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63-491: In organic chemistry , the term "reagent" denotes a chemical ingredient (a compound or mixture, typically of inorganic or small organic molecules) introduced to cause the desired transformation of an organic substance. Examples include the Collins reagent , Fenton's reagent , and Grignard reagents . In analytical chemistry , a reagent is a compound or mixture used to detect the presence or absence of another substance, e.g. by

126-510: A =4), thiols (13), malonates (13), alcohols (17), aldehydes (20), nitriles (25), esters (25), then amines (35). Amines are very basic, and are great nucleophiles/attackers. The aliphatic hydrocarbons are subdivided into three groups of homologous series according to their state of saturation : The rest of the group is classified according to the functional groups present. Such compounds can be "straight-chain", branched-chain or cyclic. The degree of branching affects characteristics, such as

189-722: A molar mass less than approximately 1000 g/mol. 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 by single and double bonds to form

252-546: A branch of organic chemistry. Although the history of biochemistry might be taken to span some four centuries, fundamental understanding of the field only began to develop in the late 19th century and the actual term biochemistry was coined around the start of 20th century. Research in the field increased throughout the twentieth century, without any indication of slackening in the rate of increase, as may be verified by inspection of abstraction and indexing services such as BIOSIS Previews and Biological Abstracts , which began in

315-423: A broad range of industrial and commercial products including, among (many) others: plastics , synthetic rubber , organic adhesives , and various property-modifying petroleum additives and catalysts . The majority of chemical compounds occurring in biological organisms are carbon compounds, so the association between organic chemistry and biochemistry is so close that biochemistry might be regarded as in essence

378-510: A carbon lattice, and that the detailed patterns of atomic bonding could be discerned by skillful interpretations of appropriate chemical reactions. The era of the pharmaceutical industry began in the last decade of the 19th century when the German company, Bayer , first manufactured acetylsalicylic acid—more commonly known as aspirin . By 1910 Paul Ehrlich and his laboratory group began developing arsenic-based arsphenamine , (Salvarsan), as

441-415: A class of hydrocarbons called biopolymer polyisoprenoids present in the latex of various species of plants, which is the basis for making rubber . Biologists usually classify the above-mentioned biomolecules into four main groups, i.e., proteins, lipids, carbohydrates, and nucleic acids. Petroleum and its derivatives are considered organic molecules, which is consistent with the fact that this oil comes from

504-500: A color change, or to measure the concentration of a substance, e.g. by colorimetry . Examples include Fehling's reagent , Millon's reagent , and Tollens' reagent . In commercial or laboratory preparations, reagent-grade designates chemical substances meeting standards of purity that ensure the scientific precision and reliability of chemical analysis , chemical reactions or physical testing. Purity standards for reagents are set by organizations such as ASTM International or

567-462: A combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds. The development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the synthetic methods developed by Adolf von Baeyer . In 2002, 17,000 tons of synthetic indigo were produced from petrochemicals . In

630-419: A common reaction is a substitution reaction written as: where X is some functional group and Nu is a nucleophile . The number of possible organic reactions is 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

693-449: A given biomolecule—for example a drug target —but are unlikely to be useful as drugs themselves, and are often starting points in the drug discovery process. However, many natural substances are hits in almost any assay in which they are tested, and therefore not useful as tool compounds. Medicinal chemists class them instead as pan-assay interference compounds . One example is curcumin . Organic chemistry Organic chemistry

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756-576: 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. Organic compounds containing bonds of carbon to nitrogen, oxygen and

819-427: A lower p K a on another molecule (intermolecular) or within the same molecule (intramolecular). Any group with a net acidic p K a that gets within range, such as an acyl or carbonyl group is fair game. Since the likelihood of being attacked decreases with an increase in p K a , acyl chloride components with the lowest measured p K a values are most likely to be attacked, followed by carboxylic acids (p K

882-584: A mathematician from National Autonomous University of Mexico (UNAM), presenting the report " DNA and RNA Physicochemical Constraints, Cellular Automata and Molecular Evolution". The work was later presented by Miramontes as his dissertation . In silico has been used in white papers written to support the creation of bacterial genome programs by the Commission of the European Community. The first referenced paper where in silico appears

945-484: A melting point, boiling point, solubility, and index of refraction. Qualitative properties include odor, consistency, and color. Organic compounds typically melt and many boil. In contrast, while inorganic materials generally can be melted, many do not boil, and instead tend 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

1008-475: A novel compound is a problem-solving task, where a synthesis is designed for a target molecule by selecting optimal reactions from optimal starting materials. Complex compounds can have tens of reaction steps that sequentially build the desired molecule. The synthesis proceeds by utilizing the reactivity of the functional groups in the molecule. For example, a carbonyl compound can be used as a nucleophile by converting it into an enolate , or as an electrophile ;

1071-552: A respectfully natural environment, or without human intervention. 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

1134-686: 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: Traditional spectroscopic methods such as infrared spectroscopy , optical rotation , and UV/VIS spectroscopy provide relatively nonspecific structural information but remain in use for specific applications. Refractive index and density can also be important for substance identification. The physical properties of organic compounds typically of interest include both quantitative and qualitative features. Quantitative information includes

1197-514: 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 several natural products . One important property of carbon

1260-469: Is a subdiscipline within chemistry 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 determines their structural formula . Study of properties includes physical and chemical properties , and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes

1323-420: 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. 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

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1386-480: Is not always clear from a list of reactants alone. The stepwise course of any given reaction mechanism can be represented using arrow pushing techniques in which curved arrows are used to track the movement of electrons as starting materials transition through intermediates to final products. Synthetic organic chemistry is an applied science as it borders engineering , the "design, analysis, and/or construction of works for practical purposes". Organic synthesis of

1449-597: Is one performed on a computer or via computer simulation software. The phrase is pseudo-Latin for 'in silicon' (correct Latin : in silicio ), referring to silicon in computer chips. It was coined in 1987 as an allusion to the Latin phrases in vivo , in vitro , and in situ , which are commonly used in biology (especially systems biology ). The latter phrases refer, respectively, to experiments done in living organisms, outside living organisms, and where they are found in nature. The earliest known use of

1512-444: 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. By 1880 an explosion in the number of chemical compounds being discovered occurred assisted by new synthetic and analytical techniques. Grignard described the situation as "chaos le plus complet" (complete chaos) due to

1575-451: Is systematically named (6a R ,9 R )- 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 . Organic molecules are described more commonly by drawings or structural formulas , combinations of drawings and chemical symbols. The line-angle formula

1638-456: 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

1701-433: Is thought to have the potential to speed the rate of discovery while reducing the need for expensive lab work and clinical trials. One way to achieve this is by producing and screening drug candidates more effectively. In 2010, for example, using the protein docking algorithm EADock (see Protein-ligand docking ), researchers found potential inhibitors to an enzyme associated with cancer activity in silico . Fifty percent of

1764-413: Is typically taught at the college or university level. It is considered a very challenging course, but has also been made accessible to students. Before the 18th century, chemists generally believed that compounds obtained from living organisms were endowed with a vital force that distinguished them from inorganic compounds . According to the concept of vitalism (vital force theory), organic matter

1827-507: The American Chemical Society . For instance, reagent-quality water must have very low levels of impurities such as sodium and chloride ions, silica , and bacteria, as well as a very high electrical resistivity . Laboratory products which are less pure, but still useful and economical for undemanding work, may be designated as technical , practical , or crude grade to distinguish them from reagent versions. In

1890-476: The chemical synthesis of natural products , drugs , and polymers , and study of individual organic molecules in the laboratory and via theoretical ( in silico ) study. The range of chemicals studied in organic chemistry includes hydrocarbons (compounds containing only carbon and hydrogen ) as well as compounds based on carbon, but also containing other elements, especially oxygen , nitrogen , sulfur , phosphorus (included in many biochemicals ) and

1953-435: The cycloalkenes and the cycloalkynes do. 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

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2016-420: The electron affinity of key atoms, bond strengths and steric hindrance . These factors can determine the relative stability of short-lived reactive intermediates , which usually directly determine the path of the reaction. The basic reaction types are: addition reactions , elimination reactions , substitution reactions , pericyclic reactions , rearrangement reactions and redox reactions . An example of

2079-407: The halogens . Organometallic chemistry is the study of compounds containing carbon– metal bonds. In addition, contemporary research focuses on organic chemistry involving other organometallics including the lanthanides , but especially the transition metals zinc, copper, palladium , nickel, cobalt, titanium and chromium. Organic compounds form the basis of all earthly life and constitute

2142-541: 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 ((CH 2 ) 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

2205-618: The 1920s as a single annual volume, but has grown so drastically that by the end of the 20th century it was only available to the everyday user as an online electronic database . Since organic compounds often exist as mixtures , a variety of techniques have also been developed to assess purity; chromatography techniques are especially important for this application, and include HPLC and gas chromatography . Traditional methods of separation include distillation , crystallization , evaporation , magnetic separation and solvent extraction . Organic compounds were traditionally characterized by

2268-495: 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

2331-473: The combination of the two is called the aldol reaction . Designing practically useful syntheses always requires conducting the actual synthesis in the laboratory. The scientific practice of creating novel synthetic routes for complex molecules is called total synthesis . Strategies to design a synthesis include retrosynthesis , popularized by E.J. Corey , which starts with the target molecule and splices it to pieces according to known reactions. The pieces, or

2394-480: The early part of the 20th century, polymers and enzymes were shown to be large organic molecules, and petroleum was shown to be of biological origin. The multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of complex natural compounds increased in complexity to glucose and terpineol . For example, cholesterol -related compounds have opened ways to synthesize complex human hormones and their modified derivatives. Since

2457-573: The field of biology, the biotechnology revolution in the 1980s grew from the development of reagents that could be used to identify and manipulate the chemical matter in and on cells. These reagents included antibodies ( polyclonal and monoclonal ), oligomers , all sorts of model organisms and immortalised cell lines , reagents and methods for molecular cloning and DNA replication , and many others. Tool compounds are an important class of reagent in biology. They are small molecules or biochemicals like siRNA or antibodies that are known to affect

2520-429: The first effective medicinal treatment of syphilis , and thereby initiated the medical practice of chemotherapy . Ehrlich popularized the concepts of "magic bullet" drugs and of systematically improving drug therapies. His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums. Early examples of organic reactions and applications were often found because of

2583-422: The fossilization of living beings, i.e., biomolecules. See also: peptide synthesis , oligonucleotide synthesis and carbohydrate synthesis . 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

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2646-437: The functional group have an intermolecular and intramolecular effect on the surrounding environment and pH level. Different functional groups have different p K a values and bond strengths (single, double, triple) leading to increased electrophilicity with lower p K a and increased nucleophile strength with higher p K a . More basic/nucleophilic functional groups desire to attack an electrophilic functional group with

2709-494: 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 . Organic reactions are chemical reactions involving organic compounds . Many of these reactions are associated with functional groups. The general theory of these reactions involves careful analysis of such properties as

2772-451: The lack of convention it was possible to have multiple names for the same compound. This led to the creation of the Geneva rules in 1892. 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

2835-710: The majority of known chemicals. The bonding patterns of carbon, with its valence of four—formal single, double, and triple bonds, plus structures with delocalized electrons —make the array of organic compounds structurally diverse, and their range of applications enormous. They form the basis of, or are constituents of, many commercial products including pharmaceuticals ; petrochemicals and agrichemicals , and products made from them including lubricants , solvents ; plastics ; fuels and explosives . The study of organic chemistry overlaps organometallic chemistry and biochemistry , but also with medicinal chemistry , polymer chemistry , and materials science . Organic chemistry

2898-567: The molecule more acidic or basic due to their electronic influence on surrounding parts of the molecule. As the p K a (aka basicity ) of the molecular addition/functional group increases, there is a corresponding dipole , when measured, increases in strength. A dipole directed towards the functional group (higher p K a therefore basic nature of group) points towards it and decreases in strength with increasing distance. Dipole distance (measured in Angstroms ) and steric hindrance towards

2961-412: 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

3024-401: The molecules were later shown to be active inhibitors in vitro . This approach differs from use of expensive high-throughput screening (HTS) robotic labs to physically test thousands of diverse compounds a day, often with an expected hit rate on the order of 1% or less, with still fewer expected to be real leads following further testing (see drug discovery ). As an example, the technique

3087-437: The organic dye now known as Perkin's mauve . His discovery, made widely known through its financial success, greatly increased interest in organic chemistry. A crucial breakthrough for organic chemistry was the concept of chemical structure, developed independently in 1858 by both Friedrich August Kekulé and Archibald Scott Couper . Both researchers suggested that tetravalent carbon atoms could link to each other to form

3150-464: The organic solute and with the organic solvent. 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

3213-422: The parent structures. Parent structures include unsubstituted hydrocarbons, heterocycles, and mono functionalized derivatives thereof. 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 include most natural products. Thus, the informally named lysergic acid diethylamide

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3276-637: The phrase was by Christopher Langton to describe artificial life , in the announcement of a workshop on that subject at the Center for Nonlinear Studies at the Los Alamos National Laboratory in 1987. The expression in silico was first used to characterize biological experiments carried out entirely in a computer in 1989, in the workshop "Cellular Automata: Theory and Applications" in Los Alamos, New Mexico, by Pedro Miramontes,

3339-769: The polarity of the molecules and their molecular weight. Some organic compounds, especially symmetrical ones, sublime . A well-known example of a sublimable organic compound is para-dichlorobenzene , the odiferous constituent of modern mothballs. Organic compounds are usually not very stable at temperatures above 300 °C, although some exceptions exist. Neutral organic compounds tend to be hydrophobic ; that is, they are less soluble in water than inorganic solvents. Exceptions include organic compounds that contain ionizable groups as well as low molecular weight alcohols , amines , and carboxylic acids where hydrogen bonding occurs. Otherwise, organic compounds tend to dissolve in organic solvents . Solubility varies widely with

3402-524: The polysaccharides), the nucleic acids (which include DNA and RNA as polymers), and the lipids . Besides, 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

3465-415: The proposed precursors, receive the same treatment, until available and ideally inexpensive starting materials are reached. Then, the retrosynthesis is written in the opposite direction to give the synthesis. A "synthetic tree" can be constructed because each compound and also each precursor has multiple syntheses. In silico In biology and other experimental sciences, an in silico experiment

3528-589: The same in a variety of molecules. Functional groups can have a decisive influence on the chemical and physical properties of organic compounds. Molecules are classified based on 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. Functional groups make

3591-430: The start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B 12 . The discovery of petroleum and the development of the petrochemical industry spurred the development of organic chemistry. Converting individual petroleum compounds into types of compounds by various chemical processes led to organic reactions enabling

3654-415: The subjects of the areas of polymer science and materials science . 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 (International Union of Pure and Applied Chemistry). Systematic nomenclature starts with the name for a parent structure within

3717-509: Was cautious about claiming he had disproved vitalism, this was the first time a substance thought to be organic was synthesized in the laboratory without biological (organic) starting materials. The event is now generally accepted as indeed disproving the doctrine of vitalism. After Wöhler, Justus von Liebig worked on the organization of organic chemistry, being considered one of its principal founders. In 1856, William Henry Perkin , while trying to manufacture quinine , accidentally produced

3780-403: Was endowed with a "vital force". During the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and alkalis . He separated the acids that, in combination with the alkali, produced the soap. Since these were all individual compounds, he demonstrated that it

3843-471: 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 inorganic starting materials (the salts potassium cyanate and ammonium sulfate ), in what is now called the Wöhler synthesis . Although Wöhler himself

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3906-502: Was utilized for a drug repurposing study in order to search for potential cures for COVID-19 (SARS-CoV-2). Efforts have been made to establish computer models of cellular behavior. For example, in 2007 researchers developed an in silico model of tuberculosis to aid in drug discovery, with the prime benefit of its being faster than real time simulated growth rates, allowing phenomena of interest to be observed in minutes rather than months. More work can be found that focus on modeling

3969-533: Was written by a French team in 1991. The first referenced book chapter where in silico appears was written by Hans B. Sieburg in 1990 and presented during a Summer School on Complex Systems at the Santa Fe Institute. The phrase in silico originally applied only to computer simulations that modeled natural or laboratory processes (in all the natural sciences), and did not refer to calculations done by computer generically. In silico study in medicine

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