The Things I learned in Organic Chemistry Magnet

Organic Chemistry is a discipline within chemistry that involves the scientific study of the structure, properties, composition, reactions, and preparation (by synthesis or by other means) of carbon based compounds, hydrocarbons, and their derivatives. These compounds may contain any number of other elements, including hydrogen, nitrogen, oxygen, the halogens as well as phosphorus, silicon and sulfur. Organic compounds are structurally diverse, and the range of application of organic compounds is enormous. They form the basis of, or are important constituents of many products (plastics, drugs, petrochemicals, food, explosives, paints, to name but a few) and, with very few exceptions, they form the basis of all earthly life processes. Organic chemistry, like all areas of science, evolves with particular waves of innovation. These innovations are motivated by practical considerations as well as theoretical innovations. The area is, however, underpinned financially by the very large applications in biochemistry, polymer science, pharmaceutical chemistry, and agrochemicals. At the beginning of the nineteenth century, chemists generally thought 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". They named these compounds "organic" and directed their investigations toward inorganic materials that seemed more easily studied.[citation needed] During the first half of the nineteenth century, it was realized that organic compounds could in fact be synthesized in the laboratory. Around 1816 Michel Chevreul started a study of soaps made from various fats and alkali. He separated the different acids that, in combination with the alkali, produced the soap. Since these were all individual compounds, he demonstrated that it was possible to make a chemical change in various fats (which traditionally come from organic sources), producing new compounds, without "vital force". In 1828 Friedrich Wöhler produced the organic chemical urea (carbamide), a constituent of urine, from the inorganic ammonium cyanate NH4OCN, in what is now called the Wöhler synthesis. Although Wöhler was, at this time as well as afterwards, cautious about claiming that he had thereby destroyed the theory of vital force, historians have looked to this event as the turning point. A great next step occurred in 1856 when William Henry Perkin, while trying to manufacture quinine, again accidentally came to manufacture the organic dye now called Perkin's mauve, which by generating a huge amount of money greatly increased interest in organic chemistry. The crucial breakthrough for organic chemistry was the concept of chemical structure, developed independently and simultaneously by Friedrich August Kekule and Archibald Scott Couper in 1858. Both men suggested that tetravalent carbon atoms could link to each other to form a carbon lattice, and that the detailed patterns of atomic bonding could be discerned by skillful interpretations of appropriate chemical reactions. The history of organic chemistry continued with the discovery of petroleum and its separation into fractions according to boiling ranges. The conversion of different compound types or individual compounds by various chemical processes created the petroleum chemistry leading to the birth of the petrochemical industry, which successfully manufactured artificial rubbers, the various organic adhesives, the property-modifying petroleum additives, and plastics. The pharmaceutical industry began in the last decade of the 19th century when acetylsalicylic acid (more commonly referred to as aspirin) manufacture was started in Germany by Bayer. The first time a drug was systematically improved was with arsphenamine (Salvarsan). Numerous derivatives of the dangerously toxic atoxyl were examined by Paul Ehrlich and his group, and the compound with best effectiveness and toxicity characteristics was selected for production. Although early examples of organic reactions and applications were often serendipitous, the latter half of the 19th century witnessed highly systematic studies of organic compounds. Beginning in the 20th century, progress of organic chemistry allowed the synthesis of highly complex molecules via multistep procedures. Concurrently, polymers and enzymes were understood to be large organic molecules, and petroleum was shown to be of biological origin. The process of finding new synthesis routes for a given compound is called total synthesis. Total synthesis of complex natural compounds started with urea, increased in complexity to glucose and terpineol, and in 1907, total synthesis was commercialized the first time by Gustaf Komppa with camphor. Pharmaceutical benefits have been substantial, for example cholesterol-related compounds have opened ways to synthesis of complex human hormones and their modified derivatives. Since the start of the 20th century, complexity of total syntheses has been increasing, with examples such as lysergic acid and vitamin B12. Today's targets feature tens of stereogenic centers that must be synthesized correctly with asymmetric synthesis. Biochemistry, the chemistry of living organisms, their structure and interactions in vitro and inside living systems, has only started in the 20th century, opening up a new chapter of organic chemistry with enormous scope. Biochemistry, like organic chemistry, primarily focuses on compounds containing carbon as well. Since organic compounds often exist as mixtures, a variety of techniques have also been developed to assess purity, especially important being chromatography techniques such as HPLC and gas chromatography. Traditional methods of separation include distillation, crystallization, and solvent extraction. 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 principle 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 allows one to obtain the "mass spec" of virtually any organic compound. • Crystallography is an unambiguous method for determining molecular geometry, the proviso being that single crystals of the material must be available and the crystal must be representative of the sample. Highly automated software allows a structure to be determined within hours of obtaining a suitable crystal. Traditional spectroscopic methods such as infrared spectroscopy, optical rotation, UV/VIS spectroscopy provide relatively nonspecific structural information but remain in use for specific classes of compounds. Additional methods are described in the article on analytical chemistry. Physical properties of organic compounds typically of interest include both quantitative and qualitative features. Quantitative information include melting point, boiling point, and index of refraction. Qualitative properties include odor, solubility, and color. Melting and boiling properties In contrast to many inorganic materials, organic compounds typically melt and many boil. 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. A well known example of a sublimable organic compound is para-dichlorobenzene, the odiferous constituent of mothballs. Organic compounds are usually not very stable at temperatures above 300 °C, although some exceptions exist. 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 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 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. Solubility in the different solvents depends upon the solvent type and on the functional groups if present. state properties Various specialized properties are of interest depending on applications, e.g. thermo-mechanical and electro-mechanical such as piezoelectricity, electrical conductivity (see organic metals), 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. The names of organic compounds is either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by recommendations 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, one must know the structures and names of the parent structures. Parent structures include unsubstituted hydrocarbons, heterocycles, and monofunctionalized derivatives thereof. Nonsystematic nomenclature is simpler and unambiguous, at least to organic chemists. Nonsystematic names do not indicate the structure of the compound. Nonsystematic names 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. With the increased use of computing, other naming methods have evolved that are intended to be interpreted by machines. Two popular formats are SMILES and InChI. 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, oxygen two, hydrogen one, and nitrogen three.