Organic Chemistry
Exothermic
An exothermic reaction is a chemical reaction that releases heat, and is the opposite of an endothermic reaction.
Ester
An inorganic or organic acid in which at least one -OH (hydroxyl) group is replaced by an -O-alkyl (alkoxy) group.
Carboxylic acid
An organic acid characterized by the presence of a carboxyl group.
Vinyl
An organic compound that contains a vinyl group (also called ethenyl), −CH=CH2.
Ether
An organic compound which contains an ether group — an oxygen atom connected to two (substituted) alkyl or aryl groups — of general formula R-O-R'.
Carbocation -
An organic ion in which a carbon atom has a positive charge, Can occur by a hyride shift or a shift of an alkyl group. The end product leads to a more stable carbocation. The group or H- will move to an adjacent positively charged carbon taking its bonding pair of electrons with it.
Alkyne
An unsaturated hydrocarbon containog triple bond.and having general formula CnH2n-2
Arene
Another name for an aromatic hydrocarbon.
Activating group
Any group which activate any molecule by increasing positive or negative charge on carbon atom.Mainly towards neucleophilic or electrophilic substitution reactions.
Nitrile
Any organic compound which has a -C≡N functional group.
Geminal -
(aka gem-diol) any organic compound having two hydroxyl functional groups (-OH) bound to the same carbon atom
Enthalpy -
(thermodynamics) a thermodynamic quantity equal to the internal energy of a system plus the product of its volume and pressure
Entropy -
(thermodynamics) a thermodynamic quantity representing the amount of energy in a system that is no longer available for doing mechanical work
Claisen condensation reaction -
- the aldol reaction with an ester. - deprotonation of the α-C of an ester and the addition of the anion to the carbonyl carbon of a second ester. - forms a β-ketoester - has a biological application in fatty acid synthesis
Fingerprint region -
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Grignard reagent -
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Ground state -
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Halohydrin formation -
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Hammond postulate -
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Hemiacetal -
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Hemiaminal -
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Hybrid orbital -
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Hybride shift -
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Hydrogen bond -
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Hyperconjugation -
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Imide -
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Imine -
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Infrared spectroscopy -
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Intermediate -
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Kekulé structure -
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Keto-enol tautomerism -
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Leaving group -
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Levorotatory -
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Lewis structure -
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Lindlar catalyst -
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Line-bond structure -
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Lone pair electrons -
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Mass spectrometry -
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Mechanism -
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Meso compound -
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Meta -
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Methylene group -
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Molecule -
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Non-bonding electrons -
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Normality -
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Nuclear magnetic resonance -
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Nucleophilic addition reaction -
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Nucleophilic aromatic substitution reaction -
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Nucleophilicity -
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Optical activity -
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Optical isomer -
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Orbital -
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Ortho -
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Oxidation -
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Oxime -
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Oxymercuration reduction reaction -
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Para -
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Pauli exclusion principle -
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Pericyclic reaction -
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Periplanar -
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Peroxide -
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Peroxyacid -
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Pi bond -
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Polar aprotic solvent -
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Polar covalent bond -
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Polar protic solvent -
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Polar reaction -
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Polarity -
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Polarizability -
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Primary -
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Prochiral -
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Prochirality center -
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Protic solvent -
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R group -
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R,S convention -
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Racemic mixture -
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Radical -
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Radical reaction -
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Rate constant -
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Rate equation -
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Rate-limiting step -
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Reducation -
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Regiochemistry -
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Regioselectivity -
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Resonance form -
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Resonance hybrid -
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Ring-flip -
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SN1 reaction -
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SN2 reaction -
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Secondary -
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Side chain -
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Sigma bond -
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Simmons-Smith reaction -
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Solvation -
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Solvent -
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Spin-spin splitting -
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Staggered conformation -
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Stereochemistry -
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Stereoisomer -
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Steric hinderance -
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Steric strain -
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Symmetry plane -
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Syn addition -
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Syn periplanar -
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Tautomers -
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Tertiary -
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Thioester -
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Thiolate ion -
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Torisional strain -
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Tosylate -
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Transition state -
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re face -
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si face -
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sp orbital -
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sp2 orbital -
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sp3 orbital -
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Claisen
1) NaOEt 2) H+ workup Make sure base matches so you don't transesterify LAST STEP MUST be to pluck off the proton in between 1,3 dicarb and then do the H+ grab!, condensation reaction which involves an ester
Equatorial bond -
A bond to a chair conformation of cyclohexane that extends from the ring roughly perpendicular to the imaginary axis through the center of the ring; a bond that lies roughly along the equator of a cyclohexane ring.
Chiral center
A carbon atom bonded to four different groups
Adam's catalyst
A catalyst for hydrogenation and hydrogenolysis in organic synthesis. Also known as platinum dioxide
Glycol
A chemical compound containing two hydroxyl groups (-OH groups). Also known as a Diol.
Hydroxylation
A chemical process that introduces one or more hydroxyl groups (-OH) into a compound (or radical) thereby oxidizing it.
Aromacity
A chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone.
Carboxylation
A chemical reaction in which a carboxylic acid group is introduced in a substrate.
Hydration
A chemical reaction in which a hydroxyl group (OH-) and a hydrogen cation (an acidic proton) are added to the two carbon atoms bonded together in the carbon-carbon double bond which makes up an alkene functional group.
Azo compound
A compound containing -N=N group.
Bicylcoalkane
A compound containing two cyclic rings.
Thiol
A compound that contains the functional group composed of a sulfur atom and a hydrogen atom (-SH).
Heterocycle
A cyclic molecule with more than 2 types of atoms as part of the ring. (e.g. Furan, a 5-membered ring with four carbons and one oxygen, or a Pyran, a 6-membered ring with five carbons and one oxygen)
Diels-Alder reaction -
A diene reacts with a dienophile (most double or triple bonds) to give a cyclic compound (bicyclic if the diene is already cyclic) Electron Releasing Groups activate dienes, EWGs activate dienophiles
Covalent bond
A form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms.
Carbonyl group
A functional group composed of a carbon atom double-bonded to an oxygen atom: C=O.
Acetyl
A functional group with chemical formula -COCH3.
Phenyl
A functional group with the formula -C6H5
Amino Acid
A fundamental unit of polypeptides or proteins.having general formula-COOHRCHNH2.eg.- glysine,alanine etc.
Achiral
A group containing atleast two identical substituents.
Acyl group
A group having alkyl or aryl group with a carbonyl group RCO-
Amide
A hydrocarbon containing amnine group attached to acyl group. eg.- RCONH2
Aldehyde
A hydrocarbon containing atleast one carbonyl gp having one hydrogen attached to it.(>C=O)
Alkyl
A hydrocarbon having formula CnH2n+1
Alkane
A hydrocarbon with all the carbon-carbon bonds are single bonds.
Alkene
A hydrocarbon with at least one carbon-carbon bond is a double-bond.
Polymer
A large molecule (macromolecule) composed of repeating structural units (monomers) typically connected by covalent chemical bonds.
Boat cyclohexane
A less-stable conformation of cyclohexane that somewhat resembles a boat.
Mole
A measure of a substance that is approximately Avogadro's Number (6.022×1023) of molecules of the substance. More simply, calculate the molecule's atomic mass and that many grams of the substance is a mole.
Molality
A measure of the concentration of a solute in a solvent given by moles of solute per kg of solvent.
Molarity
A measure of the concentration, given by moles of solute per liter of solution (solute and solvent mixed).
Hydrocarbon
A molecule consisting of hydrogens and carbons.
Acetal
A molecule with two single bonded oxygens attached to the same carbon atom.
Aliphatic
A non-cyclic, non-aromatic, hydrocarbon chain (e.g. alkanes, alkenes, and alkynes)
Cycloaddition reaction -
A pericyclic reaction in which two molecules react to form two new sigma bonds between the end atoms of their pi systems, resulting in the formation of a ring.
Hydroboration
A reaction adding BH3 or B2H6 or an alkylborane to an alkene to produce intermediate products consisting of 3 alkyl groups attached to a boron atom. This molecule is then used in other reactions, for example, to create an alcohol by reacting it with H2O2 in a basic solution.
Nucleophilic substitution reaction
A reaction in which a halide is removed from a molecule and replaced with a nucleophile.
Addition reaction
A reaction where a product is created from the coming together of 2 reactants.
Elimination reaction
A reaction where atoms and/or functional groups are removed from a reactant.
Second order reaction
A reaction whose rate is dependent on the concentration of two reactants, leading to a reaction rate of
First order reaction
A reaction whose rate is determined by the concentration of only one of its reactants leading to a reaction rate equation of
Lewis acid
A reagent that accepts a pair of electrons form a covalent bond. (see also Lewis Acids and Bases)
Lewis base
A reagent that forms covalent bonds by donating a pair of electrons. (see also Lewis Acids and Bases)
Cahn-Ingold-Prelog priorities
A rule for assigning priorities to substituents off of carbon in a double-bond or in a chiral center.
Alcohol
A saturated hydrocarbon chain with an -OH functional group.
Bimolecular reaction
A second order reaction where the concentration of two compounds determine the reaction rate.
Chain reaction
A sequence of reactions where a reactive product or by-product causes additional reactions to take place.
Amine
A simple hydrocarbon containing atleast one -NH2 group.
Unsaturated
A situation in which a compound contains double or triple bonds.
Saturated
A situation in which a compound has no double or triple bonds. Saturated can refer to the maximum amount of a solute being dissolved in a solution. Whether the context is chemical bonding or solutions will determine which meaning is appropriate.
Monomer
A small molecule that may become chemically bonded to other monomers to form a polymer.
Exergonic -
A spontaneous chemical reaction, in which there is a net release of free energy.
Endergonic
In an endergonic process, work is done on the system, and ΔG0 > 0, so the process is nonspontaneous. An exergonic process is the opposite: ΔG0 < 0, so the process is spontaneous.
Zaitsev's rule
In elimination reactions, the major reaction product is the alkene with the more highly substituted double bond. This most-substituted alkene is also the most stable.
Disulfide -
A strong covalent bond formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer.
Conjugation
A system of atoms covalently bonded with alternating single and multiple (e.g. double) bonds (e.g., C=C-C=C-C).
Chiral
A term chiral used to describe an object that is non-superposable on its mirror image
Downfield
A term used to describe the left direction on NMR charts. A peak to the left of another peak is described as being downfield from the peak.
Upfield
A term used to describe the right direction on NMR charts. A peak to the right of another peak is described as being upfield from the peak.
Chair cyclohexane -
A three-dimensional conformation of cyclohexane that resembles the rough shape of a chair. The chair form of cyclohexane is the lowest-energy conformation of the molecule., there are two main positions at which hydrogen atoms can appear. Axial and exuatorial.
Bromonium ion -
A three-membered ring containging a positively charged bromine atom; an intermediate formed in the addition of bromine to an alkene., positively charged intermediate of bromine bonded to one carbon and using its pair of electrons to stabilize the other carbon
Phenol
A toxic, colourless crystalline solid with the chemical formula C6H5OH and whose structure is that of a hydroxyl group (-OH) bonded to a phenyl ring. It is also known as carbolic acid,
β-carbon -
ATP, CO2, H2O, Carbon #3
HOMO
Acronym for Highest Occupied Molecular Orbital.
IUPAC
Acronym for International Union of Pure and Applied Chemistry.
LUMO
Acronym for Lowest Unoccupied Molecular Orbital
Acid halide
Acyl group with any halogen attached with carbon of carbonyl group.eg.- RCO-X(X=F,Cl,Br,I).
Hydrogenation
Addition of a hydrogen atoms to an alkene or alkane to produce a saturated product.
Alkylation
Addition of alkyl group in a compound.
Electrophilic addition reaction -
Alkenes behave as nucleophiles (lewis bases) in polar reactions. The C=C is electron rich, and can donate a pair of electrons to an electrophile (lewis acid). Rxn starts with attack on an electrophile (Ex: HBr) by the electrons in the C=C pi bond. The two pi electrons form a new sigma bond between a C and the H. A carbocation intermediate results as an electrophile and accepts an electron pair from the nucleophilic Br- ion to form a C-Br sigma bond.
Electrophile
Literally, electron lover. A positively or neutrally charged reagent that forms bonds by accepting electrons from a nucleophile. Elecrophiles are Lewis Acids.
Nucleophile
Literally, nucleus lover. A negatively or neutrally charged reagent that forms a bond with an electrophile by dontating both bonding electrons. Nucleophiles are Lewis Bases.
Anti bonding molecular orbital
Molecular orbitals having higher energy than bonding molecular orbitals after combination of atomic orbitals.denoted by an astric over Sigma or pi notations.
E1 reaction -
Multistep elimination where the leaving group is lost in a slow ionization step, then a proton is lost in a second step. Zaitsev rule is preffered for this orientation.
Friedel-Crafts reaction -
Reaction between an acyl halide and an aromatic ring will produce a ketone.
Substitution reaction
Reactions where one functional groups is replaced with another functional group.
NMR
See Nuclear magnetic resonance.
Saytzeff's Rule
See Zaitsev's rule
Markovnikov's rule
States that "when an unsymmetrical alkene reacts with a hydrogen halide to give an alkyl halide, the hydrogen adds to the carbon of the alkene that has the greater number of hydrogen substituents, and the halogen to the carbon of the alkene with the fewer number of hydrogen substituents."
Isotope
The different types of atoms of the same chemical element, each having a different atomic mass (mass number). Isotopes of an element have nuclei with the same number of protons (the same atomic number) but different numbers of neutrons.
Chromatography
The process of separating compounds such as a dye into its constituents
Cracking
The process whereby complex organic molecules such as heavy hydrocarbons are broken down into simpler molecules (e.g. light hydrocarbons) by the breaking of carbon-carbon bonds.
Benzyl Group
The radical or ion formed from the removal of one of the methyl hydrogens of toluene (methylbenzene).
1,3 Diaxial interaction
The steric intereaction between two methyl or larger groups attached at the 1 and 3 cis positions of cyclohexanes. The cyclohexane is in a higher energy state in the ring flip conformation that results in both 1 and 3 positions being axial due to steric strain between the 2 groups. This strain does not exist when hydrogens are bonded at these positions.
Atomic mass
Total no of nucleon i.e. no. of proton and no. of neutrons.It is denoted by A.
Atomic number
Total no. of protons is called atomic no.
Diastereomers
Two or more isomers of a molecule which are not enantiomers of one another.
Homolytic cleavage
Where bond breaks leaving each atom with one of the bonding electrons, producing two radicals.
Vinylic -
a carbocation in which the positive charge is on one of the carbons of a carbon-carbon double bond, compounds that have a halogen atom attached to one carbon atom of a double bond.
Dienophile -
a compound containing a double bond that can take part in the Diels-Alder cycloaddition reaction; most reactive are those that have electron withdrawing groups on the double bond
E2 reaction -
a concerted elimination involving a transition state where the base is abstracting a proton at the same time that the leaving group is leaving. the anti-coplanar transition state is generally preferred
Twist-boat conformation -
a conformation of cyclohexane that is somewhat more stable than a pure boat conformation
Acidity constant Ka -
a measure of acid strength, Ka= [H3O+][A-]/[HA]
Bonding molecular orbital -
a molecular orbital that is of lower energy and greater stability than the atomic orbitals from which it was formed
Dipole moment -
a property of a molecule whose charge distribution can be represented by a center of positive charge and a center of negative charge, Product of the amount of partial charge at either end of a molecule's dipole multiplied by the distance between them, given equation "p=qd". P is the dipole moment, q is the partial charge, and d is the distance separating the dipole
Enolate ion -
a resonance-stabilized anion resulting from the deprotonation of a carbon atom adjacent to a carbonyl functional group.
Van der Waals forces -
a slight attraction that develops between the oppositely charged regions of nearby molecules, Weak attractions between atoms resulting from the interaction of the electrons of one atom with the nucleus of another. This type of attraction is about one-fourth as strong as a hydrogen bond.
Fischer projection -
a system for drawing stereoisomers that shows the horizontal lines for bonds projecting forward and vertical lines for bonds projecting back with a carbon atom represented by each intersection
Conformation -
acting according to certain accepted standards
Electrophilic aromatic substitution -
aromatic compounds will act with VERY electrophilic reagents to undergo an overall substitution rxn for a H⁺ atom on the ring.
Vicinal -
belonging to or limited to a vicinity, Aldehyde HIO₄ has excessive O; diol reactant is being oxidized
Dipolar -
having equal and opposite electric charges or magnetic poles having opposite signs and separated by a small distance
Eclipsed conformation -
highest energy no separation. or 120 separation., Occurs when substituents are directly aligned, causing substantial repulsion between the substituents and an unfavorable conformation. Also called cis-conformation.
β position -
hydroxyl group located above the plane of the ring.
Concerted -
involving the joint activity of two or more
Hydrophobic
literally, "water fearing". In chemistry, molecules that aren't soluble in water.
Hydrophilic
literally, "water loving". In chemistry, these are molecules that are soluble in water.
Conformer -
organisms that do not regulate their internal conditions; they change as their external environment changes
Brønsted-Lowry Base -
proton acceptor, protons are transferred from one reactant (the acid) to another (the base)
Brønsted-Lowry Acid -
proton donor, a substance that donates a proton to another substance, A substance that can donate a hydrogen ion, H+, to another molecule or ion
Benzylic -
relating to benzyl, 2.3-2.8, Reacts a benzyl alkyl group with a diatomic bromine atom; Adds one of the bromines to the benzylic carbon, replacing a hydrogen
Dextrorotatory -
rotating to the right, an optical isomer that rotates polarized light to the right (counterclockwise to observer)
Anti conformation -
staggered conformation that is more stable since the two largest groups are at opposite ends (180 degrees apart), meaning that it is more sterically favorable
Cis-trans isomers -
stereoisomers that have the same connectivity but a different arrangement of their atoms in space as a result of the presence of either a ring or a carbon carbon double bond
E geometry -
the geometry of the atom given that all the zones where bonded., A term used to describe the stereochemistry of a carbon-carbon double bond. The two groups on each carbon are assigned priorities according to the Cahn-Ingold-Prelog sequence rules, and the two carbons are compared. If the high-priority groups on each carbon are on opposite sides of the double bond, the bond has E geometry.
Valence shell -
the outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom
Conjugate acid -
the particle formed when a base gains a hydrogen ion
Configuration
the permanent geometry of a molecule that results from the spatial arrangement of its bonds.
Decarboxylation -
the process of removing a carboxyl group from a chemical compound (usually replacing it with hydrogen)
Conjugate base -
the species that remains after a Bronsted-Lowry acid has given up a proton
Anti stereochemistry -
when the 2 Br atoms come from opposite faces of the double bond approx 180 degrees apart, The opposite of syn. An anti addition reaction is one in which the two ends of the double bond are attacked from different sides. An anti elimination reaction is one in which the two groups leave from opposite sides of the molecule.
Endothermic
An endothermic reaction is a chemical reaction that absorbs heat, and is the opposite of an exothermic reaction.
Valence bond theory -
An advanced model of chemical bonding in which electrons reside in quantum-mechanical orbitals localized on individual atoms that are a hybridized blend of standard atomic orbitals; chemical bonds result from an overlap of these orbitals.
Cycloalkane
An alkane that has one or more rings of carbon atoms in the chemical structure of its molecule.
Allyl
An alkene hydrocarbon group with the formula H2C=CH-CH2-
Enol
An alkene with a hydroxyl group affixed to one of the carbon atoms composing the double bond.
Electron
An elementary subatomic particle that carries a negative electrical charge and occupies an electron shell outside the atomic nucleus.
Isomer
Compounds with the same molecular formula but different structural formulae. There are two main forms of isomerism: structural isomerism and stereoisomerism.
α-carbon
Carbon attached to a functional group is called α-carbon
α Position
Carbon attached to a functional group is called α-carbon and the position is known as α position.
Formal Charge -
Charge assigned to an atom in a molecule or polyatmic ion, calculated by (# valence electrons) - (# 1/2 bonding electrons) - (# nonbonding electrons). Molecules containing atoms with lower formal charges tend to be more stable than those with higher formal charges.
Azide synthesis
Dutt-Wormall reaction in which a diazonium salt reacts with a sulfonamide first to a diazoaminosulfinate and then on hydrolysis the azide and a sulfinic acid.
Aldol reaction
When two similar aldehydes are reacted with each other,a product having both aldehyde(>C=O) and alcohol() group is formed.This reaction is called aldol reaction.
Entgegen
German word meaning "opposite". Represented by E in the E/Z naming system of alkenes.
Zussamen
German word meaning "together". Represented by Z in the E/Z naming system of alkenes. Simple mnemonic, Z=Zame Zide (Same Side).
Gilman reagent -
Gilman reagents are lithium and copper reagent compounds which are useful because they react with chlorides, bromides, and iodides to replace the halide group with an alkyl group.
Acid anhydride
Hydrocarbon containing two carbonyl groups.Acyl group attached with carboxylate group.eg- RCOOCOR'
Electronegativity
The ability of an atom to attract electrons towards itself in a covalent bond.
Delocalization
The ability of electrons to spread out among pi bonds to provide stabilization to electronically unstable areas of a molecule.
Benzoyl Group
The acyl of benzoic acid, with structure C6H5CO-
Bond angle
The angle formed between three atoms across at least two bonds.
Electron configuration
The arrangement of electrons in an atom or molecule
Bond
The attractive forces that create a link between atoms. Bonds may be covalent or ionic.
Bond length
The average distance between the centers of two atoms bonded together in any given molecule.
Axial bond
The bond parellel or anti parellel to axial coordinate passing center of gravity.
Alkoxide ion
The conjugate base of an alcohol without the terminal H atom. For any alcohol R-OH, the corresponding alkoxide form is R-O-.
Bond strength
The degree to which each atom linked to a central atom contributes to the valency of this central atom.
Electron shell
The orbit followed by electrons around an atomic nucleus. The atom has a number of shells and they are normally labelled K, L, M, N, O, P, and Q.
Valence electrons -
The electrons in the outermost shell (main energy level) of an atom; these are the electrons involved in forming bonds.
Gibbs free energy -
The energy in a system that can be used to drive chemical reactions. If the change in free energy of a reaction (Delta G, the free energy of the products minus the free energy of the energy of the reactants) is negative, the reaction will occur spontaneously.
Activation energy
The energy required to reactants to cross energy barrier to undergo any chemical change.denoted by Ea.
Ketone
The functional group characterized by a carbonyl group (O=C) linked to two other carbon atoms, or a chemical compound that contains a carbonyl group
Saponification
The hydrolysis of an ester under basic conditions to form an alcohol and the salt of a carboxylic acid.
IUPAC Nomenclature
The international standard set of rules for naming molecules.
Glycolysis
The metabolic pathway that converts glucose, C6H12O6, into pyruvate, C3H5O3
Mass number
The total number of protons and neutrons (together known as nucleons) in an atomic nucleus
Debye -
The unit used to express dipole moments., A unit of measure for dipole moments, where 1 Debye = 1x10^-18 esu x cm
Functional group
This is a specific group of atoms within a molecule that is responsible for the characteristic chemical reactions of that molecule. The same functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule it is a part of.
Electron-dot structure -
consists of an element's symbol, representing the atomic nucleus and inner-level electrons, that is surrounded by dots, representing the atom's valence electrons
Ultraviolet spectroscopy -
detects conjugated double bonds (double bonds separated by single bond). Provides info about length and structure of conjugated portion of molecule. More conjugated bonds allow UV light to be absorbed at higher wavelengths (Butadiene has absorption at 217 nm, tridiene have 247ish nm)