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Organic Chemistry 1

by: Michael Akinyeye

Organic Chemistry 1 227

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Michael Akinyeye
Texas A&M

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Book Notes taken out of the required material to read for the course. Correlates with lecture as well.
Organic Chemistry 1
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This 13 page Class Notes was uploaded by Michael Akinyeye on Monday July 4, 2016. The Class Notes belongs to 227 at Texas A&M University taught by Santander in Summer 2016. Since its upload, it has received 23 views. For similar materials see Organic Chemistry 1 in CHEM at Texas A&M University.


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Date Created: 07/04/16
Chapter 1 Book Notes Monday, August 31, 2015 at 4:42 PM Atomic Structure: Most of the mass for the atom is located within its positively charged nucleus. Towards the outside of the atom, the electrons become more dense, but are less dense towards the further areas. Atomic Number: Number of protons Atomic Mass: Number of protons + neutrons Isotopes: Atoms with the same atomic number but a different atomic mass (additional neutrons) The behavior of a electron can be mapped out through the wave equation which offers a wave function/orbital. This allows the behavior of an electron to be determined. Electron Shells: Show how many electrons can be held within a certain orbital and as these shells increase so does their energy. *Lowest Energy arrangement = Ground State electron configuration 3 Electron Principle’s: Aufbua’s Principle- Fill up lower energy levels first. s->p->d->f Pauli’s Exclusion Principle- Only up to 2 electrons can fill up an orbital. These two electrons must also have opposite spins. Hund’s Rule- One electron must occupy vacant orbitals until all orbitals have at least one filled. Carbon is Tetravalent: It’s able to bond 4 molecules together. Carbon is also capable of making a ring with just carbon molecules attached together to one another. *Making bonds releases energy while breaking bonds absorbs energy. Covalent Bonds- Equal sharing of electrons between atoms. *Covalent bonds help create molecules When two atoms are bonded they are still separated a certain distance because of the positive charge of each atoms nucleus. The distance they are separated is called the Bond Length. sp3 hybridized orbitals are more stable than unhybridized s and p orbitals* Carbon is capable of forming a a double bond as well as a triple bond. Lone pairs within orbitals take up more space than bonded electrons Organophosphates- Compounds that contain a phosphorous bonded with 4 oxygens and one bonded to 1 carbon. Thiols- a sulfer atom bonded with an oxygen and one carbon. Ex: methanethiol (CH3SH) Sulfides- sulfur atom bonded to two carbons. Ex: dimethyl sulfide (CH3)2S Antibonding MO- Area where electrons can’t move within. Bonding MO- Area where electrons spend most of their time. Chapter 3 Book Notes Saturday, September 5, 2015 at 4:16 PM Functional Groups: Groups in Chemistry that have specific chemical behaviors *Every molecule’s, regardless of size, is determined by the functional group it has attached to it. Alkenes, alkynes, and arenes (aromatic compounds) all contain carbon–carbon multiple bonds. Alkenes have a double bond, alkynes have a triple bond, and arenes have alternating double and single bonds in a six-membered ring of carbon atoms. Because of their structural similarities, these compounds also have chemical similarities. Alkyl halides (haloalkanes), alcohols, ethers, alkyl phosphates, amines, thiols, sulfides, and disulfides all have a carbon atom singly bonded to an electronegative atom— halogen, oxygen, nitrogen, or sulfur. Alkyl halides have a carbon atom bonded to halogen , alcohols have a carbon atom bonded to the oxygen of a hydroxyl group , ethers have two carbon atoms bonded to the same oxygen, organophosphates have a carbon atom bonded to the oxygen of a phosphate group , amines have a carbon atom bonded to a nitrogen, thiols have a carbon atom bonded to the sulfur of an group, sulfides have two carbon atoms bonded to the same sulfur, and disulfides have carbon atoms bonded to two sulfurs that are joined together. In all cases, the bonds are polar, with the carbon atom bearing a partial positive charge and the electronegative atom bearing a partial negative charge . Carbonyl groups (C=O) are found in most organic compounds. However, these compounds differ in the way they are bonded to the carbonyl group’s carbon. Aldehydes have at least one hydrogen bonded to the carbonyl group. Ketones have two carbons bonded to the carbonyl group. Carboxylic Acid have an -OH group bonded to the C=O. Esters have an ether* like oxygen bonded to the C=O Thioesters have a sulfide-like* sulfur bonded to the C=O Amindes have an amine-like* nitrogen bonded to the C=O Acid Chlorides have a chlorine bonded to the C=O Alkanes: Carbon to carbon single bonds with sp3 hybridization. They are known to be “saturated”, since they have the maximum possible amount of Hydrogens per carbon. They are also called, aliphatic (fat) because they are seen in animal fat as long carbon chains. Isomers: compounds with the same number and kinds of atoms but rearranged differently. Constitutional isomers: Compounds that just have different connections for their bonds. Alkanes are usually described by the number of carbons they have bonded, except for methane, ethane, propane, and butane* Straight-line Alkanes (Normal)- Butane & Pentane Branched-chain alkanes- 2-methylpropane (isobutane), 2-methylbutane, 2,2- domethylpropane Alkyl groups are no stable on their own. They combine with other functional groups and allow them to become larger compounds. Alkyl’s are usually brought about by removing a single hydrogen atom from a compound (Naming Alkanes) IUPAC: system of nomenclature that includes the prefix, parent, locant, and suffix. The prefix identifies the various groups in the molecule, the parent selects the main part of the molecule and tells how many carbons are within, the locant gives the position of the functional groups and substituents, and the suffix identifies the primary functional group. Properties of Alkanes: Little affinity to other substances, relatively inert. React with oxygen and halogens under the appropriate conditions Halogens = Fluorine, Chlorine, Bromine, Iodine, Astatine *Dispersion forces increase as molecule size increases... Accounting for the higher melting and boiling points of larger alkanes Comformations of Ethane: Stereochemistry- Branch of Chemistry concerned with the 3D aspects of molecules. Conformations- Different arrangements of atoms from bond rotation. Conformers/conformational isomers- molecules that have different arrangements. *Different ways to view conformations staggered conformation (more common for ethane) The three-dimensional arrangement of atoms around a carbon–carbon single bond in which the bonds on one carbon bisect the bond angles on the second carbon as viewed end-on. More Stable* eclipsed conformation The geometric arrangement around a carbon–carbon single bond in which the bonds to substituents on one carbon are parallel to the bonds to substituents on the neighboring carbon as viewed in a Newman projection. Least stable* torsional strain The strain in a molecule caused by electron repulsion between eclipsed bonds. Torsional strain is also called eclipsing strain. Energy of molecule as it goes through rotations Conformation of Other Alkanes: As Alkanes get larger, they get more complexed since not all the staggered conformations and eclipsed conformations have the same energy. anti conformation The geometric arrangement around a carbon–carbon single bond in which the two largest substituents are apart as viewed in a Newman projection gauche conformation The conformation of butane in which the two methyl groups lie apart as viewed in a Newman projection. This conformation has steric strain. Steric strain The strain imposed on a molecule when two groups are too close together and try to occupy the same space. Steric strain is responsible both for the greater stability of trans versus cis alkenes and for the greater stability of equatorially substituted versus axially substituted cyclohexanes. Chapter 2 Book Notes Tuesday, September 1, 2015 at 1:25 PM When a bond has an unequal distribution of electrons, one atom will have a partial negative charge while the other has a partial positive charge. This type of bond is known as a Polar Covalent bond. The higher the Electronegativity the more likely that element will attract electrons. An inductive effect is the shifting of electrons in a sigma bond in response to the electronegativity of nearby atoms. Net molecular polarity is defined as a dipole moment Formal Charge = (# of valence electrons in free atom) - (# of valence electrons in bonded atom)= (# of valence electrons in free atom) - (# of bonding electrons/2 + number of nonbonding electrons) Formal charge often gives a hint to the reactivity of an atom The resonance structure of a certain compound is just the different ways certain atoms can be arranged. Even though it will look visibly different the compound will still have the same properties. Resonance Hybrids keep the same shape but can change where certain bonds are formed.* Ex: Benzene Rules for resonance structures: 1) Individual resonance forms are imaginary, not real. 2) Resonance forms only differ in where their pi bons and non bonding electrons are placed. *Curved arrows on a molecular drawing detail the movement of the electron and not the atom. 3) Different resonance forms don’t have to be equivalent. 4) Resonance forms must follow the valency rules. 5) Resonance Hybrid is more stable than any other resonance form *Any three atom grouping as two resonance structures. Bronsted-Lowry Acid: Donates H+ ions Bronsted-Lowry Base: Accepts H+ ions Conjugate Acid: Gains a proton Conjugate Base: Loses a proton Determining the Ka of a solution: The more positive the Ka, the stronger the acid. If it’s negative, it is most likely a weak acid. The more negative the pKa the more acidic the solution. The more positive it is, the more basic the solution is. Kw = [H3O+][OH-] = 1x10^-14 Organic Acids are characterized by the bondings of the Hydrogen atoms they have. One bonds with the available Oxygen and the other bonds with the available Carbon. *Anions are typically stabilized by having the extra electron attached to the most electronegative atom. Organic Bases are characterized by having a lone pair of electron that can bond to an H+ ion Zwitterion form: When an molecule undergoes acid/base reactions.* Lewis Acid: Accepts electron pairs. Lewis Base: Donates electron pairs. *Most oxygen and Nitrogen containing compounds form Lewis Bases Noncovalent interaction/Van Der waals interactions: dipole-dipole, dispersion forces and hydrogen bonds. Dipole-Dipole forces are between two polar molecules and result in a attraction or repulsion Dispersion forces deal with the uncertain changes of molecules in an area. These changes could give molecules a slight positive or negative charge that will change its behavior Hydrogen bond involves a hydrogen bonded with an oxygen or nitrogen and an unshared electron pair of a oxygen or nitrogen Chapter 4 Book Notes Monday, September 14, 2015 at 10:01 PM Saturated cyclic hydrocarbons are called cycloalkanes- An alkane that contains a ring of carbons. Larger cycloalkanes have increasing rotational freedom, and very large rings ( and up) are so floppy that they are nearly indistinguishable from open-chain alkanes. The common ring sizes , however, are severely restricted in their molecular motions. There are two different 1,2-dimethylcyclopropane isomers, one with the methyl groups on the same face of the ring (cis) and the other with the methyl groups on opposite faces of the ring (trans). The two isomers do not interconvert. Stability of Cycloalkane: smaller and larger ring sizes exhibit Angle Strain. Angle strain The strain introduced into a molecule when a bond angle is deformed from its ideal value(109.5). Angle strain is particularly important in small-ring cycloalkanes, where it results from compression of bond angles to less than their ideal tetrahedral values. The higher the strain a cycloalkane compound has the more energy (heat) will be released by combustion. Cycloalkane strain energies, calculated by taking the difference between cycloalkane ‍ heat of combustion per and acyclic alkane heat of combustion per , and multiplying by the number of units in a ring. Small and medium rings are strained, but cyclohexane rings and very large rings are strain-free. • Angle strain—the strain due to expansion or compression of bond angles • Torsional strain—the strain due to eclipsing of bonds between neighboring atoms • Steric strain—the strain due to repulsive interactions when atoms approach each other too closely Cyclopropanes are the most angle strained of all the rings compounds Cyclobutanes have a slightly higher angle strain than Cyclopropane, but a lesser torsional strain. This is because of the slight bend that the geometric model has. Although planar cyclopentane has practically no angle strain, it has a large torsional strain. Cyclopentane therefore twists to adopt a puckered, nonplanar conformation that strikes a balance between increased angle strain and decreased torsional strain. Four of the cyclopentane carbon atoms are in approximately the same plane, with the fifth carbon atom bent out of the plane. Most of the hydrogens are nearly staggered with respect to their neighbors Cyclohexane adopts a strain-free, three-dimensional shape called a chair conformation-chair conformation: 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. The cyclohexane doesn’t have angle strain nor torsional strain. The strain-free chair conformation of cyclohexane. All bond angles are , close to the ideal tetrahedral angle, and all neighboring bonds are staggered\ In addition to the chair conformation of cyclohexane, there is an alternative conformation of cyclohexane that bears a slight resemblance to a boat. Boat cyclohexane has no angle strain but has a large number of eclipsing interactions that make it less stable than chair cyclohexane. A “twist” on this alternative can be found in twist-boat conformation, which is also nearly free of angle strain. *The chair conformation affects the chemistry of the molecule (ex: Glucose) Axial and equatorial positions in chair cyclohexane. The six axial hydrogens are parallel to the ring axis, and the six equatorial hydrogens are in a band around the ring equator. A ring-flip in chair cyclohexane interconverts axial and equatorial positions. What is axial in the starting structure becomes equatorial in the ring-flipped structure, and what is equatorial in the starting structure is axial after ring-flip. Cyclohexane rings flip rapidly between chair conformations at room temperature. The same is true of other monosubstituted cyclohexanes: a substituent is almost always more stable in an equatorial position than in an axial position. The energy difference between axial and equatorial conformations is due to steric strain caused by 1,3-diaxial interactionsThe strain energy caused by a steric interaction between axial groups three carbon atoms apart in chair cyclohexane. Conformations of Disubstituted Cyclohexanes: *Less strain makes the molecule more favorable Conformations of Polycyclic Molecules: Polycyclic compound (ex: Steroids-testosterone) Chapter 5 Book Notes Sunday, September 27, 2015 at 3:25 PM Tetrahedral carbon atoms and their mirror images. Molecules of the type and are identical to their mirror images, but a molecule of the type is not. A molecule is related to its mirror image in the same way that a right hand is related to a left hand. Molecules that aren’t the same as their mirror images are Enantiomers (optical isomers). You will not be able to superimpose the two molecules. They will end up only allowing two groups to match up. Molecule that isn’t identical to it’s mirror image is said to be chiral. You will not be able to take a chiral molecule and its enantiomer and place the other inside it so the atoms coincide. A molecule is not chiral if it has a plane of symmetry. If a molecule has a plane of symmetry it is achiral. chirality centers An atom (usually carbon) that is bonded to four different groups. Achiral = symmetric Chiral = asymmetric Polarizer oscillates light waves in a single plane and the light is said to be plane-polarized For some molecules, when light is passed through the solution the plane of polarization is rotated through an angle. This means the organic substances are optically active. levorotatory An optically active substance that rotates the plane of polarization of plane-polarized light in a left-handed (counterclockwise) direction. dextrorotatory A word used to describe an optically active substance that rotates the plane of polarization of plane-polarized light in a right-handed (clockwise) direction. (Step 1) Look at the four atoms directly attached to the chirality center, and rank them according to atomic number. The atom with the highest atomic number has the highest ranking (▯irst), and the atom with the lowest atomic number (usually hydrogen) has the lowest ranking (fourth). When different isotopes of the same element are compared, such as deuterium and protium , the heavier isotope ranks higher than the lighter isotope. Thus, atoms commonly found in organic compounds have the following order. (Step 2) If a decision can’t be reached by ranking the ▯irst atoms in the substituent, look at the second, third, or fourth atoms away from the chirality center until the ▯irst difference is found. A substituent and a substituent are equivalent by rule 1 because both have carbon as the ▯irst atom. By rule 2, however, ethyl ranks higher than methyl because ethyl has a carbon as its highest second atom, while methyl has only hydrogen as its second atom. Look at the following pairs of examples to see how the rule works: (Step 3) Multiple-bonded atoms are equivalent to the same number of single-bonded atoms. For example, an aldehyde substituent , which has a carbon atom doubly bonded to oneoxygen, is equivalent to a substituent having a carbon atom singly bonded to two oxygens: If a curved arrow drawn from the highest to second-highest to third- highest ranked substituent is clockwise, we say that the chirality center has the Rconfiguration (Latin rectus, meaning “right”). If an arrow from is counterclockwise, the chirality center has the S configuration (Latin sinister, meaning “left”) Molecules like lactic acid, alanine, and glyceraldehyde are relatively simple because each has only one chirality center and only two stereoisomers. The situation becomes more complex, however, with molecules that have more than one chirality center. Diastereomers Non–mirror-image stereoisomers; diastereomers have the same configuration at one or more chirality centers but differ at other chirality centers. Note carefully the difference between enantiomers and diastereomers: enantiomers have opposite con▯igurations at all chirality centers, whereas diastereomers have opposite con▯igurations at some (one or more) chirality centers but the same con▯iguration at others. epimers Diastereomers that differ in configuration at only one chirality center but are the same at all others. meso compounds (me-zo) Compounds that contain chirality centers but are nevertheless achiral because they contain a symmetry plane. racemate A mixture consisting of equal parts (+) and (−) enantiomers of a chiral substance; also called a racemic mixture. 50/50 The most common method of resolution uses an acid–base reaction between the racemate of a chiral carboxylic acid and an amine base to yield an ammonium salt Nitrogen, phosphorus, and sulfur are all commonly encountered in organic molecules, and can all be chirality centers. We know, for instance, that trivalent nitrogen is tetrahedral, with its lone pair of electrons acting as the fourth “substituent” A similar situation occurs in trivalent phosphorus compounds, or phosphines. It turns out, though, that inversion at phosphorus is substantially slower than inversion at nitrogen, so stable chiral phosphines can be isolated. Divalent sulfur compounds are achiral, but trivalent sulfur compounds called sulfonium salts can be chiral. Like phosphines, sulfonium salts undergo relatively slow inversion, so chiral sulfonium salts are con▯igurationally stable and can be isolated. A molecule is said to be prochiral if it can be converted from achiral to chiral in a single chemical step. In addition to compounds with planar, -hybridized atoms, compounds with tetrahedral, -hybridized atoms can also be prochiral. An - hybridized atom is said to be a prochirality center if, by changing one of its attached groups, it becomes a chirality center. The face on which the arrows curve clockwise is designated Re face (similar to R), and the face on which the arrows curve counterclockwise is designated Si face (similar to S). In this example, addition of hydrogen from the Re face gives (S)-butan-2-ol, and addition from the Si face gives (R)-butan-2-ol. When one face is Re or Si, the other face will be the opposite no matter what. The newly introduced atom ranks higher than the remaining atom, but it remains lower than other groups attached to the carbon. Of the two identical atoms in the original compound, that atom whose replacement leads to an R chirality center is said to be pro-R and that atom whose replacement leads to an S chirality center is pro-S. Chapter 6 Book Notes Monday, October 5, 2015 at 4:45 PM Four generic organic reactions: Addition: two reactant add together to form a single product with no atoms “left over”. Elimination: Opposite of addition reactions. They occur when a single reactant splits into two products, often with the formation of small molecule such as water or HBr. Substitution: Two reactants exchange parts to give two new products. Rearrangement: A single reactant undergoes a reorganization of bonds and atoms to yield an isomeric product. Two ways bonds can break: symmetrically(homolytic) and unsymmetrically(heterolytic) Two ways bonds can me formed: Symmetrically (radical) and unsymmetrical (polar) A radical is a chemical species that is neutral but has an odd number of electrons A Polar reaction involves species that have an even number of electrons that only have electron pairs available. Polar processes/reactions are more common Radical Reactions are highly reative due to the unpaired nature of the chemical species. (These reactions are often less likely to occur.) Steps of a radical reaction: Initiation: Use of light to break the bond between the two chlorines to form 2 chlorine radicals. Propagation: Reactive chlorine radical collides with the methane molecule and then the methyl reacts further with the Cl2. Termination: One or two radicals come together to make a stable product. Polar reactions occur because of the electrical attraction between positively polarized and negatively polarized centers on functional groups in molecules. *Most metals are less electronegative than carbon Nucleophiles: Lewis Base (Neutral or negative) Electrophiles: Lewis Acid (Neutral or positive) (electrophilic addition reaction) A comparison of carbon–carbon single and double bonds. A double bond is both more accessible to approaching reactants than a single bond and more electron-rich (more nucleophilic). An electrostatic potential map of ethylene indicates that the double bond is the region of highest negative charge. carbocation A carbon cation, or substance that contains a trivalent, positively charged carbon atom having six electrons in its outer shell ‍all polar reactions take place between an electron-poor site and an electron- rich site and involve the donation of an electron pair from a nucleophile to an electrophile. Rules for curved arrows for Polar Reactions: 1) Electrons usually move from ta nucleophilic source to an electrophilic sink. The electrophilic sink must be able to accept an electron pair. 2) The nucleophile can either be negatively charged or neutral. If the nucleophile is neutral, the atom that donates the electron pair acquires a positive charge. 3) The electrophile can be either positively charged or neutral. If the electrophile is neutral, the atom that ultimately accepts the electron pair acquires a negative charge. 4) Octet rule must be followed Just like all reactions, these organic reactions must follow the direction of the equilibrium constant. If Keq is much larger than 1, then the product concentration term [C][D] is much larger than the reactant concentration term [A][B] , and the reaction proceeds as written from left to right. If Keq is near 1, appreciable amounts of both reactant and product are present at equilibrium. And if Keq is much smaller than 1 , the reaction does not take place as written but instead goes in the reverse direction, from right to left. Gibbs free-energy change The free-energy change that occurs during a reaction, given by the equation . A reaction with a negative free-energy change is spontaneous, and a reaction with a positive free-energy change is nonspontaneous. exergonic A reaction that has a negative free-energy change and is therefore spontaneous. On an energy diagram, the product of an exergonic reaction has a lower energy level than that of the reactants. endergonic A reaction that has a positive free-energy change and is therefore nonspontaneous. In an energy diagram, the product of an endergonic reaction has a higher energy level than the reactants. enthalpy change The heat of reaction. The enthalpy change that occurs during a reaction is a measure of the difference in total bond energy between reactants and products. exothermic A reaction that releases heat and therefore has a negative enthalpy change. endothermic A reaction that absorbs heat and therefore has a positive enthalpy change. bond dissociation energy (D) The amount of energy needed to break a bond and produce two radical fragments. In an exothermic reaction, more heat is released than is absorbed. But because making bonds in the products releases heat and breaking bonds in the reactants absorbs heat, the bonds in the products must be stronger than the bonds in the reactants. In other words, exothermic reactions are favored by products with strong bonds and by reactants with weak, easily broken bonds. The reaction coordinate, represents the progress of the reaction from beginning to end. *Reactions with activation energies less than take place at or below room temperature, while reactions with higher activation energies normally require a higher temperature to give the reactants enough energy to climb the activation barrier. The net energy change for the step, is represented in the diagram as the difference in level between reactant and product. Since the carbocation is higher in energy than the starting alkene, the step is endergonic, has a positive value of , and absorbs energy. intermediate A species that is formed during the course of a multistep reaction but is not the final product. Intermediates are more stable than transition states but may or may not be stable enough to isolate. An energy diagram for a typical, enzyme-catalyzed biological reaction versus an uncatalyzed laboratory reaction. The biological reaction involves many steps, each of which has a relatively small activation energy and small energy change. The end result is the same, however. Chapter 8 Book Notes Saturday, October 24, 2015 at 11:32 AM Basic process of Addition and Elimination react The two most common elimination reactions are dehydrohalogenation (loss of a HX from an alkyl halide) and dehydration (the loss of water from an alcohol). Dehydrohalogenation: Dehydration: Carried out with the use of a strong acid and the solvent THF Halogenation: When halogenation reaction is carried out an cycloalkene, such as cyclopentene, only the trans stereoisomer of the dihalide addition product is formed, rather than the mixture of cis and trans that might have been expected if a planar carbocation intermediate were involved Displays a Bromonium ion intermediate instead of a carbocation Anti stereochemistry: The opposite of syn. An anti addition reaction is one in which the two ends of the double bond are attached from different sides. An anti elimination reaction is one in which the two groups leave from opposite sides of the molecule. Halohydrins (Addition of HOX): The addition of hypohalous acids (HO-Cl or HO- Br) Happen indirectly with Br2 or Cl2 in the presence of water Addition of Water by Oxymercuration: Acid-catalyzed hydration of isolated double bonds is uncommon - it often involves the formation of an anion intermediate followed by protonation by an acid. Oxymercuration - Involves a electrophilic addition of Hg2+ to the alkene on reaction with mercury (II) acetate in aqueous (THF) solvent. The intermediate is treated with NaBH4 (Sodium borohydride) Demercuration occurs to produce an alcohol. Alkene ocymercuration is analogous to halohydrin formation. The regiochemistry of the reaction corresponds to markovnikov addition of water Hydroboration: Involves the addition of BH bond of borane to an alkene to yield an organoborane intermediate RBH2. The three C-B bonds are broken and replaced with alcohol groups During the addition of this reaction, the H and BH2 are added to the same face of the molecule and this symbolizes syn stereochemistry. There is also no development of a carbocation intermediate during this reaction* Reduction of Alkenes: Hydrogenation (The gaining of electrons) Hydrogenation usually occurs with syn stereochemistry. Both hydrogens add to the double bond from the same face. Hydrogen atoms cannot form on the top face of the molecule because the methyl group is blocking their entry. Aldehydes, ketones, esters, and nitriles are not reduced by hydrogenation (double bonds are still reduced) Epoxidation and Hydroxylation Oxidation: loss of electron density for carbon, caused either by bond formation between carbon and a more electronegative atom or by bond-breaking between carbon and a less electronegative atom-usually hydrogen. Epoxides are cyclic ether with an oxygen atom in a three membered ring Synthesis of epoxides involves the use of halohydrins, prepared by electrophilic addition of HO-X to alkenes. When a halohydrin is treated with base, HX is eliminated and an epoxide is produced Hydroxylation is the addition of an -OH group to each of the two double bond carbons. Resembles Alkene Bromination* With Osmium tetroxide (OsO4) the stereochemistry of the Hydroxylation reaction becomes syn, and does not involve a carbocation intermediate. The cyclick osmate is then cleved using NaHSO3 Cleavage to Carbonyl Compounds: Cleavage with the use of Ozone: Carbon to Carbon double bonds are cleaved and then replaced with an oxygen Potassium PErmanganate also works like Ozone in the way it cleaves. Cleavage with HIO4* Cyclopropane Synthesis: Carbene is a neutral molecule containing a divalent carbon with only 6 electrons in its valence shell Simmons-Smith reaction: The reaction of an alkene with CH2I2 and Zu-Cu to yield cyclopropane Biological Additions of Radicals Radical addition reactions usually go on uncontrollably until their resources are depleted Electrophilic Addition reactions are quenched quickly Chapter 10 Book Notes Sunday, November 8, 2015 at 1:14 PM Alkyl halides = haloalkanes If different halogens are present, number each one and list them in alphabetical order when writing the name If the parent chain can be properly numbered from either end by step 2, begin at the end nearer the substituent that had the alphabetical precedence C-X(halogen) bond strenths decrease going down the periodic table Mechanism of radical chlorination of methane The chlorination of methane does not stop cleanly at the monochlorinated stage but continues to give a mixture of dichloro, trichloro, and even tetrachloro products Preparing Alkyl Halides from Alkenes: Allylic Bromination The Mechanism of Allylic bromination New Ranking of stability* (resonance) A allyl radical with two resonance forms is more stable than a typical alkyl radical which has only a single structure. The two products are not formed in equal amounts, however because the intermediate allylic radical is not symmetrical and reaction at the ends is not equally likely. Reaction at the less hindered, primary end is favored. Preparing Alkyl Halides from Alcohols: The yields of these SOCl2 and PBr3 reactions are generally high and other functional groups such as ethers, carbonyls, and aromatic rings dont usually interfere Reactions of Alkyl Halides: Grignard Reagents (RMgX) A Grignard reagent is formally the magnesium salt of a carbon acid and is thus a carbon anion or carbanion Organometallic Coupling Reaction: Alkyllithiums are both nucleophiles and strong bases Gilman reagents: lithium diorganocopper compounds are useful because they undergo a coupling reaction with organochlorides, bromides and iodides. R-B(OH)2 with an aromatic or vinyl substituted organohalide in the presence of a base and a palladium catalyst. Suzuki-Miyaura reaction- Oxidation and Reduction in Organic Chemistry The chlorination reaction of methane to yield chloromethane is an oxidation because a C-H bond is broken and Cl-Cl bond is formed. The conversion of an alkyl chloride to an alkane via Grignard reagent followed by protonation is reduction Chapter 7 Book Notes Monday, October 5, 2015 at 4:46 PM alkene A hydrocarbon that contains a carbon–carbon double bond, 䠼 Steam cracking is an example of a reaction whose energetics are dominated by entropy rather than by enthalpy in the free-energy equation . Alkenes are referred to as unsaturated. degree of unsaturation The number of rings and/or multiple bonds in a molecule. Organohalogen compounds (C,H,X, where X=F,Cl ,Br , or I ) A halogen substituent acts as a replacement for hydrogen in an organic molecule, so we can add the number of halogens and hydrogens to arrive at an equivalent hydrocarbon formula from which the degree of unsaturation can be found. For example, the formula C4H6Br2 is equivalent to the hydrocarbon formula C4H8 and thus corresponds to one degree of unsaturation. Organooxygen compounds (C,H,O ) Oxygen forms two bonds, so it doesn’t affect the formula of an equivalent hydrocarbon and can be ignored when calculating the degree of unsaturation. You can convince yourself of this by seeing what happens when an oxygen atom is inserted into an alkane bond: C-C becomes C-O-C or C-H becomes C-O-H , and there is no change in the number of hydrogen atoms. For example, the formula C5H8O is equivalent to the hydrocarbon formula C5H8 and thus corresponds to two degrees of unsaturation. Organonitrogen compounds (C,H,N ) Nitrogen forms three bonds, so an organonitrogen compound has one more hydrogen than a related hydrocarbon. We therefore subtract the number of nitrogens from the number of hydrogens to arrive at the equivalent hydrocarbon formula. Again, you can convince yourself of this by seeing what happens when a nitrogen atom is inserted into an alkane bond: C-C becomes C- NH-C or C-H becomes C-NH2 , meaning that one additional hydrogen atom has been added. We must therefore subtract this extra hydrogen atom to arrive at the equivalent hydrocarbon formula. For example, the formula C5H9N is equivalent to C5H8 and thus has two degrees of unsaturation. Naming Alkenes: 1)Name the parent hydrocarbon. Find the longest carbon chain containing the double bond, and name the compound accordingly, using the suf▯ix -ene: 2)Number the carbon atoms in the chain. Begin at the end nearer the double bond or, if the double bond is equidistant from the two ends, begin at the end nearer the ▯irst branch point. This rule ensures that the double-bond carbons receive the lowest possible numbers. 3) Write the full name. Number the substituents according to their positions in the chain, and list them alphabetically. Indicate the position of the double bond by giving the number of the ▯irst alkene carbon and placing that number directly before the parent name. If more than one double bond is present, indicate the position of each and use one of the suf▯ixes -diene, -triene, and so on. Note also that a =CH2 substituent is called a methylene group, a H2C=CH- substituent is called a vinyl group, and a H2C=CHCH2- substituent is called an allyl group. The cis–trans naming system used in the previous section works only with disubstituted alkenes—compounds that have two substituents other than hydrogen on the double bond. With trisubstituted and tetrasubstituted double bonds, a more general method is needed for describing double-bond geometry. (Trisubstituted means three substituents other than hydrogen on the double bond; tetrasubstituted means four substituents other than hydrogen.) Rules for naming Alkenes: 1)Considering each of the double-bond carbons separately, look at the two substituents attached and rank them according to the atomic number of the ▯irst atom in each. An atom with higher atomic number ranks higher than an atom with lower atomic number. 2)If a decision can’t be reached by ranking the ▯irst atoms in the two substituents, look at the second, third, or fourth atoms away from the double-bond until the ▯irst difference is found. 3)Multiple-bonded atoms are equivalent to the same number of single-bonded atoms. Z geometry A term used to describe the stereochemistry of a carbon–carbon double bond. The two groups on each carbon are ranked according to the Cahn–Ingold–Prelog sequence rules, and the two carbons are compared. If the higher ranked groups on each carbon are on the same side of the double bond, the bond has Z geometry. E geometry A term used to describe the stereochemistry of a carbon–carbon double bond. The two groups on each carbon are ranked according to the Cahn–Ingold–Prelog sequence rules, and the two carbons are compared. If the higher-ranked groups on each carbon are on opposite sides of the double bond, the bond has E geometry. Trans is more stable than Cis. Cis alkenes are less stable than their trans isomers because of steric strain between the two larger substituents on the same side of the double bond. Hydrogenation process The stability order of substituted alkenes is due to a combination of two factors. One is a stabilizing interaction between the bond and adjacent bonds on substituents. hyperconjugation An electronic interaction that results from overlap of a vacant p orbital on one atom with a neighboring C-H sigma bond. Hyperconjugation is important in stabilizing carbocations and substituted alkenes. electrophilic addition reactions Addition of an electrophile to a carbon–carbon double bond to yield a saturated product. Mechanism of the electrophilic addition of to 2-methylpropene. The reaction occurs in two steps, protonation and bromide addition, and involves a carbocation intermediate. The energy level of the intermediate is higher than that of the starting alkene, but the reaction as a whole is exergonic (negative Free Energy ). The ▯irst step, protonation of the alkene to yield the intermediate cation, is relatively slow. But once the cation intermediate is formed, it rapidly reacts to yield the ▯inal alkyl bromide product. Energy diagram for the two-step electrophilic addition of to 2-methylpropene. The first step is slower than the second step. regiospecific A term describing a reaction that occurs with a specific regiochemistry to give a single product rather than a mixture of products. Markovnikov’s rule A guide for determining the regiochemistry (orientation) of electrophilic addition reactions. In the addition of to an alkene, the hydrogen atom bonds to the alkene carbon that has fewer alkyl substituents. *Carbocations are planar Thermodynamic measurements show that, indeed, the stability of carbocations increases with increasing substitution so that the stability order is tertiary > secondary > primary > methyl. More highly substituted alkyl halides dissociate more easily than less highly substituted ones. A comparison of inductive stabilization for methyl, primary, secondary, and tertiary carbocations. The more alkyl groups that are bonded to the positively charged carbon, the more electron density shifts toward the charge, making the charged carbon less electron-poor (blue in electrostatic potential maps). Electrophilic addition to an unsymmetrically substituted alkene gives the more highly substituted carbocation intermediate. A more highly substituted carbocation forms faster than a less highly substituted one and, once formed, rapidly goes on to give the ▯inal product. A more highly substituted carbocation is more stable than a less highly substituted one. That is, the stability order of carbocations is tertiary > secondary > primary > methyl. Carbocation stability is determined by the free energy change. Energy diagrams for two similar competing reactions. In (a), the faster reaction yields the more stable intermediate. In (b), the slower reaction yields the more stable intermediate. The curves shown in (a) represent the typical situation. Hammond postulate A postulate stating that we can get a picture of what a given transition state looks like by looking at the structure of the nearest stable species. Exergonic reactions have transition states that resemble reactant; endergonic reactions have transition states that resemble product. Energy diagrams for endergonic and exergonic steps. (a) In an endergonic step, the energy levels of transition state and product are closer. (b) In an exergonic step, the energy levels of transition state and reactant are closer. The formation of a carbocation by protonation of an alkene is an endergonic step. Thus, the transition state for alkene protonation structurally resembles the carbocation intermediate, and any factor that stabilizes the carbocation will also stabilize the nearby transition state. hydride shift The shift of a hydrogen atom and its electron pair to a nearby cationic center. In this instance, a secondary carbocation rearranges to a more stable tertiary carbocation by the shift of a methyl group. Chapter 9 Book Notes Wednesday, October 28, 2015 at 9:52 PM Naming Alkynes: Make sure the triple bond on the alkyne has the smallest number* Compounds with more than one triple bond: diynes, triynes, etc. Also incorporates double bonds: Elimination Reactions of Dihalides: Addition of HX and X2: The two additions of the HBr allow for a dihalide to be formed This shows the addition breaks the triple bond one bond at a time until only left with a sigma bond. Also applies to X2 compounds* Hydration of Alkynes: Can be done through the addition of water +Mercury (Markovnikov product) and the indirect addition of water by hydroboration-oxidation (non Markovnikov) Mercury-Catalyzed Hydration of Alkynes: -OH group from reaction attaches to the most substituated carbon (Markovnikov) the alcohol group then becomes a ketone Tautermerize: the rearrangement of the hydrogen ion Internal Ketones produce more than one product* Hydroboration-Oxidation of Alkynes: Formation of a ketone (or an aldehyde depending on where the triple bond is) after the reaction is because of the process of tautomerization Reduction of Alkynes: The addition of H2 breaks the triple bond per mole used (over a metal catalyst) IF a Lindlar catalyst is used the hydrogenation is stopped at the Alkene phase. (Syn addition) The use of Lithium and Ammonia (l) also does the same process that the Lindlar catalyst accomplishes (Transforms the Alkyne into a Alkene) (Trans addition) Oxidative Cleavage of Alkynes: Alkyne Acidity: Formation of Acetylide Anions Removal of the terminal hydrogen to form a acetylide anion Alkylation of Acetylide Anions: The simple introduction of an alkyl group onto a molecule to replace the removed hydrogen Chapter 11 Book Notes Monday, November 9, 2015 at 3:24 PM Nucleophilic substitution reactions: the substitution of one nucleophile (Cl- or OH-) Inversion of the stereochemical configuration: Kinetics refers to the rate of the reaction 2nd order reaction is bimolecular and the kinetics are therefore dependent on the concentration of two reactants Reaction rate = Rate of disappearance of reactant (Sn2 reaction- substitution, nucleophilic, bimolecular) Take places in a single step without intermediates when the incoming nucleophile reacts with the alkyl halide or tosylate from a direction opposite the group that is displaced (leaving group) Rate of reaction is determined by the activation energy A higher reactant energy level corresponds to a faster reaction (smaller activation energy) A higher transition state energy level corresponds to a slower reaction As a substituent leaves in an Sn2 reaction, the side it’s leaving from is slightly hindered so it’s most likely that the incoming substituent comes from the opposite side The nucleophile is also a major component to the Sn2 reaction. (Nucleophile is anything neutral or negatively charged and has unshared pair of electrons) Nucleophlilicity roughly parallels basicity Nucleophlilicity usually increases going down a column of the periodic table Negatively charged nucleophiles are usually more reactive than neutral ones To carry out an Sn2 reaction with an alcohol it’s necessary to convert the OH- into a better leaving group. Protic solvents (contain -OH or -NH groups) are generally the worst for Sn2 reactions. Polar aprotic solvents that don’t have -OH or -NH groups are the best. Solvation - clustering of solvent molecules around a solute particle to stabilize it. Protic solvents in Sn2 reactions decrease the rate of reaction by lowering the groundstate energy of the nucleophile Sn1 reactions: (Basically the reverse of Sn2 reactions) 1st order reaction that does NOT depend on the concentration or addition of the nucleophile Reaction rate = Rate of disappearance of alkyl halide The step with the highest transition state is the rate limiting step Carbocation is formed in the reaction* More likely to bond to the side that the substituent is not on Side that is not shielded is slightly more favored (results in unequally favored diasteromers) Substrate The more stable the carbocation intermediate, the faster the Sn1 reaction. (Resonance stabilized allyl and benzyl cations) Order of Carbocation stability: Leaving Group: Best leaving group is determined by which one is the most stable. The leaving group is directly involved in the rate limiting step. Tertiary alcohols form the most stable carbocations* The Solvent: Effects Sn1 reactions largely due to stabilization or destabilization of the transition state. Solvent molecules orient around the carbocation so that the electron-rich ends of the solvent dipoles face the positive charge, thereby lowering the energy of the ion and favoring its formation. Sn1 reactions take place much more rapidly in strongly polar solvents such as water and methanol than in less polar solvents such as ether and chloroform. Favor aprotic solvents because the transition state energy leading to carbocation intermediate is lowered by solvation Elimination Reactions: Zaitsev’s Rule Elimination reaction produce more than one product due to the change in possible stereochemistry for alkenes. The more highly substituted alkene product predominates E1 reaction: The C-X bond breaks first to give a carbocation intermediate which undergoes subsequent base abstraction of H+ to yield the alkene. E1 reaction (elimination, unimolecular)- the first step is rate limiting and a carbocation intermediate is present Almost like an Sn1 reaction, but instead of a substitution, a loss of an H results in a double bond between the carbon atoms The best E1 substrates are also the best Sn1 substrates and mixtures of substitution and elimination products are usually obtained E2 reaction: Base-induced C-H bond cleavage is simultaneous with C-X bond cleavage, giving the alkene in a single step. Occurs when an alkyl halide is treated with a strong base. Take place in one step without intermediates. Stereochemistry of E2 reactions: • periplanar geometry- all the four reacting atoms lie in the same plane. • synperiplanar- H and the X are on the same side of the molecule • anti periplanar- The H and the X are on opposite sides of the molecule In an E2 reaction, an electron pair from a neighboring C-H bond also pushes out the leaving group on the opposite side of the molecule For E2 reactions, they can only occur on cyclohexanes only if the hydrogen and the leaving group are trans diaxial. Different conformations results in different alkene arrangements. E1cB reaction (cB = conjugate base): base abstraction of the proton occurs first, giving a carbanion intermediate. Involves a carbanion intermediate. Base-induced abstraction of a proton in a slow, rate limiting step gives san anion. This reaction is common in substrated that have a poor leaving group such as -OH. The poor leaving group disfavors the alternative E1 and E2 possibilities and the carbonyl group makes the adjacent hydrogen unusually acidic by resonance stabilization of the anion intermediate. Chapter 17 Book Notes Friday, November 20, 2015 at 5:52 PM Naming Alcohols and Phenols Alcohols and Phenols are both weakly basic and acidic. Weak acids dissociate slightly in dilute aqueous solution by donating a proton to water, generating H3O+ and an alkoxide ion or a phenoxide ion More accesible = more acidic molecule Phenols are more acidic than alcohols because the phenoxoide anion is resonance-stabilized Alcohols from Carbonyl Compounds: Reduction Any kind of carbonyl compound can be reduced, including aldehydes, keyones, carboxylic acids, and esters Reduction of aldehydes and Ketones Aldehydes are easily reduced to give primary alcohols and ketones are reduced to give secondary alcohols Lithium aluminum hydride (LiAlH4) is another reducing agent for the reduction of aldehydes and ketones. Reduction of Carboxylic Acids and Esters: Carboxylic acids and esters are reduced to give primary alcohols Alcohols from Carbonyl Compounds: Grignard Reaction A carbonyl reduction involves addition of a hydride ion nucleophile to the C=O bond, Grignard reaction involves addition of a carbanion nucleophile Ester react with Grignard reagents to yield alcohols in which two of the substituents bonded to the hydroxyl- bearing carbon have come from the Grignard reagent, just as LiAlH4 reduction og an ester adds two hydrogens The Grignard reaction has limitations. The reagents cant be prepared from an organohalide if other reactive functional groups are present in the same molecule. A compound that is both an alkyl halide and a ketone can’t form a Grignard reagent because it would react with itself Conversion of Alcohols into Alkyl Halides Tertiary alcohols react with either HCl or HBr by an Sn1 mechanism through a carbocation intermediate. Primary and secondary alcohols are much more resistant to acid, and are best converted into halides by treatment with either SOCl2 or PBr3 through an Sn2 mechanism Conversion of Alcohols into Tosylates Only the O-H bond of the alcohol is broken in this reaction; the C-O bond remains intact so no change of configuration occurs if the oxygen is attached to a chirality center Two inversions occur: Dehydration of Alcohols to Yield Alkenes: Acid catalyzed dehydration usually follow Zaitsev’s rule and yield the mot stable alkene as the major product. Mechanism: E2 Elimination of secondary or tertiary alcohol Mechanism: E1cB mechanism on a substrate in which the -OH group is two carbons away from a carbonyl group. Conversion of Alcohols into Esters Alcohols react with carboxylic acids to give esters a reaction that is common in both the laboratory and living organisms. Oxidation of Alcohols Primary alcohols yield aldehydes or carboxylic acids, secondary alcohols yield ketones, but tertiary alcohols dont normally react with most oxidizing agents. The oxidation of a primary or secondary alcohol can be accomplished by any of a large number reagents, including KMnO4, CrO3, and Na2Cr2O7. CrO3 or Na2Cr2O7 are a common choice for preparing an aldehyde from a primary alcohol - Dess-Martin periodinane (CrO3) - oxidize primary alcohols directly to carboxylic acids \ Protection of Alcohols Incompatibility* when this happens- protecting the interfering functional group. Protection involves three steps: 1)introducing a protecting group to block the interfering function 2) carrying out the desired reaction 3) removing the protecting group Chapter 18 Book Notes Saturday, November 28, 2015 at 1:33 PM Names and properties of Ethers If other functional groups are present, the ether part is considered an alkoxy substituent Preparing Ethers Prepared industrially by the sulfuric-acid catalyzed reaction of alcohols. The reaction occurs by Sn2 displacement of water from a protonated ethanol molecule by the oxygen atom of a second ethanol. (Limited to use with primary alcohols because secondary & rertiary alcohols dehydrate by an E1 mechanism to yield alkenes The Williamson Ether Synthesis alkoxide ion reacts with a primary alkyl halide or tosylate in an Sn2 reaction Another variation:* Alkoxymercuration of Alkenes When an alkene is treated with an alcohol in the presence of mercuric acetate or mercuric trifuoroacetate. Demercuration with NaBH4 hen yields an ether. The net result is Markovnikov addition of the alcohol to the alkene Reaction of Ethers: Acidic Cleavage Halogens, dilute acids, bases, and nucleophiles have no effect on most ethers. Ethers undergo only truly general reaction when cleaved by strong acids. HBr & HI Usually considered nucleophilic substitution reaction. The I- and Br- usually attack the protonated ether at the less hindered site. Ethers with a tertiary, benzylic, or allylic group cleave by either an Sn1 or E1 mechanism because these substrates can produce stable carbocations. Reaction of Ethers: Claisen Rearrangment The pericyclic conversion of an allyl phenyl ether to an o-allylphenol or an allyl vinyl ether to a unsaturated ketone by heating Takes place in a single step through a pericyclic mechanism. Cyclic Ethers: Epoxides The epoxide ring doesn’t actually have a double bond* Alkene -> Alcohol -> HX -> Epoxide ring Reactions of Epoxides: Ring Opening The epoxide cleavage takes place by Sn2 like backside attack of a nucleophile on the protonated epoxide giving a tran-1,2-diol product Also... When one of the epoxide carbon atoms is tertiary, nucelophilic attack occurs primarily at the more highly substituted site (Sn1) Base-Catalyzed Epoxide Opening Epoxides can be cleaved by bases and nucleophiles as well as by acids. The attack of the nucleophile takes place at te less hindered epoxide carbon Crown Ethers Thiols and Sulfides Thiols are usually prepared from alkyl halides by Sn2 displacement with a sulfur nucleophile such as hydrosulfide anion, -SH Thiols can be oxidized by Br2 or I2 to yield disulfides Sulfides similar to the Williamson synthesis of ethers* Diakyjk sulfides react rapidly with primary alkyl halides by an Sn2 mechanism to give sulfonium ions Sulfides are easily oxidized as well. They can form sulfoxides and sulfones


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