George Mason University

George Mason University
General Chemistry 212 Chapter 15 Organic Chemistry Acknowledgements Course Text: Chemistry: the Molecular Nature of Matter and Change, 7th edition, 2011, McGraw-Hill Martin S. Silberberg & Patricia Amateis The Chemistry 211/212 General Chemistry courses taught at George Mason are intended for those students enrolled in a science /engineering oriented curricula, with particular emphasis on chemistry, biochemistry, and biology The material on these slides is taken primarily from the course text but the instructor has modified, condensed, or otherwise reorganized selected material. Additional material from other sources may also be included. Interpretation of course material to clarify concepts and solutions to problems is the sole responsibility of this instructor. 4/24/2017

Organic Chemistry Life on earth is based on a vast variety of reactions and compounds based on the chemistry of Carbon – Organic Chemistry Organic compounds contain Carbon atoms, nearly always bonded to other Carbon atoms, Hydrogen, Nitrogen, Oxygen, Halides and selected others (S, P) Carbonates, Cyanides, Carbides, and other carbon- containing ionic compounds are NOT organic compounds Carbon, a group 4A compound, exhibits the unique property of forming bonds with itself (catenation) and selected other elements to form an extremely large number of compounds – about 9 million Most organic molecules have much more complex structures than most inorganic molecules

Organic Chemistry Bond Properties, Catenation, Molecular Shape
The diversity of organic compounds is based on the ability of Carbon atoms to bond to each other (catenation) to form straight chains, branched chains, and cyclic structures – aliphatic, aromatic Carbon is in group 4 of the Periodic Chart and has 4 valence electrons – 2s22p2 This configuration would suggest that compounds of Carbon would have two types of bonding orbitals each with a different energy If fact, all four Carbon bonds are of equal energy This equalization of energy arises from the hybridization of the 2s & 2p orbitals resulting in 4 sp3 hybrid orbitals of equal energy

Organic Chemistry Hybrid orbitals are orbitals used to describe bonding that is obtained by taking combinations of atomic orbitals of an isolated atom In the case of Carbon, one “s” orbital and three “p” orbitals, are combined to form 4 sp3 hybrid orbitals The Carbon atom in a typical sp3 hybrid structure has 4 bonded pairs and zero unshared electrons, therefore, Tetrahedral structure AXaEb (a + b) = AX4 The four sp3 hybrid orbitals take the shape of a Tetrahedron

Organic Chemistry 2p sp3 sp3 2s 1s 1s 1s C-H bonds Energy C atom
(ground state) C atom (hybridized state) C atom (in CH4)

Organic Chemistry Shape of sp3 hybrid orbital different than either s or p

Organic Chemistry The bonds formed by these 4 sp3 hybridized orbitals are short and strong The C-C bond is short enough to allow side-to- side overlap of half-filled, unhybridized p orbitals and the formation of “multiple” bonds Multiple bonds restrict rotation of attached groups The properties of Organic molecules allow for many possible molecular shapes

Organic Chemistry Electron Configuration, Electronegativity, and Covalent Bonding Carbon ground-state configuration – [He 2s22p2] Hybridized configuration – sp3 Forming a C4+ or C4- ion is energetically very difficult (impossible?): Required energy Ionization Energy for C4+ - IE1<IE2<IE3<IE4 Electron Affinity for C EA1<EA2<EA3<EA4 Electronegativity is midway between metallic and most nonmetallic elements Carbon, thus, shares electrons to bond covalently in all its elemental forms

Organic Chemistry Molecular Stability
Silicon and a few other elements also catenate, but the unique properties of Carbon make chains of carbon very stable Atomic Size and Bond strength Bond strength decreases as atom size and bond length increase, thus, C-C bond strength is the highest in group 4A Relative Heats of Reaction Energy difference between a C-C Bond (346 kJ/mol) vs C-O Bond (358 kJ/mol) is small Si-Si (226 kJ/mo) vs Si-O (368 kJ/mol) difference represents heat lost in bond formation Thus, Carbon bonds are more stable than Silicon

Organic Chemistry Orbitals available for Reaction
Unlike Carbon, Silicon has low-energy “d” orbitals that can be attacked by lone pairs of incoming reactants Thus, Ethane (CH3-CH3) with its sp3 hybridized orbitals is very stable, does not react with air unless considerable energy (a spark) is applied Whereas, Disilane (SiH3 – SiH3) breaks down in water and ignites spontaneously in air

Organic Chemistry Chemical Diversity of Organic Molecules
Bonding to Heteroatoms (N, O, X, S, P) Electron Density and Reactivity Most reactions start (a new bond forms) when a region of high electron density on one molecule meets a region of low electron density of another C-C bond: “Nonreactive” – The electronegativities of most C-C bonds in a molecule are equal and the bonds are nonpolar C-H bond: “Nonreactive” – the bond is nonpolar and the electronegativities of both H(2.1) & C(2.5) are close C-O bond: “Reactive” – polar bond Bonds to other Heteroatoms: Bonds are long & weak, and thus, reactive 4/24/2017

Carbon Geometry The combination of single, double, and triple bonds in an organic molecule will determine the molecular geometry sp sp sp sp Tetrahedral trigonal planar linear linear AX AX AX AX2 Review Chapter 11 – Multiple bonding in carbon compounds

Hydrocarbons Compounds containing only C and H
Saturated Hydrocarbons: Alkanes only single () bonds Unsaturated Hydrocarbons: Alkenes Alkynes Double (=) Bonds Triple () bonds Aromatic Hydrocarbons (Benzene rings) (6-C ring with alternating double and single bonds)

Hydrocarbons A shorter bond is a stronger bond
A close relationship exists among Bond Order, Bond Length, and Bond Energy Two nuclei are more strongly attracted to two shared electrons pairs than to one: The atoms are drawn closer together and are more difficult to pull part For a given pair of atoms, a higher bond order results in a shorter bond length and a higher bond energy, i.e., A shorter bond is a stronger bond The Relation of Bond Order, Bond Length, and Bond Energy

Hydrocarbons Alkanes (Aliphatic Hydrocarbons)
Normal-chain: linear series of C atoms C-C-C-C-C-C- Branched-chain: branching nodes for C atoms Cycloalkanes: C atoms arranged in rings Methyl Propane Cyclohexane

Hydrocarbons Methane Propane Ethane Butane Alkanes: CnH2n+2
Straight Chained Alkanes C H C H Methane Propane C H C H Ethane Butane

Hydrocarbons Branched Chained Alkanes Cycloalkanes
3-Ethyl-4-MethylHexane Cyclobutane Methylcyclopropane

Hydrocarbons Molecular Formulas of n-Alkanes Methane: C-1: CH4
Ethane: C-2: CH3CH3 Propane: C-3: CH3CH2CH3 Butane: C-4: CH3CH2CH2CH3 Pentane: C-5: CH3CH2CH2CH2CH3 Hexane: C-6: CH3(CH2)4CH3 Heptane: C-7: CH3(CH2)5CH3 Octane: C-8: CH3(CH2)6CH3 Nonane: C-9: CH3(CH2)7CH3 Decane: C-10: CH3(CH2)8CH3

Physical Properties of Straight–Chain Alkanes
Hydrocarbons Straight Chain (n) Alkanes Physical Properties of Straight–Chain Alkanes

Lubricants, Asphalt, Wax
Hydrocarbons Petroleum Fractions Boiling Point Name Carbon Atoms Use < 20 0C Gases C1 to C4 Heating, Cooking C Gasoline C5 to C12 Fuel C Kerosene C12 to C15 C Fuel oil C15 to C18 Diesel Fuel > 400 0C over C18 Lubricants, Asphalt, Wax

Hydrocarbons Cycloalkanes: CnH2n Cyclohexane Cyclopropane Cyclobutane

Hydrocarbons Butane Isobutane C4H10 C4H10 Structural Isomers
Structural (or constitutional) isomers are compounds with the same molecular formula, but different structural formulas. Created by branching, etc. C H 3 H 3 C Butane Isobutane C4H10 C4H10

C5H12 Hydrocarbons Structural Isomers of Pentane Pentane
2-Methylbutane 2,2-Dimethylpropane

Hydrocarbons Chiral Molecules & Optical Isomerism
Another type of isomerism exhibited by some alkanes and many other organic compounds is called Stereoisomerism Sterioisomers are molecules with the same arrangement of atoms but different orientations of groups in space Optical Isomerism is a type of stereoisomerism, where two objects are mirror images of each other and cannot be superimposed (also called enantiomers) Optical isomers are not superimposable because each is asymmetric: there is no plane of symmetry that divides an object into two identical parts

Hydrocarbons Chiral Molecules & Optical Isomerism
An asymmetric molecule is called “Chiral” The Carbon atom in an optically active asymmetric (l) organic molecule (the Chiral atom) is bonded to four (4) different groups. Mirror images 1C1 & 1C2 of molecule 1 (left) can be moved to the right to sit on top of 2C1 & 2C2 of molecule 2, i.e., 1C & 2C groups can be superimposed But, the two groups on C3 are opposite  The two forms are optical isomers and cannot be superimposed, i.e., no plane of symmetry to divide molecule into equal parts C-3 is the “Chiral” Carbon Optical Isomers of 3-methylhexane

Hydrocarbons recemic mixture
Optical Isomers In their physical properties, Optical Isomers differ only in the direction each isomer rotates the plane of polarized light One of the isomers – dextrorotary isomer - rotates the plane in a clockwise direction (d or +) The other isomer – levorotary isomer - rotates the plane in a counterclockwise direction (l or -) An equimolar mixture of the dextrorotary (d or +) and levorotary (l or -) isomers: recemic mixture does not rotate the plane of light because the dextrorotation cancels the levoratation

Hydrocarbons Optical Isomers In their chemical properties, optical isomers differ only in a chiral (asymmetric) chemical environment An optically active isomer is distinguished by the chiral atom being attached to 4 distinct groups If the attached groups are not distinct the molecule is NOT optically active An isomer of an optically active reactant added to a mixture of optically active isomers of an another compound will produce products of different properties – solubility, melting point, etc.

Nomenclature of Alkanes
Determine the longest continuous chain of carbon atoms. The base name is that of this straight-chain alkane. Any chain branching off the longest chain is named as an “alkyl” group, changing the suffix –ane to –yl For multiple alkyl groups of the same type, indicate the number with the prefix di, tri, … Ex. Dimethyl, Tripropyl, Tertbutyl The location of the branch is indicated with the number of the carbon to which is attached Note: The numbering of the longest chain begins with the end carbon closest to the carbon with the first substituted chain or functional group

Nomenclature Example CH3 H2C CH CH2 HC (Con’t)

Substituted Heptane (7 C)
Nomenclature Example Determine the longest chain in the molecule 7 Carbons CH3 H2C CH CH2 HC Substituted Heptane (7 C) (Con’t)

3,5-dimethyl-4-ethylheptane
Nomenclature Example The base chain is 7 carbons – Heptane Add the name of each chain substituted on the base chain “methyl” groups at Carbon 3 and Carbon 5 “ethyl” group at Carbon 4 1 2 3 4 5 6 7 CH3 H2C CH CH2 HC 3,5-dimethyl-4-ethylheptane

Nomenclature Example Guidelines for numbering substituted carbon chains The numbering scheme used in developing the name of a organic compound begins with the end carbon closest to the carbon with the first substituted group or functional group

Hydrocarbons Reactions of Alkanes
Combustion (reaction with oxygen) – Burning C5H12(g) + 8 O2(g)  5 CO2(g) + 6 H2O(l) Substitution (for a Hydrogen) C5H12(g) + Cl2(g)  C5H11Cl(g) + HCl(g)

Hydrocarbons Alkenes When a Carbon atom forms a double bond with another Carbon atom, it is now bonded to 2 other atoms instead of 3 as in an Alkane The Geometry now changes from 4 sp3 orbitals (Tetrahedral AX4E0) to 3 sp2 hybrid orbitals and 1 unhybridized 2p orbital (AX3E0 Trigonal Planar) lying perpendicular to the plane of the trigonal sp2 hybrid orbitals Review Chapter Geometry

Hydrocarbons Alkenes Two sp2 orbitals of each carbon form C – H sigma () bonds by overlapping the 1 s orbitals of the two H atoms The 3rd sp2 orbital forms a C-C () bond with the other Carbon A Pi () bond forms when the two unhybridized 2p orbitals (one from each carbon) overlap side-to-side, one above and one below the C-C sigma bond A double bond always consists of 1  and 1  bond

Hydrocarbons Alkenes: CnH2n
Alkenes substitute the single sigma bond () with a double bond – a combination of a sigma bond and a Pi () bond The double-bonded (-C=C-) atoms are sp2 hybridized The carbons in an Alkene structure are bonded to fewer than the maximum 4 atoms Alkenes are considered: unsaturated hydrocarbons H H H H C C C C H H H CH3 Ethene or Ethylene Propene

Hydrocarbons Molecular Formulas of Alkenes Conjugated Molecules
Ethene: CH2=CH2 Propene: CH2=CHCH3 Butene: CH2=CHCH2CH3 Pentene: CH2=CHCH2CH2CH3 Decene: CH2=CH(CH2)7CH3 Conjugated Molecules Alkene (or aromatic) with alternating Sigma bonds and Pi bonds) Ex. 2,5-Dimethyl-2,4-Hexadiene CH3CH3=CH-CH=C(CH3CH3)

CH3CH=CH2 + HBr  CH3CHBrCH(H2)
Hydrocarbons Reactions of Alkenes Addition Reactions CH3CH=CH2 + HBr  CH3CHBrCH(H2) Why does the Bromine (Br) attach to the middle carbon? Markownikov’s Rule: When a double bond is broken, the H atom being added adds to the carbon that already has the most Hydrogens CH2 → CH3

Hydrocarbons An addition reaction occurs when an unsaturated reactant (alkene, alkyne) becomes saturated ( bonds are eliminated) Carbon atoms are bonded to more atoms in the “Product” than in the reactant (Ethene is reduced) Addition Reaction – Heat of Formation Reaction is Exothermic Formation of two strong  bonds from a single  bond and a relatively weak  bond Reactants (bonds broken Product (bonds formed) 1 C = C = kJ 1 C – C = – kJ 4 C – H = kJ 5 C – H = – kJ 1 H – C = kJ 1 C – Cl = – kJ Total = kJ Total = – kJ

A saturated molecule becomes “unsaturated”
Hydrocarbons Elimination Reactions The reverse of “addition reaction”: A saturated molecule becomes “unsaturated” Typical groups “Eliminated” include: Pairs of Halogens – Cl2, Br2, I2 H atom and Halogen – HCL, HBr H atom and Hydroxyl (OH) – Driving force – Formation of a small, stable molecule, such as HCl, H2O, which increases Entropy of the system

Hydrocarbons Substitution Reactions
A substitution reaction occurs when an atom (or group) from an added reagent substitutes for an atom or group already attached to a carbon Carbon atom is still bonded to the same number of atoms in the product as in the reactant Carbon atom may be saturated or unsaturated “X” & “y” may be many different atoms (not C) Reaction of “Acetyl Chloride” and “isopentylalcohol” to form “banana oil”, an ester

Hydrocarbons Nomenclature of Alkenes
Alkenes (-C=C-) are named just as alkanes, except that the –ane suffix is changed to –ene Alkynes (-CC-) are named in the same way, except that the suffix –yne is used In either case, the position of the double bond is indicated by the number of the carbon

Hydrocarbons CH2CH3 H3CHC CH2CHCH3 CH2CH2CH3
Nomenclature of Alkenes - Example First, find the longest carbon chain containing the double bond CH2CH3 6 7 H3CHC C CH2CHCH3 1 2 3 4 5 3-propyl-5-methyl-2-heptene CH2CH2CH3

Hydrocarbons trans-2-butene cis-2-butene Alkenes – Geometric Isomerism
In Alkanes, the C-C bond allows rotation of bonded groups; the groups continually change relative positions In Alkenes with the C=C bond, the double bond restricts rotation around the bond Geometric isomers are compounds joined together in the same way, but have different geometries The similar groups attached to the two carbon atoms of the C=C bond are on the same side of the double bond in one isomer and on the opposite side for the other isomer H3C CH3 H3C H C C C C CH3 H H H cis-2-butene trans-2-butene

Hydrocarbons Alkynes General Formula - CnH2n-2
The Carbon-Carbon (-C-C-) bond is replaced by a triple bond Each Carbon of an Alkyne structure (-CC-) can only bond to one other Carbon in a linear structure Each C is sp hybridized (sp – linear geometry) Alkyne compound names are appended by the suffix “yne” The  electrons in both alkenes (-C=C-) and alkynes (-CC-) are “electron rich” and act as functional groups Alkenes and alkynes are much more “reactive” than alkanes

Hydrocarbons Alkynes Ethyne or Acetylene Propyne A Terminal Acetylene
3 CH2 CH2 H3C C C CH3 3-Hexyne

Aromatic Hydrocarbons
Aromatic Hydrocarbons are “Planar” molecules consisting of one or more 6-carbon rings Although often drawn depicting alternating  and  bonds, the 6 aromatic ring bonds are identical with values of length and strength between those of –C-C– & –C=C – bonds The actual structure consists of 6  bonds and 3 pairs of  electrons “delocalized” over all 6 carbon atoms The bond between any two carbons “resonates” between a single bond and a double bond The orbital picture shows the two “lobes” of the delocalized  cloud above and below the hexagonal plane of the -bonded carbon atoms 4/24/2017

Molecular Orbitals of Benzene

Benzene Benzene Condensed Resonance Form of Benzene

Substituted Benzenes CH3 CH3 CH3 C2CH3 Methylbenzene (Toluene) 3,4-Dimethyl-ethylbenzene m,p-Dimethyl-ethylbenzene

Aromatic Compounds Substituted Benzenes Toluene Methyl Benzene Anisole
(Methoxybenzene) Dinitroanizole Methoxybenzoate Nitrobenzene Tribromobenzene (isomers)

Aromatic Compounds Benzene ring naming conventions - ring site locations Starting at the carbon containing the first substituted group, number the carbons 1 thru 6 moving clockwise Alternate names: 2 (ortho); 3 (meta); 4 (para) CH3 CH3 2 (o) 3 (m) 4 (p) 1 5 (m) 6 (o) CH3 3 (m) 2 (o) 4 (p) 1 5 (m) 6 (o) 1 6 (o) 2 (o) 5 (m) 3 (m) 4 (p) CH3 ortho-toluene 1,2-dimethylbenzene meta-toluene 1,3-dimethylbenzene para-toluene 1,4-dimethylbenzene

Reactions of Aromatic Compounds
The stability of the Benzene ring favors “substitution” reactions The “delocalization” of the pi bonds makes it very difficult to break a –C=C- bond for an “addition” reaction

Reactivity – Alkenes vs Aromatics
The double bond (-C=C-) is electron–rich  Electrons are readily attracted to the partially positive H atoms of hydronium atoms (H3O+) and hydrohalic acids (HX), to yield alcohols and alkyl Halides, respectively

Reactivity – Alkenes vs Aromatics
The pi electrons in an alkene double bond represent a localized overlap of unhybridized 2p orbitals, where two regions of electron density are located above and below the  bond The localized nature of alkene double bonds is very different from the “delocalized” unsaturation of aromatic structures Although aromatic rings are commonly depicted as having alternating sigma () and () bonds, the () bonds are actually delocalized over all 6 –C– () bonds The reactivity of benzene is much less than a typical alkene because the  electrons are “delocalized” requiring much more energy to break up the ring structure to accommodate an “addition” reaction “Substitution” is much more likely from an energy perspective because the delocalization is retained

Redox Processes in Organic Reactions
“Oxidation Number” is not applicable for carbon atoms Oxidation-Reduction in organic reactions is based on movement of “electron density” around Carbon atom The number of bonds joining a carbon atom and a “more” electronegative atom (group) vs. the number of bonds joining a carbon atom to a “Less” electronegative atom (group) The more electronegative atoms will attract electron density away from the carbon atom Less electronegative atoms will donate electron density to the carbon atom When a C atom forms more bonds to Oxygen or fewer bonds to Hydrogen, the compound is oxidized When a C atom forms fewer bonds to Oxygen or more bonds to Hydrogen, the compound is reduced

Combustion Reactions (burning in Oxygen) Ethane is converted to Carbon Dioxide (CO2) and water (H2O) Each Carbon in CO2 has more bonds to Oxygen than in ethane (none) and few bonds to Hydrogen Reaction is “Oxidation” Oxidation of Propanol C-2 has one fewer bonds to H and one more bond to O in 2-propanone - Oxidation

Hydrogenation of Ethene Each carbon has more bonds to H in Ethane than in Ethene Ethene is reduced, H2 is oxidized (loses e-)

Organic Reactions Functional groups
A functional group is a reactive portion of a molecule that undergoes predictable reactions The reaction of an organic compound takes place at the functional group A functional group is a combination of bonded atoms that reacts as a group in a characteristic way Each functional group has its own pattern of reactivity The distribution of electron density in a functional group affects its reactivity Vary from carbon-carbon bonds (single, double, triple) to several combinations of carbon-heteroatom bonds A particular bond may be a functional group itself or part of one or more functional groups

Organic Reactions Functional Groups (Con’t)
Electron density can be low at one end of a bond and higher at the other end, as in a dipole, an intermolecular force The Intermolecular Forces that affect physical properties and solubility also affect reactivity Alkene (-C=C-) and Alkyne (-CC-) bonds have high electron density, thus are functional groups with high reactivity Classification of Functional Groups Functional groups with only single bonds undergo “substitution” reactions Functional groups with “double” or “triple” bonds undergo “addition” reactions Functional groups with both single and double bonds undergo substitution reactions 4/24/2017

Functional Groups Oxygen containing functional groups:
alcohols, ethers, aldehydes, ketones, esters, carboxylic acids, anhydrides, acid halides Nitrogen containing functional groups: amines, amides, nitriles, nitro Compounds containing Carbonyl Group (C=O) acids, esters, ketones, aldehydes, anhydrides, amides, acid halides Compounds containing Halides alkyl halides, aryl halides, acid halides Compounds containing double & triple bonds alkenes, alkynes, aryl structures (benzene rings)

Functional Groups

Alcohols Functional Groups with “only” single bonds
An alcohol, general formula – R-OH, is a compound obtained by substituting an -OH group for an –H atom in a hydrocarbon primary alcohol: one carbon attached to the carbon with the –OH group secondary alcohol: two carbons attached to the carbon with the –OH group tertiary alcohol: three carbons attached to the carbon with the –OH group

Alcohols Alcohol Nomenclature
t-butanol (tertiary alcohol) sec-butanol (secondary alcohol) CH3 – CH2 – CH2 – OH Propanol (n-propyl alcohol) (primary alcohol) Alcohol Nomenclature Drop final “e” from hydrocarbon and add suffix “ol” OH CH3CH2CH2CH2CH3 CH2CH2CH2CH3 CH3 4,6-dimethyl-3-octanol (a secondary alcohol)

Alcohols Alcohol Reactions Alcohol structure similar to water
(R-OH vs H-OH) Alcohols react with very active metals to release H2 Alcohols form strongly basic “Alkoxide (R-O-) Ions High melting points and boiling points of alcohols result from Hydrogen Bonding Alcohols dissolve “Polar” molecules Alcohols dissolve “some” salts

Alcohols Alcohol Reactions Elimination Reactions
Elimination of a H atom and a hydroxide ion (OH) from a cyclic compound in the presence of acid results in the formation of an “alkene” Removal of 2 H atoms from a secondary alcohol in the presence of an oxidizing agent, such as K2CrO7 results in the formation of a “Ketone”

Alcohols Alcohols Reactions Oxidation
For Alcohols with the OH group at the end of a chain (primary alcohol) oxidation to an organic acid can occur in air Substitution Reactions Substitution results in products with other single bonded functional groups, such as the formation of Haloalkanes

Haloalkanes A Haloalkane (Alkyl Halide) is a Halogen (X = F, Cl, Br, I) bonded to a carbon atom Elimination Reactions Elimination of HX in the presence of a strong base will produce an Alkene

Haloalkanes Haloalkanes Substitution Reactions
Halides of Carbon and most other non-metals, such as Boron (B), Silicon (Si), Phosphorus (P), all undergo substitution reactions The process involves an attack on the slightly positive central atom, such as C, etc. by an OH- group -CN, -SH, -OR, and –NH2 groups also substitute for the halide

Ethers H-O-H water R-O-H alcohol (OH group – Hydroxyl group)
R-O-R ether (R-O group – Alkoxy group) where R = any group Ether Nomenclature: If R-C-O-CH3 group is part of structure, add “Methoxy” to name If R-C-O-CH2-CH3 group is part of structure, add “Ethoxy” to name

Ether Nomenclature 4,6-dimethyl-3-ethoxyoctane OCH2CH3 CH3CH2CH2CH2CH3
4,6-dimethyl-3-ethoxyoctane

Amines An Amine is a compound derived by substituting one or more Hydrocarbon groups for Hydrogens in Ammonia, NH3 Naming convention Drop the final “e” from the alkane name and add “amine” (ethanamine) or append “amine” to alkyl name (Methylamine) Types primary amine: one carbon attached to the Nitrogen secondary amine: two carbons attached to the Nitrogen. tertiary amine: three carbons attached to the Nitrogen

Amine Examples : : : CH3 CH3 CH3
Methylamine (Primary Amine) Dimethylamine (Secondary Amine) Trimethylamine (Tertiary Amine) Trigonal pyramidal Shape – AX3E The pair of “unbonded” electrons common to all amines is the key to all amine reactivity Amines act as bases by donating the pair of unshared electrons

Amines Reactions Primary and secondary Amines can form H–bonds
Higher melting points and boiling points than Hydrocarbons or Alkyl Halides of similar mass Trimethyl Amines cannot form Hydrogen Bonds and have generally lower melting points Amines of low molecular mass are water soluble and weakly basic (donate electrons) Reaction with water proceeds slowly and produces OH- ions

Amines Amine Reactions Substitution Reactions
The pair of unbonded electrons on the Nitrogen attacks the partially positive Carbon in Alkyl Halides to displace the Halogen (X-) and form a “larger” amine

Carbonyl Group Functional Groups with Double Bonds
The Carbonyl group is a Carbon doubly bonded to an Oxygen (C=O) Very versatile group appearing in several types of compounds Aldehydes Ketones Carboxylic acids Esters Anydrides Acid Halides Amides

H R C O C O Aldehydes and Ketones
An Aldehyde is distinguished from a Ketone by the Hydrogen atom attached to the Carbonyl Carbon If two Hydrogens are attached to the Carbonyl atom, the compound is specific – Formaldehyde (CH2O) R H C O R C O C O H Aldehyde (- al) Formaldehyde Ketone (-one)

Aldehydes and Ketones Butanal (Butyraldehyde) Aldehydes
In Aldehydes the Carbonyl group always appears at the end of a “chain Aldehyde names drop the final “e” from the alkane names and “-al” – Propanal, Isobutanal, etc. Alternate naming conventions: Benzaldehyde, Propionaldehyde Butanal (Butyraldehyde)

Aldehydes and Ketones Ketones
The Carbonyl Carbon always occurs within a chain as it is bonded to two other Alkyl groups (R, R’) Ketones are named by numbering the carbonyl C, dropping the final “e” from the alkane name, and adding “-one”, 4-Heptanone Alternate naming conventions: Use the Alkyl root and add “ketone” 4-Heptanone (Dipropylketone) Methylisopropylketone (3-methyl-2-butanone)

Aldehydes and Ketones Like the –C=C= bond, the Carbonyl (–C=O) bond is electron-rich Unlike the –C=C= bond, the –C=O bond is highly polar A - The  and  bonds that make up the C═O bond of the carbonyl group B - The charged resonance form shows that the C═O bond is polar (ΔEN = 1.0)

Aldehydes and Ketones Aldehydes and Ketones are formed by oxidation of Alcohols The C=O is an unsaturated structure, thus, carbonyl compounds can undergo “addition” reactions and be reduced (forms more bonds to H) to form alcohols

Aldehydes and Ketones Organometallic compounds
The Carbonyl group exhibits polarity with the Carbon atom bearing a slight positive charge and the Oxygen bearing a negative charge An addition reaction to the Carbonyl group would involve an electron-rich group bonding to the positive carbon and an electron-poor group bonding to the negative Oxygen Organometallic compounds have a metal atom (Li or Mg) attached to an “R” group through a polar covalent bond

Aldehydes and Ketones Organometallic compounds
The two-step addition of an organometallic compound to a Carbonyl group produces an Alcohol with a different Carbon skeleton Aldehyde & Lithium Organometallic Acetone (ketone) & Ethyllithium

Carboxylic Acids Carboxylic Acids are formed by adding an “Hydroxyl” group to the Carbonyl Carbon Different R groups lead to many different carboxylic acids Carboxylic Acids have the “- oic” suffix with “acid” Example: Ethanoic acid (Acetic acid) – C2H4O2 HO Acidic Hydrogen (Hydroxyl Group) C O CH3 Carboxyl Group Carbonyl Group

Carboxylic Acids Carboxylic Acids are named by dropping the “-e” from the alkane name and adding “-oic acid” Common names are often used Carboxylic Acids are “Weak Acids” in solution Typically >99% of an organic acid is “undissociated” Carboxylic acid molecules react completely with strong base to form salt & water Carboxylate anion

Carboxylic Acids Carboxylic acids with long hydrocarbon chains are referred to as “fatty acids” Fatty acid skeletons have an “even” number of Carbon atoms (16-18 most common) Animal fatty acids have “saturated” hydrocarbon chains Vegetable sources are generally “unsaturated”, with the -C=C- in the “cis” configuration Fatty acid salts are the “soaps”, with the “cation” usually from Group 1A of 2A

Examples Straight chain saturated (Aliphatic) carboxylic acids Name
Formula Methanoic (Formic) Acid HCOOH Ethanoic (Acetic) Acid CH3COOH Propionic Acid CH3CH2COOH Butanoic (Butyric) Acid CH3CH2CH2COOH Pentanoic Acid CH3CH2CH2CH2COOH 4/24/2017

Esters Esterification is a dehydration-condensation reaction between a Carboxylic acid and an alcohol to form an Ester The Hydroxyl group (OH) from the Alcohol reacts with the Carboxyl group to form the Ester and Water R1COOH + R2OH  R1COOR2 + H2O Ester group occurs commonly in “Lipids,” a large group of fatty biological substances, such as “triglycerides

Esters Hydrolysis is the opposite of Dehydration-Condensation (Esterification) in which the Oxygen atom from water is attracted to the partially positive Carbon of the ester carbonyl group, cleaving (lysing) the molecule into two parts One part gets the –OH and one part gets the H In Saponification, the process used in the manufacture of soap, the ester bonds in animal or vegetable fats are “Hydrolyzed” with a strong base

Amides Amides are derived from the reaction of an Amine with a Carboxylic acid or an Ester Amides are named by denoting the “amine” portion from the amine and the replacing the “-oic acid” from the Carboxylic acid with “-amide”

Amides R1COOH + R2NH2  R1CONHR2 + H2O
The partially negative N (2 unbonded e-) of the amine is attracted to the partially positive carbonyl carbon of the ester In the Amine & Acid reaction water is lost In the Amine & Ester reaction an alcohol (ROH) is lost Amides can be “Hydrolyzed” in hot water to reform the acid and the amine R1COOH + R2NH2  R1CONHR2 + H2O

Functional Groups with Triple Bonds
Principal Groups with triple bonds Alkynes (Acetylenes) -CC- Addition reactions with H2O, H2, HX, X2, others Nitriles -CN Produced by substituting a cyanide ion (-C N-) for a Halide ion (X-) in a reaction with an alkyl halide Nitriles can be reduced to form amines or hydrolyzed to carboxylic acids

Polyethylene Polystyrene Polyvinyl chloride
Polymers Polymers are extremely large molecules consisting of “monomeric” repeating units Naming polymers Add prefix “poly-” to the monomer name Polyethylene Polystyrene Polyvinyl chloride Polymer Types Addition Monomers undergo addition with each other (chain reactions) Monomers of most addition polymers have the group

Addition Polymers 4/24/2017

Addition Polymers Free-radical polymerization of Ethene, CH2=CH2 ,to polyethylene

Condensation Polymers
Condensation polymers have “two” functional groups A – R – B Monomers link when group A on one undergoes a “dehydration-condensation” reaction with a B group on another monomer Many condensation polymers are “Copolymer”, consisting of two or more different repeating units Condensation of Carboxylic acid & Amine monomers forms “polyamides” (nylons) Carboxylic Acid and Alcohol monomers form polyesters

Biological Macromolecules
Natural Polymers Polysaccharides Proteins Nucleic acids Intermolecular forces stabilize the very large molecules in the aqueous medium of living cells Structures that make wood strong; hair curly, fingernails hard Speed up many natural reaction inside cells Defend living organisms against infection Possess genetic information organisms need to synthesis other biomolecules

Sugars & Polysaccharides
Carbohydrates – substances that provide energy through oxidation Monosaccharides Glucose & simple sugars Consist of carbon chains with attached hydroxyl and carbonyl groups Serve as monomer units of polysaccharides Polysaccharides Consist mainly of Glucose units with differences in aromatic ring position of the links, orientation of certain bonds and the extent of cross-linking Cellulose Starch Glycogen

Cellulose Most abundant organic chemical on earth 50% of carbon in plants occurs in stems & leaves Cotton is 90% cellulose Wood strength comes from Hydrogen bonds between cellulose chains Humans lack enzyme to links to the C1 & C4 bonds between units making it impossible to digest Other animals – cows, sheep, termites, however, have microorganisms in their digestive tracts that can digest cellulose 4/24/2017

Starch A mixture of polysaccharides of glucose Energy store in plants Starch is broken down by hydrolysis of the bonds between units, releasing glucose, which is oxidized in a multistep process Glycogen Energy storage molecule in animals Occurs in molecules made from 1000 to 500,000 glucose units The cross-linking between the C1 & C4 bonds is similar to starch, but is more highly cross-linked between the C1 & C6 bonds 4/24/2017

Amino Acids & Proteins Amino Acids
An amino acid has a carboxyl group (COOH) and an amine group (NH2) attached to an “-carbon”, the 2nd C atom in a Carbon-Carbon (C-C) chain In the aqueous cell fluid, the NH2 (amino) and COOH (carboxyl) groups of amino acids are charged because the carboxyl group transfers an H+ ion to H2O to form H3O+ (acid), which transfers the H+ to the amine group

Amino Acids & Proteins Proteins
Proteins are unbranched polyamide polymers made up of amino acids linked together by “Peptide” bonds” A “Peptide” (amide) bond is formed by a dehydration- condensation reaction in which the Carboxyl group of one monomer reacts with the Amine group of the next monomer releasing water “dipeptide” A “Polypeptide chain” is a polymer formed by the linking of many amino acids by peptide bonds A “Protein” is a polypeptide with a “biological” function

Amino Acids & Proteins Peptide Bonds C=O :N-H

See Examples on Next Slide
Amino Acids & Proteins About 20 different amino acids occur in proteins See Examples on Next Slide The R groups are screened gray The -carbons (boldface), with carboxyl and amino groups, are screened yellow The amino acids are shown with the charges they have under physiological conditions They are grouped by polarity, acid-base character, and presence of an aromatic ring The R groups, which dangle from the -carbons on alternate sides of the chain, play a major role in the shape and function of proteins

Amino Acids & Proteins 4/24/2017

Amino Acids & Proteins Hierarchy of Protein Structure
Each type of protein has its own amino acid composition – a specific number and proportion of various amino acids The role of a protein in a cell, however, is not determined by its composition The “sequence” of amino acids determines the protein’s shape and function in the cell Proteins range from 50 to several thousand amino acids The number of possible sequences of the 20 types of amino acid, even in the smaller proteins, is extremely large (20n where ‘n’ is the number of amino acids) Only a small fraction of the possible combinations occur in actual proteins – 105 for a human being

Amino Acids & Proteins Protein Native Shapes
Proteins have unique shapes that unfold during synthesis in a cell Simple Complex Long rods Baskets Undulating sheets Y-Shapes Spheroid Blobs Globular Forms

Amino Acids & Proteins Hierarchy of Protein Structure
Primary (1o) – Basic Level (sequence of covalently bonded amino acids in polypeptide chain) Secondary (2o) – Shapes called -helices and -pleated sheets formed as a result of H bonding between nearby peptide groupings Tertiary (3o) – 3-dimensional folding of whole polypeptide chain Quarternary (4o) – Most complex, proteins made up of several polypeptide chains

Structural Hierarchy of Proteins
Amino Acids & Proteins Structural Hierarchy of Proteins 4/24/2017

Amino Acids & Proteins Protein Structure and Function
Two broad classes of proteins differ in the complexity of their amino acid composition and sequence, thus, their structure and function Fibrous Proteins Relatively simple amino acid compositions and correspondingly simple structures Includes “Colagen”, the most common animal protein (30% glycine; 20% proline) Globular Proteins More complex, containing up to all 20 amino acids in varying proportions

Amino Acids & Proteins Nucleotides and Nucleic Acids
Nucleic Acids – Unbranched polymers that consist of linked monomer units called mononucleotides Mononucleotides consist of: Nitrogen-containing base Sugar Phosphate group Nucleic Acid Types Ribonucleic Acid (RNA) Deoxyribonucleic Acid (DNA) RNA & DNA differ in sugar portions of mononucleotides RNA contains Ribose, a 5-Carbon sugar DNA contains deoxyribose (H substitutes for OH on the 2’ position of Ribose

– sugar – phosphate – sugar – phosphate –
Amino Acids & Proteins Nucleic Acid Precursors Nucleoside Triphosphates – Cellular precursors that form a nucleic acid Dehydration-condensation reactions between cellular precursors: Releases inorganic diphosphate (H2P2O72-) Creates Phosphodiester bonds to form a “polynucleotide” Sets up the repeating pattern of the nucleic acid backbone – sugar – phosphate – sugar – phosphate –

Amino Acids & Proteins DNA Phosphate group 2’-deoxyribose (a Sugar)
Base: Attached to each sugar is one of four N containing bases, either a Pyrimidine (six-membered ring) Pyrimidines – Thymine (T) & Cytosine (C) or a Purine (six- and five- membered rings sharing a side) Purines – Guanine (G) & Adenine (A) RNA Sugar in RNA is Ribose Uracil (U) substitutes for Thymine (T)

Amino Acids & Proteins Nucleic Acid Precursors
In a cell, nucleic acids are constructed from nucleoside triphosphates, precursors of the mononucleic units Each mononucleic unit consists of: an N-containing base a sugar a triphosphate group Nitrogen Containing Bases: Pyrimidines Thymine (DNA) Uracil (RNA) Cytosine Purines Guanine Adenine

Amino Acids & Proteins Base Pairing
In the nucleus of a cell, DNA exists as two chains wrapped around each other in a “double Helix” Each base in one chain “Pairs” with a base in the other through Hydrogen Bonding A double-helical DNA molecule may contain many millions of H-Bonded bases Base Pair Features A Pyrimidine (Pyr) is always paired with a Purine (Pur) Each base is always paired with the same partner Thymine (T) (Pyr) with Adenine (A) (Pur) Cytosine (C) (Pyr) with Guanine (G) (Pur) Thus, base sequence on one chain is the complement of the sequence on the other chain Ex. A-C-T on one chain paired with T-G-A on another

Practice Problem Write the sequence of the complimentary DNA strand that pairs with each of the following: a GGTTAC Ans: CCAATG b CCCGAA Ans: GGGCTT

Practice Problem Write the base sequence of the DNA template from which the RNA sequence below was derived GUA UCA AUG AAC UUG (RNA) Ans: CAT AGT TAC TTG AAC (DNA) (note: Uracil (U) substitutes for Thymine (T) in RNA) How many amino acids are coded for in this sequence? Ans: five (CAT) (AGT) (TAC) (TTG) (AAC) Each 3-base sequence is a word, each word codes for a specific amino acid

Nucleic Acids (N-Containing Bases)
Pyrimidines Thymine Uracil Cytosine Purines Guanine Adenine

Nucleic acid precursors and their linkage
.

The Double Helix of DNA

SEQUENCE  STRUCTURE  FUNCTION
Amino Acids & Proteins Protein Synthesis A protein consists of a sequence of Amino Acids The Protein’s Amino Acid sequence determines its structure, which in turn determines its function SEQUENCE  STRUCTURE  FUNCTION The DNA base sequence contains an information template that is carried by the RNA base sequence (messenger and transfer) to create the protein amino acid sequence In other words, the DNA sequence determines the RNA sequence, which determines the protein amino acid sequence In Genetic Code, each base acts as a “Letter” Each three-base sequence is a “Word” Each word codes for a specific Amino Acid Ex. C-A-C codes for Histidine A-A-G codes for Lysine

Amino Acids & Proteins One Amino Acid at a time is positioned and linked to the next in the process of protein synthesis Outline of Synthesis DNA occurs in cell nucleus Genetic message is decoded outside of cell RNA serves as messenger to synthesis site Portion of DNA is unwound and one chain segment acts as a template for the formation of a complementary chain of messenger RNA (mRNA) mRNA made by individual mononucleoside triphosphates linking together The DNA code words are transcribed into RNA code words through base pairing mRNA leaves the nucleus and binds, again through base-pairing, to an RNA rich-rich particle called a “Ribosome”

Amino Acids & Proteins Synthesis Outline (con’t)
The words (3-base sequences) in the RNA are then decoded by molecules of transfer RNA (tRNA) The smaller nucleic acid “shuttles” have two key portions on opposite ends of their structures A three-base sequence (word) which is a complement of a word on the nRNA A binding site for the amino acid coded by that word The Ribosome moves along the bound mRNA, one word at a time, while tRNAs bind to the mRNA The Amino acids are positioned near one another in preparation of peptide bond formation and synthesis of the protein

Amino Acids & Proteins Synthesis Outline (con’t) Net result
Protein Synthesis involves the DNA message of three- base words being transcribed into the RNA message of three-base words, which is then translated into a sequence of amino acids that are linked to make a protein DNA Base Sequence  RNA Base Sequence  Protein Amino Acid Sequence

George Mason University

Similar presentations

Presentation on theme: "George Mason University"— Presentation transcript:

Similar presentations

About project

Feedback

Log in

Auth with social network:

George Mason University

Similar presentations

Presentation on theme: "George Mason University"— Presentation transcript:

Similar presentations

About project

Feedback