~~~~Organic Chemistry~~~~

 

An Online  Tutorial

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Overview

Organic Chemistry is a specific discipline within the field of chemistry. It is the scientific study of the structure, properties, composition, reactions, and preparation by synthesis (or other means) of chemical compounds of carbon and hydrogen, which may contain any number of other elements. A list of such elements includes nitrogen, oxygen, and the halogens (fluorine, chlorine, bromine, iodine). They may also contain the elements phosphorus or sulfur.

Because of their unique properties, multi-carbon hydrocarbon compounds exhibit extremely large variety and the range of application of organic compounds is enormous. They form the chemical basis of many products (e.g. paints, plastics, explosives, pharmaceuticals, fossil fuels, petrochemicals ) and of course they form the basis of all life processes.

Inorganic chemistry is the branch of chemistry concerned with the properties and behavior of inorganic compounds. Major branches of inorganic groups include minerals from the earth's crust (e.g. SiO2, Mg0, Al2O3) and other compounds containing non-metallic elements like silicon, phosphorus, sulfur, chlorine and oxygen (e.g. water). Also important are compounds of elements of Groups I, II with Group VII elements to form ionically bonded salts (e.g. NaCl, table salt). Also included are simple carbon compounds which do not contain C-C bonds (e.g. its oxides, acids, salts, carbides, and minerals) as well as metal alloys and hydrated metal complexes. Many inorganic species exist in living organisms and are essential to life. Examples include the sodium, potassium, and chloride ions as well as the phosphate and nitrate ions. The distinction between what constitutes an organic compound and what constitutes an inorganic compound  is far from absolute. Overlap exists most notably in the field of organometallic chemistry.

The original definition of organic chemistry came from the misperception that these compounds were always related to life and vital functions. Those compounds that are related to life processes are dealt with in the branch of organic chemistry which is called biochemistry. Living organisms maintain themselves by continuously processing the nutrient molecules contained in edible matter, or food. These molecules provide building blocks for new living matter and energy to sustain the vital functions of life. Nutrients include organic compounds such as complex carbohydrates (polysaccharides such as starch, glycogen, cellulose), fats, proteins, and vitamins, as well as metallic elements or minerals such as iron and copper, and water. 

The human body is composed of chemical compounds such as water, amino acids (or proteins ), fatty acids (or lipids ), nucleic acids (DNA / RNA), and carbohydrates (or sugars). These compounds in turn consist of elements such as carbon, hydrogen, oxygen, nitrogen, and phosphorus, and may or may not contain minerals such as calcium, iron, or zinc. Minerals ubiquitously occur in the form of salts and electrolytes. All of these chemical compounds and elements occur in various forms and combinations (e.g. hormones, phospholipids, and crystalline hydroxyapatite or bone), both in the human body and in the vital organisms (plants and animals) that we consume for fuel. The science of nutrition is an attempt to understand how specific nutrients and other body fuels are used by the body, and how an improper balance of nutrient and fuel intake can result in poor health.

Functional groups. Many elements present themselves in functional groups which have decisive influence on the chemical and physical properties of an organic compound. The different shapes and chemical reactivities of the substituents (atoms and functional groups) of organic hydrocarbons provide an astonishing variety of functions, like those of enzyme catalysts in biochemical reactions of live systems. The automatic propagating nature of these is what life is all about.

The central message of chemistry is that the properties of any substance are a direct result of its molecular structure. The simple fact is that a number of elements, or groups of elements, present themselves in functional groups which have decisive influence on the chemical and physical characteristics of the compound. Thus, in a manner similar to groups or families in the Periodic Table, compounds containing the same atomic or molecular constituents typically have similar chemical characteristics. Examples are miscibility, acidity/ alkalinity (pH), chemical reactivity, electron affinity, oxidation resistance, and others.

The objective of this Online tutorial is to emphasize the fundamental connection between structure and properties using the methods best suited for such an approach. Thus the reader will find a specific focus on the characterization of the structural units within a compound that are most closely identified with its chemical and physical properties. 

Speaking universally: because of the special properties of carbon, it is likely that life on other star systems will be found to be carbon-based, in spite of speculations about the possibility of substituting silicon, which lies just below carbon in the periodic table. Modern Trends in organic chemistry include chiral synthesis, green chemistry, microwave chemistry, fullerenes (or buckyballs) and microwave (rotational) spectroscopy.

Classification is not possible without having a full description of the individual compounds. One way of describing the molecule is by drawing its structural formula. Because of the difficulty due to the very large number and variety of organic compounds, chemists realized early on that the establishment of an internationally accepted system of naming organic compounds was of paramount importance. 

The Geneva Nomenclature was born in 1892 as a result of a number of international meetings on the subject. It was also realized that as the family of organic compounds grew, the system would have to be expanded and modified. This task was ultimately taken on by the International Union on Pure and Applied Chemistry, IUPAC. Since the complexity of organic structures increases in biochemical compounds, the IUPAC organization joined forces with IUBMB, the International Union of Biochemistry and Molecular Biology, to produce a list of joint recommendations on nomenclature.

Organic substances are classified by their molecular structural arrangement and by what other atoms are present with the chief (carbon) constituent in their makeup. In a structural formula, hydrogen is implicitly assumed to occupy all free valencies of an appropriate carbon atom, which remain after accounting for branching, other element(s) and/or multiple bonding.

A homologous series is a series of organic compounds with a similar general formula, possessing similar chemical properties due to the presence of the same functional group, and exhibiting a gradation in physical properties resulting from an increase in molecular size and mass (see relative molecular mass). Organic compounds in the same homologous series vary by a CH₂ group or unit. The alkane homologous series begins with: 

Methane (CH₄), ethane (C₂H₆), propane (C₃H₈), butane (C₄H₁₀), and pentane (C₅H₁₂).           Each member differs from the previous one by a -CH₂- group. 

Alkanes (paraffins), Alkenes (olefins), Alkynes (acetylenes) and Ethers (methoxyethane) all form such series in which members differ in mass by 14, 12, and 10 atomic mass units, respectively. Even while the general formulas are the same, they have different structures that can lead the exact same compound to different properties, although they will always present the same chemical properties while as a homologous compound.

Classification normally starts with the hydrocarbons: compounds which contain only carbon and hydrogen. On the basis of molecular structure, hydrocarbons are divided into two main classes: aliphatic and aromatic. Aliphatic hydrocarbons are further subdivided into families: alkanes, alkenes, alkynes, and their (ali)cyclic analogs (cycloalkanes, cycloalkenes, etc.).      

Referring to the hydrocarbon types below, many, if not all of the functional groups which are typically present within aliphatic compounds are also represented within the aromatic and alicyclic group of compounds, unless they are dehydrated, which would lead to non-reacting co-optional groups.

Two overarching chain type categories exist: "open chain" aliphatic compounds (straight chain, or branched) and "closed chain" (or unbranched) alicyclic compounds. Those in which both open chain and cyclic parts are present are normally classed with the alicyclics. 

Aliphatic compounds are subdivided into three groups (or homologous series) according to their state of saturation. Saturated compounds have the maximum number of hydrogen atoms possible. There are no double bonded carbon atom pairs. Thus, in any hydrocarbon chain, every carbon atom is attached to two hydrogen atoms. 

The majority of the aliphatics have a backbone (or skeleton) consisting of straight chains of carbon atoms (either branched or unbranched). Of the closed-chain (alicyclic) hydrocarbons, alkanes are saturated, as opposed to the alkenes and alkynes which are unsaturated. Thus, unsaturated is a term which is used to describe any carbon structure containing double or occasionally triple bonds (or pi-bonds). The degree of unsaturation is a method of specifying the amount that a compound is partially saturated The term is applied similarly to the fatty acid constituents of lipids, where the fat is described as saturated or unsaturated, depending on whether the constituent fatty acids contain carbon-carbon double bonds. 

Alkanes (paraffins) are white or colorless, odorless, tasteless, water-insoluble, relatively stable solid substances (not very reactive), and obtained from crude oil. They are used in the formation of candles, for forming preservative coatings and seals, and for waterproofing paper, etc. An alkane is an acyclic saturated hydrocarbon ; a long chain of carbon atoms linked together by single (covalent) bonds. The general formula for alkanes is: 

                                                            C_nH_2n+2  

The simplest possible alkane is therefore methane, CH₄. The next simplest is ethane, C₂H₆ . The series continues indefinitely. Each carbon atom in an alkane has sp³ hybridization.

Alkenes (olefins) contain double-bonded carbon atoms. They can be mono-olefins with a single double bond, di-olefins, or di-enes with two double bonds, or poly-olefins with more than two double bonds.

Alkynes contain a triple bond. The alkynes are named after the shortest member of the homologue series: the acetylenes or alkynes. 

The rest of the group is classed according to the functional groups present.

From another aspect aliphatics can be straight chain or branched chain compounds, and the degree of branching also affects characteristics (much like the octane number or cetane number in petroleum chemistry).

Cyclic Compounds: Aromatics & Alicyclics 

Cyclic hydrocarbon compounds divide into: 

1) Cyclic aliphatics (or alicyclics)  

2) Aromatics (or arenes).

Cyclic compounds can, again, be saturated (alicyclic) or unsaturated (alicyclic or aromatic). Because of the bonding angle of carbon, the most stable configuration of the cyclic compounds contain six carbon atoms. Rings with five carbon atoms (pentagons) are also frequent, and others (squares & triangles) also exist. Saturated cyclic compounds contain single bonds only, whereas aromatic rings have an alternating (or conjugated) double bond.

Alicyclic compounds include the cycloalkanes (cycloparaffins) which do not contain double bonds, while the cycloalkenes (cyclo-olefins) do. The simplest member of the cycloalkane family is cyclopropane. A notable group amongst the alicyclics is represented by the terpenes (major components of resin or turpentine)..

Aromatic compounds differ in that they contain conjugated or alternating double bonds. One of the simplest example of this is benzene. The unique structure of benzene was formulated by a German chemist named Kekulé who first proposed the electron delocalization or structural resonance principles. This method justified the use of an alternating sequence of single and double bonds within a 6-membered hexagonal ring of carbon atoms.

Heterocyclic compounds. Those compounds with other elements in the ring are called heterocyclic and the atom substituting the carbon is a heteroatom. The heteroatom of heterocyclic molecules is generally O, S, or N, but most often nitrogen, and the heterocyclics of living systems are compounds with nitrogen. 

Examples of groups among the heterocyclics are the aniline dyes, the great majority of the compounds discussed in biochemistry such as alkaloids, many compounds related to vitamins, steroids, nucleic acids (e.g. DNA, RNA) and also numerous medicines. Heterocyclics with relatively simple strucures are pyrrole (5-membered) and indole (6-membered carbon ring).

Classification normally starts with the hydrocarbons: compounds which contain only carbon and hydrogen. Compounds in each set have the same little group of atoms called the functional group. Most chemical properties of organic compounds are due to the presence of the functional group.

A number of elements, or groups of elements, present themselves in functional groups which have decisive influence on the chemical and physical characteristics of the compound. Thus, in a manner similar to groups or families in the Periodic Table, compounds containing the same atomic or molecular constituents typically have similar characteristics. Examples are miscibility with water, acidity/ alkalinity, chemical reactivity, oxidation resistance, or others. Some functional groups are also radicals, similar to those in inorganic chemistry, defined as atomic configurations which pass during chemical reactions from one chemical compound into another without change.

Some of the elements of the functional groups (O, S, N, and halogens: F, Cl, Br, I) may stand alone and the group name is not strictly appropriate. But because of their decisive effect on the physical properties / characteristics of the compounds in which they are present, they are classed with the functional groups. Their specific effect on the properties lends excellent means for characterization and classification.

For example, the characteristics of the cyclic hydrocarbons are altered if there are functional groups present, creating heterocyclic compounds . But additionally here some of the elements which are classed with the functional groups can form part of the ring itself. 

Synthetic Polymers: Plastics & Rubber

One important property of carbon in organic chemistry is that it can form certain compounds, the individual molecules of which are capable of attaching themselves to one another, thereby forming a chain or a network. The process is called polymerization and the chains or networks polymers, while the source compound is a monomer. Two main groups of polymers exist: those artificially manufactured are referred to as industrial polymers or synthetic polymers (plastics) and those naturally occurring as biopolymers.

The key feature that distinguishes polymers from other molecules is the repetition of many identical, similar, or complementary molecular subunits in these chains. These subunits, the monomers, are small molecules of low to moderate molecular weight, and are linked to each other during polymerization.

Instead of being identical, similar monomers can have various chemical substituents. Thus, functional groups can affect the chemical properties of monomers, such as solubility and chemical reactivity. In addition, functional groups can affect the physical properties of monomers, such as hardness, density, mechanical or tensile strength, abrasion resistance, heat resistance, transparency, color, etc.). In proteins, these differences give the polymer the ability to adopt a biologically-active conformation in preference to others (see self-assembly).

People have been using natural organic polymers for centuries in the form of waxes and shellac - a thermoplastic polymer.  A plant polymer named cellulose provides the tensile strength for natural fibers and ropes, and by the early 19th century natural rubber was in widespread use.

Eventually, inventors learned to improve the properties of natural polymers. Natural rubber was sensitive to temperature, becoming sticky and smelly in hot weather and brittle in cold weather. In 1834, two inventors, Friedrich Ludersdorf of Germany and Nathaniel Hayward of the U.S., independently discovered that adding sulfur to raw rubber helped prevent the material from becoming sticky.

In 1907, the invention and refinement of a synthetic polymer commonly known as Bakelite signaled the dawning of the Age of Plastics. Bakelite is a brand named for a material based on a thermosetting phenol formaldehyde resin called polyoxybenzylmethylenglycolanhydride. First discovered in 1872 by Dr. Leo Baekeland, it is formed by the reaction under heat and pressure of phenol and formaldehyde, generally with a wood flour filler. It was the first plastic made from synthetic polymers. It was used for its nonconductive and heat-resistant properties in radio and telephone casings as well as electrical insulators. Since the invention of the first artificial polymer, the family has quickly grown with the invention of others. 

Common synthetic organic polymers are polyethylene (or polythene), polypropylene, nylon, polytetrafluoroethyleneteflon PTFE (fluorine-based Teflon or Gore-tex), rayon (or cellophane, a cellulose based fiber), polystyrene (or styrofoam), polyurethane (epoxy), polyesters, polymethylmethacrylate PMMA (acrylic or plexiglas), polyvinylchloride (PVC), and polyisobutylene (butyl rubber), Tupperware, Formica plastic laminate, and high-strength Kevlar. Also important are both natural and synthetic rubber as well as the polymerized butadiene, a component of synthetic rubber. 

Most of these examples are generic terms, and many varieties of each of these may exist, with their physical characteristics finely tuned for a specific use. Changing the conditions of polymerization changes the chemical composition of the product by altering chain length (degree of polymerization), branching, or tacticity. With a single monomer as a start the product is a homopolymer. Further, secondary components may be added to create a heteropolymer (co-polymer) and the degree of clustering of the different components can also be controlled. Physical characteristics (hardness, density, mechanical or tensile strength, abrasion resistance, heat resistance, transparency, color, etc.) will depend on the final composition.

Plastic can be classified in many ways but most commonly by their polymer backbone (polyvinyl chloride, polyethylene, acrylic, silicone, urethane, etc.). Other classifications include thermoplastic vs. thermoset, elastomer, engineering plastic, addition or condensation, and glass transition temperature or T_g. Many plastics are partially crystalline and partially amorphous in molecular structure, giving them both a melting point (the temperature at which the attractive intermolecular forces are overcome) and one or more glass transitions (temperatures at which the degree of cross-linking is substantially reduced).

The vast majority of plastics are composed of polymers of carbon alone -- or with oxygen, nitrogen, chlorine or sulfur in the backbone. The development of plastics has come from the use of natural materials (e.g., chewing gum, shellac) to the use of chemically modified natural materials (e.g., natural rubber, nitrocellulose) and finally to completely manmade molecules (e.g., epoxy, polyvinyl chloride, polyethylene).

Rubber is an elastic hydrocarbon polymer which occurs as a milky emulsion (known as latex) in the sap of several varieties of plants. Synthetic rubber is made through the polymerization of a variety of monomers. The major commercial source of natural sap used to create rubber is the Para rubber tree. This is largely because it responds to wounding by producing more latex. The chemical process of vulcanization is a type of cross-linking and it changes the property of rubber to the hard, durable material we associate with tires.

The only other element that can produce polymers is silicon. The silicones, however, show one major difference from carbon based polymers. Unlike the direct C-C bonds of those based on carbon in silicones, the Si atoms are joined indirectly through oxygen links (e.g. Silica Si02 -- beach sand, quartz or window glass). Silicones, or polysiloxanes, are inorganic-organic polymers with the chemical formula [R₂SiO]_n, where R = organic groups such as methyl, ethyl, and phenyl. These materials consist of an inorganic silicon-oxygen backbone (...-Si-O-Si-O-Si-O-...) with organic side groups attached to the silicon atoms, which are four-coordinated. In some cases organic side groups can be used to link two or more of these -Si-O- backbones together. By varying the -Si-O- chain lengths, functional side groups, and crosslinking, silicones can be synthesized with a wide variety of properties and compositions.

Biomolecules

Biomolecular chemistry is a major category within organic chemistry. Many complex multi-functional group molecules are important in living organisms. Some are long-chain biopolymers. Biopolymers are a special class of polymers found only in living organisms. Starch, proteins and polypeptides (e.g. DNA, RNA) are all examples of biopolymers, in which the monomer units, respectively, are carbohydrates (sugars), amino acids, and nucleic acids. The main classes of biopolymers are carbohydrates, amino acids and proteins, polysaccharides (e.g. starch, glycogen, cellulose), lipids (fatty acids or carboxylic acids) and nucleic acids.

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Organic compounds are generally covalently bonded. This allows for unique structures such as long carbon chains and rings. The reason carbon is excellent at forming unique structures and that there are so many carbon compounds is that carbon atoms form very stable covalent bonds with one another (catenation). Thus, In contrast to inorganic materials with higher strength ionic bonds, covalently bonded organic compounds typically melt, boil, sublimate, or decompose below 300°C. 

Solubility often depends upon the solvent type and on the functional groups present. Like inorganic salts, organic compounds may also form crystals. Organic compounds tend to be less soluble in water compared to many inorganic salts. Exceptions to this rule include certain ionic organic compounds, low molecular weight alcohols and carboxylic acids (where hydrogen bonding occurs).

Organic compounds tend rather to dissolve in organic solvents such as pure substances like ether or ethyl alcohol. They also dissolve in mixtures, such as the paraffinic solvents including various petroleum ethers and white spirits, or the range of pure or mixed aromatic solvents obtained from petroleum or tar fractions by physical separation or by chemical conversion. 

A unique property of carbon in organic compounds is that its valency does not always have to be taken up by atoms of other elements. Unsaturated hydrocarbon compounds contain carbon-carbon double bonds or triple bonds. Double bonds alternating with single bonds in a chain are called conjugated double bonds (alternating single and double or multiple bonds (e.g., C=C-C=C-C). An aromatic structure is a special case in which the conjugated chain is a closed ring.

Physical Properties

Physical properties of elements and compounds which provide conclusive evidence of chemical composition include odor, color, volume, density (mass / volume), melting point, boiling point, heat capacity, physical form @ room temp. (solid, liquid or gas), hardness, porosity, and index of refraction. Physical properties which constitute the emerging study of the science of materials in the solid state include include the following:

Thermo-Mechanical properties such as thermal conductivity focus on the mechanical stability of a material at elevated temperatures. Also important is the specific heat capacity of a material to store energy in the form of heat (or thermal vibrations). In the aerospace industry, high performance materials used in the design of aircraft and/or spacecraft exteriors must have a high resistance to thermal shock. Thus, synthetic fibers spun out of organic polymers and polymer/ ceramic /metal composite materials and fiber-reinforced polymers are now being designed with this purpose in mind.  

Mechanical properties are important in structural and building materials as well as textile fabrics. They include the many properties used to describe the strength of materials such as:  elasticity / plasticity, tensile strength, compressive strength, shear strength, fracture toughness & ductility (low in brittle materials),  and indentation hardness.          

Electro-Mechanical properties. Piezoelectricity is the ability of crystals to generate a voltage in response to an applied mechanical stress. The piezoelectric effect is reversible in that piezoelectric crystals, when subjected to an externally applied voltage, can change shape by a small amount. Polymer materials like rubber, wool, hair, wood fiber, and silk often behave as electrets. The polymer polyvinylidene fluoride, PVDF, exhibits a piezoelectric response several times larger than quartz (crystalline SiO2). The deformation (~ 0.1% ) lends itself to useful technical applications such as "light amplification by stimulated emission of radiation" (or lasers), high voltage sources and loudspeakers, as well as chemical, biological, and acousto-optic sensors and/or transducers. 

Electrical properties include conductivity, resistance, impedance and capacitance. Electrical conductors (metals & alloys) are contrasted with electrical insulators (glasses & ceramics). Semiconductors (Si, GaAs) behave somewhere in between, showing electrical conduction only beyond a threshold applied voltage. Alternatively, ionic superconductors are at the extreme end of the conductivity spectrum, with highly mobile ions acting as charge carriers moving thru a low temperature crystalline lattice with virtually negligible resistance.  

Dielectric properties. A dielectric, or electrical insulator, is a substance that is highly resistant to the flow of electric current. A dielectric tends to concentrate an applied electric field (e-field) within itself. The use of many plastics as dielectrics in capacitors presents several advantages. A capacitor is an electrical device that can store energy in the electric field between a pair of closely spaced conductors (called 'plates'). When voltage is applied to the capacitor, electric charges of equal magnitude, but opposite polarity, build up on each plate. Capacitors are used in electrical circuits as energy-storage devices. They can also be used to differentiate between high-frequency and low-frequency signals which makes them useful in electronic filters.

Electro-Optical and Far-Infrared properties. Optically transparent materials focus on the response of a material to incoming lightwaves of a range of wavelengths. Frequency selective optical filters can be utilized to alter or enhance the brightness and contrast of a digital image. Guided lightwave transmission involves the emerging field of fiber optics and the ability of certain glassy compositions as medium of transmission for a range of frequencies simultaneously (multi-mode optical waveguides) with little or no interference between competing waveforms. This resonant mode of energy & data transmission vie electromagnetic wave propagation, though low powered, is virtually lossless. Optical waveguides are used as components in integrated optical circuits (e.g. light-emitting diodes LED's) or as the transmission medium in local and long haul optical communication systems. Also of value to the emerging materials scientist is the sensitivity of materials to radiation in the thermal infrared portion of the electromagnetic spectrum. This heat-seeking ability is responsible for such diverse optical phenomena as night vision and infrared luminescence.

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Organic compounds consist of carbon atoms, hydrogen atoms, and functional groups. The valence of carbon is 4, and hydrogen is 1, functional groups are generally 1. From the number of carbon atoms and hydrogen atoms in a molecule the degree of unsaturation can be obtained. Many, but not all structures can be envisioned by the simple valence rule that there will be one bond for each valence number. The knowledge of the chemical formula for an organic compound is not sufficient information because many isomers can exist.

Organic compounds often exist as mixtures. Because many organic compounds have relatively low boiling points and/or dissolve easily in organic solvents there exist many methods for separating mixtures into pure constituents that are specific to organic chemistry such as distillation, crystallization and chromatography techniques. 

Methods for deducing the structure an organic compound include:

·   Elemental Analysis  ·  Atomic spectroscopy  ·  Mass spectrometry  ·  X-ray fluorescence 

·   X-ray photoelectron spectroscopy   ·   Auger electron spectroscopy.

·   NMR spectrometry  ·   IR spectroscopy   ·  UV/VIS spectroscopy  

·   X-ray diffraction   ·   Neutron diffraction   ·   Electron diffraction 

While this website is primarily organized according to hydrocarbon groups by degree of bond saturation and geometry (e.g. open chains vs. closed chains), we emphasize reaction mechanisms and strongly encourage students to recognize similarities and trends in mechanisms among different functional groups.    

Organic reactions are chemical reactions involving organic compounds. While pure hydrocarbons undergo certain limited classes of reactions, many more reactions which organic compounds undergo are largely determined by functional groups. The general theory of these reactions involves careful analysis of such properties as the electron affinity of key atoms, bond strengths and steric hindrance. These issues can determine the relative stability of metastable (or short-lived) reactive intermediates, which often determine the path of the reaction sequence.

The basic reaction types are: addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions and redox reactions .

An example of a substitution reaction is written as:

                     Nu ⁻    +     C - X          →         C - Nu     +     X ⁻

where X is some functional group and Nu is a nucleophile.

The number of possible organic reactions is basically infinite. However, certain general patterns are observed that can be used to describe many common or useful reactions. Each reaction has a stepwise reaction mechanism that explains how it happens in sequence -- although the detailed description of steps is not always clear from a list of reactants alone.

A reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs. Although only the net chemical change is directly observable for most chemical reactions, experiments can often be designed that suggest the possible sequence of steps in a reaction mechanism. A mechanism describes in detail exactly what takes place at each stage of a chemical transformation.

The mechanism includes a description of which bonds are broken and in what order, which bonds are formed and in what order, and what the relative rates of the steps are. The mechanism includes a description of the transition state -- the highest energy state or conformation in the process of any chemical or physical transformation. The transition state can be considered a reaction intermediate or activated complex which is in metastable state, since both reactants and products represent lower energy configurations.

Note that only in an irreversible reaction can we assume that all reactants will indeed proceed to the formation of products. Chemical equilibrium is the state in which the concentrations of the reactants and products have no net change over time. Usually, this state results when the forward reactions proceed at the same rate as their reverse reactions.

A complete mechanism must also account for all reactants used, the function of a catalyst, stereochemistry, the qualitative composition of all products formed and the quantitative amounts of each product. A reaction mechanism must also account for the order in which molecules react. Often what appears to be a single step conversion is in fact a multi-step reaction sequence.

Physical chemistry includes the study of chemical kinetics or reaction kinetics, which emphasize the role of  reaction rates in a chemical reactions. Analyzing the influence of different reaction conditions on the reaction rate gives information about the reaction mechanism and the transition state of a chemical reaction. The law of mass action  states that the speed or rate of any chemical reaction is proportional to the quantity (or concentration) of the reacting substances.

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There are many important aspects of a specific chemical reaction, including reaction rates, chemical kinetics, and chemical equilibrium. The most important factors influencing the rate of a reaction are temperature, concentration, and pressure.

There are physical and chemical driving forces which determine whether or not any given chemical reaction will occur spontaneously in nature. The driving force is determined by the Gibbs Free Energy change of the reaction, D G, which is determined by the differences in the free energy of the reactants and products.

The heat that is either produced or consumed by the reaction is found from the total Enthalpy change, D H. A less significant thermodynamic variable included in the driving force is the change in Entropy, D S. These parameters are all related by the following equation, where T is the absolute temperature:

                                                D G   =    D H   -   T D S

Other concerns include whether side reactions occur from the same reaction conditions. Any side reactions which occur typically produce undesired compounds which may be anywhere from very easy or very difficult to separate from the desired compound.