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COURSE STRUCTURE : BIOLOGY, CHEMISTRY AND PHYSICS
Organic chemistry is a chemistry subdiscipline involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms. Study of structure includes many physical and chemical methods to determine the chemical composition and the chemical constitution of organic compounds and materials. Study of properties includes both physical properties and chemical properties, and uses similar methods as well as methods to evaluate chemical reactivity, with the aim to understand the behavior of the organic matter in its pure form (when possible), but also in solutions, mixtures, and fabricated forms. The study of organic reactionsincludes probing their scope through use in preparation of target compounds (e.g., natural products, drugs, polymers, etc.) by chemical synthesis, as well as the focused study of the reactivities of individual organic molecules, both in the laboratory and via theoretical (in silico) study.
The range of chemicals studied in organic chemistry include hydrocarbons (compounds containing only carbon and hydrogen), as well as myriad compositions based always on carbon, but also containing other elements, especially oxygen, nitrogen, sulfur, phosphorus (these included in many organic chemicals in biology) and the radiostable elements of the halogens.
In the modern era, the range extends further into the periodic table, with main group elements, including:
- Group 1 and 2 organometallic compounds, i.e., involving alkali (e.g., lithium, sodium, and potassium) or alkaline earth metals (e.g., magnesium)
- Metalloids (e.g., boron and silicon) or other metals (e.g., aluminium and tin)
In addition, much modern research focuses on organic chemistry involving further organometallics, including the lanthanides, but especially the transition metals; (e.g., zinc, copper, palladium, nickel, cobalt, titanium and chromium)
Finally, organic compounds form the basis of all earthly life and constitute a significant part of human endeavors in chemistry. The bonding patterns open to carbon, with its valence of four—formal single, double, and triple bonds, as well as various structures with delocalized electrons—make the array of organic compounds structurally diverse, and their range of applications enormous. They either form the basis of, or are important constituents of, many commercial products including pharmaceuticals; petrochemicals and products made from them (including lubricants, solvents, etc.); plastics; fuels and explosives; etc. As indicated, the study of organic chemistry overlaps with organometallic chemistry and biochemistry, but also with medicinal chemistry, polymer chemistry, as well as many aspects of material science.
Three representations of an organic compound, 5α-Dihydroprogesterone (5α-DHP), a steroid hormone. For molecules showing color, the carbon atoms are in black, hydrogens in gray, and oxygen’s in red. In the line angle representation, carbon atoms are implied at every terminus of a line and vertex of multiple lines, and hydrogen atoms are implied to fill the remaining needed valences.
Characterization
Organic compounds were traditionally characterized by a variety of chemical tests, called “wet methods”, but such tests have been largely displaced by spectroscopic or other computer-intensive methods of analysis. Listed in approximate order of utility, the chief analytical methods are:
- Nuclear magnetic resonance (NMR) spectroscopy is the most commonly used technique, often permitting complete assignment of atom connectivity and even stereochemistry using correlation spectroscopy. The principal constituent atoms of organic chemistry – hydrogen and carbon – exist naturally with NMR-responsive isotopes, respectively 1H and 13C.
- Elemental analysis: A destructive method used to determine the elemental composition of a molecule. See also mass spectrometry, below.
- Mass spectrometry indicates the molecular weight of a compound and, from the fragmentation patterns, its structure. High resolution mass spectrometry can usually identify the exact formula of a compound and is used in lieu of elemental analysis. In former times, mass spectrometry was restricted to neutral molecules exhibiting some volatility, but advanced ionization techniques allow one to obtain the “mass spec” of virtually any organic compound.
- Crystallography can be useful for determining molecular geometry when a single crystal of the material is available and the crystal is representative of the sample. Highly automated software allows a structure to be determined within hours of obtaining a suitable crystal.
Properties
Melting and boiling properties
Organic compounds typically melt and many boil. In contrast, while inorganic materials generally can be melted, many do not boil, tending instead to degrade. In earlier times, the melting point (m.p.) and boiling point (b.p.) provided crucial information on the purity and identity of organic compounds. The melting and boiling points correlate with the polarity of the molecules and their molecular weight. Some organic compounds, especially symmetrical ones, sublime, that is they evaporate without melting.
Solubility
Neutral organic compounds tend to be hydrophobic; that is, they are less soluble in water than in organic solvents. Exceptions include organic compounds that contain ionizable (which can be converted in ions) groups as well as low molecular weight alcohols, amines, and carboxylic acids where hydrogen bonding occurs. Organic compounds tend to dissolve in organic solvents. Solvents can be either pure substances like ether or ethyl alcohol, or mixtures, such as the paraffinic solvents such as the various petroleum ether 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.
Solid state properties
Various specialized properties of molecular crystals and organic polymers with conjugated systems are of interest depending on applications, e.g. thermo-mechanical and electro-mechanical such as piezoelectricity, electrical conductivity (see conductive polymers and organic semiconductors), and electro-optical (e.g. non-linear optics) properties. For historical reasons, such properties are mainly the subjects of the areas of polymer science and materials science
Nomenclature
The names of organic compounds are either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by specifications from IUPAC. Systematic nomenclature starts with the name for a parent structure within the molecule of interest. This parent name is then modified by prefixes, suffixes, and numbers to unambiguously convey the structure. Given that millions of organic compounds are known, rigorous use of systematic names can be cumbersome. Thus, IUPAC recommendations are more closely followed for simple compounds, but not complex molecules. To use the systematic naming.
Nonsystematic nomenclature is simpler and unambiguous, at least to organic chemists. Nonsystematic names do not indicate the structure of the compound. They are common for complex molecules, which includes most natural products. Thus, the informally named lysergic acid diethylamide is systematically named (6aR,9R)-N,N-diethyl-7-methyl-4,6,6a,7,8,9-hexahydroindolo-[4,3-fg] quinoline-9-carboxamide.
Structural drawings
Organic molecules are described more commonly by drawings or structural formulas, combinations of drawings and chemical symbols. The line-angle formula is simple and unambiguous. In this system, the endpoints and intersections of each line represent one carbon, and hydrogen atoms can either be notated explicitly or assumed to be present as implied by tetravalent carbon. The depiction of organic compounds with drawings is greatly simplified by the fact that carbon in almost all organic compounds has four bonds, nitrogen three, oxygen two, and hydrogen one.
Classification of organic compounds
Functional groups
The concept of functional groups is central in organic chemistry, both as a means to classify structures and for predicting properties. A functional group is a molecular module, and the reactivity of that functional group is assumed, within limits, to be the same in a variety of molecules. Functional groups can have decisive influence on the chemical and physical properties of organic compounds. Molecules are classified on the basis of their functional groups. Alcohols, for example, all have the subunit C-O-H. All alcohols tend to be somewhat hydrophilic, usually form esters, and usually can be converted to the corresponding halides. Most functional groups feature heteroatoms (atoms other than C and H). Organic compounds are classified according to functional groups, alcohols, carboxylic acids, amines, etc.
Aliphatic compounds
Main article: Aliphatic compound
The aliphatic hydrocarbons are subdivided into three groups of homologous series according to their state of saturation:
- alkanes (paraffins): aliphatic hydrocarbons without any double or triple bonds, i.e. just C-C, C-H single bonds
- alkenes (olefins): aliphatic hydrocarbons which contain one or more double bonds, i.e. di-olefins (dienes) or poly-olefins.
- alkynes (acetylenes): aliphatic hydrocarbons which have one or more triple bonds.
The rest of the group is classed according to the functional groups present. Such compounds can be “straight-chain”, branched-chain or cyclic. The degree of branching affects characteristics, such as the octane number or cetane number in petroleum chemistry.
Both saturated (alicyclic) compounds and unsaturated compounds exist as cyclic derivatives. The most stable rings contain five or six carbon atoms, but large rings (macrocycles) and smaller rings are common. The smallest cycloalkane family is the three-membered cyclopropane ((CH2)3). Saturated cyclic compounds contain single bonds only, whereas aromatic rings have an alternating (or conjugated) double bond. Cycloalkanes do not contain multiple bonds, whereas the cycloalkenes and the cycloalkynes do.
Aromatic compounds
Benzene is one of the best-known aromatic compounds as it is one of the simplest and most stable aromatics.
Aromatic hydrocarbons contain conjugated double bonds. This means that every carbon atom in the ring is sp2 hybridized, allowing for added stability. The most important example is benzene, the structure of which was formulated by Kekulé who first proposed the delocalization or resonance principle for explaining its structure. For “conventional” cyclic compounds, aromaticity is conferred by the presence of 4n + 2 delocalized pi electrons, where n is an integer. Particular instability (antiaromaticity) is conferred by the presence of 4n conjugated pi electrons.
Heterocyclic compounds
Main article: Heterocyclic compound
The characteristics of the cyclic hydrocarbons are again altered if heteroatoms are present, which can exist as either substituents attached externally to the ring (exocyclic) or as a member of the ring itself (endocyclic). In the case of the latter, the ring is termed a heterocycle. Pyridine and furan are examples of aromatic heterocycles while piperidine and tetrahydrofuran are the corresponding alicyclic heterocycles. The heteroatom of heterocyclic molecules is generally oxygen, sulfur, or nitrogen, with the latter being particularly common in biochemical systems.
Heterocycles are commonly found in a wide range of products including aniline dyes and medicines. Additionally, they are prevalent in a wide range of biochemical compounds such as alkaloids, vitamins, steroids, and nucleic acids (e.g. DNA, RNA).
Rings can fuse with other rings on an edge to give polycyclic compounds. The purine nucleoside bases are notable polycyclic aromatic heterocycles. Rings can also fuse on a “corner” such that one atom (almost always carbon) has two bonds going to one ring and two to another. Such compounds are termed spiro and are important in a number of natural products.
Polymers
Main article: Polymer
This swimming board is made of polystyrene, an example of a polymer.
One important property of carbon is that it readily forms chains, or networks, that are linked by carbon-carbon (carbon-to-carbon) bonds. The linking process is called polymerization, while the chains, or networks, are called polymers. The source compound is called a monomer.
Two main groups of polymers exist: synthetic polymers and biopolymers. Synthetic polymers are artificially manufactured, and are commonly referred to as industrial polymers. Biopolymers occur within a respectfully natural environment, or without human intervention.
Since the invention of the first synthetic polymer product, bakelite, synthetic polymer products have frequently been invented.
Common synthetic organic polymers are polyethylene (polythene), polypropylene, nylon, teflon (PTFE), polystyrene, polyesters, polymethylmethacrylate (called perspex and plexiglas), and polyvinylchloride (PVC).
Both synthetic and natural rubber are polymers.
Varieties of each synthetic polymer product may exist, for purposes of a specific use. Changing the conditions of polymerization alters the chemical composition of the product and its properties. These alterations include the chain length, or branching, or the tacticity.
With a single monomer as a start, the product is a homopolymer.
Secondary component(s) may be added to create a heteropolymer (co-polymer) and the degree of clustering of the different components can also be controlled.
Physical characteristics, such as hardness, density, mechanical or tensile strength, abrasion resistance, heat resistance, transparency, colour, etc. will depend on the final composition.
Biomolecules
Maitotoxin, a complex organic biological toxin.
Biomolecular chemistry is a major category within organic chemistry which is frequently studied by biochemists. Many complex multi-functional group molecules are important in living organisms. Some are long-chain biopolymers, and these include peptides, DNA, RNA and the polysaccharides such as starches in animals and celluloses in plants. The other main classes are amino acids (monomer building blocks of peptides and proteins), carbohydrates (which includes the polysaccharides), the nucleic acids (which include DNA and RNA as polymers), and the lipids. In addition, animal biochemistry contains many small molecule intermediates which assist in energy production through the Krebs cycle, and produces isoprene, the most common hydrocarbon in animals. Isoprenes in animals form the important steroid structural (cholesterol) and steroid hormone compounds; and in plants form terpenes, terpenoids, some alkaloids, and a class of hydrocarbons called biopolymer polyisoprenoids present in the latex of various species of plants, which is the basis for making rubber.
- Peptide Synthesis
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- See also Peptide synthesis
- Oligonucleotide Synthesis
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- See also Oligonucleotide synthesis
- Carbohydrate Synthesis
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- See also Carbohydrate synthesis
Small molecules
Molecular models of caffeine.
In pharmacology, an important group of organic compounds is small molecules, also referred to as ‘small organic compounds’. In this context, a small molecule is a small organic compound that is biologically active, but is not a polymer. In practice, small molecules have a molar massless than approximately 1000 g/mol.
Fullerenes
Fullerenes and carbon nanotubes, carbon compounds with spheroidal and tubular structures, have stimulated much research into the related field of materials science. The first fullerene was discovered in 1985 by Sir Harold W. Kroto of the United Kingdom and by Richard E. Smalley and Robert F. Curl, Jr., of the United States. Using a laser to vaporize graphite rods in an atmosphere of helium gas, these chemists and their assistants obtained cagelike molecules composed of 60 carbon atoms (C60) joined together by single and double bonds to form a hollow sphere with 12 pentagonal and 20 hexagonal faces—a design that resembles a football, or soccer ball. In 1996 the trio was awarded the Nobel Prize for their pioneering efforts. The C60 molecule was named buckminsterfullerene (or, more simply, the buckyball) after the American architect R. Buckminster Fuller, whose geodesic dome is constructed on the same structural principles.
Others
Organic compounds containing bonds of carbon to nitrogen, oxygen and the halogens are not normally grouped separately. Others are sometimes put into major groups within organic chemistry and discussed under titles such as organosulfur chemistry, organometallic chemistry, organophosphorus chemistry and organosilicon chemistry.
