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Theoretical chemistry

Theoretical chemistry is the branch of chemistry which develops theoretical generalizations that are part of the theoretical arsenal of modern chemistry: for example, the concepts of chemical bonding, chemical reaction, valence, the surface of potential energy, molecular orbitals, orbital interactions, and molecule activation. Overview Theoretical chemistry unites principles and concepts common to all branches of chemistry. Within the framework of theoretical chemistry, there is a systematization of chemical laws, principles and rules, their refinement and detailing, the construction of a hierarchy. The central place in theoretical chemistry is occupied by the doctrine of the interconnection of the structure and properties of molecular systems. It uses mathematical and physical methods to explain the structures and dynamics of chemical systems and to correlate, understand, and predict their thermodynamic and kinetic properties. In the most general sense, it is explanation of chemical phenomena by methods of theoretical physics. In contrast to theoretical physics, in connection with the high complexity of chemical systems, theoretical chemistry, in addition to approximate mathematical methods, often uses semi-empirical and empirical methods. In recent years, it has consisted primarily of quantum chemistry, i.e., the application of quantum mechanics to problems in chemistry. Other major components include molecular dynamics, statistical thermodynamics and theories of electrolyte solutions, reaction networks, polymerization, catalysis, molecular magnetism and spectroscopy. Modern theoretical chemistry may be roughly divided into the study of chemical structure and the study of chemical dynamics. The former includes studies of: electronic structure, potential energy surfaces, and force fields; vibrational-rotational motion; equilibrium properties of condensed-phase systems and macro-molecules. Chemical dynamics includes: bimolecular kinetics and the collision theory of reactions and energy transfer; unimolecular rate theory and metastable states; condensed-phase and macromolecular aspects of dynamics. Branches of theoretical chemistry Quantum chemistry The application of quantum mechanics or fundamental interactions to chemical and physico-chemical problems. Spectroscopic and magnetic properties are between the most frequently modelled. Computational chemistryThe application of scientific computing to chemistry, involving approximation schemes such as Hartree–Fock, post-Hartree–Fock, density functional theory, semiempirical methods (such as PM3) or force field methods. Molecular shape is the most frequently predicted property. Computers can also predict vibrational spectra and vibronic coupling, but also acquire and Fourier transform Infra-red Data into frequency information. The comparison with predicted vibrations supports the predicted shape. Molecular modelling Methods for modelling molecular structures without necessarily referring to quantum mechanics. Examples are molecular docking, protein-protein docking, drug design, combinatorial chemistry. The fitting of shape and electric potential are the driving factor in this graphical approach. Molecular dynamics Application of classical mechanics for simulating the movement of the nuclei of an assembly of atoms and molecules. The rearrangement of molecules within an ensemble is controlled by Van der Waals forces and promoted by temperature. Molecular mechanics Modeling of the intra- and inter-molecular interaction potential energy surfaces via potentials. The latter are usually parameterized from ab initio calculations. Mathematical chemistry Discussion and prediction of the molecular structure using mathematical methods without necessarily referring to quantum mechanics. Topology is a branch of mathematics that allows researchers to predict properties of flexible finite size bodies like clusters. Chemical kinetics Theoretical study of the dynamical systems associated to reactive chemicals, the activated complex and their corresponding differential equations. Cheminformatics (also known as chemoinformatics) The use of computer and informational techniques, applied to crop information to solve problems in the field of chemistry. Chemical engineering The application of chemistry to industrial processes to conduct research and development. This allows for development and improvement of new and existing products and manufacturing processes. Chemical thermodynamics The study of the relationship between heat, work, and energy in chemical reactions and processes, with focus on entropy, enthalpy, and Gibbs free energy to understand reaction spontaneity and equilibrium. Statistical mechanics The application of statistical mechanics to predict and explain thermodynamic properties of chemical systems, connecting molecular behavior with macroscopic properties. Closely related disciplines Historically, the major field of application of theoretical chemistry has been in the following fields of research: Atomic physics: The discipline dealing with electrons and atomic nuclei. Molecular physics: The discipline of the electrons surrounding the molecular nuclei and of movement of the nuclei. This term usually refers to the study of molecules made of a few atoms in the gas phase. But some consider that molecular physics is also the study of bulk properties of chemicals in terms of molecules. Physical chemistry and chemical physics: Chemistry investigated via physical methods like laser techniques, scanning tunneling microscope, etc. The formal distinction between both fields is that physical chemistry is a branch of chemistry while chemical physics is a branch of physics. In practice this distinction is quite vague. Many-body theory: The discipline studying the effects which appear in systems with large number of constituents. It is based on quantum physics – mostly second quantization formalism – and quantum electrodynamics. Hence, theoretical chemistry has emerged as a branch of research. With the rise of the density functional theory and other methods like molecular mechanics, the range of application has been extended to chemical systems which are relevant to other fields of chemistry and physics, including biochemistry, condensed matter physics, nanotechnology or molecular biology. See also List of unsolved problems in chemistry Bibliography Attila Szabo and Neil S. Ostlund, Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, Dover Publications; New Ed edition (1996) , Robert G. Parr and Weitao Yang, Density-Functional Theory of Atoms and Molecules, Oxford Science Publications; first published in 1989; , D. J. Tannor, V. Kazakov and V. Orlov, Control of Photochemical Branching: Novel Procedures for Finding Optimal Pulses and Global Upper Bounds, in Time Dependent Quantum Molecular Dynamics, J. Broeckhove and L. Lathouwers, eds., 347-360 (Plenum, 1992) Chemistry Physical chemistry Chemical physics

Physical chemistry

Physical chemistry is the study of macroscopic and microscopic phenomena in chemical systems in terms of the principles, practices, and concepts of physics such as motion, energy, force, time, thermodynamics, quantum chemistry, statistical mechanics, analytical dynamics and chemical equilibria. Physical chemistry, in contrast to chemical physics, is predominantly (but not always) a supra-molecular science, as the majority of the principles on which it was founded relate to the bulk rather than the molecular or atomic structure alone (for example, chemical equilibrium and colloids). Some of the relationships that physical chemistry strives to understand include the effects of: Intermolecular forces that act upon the physical properties of materials (plasticity, tensile strength, surface tension in liquids). Reaction kinetics on the rate of a reaction. The identity of ions and the electrical conductivity of materials. Surface science and electrochemistry of cell membranes. Interaction of one body with another in terms of quantities of heat and work called thermodynamics. Transfer of heat between a chemical system and its surroundings during change of phase or chemical reaction taking place called thermochemistry Study of colligative properties of number of species present in solution. Number of phases, number of components and degree of freedom (or variance) can be correlated with one another with help of phase rule. Reactions of electrochemical cells. Behaviour of microscopic systems using quantum mechanics and macroscopic systems using statistical thermodynamics. Calculation of the energy of electron movement in molecules and metal complexes. Key concepts The key concepts of physical chemistry are the ways in which pure physics is applied to chemical problems. One of the key concepts in classical chemistry is that all chemical compounds can be described as groups of atoms bonded together and chemical reactions can be described as the making and breaking of those bonds. Predicting the properties of chemical compounds from a description of atoms and how they bond is one of the major goals of physical chemistry. To describe the atoms and bonds precisely, it is necessary to know both where the nuclei of the atoms are, and how electrons are distributed around them. Disciplines Quantum chemistry, a subfield of physical chemistry especially concerned with the application of quantum mechanics to chemical problems, provides tools to determine how strong and what shape bonds are, how nuclei move, and how light can be absorbed or emitted by a chemical compound. Spectroscopy is the related sub-discipline of physical chemistry which is specifically concerned with the interaction of electromagnetic radiation with matter. Another set of important questions in chemistry concerns what kind of reactions can happen spontaneously and which properties are possible for a given chemical mixture. This is studied in chemical thermodynamics, which sets limits on quantities like how far a reaction can proceed, or how much energy can be converted into work in an internal combustion engine, and which provides links between properties like the thermal expansion coefficient and rate of change of entropy with pressure for a gas or a liquid. It can frequently be used to assess whether a reactor or engine design is feasible, or to check the validity of experimental data. To a limited extent, quasi-equilibrium and non-equilibrium thermodynamics can describe irreversible changes. However, classical thermodynamics is mostly concerned with systems in equilibrium and reversible changes and not what actually does happen, or how fast, away from equilibrium. Which reactions do occur and how fast is the subject of chemical kinetics, another branch of physical chemistry. A key idea in chemical kinetics is that for reactants to react and form products, most chemical species must go through transition states which are higher in energy than either the reactants or the products and serve as a barrier to reaction. In general, the higher the barrier, the slower the reaction. A second is that most chemical reactions occur as a sequence of elementary reactions, each with its own transition state. Key questions in kinetics include how the rate of reaction depends on temperature and on the concentrations of reactants and catalysts in the reaction mixture, as well as how catalysts and reaction conditions can be engineered to optimize the reaction rate. The fact that how fast reactions occur can often be specified with just a few concentrations and a temperature, instead of needing to know all the positions and speeds of every molecule in a mixture, is a special case of another key concept in physical chemistry, which is that to the extent an engineer needs to know, everything going on in a mixture of very large numbers (perhaps of the order of the Avogadro constant, 6 x 1023) of particles can often be described by just a few variables like pressure, temperature, and concentration. The precise reasons for this are described in statistical mechanics, a specialty within physical chemistry which is also shared with physics. Statistical mechanics also provides ways to predict the properties we see in everyday life from molecular properties without relying on empirical correlations based on chemical similarities. History The term "physical chemistry" was coined by Mikhail Lomonosov in 1752, when he presented a lecture course entitled "A Course in True Physical Chemistry" before the students of Petersburg University. In the preamble to these lectures he gives the definition: "Physical chemistry is the science that must explain under provisions of physical experiments the reason for what is happening in complex bodies through chemical operations". Modern physical chemistry originated in the 1860s to 1880s with work on chemical thermodynamics, electrolytes in solutions, chemical kinetics and other subjects. One milestone was the publication in 1876 by Josiah Willard Gibbs of his paper, On the Equilibrium of Heterogeneous Substances. This paper introduced several of the cornerstones of physical chemistry, such as Gibbs energy, chemical potentials, and Gibbs' phase rule. The first scientific journal specifically in the field of physical chemistry was the German journal, Zeitschrift für Physikalische Chemie, founded in 1887 by Wilhelm Ostwald and Jacobus Henricus van 't Hoff. Together with Svante August Arrhenius, these were the leading figures in physical chemistry in the late 19th century and early 20th century. All three were awarded the Nobel Prize in Chemistry between 1901 and 1909. Developments in the following decades include the application of statistical mechanics to chemical systems and work on colloids and surface chemistry, where Irving Langmuir made many contributions. Another important step was the development of quantum mechanics into quantum chemistry from the 1930s, where Linus Pauling was one of the leading names. Theoretical developments have gone hand in hand with developments in experimental methods, where the use of different forms of spectroscopy, such as infrared spectroscopy, microwave spectroscopy, electron paramagnetic resonance and nuclear magnetic resonance spectroscopy, is probably the most important 20th century development. Further development in physical chemistry may be attributed to discoveries in nuclear chemistry, especially in isotope separation (before and during World War II), more recent discoveries in astrochemistry, as well as the development of calculation algorithms in the field of "additive physicochemical properties" (practically all physicochemical properties, such as boiling point, critical point, surface tension, vapor pressure, etc.—more than 20 in all—can be precisely calculated from chemical structure alone, even if the chemical molecule remains unsynthesized), and herein lies the practical importance of contemporary physical chemistry. See Group contribution method, Lydersen method, Joback method, Benson group increment theory, quantitative structure–activity relationship Journals Some journals that deal with physical chemistry include Zeitschrift für Physikalische Chemie (1887) Journal of Physical Chemistry A (from 1896 as Journal of Physical Chemistry, renamed in 1997) Physical Chemistry Chemical Physics (from 1999, formerly Faraday Transactions with a history dating back to 1905) Macromolecular Chemistry and Physics (1947) Annual Review of Physical Chemistry (1950) Molecular Physics (1957) Journal of Physical Organic Chemistry (1988) Journal of Physical Chemistry B (1997) ChemPhysChem (2000) Journal of Physical Chemistry C (2007) Journal of Physical Chemistry Letters (from 2010, combined letters previously published in the separate journals) Historical journals that covered both chemistry and physics include Annales de chimie et de physique (started in 1789, published under the name given here from 1815 to 1914). Branches and related topics Chemical thermodynamics Chemical kinetics Statistical mechanics Quantum chemistry Electrochemistry Photochemistry Surface chemistry Solid-state chemistry Spectroscopy Biophysical chemistry Materials science Physical organic chemistry Micromeritics See also List of important publications in chemistry#Physical chemistry List of unsolved problems in chemistry#Physical chemistry problems Physical biochemistry :Category:Physical chemists References External links The World of Physical Chemistry (Keith J. Laidler, 1993) Physical Chemistry from Ostwald to Pauling (John W. Servos, 1996) Physical Chemistry: neither Fish nor Fowl? (Joachim Schummer, The Autonomy of Chemistry, Würzburg, Königshausen & Neumann, 1998, pp. 135–148) The Cambridge History of Science: The modern physical and mathematical sciences (Mary Jo Nye, 2003)

Chemical reaction

A chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. When chemical reactions occur, the atoms are rearranged and the reaction is accompanied by an energy change as new products are generated. Classically, chemical reactions encompass changes that only involve the positions of electrons in the forming and breaking of chemical bonds between atoms, with no change to the nuclei (no change to the elements present), and can often be described by a chemical equation. Nuclear chemistry is a sub-discipline of chemistry that involves the chemical reactions of unstable and radioactive elements where both electronic and nuclear changes can occur. The substance (or substances) initially involved in a chemical reaction are called reactants or reagents. Chemical reactions are usually characterized by a chemical change, and they yield one or more products, which usually have properties different from the reactants. Reactions often consist of a sequence of individual sub-steps, the so-called elementary reactions, and the information on the precise course of action is part of the reaction mechanism. Chemical reactions are described with chemical equations, which symbolically present the starting materials, end products, and sometimes intermediate products and reaction conditions. Chemical reactions happen at a characteristic reaction rate at a given temperature and chemical concentration. Some reactions produce heat and are called exothermic reactions, while others may require heat to enable the reaction to occur, which are called endothermic reactions. Typically, reaction rates increase with increasing temperature because there is more thermal energy available to reach the activation energy necessary for breaking bonds between atoms. A reaction may be classified as redox in which oxidation and reduction occur or non-redox in which there is no oxidation and reduction occurring. Most simple redox reactions may be classified as a combination, decomposition, or single displacement reaction. Different chemical reactions are used during chemical synthesis in order to obtain the desired product. In biochemistry, a consecutive series of chemical reactions (where the product of one reaction is the reactant of the next reaction) form metabolic pathways. These reactions are often catalyzed by protein enzymes. Enzymes increase the rates of biochemical reactions, so that metabolic syntheses and decompositions impossible under ordinary conditions can occur at the temperature and concentrations present within a cell. The general concept of a chemical reaction has been extended to reactions between entities smaller than atoms, including nuclear reactions, radioactive decays and reactions between elementary particles, as described by quantum field theory. History Chemical reactions such as combustion in fire, fermentation and the reduction of ores to metals were known since antiquity. Initial theories of transformation of materials were developed by Greek philosophers, such as the Four-Element Theory of Empedocles stating that any substance is composed of the four basic elements – fire, water, air and earth. In the Middle Ages, chemical transformations were studied by alchemists. They attempted, in particular, to convert lead into gold, for which purpose they used reactions of lead and lead-copper alloys with sulfur. The artificial production of chemical substances already was a central goal for medieval alchemists. Examples include the synthesis of ammonium chloride from organic substances as described in the works (c. 850–950) attributed to Jābir ibn Ḥayyān, or the production of mineral acids such as sulfuric and nitric acids by later alchemists, starting from c. 1300. The production of mineral acids involved the heating of sulfate and nitrate minerals such as copper sulfate, alum and saltpeter. In the 17th century, Johann Rudolph Glauber produced hydrochloric acid and sodium sulfate by reacting sulfuric acid and sodium chloride. With the development of the lead chamber process in 1746 and the Leblanc process, allowing large-scale production of sulfuric acid and sodium carbonate, respectively, chemical reactions became implemented into the industry. Further optimization of sulfuric acid technology resulted in the contact process in the 1880s, and the Haber process was developed in 1909–1910 for ammonia synthesis. From the 16th century, researchers including Jan Baptist van Helmont, Robert Boyle, and Isaac Newton tried to establish theories of experimentally observed chemical transformations. The phlogiston theory was proposed in 1667 by Johann Joachim Becher. It postulated the existence of a fire-like element called "phlogiston", which was contained within combustible bodies and released during combustion. This proved to be false in 1785 by Antoine Lavoisier who found the correct explanation of the combustion as a reaction with oxygen from the air. Joseph Louis Gay-Lussac recognized in 1808 that gases always react in a certain relationship with each other. Based on this idea and the atomic theory of John Dalton, Joseph Proust had developed the law of definite proportions, which later resulted in the concepts of stoichiometry and chemical equations. Regarding the organic chemistry, it was long believed that compounds obtained from living organisms were too complex to be obtained synthetically. According to the concept of vitalism, organic matter was endowed with a "vital force" and distinguished from inorganic materials. This separation was ended however by the synthesis of urea from inorganic precursors by Friedrich Wöhler in 1828. Other chemists who brought major contributions to organic chemistry include Alexander William Williamson with his synthesis of ethers and Christopher Kelk Ingold, who, among many discoveries, established the mechanisms of substitution reactions. Characteristics The general characteristics of chemical reactions are: Evolution of a gas Formation of a precipitate Change in temperature Change in state Equations Chemical equations are used to graphically illustrate chemical reactions. They consist of chemical or structural formulas of the reactants on the left and those of the products on the right. They are separated by an arrow (→) which indicates the direction and type of the reaction; the arrow is read as the word "yields". The tip of the arrow points in the direction in which the reaction proceeds. A double arrow pointing in opposite directions is used for equilibrium reactions. Equations should be balanced according to the stoichiometry, the number of atoms of each species should be the same on both sides of the equation. This is achieved by scaling the number of involved molecules (A, B, C and D in a schematic example below) by the appropriate integers a, b, c and d. More elaborate reactions are represented by reaction schemes, which in addition to starting materials and products show important intermediates or transition states. Also, some relatively minor additions to the reaction can be indicated above the reaction arrow; examples of such additions are water, heat, illumination, a catalyst, etc. Similarly, some minor products can be placed below the arrow, often with a minus sign. Retrosynthetic analysis can be applied to design a complex synthesis reaction. Here the analysis starts from the products, for example by splitting selected chemical bonds, to arrive at plausible initial reagents. A special arrow (⇒) is used in retro reactions. Elementary reactions The elementary reaction is the smallest division into which a chemical reaction can be decomposed, it has no intermediate products. Most experimentally observed reactions are built up from many elementary reactions that occur in parallel or sequentially. The actual sequence of the individual elementary reactions is known as reaction mechanism. An elementary reaction involves a few molecules, usually one or two, because of the low probability for several molecules to meet at a certain time. The most important elementary reactions are unimolecular and bimolecular reactions. Only one molecule is involved in a unimolecular reaction; it is transformed by isomerization or a dissociation into one or more other molecules. Such reactions require the addition of energy in the form of heat or light. A typical example of a unimolecular reaction is the cis–trans isomerization, in which the cis-form of a compound converts to the trans-form or vice versa. In a typical dissociation reaction, a bond in a molecule splits (ruptures) resulting in two molecular fragments. The splitting can be homolytic or heterolytic. In the first case, the bond is divided so that each product retains an electron and becomes a neutral radical. In the second case, both electrons of the chemical bond remain with one of the products, resulting in charged ions. Dissociation plays an important role in triggering chain reactions, such as hydrogen–oxygen or polymerization reactions. AB -> A + B Dissociation of a molecule AB into fragments A and B For bimolecular reactions, two molecules collide and react with each other. Their merger is called chemical synthesis or an addition reaction. A + B -> AB Another possibility is that only a portion of one molecule is transferred to the other molecule. This type of reaction occurs, for example, in redox and acid-base reactions. In redox reactions, the transferred particle is an electron, whereas in acid-base reactions it is a proton. This type of reaction is also called metathesis. HA + B -> A + HB for example NaCl + AgNO3 -> NaNO3 + AgCl(v) Chemical equilibrium Most chemical reactions are reversible; that is, they can and do run in both directions. The forward and reverse reactions are competing with each other and differ in reaction rates. These rates depend on the concentration and therefore change with the time of the reaction: the reverse rate gradually increases and becomes equal to the rate of the forward reaction, establishing the so-called chemical equilibrium. The time to reach equilibrium depends on parameters such as temperature, pressure, and the materials involved, and is determined by the minimum free energy. In equilibrium, the Gibbs free energy of reaction must be zero. The pressure dependence can be explained with the Le Chatelier's principle. For example, an increase in pressure due to decreasing volume causes the reaction to shift to the side with fewer moles of gas. The reaction yield stabilizes at equilibrium but can be increased by removing the product from the reaction mixture or changed by increasing the temperature or pressure. A change in the concentrations of the reactants does not affect the equilibrium constant but does affect the equilibrium position. Thermodynamics Chemical reactions are determined by the laws of thermodynamics. Reactions can proceed by themselves if they are exergonic, that is if they release free energy. The associated free energy change of the reaction is composed of the changes of two different thermodynamic quantities, enthalpy and entropy: . : free energy, : enthalpy, : temperature, : entropy, : difference (change between original and product) Reactions can be exothermic, where ΔH is negative and energy is released. Typical examples of exothermic reactions are combustion, precipitation and crystallization, in which ordered solids are formed from disordered gaseous or liquid phases. In contrast, in endothermic reactions, heat is consumed from the environment. This can occur by increasing the entropy of the system, often through the formation of gaseous or dissolved reaction products, which have higher entropy. Since the entropy term in the free-energy change increases with temperature, many endothermic reactions preferably take place at high temperatures. On the contrary, many exothermic reactions such as crystallization occur preferably at lower temperatures. A change in temperature can sometimes reverse the sign of the enthalpy of a reaction, as for the carbon monoxide reduction of molybdenum dioxide: 2CO(g) + MoO2(s) -> 2CO2(g) + Mo(s); This reaction to form carbon dioxide and molybdenum is endothermic at low temperatures, becoming less so with increasing temperature. ΔH° is zero at , and the reaction becomes exothermic above that temperature. Changes in temperature can also reverse the direction tendency of a reaction. For example, the water gas shift reaction CO(g) + H2O({v}) <=> CO2(g) + H2(g) is favored by low temperatures, but its reverse is favored by high temperatures. The shift in reaction direction tendency occurs at . Reactions can also be characterized by their internal energy change, which takes into account changes in the entropy, volume and chemical potentials. The latter depends, among other things, on the activities of the involved substances. : internal energy, : entropy, : pressure, : chemical potential, : number of molecules, : small change sign Kinetics The speed at which reactions take place is studied by reaction kinetics. The rate depends on various parameters, such as: Reactant concentrations, which usually make the reaction happen at a faster rate if raised through increased collisions per unit of time. Some reactions, however, have rates that are independent of reactant concentrations, due to a limited number of catalytic sites. These are called zero order reactions. Surface area available for contact between the reactants, in particular solid ones in heterogeneous systems. Larger surface areas lead to higher reaction rates. Pressure – increasing the pressure decreases the volume between molecules and therefore increases the frequency of collisions between the molecules. Activation energy, which is defined as the amount of energy required to make the reaction start and carry on spontaneously. Higher activation energy implies that the reactants need more energy to start than a reaction with lower activation energy. Temperature, which hastens reactions if raised, since higher temperature increases the energy of the molecules, creating more collisions per unit of time, The presence or absence of a catalyst. Catalysts are substances that make weak bonds with reactants or intermediates and change the pathway (mechanism) of a reaction which in turn increases the speed of a reaction by lowering the activation energy needed for the reaction to take place. A catalyst is not destroyed or changed during a reaction, so it can be used again. For some reactions, the presence of electromagnetic radiation, most notably ultraviolet light, is needed to promote the breaking of bonds to start the reaction. This is particularly true for reactions involving radicals. Several theories allow calculating the reaction rates at the molecular level. This field is referred to as reaction dynamics. The rate v of a first-order reaction, which could be the disintegration of a substance A, is given by: Its integration yields: Here k is the first-order rate constant, having dimension 1/time, [A](t) is the concentration at a time t and [A]0 is the initial concentration. The rate of a first-order reaction depends only on the concentration and the properties of the involved substance, and the reaction itself can be described with a characteristic half-life. More than one time constant is needed when describing reactions of higher order. The temperature dependence of the rate constant usually follows the Arrhenius equation: where Ea is the activation energy and kB is the Boltzmann constant. One of the simplest models of reaction rate is the collision theory. More realistic models are tailored to a specific problem and include the transition state theory, the calculation of the potential energy surface, the Marcus theory and the Rice–Ramsperger–Kassel–Marcus (RRKM) theory. Reaction types Four basic types Synthesis In a synthesis reaction, two or more simple substances combine to form a more complex substance. These reactions are in the general form: A + B->AB Two or more reactants yielding one product is another way to identify a synthesis reaction. One example of a synthesis reaction is the combination of iron and sulfur to form iron(II) sulfide: 8Fe + S8->8FeS Another example is simple hydrogen gas combined with simple oxygen gas to produce a more complex substance, such as water. Decomposition A decomposition reaction is when a more complex substance breaks down into its more simple parts. It is thus the opposite of a synthesis reaction and can be written as AB->A + B One example of a decomposition reaction is the electrolysis of water to make oxygen and hydrogen gas: 2H2O->2H2 + O2 Single displacement In a single displacement reaction, a single uncombined element replaces another in a compound; in other words, one element trades places with another element in a compound These reactions come in the general form of: A + BC->AC + B One example of a single displacement reaction is when magnesium replaces hydrogen in water to make solid magnesium hydroxide and hydrogen gas: Mg + 2H2O->Mg(OH)2 (v) + H2 (^) Double displacement In a double displacement reaction, the anions and cations of two compounds switch places and form two entirely different compounds. These reactions are in the general form: AB + CD->AD + CB For example, when barium chloride (BaCl2) and magnesium sulfate (MgSO4) react, the SO42− anion switches places with the 2Cl− anion, giving the compounds BaSO4 and MgCl2. Another example of a double displacement reaction is the reaction of lead(II) nitrate with potassium iodide to form lead(II) iodide and potassium nitrate: Pb(NO3)2 + 2KI->PbI2(v) + 2KNO3 Forward and backward reactions According to Le Chatelier's Principle, reactions may proceed in the forward or reverse direction until they end or reach equilibrium. Forward reactions Reactions that proceed in the forward direction (from left to right) to approach equilibrium are often called spontaneous reactions, that is, is negative, which means that if they occur at constant temperature and pressure, they decrease the Gibbs free energy of the reaction. They require less energy to proceed in the forward direction. Reactions are usually written as forward reactions in the direction in which they are spontaneous. Examples: Reaction of hydrogen and oxygen to form water. + Dissociation of acetic acid in water into acetate ions and hydronium ions. + + Backward reactions Reactions that proceed in the backward direction to approach equilibrium are often called non-spontaneous reactions, that is, is positive, which means that if they occur at constant temperature and pressure, they increase the Gibbs free energy of the reaction. They require input of energy to proceed in the forward direction. Examples include: Charging a normal DC battery (consisting of electrolytic cells) from an external electrical power source Photosynthesis driven by absorption of electromagnetic radiation usually in the form of sunlight + + → + Combustion In a combustion reaction, an element or compound reacts with an oxidant, usually oxygen, often producing energy in the form of heat or light. Combustion reactions frequently involve a hydrocarbon. For instance, the combustion of 1 mole (114 g) of octane in oxygen C8H18(l) + 25/2 O2(g)->8CO2 + 9H2O(l) releases 5500 kJ. A combustion reaction can also result from carbon, magnesium or sulfur reacting with oxygen. 2Mg(s) + O2->2MgO(s) S(s) + O2(g)->SO2(g) Oxidation and reduction Redox reactions can be understood in terms of the transfer of electrons from one involved species (reducing agent) to another (oxidizing agent). In this process, the former species is oxidized and the latter is reduced. Though sufficient for many purposes, these descriptions are not precisely correct. Oxidation is better defined as an increase in oxidation state of atoms and reduction as a decrease in oxidation state. In practice, the transfer of electrons will always change the oxidation state, but there are many reactions that are classed as "redox" even though no electron transfer occurs (such as those involving covalent bonds). In the following redox reaction, hazardous sodium metal reacts with toxic chlorine gas to form the ionic compound sodium chloride, or common table salt: 2Na(s) + Cl2(g)->2NaCl(s) In the reaction, sodium metal goes from an oxidation state of 0 (a pure element) to +1: in other words, the sodium lost one electron and is said to have been oxidized. On the other hand, the chlorine gas goes from an oxidation of 0 (also a pure element) to −1: the chlorine gains one electron and is said to have been reduced. Because the chlorine is the one reduced, it is considered the electron acceptor, or in other words, induces oxidation in the sodium – thus the chlorine gas is considered the oxidizing agent. Conversely, the sodium is oxidized or is the electron donor, and thus induces a reduction in the other species and is considered the reducing agent. Which of the involved reactants would be a reducing or oxidizing agent can be predicted from the electronegativity of their elements. Elements with low electronegativities, such as most metals, easily donate electrons and oxidize – they are reducing agents. On the contrary, many oxides or ions with high oxidation numbers of their non-oxygen atoms, such as , , , , or , can gain one or two extra electrons and are strong oxidizing agents. For some main-group elements the number of electrons donated or accepted in a redox reaction can be predicted from the electron configuration of the reactant element. Elements try to reach the low-energy noble gas configuration, and therefore alkali metals and halogens will donate and accept one electron, respectively. Noble gases themselves are chemically inactive. The overall redox reaction can be balanced by combining the oxidation and reduction half-reactions multiplied by coefficients such that the number of electrons lost in the oxidation equals the number of electrons gained in the reduction. An important class of redox reactions are the electrolytic electrochemical reactions, where electrons from the power supply at the negative electrode are used as the reducing agent and electron withdrawal at the positive electrode as the oxidizing agent. These reactions are particularly important for the production of chemical elements, such as chlorine or aluminium. The reverse process, in which electrons are released in redox reactions and chemical energy is converted to electrical energy, is possible and used in batteries. Complexation In complexation reactions, several ligands react with a metal atom to form a coordination complex. This is achieved by providing lone pairs of the ligand into empty orbitals of the metal atom and forming dipolar bonds. The ligands are Lewis bases, they can be both ions and neutral molecules, such as carbon monoxide, ammonia or water. The number of ligands that react with a central metal atom can be found using the 18-electron rule, saying that the valence shells of a transition metal will collectively accommodate 18 electrons, whereas the symmetry of the resulting complex can be predicted with the crystal field theory and ligand field theory. Complexation reactions also include ligand exchange, in which one or more ligands are replaced by another, and redox processes which change the oxidation state of the central metal atom. Acid–base reactions In the Brønsted–Lowry acid–base theory, an acid–base reaction involves a transfer of protons (H+) from one species (the acid) to another (the base). When a proton is removed from an acid, the resulting species is termed that acid's conjugate base. When the proton is accepted by a base, the resulting species is termed that base's conjugate acid. In other words, acids act as proton donors and bases act as proton acceptors according to the following equation: \underset{acid}{HA} + \underset{base}{B} <=> \underset{conjugated\ base}{A^-} + \underset{conjugated\ acid}{HB+} The reverse reaction is possible, and thus the acid/base and conjugated base/acid are always in equilibrium. The equilibrium is determined by the acid and base dissociation constants (Ka and Kb) of the involved substances. A special case of the acid-base reaction is the neutralization where an acid and a base, taken at the exact same amounts, form a neutral salt. Acid-base reactions can have different definitions depending on the acid-base concept employed. Some of the most common are: Arrhenius definition: Acids dissociate in water releasing H3O+ ions; bases dissociate in water releasing OH− ions. Brønsted–Lowry definition: Acids are proton (H+) donors, bases are proton acceptors; this includes the Arrhenius definition. Lewis definition: Acids are electron-pair acceptors, and bases are electron-pair donors; this includes the Brønsted-Lowry definition. Precipitation Precipitation is the formation of a solid in a solution or inside another solid during a chemical reaction. It usually takes place when the concentration of dissolved ions exceeds the solubility limit and forms an insoluble salt. This process can be assisted by adding a precipitating agent or by the removal of the solvent. Rapid precipitation results in an amorphous or microcrystalline residue and a slow process can yield single crystals. The latter can also be obtained by recrystallization from microcrystalline salts. Solid-state reactions Reactions can take place between two solids. However, because of the relatively small diffusion rates in solids, the corresponding chemical reactions are very slow in comparison to liquid and gas phase reactions. They are accelerated by increasing the reaction temperature and finely dividing the reactant to increase the contacting surface area. Reactions at the solid/gas interface The reaction can take place at the solid|gas interface, surfaces at very low pressure such as ultra-high vacuum. Via scanning tunneling microscopy, it is possible to observe reactions at the solid|gas interface in real space, if the time scale of the reaction is in the correct range. Reactions at the solid|gas interface are in some cases related to catalysis. Photochemical reactions In photochemical reactions, atoms and molecules absorb energy (photons) of the illumination light and convert it into an excited state. They can then release this energy by breaking chemical bonds, thereby producing radicals. Photochemical reactions include hydrogen–oxygen reactions, radical polymerization, chain reactions and rearrangement reactions. Many important processes involve photochemistry. The premier example is photosynthesis, in which most plants use solar energy to convert carbon dioxide and water into glucose, disposing of oxygen as a side-product. Humans rely on photochemistry for the formation of vitamin D, and vision is initiated by a photochemical reaction of rhodopsin. In fireflies, an enzyme in the abdomen catalyzes a reaction that results in bioluminescence. Many significant photochemical reactions, such as ozone formation, occur in the Earth atmosphere and constitute atmospheric chemistry. Catalysis In catalysis, the reaction does not proceed directly, but through a reaction with a third substance known as catalyst. Although the catalyst takes part in the reaction, forming weak bonds with reactants or intermediates, it is returned to its original state by the end of the reaction and so is not consumed. However, it can be inhibited, deactivated or destroyed by secondary processes. Catalysts can be used in a different phase (heterogeneous) or in the same phase (homogeneous) as the reactants. In heterogeneous catalysis, typical secondary processes include coking where the catalyst becomes covered by polymeric side products. Additionally, heterogeneous catalysts can dissolve into the solution in a solid-liquid system or evaporate in a solid–gas system. Catalysts can only speed up the reaction – chemicals that slow down the reaction are called inhibitors. Substances that increase the activity of catalysts are called promoters, and substances that deactivate catalysts are called catalytic poisons. With a catalyst, a reaction that is kinetically inhibited by high activation energy can take place in the circumvention of this activation energy. Heterogeneous catalysts are usually solids, powdered in order to maximize their surface area. Of particular importance in heterogeneous catalysis are the platinum group metals and other transition metals, which are used in hydrogenations, catalytic reforming and in the synthesis of commodity chemicals such as nitric acid and ammonia. Acids are an example of a homogeneous catalyst, they increase the nucleophilicity of carbonyls, allowing a reaction that would not otherwise proceed with electrophiles. The advantage of homogeneous catalysts is the ease of mixing them with the reactants, but they may also be difficult to separate from the products. Therefore, heterogeneous catalysts are preferred in many industrial processes. Reactions in organic chemistry In organic chemistry, in addition to oxidation, reduction or acid-base reactions, a number of other reactions can take place which involves covalent bonds between carbon atoms or carbon and heteroatoms (such as oxygen, nitrogen, halogens, etc.). Many specific reactions in organic chemistry are name reactions designated after their discoverers. One of the most industrially important reactions is the cracking of heavy hydrocarbons at oil refineries to create smaller, simpler molecules. This process is used to manufacture gasoline. Specific types of organic reactions may be grouped by their reaction mechanisms (particularly substitution, addition and elimination) or by the types of products they produce (for example, methylation, polymerisation and halogenation). Substitution In a substitution reaction, a functional group in a particular chemical compound is replaced by another group. These reactions can be distinguished by the type of substituting species into a nucleophilic, electrophilic or radical substitution. In the first type, a nucleophile, an atom or molecule with an excess of electrons and thus a negative charge or partial charge, replaces another atom or part of the "substrate" molecule. The electron pair from the nucleophile attacks the substrate forming a new bond, while the leaving group departs with an electron pair. The nucleophile may be electrically neutral or negatively charged, whereas the substrate is typically neutral or positively charged. Examples of nucleophiles are hydroxide ion, alkoxides, amines and halides. This type of reaction is found mainly in aliphatic hydrocarbons, and rarely in aromatic hydrocarbon. The latter have high electron density and enter nucleophilic aromatic substitution only with very strong electron withdrawing groups. Nucleophilic substitution can take place by two different mechanisms, SN1 and SN2. In their names, S stands for substitution, N for nucleophilic, and the number represents the kinetic order of the reaction, unimolecular or bimolecular. The SN1 reaction proceeds in two steps. First, the leaving group is eliminated creating a carbocation. This is followed by a rapid reaction with the nucleophile. In the SN2 mechanisms, the nucleophile forms a transition state with the attacked molecule, and only then the leaving group is cleaved. These two mechanisms differ in the stereochemistry of the products. SN1 leads to the non-stereospecific addition and does not result in a chiral center, but rather in a set of geometric isomers (cis/trans). In contrast, a reversal (Walden inversion) of the previously existing stereochemistry is observed in the SN2 mechanism. Electrophilic substitution is the counterpart of the nucleophilic substitution in that the attacking atom or molecule, an electrophile, has low electron density and thus a positive charge. Typical electrophiles are the carbon atom of carbonyl groups, carbocations or sulfur or nitronium cations. This reaction takes place almost exclusively in aromatic hydrocarbons, where it is called electrophilic aromatic substitution. The electrophile attack results in the so-called σ-complex, a transition state in which the aromatic system is abolished. Then, the leaving group, usually a proton, is split off and the aromaticity is restored. An alternative to aromatic substitution is electrophilic aliphatic substitution. It is similar to the nucleophilic aliphatic substitution and also has two major types, SE1 and SE2 In the third type of substitution reaction, radical substitution, the attacking particle is a radical. This process usually takes the form of a chain reaction, for example in the reaction of alkanes with halogens. In the first step, light or heat disintegrates the halogen-containing molecules producing radicals. Then the reaction proceeds as an avalanche until two radicals meet and recombine. X. + R-H -> X-H + R. R. + X2 -> R-X + X. Reactions during the chain reaction of radical substitution Addition and elimination The addition and its counterpart, the elimination, are reactions that change the number of substituents on the carbon atom, and form or cleave multiple bonds. Double and triple bonds can be produced by eliminating a suitable leaving group. Similar to the nucleophilic substitution, there are several possible reaction mechanisms that are named after the respective reaction order. In the E1 mechanism, the leaving group is ejected first, forming a carbocation. The next step, the formation of the double bond, takes place with the elimination of a proton (deprotonation). The leaving order is reversed in the E1cb mechanism, that is the proton is split off first. This mechanism requires the participation of a base. Because of the similar conditions, both reactions in the E1 or E1cb elimination always compete with the SN1 substitution. The E2 mechanism also requires a base, but there the attack of the base and the elimination of the leaving group proceed simultaneously and produce no ionic intermediate. In contrast to the E1 eliminations, different stereochemical configurations are possible for the reaction product in the E2 mechanism, because the attack of the base preferentially occurs in the anti-position with respect to the leaving group. Because of the similar conditions and reagents, the E2 elimination is always in competition with the SN2-substitution. The counterpart of elimination is an addition where double or triple bonds are converted into single bonds. Similar to substitution reactions, there are several types of additions distinguished by the type of the attacking particle. For example, in the electrophilic addition of hydrogen bromide, an electrophile (proton) attacks the double bond forming a carbocation, which then reacts with the nucleophile (bromine). The carbocation can be formed on either side of the double bond depending on the groups attached to its ends, and the preferred configuration can be predicted with the Markovnikov's rule. This rule states that "In the heterolytic addition of a polar molecule to an alkene or alkyne, the more electronegative (nucleophilic) atom (or part) of the polar molecule becomes attached to the carbon atom bearing the smaller number of hydrogen atoms." If the addition of a functional group takes place at the less substituted carbon atom of the double bond, then the electrophilic substitution with acids is not possible. In this case, one has to use the hydroboration–oxidation reaction, wherein the first step, the boron atom acts as electrophile and adds to the less substituted carbon atom. In the second step, the nucleophilic hydroperoxide or halogen anion attacks the boron atom. While the addition to the electron-rich alkenes and alkynes is mainly electrophilic, the nucleophilic addition plays an important role in the carbon-heteroatom multiple bonds, and especially its most important representative, the carbonyl group. This process is often associated with elimination so that after the reaction the carbonyl group is present again. It is, therefore, called an addition-elimination reaction and may occur in carboxylic acid derivatives such as chlorides, esters or anhydrides. This reaction is often catalyzed by acids or bases, where the acids increase the electrophilicity of the carbonyl group by binding to the oxygen atom, whereas the bases enhance the nucleophilicity of the attacking nucleophile. Nucleophilic addition of a carbanion or another nucleophile to the double bond of an alpha, beta-unsaturated carbonyl compound can proceed via the Michael reaction, which belongs to the larger class of conjugate additions. This is one of the most useful methods for the mild formation of C–C bonds. Some additions which can not be executed with nucleophiles and electrophiles can be succeeded with free radicals. As with the free-radical substitution, the radical addition proceeds as a chain reaction, and such reactions are the basis of the free-radical polymerization. Other organic reaction mechanisms In a rearrangement reaction, the carbon skeleton of a molecule is rearranged to give a structural isomer of the original molecule. These include hydride shift reactions such as the Wagner-Meerwein rearrangement, where a hydrogen, alkyl or aryl group migrates from one carbon to a neighboring carbon. Most rearrangements are associated with the breaking and formation of new carbon-carbon bonds. Other examples are sigmatropic reaction such as the Cope rearrangement. Cyclic rearrangements include cycloadditions and, more generally, pericyclic reactions, wherein two or more double bond-containing molecules form a cyclic molecule. An important example of cycloaddition reaction is the Diels–Alder reaction (the so-called [4+2] cycloaddition) between a conjugated diene and a substituted alkene to form a substituted cyclohexene system. Whether a certain cycloaddition would proceed depends on the electronic orbitals of the participating species, as only orbitals with the same sign of wave function will overlap and interact constructively to form new bonds. Cycloaddition is usually assisted by light or heat. These perturbations result in a different arrangement of electrons in the excited state of the involved molecules and therefore in different effects. For example, the [4+2] Diels-Alder reactions can be assisted by heat whereas the [2+2] cycloaddition is selectively induced by light. Because of the orbital character, the potential for developing stereoisomeric products upon cycloaddition is limited, as described by the Woodward–Hoffmann rules. Biochemical reactions Biochemical reactions are mainly controlled by complex proteins called enzymes, which are usually specialized to catalyze only a single, specific reaction. The reaction takes place in the active site, a small part of the enzyme which is usually found in a cleft or pocket lined by amino acid residues, and the rest of the enzyme is used mainly for stabilization. The catalytic action of enzymes relies on several mechanisms including the molecular shape ("induced fit"), bond strain, proximity and orientation of molecules relative to the enzyme, proton donation or withdrawal (acid/base catalysis), electrostatic interactions and many others. The biochemical reactions that occur in living organisms are collectively known as metabolism. Among the most important of its mechanisms is the anabolism, in which different DNA and enzyme-controlled processes result in the production of large molecules such as proteins and carbohydrates from smaller units. Bioenergetics studies the sources of energy for such reactions. Important energy sources are glucose and oxygen, which can be produced by plants via photosynthesis or assimilated from food and air, respectively. All organisms use this energy to produce adenosine triphosphate (ATP), which can then be used to energize other reactions. Decomposition of organic material by fungi, bacteria and other micro-organisms is also within the scope of biochemistry. Applications Chemical reactions are central to chemical engineering, where they are used for the synthesis of new compounds from natural raw materials such as petroleum, mineral ores, and oxygen in air. It is essential to make the reaction as efficient as possible, maximizing the yield and minimizing the number of reagents, energy inputs and waste. Catalysts are especially helpful for reducing the energy required for the reaction and increasing its reaction rate. Some specific reactions have their niche applications. For example, the thermite reaction is used to generate light and heat in pyrotechnics and welding. Although it is less controllable than the more conventional oxy-fuel welding, arc welding and flash welding, it requires much less equipment and is still used to mend rails, especially in remote areas. Monitoring Mechanisms of monitoring chemical reactions depend strongly on the reaction rate. Relatively slow processes can be analyzed in situ for the concentrations and identities of the individual ingredients. Important tools of real-time analysis are the measurement of pH and analysis of optical absorption (color) and emission spectra. A less accessible but rather efficient method is the introduction of a radioactive isotope into the reaction and monitoring how it changes over time and where it moves to; this method is often used to analyze the redistribution of substances in the human body. Faster reactions are usually studied with ultrafast laser spectroscopy where utilization of femtosecond lasers allows short-lived transition states to be monitored at a time scaled down to a few femtoseconds. See also Chemical equation Chemical reaction Substrate Reagent Catalyst Product Chemical reaction model Chemist Chemistry Combustion Limiting reagent List of organic reactions Mass balance Microscopic reversibility Organic reaction Reaction progress kinetic analysis Reversible reaction References Bibliography Chemistry Change

Chemistry

Chemistry is the scientific study of the properties and behavior of matter. It is a physical science within the natural sciences that studies the chemical elements that make up matter and compounds made of atoms, molecules and ions: their composition, structure, properties, behavior and the changes they undergo during reactions with other substances. Chemistry also addresses the nature of chemical bonds in chemical compounds. In the scope of its subject, chemistry occupies an intermediate position between physics and biology. It is sometimes called the central science because it provides a foundation for understanding both basic and applied scientific disciplines at a fundamental level. For example, chemistry explains aspects of plant growth (botany), the formation of igneous rocks (geology), how atmospheric ozone is formed and how environmental pollutants are degraded (ecology), the properties of the soil on the Moon (cosmochemistry), how medications work (pharmacology), and how to collect DNA evidence at a crime scene (forensics). Chemistry has existed under various names since ancient times. It has evolved, and now chemistry encompasses various areas of specialisation, or subdisciplines, that continue to increase in number and interrelate to create further interdisciplinary fields of study. The applications of various fields of chemistry are used frequently for economic purposes in the chemical industry. Etymology The word chemistry comes from a modification during the Renaissance of the word alchemy, which referred to an earlier set of practices that encompassed elements of chemistry, metallurgy, philosophy, astrology, astronomy, mysticism, and medicine. Alchemy is often associated with the quest to turn lead or other base metals into gold, though alchemists were also interested in many of the questions of modern chemistry. The modern word alchemy in turn is derived from the Arabic word . This may have Egyptian origins since is derived from the Ancient Greek , which is in turn derived from the word , which is the ancient name of Egypt in the Egyptian language. Alternately, may derive from 'cast together'. Modern principles The current model of atomic structure is the quantum mechanical model. Traditional chemistry starts with the study of elementary particles, atoms, molecules, substances, metals, crystals and other aggregates of matter. Matter can be studied in solid, liquid, gas and plasma states, in isolation or in combination. The interactions, reactions and transformations that are studied in chemistry are usually the result of interactions between atoms, leading to rearrangements of the chemical bonds which hold atoms together. Such behaviors are studied in a chemistry laboratory. The chemistry laboratory stereotypically uses various forms of laboratory glassware. However glassware is not central to chemistry, and a great deal of experimental (as well as applied/industrial) chemistry is done without it. A chemical reaction is a transformation of some substances into one or more different substances. The basis of such a chemical transformation is the rearrangement of electrons in the chemical bonds between atoms. It can be symbolically depicted through a chemical equation, which usually involves atoms as subjects. The number of atoms on the left and the right in the equation for a chemical transformation is equal. (When the number of atoms on either side is unequal, the transformation is referred to as a nuclear reaction or radioactive decay.) The type of chemical reactions a substance may undergo and the energy changes that may accompany it are constrained by certain basic rules, known as chemical laws. Energy and entropy considerations are invariably important in almost all chemical studies. Chemical substances are classified in terms of their structure, phase, as well as their chemical compositions. They can be analyzed using the tools of chemical analysis, e.g. spectroscopy and chromatography. Scientists engaged in chemical research are known as chemists. Most chemists specialize in one or more sub-disciplines. Several concepts are essential for the study of chemistry; some of them are: Matter In chemistry, matter is defined as anything that has rest mass and volume (it takes up space) and is made up of particles. The particles that make up matter have rest mass as well – not all particles have rest mass, such as the photon. Matter can be a pure chemical substance or a mixture of substances. Atom The atom is the basic unit of chemistry. It consists of a dense core called the atomic nucleus surrounded by a space occupied by an electron cloud. The nucleus is made up of positively charged protons and uncharged neutrons (together called nucleons), while the electron cloud consists of negatively charged electrons which orbit the nucleus. In a neutral atom, the negatively charged electrons balance out the positive charge of the protons. The nucleus is dense; the mass of a nucleon is approximately 1,836 times that of an electron, yet the radius of an atom is about 10,000 times that of its nucleus. The atom is also the smallest entity that can be envisaged to retain 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). Element A chemical element is a pure substance which is composed of a single type of atom, characterized by its particular number of protons in the nuclei of its atoms, known as the atomic number and represented by the symbol Z. The mass number is the sum of the number of protons and neutrons in a nucleus. Although all the nuclei of all atoms belonging to one element will have the same atomic number, they may not necessarily have the same mass number; atoms of an element which have different mass numbers are known as isotopes. For example, all atoms with 6 protons in their nuclei are atoms of the chemical element carbon, but atoms of carbon may have mass numbers of 12 or 13. The standard presentation of the chemical elements is in the periodic table, which orders elements by atomic number. The periodic table is arranged in groups, or columns, and periods, or rows. The periodic table is useful in identifying periodic trends. Compound A compound is a pure chemical substance composed of more than one element. The properties of a compound bear little similarity to those of its elements. The standard nomenclature of compounds is set by the International Union of Pure and Applied Chemistry (IUPAC). Organic compounds are named according to the organic nomenclature system. The names for inorganic compounds are created according to the inorganic nomenclature system. When a compound has more than one component, then they are divided into two classes, the electropositive and the electronegative components. In addition the Chemical Abstracts Service has devised a method to index chemical substances. In this scheme each chemical substance is identifiable by a number known as its CAS registry number. Molecule 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. However, this definition only works well for substances that are composed of molecules, which is not true of many substances (see below). 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. Thus, molecules exist as electrically neutral units, unlike ions. When this rule is broken, giving the "molecule" a charge, the result is sometimes named a molecular ion or a polyatomic ion. However, the discrete and separate nature of the molecular concept usually requires that molecular ions be present only in well-separated form, such as a directed beam in a vacuum in a mass spectrometer. Charged polyatomic collections residing in solids (for example, common sulfate or nitrate ions) are generally not considered "molecules" in chemistry. Some molecules contain one or more unpaired electrons, creating radicals. Most radicals are comparatively reactive, but some, such as nitric oxide (NO) can be stable. The "inert" or noble gas elements (helium, neon, argon, krypton, xenon and radon) are composed of lone atoms as their smallest discrete unit, but the other isolated chemical elements consist of either molecules or networks of atoms bonded to each other in some way. Identifiable molecules compose familiar substances such as water, air, and many organic compounds like alcohol, sugar, gasoline, and the various pharmaceuticals. However, not all substances or chemical compounds consist of discrete molecules, and indeed most of the solid substances that make up the solid crust, mantle, and core of the Earth are chemical compounds without molecules. These other types of substances, such as ionic compounds and network solids, are organized in such a way as to lack the existence of identifiable molecules per se. Instead, these substances are discussed in terms of formula units or unit cells as the smallest repeating structure within the substance. Examples of such substances are mineral salts (such as table salt), solids like carbon and diamond, metals, and familiar silica and silicate minerals such as quartz and granite. One of the main characteristics 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. Substance and mixture A chemical substance is a kind of matter with a definite composition and set of properties. A collection of substances is called a mixture. Examples of mixtures are air and alloys. Mole and amount of substance The mole is a unit of measurement that denotes an amount of substance (also called chemical amount). One mole is defined to contain exactly particles (atoms, molecules, ions, or electrons), where the number of particles per mole is known as the Avogadro constant. Molar concentration is the amount of a particular substance per volume of solution, and is commonly reported in mol/dm3. Phase In addition to the specific chemical properties that distinguish different chemical classifications, chemicals can exist in several phases. 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. The most familiar examples of phases are solids, liquids, and gases. 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. Bonding 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. The chemical bond can be a covalent bond, an ionic bond, a hydrogen bond or just because of Van der Waals force. Each of these kinds of bonds 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. An ionic bond is formed when a metal loses one or more of its electrons, becoming a positively charged cation, and the electrons are then gained by the non-metal atom, becoming a negatively charged anion. The two oppositely charged ions attract one another, and the ionic bond is the electrostatic force of attraction between them. For example, sodium (Na), a metal, loses one electron to become an Na+ cation while chlorine (Cl), a non-metal, gains this electron to become Cl−. The ions are held together due to electrostatic attraction, and that compound sodium chloride (NaCl), or common table salt, is formed. In a covalent bond, one or more pairs of valence electrons are shared by two atoms: the resulting electrically neutral group of bonded atoms is termed a molecule. Atoms will share valence electrons in such a way as to create a noble gas electron configuration (eight electrons in their outermost shell) for each atom. Atoms that tend to combine in such a way that they each have eight electrons in their valence shell are said to follow the octet rule. However, some elements like hydrogen and lithium need only two electrons in their outermost shell to attain this stable configuration; these atoms are said to follow the duet rule, and in this way they are reaching the electron configuration of the noble gas helium, which has two electrons in its outer shell. 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. Energy 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 structures, 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 a 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 to occur 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. The term chemical energy is often used to indicate the potential of a chemical substance to undergo a transformation through a chemical reaction or to transform other chemical substances. Reaction When a chemical substance is transformed as a result of its interaction with another substance or with energy, a chemical reaction is said to have occurred. A 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 as with the system environment, which may be designed vessels—often laboratory glassware. Chemical reactions can result in the formation or dissociation of molecules, that is, molecules breaking apart to form two or more 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 examples of common 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 in 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'). Ions and salts An ion is a charged species, an atom or a molecule, that has lost or gained one or more electrons. When an atom loses an electron and thus has more protons than electrons, the atom is a positively charged ion or cation. When an atom gains an electron and thus has more electrons than protons, the atom is a negatively charged ion or anion. Cations and anions can form a crystalline lattice of neutral salts, such as the Na+ and Cl− ions forming sodium chloride, or NaCl. Examples of polyatomic ions that do not split up during acid–base reactions are hydroxide (OH−) and phosphate (PO43−). Plasma is composed of gaseous matter that has been completely ionized, usually through high temperature. 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 that 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. 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 measures 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. Redox Redox (-) reactions include all chemical reactions in which atoms have their oxidation state changed by either gaining electrons (reduction) or losing electrons (oxidation). 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. Equilibrium 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, as 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. Chemical laws 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 laws of diffusion Gay-Lussac's law (1809, relating pressure and temperature) Le Chatelier's principle 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 continues to be conserved in isolated systems, even in modern physics. However, special relativity shows that due to mass–energy equivalence, whenever non-material "energy" (heat, light, kinetic energy) is removed from a non-isolated system, some mass will be lost with it. High energy losses result in loss of weighable amounts of mass, an important topic 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 History The history of chemistry spans a period from the ancient past to the present. Since several millennia BC, civilizations were using technologies that would eventually form the basis of the various branches of chemistry. Examples include extracting metals from ores, making pottery and glazes, fermenting beer and wine, extracting chemicals from plants for medicine and perfume, rendering fat into soap, making glass, and making alloys like bronze. Chemistry was preceded by its protoscience, alchemy, which operated a non-scientific approach to understanding the constituents of matter and their interactions. Despite being unsuccessful in explaining the nature of matter and its transformations, alchemists set the stage for modern chemistry by performing experiments and recording the results. Robert Boyle, although skeptical of elements and convinced of alchemy, played a key part in elevating the "sacred art" as an independent, fundamental and philosophical discipline in his work The Sceptical Chymist (1661). While both alchemy and chemistry are concerned with matter and its transformations, the crucial difference was given by the scientific method that chemists employed in their work. Chemistry, as a body of knowledge distinct from alchemy, became an established science with the work of Antoine Lavoisier, who developed a law of conservation of mass that demanded careful measurement and quantitative observations of chemical phenomena. The history of chemistry afterwards is intertwined with the history of thermodynamics, especially through the work of Willard Gibbs. Definition The definition of chemistry has changed over time, as new discoveries and theories add to the functionality of the science. The term "chymistry", in the view of noted scientist Robert Boyle in 1661, meant the subject of the material principles of mixed bodies. In 1663, the chemist Christopher Glaser described "chymistry" as a scientific art, by which one learns to dissolve bodies, and draw from them the different substances on their composition, and how to unite them again, and exalt them to a higher perfection. The 1730 definition of the word "chemistry", as used by Georg Ernst Stahl, meant the art of resolving mixed, compound, or aggregate bodies into their principles; and of composing such bodies from those principles. In 1837, Jean-Baptiste Dumas considered the word "chemistry" to refer to the science concerned with the laws and effects of molecular forces. This definition further evolved until, in 1947, it came to mean the science of substances: their structure, their properties, and the reactions that change them into other substances – a characterization accepted by Linus Pauling. More recently, in 1998, Professor Raymond Chang broadened the definition of "chemistry" to mean the study of matter and the changes it undergoes. Background Early civilizations, such as the Egyptians Babylonians and Indians amassed practical knowledge concerning the arts of metallurgy, pottery and dyes, but did not develop a systematic theory. A basic chemical hypothesis first emerged in Classical Greece with the theory of four elements as propounded definitively by Aristotle stating that fire, air, earth and water were the fundamental elements from which everything is formed as a combination. Greek atomism dates back to 440 BC, arising in works by philosophers such as Democritus and Epicurus. In 50 BCE, the Roman philosopher Lucretius expanded upon the theory in his poem De rerum natura (On The Nature of Things). Unlike modern concepts of science, Greek atomism was purely philosophical in nature, with little concern for empirical observations and no concern for chemical experiments. An early form of the idea of conservation of mass is the notion that "Nothing comes from nothing" in Ancient Greek philosophy, which can be found in Empedocles (approx. 4th century BC): "For it is impossible for anything to come to be from what is not, and it cannot be brought about or heard of that what is should be utterly destroyed." and Epicurus (3rd century BC), who, describing the nature of the Universe, wrote that "the totality of things was always such as it is now, and always will be". In the Hellenistic world the art of alchemy first proliferated, mingling magic and occultism into the study of natural substances with the ultimate goal of transmuting elements into gold and discovering the elixir of eternal life. Work, particularly the development of distillation, continued in the early Byzantine period with the most famous practitioner being the 4th century Greek-Egyptian Zosimos of Panopolis. Alchemy continued to be developed and practised throughout the Arab world after the Muslim conquests, and from there, and from the Byzantine remnants, diffused into medieval and Renaissance Europe through Latin translations. The Arabic works attributed to Jabir ibn Hayyan introduced a systematic classification of chemical substances, and provided instructions for deriving an inorganic compound (sal ammoniac or ammonium chloride) from organic substances (such as plants, blood, and hair) by chemical means. Some Arabic Jabirian works (e.g., the "Book of Mercy", and the "Book of Seventy") were later translated into Latin under the Latinized name "Geber", and in 13th-century Europe an anonymous writer, usually referred to as pseudo-Geber, started to produce alchemical and metallurgical writings under this name. Later influential Muslim philosophers, such as Abū al-Rayhān al-Bīrūnī and Avicenna disputed the theories of alchemy, particularly the theory of the transmutation of metals. Improvements of the refining of ores and their extractions to smelt metals was widely used source of information for early chemists in the 16th century, among them Georg Agricola (1494–1555), who published his major work De re metallica in 1556. His work, describing highly developed and complex processes of mining metal ores and metal extraction, were the pinnacle of metallurgy during that time. His approach removed all mysticism associated with the subject, creating the practical base upon which others could and would build. The work describes the many kinds of furnace used to smelt ore, and stimulated interest in minerals and their composition. Agricola has been described as the "father of metallurgy" and the founder of geology as a scientific discipline. Under the influence of the new empirical methods propounded by Sir Francis Bacon and others, a group of chemists at Oxford, Robert Boyle, Robert Hooke and John Mayow began to reshape the old alchemical traditions into a scientific discipline. Boyle in particular questioned some commonly held chemical theories and argued for chemical practitioners to be more "philosophical" and less commercially focused in The Sceptical Chemyst. He formulated Boyle's law, rejected the classical "four elements" and proposed a mechanistic alternative of atoms and chemical reactions that could be subject to rigorous experiment. In the following decades, many important discoveries were made, such as the nature of 'air' which was discovered to be composed of many different gases. The Scottish chemist Joseph Black and the Flemish Jan Baptist van Helmont discovered carbon dioxide, or what Black called 'fixed air' in 1754; Henry Cavendish discovered hydrogen and elucidated its properties and Joseph Priestley and, independently, Carl Wilhelm Scheele isolated pure oxygen. The theory of phlogiston (a substance at the root of all combustion) was propounded by the German Georg Ernst Stahl in the early 18th century and was only overturned by the end of the century by the French chemist Antoine Lavoisier, the chemical analogue of Newton in physics. Lavoisier did more than any other to establish the new science on proper theoretical footing, by elucidating the principle of conservation of mass and developing a new system of chemical nomenclature used to this day. English scientist John Dalton proposed the modern theory of atoms; that all substances are composed of indivisible 'atoms' of matter and that different atoms have varying atomic weights. The development of the electrochemical theory of chemical combinations occurred in the early 19th century as the result of the work of two scientists in particular, Jöns Jacob Berzelius and Humphry Davy, made possible by the prior invention of the voltaic pile by Alessandro Volta. Davy discovered nine new elements including the alkali metals by extracting them from their oxides with electric current. British William Prout first proposed ordering all the elements by their atomic weight as all atoms had a weight that was an exact multiple of the atomic weight of hydrogen. J.A.R. Newlands devised an early table of elements, which was then developed into the modern periodic table of elements in the 1860s by Dmitri Mendeleev and independently by several other scientists including Julius Lothar Meyer. The inert gases, later called the noble gases were discovered by William Ramsay in collaboration with Lord Rayleigh at the end of the century, thereby filling in the basic structure of the table. At the turn of the twentieth century the theoretical underpinnings of chemistry were finally understood due to a series of remarkable discoveries that succeeded in probing and discovering the very nature of the internal structure of atoms. In 1897, J.J. Thomson of the University of Cambridge discovered the electron and soon after the French scientist Becquerel as well as the couple Pierre and Marie Curie investigated the phenomenon of radioactivity. In a series of pioneering scattering experiments Ernest Rutherford at the University of Manchester discovered the internal structure of the atom and the existence of the proton, classified and explained the different types of radioactivity and successfully transmuted the first element by bombarding nitrogen with alpha particles. His work on atomic structure was improved on by his students, the Danish physicist Niels Bohr, the Englishman Henry Moseley and the German Otto Hahn, who went on to father the emerging nuclear chemistry and discovered nuclear fission. The electronic theory of chemical bonds and molecular orbitals was developed by the American scientists Linus Pauling and Gilbert N. Lewis. The year 2011 was declared by the United Nations as the International Year of Chemistry. It was an initiative of the International Union of Pure and Applied Chemistry, and of the United Nations Educational, Scientific, and Cultural Organization and involves chemical societies, academics, and institutions worldwide and relied on individual initiatives to organize local and regional activities. Organic chemistry was developed by Justus von Liebig and others, following Friedrich Wöhler's synthesis of urea. Other crucial 19th century advances were; an understanding of valence bonding (Edward Frankland in 1852) and the application of thermodynamics to chemistry (J. W. Gibbs and Svante Arrhenius in the 1870s). Practice In the practice of chemistry, pure chemistry is the study of the fundamental principles of chemistry, while applied chemistry applies that knowledge to develop technology and solve real-world problems. Subdisciplines Chemistry is typically divided into several major sub-disciplines. There are also several main cross-disciplinary and more specialized fields of chemistry. Analytical chemistry is the analysis of material samples to gain an understanding of their chemical composition and structure. Analytical chemistry incorporates standardized experimental methods in chemistry. These methods may be used in all subdisciplines of chemistry, excluding purely theoretical chemistry. Biochemistry is the study of the chemicals, chemical reactions and interactions that take place at a molecular level in living organisms. Biochemistry is highly interdisciplinary, covering medicinal chemistry, neurochemistry, molecular biology, forensics, plant science and genetics. Inorganic chemistry is the study of the properties and reactions of inorganic compounds, such as metals and minerals. The distinction between organic and inorganic disciplines is not absolute and there is much overlap, most importantly in the sub-discipline of organometallic chemistry. Materials chemistry is the preparation, characterization, and understanding of solid state components or devices with a useful current or future function. The field is a new breadth of study in graduate programs, and it integrates elements from all classical areas of chemistry like organic chemistry, inorganic chemistry, and crystallography with a focus on fundamental issues that are unique to materials. Primary systems of study include the chemistry of condensed phases (solids, liquids, polymers) and interfaces between different phases. Neurochemistry is the study of neurochemicals; including transmitters, peptides, proteins, lipids, sugars, and nucleic acids; their interactions, and the roles they play in forming, maintaining, and modifying the nervous system. Nuclear chemistry is the study of how subatomic particles come together and make nuclei. Modern transmutation is a large component of nuclear chemistry, and the table of nuclides is an important result and tool for this field. In addition to medical applications, nuclear chemistry encompasses nuclear engineering which explores the topic of using nuclear power sources for generating energy Organic chemistry is the study of the structure, properties, composition, mechanisms, and reactions of organic compounds. An organic compound is defined as any compound based on a carbon skeleton. Organic compounds can be classified, organized and understood in reactions by their functional groups, unit atoms or molecules that show characteristic chemical properties in a compound. Physical chemistry is the study of the physical and fundamental basis of chemical systems and processes. In particular, the energetics and dynamics of such systems and processes are of interest to physical chemists. Important areas of study include chemical thermodynamics, chemical kinetics, electrochemistry, statistical mechanics, spectroscopy, and more recently, astrochemistry. Physical chemistry has large overlap with molecular physics. Physical chemistry involves the use of infinitesimal calculus in deriving equations. It is usually associated with quantum chemistry and theoretical chemistry. Physical chemistry is a distinct discipline from chemical physics, but again, there is very strong overlap. Theoretical chemistry is the study of chemistry via fundamental theoretical reasoning (usually within mathematics or physics). In particular the application of quantum mechanics to chemistry is called quantum chemistry. Since the end of the Second World War, the development of computers has allowed a systematic development of computational chemistry, which is the art of developing and applying computer programs for solving chemical problems. Theoretical chemistry has large overlap with (theoretical and experimental) condensed matter physics and molecular physics. Others subdivisions include electrochemistry, femtochemistry, flavor chemistry, flow chemistry, immunohistochemistry, hydrogenation chemistry, mathematical chemistry, molecular mechanics, natural product chemistry, organometallic chemistry, petrochemistry, photochemistry, physical organic chemistry, polymer chemistry, radiochemistry, sonochemistry, supramolecular chemistry, synthetic chemistry, and many others. Interdisciplinary Interdisciplinary fields include agrochemistry, astrochemistry (and cosmochemistry), atmospheric chemistry, chemical engineering, chemical biology, chemo-informatics, environmental chemistry, geochemistry, green chemistry, immunochemistry, marine chemistry, materials science, mechanochemistry, medicinal chemistry, molecular biology, nanotechnology, oenology, pharmacology, phytochemistry, solid-state chemistry, surface science, thermochemistry, and many others. Industry The chemical industry represents an important economic activity worldwide. The global top 50 chemical producers in 2013 had sales of US$980.5 billion with a profit margin of 10.3%. Professional societies American Chemical Society American Society for Neurochemistry Chemical Institute of Canada Chemical Society of Peru International Union of Pure and Applied Chemistry Royal Australian Chemical Institute Royal Netherlands Chemical Society Royal Society of Chemistry Society of Chemical Industry World Association of Theoretical and Computational Chemists List of chemistry societies See also Comparison of software for molecular mechanics modeling Glossary of chemistry terms International Year of Chemistry List of chemists List of compounds List of important publications in chemistry List of unsolved problems in chemistry Outline of chemistry Periodic systems of small molecules Philosophy of chemistry Science tourism References Bibliography Further reading Popular reading Atkins, P. W. Galileo's Finger (Oxford University Press) Atkins, P. W. Atkins' Molecules (Cambridge University Press) Kean, Sam. The Disappearing Spoon – and Other True Tales from the Periodic Table (Black Swan) London, England, 2010 Levi, Primo The Periodic Table (Penguin Books) [1975] translated from the Italian by Raymond Rosenthal (1984) Stwertka, A. A Guide to the Elements (Oxford University Press) Introductory undergraduate textbooks Atkins, P.W., Overton, T., Rourke, J., Weller, M. and Armstrong, F. Shriver and Atkins Inorganic Chemistry (4th ed.) 2006 (Oxford University Press) Chang, Raymond. Chemistry 6th ed. Boston, Massachusetts: James M. Smith, 1998. Voet and Voet. Biochemistry (Wiley) Advanced undergraduate-level or graduate textbooks Atkins, P. W. Physical Chemistry (Oxford University Press) Atkins, P. W. et al. Molecular Quantum Mechanics (Oxford University Press) McWeeny, R. Coulson's Valence (Oxford Science Publications) Pauling, L. The Nature of the chemical bond (Cornell University Press) Pauling, L., and Wilson, E. B. Introduction to Quantum Mechanics with Applications to Chemistry (Dover Publications) Smart and Moore. Solid State Chemistry: An Introduction (Chapman and Hall) Stephenson, G. Mathematical Methods for Science Students (Longman) External links General Chemistry principles, patterns and applications.

Analysis

Analysis (: analyses) is the process of breaking a complex topic or substance into smaller parts in order to gain a better understanding of it. The technique has been applied in the study of mathematics and logic since before Aristotle (384–322 B.C.), though analysis as a formal concept is a relatively recent development. The word comes from the Ancient Greek (analysis, "a breaking-up" or "an untying;" from ana- "up, throughout" and lysis "a loosening"). From it also comes the word's plural, analyses. As a formal concept, the method has variously been ascribed to René Descartes (Discourse on the Method), and Galileo Galilei. It has also been ascribed to Isaac Newton, in the form of a practical method of physical discovery (which he did not name). The converse of analysis is synthesis: putting the pieces back together again in a new or different whole. Science and technology Chemistry The field of chemistry uses analysis in three ways: to identify the components of a particular chemical compound (qualitative analysis), to identify the proportions of components in a mixture (quantitative analysis), and to break down chemical processes and examine chemical reactions between elements of matter. For an example of its use, analysis of the concentration of elements is important in managing a nuclear reactor, so nuclear scientists will analyze neutron activation to develop discrete measurements within vast samples. A matrix can have a considerable effect on the way a chemical analysis is conducted and the quality of its results. Analysis can be done manually or with a device. Types of Analysis A) Qualitative Analysis: It is concerned with which components are in a given sample or compound. Example: Precipitation reaction B) Quantitative Analysis: It is to determine the quantity of individual component present in a given sample or compound. Example: To find concentration by uv-spectrophotometer. Isotopes Chemists can use isotope analysis to assist analysts with issues in anthropology, archeology, food chemistry, forensics, geology, and a host of other questions of physical science. Analysts can discern the origins of natural and man-made isotopes in the study of environmental radioactivity. Computer science Requirements analysis – encompasses those tasks that go into determining the needs or conditions to meet for a new or altered product, taking account of the possibly conflicting requirements of the various stakeholders, such as beneficiaries or users. Competitive analysis (online algorithm) – shows how online algorithms perform and demonstrates the power of randomization in algorithms Lexical analysis – the process of processing an input sequence of characters and producing as output a sequence of symbols Object-oriented analysis and design – à la Booch Program analysis (computer science) – the process of automatically analysing the behavior of computer programs Semantic analysis (computer science) – a pass by a compiler that adds semantical information to the parse tree and performs certain checks Static code analysis – the analysis of computer software that is performed without actually executing programs built from that Structured systems analysis and design methodology – à la Yourdon Syntax analysis – a process in compilers that recognizes the structure of programming languages, also known as parsing Worst-case execution time – determines the longest time that a piece of software can take to run Engineering Analysts in the field of engineering look at requirements, structures, mechanisms, systems and dimensions. Electrical engineers analyse systems in electronics. Life cycles and system failures are broken down and studied by engineers. It is also looking at different factors incorporated within the design. Mathematics Modern mathematical analysis is the study of infinite processes. It is the branch of mathematics that includes calculus. It can be applied in the study of classical concepts of mathematics, such as real numbers, complex variables, trigonometric functions, and algorithms, or of non-classical concepts like constructivism, harmonics, infinity, and vectors. Florian Cajori explains in A History of Mathematics (1893) the difference between modern and ancient mathematical analysis, as distinct from logical analysis, as follows: The terms synthesis and analysis are used in mathematics in a more special sense than in logic. In ancient mathematics they had a different meaning from what they now have. The oldest definition of mathematical analysis as opposed to synthesis is that given in [appended to] Euclid, XIII. 5, which in all probability was framed by Eudoxus: "Analysis is the obtaining of the thing sought by assuming it and so reasoning up to an admitted truth; synthesis is the obtaining of the thing sought by reasoning up to the inference and proof of it." The analytic method is not conclusive, unless all operations involved in it are known to be reversible. To remove all doubt, the Greeks, as a rule, added to the analytic process a synthetic one, consisting of a reversion of all operations occurring in the analysis. Thus the aim of analysis was to aid in the discovery of synthetic proofs or solutions. James Gow uses a similar argument as Cajori, with the following clarification, in his A Short History of Greek Mathematics (1884): The synthetic proof proceeds by shewing that the proposed new truth involves certain admitted truths. An analytic proof begins by an assumption, upon which a synthetic reasoning is founded. The Greeks distinguished theoretic from problematic analysis. A theoretic analysis is of the following kind. To prove that A is B, assume first that A is B. If so, then, since B is C and C is D and D is E, therefore A is E. If this be known a falsity, A is not B. But if this be a known truth and all the intermediate propositions be convertible, then the reverse process, A is E, E is D, D is C, C is B, therefore A is B, constitutes a synthetic proof of the original theorem. Problematic analysis is applied in all cases where it is proposed to construct a figure which is assumed to satisfy a given condition. The problem is then converted into some theorem which is involved in the condition and which is proved synthetically, and the steps of this synthetic proof taken backwards are a synthetic solution of the problem. Psychotherapy Psychoanalysis – seeks to elucidate connections among unconscious components of patients' mental processes Transactional analysis Transactional analysis is used by therapists to try to gain a better understanding of the unconscious. It focuses on understanding and intervening human behavior. Signal processing Finite element analysis – a computer simulation technique used in engineering analysis Independent component analysis Link quality analysis – the analysis of signal quality Path quality analysis Fourier analysis Statistics In statistics, the term analysis may refer to any method used for data analysis. Among the many such methods, some are: Analysis of variance (ANOVA) – a collection of statistical models and their associated procedures which compare means by splitting the overall observed variance into different parts Boolean analysis – a method to find deterministic dependencies between variables in a sample, mostly used in exploratory data analysis Cluster analysis – techniques for finding groups (called clusters), based on some measure of proximity or similarity Factor analysis – a method to construct models describing a data set of observed variables in terms of a smaller set of unobserved variables (called factors) Meta-analysis – combines the results of several studies that address a set of related research hypotheses Multivariate analysis – analysis of data involving several variables, such as by factor analysis, regression analysis, or principal component analysis Principal component analysis – transformation of a sample of correlated variables into uncorrelated variables (called principal components), mostly used in exploratory data analysis Regression analysis – techniques for analysing the relationships between several predictive variables and one or more outcomes in the data Scale analysis (statistics) – methods to analyse survey data by scoring responses on a numeric scale Sensitivity analysis – the study of how the variation in the output of a model depends on variations in the inputs Sequential analysis – evaluation of sampled data as it is collected, until the criterion of a stopping rule is met Spatial analysis – the study of entities using geometric or geographic properties Time-series analysis – methods that attempt to understand a sequence of data points spaced apart at uniform time intervals Business Business Financial statement analysis – the analysis of the accounts and the economic prospects of a firm Financial analysis – refers to an assessment of the viability, stability, and profitability of a business, sub-business or project Gap analysis – involves the comparison of actual performance with potential or desired performance of an organization Business analysis – involves identifying the needs and determining the solutions to business problems Price analysis – involves the breakdown of a price to a unit figure Market analysis – consists of suppliers and customers, and price is determined by the interaction of supply and demand Sum-of-the-parts analysis – method of valuation of a multi-divisional company Opportunity analysis – consists of customers trends within the industry, customer demand and experience determine purchasing behavior Economics Agroecosystem analysis Input–output model if applied to a region, is called Regional Impact Multiplier System Government Intelligence The field of intelligence employs analysts to break down and understand a wide array of questions. Intelligence agencies may use heuristics, inductive and deductive reasoning, social network analysis, dynamic network analysis, link analysis, and brainstorming to sort through problems they face. Military intelligence may explore issues through the use of game theory, Red Teaming, and wargaming. Signals intelligence applies cryptanalysis and frequency analysis to break codes and ciphers. Business intelligence applies theories of competitive intelligence analysis and competitor analysis to resolve questions in the marketplace. Law enforcement intelligence applies a number of theories in crime analysis. Policy Policy analysis – The use of statistical data to predict the effects of policy decisions made by governments and agencies Policy analysis includes a systematic process to find the most efficient and effective option to address the current situation. Qualitative analysis – The use of anecdotal evidence to predict the effects of policy decisions or, more generally, influence policy decisions Humanities and social sciences Linguistics Linguistics explores individual languages and language in general. It breaks language down and analyses its component parts: theory, sounds and their meaning, utterance usage, word origins, the history of words, the meaning of words and word combinations, sentence construction, basic construction beyond the sentence level, stylistics, and conversation. It examines the above using statistics and modeling, and semantics. It analyses language in context of anthropology, biology, evolution, geography, history, neurology, psychology, and sociology. It also takes the applied approach, looking at individual language development and clinical issues. Literature Literary criticism is the analysis of literature. The focus can be as diverse as the analysis of Homer or Freud. While not all literary-critical methods are primarily analytical in nature, the main approach to the teaching of literature in the west since the mid-twentieth century, literary formal analysis or close reading, is. This method, rooted in the academic movement labelled The New Criticism, approaches texts – chiefly short poems such as sonnets, which by virtue of their small size and significant complexity lend themselves well to this type of analysis – as units of discourse that can be understood in themselves, without reference to biographical or historical frameworks. This method of analysis breaks up the text linguistically in a study of prosody (the formal analysis of meter) and phonic effects such as alliteration and rhyme, and cognitively in examination of the interplay of syntactic structures, figurative language, and other elements of the poem that work to produce its larger effects. Music Musical analysis – a process attempting to answer the question "How does this music work?" Musical Analysis is a study of how the composers use the notes together to compose music. Those studying music will find differences with each composer's musical analysis, which differs depending on the culture and history of music studied. An analysis of music is meant to simplify the music for you. Schenkerian analysis Schenkerian analysis is a collection of music analysis that focuses on the production of the graphic representation. This includes both analytical procedure as well as the notational style. Simply put, it analyzes tonal music which includes all chords and tones within a composition. Philosophy Philosophical analysis – a general term for the techniques used by philosophers Philosophical analysis refers to the clarification and composition of words put together and the entailed meaning behind them. Philosophical analysis dives deeper into the meaning of words and seeks to clarify that meaning by contrasting the various definitions. It is the study of reality, justification of claims, and the analysis of various concepts. Branches of philosophy include logic, justification, metaphysics, values and ethics. If questions can be answered empirically, meaning it can be answered by using the senses, then it is not considered philosophical. Non-philosophical questions also include events that happened in the past, or questions science or mathematics can answer. Analysis is the name of a prominent journal in philosophy. Other Aura analysis – a pseudoscientific technique in which supporters of the method claim that the body's aura, or energy field is analysed Bowling analysis – Analysis of the performance of cricket players Lithic analysis – the analysis of stone tools using basic scientific techniques Lithic analysis is most often used by archeologists in determining which types of tools were used at a given time period pertaining to current artifacts discovered. Protocol analysis – a means for extracting persons' thoughts while they are performing a task See also Formal analysis Metabolism in biology Methodology Scientific method References External links Abstraction Critical thinking skills Emergence Empiricism Epistemological theories Intelligence Mathematical modeling Metaphysics of mind Methodology Ontology Philosophy of logic Rationalism Reasoning Research methods Scientific method Theory of mind

Anabolism

Anabolism is the set of metabolic pathways that construct macromolecules like DNA or RNA from smaller units. These reactions require energy, known also as an endergonic process. Anabolism is the building-up aspect of metabolism, whereas catabolism is the breaking-down aspect. Anabolism is usually synonymous with biosynthesis. Pathway Polymerization, an anabolic pathway used to build macromolecules such as nucleic acids, proteins, and polysaccharides, uses condensation reactions to join monomers. Macromolecules are created from smaller molecules using enzymes and cofactors. Energy source Anabolism is powered by catabolism, where large molecules are broken down into smaller parts and then used up in cellular respiration. Many anabolic processes are powered by the cleavage of adenosine triphosphate (ATP). Anabolism usually involves reduction and decreases entropy, making it unfavorable without energy input. The starting materials, called the precursor molecules, are joined using the chemical energy made available from hydrolyzing ATP, reducing the cofactors NAD+, NADP+, and FAD, or performing other favorable side reactions. Occasionally it can also be driven by entropy without energy input, in cases like the formation of the phospholipid bilayer of a cell, where hydrophobic interactions aggregate the molecules. Cofactors The reducing agents NADH, NADPH, and FADH2, as well as metal ions, act as cofactors at various steps in anabolic pathways. NADH, NADPH, and FADH2 act as electron carriers, while charged metal ions within enzymes stabilize charged functional groups on substrates. Substrates Substrates for anabolism are mostly intermediates taken from catabolic pathways during periods of high energy charge in the cell. Functions Anabolic processes build organs and tissues. These processes produce growth and differentiation of cells and increase in body size, a process that involves synthesis of complex molecules. Examples of anabolic processes include the growth and mineralization of bone and increases in muscle mass. Anabolic hormones Endocrinologists have traditionally classified hormones as anabolic or catabolic, depending on which part of metabolism they stimulate. The classic anabolic hormones are the anabolic steroids, which stimulate protein synthesis and muscle growth, and insulin. Photosynthetic carbohydrate synthesis Photosynthetic carbohydrate synthesis in plants and certain bacteria is an anabolic process that produces glucose, cellulose, starch, lipids, and proteins from CO2. It uses the energy produced from the light-driven reactions of photosynthesis, and creates the precursors to these large molecules via carbon assimilation in the photosynthetic carbon reduction cycle, a.k.a. the Calvin cycle. Amino acid biosynthesis All amino acids are formed from intermediates in the catabolic processes of glycolysis, the citric acid cycle, or the pentose phosphate pathway. From glycolysis, glucose 6-phosphate is a precursor for histidine; 3-phosphoglycerate is a precursor for glycine and cysteine; phosphoenol pyruvate, combined with the 3-phosphoglycerate-derivative erythrose 4-phosphate, forms tryptophan, phenylalanine, and tyrosine; and pyruvate is a precursor for alanine, valine, leucine, and isoleucine. From the citric acid cycle, α-ketoglutarate is converted into glutamate and subsequently glutamine, proline, and arginine; and oxaloacetate is converted into aspartate and subsequently asparagine, methionine, threonine, and lysine. Glycogen storage During periods of high blood sugar, glucose 6-phosphate from glycolysis is diverted to the glycogen-storing pathway. It is changed to glucose-1-phosphate by phosphoglucomutase and then to UDP-glucose by UTP--glucose-1-phosphate uridylyltransferase. Glycogen synthase adds this UDP-glucose to a glycogen chain. Gluconeogenesis Glucagon is traditionally a catabolic hormone, but also stimulates the anabolic process of gluconeogenesis by the liver, and to a lesser extent the kidney cortex and intestines, during starvation to prevent low blood sugar. It is the process of converting pyruvate into glucose. Pyruvate can come from the breakdown of glucose, lactate, amino acids, or glycerol. The gluconeogenesis pathway has many reversible enzymatic processes in common with glycolysis, but it is not the process of glycolysis in reverse. It uses different irreversible enzymes to ensure the overall pathway runs in one direction only. Regulation Anabolism operates with separate enzymes from catalysis, which undergo irreversible steps at some point in their pathways. This allows the cell to regulate the rate of production and prevent an infinite loop, also known as a futile cycle, from forming with catabolism. The balance between anabolism and catabolism is sensitive to ADP and ATP, otherwise known as the energy charge of the cell. High amounts of ATP cause cells to favor the anabolic pathway and slow catabolic activity, while excess ADP slows anabolism and favors catabolism. These pathways are also regulated by circadian rhythms, with processes such as glycolysis fluctuating to match an animal's normal periods of activity throughout the day. Etymology The word anabolism is from Neo-Latin, with roots from , "upward" and , "to throw". References Metabolism

Metabolism

Metabolism (, from metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks of proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transportation of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary (or intermediate) metabolism. Metabolic reactions may be categorized as catabolic—the breaking down of compounds (for example, of glucose to pyruvate by cellular respiration); or anabolic—the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy. The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy and will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts—they allow a reaction to proceed more rapidly—and they also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells. The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The basal metabolic rate of an organism is the measure of the amount of energy consumed by all of these chemical reactions. A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants. These similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention is likely due to their efficacy. In various diseases, such as type II diabetes, metabolic syndrome, and cancer, normal metabolism is disrupted. The metabolism of cancer cells is also different from the metabolism of normal cells, and these differences can be used to find targets for therapeutic intervention in cancer. Key biochemicals Most of the structures that make up animals, plants and microbes are made from four basic classes of molecules: amino acids, carbohydrates, nucleic acid and lipids (often called fats). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or on breaking them down and using them to obtain energy, by their digestion. These biochemicals can be joined to make polymers such as DNA and proteins, essential macromolecules of life. Amino acids and proteins Proteins are made of amino acids arranged in a linear chain joined by peptide bonds. Many proteins are enzymes that catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle. Amino acids also contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle (tricarboxylic acid cycle), especially when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress. Lipids Lipids are the most diverse group of biochemicals. Their main structural uses are as part of internal and external biological membranes, such as the cell membrane. Their chemical energy can also be used. Lipids contain a long, non-polar hydrocarbon chain with a small polar region containing oxygen. Lipids are usually defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as ethanol, benzene or chloroform. The fats are a large group of compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty acids by ester linkages is called a triacylglyceride. Several variations of the basic structure exist, including backbones such as sphingosine in sphingomyelin, and hydrophilic groups such as phosphate in phospholipids. Steroids such as sterol are another major class of lipids. Carbohydrates Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals). The basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways. Nucleotides The two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group which is attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, and its interpretation through the processes of transcription and protein biosynthesis. This information is protected by DNA repair mechanisms and propagated through DNA replication. Many viruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic-group-transfer reactions. Coenzymes Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups of atoms and their bonds within molecules. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled. One central coenzyme is adenosine triphosphate (ATP), the energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day. ATP acts as a bridge between catabolism and anabolism. Catabolism breaks down molecules, and anabolism puts them together. Catabolic reactions generate ATP, and anabolic reactions consume it. It also serves as a carrier of phosphate groups in phosphorylation reactions. A vitamin is an organic compound needed in small quantities that cannot be made in cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells. Nicotinamide adenine dinucleotide (NAD+), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to transfer hydrogen atoms to their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions. Mineral and cofactors Inorganic elements play critical roles in metabolism; some are abundant (e.g. sodium and potassium) while others function at minute concentrations. About 99% of a human's body weight is made up of the elements carbon, nitrogen, calcium, sodium, chlorine, potassium, hydrogen, phosphorus, oxygen and sulfur. Organic compounds (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen; most of the oxygen and hydrogen is present as water. The abundant inorganic elements act as electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride, phosphate and the organic ion bicarbonate. The maintenance of precise ion gradients across cell membranes maintains osmotic pressure and pH. Ions are also critical for nerve and muscle function, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell's fluid, the cytosol. Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules. Transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant of those. Metal cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such as ferritin or metallothionein when not in use. Catabolism Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions which build molecules. The exact nature of these catabolic reactions differ from organism to organism, and organisms can be classified based on their sources of energy, hydrogen, and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of hydrogen atoms or electrons by organotrophs, while lithotrophs use inorganic substrates. Whereas phototrophs convert sunlight to chemical energy, chemotrophs depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, hydrogen, hydrogen sulfide or ferrous ions to oxygen, nitrate or sulfate. In animals, these reactions involve complex organic molecules that are broken down to simpler molecules, such as carbon dioxide and water. Photosynthetic organisms, such as plants and cyanobacteria, use similar electron-transfer reactions to store energy absorbed from sunlight. The most common set of catabolic reactions in animals can be separated into three main stages. In the first stage, large organic molecules, such as proteins, polysaccharides or lipids, are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on acetyl-CoA is oxidized to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing more energy while reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH. Digestion Macromolecules cannot be directly processed by cells. Macromolecules must be broken into smaller units before they can be used in cell metabolism. Different classes of enzymes are used to digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple sugars known as monosaccharides. Microbes simply secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their guts, including the stomach and pancreas, and in salivary glands. The amino acids or sugars released by these extracellular enzymes are then pumped into cells by active transport proteins. Energy from organic compounds Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells after they have been digested into monosaccharides such as glucose and fructose. Once inside, the major route of breakdown is glycolysis, in which glucose is converted into pyruvate. This process generates the energy-conveying molecule NADH from NAD+, and generates ATP from ADP for use in powering many processes within the cell. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA and fed into the citric acid cycle, which enables more ATP production by means of oxidative phosphorylation. This oxidation consumes molecular oxygen and releases water and the waste product carbon dioxide. When oxygen is lacking, or when pyruvate is temporarily produced faster than it can be consumed by the citric acid cycle (as in intense muscular exertion), pyruvate is converted to lactate by the enzyme lactate dehydrogenase, a process that also oxidizes NADH back to NAD+ for re-use in further glycolysis, allowing energy production to continue. The lactate is later converted back to pyruvate for ATP production where energy is needed, or back to glucose in the Cori cycle. An alternative route for glucose breakdown is the pentose phosphate pathway, which produces less energy but supports anabolism (biomolecule synthesis). This pathway reduces the coenzyme NADP+ to NADPH and produces pentose compounds such as ribose 5-phosphate for synthesis of many biomolecules such as nucleotides and aromatic amino acids. Fats are catabolized by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates. Steroids are also broken down by some bacteria in a process similar to beta oxidation, and this breakdown process involves the release of significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for energy. M. tuberculosis can also grow on the lipid cholesterol as a sole source of carbon, and genes involved in the cholesterol-use pathway(s) have been validated as important during various stages of the infection lifecycle of M. tuberculosis. Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide to produce energy. The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example α-ketoglutarate formed by deamination of glutamate. The glucogenic amino acids can also be converted into glucose, through gluconeogenesis. Energy transformations Oxidative phosphorylation In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the citric acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell's inner membrane. These proteins use the energy from reduced molecules like NADH to pump protons across a membrane. Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient. This force drives protons back into the mitochondrion through the base of an enzyme called ATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate—turning it into ATP. Energy from inorganic compounds Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. These organisms can use hydrogen, reduced sulfur compounds (such as sulfide, hydrogen sulfide and thiosulfate), ferrous iron (Fe(II)) or ammonia as sources of reducing power and they gain energy from the oxidation of these compounds. These microbial processes are important in global biogeochemical cycles such as acetogenesis, nitrification and denitrification and are critical for soil fertility. Energy from light The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can, however, operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds. In many organisms, the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves the storage of energy as a proton concentration gradient. This proton motive force then drives ATP synthesis. The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres. Reaction centers are classified into two types depending on the nature of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two. In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast. These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then be used to reduce the coenzyme NADP+. Anabolism Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from smaller and simpler precursors. Anabolism involves three basic stages. First, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids. Anabolism in organisms can be different according to the source of constructed molecules in their cells. Autotrophs such as plants can construct the complex organic molecules in their cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from oxidation reactions. Carbon fixation Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide (CO2). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO2 into glycerate 3-phosphate, which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of the Calvin–Benson cycle. Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions. In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin–Benson cycle, a reversed citric acid cycle, or the carboxylation of acetyl-CoA. Prokaryotic chemoautotrophs also fix CO2 through the Calvin–Benson cycle, but use energy from inorganic compounds to drive the reaction. Carbohydrates and glycans In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as glucose and then used to assemble polysaccharides such as starch. The generation of glucose from compounds like pyruvate, lactate, glycerol, glycerate 3-phosphate and amino acids is called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis. However, this pathway is not simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately, and prevents both pathways from running simultaneously in a futile cycle. Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic machinery. As a result, after long-term starvation, vertebrates need to produce ketone bodies from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. In other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose. Other than fat, glucose is stored in most tissues, as an energy resource available within the tissue through glycogenesis which was usually being used to maintained glucose level in blood. Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate glucose (UDP-Glc) to an acceptor hydroxyl group on the growing polysaccharide. As any of the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures. The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by the enzymes oligosaccharyltransferases. Fatty acids, isoprenoids and sterol Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty acid synthase reactions are carried out by a single multifunctional type I protein, while in plant plastids and bacteria separate type II enzymes perform each step in the pathway. Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plant natural products. These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate. These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. One important reaction that uses these activated isoprene donors is sterol biosynthesis. Here, the isoprene units are joined to make squalene and then folded up and formed into a set of rings to make lanosterol. Lanosterol can then be converted into other sterols such as cholesterol and ergosterol. Proteins Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food. Some simple parasites, such as the bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Nonessensial amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid. Amino acids are made into proteins by being joined in a chain of peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA. Nucleotide synthesis and salvage Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy. Consequently, most organisms have efficient systems to salvage preformed nucleotides. Purines are synthesized as nucleosides (bases attached to ribose). Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate. Xenobiotics and redox metabolism All organisms are constantly exposed to compounds that they cannot use as foods and that would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called xenobiotics. Xenobiotics such as synthetic drugs, natural poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include cytochrome P450 oxidases, UDP-glucuronosyltransferases, and glutathione S-transferases. This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III). In ecology, these reactions are particularly important in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills. Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even persistent organic pollutants such as organochloride compounds. A related problem for aerobic organisms is oxidative stress. Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide. These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases and peroxidases. Thermodynamics of living organisms Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work. The second law of thermodynamics states that in any isolated system, the amount of entropy (disorder) cannot decrease. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are open systems that exchange matter and energy with their surroundings. Living systems are not in equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments. The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms, metabolism maintains order by creating disorder. Regulation and control As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis. Metabolic regulation also allows organisms to respond to signals and interact actively with their environments. Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway). For example, an enzyme may show large changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway. There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self-regulates to respond to changes in the levels of substrates or products; for example, a decrease in the amount of product can increase the flux through the pathway to compensate. This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway. Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of water-soluble messengers such as hormones and growth factors and are detected by specific receptors on the cell surface. These signals are then transmitted inside the cell by second messenger systems that often involved the phosphorylation of proteins. A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin. Insulin is produced in response to rises in blood glucose levels. Binding of the hormone to insulin receptors on cells then activates a cascade of protein kinases that cause the cells to take up glucose and convert it into storage molecules such as fatty acids and glycogen. The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating protein phosphatases and producing a decrease in the phosphorylation of these enzymes. Evolution The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all three domains of living things and were present in the last universal common ancestor. This universal ancestral cell was prokaryotic and probably a methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism. The retention of these ancient pathways during later evolution may be the result of these reactions having been an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps. The first pathways of enzyme-based metabolism may have been parts of purine nucleotide metabolism, while previous metabolic pathways were a part of the ancient RNA world. Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway. The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with novel functions created from pre-existing steps in the pathway. An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the MANET database) These recruitment processes result in an evolutionary enzymatic mosaic. A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules. As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host. Similar reduced metabolic capabilities are seen in endosymbiotic organisms. Investigation and manipulation Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products. The enzymes that catalyze these chemical reactions can then be purified and their kinetics and responses to inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell. An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 26.500 genes. However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior. These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomic and DNA microarray studies. Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research. These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites. Bacterial metabolic networks are a striking example of bow-tie organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies. A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants or bacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such as antibiotics or industrial chemicals such as 1,3-propanediol and shikimic acid. These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes. History The term metabolism is derived from the Ancient Greek word μεταβολή—"metabole" for "a change" which is derived from μεταβάλλειν—"metaballein", meaning "to change" Greek philosophy Aristotle's The Parts of Animals sets out enough details of his views on metabolism for an open flow model to be made. He believed that at each stage of the process, materials from food were transformed, with heat being released as the classical element of fire, and residual materials being excreted as urine, bile, or faeces. Ibn al-Nafis described metabolism in his 1260 AD work titled Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of Kamil on the Prophet's Biography) which included the following phrase "Both the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change." Application of the scientific method and Modern metabolic theories The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medicina. He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration". In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue. In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." This discovery, along with the publication by Friedrich Wöhler in 1828 of a paper on the chemical synthesis of urea, and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry. It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry. The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle. See also , a "metabolism first" theory of the origin of life Microphysiometry Oncometabolism References Further reading Introductory Advanced External links General information The Biochemistry of Metabolism (archived 8 March 2005) Sparknotes SAT biochemistry Overview of biochemistry. School level. MIT Biology Hypertextbook Undergraduate-level guide to molecular biology. Human metabolism Topics in Medical Biochemistry Guide to human metabolic pathways. School level. THE Medical Biochemistry Page Comprehensive resource on human metabolism. Databases Flow Chart of Metabolic Pathways at ExPASy IUBMB-Nicholson Metabolic Pathways Chart SuperCYP: Database for Drug-Cytochrome-Metabolism Metabolic pathways Metabolism reference Pathway Underwater diving physiology

Chemical property

A chemical property is any of a material's properties that becomes evident during, or after, a chemical reaction; that is, any attribute that can be established only by changing a substance's chemical identity. Simply speaking, chemical properties cannot be determined just by viewing or touching the substance; the substance's internal structure must be affected greatly for its chemical properties to be investigated. When a substance goes under a chemical reaction, the properties will change drastically, resulting in chemical change. However, a catalytic property would also be a chemical property. Chemical properties can be contrasted with physical properties, which can be discerned without changing the substance's structure. However, for many properties within the scope of physical chemistry, and other disciplines at the boundary between chemistry and physics, the distinction may be a matter of researcher's perspective. Material properties, both physical and chemical, can be viewed as supervenient; i.e., secondary to the underlying reality. Several layers of superveniency are possible. Chemical properties can be used for building chemical classifications. They can also be useful to identify an unknown substance or to separate or purify it from other substances. Materials science will normally consider the chemical properties of a substance to guide its applications. Examples Heat of combustion Enthalpy of formation Toxicity Chemical stability in a given environment Flammability (the ability to burn) Preferred oxidation state(s) Ability to corrode Combustibility Acidity and basicity See also Chemical structure Material properties Biological activity Quantitative structure–activity relationship (QSAR) Lipinski's Rule of Five, describing molecular properties of drugs References

Biochemistry

"Biochemistry or biological chemistry is the study of chemical processes within and relating to livi(...TRUNCATED)

Biosynthesis

"Biosynthesis, i.e., chemical synthesis occurring in biological contexts, is a term most often refer(...TRUNCATED)