Introductory Organic Chemistry

Published by ryan z.

None

• Reaction

  When two or more molecules interact to form products that are distinct from the original molecules, reactants.

• Functional Group

  Functional Group can affect Reaction

  Structural features within molecules. Have characteristic properties and chemical behaviors that is similar throughout every molecule of which it is a part.

• Alkene

  Alkene has a Functional Group

  Hydrocarbons with carbon-carbon double bonds (C=H) in addition to C-C and C-H. Molecular formula CnH(2n).

• Alkyne

  Alkyne has a Functional Group

  Hydrocarbons with carbon-carbon triple bonds in addition to C-C and C-H. Molecular formula CnH(2n-2).

• Aromatic Compounds

  Aromatic Compounds has a Functional Group

  Hydrocarbons with an arene (aromatic ring), a six-carbon ring containing in total 3 pi-bonds between carbons. Resonance makes it such that each carbon-carbon bond in the ring is effectively 1.5 of a regular bond. Functional group name: arene.

• Alkyl Halide

  Alkyl Halide has a Functional Group

  

  A molecule formed by substituting a halogen for a hydrogen in a hydrocarbon. All atoms are sp3 hybridized.

• Carbonyl

  Carbonyl is a Functional Group

  

  A type of functional group consisting of a carbon double bonded to an oxygen and 2 different groups.

• Carboxylic Acid Derivative

  Carboxylic Acid Derivative have Carbonyl

  A molecule that can be formed from carboxylic acid(s). Includes aldehydes, ketones, esters, and nitriles, technically.

• Thiol

  Thiol has a Functional Group

  

  A molecule formed by substiting a SH group for a hydrogen in a hydrocarbon. All atoms are sp3 hybridized.

• Sulfide

  Sulfide has a Functional Group

  

  A molecule formed by substiting a S-R group for a hydrogen in a hydrocarbon. All atoms are sp3 hybridized.

• Acid Halide

  Acid Halide has a Functional Group

  

  A molecule formed by substituting a halogen for the OH (hydroxyl) group on a carboxylic acid.

• Acid Anhydride

  Acid Anhydride has a Functional Group

  

  A molecule formed by combining two carboxylic acids in a dehydration synthesis (condensation) reaction.

• Carbamate

  Carbamate has a Functional Group

  

  An organic molecule that from one side is an ester, and from the other is an amide.

• Imide

  Imide has a Functional Group

  

  An organic molecule formed by combining two amides.

• Constitutional Isomer

  Constitutional Isomer may be related to Functional Group

  Compounds with the same molecular formula but different connectivity between the atoms. May be caused by branching, different functional groups, or different positions of functional groups.

• IR Spectroscopy

  IR Spectroscopy can be used to find Functional Group

  A type of absorption spectroscopy useful for identifying functional groups in a molecule. A sample is irradiated by IR radiation and absorbances, measured in in wavenumber (1/wavelength), are observed. Certain wavenumbers of absorption correspond to certain special vibrations (stretching [symmetric/asymmetric], in-plane bending vibration [scissoring], out-of-plane bending vibration [twisting]) of certain bonds, which can give clues about functional groups present. Only vibrations that result in a change in dipole in a molecule will be IR active (more change in dipole, more intense the absorption) (eg. internal alkynes often not seen).

• Hooke's Law

  Hooke's Law related to IR Spectroscopy

  

  Hooke's Law is used to describe springs. Bonds can be treated like springs. Main takeaways: 1) The stronger the bond (presence of double/triple bonds), the more energy it will require for a transition and thus the higher the frequency (and wavenumber) absorptions are found at. 2) The mass of the atoms involved impact the energy required for a transition (the lighter the atoms are, the higher the frequency and wavenumber).

• Inductive Effects

  Inductive Effects is a factor affecting IR Spectroscopy

  

  Electronegative electron withdrawing groups (EWG) can pull electron density away from bonds near itself, making nearby bonds longer/shorter and thus stronger/weaker. The more electronegative the group, the shorter it makes nearby bonds, the stronger the bonds become, the higher the corresponding wavenumber tends to be. Vice versa. Can be seen on carbonyl of different functional groups (when other non-carbon groups attached, there is a shift to a higher wavenumber)

• Resonance Effects (IR Spectroscopy)

  Resonance Effects (IR Spectroscopy) is a factor affecting IR Spectroscopy

  

  When a functional group is connected to an atom/double bond via conjugation (delocalized electrons, related to resonance), bonds and lengthened/weakened (as what would normally be a double bond is effectively less than a full double bond). A weakened bond means lower wavenumber absorbance. The more resonance it displays, the more weak the bonds become. If conformational strain makes the bonds go out of conjugation, the effect is not as pronounced. (Eg. acid halides can have a higher wavenumber than other carbonyl-containing carboxylic acid derivatives, as the alternative resonance form requires pi-bonds to a halogen, which does not form as readily with elements below period 2, and thus resonance is not as strong).

• H-Bonding Effects (IR Spectroscopy)

  H-Bonding Effects (IR Spectroscopy) is a factor affecting IR Spectroscopy

  

  When hydrogen bonding occurs, it is observed in IR spectra as a broad, strong absorption at around 2900-3500 cm-1. Dimerization (shown above) can occur with carboxylic acids, which results in the weakening of both O-H and C=O bonds as the two molecules are pulled together by hydrogen bonding. Any hydrogen bonding in other molecules can cause this. This causes a shift to lower wavenumbers in the IR spectrum for the dimer. This can be minimized by using non-polar solvents and low dilutions of the sample.

• Reaction Mechanism

  Reaction Mechanism is used to describe Reaction

  A detailed accounting of how the electrons move in a reaction, leading to a representation of bond formation and breaking as the reaction occurs. This is on a molecular level. Basic Guidelines: 1)Identify nucleophile and electrophile. First mechanistic arrow goes from nucleophile to electrophile. 2) Use a regular curly mechanistic arrow to represent the movement of a pair of electrons. These indicate formation/breaking of bonds, not movement of atoms. 3) Check that the octet rule is not violated after formation of the new bond. If it is, then a bond needs to be broken. 4) Account for charges (taking e- density away makes original source of e- more positive, vice versa(.

• Nucleophile (Nu)

  Nucleophile (Nu) is related to Reaction Mechanism

  "Loves Nucleus": has electron (e-) density that it can donate. This may be in the form of a lone pair, negative charge, or pi-bonding electrons.

• Nucleophile Strength

  Nucleophile Strength is related to Nucleophile (Nu)

  Strength of different nucleophiles can be compared given the solvent and concentration remain constant. Generally, good nucleophiles are less stable than poor ones. Negatively charged nucleophiles are stronger than their neutral counterparts; less sterically hindered nucleophiles are better; electronegativity inversely proportional to nucleophilicity; atomic size proportional to nucleophilicity; negative charges stabilized by resonance are less good nucleophiles; when comparing two nucleophiles with identical attacking atoms, the stronger Lewis base is the stronger nucleophile.

• Electrophile (E+)

  Electrophile (E+) is related to Reaction Mechanism

  "Loves Electrons": is electron (e-)-deficient. This can take the form of polarized/weak bonds or a positive charge, along with other things such as empty orbitals.

• Acid/Base

  Acid/Base can influence Reaction

  Definition depends. Review Lewis and Bronsted-Lowry definitions.

• Acidity

  Acidity describes Acid/Base

  How acidic a substance is. Acid strength can be quantified by Ka and pKa. Strong acids have a low pKa, weak acids have a high pKa.

• Electronegativity (Acidity)

  Electronegativity (Acidity) influences Acidity

  Hydrogens attached to more electronegative atoms are more acidic; the negative charge formed upon ionization can be stabilized by being carried on the more electronegative atom.

• Polarizability (Acidity)

  Polarizability (Acidity) influences Acidity

  Polarizability, the ability of an atom to distort its electron density in response to some external influence, increases with atomic size (down a group). Increased distortion of electron density means more delocalization and thus increased stability of the charge formed upon dissociation. Thus, increased polarizability leads to increased acidity.

• Resonance (Acidity)

  Resonance (Acidity) influences Acidity

  Resonance can stabilize an anion due to delocalization of electrons and thus of the charge formed upon dissociation of an acid. Increased resonance results in the lowering of the pKa and increased acidity.

• Inductive Effects (Acidity)

  Inductive Effects (Acidity) influences Acidity

  Slightly less effective than resonance. The shifting of e- in a bond in response to electronegativity of neary atoms, which pull e- density away from other parts of the molecule. More electronegative substituents present, the more the resultant charge from dissociation is stabilized, and thus the more acidic a substance is. Secondarily, it makes the bond with hydrogen more polar, allowing it to easier dissociate.

• Atom Hybridization (Acidity)

  Atom Hybridization (Acidity) influences Acidity

  Is related to the amount of s-character of the hybridization on the atom bearing the charge in a conjugate base. The more s-character, the closer the electrons are held, and thus the more stable the charge will be and the more acidic the substance will be.

• Hydrocarbon

  Molecules containing only carbon and hydrogen atoms. May have carbon-carbon multiple bonds in addition to carbon-carbon single bonds and carbon-hydrogen single bonds.

• Alkane

  Alkane is a Hydrocarbon

  Hydrocarbons with only carbon-carbon single (C-C) bonds and/or carbon-hydrogen single bonds (C-H). All carbons are sp3 hybridized. Do not have functional groups, as these bonds are relatively unreactive. Molecular formula CnH(2n+2)

• Conformational Isomer (Conformers)

  Conformational Isomer (Conformers) related to Alkane

  

  Isomers that result from rotation about single bonds, often in acyclic alkanes. Some isomers are more energetically favorable than others, even if they interconvert rapidly and thus cannot be isolated.

• Sawhorse Representation

  Sawhorse Representation is used to examine Conformational Isomer (Conformers)

  

  A way of examining bond rotation on a 2-dimensional page.

• Newman Projection

  Newman Projection is used to examine Conformational Isomer (Conformers)

  

  A way of examining bond rotation on a 2-dimensional page. More commonly used, easier to interpret. An end-on view of a single C-C single bond. The Newman projection shown here is of ethane, with eclipsed conformer on the left and staggered on the right.

• Strain (Conformers)

  Strain (Conformers) related to Conformational Isomer (Conformers)

  Energy penalty resulting from interactions between groups causing a less energetically favorable conformer.

• Torsional Strain

  Torsional Strain is a type of Strain (Conformers)

  Strain resulting from the eclipsing of bonds. For every H/H eclipsing interaction there is a 4.0 kJ/mol energy cost; for every CH_{3/H eclipsing interaction there is 6.0 kJ/mol torsional strain.}

• Steric Strain

  Steric Strain is a type of Strain (Conformers)

  Energy penalty resulting from the repulsive interaction that result when two groups are forced very close together. The nuclei of the atoms of one group are trying to occupy the same space as the other nuclei of the other group, as opposed to bonds. Occurs between large groups. CH₃/CH₃ eclipsed has energy penalty of 11.0 kJ/mol resulting from torsional+steric strain; CH₃/CH₃ gauche has energy penalty of 3.8 kJ/mol resulting from steric strain.

• Ring Strain

  Ring Strain is a type of Strain (Conformers)

  Term used to describe strain within cycloalkanes. Three factors contribute to it: Torsional Strain, Steric Strain, and Angle Strain (strain due to compression/expansion of regular sp^{3-hybridized bond angles).}

• Conformations of Butane

  Conformations of Butane is an example of Conformational Isomer (Conformers)

  

  A good example to illustrate more complicated conformational isomers.

• Cycloalkane

  Cycloalkane is a type of Alkane

  An alkane in a ring formation.

• Cycloalkane Conformation

  Cycloalkane Conformation describe the shape of Cycloalkane

  The various conformations that cycloalkanes can take on.

• Cyclopropane (Conformation)

  Cyclopropane (Conformation) is a Cycloalkane Conformation

  

  The only planar cycloalkane, cyclopropane has the most ring strain out of all the cycloalkanes. The internal bond angles are compressed to 60 degrees (maximum angle strain), and all groups on neighboring carbons are eclipsed (maximum torsional strain). Cyclopropane bonds do not overlap head-to-head; see image. These are called "bent bonds" or "banana bonds", resulting in poor overlap of orbitals, making the bonds weaker and more reactive than normal C-C single bonds.

• Cyclobutane (Conformation)

  Cyclobutane (Conformation) is a Cycloalkane Conformation

  

  Cyclobutane experiences around the same amount of ring strain as cyclopropane; its internal bond angles are compressed to around 88 degrees, but increased numbers of groups on more carbon atoms leads to increased torsional strain from eclipsing interactions. To alleviate torsional strain, cyclobutane adopts a "puckered" or "butterfly" conformation at the cost of increasing angle strain slightly.

• Gauche, Anti Interactions

  Gauche, Anti Interactions seen in Cyclobutane (Conformation)

  

  Interactions present in alkanes such as cyclobutane, where two of the bonds down the central bond in a Newman projection are to larger substituents. Gauche interactions have an energy penalty compared to Anti. See image.

• 1,2-cis/trans-disubstitued Cyclohexanes (Conformers)

  1,2-cis/trans-disubstitued Cyclohexanes (Conformers) may demonstrate Gauche, Anti Interactions

  

  1,2-cis-disubstituted cyclohexanes have gauche interactions between the substituents, and a ring flip produces another chair conformer with the same interactions and equal energy. Note that ring flip does not convert between cis and trans isomers. For example, in 1,2-cis-dimethylcyclohexane, both chair forms have 1 CH₃/CH₃ gauche interaction, and two CH₃/H diaxial interactions. On the other hand, 1,2-trans-disubstituted cyclohexanes have a more stable form: when both groups are equatorial rather than axial (when axial, there are CH₃/H diaxial interactions in the case of 1,2--trans-dimethylcyclohexane).

• Cyclopentane (Conformation)

  Cyclopentane (Conformation) is a Cycloalkane Conformation

  

  Cyclopentane experiences very little ring strain (internal bond angles at 108 degrees, similar to tetrahedral geometry). Increased torsional strain results from the presence of more groups as the number of carbon atoms increase; to alleviate this, cyclopentane adopts an envelope conformation (note that there is still significant torsional strain with neighboring, partially eclipsed carbons). Each carbon atom can pucker out of the plane just as easily (interchange due to low energy barrier). The most stable form is when only one carbon atom is out of plane.

• Cyclohexane (Conformation)

  Cyclohexane (Conformation) is a Cycloalkane Conformation

  

  Cyclohexane has no ring strain when in the chair conformation: all internal angles are 109.5 degrees, and groups on neighboring carbons are all staggered (no torsional strain). Chair formation is particularly stable; >99% of molecules exist in that formation at any given time. Cyclohexane is conformationally flexible at room temperature.

• Alkyl Group

  Alkyl Group originate from Hydrocarbon

  A substituent that results from the removal of hydrogen from an alkane. Generically represented by "R". Have common names and abbreviations (general naming guideline: take out "ane" from hydrocarbon name and add "yl" to the end. Eg. methane->meth->methyl).

• Isopropyl

  Isopropyl is a Alkyl Group

  

  An alkyl group resulting from the removal of a hydrogen from the middle carbon. Can be denoted by "i-Pr". See image.

• Isobutyl

  Isobutyl is a Alkyl Group

  

  A type of alkyl group. See image. Can be denoted by "i-Bu"

• sec-butyl

  sec-butyl is a Alkyl Group

  

  An alkyl group resulting from the removal of a hydrogen from the secondary carbon of butane. Can be denoted by "s-Bu". "sec" does not count when looking at alphabetical ordering of groups in nomenclature.

• tert-butyl

  tert-butyl is a Alkyl Group

  

  An alkyl group. See image. Can be denoted by ^tBu. "tert" does not count when looking at alphabetical ordering of groups in nomenclature.

• Stereochemistry

  The study of how atoms may be arranged spatially within a given molecule.

• Substituent

  Substituent may affect Stereochemistry

  General term for an atom or group of atoms taking the place of another atom/group, or occupying a specific location in a molecule, that can be found as a part of an organic molecule. May be found as a branch.

• Phenyl (Substituent)

  Phenyl (Substituent) is a Substituent

  

  A substituent that results from the removal of a hydrogen from benzene. The hydrogens directly attached to the aromatic ring are reactive. May be represented by "Ph". Is a common hydrocarbon fragment.

• Benzyl (Substituent)

  Benzyl (Substituent) is a Substituent

  

  A substituent that results from the removal of a hydrogen from the methyl group of methylbenzene. The hydrogens directly attached to the former methyl group are reactive. May be represented by "Bn". Is a common hydrocarbon fragment.

• Allyl (Substituent)

  Allyl (Substituent) is a Substituent

  

  A substituent that results from the removal of a hydrogen from the sp3-hybridized carbon on propene. Is a common hydrocarbon fragment.

• Chirality

  Chirality related to Stereochemistry

  

  A property of a given molecule. Chiral molecules lack a plane of symmetry and cannot be rotated and superimposed on their mirror image. The presence of one of more stereogenic centers makes a molecule chiral, given that it does not have a plane of symmetry.

• Stereogenic Center (or Stereocenter)

  Stereogenic Center (or Stereocenter) can be used to determine Chirality

  

  A sp³-hybridized atom with 4 different substituents, where interchanging two of the substituents creates a different stereoisomer. Sometimes denoted with an asterisk (*).

• R/S Nomenclature (Stereogenic Centers)

  R/S Nomenclature (Stereogenic Centers) describes Stereogenic Center (or Stereocenter)

  

  A method of designating stereochemistry around a stereogenic center by looking at the structure of the molecule. 1) Assign group priorities using Cahn-Ingold-Prelog rules (#1-4, 1 being highest priority). 2) Rotate the molecule so that lowest priority group in the back. 3) Assign: R (Latin for right, rectus) if priorities increase in clockwise manner; S (Latin for left, sinister) if priorities increase in anticlockwise manner.

• Enantiomer

  Enantiomer related to Chirality

  

  Stereoisomers that are non-superimposable mirror images of one another. Not possible to rotate molecule so that it can be superimposed on mirror image. An Enantionmeric Pair are two molecules that are enantiomers of each other.

• Racemic Mixture

  Racemic Mixture related to Enantiomer

  A 1:1 mixture of enantiomers, usually what is generated in non-selective reactions (not in stereoselective reactions).

• Optical Activity (Enantiomers)

  Optical Activity (Enantiomers) is a property exhibited by Enantiomer

  

  A property of enantiomers. Measured by a polarimeter. Each enantiomer in an enantiomeric pair will rotate plane-polarized light in a certain direction (opposite to the direction that the other enantiomer in the enantiomeric pair rotates light). Light is rotated in the same magnitude for each enantiomer in an enantiomeric pair, only in opposite directions. Clockwise (Left rotation; Levorotatory)-->assigned "L". Anticlockwise (Right rotation; dextrorotatory)-->assigned "D". No correlation between R and S configurations of stereogenic centers and optical activity. Racemic mixtures have a specific rotation of 0 degrees. Useful because enantiomers have identical physical properties and only exhibit different chemical properties when interacting with other chiral substances (eg. enzymes, chiral catalysts, etc.)

• Meso Compounds

  Meso Compounds related to Chirality

  

  An achiral molecule that has (a) stereogenic center(s) but is achiral because there is an internal plane of symmetry (can be flipped to be superimposed on the other.

• Double Bond Stereochemistry

  Double Bond Stereochemistry a subset of Stereochemistry

  The stereochemistry of double bonds.

• Cahn-Ingold-Prelog Rules

  Cahn-Ingold-Prelog Rules related to Double Bond Stereochemistry

  

  A system of rules to assign priorities to substituents on each double bond carbon in an alkene, which can be used to designate stereochemistry in alkenes with more than two substituents. 1) For each carbon of the double bond, look at the atoms attached to the double bond. The higher the atomic number, the higher the priority. 2) If priority can't be assigned with the first atom, follow rule one for the second, then third atom, etc. 3) Multiple bond atoms are counted the same way as several single bonds to the same atom.

• E/Z Nomenclature

  E/Z Nomenclature nomenclature for Double Bond Stereochemistry

  

  A system for naming tri- and tetra-substituted double bonds regarding double bond stereochemistry. First, split the double bond in half. Next, assign either E or Z. E: highest priority groups are on opposite sides. Z: highest priority groups are on the same side. Memory device: "Z: 'zame zide' rhymes with 'same side', but s cannot be replaced with e easily".

• sp3-Hybridized Carbon Stereochemistry

  sp3-Hybridized Carbon Stereochemistry a subset of Stereochemistry

  Stereochemistry for molecules with sp³-hybridized carbons. Can be represented b

• Isomer

  

  Compounds with identical molecular formulas but different structures.

• Stereoisomer

  Stereoisomer is a type of Isomer

  

  Compounds with the same molecular formula and atom connectivity but different ways in which the atoms are arranged in space. May form with ringed compounds (when there is a ring, bonds don't freely rotate), or with presence of pi-bonds.

• Cis-Trans Isomerism

  Cis-Trans Isomerism is used to describe Stereoisomer

  

  A way of describing a set of stereoisomers where a certain set of 2 substituents is oriented differently in space. Cis: the substituents are facing the same direction. Trans: the substitutents are facing different directions.

• Diastereomers

  Diastereomers include Cis-Trans Isomerism

  

  Stereoisomers that are not enantiomers (mirror images) of each other. Can occur when molecules have two or more stereogenic centers. These include cis and trans isomers. One way to distinguish them from enantiomers is to assign stereochemistry to each stereogenic center in a molecule and observe the relationships between one another. Diastereomers will have some (but NOT all) of the stereogenic centers' configurations changed; enantiomers will have all the stereocenters changed in configuration.

• Nomenclature (Molecules with Multiple Stereogenic Centers)

  Nomenclature (Molecules with Multiple Stereogenic Centers) related to Stereoisomer

  As molecules with two or more stereocenters can have many stereoisomers (and often are chiral molecules); for n stereogenic centers, there are 2ⁿ potential stereoisomers (some may be identical to each other). R/S configuration of each stereogenic center is analyzed separately and integrated into the front of the name surrounded by brackets and using numbers to link the configuration to the carbon atom. Commas separate the different configurations. Example: Name: (1R,2R)-1,2-dimethylcyclopentane.

• Chair (Conformation)

  

  A very stable conformation adopted by 6-membered rings. See "Cyclohexane (Conformation)".

• Ring Flip (Chair Conformations)

  Ring Flip (Chair Conformations) is related to Chair (Conformation)

  

  When the chair conformation interconverts between the two possible chair forms. All axial hydrogens become equatorial hydrogens, all equatorial hydrogens become axial hydrogens. Ring flip occurs via a series of bond rotations that turn one chair conformer to another via a series of intermediate conformers with higher ring strain (generally, flattening out of a cycloalkane causes an increase in torsional and angle strain).

• 1,3-diaxial interactions

  1,3-diaxial interactions may be seen in Chair (Conformation)

  

  These interactions result when there is a substituent in the axial position of a chair conformer. These create steric strain. Thus, substituents are usually preferentially placed in the equatorial position. For example there is a 7.6 kJ/mol energy difference between the image shown and the conformer if the methyl group were placed in an equatorial position. Each CH₃/H diaxial interaction costs 3.8 kJ/mol of energy; larger substituents have a larger energy penalty. If the ring flip is treated as an equilibrium, the dominant conformer can be determined, and a K_eq value can be determined.

• Dipole

  An unequal distribution of electron density caused by a difference in electronegativity between two atoms engaged in a polar covalent bond. Bond polarity may be represented either with (\delta )+, (\delta )-, or vector arrows (pointing towards the more electronegative atom, with +-> type of vector arrow. The other type, -->, not discussed in this course). These represent bond diploles, which have dipole moments (measured in D, debye). May lead to formation of polar molecules if there is overall dipole moment in molecule (see geometry of molecule; sometimes dipole moments cancel out).

• Heteroatom

  Heteroatom may cause Dipole

  Any atom other than carbon or hydrogen that is present in the structure of an organic compound. Causes polarization of covalent bonds towards the more electronegative atom. Often more electronegative than both carbon and hydrogen.

• The Levelling Effect

  In water, hydronium ions are the strongest acidic species that can exist, and hydroxide ions are the strongest basic species. Stronger acids/bases will always react with water to form these ions. Recall that strong acids are ones that completely dissociate/ionize in water.

• Fischer Projection

  

  A flattened out depiction of stereochemistry useful for drawing enantiomers/diastereomers (with multiple stereogenic centers, especially for carbohydrates).