In organic chemistry Organic chemistry is a discipline within chemistry that involves the scientific study of the structure, properties, composition, reactions, and preparation 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 and biochemistry Biochemistry is the study of the chemical processes in living organisms. It deals with the structures and functions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules. Over the last 40 years biochemistry has become so successful at explaining living processes that now almost all areas of the life, a substituent is an atom or group of atoms substituted in place of a hydrogen Hydrogen is the chemical element with atomic number 1. It is represented by the symbol H. With an average atomic weight of 1.00794 u (1.007825 u for Hydrogen-1), hydrogen is the lightest and most abundant chemical element, constituting roughly 75 % of the Universe's elemental mass. Stars in the main sequence are mainly composed of hydrogen in its atom on the parent chain The IUPAC nomenclature of organic chemistry is a systematic method of naming organic chemical compounds as recommended by the International Union of Pure and Applied Chemistry . Ideally, every organic compound should have a name from which an unambiguous structural formula can be drawn. There is also an IUPAC nomenclature of inorganic chemistry of a hydrocarbon In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons from which one hydrogen atom has been removed are functional groups, called hydrocarbyls. Aromatic hydrocarbons , alkanes, alkenes, cycloalkanes and alkyne-based compounds are different types of hydrocarbons. The terms substituent, side chain, group, branch, or pendant group are used almost interchangeably to describe branches from a parent structure,^[1] though certain distinctions are made in the context of polymer A polymer is a large molecule composed of repeating structural units typically connected by covalent chemical bonds. While polymer in popular usage suggests plastic, the term actually refers to a large class of natural and synthetic materials with a wide variety of properties chemistry.^[2] In polymers A polymer is a large molecule composed of repeating structural units typically connected by covalent chemical bonds. While polymer in popular usage suggests plastic, the term actually refers to a large class of natural and synthetic materials with a wide variety of properties, side chains extend from a backbone structure. In proteins Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded side chains are attached to the alpha carbon The alpha carbon in organic chemistry refers to the first carbon that attaches to a functional group . By extension, the second carbon is the beta carbon, and so on atoms of the amino acid Amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. These molecules contain the key elements of carbon, hydrogen, oxygen, and nitrogen. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula backbone. This word may also be confused with the word substitute such as a substitute teacher.

The suffix -yl is used when naming organic compounds An organic compound is any member of a large class of chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of compounds such as carbonates, simple oxides of carbon and cyanides, as well as the allotropes of carbon, are considered inorganic. The distinction between "organic" and " that contain a single bond Bond order is the number of chemical bonds between a pair of atoms. For example, in diatomic nitrogen N≡N the bond order is 3, while in acetylene H−C≡C−H the bond order between the two carbon atoms is also 3, and the C−H bond order is 1. Bond order gives an indication to the stability of a bond. In a more advanced context, bond order replacing one hydrogen; -ylidene and -ylidyne are used with double bonds A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms, and other covalent bonds. In short, the attraction-to-repulsion stability that forms between atoms when they share electrons is known as covalent bonding and triple bonds A triple bond in chemistry is a chemical bond between two chemical elements involving six bonding electrons instead of the usual two in a covalent single bond. The most common triple bond, that between two carbon atoms, can be found in alkynes. Other functional groups containing a triple bond are cyanides and isocyanides. Some diatomic molecules, respectively. In addition, when naming hydrocarbons that contain a substituent, positional numbers are used to indicate which carbon atom the substituent is attached to when such information is needed to distinguish between structural isomers In chemistry, isomers are compounds with the same molecular formula but different structural formulas. The word is derived from the Greek ισομερης, isomerès; isos = "equal", méros = "part". There are many different classes of isomers, like stereoisomers, enantiomers, geometrical isomers, et cetera . Isomers do not. The polar effect The Polar effect or electronic effect in chemistry is the effect exerted by a substituent on modifying electrostatic forces operating on a nearby reaction center. The main contributors to the polar effect are the inductive effect, mesomeric effect and the through-space electronic field effect exerted by a substituent is a combination of the inductive effect The inductive effect in chemistry is an experimentally observable effect of the transmission of charge through a chain of atoms in a molecule by electrostatic induction. The net polar effect exerted by a substituent is a combination of this inductive effect and the mesomeric effect and the mesomeric effect The mesomeric effect or resonance effect in chemistry is a property of substituents or functional groups in a chemical compound. The effect is used in a qualitative way and describes the electron withdrawing or releasing properties of substituents based on relevant resonance structures and is symbolized by the letter M. The mesomeric effect is. Additional Steric effects Steric effects arise from the fact that each atom within a molecule occupies a certain amount of space. If atoms are brought too close together, there is an associated cost in energy due to overlapping electron clouds , and this may affect the molecule's preferred shape (conformation) and reactivity result from the volume occupied by a substituent.

The phrases most-substituted and least-substituted are frequently used to describe molecules and predict their products. For example:

• Markovnikov's rule In organic chemistry, Markovnikov's rule or Markownikoff's rule is an observation based on Zaitsev's rule. It was formulated by the Russian chemist Vladimir Vasilevich Markovnikov in 1870 predicts that the hydrogen adds to the carbon of the alkene functional group that has the greater number of hydrogen substituents.
• Zaitsev's rule In chemistry, Zaitsev's rule, Saytzeff's rule or Saytsev's rule named after Alexander Mikhailovich Zaitsev is a rule that states that if more than one alkene can be formed during dehalogenation by an elimination reaction, the more stable alkene is the major product. In general, the compound that has a more highly substituted C=C double bond is predicts that the major reaction product is the alkene with the more highly substituted (more stable) double bond.

Nomenclature

The suffix An affix is a morpheme that is attached to a word stem to form a new word. Affixes may be derivational, like English -ness and pre-, or inflectional, like English plural -s and past tense -ed. They are bound morphemes by definition; prefixes and suffixes may be separable affixes. Affixation is, thus, the linguistic process speakers use to form new -yl is used in Organic chemistry Organic chemistry is a discipline within chemistry that involves the scientific study of the structure, properties, composition, reactions, and preparation 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 to form names of radicals In chemistry, radicals are atoms, molecules, or ions with unpaired electrons on an open shell configuration. Radicals may have positive, negative or zero charge. By convention, metals and their ions or complexes with unpaired electrons are not radicals. The unpaired electrons cause radicals to be highly chemically reactive, either separate or chemically bonded parts of molecules. It can be traced back to the word methylene Methylene groups in a chain or ring contribute to its size and lipophilicity. Methylene was also the old original name for methanol (methy = "wine" + hȳlē = wood) Methanol, also known as methyl alcohol, wood alcohol, wood naphtha or wood spirits, is a chemical with formula C , evolving through the gradual regularization of chemical names to its current meaning.

The use of the suffix is determined by the number of hydrogen atoms that the substituent replaces on a parent compound (and also, usually, on the substituent). According to 1993 IUPAC The International Union of Pure and Applied Chemistry , pronounced /ˈaɪjuːpæk/, is an international federation of National Adhering Organizations that represents chemists in individual countries. It is a member of the International Council for Science (ICSU). The international headquarters of IUPAC is located in Zürich, Switzerland. The guidelines:^[3]

• -yl means that one hydrogen is replaced.

• -ylidene means that two hydrogens are replaced by a double bond A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms, and other covalent bonds. In short, the attraction-to-repulsion stability that forms between atoms when they share electrons is known as covalent bonding between parent and substituent. The term "-ylidine" is encountered sporadically, and is often used synonymously with -ylidene. The spelling "-ylidine" seems to be a rare usage in some contexts, but it appears notably in manufacturer's publications about Sunitinib EU EMEA:link, US FDA:link ^[4] PubChem PubChem is a database of chemical molecules. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and indexes 740110 results for "-ylidene", of which 14 use synonyms that replace the suffix freely with "-ylidine". An additional four compound entries contain "-ylidine" without listing "-ylidene" as a synonym. The word "-ylidine" is not in IUPAC guidelines.
• -ylidyne means that three hydrogens are replaced by a triple bond A triple bond in chemistry is a chemical bond between two chemical elements involving six bonding electrons instead of the usual two in a covalent single bond. The most common triple bond, that between two carbon atoms, can be found in alkynes. Other functional groups containing a triple bond are cyanides and isocyanides. Some diatomic molecules, between parent and substituent.

• -di, -tri, -tetra indicate multiple bonds of the same type link the substituent and parent group (-diyl, -triyl, -tetrayl, -diylidine), and multiple suffixes are added to indicate different bond types (-ylylidine, -ylylidyne, -diylylidine)

The parent compound name can be altered in two different ways.

• For many common compounds the substituent is linked at one end (the 1 position), which is therefore not explicitly numbered in the formula. The substituent name is modified by stripping "-ane" (see Alkane Alkanes are chemical compounds that consist only of the elements carbon (C) and hydrogen (H) (i.e., hydrocarbons), wherein these atoms are linked together exclusively by single bonds (i.e., they are saturated compounds) without any cyclic structure (i.e. loops). Alkanes belong to a homologous series of organic compounds in which the members differ) and adding the appropriate suffix. This is "recommended only for saturated acyclic and monocyclic hydrocarbon substituent groups and for the mononuclear parent hydrides of silicon, germanium, tin, lead, and boron". Thus, if there is a carboxylic acid Carboxylic acids are organic acids characterized by the presence of at least one carboxyl group. A carboxyl group is a functional group consisting of a carbonyl and a hydroxyl, which has the formula -C(=O)OH, usually written -COOH or -CO2H. Carboxylic acids are Brønsted-Lowry acids — they are proton donors. Salts and anions of carboxylic acids called "X-ic acid", an alcohol In chemistry, an alcohol is any organic compound in which a hydroxyl functional group (-O ending "X-anol" (or "X-yl alcohol"), or an alkane called "X-ane", then "X-yl" typically denotes the same carbon chain lacking these groups but modified by attachment to some other parent molecule.

• The more general method omits only the terminal "e" of the substituent name, but requires explicit numbering of each -yl prefix, even at position 1 (except for -ylidyne, which as a triple bond A triple bond in chemistry is a chemical bond between two chemical elements involving six bonding electrons instead of the usual two in a covalent single bond. The most common triple bond, that between two carbon atoms, can be found in alkynes. Other functional groups containing a triple bond are cyanides and isocyanides. Some diatomic molecules, must terminate the substituent carbon chain). Pentan-1-yl is an example of a name by this method, and is synonymous with Pentyl from the previous guideline.

Note that some popular terms such as "vinyl A vinyl compound is any organic compound that contains a vinyl group . Vinyl groups (formula −C " represent only a portion of the full chemical name.

Structures

In a chemical structural formula The structural formula of a chemical compound is a graphical representation of the molecular structure, showing how the atoms are arranged. The chemical bonding within the molecule is also shown, either explicitly or implicitly. There are three common representations used in publications: text, Lewis type and line-angle formula. Also several other, an organic substituent such as methyl In chemistry, a methyl group is a hydrophobic alkyl functional group named after methylene (RC , ethyl, aryl In the context of organic molecules, aryl refers to any functional group or substituent derived from a simple aromatic ring, be it phenyl, thiophene, indolyl, etc . "Aryl" is used for the sake of abbreviation or generalization can be written as R (or R₁, R₂, etc.) This is a generic placeholder, the R derived from radical In chemistry, radicals are atoms, molecules, or ions with unpaired electrons on an open shell configuration. Radicals may have positive, negative or zero charge. By convention, metals and their ions or complexes with unpaired electrons are not radicals. The unpaired electrons cause radicals to be highly chemically reactive or rest, which may replace any portion of the formula as the author finds convenient. The first to use this symbol was Charles Frédéric Gerhardt in 1844.

The symbol X is often used to denote electronegative substituents such as the halides A halide is a binary compound, of which one part is a halogen atom and the other part is an element or radical that is less electronegative than the halogen, to make a fluoride, chloride, bromide, iodide, or astatide compound. Many salts are halides. All Group 1 metals form halides with the halogens and they are white solids. ^[5]

Number crunching

One cheminformatics Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery. These methods can also be used in chemical and allied industries in various other forms study ^[1] identified 849,574 unique substituents up to 12 non-hydrogen atoms large and containing only C,H,N,O,S,P,Se and the halogens in a set of 3,043,941 molecules. Fifty common substituents are found in only 1% of this set, and 438 in 0.1%. 64% of the substituents are unique to just one molecule. The top 5 consists of the phenyl where the six carbon atoms are arranged in a cyclic ring structure. This hydrophobic, highly-stable and aromatic hydrocarbon unit can be found in many organic compounds. It can be thought of as being derived from benzene . In fact, in chemical literature benzene itself is sometimes denoted as PhH, chlorine Chlorine (pronounced /ˈklɔəriːn/ KLOR-een, from the Greek word 'χλωρóς' , is the chemical element with atomic number 17 and symbol Cl. It is a halogen, found in the periodic table in group 17 (formerly VII, VIIa, or VIIb). As the chloride ion, which is part of common salt and other compounds, it is abundant in nature and necessary to, methoxy In chemistry , methoxy refers to the functional group consisting of a methyl group bound to oxygen. It has the formula:, hydroxyl In chemistry, hydroxyl is a compound containing an oxygen atom bound covalently with a hydrogen atom. The neutral form of this group is a hydroxyl radical. The hydroxyl anion is called hydroxide; it is a diatomic ion with a single negative electronic charge. In discussions of synthetic methods in organic chemistry the hydroxyl group (–OH) is, and ethyl In chemistry, an ethyl group is an alkyl functional group derived from ethane . It has the formula -C2H5 and is very often abbreviated -Et substituent. The total number of organic substituents in organic chemistry is estimated at 3.1 million, creating a total of 6.7×10²³ molecules. Or, since you can increase the carbon chain length of a substituent an infinite amount, provided it is not long enough to become part of the parent carbon chain (which can also be infinite in length), you can have an infinite number of substituents, simply by increasing carbon chain length. For instance, the substituents methyl (-CH₃) and pentyl (C₅H₁₁)

See also

• Functional groups In organic chemistry, functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction regardless of the size of the molecule it is a part of. However, its relative reactivity can be are a subset of substituents

External links

• Database of 21,000 substituents and 49,000 linkers extracted from bioactive molecules

References

1. ^ Cheminformatics Analysis of Organic Substituents: Identification of the Most Common Substituents, Calculation of Substituent Properties, and Automatic Identification of Drug-like Bioisosteric Groups Peter Ertl J. Chem. Inf. Comput. Sci.; 2003; 43(2) pp 374 – 380 Abstract Download reprint

1. ^ D.R. Bloch (2006). "Organic Chemistry Demystified". http://books.google.com/books?id=yVPcSIn5xjAC&pg=PT88&lpg=PT88.
2. ^ "PAC, 1996, 68, 2287. Glossary of basic terms in polymer science (IUPAC Recommendations 1996)". IUPAC Gold Book. doi A digital object identifier is a character string used to uniquely identify an electronic document or other object. Metadata about the object is stored in association with the DOI name and this metadata may include a location, such as a URL, where the object can be found. The DOI for a document is permanent, whereas its location and other metadata:doi:10.1351/pac199668122287. http://goldbook.iupac.org/src_PAC1996682287.html. This distinguishes a pendant group as neither oligomeric nor polymeric, whereas a pendant chain must be oligomeric or polymeric.
3. ^ "R-2.5 Substituent Prefix Names Derived from Parent Hydrides". IUPAC. 1993. http://www.acdlabs.com/iupac/nomenclature/93/r93_271.htm.
4. ^ http://www.pfizerpro.com/product_info/sutent_pi_description.aspx
5. ^ Jensen, W. B. (2010). "Why Is “R” Used To Symbolize Hydrocarbon Substituents?". Journal of Chemical Education 87: 360–361. doi A digital object identifier is a character string used to uniquely identify an electronic document or other object. Metadata about the object is stored in association with the DOI name and this metadata may include a location, such as a URL, where the object can be found. The DOI for a document is permanent, whereas its location and other metadata:10.1021/ed800139p.

6. wikipedia.org

Categories: Organic chemistry | Chemical nomenclature

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