condensates and the paramagnetic and ferromagnetic phases of magnetic materials. While most familiar phases deal with three-dimensional systems, it is also possible to define analogs in two-dimensional systems, which has received attention for its relevance to systems in biology.
It is a concept related to the ability of atoms of various substances to lose or gain electrons. Substances that have the ability to oxidize other substances are said to be oxidative and are known as oxidizing agents, oxidants or oxidizers. An oxidant removes electrons from another substance. Similarly, substances that have the ability to reduce other substances are said to be reductive and are known as reducing agents, reductants, or reducers. A reductant transfers electrons to another substance, and is thus oxidized itself. And because it "donates" electrons it is also called an electron donor. Oxidation and reduction properly refer to a change in oxidation number—the actual transfer of electrons may never occur. Thus, oxidation is better defined as an increase in oxidation number, and reduction as a decrease in oxidation number.
When a chemical substance is transformed as a result of its interaction with another or energy, a chemical reaction is said to have occurred. Chemical reaction is therefore a concept related to the 'reaction' of a substance when it comes in close contact with another, whether as a mixture or a solution; exposure to some form of energy, or both. It results in some energy exchange between the constituents of the reaction as well with the system environment which may be a designed vessels which are often laboratory glassware. Chemical reactions can result in the formation or dissociation of molecules, that is, molecules breaking apart to form two or more smaller molecules, or rearrangement of atoms within or across molecules. Chemical reactions usually involve the making or breaking of chemical bonds. Oxidation, reduction, dissociation, acid-base neutralization and molecular rearrangement are some of the commonly used kinds of chemical reactions.
A chemical reaction can be symbolically depicted through a chemical equation. While in a non-nuclear chemical reaction the number and kind of atoms on both sides of the equation are equal, for a nuclear reaction this holds true only for the nuclear particles viz. protons and neutrons.
The sequence of steps in which the reorganization of chemical bonds may be taking place in the course of a chemical reaction is called its mechanism. A chemical reaction can be envisioned to take place in a number of steps, each of which may have a different speed. Many reaction intermediates with variable stability can thus be envisaged during the course of a reaction. Reaction mechanisms are proposed to explain the kinetics and the relative product mix of a reaction. Many physical chemists specialize in exploring and proposing the mechanisms of various chemical reactions. Several empirical rules, like the Woodward-Hoffmann rules often come handy while proposing a mechanism for a chemical reaction.
According to the IUPAC gold book a chemical reaction is a process that results in the interconversion of chemical species". Accordingly, a chemical reaction may be an elementary reaction or a stepwise reaction. An additional caveat is made, in that this definition includes cases where the interconversion of conformers is experimentally observable. Such detectable chemical reactions normally involve sets of molecular entities as indicated by this definition, but it is often conceptually convenient to use the term also for changes involving single molecular entities (i.e. 'microscopic chemical events').
Although the concept of equilibrium is widely used across sciences, in the context of chemistry, it arises whenever a number of different states of the chemical composition are possible. For example, in a mixture of several chemical compounds that can react with one another, or when a substance can be present in more than one kind of phase. A system of chemical substances at equilibrium even though having an unchanging composition is most often not static; molecules of the substances continue to react with one another thus giving rise to a dynamic equilibrium. Thus the concept describes the state in which the parameters such as chemical composition remain unchanged over time. Chemicals present in biological systems are invariably not at equilibrium; rather they are far from equilibrium.
In the context of chemistry, energy is an attribute of a substance as a consequence of its atomic, molecular or aggregate structure. Since a chemical transformation is accompanied by a change in one or more of these kinds of structure, it is invariably accompanied by an increase or decrease of energy of the substances involved. Some energy is transferred between the surroundings and the reactants of the reaction in the form of heat or light; thus the products of a reaction may have more or less energy than the reactants. A reaction is said to be exergonic if the final state is lower on the energy scale than the initial state; in the case of endergonic reactions the situation is the reverse. A reaction is said to be exothermic if the reaction releases heat to the surroundings; in the case of endothermic reactions, the reaction absorbs heat from the surroundings.
Chemical reactions are invariably not possible unless the reactants surmount an energy barrier known as the activation energy. The speed of a chemical reaction (at given temperature T) is related to the activation energy E, by the Boltzmann's population factor - that is the probability of molecule to have energy greater than or equal to E at the given temperature T. This exponential dependence of a reaction rate on temperature is known as the Arrhenius equation. The activation energy necessary for a chemical reaction can be in the form of heat, light, electricity or mechanical force in the form of ultrasound.
A related concept free energy, which also incorporates entropy considerations, is a very useful means for predicting the feasibility of a reaction and determining the state of equilibrium of a chemical reaction, in chemical thermodynamics. A reaction is feasible only if the total change in the Gibbs free energy is negative, ; if it is equal to zero the chemical reaction is said to be at equilibrium.
There exist only limited possible states of energy for electrons, atoms and molecules. These are determined by the rules of quantum mechanics, which require quantization of energy of a bound system. The atoms/molecules in a higher energy state are said to be excited. The molecules/atoms of substance in an excited energy state are often much more reactive; that is, more amenable to chemical reactions.
The phase of a substance is invariably determined by its energy and the energy of its surroundings. When the intermolecular forces of a substance are such that the energy of the surroundings is not sufficient to overcome them, it occurs in a more ordered phase like liquid or solid as is the case with water (H2O); a liquid at room temperature because its molecules are bound by hydrogen bonds. Whereas hydrogen sulfide (H2S) is a gas at room temperature and standard pressure, as its molecules are bound by weaker dipole-dipole interactions.
The transfer of energy from one chemical substance to another depends on the size of energy quanta emitted from one substance. However, heat energy is often transferred more easily from almost any substance to another because the phonons responsible for vibrational and rotational energy levels in a substance have much less energy than photons invoked for the electronic energy transfer. Thus, because vibrational and rotational energy levels are more closely spaced than electronic energy levels, heat is more easily transferred between substances relative to light or other forms of electronic energy. For example, ultraviolet electromagnetic radiation is not transferred with as much efficacy from one substance to another as thermal or electrical energy.
The existence of characteristic energy levels for different chemical substances is useful for their identification by the analysis of spectral lines. Different kinds of spectra are often used in chemical spectroscopy, e.g. IR, microwave, NMR, ESR, etc. Spectroscopy is also used to identify the composition of remote objects - like stars and distant galaxies - by analyzing their radiation spectra.
Chemical reactions are governed by certain laws, which have become fundamental concepts in chemistry. Some of them are:
- Avogadro's law
- Beer-Lambert law
- Boyle's law (1662, relating pressure and volume)
- Charles's law (1787, relating volume and temperature)
- Fick's law of diffusion
- Gay-Lussac's law (1809, relating pressure and temperature)
- Henry's law
- Hess's Law
- Law of conservation of energy leads to the important concepts of equilibrium, thermodynamics, and kinetics.
- Law of conservation of mass, according to the modern physics it is actually energy that is conserved, and that energy and mass are related; a concept which becomes important in nuclear chemistry.
- Law of definite composition, although in many systems (notably biomacromolecules and minerals) the ratios tend to require large numbers, and are frequently represented as a fraction.
- Law of multiple proportions
- Raoult's Law
- General Chemistry Online - Companion Notes: Matter
- visionlearning: Chemical Bonding by Anthony Carpi, Ph
- Official SI Unit definitions
- Hill, J.W.; Petrucci, R.H.; McCreary, T.W.; Perry, S.S. (2005). General Chemistry (4th ed.). Pearson Prentice Hall. p. 37. Unknown parameter
- IUPAC Nomenclature of Organic Chemistry
- IUPAC Provisional Recommendations for the Nomenclature of Inorganic Chemistry (2004) 
- "The Lewis Acid-Base Concept". Apsidium. May 19, 2003. Archived from the original on 2008-05-27. Retrieved 2010-07-31.
- History of Acidity
- Chemical Reaction Equation- IUPAC Goldbook
- Gold Book Chemical Reaction IUPAC Goldbook
- Reilly, Michael. (2007). Mechanical force induces chemical reaction, NewScientist.com news service, Reilly [dead link]
- Changing States of Matter - Chemforkids.com