Structure & Reactivity in Organic, Biological and Inorganic Chemistry
Acet - a prefix used for carboxylic acid derivatives and related compounds that have two carbons in the carbonyl-containing part of the structure. Synonymous with "ethano". An example is acetic acid or ethanoic acid, CH3CO2H.
Acetylene - a term for a specific compound, also called ethyne, containing two carbons and a triple bond, formula C2H2. Also a common term for compounds containing carbon-carbon triple bonds, more formally referred to as alkynes.
Acid chloride - a compound containing a carbonyl attached to a chlorine atom, of general formula RCOCl. This functional group is an example of a carboxylic acid derivative. Also called acyl chloride.
Acyl - a general term for a carbon-containing group with a carbonyl which is joined to something else, usually a heteroatom or a metal.
Alcohol - a compound containing an OH group that is attached to carbon, but not to a carbonyl. An example is ethanol, CH3CH2OH.
Aldehyde - a compound containing a carbonyl at the end of a chain, so that a hydrogen atom is also attached to the carbonyl. An example is propanal, CH3CH2CHO.
Aliphatic - an archaic adjective used to describe compounds or parts of compounds that contain chains of carbon atoms, in contrast with cyclic (or, archaically, alicylic). Also sometimes used to describe saturated or parrafinic hydrocarbons, in which all the carbons are tetrahedral and attached to each other via single bonds only.
Aliphatic Nucleophilic Substitution - a type of reaction in which a nucleophile replaces a leaving group (that is, one group is exchanged for another) at an electrophilic, tetrahedral carbon.
Alkane - a hydrocarbon composed of only tetrahedral carbons, connected to each other via single bonds only. Also called a saturated hydrocarbon. An example is ethane, CH3CH3.
Alkene - a hydrocarbon containing one or more double bonds between carbons. An example is ethene, CH2CH2.
Alkyne - a hydrocarbon containing one or more triple bonds between carbons. An example is ethyne, CHCH.
Amide - a compound containing a nitrogen that is attached to a carbonyl. An example is methanamide, also called formamide, HCONH2.
Amine - a compound containing a nitrogen that is not attached to a carbonyl. An example is ethylamine, CH3CH2NH2.
Amino - an NH2 group covalently attached (through the nitrogen) to a larger molecule. May also be used, with modifications, to describe similar groups, such as methylamino, CH3NH.
Angular - a bonding arrangement in which two atoms are connected to a middle atom, A-B-C, with the three atoms forming a bent geometry rather than linear. This arrangement is usually seen where the middle atom has one or more lone pairs as well as its neighbouring atoms. An example of a compound with this geometry is water, H2O.
Aromatic - a cyclic, unsaturated compound that is unusually stable compared to other unsaturated compounds. Aromatics generally undergo different reactions than alkenes. In order to achieve aromaticity, the compound must be planar and possess an odd number of electron pairs in its pi system (the electrons that can participate in pi bonding).
Arrow convention - a number of different arrow conventions are used in chemistry to convey specific ideas. A thorough knowledge of arrow conventions is indispensable on class tests.
Aufbau process - the rules followed in populating energy levels with electrons in an atom.
Benzene - the most common example of an aromatic compound, formula C6H6.
Beta-elimination - in organometallic chemistry, a reaction analogous to 1,2-elimination in organic chemistry, but in which a metal center attached to the alkyl chain undergoing elimination is analogous to both the base and the leaving group in an organic 1,2-elimination.
Bis - a prefix that indicates there are two identical groups in a structure. Used for complicated subunits, or where the subunit itself contains a number of identical groups. An example of usage is in bis(triphenylphosphine) palladium, (PPh3)2Pd.
Bohr atom (or Bohr model of the atom) - an early view of the atom in which electrons were presumed to orbit at fixed distances from the nucleus. This model was used to explain the emission of very specific wavelengths of light when different elements were excited.
Bronsted-Lowry acid - concerns a specific case of Lewis acidity, in which a proton, H+, is the Lewis acid. In this case, the molecule that provides the proton for the reaction is described as a Bronsted acid.
Bronsted-Lowry base - a specific example of a Lewis base, in which the lone pair from the base is donated specifically to a proton, H+. Most commonly, small atoms that can form good covalent bonds with hydrogen, such as oxygen (especially oxygen anions) and nitrogen (even if uncharged), are responsible for the Bronsted basicity of a molecule.
But - ("byoot") a prefix in the name of organic compound meaning a group contains four carbons. An example is butylamine, CH3CH2CH2CH2NH2.
Carbonyl - a common structural unit in which a carbon is double bonded to an oxygen, C=O.
Carboxylic acid - a compound containing an OH group attached to a carbonyl. An example is ethanoic acid, CH3CO2H.
Cis - a prefix, usually italicized, that indicates two substituents are present on the double bond of an alkene or on a ring, and that the substituents are on the same side of the alkene or the same face of the ring. Examples are cis-1,2-dimethylcylohexane and cis-2-butene.
Conformation - a shape adopted by a flexible molecules by rotating or twisting neighbouring groups around its sigma bonds. Many molecules can adopt a variety of different shapes in this way.
Conformer - a stable conformation, one of the most likely shapes for a molecule to adopt.
Dec - a prefix in the name of an organic compound meaning a group contains nine carbons. An example is decane, CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3.
Drying agent - a compound used to remove traces of water from an organic solution. Drying agents can work by reacting with the water, usually turning it into a metal hydroxide and hydrogen; by capturing the water in cave-like pores; or by strongly binding to oxygen in a Lewis acid-base adduct.
E - a prefix, usually italicized, that indicates two high-priority substituents on the double bond of an alkene are on opposite sides of the alkene. From the German entgegen (opposite). Loosely analogous to the prefix trans, but can be used for compounds with more than two substituents on the double bond. Whether a compound is called E or the complementary term, Z, is determined using specific rules (modified Cahn-Ingold-Prelog Rules).
Electron affinity - the energy released when a free electron is adopted by an atom.
Electronegativity - the ability of an atom to draw electrons toward itself.
Electrophile - an atom or compound that attracts electrons; analogous to a Lewis acid, or to the proton in a Bronsted-Lowry acid
Element - a material composed of only one type of atom, or conversely, a unique type of atom that, when combined with other, different types of atoms, can make up new compounds with new properties.
Elimination - a type of reaction in which part of a molecule is lost, without being replaced by something else. A common elimination reaction is 1,2-elimination in organic chemistry: H-CH2-CH2-Cl = CH2=CH2 + HCl
Ester - a compound with an oxygen connecting a carbonyl and a second carbon group which is not a carbonyl. An example is methyl ethanoate, CH3CO2CH3.
Eth - a prefix in the name of organic compound meaning a group contains two carbons. An example is ethane, CH3CH3.
Ether - a compound with an oxygen connecting two separate carbon groups, but in which the oxygen is not attached to a carbonyl. An example is methyl ether, CH3OCH3
Form - a prefix used for carboxylic acid derivatives and related compounds that have only one carbon in the carbonyl-containing part of the structure. Synonymous with "methano". An example is formic acid or methanoic acid, HCO2H.
Functional Group - a specific group of atoms having characteristic reactivity and physical properties. Examples include alcohols, ethers and aromatics.
Halogen - Elements from Group 7 of the periodic table: fluorine, chlorine, bromine, iodine.
Hex - a prefix in the name of organic compound meaning a group contains six carbons. An example is hexanol, CH3CH2CH2CH2CH2CH2OH.
Hept - a prefix in the name of organic compound meaning a group contains seven carbons. An example is 1-heptene, CH3CH2CH2CH2CH2CH=CH2.
High spin - a description of the electronic configuration of certain transition metal ions, in which frontier d electrons populate a higher energy level rather than pair up in a energy level.
Hybridization - a mathematical approach for simplifying molecular orbital calculations and other MO considerations. Rather than treating each (atomic) basis orbital separately, the orbitals involved in direct sigma bonds with neighbouring atoms are averaged and treated as though identical. This approach is particularly useful for boron and carbon (and sometimes nitrogen), in which the atomic orbitals are close enough to each other in energy to justify this approximation.
Hydroxy - an OH group covalently attached (through the oxygen) to a larger molecule.
Integral - the measurement of the area of a peak in spectroscopy. The peak area is proportional to the number of molecules or atoms absorbing or fluorescing at that frequency.
Ionization energy - the energy it costs to strip an electron away from a particular atom.
Ketone - a compound containing a carbonyl bonded to carbons on both sides. An example is 2-butanone, CH3COCH2CH3.
Law of definite proportions - as described by Dalton, the fact that atoms combine in specific ratios to form specific compounds with specific properties.
Lewis acid - A compound or atom that can accept lone pairs from another atom or compound, forming a covalent bond in the process. The most general definition of an acid.
Lewis base - A compound or atom that can donate lone pairs to another atom or compound, forming a covalent bond in the process. The most general definition of a base.
Linear - a bonding arrangement in which two atoms are connected to a middle atom, A-B-C, with all three atoms forming one straight line.
Lone pair - casual term for a non-bonding pair of electrons.
Low spin - a description of the electronic configuration of certain transition metal ions, in which frontier d electrons pair up in a lower energy level rather than populate the next energy level.
Meth - a prefix in the name of organic compound meaning a group contains one carbon. An example is methanol, CH3OH.
Nomenclature - a standard system used in naming things. For example, the nomenclature of inorganic chemistry uses the suffix "ide" for simple anions, as in chloride or hydroxide, to distinguish them from neutral species like chlorine or hydroxyl radical.
Non - a prefix in the name of organic compound meaning a group contains nine carbons. An example is nonane, CH3CH2CH2CH2CH2CH2CH2CH2CH3.
Nucleophile - an atom or compound that attracts nuclei or positive charges; analogous to a Lewis base. A nucleophile requires a pair of electrons, which can be either a lone pair or a pi bonding pair, and sometimes has a negative charge.
Oct - a prefix in the name of organic compound meaning a group contains eight carbons. An example is octanal, CH3CH2CH2CH2CH2CH2CH2CHO.
Olefin - a common term for a carbon-carbon double bond or alkene, still frequently used in industry.
Pent - a prefix in the name of organic compound meaning a group contains five carbons. An example is pentanol, CH3CH2CH2CH2CH2OH.
Percent Composition (% Composition) - the make-up of a mixture or alloy by percentages of each component. For example, a steel might be 99% iron, 0.8% manganese and 0.2% carbon. The persent composition of mixtures of organic compounds can be determined by NMR analysis.
Periodic Table (of the Elements) - an organized chart that displays the elements in rows and columns according to similarities in their properties and, underlying those properties, according to electronic configuration.
Periodicity - the predictable variation of properties of the elements across the periodic table.
Phenol - a special case of an alcohol in which the OH is directly connected to one of the carbons in a benzene ring. Because of resonance considerations, phenols are much more acidic than regular alcohols.
Polymer - a macromolecule composed of many repeating units, useful for having particular physical properties that can be applied in materials science.
Prefix - in organic nomenclature of the simplest compounds, the prefix states the number of carbons in the chain. Alternatively, in more complicated compounds, additional prefixes are added to the front of the name to indicate how many carbons are found in each of various branches of the structure, with numbers indicating where these branches are found in the structure.
Pyramidal - a bonding arrangement in which three atoms are connected to one central atom, with the central atom at the apex of a pyramid. This arrangement is usually seen where the central atom has one or more lone pairs as well as its neighbouring atoms. An example of a compound with this geometry is ammonia, NH3.
Quinone - an oxidized form of a dihydroxybenzene, in which the six-membered ring contains two double bonds and two carbonyls.
R - a prefix, usually italicized, that indicates a molecule contains a chiral center, and that the three highest-priority substituents around the chiral center have a clockwise relationship from first to third priority when viewed in the foreground of the molecule. From the Latin rectus (right). An example is R-alanine (aka L-alanine, for different reasons).
S - a prefix, usually italicized, that indicates a molecule contains a chiral center, and that the three highest-priority substituents around the chiral center have a counter-clockwise relationship from first to third priority when viewed in the foreground of the molecule. From the Latin sinistere (left). An example is S-alanine (aka D-alanine, for different reasons).
Schrodinger wave equation - a crucial development in quantum mechanics in which the electron is described mathematically as a wave. Solutions to this equation provide the energy and the probable location of the electron.
SN1 - one of the two limiting cases of aliphatic nucleophilic substitution reactions, so designated by K.U. Ingold because one molecule (the electrophile) takes part in the rate-determining step.
SN2 - one of the two limiting cases of aliphatic nucleophilic substitution reactions, so designated by K.U. Ingold because two molecules (the electrophile and the nucleophile) take part in the rate-determining step.
sp - a label that, in organic chemistry, corresponds to a linear geometry at carbon. This term comes from the hybridization approach to molecular orbital calculations. If a central carbon is bonded to two neighbours in a straight line, only the carbon s orbital and one p orbital would directly overlap the neighbours, whereas the other two p orbitals would lie off the bond axis. These p orbitals would potentially be available for pi bonding, however.
sp2 - a label that, in organic chemistry, corresponds to a trigonal planar geometry at carbon. This term comes from the hybridization approach to molecular orbital calculations. If a central carbon is bonded to three neighbours in a plane, only the carbon s orbital and two of the p orbitals would directly overlap the neighbours, whereas the other p orbital would lie out of the plane. This p orbital would potentially be available for pi bonding, however.
sp3- a label that, in organic chemistry, corresponds to a tetrahedral geometry at carbon. This term comes from the hybridization approach to molecular orbital calculations. If a central carbon is bonded to four neighbours in a tetrahedron, the carbon s orbital could overlap with any of the neighbours and all three p orbitals would be needed for overlap with the neighbours in three dimensions.
Spectrochemical series - a ranking of ligands in terms of the strength of binding to transition metals, characterized by Δ, the ligand field splitting.
Substituent - an atom or group of atoms attached to a specific structure; usually assumed to be something other than hydrogen.
Substitution - a reaction in which one atom or group of atoms replaces another.
Suffix - in organic nomenclature, the suffix indicates the main functional group in the compound. If there are multiple functional groups, the main one is arbitrarily considered that which contains the most bonds to oxygen.
Tetrahedral - a geometry in which four atoms, all bonded to the same central atom, point to alternating corners of a cube. An example is methane, CH4. Alternatively, can also be used to describe the arrangement of a mixture of atoms and lone pairs, as in ammonia, NH3.
Trigonal Planar - a geometry in which three atoms, all bonded to the same central atom, point to the corners of an equilateral triangle. An example is free, monomeric borane, BH3.
Trans - a prefix, usually italicized, that indicates two substituents are present on the double bond of an alkene or on a ring, and that the substituents are on opposite sides of the alkene or opposite faces of the ring. Examples are trans-1,2-dimethylcylohexane and trans-2-butene.
Z - a prefix, usually italicized, that indicates two high-priority substituents on the double bond of an alkene are the same side of the double bond. From the German zusammen (together). Loosely analogous to the prefix cis, but can be used for compounds with more than two substituents on the double bond. Whether a compound is called Z or the complementary term, E, is determined using specific rules (Cahn-Ingold-Prelog Rules).
Zeolite - an inorganic compound of metal oxides with an open, cage-like structure. Zeolites are important because they can be used to catalyse certain reactions. Also, zeolites with well-controlled pore sizes can be used to selectively absorb certain molecules, such as water, and consequently they can be used as drying agents.
These materials are protected by copyright 2008, Chris P. Schaller
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