Presentation is loading. Please wait.

Presentation is loading. Please wait.

Biomass Fundamentals Modules 3-5: Fundamental Concepts of Organic Chemistry A capstone course for BioSUCCEED: Bio products S ustainability: a U niversity.

Similar presentations


Presentation on theme: "Biomass Fundamentals Modules 3-5: Fundamental Concepts of Organic Chemistry A capstone course for BioSUCCEED: Bio products S ustainability: a U niversity."— Presentation transcript:

1 Biomass Fundamentals Modules 3-5: Fundamental Concepts of Organic Chemistry A capstone course for BioSUCCEED: Bio products S ustainability: a U niversity C ooperative C enter of E xcellence in ED ucation The USDA Higher Education Challenge Grants program gratefully acknowledged for support

2 This course would not be possible without support from: USDA Higher Education Challenge (HEC) Grants Program

3 Atomic view of matter Democritus (ca. 460 BC – ca. 370 BC) was an ancient Greek materialist philosopher who indicated that: All matter was composed of discrete smaller particles called “atoms” that retained the fundamental identity of that matter. The “atomic” viewpoint he espoused was very clever: e.g., oily substances were made of atoms that slid past each other Quiz M3/5.1 1.What is a element: (a) a compound; (b) a molecule; (c) smallest identifiable part of anything; (d) earth, wind, water, and fire 2. How do atoms form compounds: (a) ionic coupling; (b) covalent coupling; (c) coordination; (d) none of the above 3. What is the smallest element on record: (a) iron; (b) aluminum; (c) hydrogen; (d) beryllium 1.What is a element: (a) a compound; (b) a molecule; (c) smallest identifiable part of anything; (d) earth, wind, water, and fire 2. How do atoms form compounds: (a) ionic coupling; (b) covalent coupling; (c) coordination; (d) none of the above 3. What is the smallest element on record: (a) iron; (b) aluminum; (c) hydrogen; (d) beryllium

4 Atom and molecules What are they? Atoms as described previously are the building blocks of matter – Made up of three primary subatomic particles: the neutrons and protons (nucleus, positively charged) comprise the atomic weight, whereas the protons are the atomic number (identity); the last subatomic particle, the electrons, balance the charge (they are negative) and engage in chemical reactions (bonding, oxidation, reduction, polymerization, etc.) – The protons CANNOT be divided without losing the identity of the material they represent; e.g., a carbon atom has 6 protons, 6 neutrons, and 6 electrons – if you change the number of neutrons you get an ISOTOPE of the element, if you change the number of electrons, you get an ION (CATION or ANION), but if you change the protons, you GET A DIFFERENT ATOM!!! Molecules are combinations of atoms This is a natural and stable isotope of carbon 1.1% of all natural carbon is in this form It is also resonance frequency active meaning that it is amenable to imaging by NMR spectrometers, hence providing a structural profile of a substance Carbon dating is done using the 14 C 12 isotope which can date up to 60K years

5 Bohr’s concept of an atom Quiz M3/5.2 The Bohr model was proposed in 1915 by Niels Bohr who suggested that the electrons (recall) orbit the nucleus of the atom [see model at right  ]Niels Bohr He indicated that each electron had its own position (or orbit), but jumping/falling was allowed whose energy consequences resulted in radiative emission This lead to the concept of quantization of energy, or the idea that discrete (separate) energy levels in matter were allowed, viz., energy paths are NOT a continuum, but broken into LEVELS or orbits 1. Where do the electrons in an atom reside: (a) inside nucleus; (b) in orbits; (c) paired; (d) both b & c 2. What forms of energy are released by electronic transitions: (a) heat; (b) light; (c) vibrational; (d) all of the above 3. Is all matter “quantized:” (a) yes; (b) no 1. Where do the electrons in an atom reside: (a) inside nucleus; (b) in orbits; (c) paired; (d) both b & c 2. What forms of energy are released by electronic transitions: (a) heat; (b) light; (c) vibrational; (d) all of the above 3. Is all matter “quantized:” (a) yes; (b) no

6 Overview of periodic table All the elements are described!!! The “periodic” table is so named because the properties of all of the elements are periodic functions of their atomic number elements Although Mendeleev is credited for the Table, many others had enormous contributions to its development It is now a wonderful teaching tool to describe the properties (physical and chemical) of all the elements in the UNIVERSE Many contributors to this:

7 Molecular bonding I Petro-economy vs. bio-economy During the 18 th century, Antoine Lavoisier began the science of elemental analysis (chemical analysis) by measuring the amount of carbon dioxide and water when a substance was completely combusted. – For example, organic substance + 2O 2  ____CO 2 + ____H 2 O We learned from a great British experimentalist, Sir Davy, that chemical bonds can be broken by electrolysis: – A-----B  A + + B - (electrically charged) Quiz M3/5.3 If we determine that 36g of water are collected and 88 g of carbon dioxide are collected, while 2 moles or 64 g of oxygen are consumed by the organic substance, then what is the organic substance?

8 Molecular bonding II Charged, but charges must cancel according to the conservation of charge. Salts are classic examples. Please list several here (see periodic table): – In 1916, Kossel (Germany) introduced concept of stable ion formation to approach “Noble Gas” configurations. – Li + Be +2 B +3 C +4 N -3 O -2 F -1 Ne 0 Ionization is the tendency to lose an electron. The ionization energy decreases, becomes more negative as one goes to the lower left of the periodic table. Electron Affinity is the attraction an atom has for an electron. The more negative this value is, the higher the affinity - it increases as one goes to the upper right of the periodic table. The affinity can be described by classical coulombic laws of physics: E = q 1 q 2 /r 2 , where q are the charge on the particles, r is the distance between them, and epsilon (  ) is the shielding factor between them (as this increases, the attraction is minimized). ESSAY At this point, describe in a page or less, why the properties of ionic substances are so important to life. Think about electrolytes and find out how they influence the overall metabolic activity of living organisms Ionic bonding

9 Molecular bonding III This is the most important bond that we will be dealing with in our studies -Do you think that a covalent compound would conduct electricity? In 1916 (same year as Kossel’s work on ionic bonds), G.N. Lewis proposed the concept of a chemical bond in which electrons are equally shared between atomic partners and introduced the concept of the “Lewis Dot Structure:”Kossel’s A classic representation of the concept of covalent bonding between C and H atoms; shown above is methane, the simplest hydrocarbon in the universe Covalent bonding

10 Molecular bonding IV The concept of BOND ORDER involves the number of bonds between atoms, considering that two electrons make up one stable bond. In the previous slide (see notes section), we have three forms of C 2 in which each one represents a different bond orderprevious slide C-C bonds have bond order of 1 (2 electrons) C=C bonds (double bonds or “unsaturated” bonds) have a bond order of 2 The higher the bond order, the tighter the bond, the more energy it contains, and hence, more difficult to break Formal charge is the charge assigned to an atom in a compound that mathematically allows to obtain the overall charge of the molecule (Following always holds  O = -2; H = +1) 1. Acetylene has a bond order of: (a) 1; (2) 2; (3) 3; (4) 4 2. True or false: the higher the bond order, the stronger the bond 3. What is the formal charge of N in [NO 3 ] -1 ? 1. Acetylene has a bond order of: (a) 1; (2) 2; (3) 3; (4) 4 2. True or false: the higher the bond order, the stronger the bond 3. What is the formal charge of N in [NO 3 ] -1 ? Quiz M3/5.4 Bond order & Formal charge

11 Molecular structural paradigms I A Lewis acid is an electron acceptor A Lewis base is an electron donor A lot of chemical reactivity can be explained using these two concepts Lewis Acids & Bases Shown above is an example of a classic Lewis acid and Lewis base reaction: ammonia (NH 3 ), the Lewis base, directing its lone pair of electrons by virtue of electrostatic forces to the empty p orbital of boron trifluoride (BF 3 ) forming a coordination complex/adduct.

12 ALKANES Hydrocarbons can be saturated or unsaturated Alkane (CH 4 ), alkene (CH 2 CH 2 ), alkyne (CH 1 CH 1 ) Benzene (“tri-alkene” with RESONANCE) see 2.2d computer animation

13 Polar Covalent Bonds Dipolar bonding (force of dipole = charge x distance) Polar (CHCl 3 ) and non-polar (CCl 4 ) How about water and ammonia?

14 Functional Groups

15 Alkyl Halides, Alcohols, and Organic Chemistry’s Most Wanted Primary, secondary, and tertiary designate degree of carbon substitution on carbon bearing halide (-Cl, -Br, -I) or alcohol (-OH) Ethers: CH 3 OCH 3 (dimethyl ether) or R-O-R Amines: NH 3 (ammonia), NHR, NR 2, NR 4 where N formal charge = +1 Aldehydes, Ketones: RR’C=O, R=H (Aldehyde)

16 Alkyl Halides, Alcohols, and Organic Chemistry’s Most Wanted Carboxylic acids: RCOOH Amides: RCONH 2 Esters: RCOOR (similar to carboxylic acids)

17 Intermolecular Forces Forces such as ion-ion between atoms or molecules that affects melting/boiling points dipole-dipole forces are very important hydrogen bonding van der Waals forces (see 2.15 computer animation

18 Structure and Preparation of Alkenes: Elimination Reactions

19 Common Alkenyl Groups Vinyl (CH 2 =CH-) Allyl (CH 2 =CHCH 2- ) Isopropenyl(CH 2 =CH(CH 3 )-) Exo vs. Endo Alkene Structures

20 p orbitals are indeed “perpendicular” They are perpendicular to molecular axis The molecule is planar Substituents are “fixed” Isomerism leads to cis and trans forms EZ Notation (relates to atomic number of substitutents)

21 Stabilities C n H 2n + aO 2  bCO 2 + cH 2 O Isomers of highest energy have the highest heat of combustion and are the least stable (i.e., more stable forms release less energy, reflective of generation) Degree of substitution affects the stability status of alkenes (mono, di, tri, tetra alkyl groups stabilize sp 2 orbitals) Steric strain among substituents affects stability – less strain, lower heat of combustion

22 ELIMINATION REACTIONS X-CH 2 -CH 2 -Y  CH 2 =CH 2 + X-Y (what general reaction concept is this an example of?) Dehydration of alcohols – H-CH 2 CH 2 OH + ?  CH 2 =CH 2 + H 2 O (need to make OH good leaving group – how?) – Identify the alkene obtained by he dehydration of the following: 1.) 3-ethyl-3-propanol 2.) 1- propanol 3.) 2-butanol

23 ZAITSEF RULE Look at 2-butanol dehydration products. Which is preferred? Regioselectivity is rule “du jour” – elimination reactions of alcohols yield the most highly substituted alkene as the major product What is the mechanism of reaction? (think of carbocation formation) – use smartboard page

24 Rearrangements (RAR) – bizarre!!! (CH 3 ) 3 CCH(OH)CH 3 + H +  (CH 3 ) 2 C=C(CH 3 ) 2 (64%) + CH 2 =C(CH 3 ) 2 (33%) Sigmatropic RAR of methyl groups (move like a proton does or a doublebond) Hydride shifts like methyl shifts also occur (see 1-butanol)

25 Dehydrohalogenation Same as dehydration, except leaving group is a halide Instead of acid catalysis, requires a strong base (alkoxide – which are best?) 1-chlorocyclohexane + Sodium ethoxide/ethanol, 55C  ? Mechanism? It is second order!! The best substrates (R-X) have the heaviest halides

26 Conformations Need model kit! Shapes of alkane are very much zig-zag because of tetrahedral nature of sp 3 hybridized orbitals (build propane, butane, pentane, isobutane, isopentane, neopentane) Isomer numbers grow exponentially as number of carbons increase

27 Nomenclature and Boiling Point Branched: “alkyl” Alkene: Propane becomes propene Alkyne: Propene becomes propyne Note that branching causes lower bp since less surface area (van der Waals) for attraction

28 Sigma Bonds and Rotation C-C bonds can rotate and give rise to temporary “conformations;” Newman projection formulae are great ways of visualizing these rotations Sawhorse is a simpler method for visualization Ethane: a torsional barrier exists (see p. 88) staggered and eclipsed conformations

29 Conformational Analysis Anti, eclipsed, and gauche conformations Draw potential energy diagram (PE vs. torsion angle - see p. 91) Ring strain is fairly significant, in cyclopropane causing bonds to deviate from ideality by almost 50 degrees

30 Cyclohexane Conformations See 4.12 computer animation Boat, half-boat, and chair More than 99% of cyclohexane is in the chair (p. 159 Solomon for diagram) Axial and equatorial hydrogen atoms or other substituents

31 Cis-Trans Isomerism Distinguish between cis and trans-1,2- dimethylcyclopentane How about trans-1,6- dimethylcyclohexane What happens to the axial nature of these methyls in going from one chair to the other?

32 Cyclic Alkanes Cyclopropane - see p. 103 Cyclopentane - see p. 105 What is positional preference (axial or equatorial) of a large, bulky group (like t- butyl) on the 1 position of a cyclohexane? Heterocyclics: epoxides, tetrahydrofuran, piperidine

33 Enantiomers Mirror images (assemble CHClBrI) are not superimposable if they are dysymmetric (chiral) – hand Asymmetric (w/o symmetry) geometry defines a tetrahedral system Stereoisomers have the same exact atoms in the same pattern (connection), but differ in spatial arrangements of these atoms – ENANTIOMERS!!! Stereogenic centers are chiral centers

34 How to define achiral centers Plane of symmetry or center of symmetry must be present for an achiral center Achiral molecules do not possess optical activity: rotate the plane of plane-polarized light (light that has been polarized – one direction of propagation for the electric field) Enantiomeric excess must be present for net rotation of plane-polarized light

35 Configuration Stereogenic centers have absolute configurations designated as either (+) or (-) for the two enantiomers: sign for rotation of light The same relative configurations of different compounds may not have same rotation (+ or - )

36 Cahn-Ingold-Prelog R-S System Like E/Z, cis/trans for alkenes, this system ranks absolute configurations at a stereogenic center – Rank substituents according to decreasing AW – Orient molecule with the lowest ranked substituent at back – Look at direction of decreasing ranking (clockwise or counterclockwise?) If clockwise (R, rectus, right; S, sinister, left)

37 Fisher Projection Formulae H CH 3 + OH represents a tetrahedral carbon CH 2 CH 3 The horizontal bar substituents point toward you, whereas the vertical substituents point away Enantiomers differ in ability to interact with receptors

38 Elimination Bimolecular Must be bimolecular since fastest reactions occur with weakest R-X bonds Regioselectivity is also a factor in deciding where elimination occurs Must be periplanar transition state (look at cis vs trans 4-t-butylcyclohexylbromide – use model kits)

39 Reactions that Generate Stereogenic Centers Epoxidation (propene) Hydrobromination (2-butene) Chiral molecules with 2 stereogenic centers possess diastereomeric properties (R,R  S,S; R,S  S,R, but R,R is not an enantiomer of R,S and these two are diastereomers  stereoisomers R,R and S,S have rotations equal in magnitude but different in sign, likewise R,S and S,R have rotations equal to each other, but opposite in sign Erythro: like substituents on same side of Fisher projection form, threo is opposite

40 Reactions that Generate Stereogenic Centers Epoxidation (propene) Hydrobromination (2-butene) Chiral molecules with 2 stereogenic centers possess diastereomeric properties (R,R  S,S; R,S  S,R, but R,R is not an enantiomer of R,S and these two are diastereomers  stereoisomers R,R and S,S have rotations equal in magnitude but different in sign, likewise R,S and S,R have rotations equal to each other, but opposite in sign Erythro: like substituents on same side of Fisher projection form, threo is opposite

41 E1: Elimination Unimolecular Rate = k[alkyl halide] Mechanism involved formation of carbocation

42 Alcohols and Alkyl Halides C-X bond is polarized; dipole moment is strong! Classes of alcohols: primary, sec, tert Bonding is polar covalent Polarizability (induced dipole-dipole interactions)

43 Acid/Base Theory B: + H-A  B + -H + :A - What is base, acid, conjugates? HA + H 2 O  H 3 O + + A - K a = ? pK a = -logK a Acid dissociation constants (as you go from lower to higher pK a s, acidity decreases) – why?

44 Acid/Base Reactions: Mechanism HBr + H 2 O  Show reaction mechanism and TS diagram Alkoxide ions (anions) – which are more stable (primary, sec, tert?)

45 Alkyl Halides Preparation Alcohols + alkyl halides Mechanism (animation 6.11) Bonding and stability Carbon’s inductive effect*

46 S N 1 Mechanism Unimolecular in nature, kinetics Nucleophile (“Lover of Nucleus”) attack is non-directional RDS E act lower for higher C sub centers

47 Free Radicals Consider them “electrophilic” – they have an unfilled 2p orbital Stability like carbocations Homolytic cleavage is how they are generated

48 Enantiomers Mirror images (assemble CHClBrI) are not superimposable if they are dysymmetric (chiral) – hand Asymmetric (w/o symmetry) geometry defines a tetrahedral system Stereoisomers have the same exact atoms in the same pattern (connection), but differ in spatial arrangements of these atoms – ENANTIOMERS!!! Stereogenic centers are chiral centers

49 How to define achiral centers Plane of symmetry or center of symmetry must be present for an achiral center Achiral molecules do not possess optical activity: rotate the plane of plane-polarized light (light that has been polarized – one direction of propagation for the electric field) Enantiomeric excess must be present for net rotation of plane-polarized light

50 Configuration Stereogenic centers have absolute configurations designated as either (+) or (-) for the two enantiomers: sign for rotation of light The same relative configurations of different compounds may not have same rotation (+ or - )

51 Cahn-Ingold-Prelog R-S System Like E/Z, cis/trans for alkenes, this system ranks absolute configurations at a stereogenic center – Rank substituents according to decreasing AW – Orient molecule with the lowest ranked substituent at back – Look at direction of decreasing ranking (clockwise or counterclockwise?) If clockwise (R, rectus, right; S, sinister, left)

52 Fisher Projection Formulae H CH 3 + OH represents a tetrahedral carbon CH 2 CH 3 The horizontal bar substituents point toward you, whereas the vertical substituents point away Enantiomers differ in ability to interact with receptors

53 Reactions that Generate Stereogenic Centers Epoxidation (propene) Hydrobromination (2-butene) Chiral molecules with 2 stereogenic centers possess diastereomeric properties (R,R  S,S; R,S  S,R, but R,R is not an enantiomer of R,S and these two are diastereomers  stereoisomers R,R and S,S have rotations equal in magnitude but different in sign, likewise R,S and S,R have rotations equal to each other, but opposite in sign Erythro: like substituents on same side of Fisher projection form, threo is opposite

54 Reactions that Generate Stereogenic Centers Epoxidation (propene) Hydrobromination (2-butene) Chiral molecules with 2 stereogenic centers possess diastereomeric properties (R,R  S,S; R,S  S,R, but R,R is not an enantiomer of R,S and these two are diastereomers  stereoisomers R,R and S,S have rotations equal in magnitude but different in sign, likewise R,S and S,R have rotations equal to each other, but opposite in sign Erythro: like substituents on same side of Fisher projection form, threo is opposite

55 Achiral molecules with 2 stereogenic centers Meso forms are R,S/S,R forms that are superimposable on each other (achiral, and thus optically inactive) – 2,3-butanediol (2S, 3R form) Reactions that produce diastereomers: bromination – 2-butene yields the meso forms (homework)

56 “Nucleophilic” “Seeking the nucleus” R-X + Y:-  RY + X- C-X bond is polarized toward the halogen Common nucleophiles include alkoxide, sulfide, cyanide, and azide Substrate is sp 3 hybidized

57 Halogen Substitution Reactions Halide-halide exchange: Nucleophilic component must be soluble in medium and salt product should fall out! RCH 2 CH 2 Br + NaI/acetone  RCH 2 CH 2 I + NaBr (solid) Halide leaving group is based on relative acidity (RF< { "@context": "http://schema.org", "@type": "ImageObject", "contentUrl": "http://images.slideplayer.com/3411299/12/slides/slide_56.jpg", "name": "Halogen Substitution Reactions Halide-halide exchange: Nucleophilic component must be soluble in medium and salt product should fall out.", "description": "RCH 2 CH 2 Br + NaI/acetone  RCH 2 CH 2 I + NaBr (solid) Halide leaving group is based on relative acidity (RF<

58 S N 2 Reaction CH 3 Br + - OH  CH 3 OH + Br - Rate = k? Hughes and Ingold defined a concerted bimolecular process Simple primary and secondary carbon substrates are typical electrophiles Retention of configuration vs. Inversion of configuration are two pathways (RR’R’’-C-X + N: -  ?)

59 Principles of S N 2 Reactions Pentacoordinate TS, lower E product and halide LG Solvents influence the generation of the TS and the solvation of the final products/leaving group

60 Steric Effects in S N 2 (Reactivity) Alkyl Bromide StructureClass Relative Rate Methyl bromide CH 3 BrUnsub.221,000 Ethyl bromide CH 3 CH 2 BrPrimary1,350 Isopropyl bromide (CH 2 ) 2 CH Br Secondary1 t-butyl bromide (CH 3 ) 3 C-BrTertiary<<1

61 Substitution with LiI/Acetone Alkyl BromideStructureRel. Rate Ethyl bromideCH 3 CH 2 Br1.0 Propyl bromideCH 3 CH 2 CH 2 Br0.8 i-butyl bromide (CH 3 ) 2 CHCH 2 Br Neopentyl bromide (CH 3 ) 3 CCH 2 Br

62 Nucleophilicity ReactivityNucleophile Rel. Reactivity Very goodI -, HS -, RS Good Br -, HO -, RO -, CN -, N Fair NH 3, Cl -, F -, RCO WeakH 2 O, ROH1 PoorRCO 2 H10 -2

63 S N 1 Mechanism STERIC HINDRANCE defines the operability of this mechanism! Unimolecular (single order) (CH 3 ) 3 C-Br + H 2 O  Reactivity for S N 1 is reversed compared to S N 2: (methyl { "@context": "http://schema.org", "@type": "ImageObject", "contentUrl": "http://images.slideplayer.com/3411299/12/slides/slide_62.jpg", "name": "S N 1 Mechanism STERIC HINDRANCE defines the operability of this mechanism.", "description": "Unimolecular (single order) (CH 3 ) 3 C-Br + H 2 O  Reactivity for S N 1 is reversed compared to S N 2: (methyl

64 Relative Rate of S N 1 Solvolysis of t-butyl chloride Solvent Dielectric constant Rel. Rate Acetic acid61 Methanol334 Formic acid585,000 Water78150,000

65 Notable Carbocations The allylic group is very prominent [CH 2 =CHCH 2 +  + CH 2 CH=CH 2 ] and serves to highlight resonance well Hand-in Exercise (HIE): Draw the allylic cation in a cyclopentene system with the two resonant structures 3-chloro-3-methyl-1-butene undergoes bond homolysis at the chloro position to give an allylic carbocation [(CH 3 ) 2 CH + CH=CH 2 ] which can make an alcohol upon reaction with water – it can form 2 isomeric forms, name them (HIE)!

66 Dienes 1,4-pentadiene is a classic diene (CH 2 =CHCH 2 CH=CH 2 ) – (HIE) are they conjugated? Isolated double bonds are separated by at least on sp 3 carbon 1,3-butadiene has all sp 2 carbons (C 1 H2=C 2 HC 3 H=C 4 H 2 ) Allenes are cumulated dienes, i.e., have a central sp hybridized carbon (CH 2 =C=CH 2 )

67 Aromaticity Special property associated with benzene Reactivity is attenuated relative to analogous triene (the imaginary cyclohexatriene) Bonds in benzene are all the same Exhibits “resonance,” a special property related to the conjugation of the six  electrons

68 Chemical Characteristics of Benzene Planar molecule with all carbons in sp 2 hybridization 3 bonding orbitals filled and 3 empty anti-bonding orbitals Benzene can be substituted, but requires catalysts or strong conditions Typical substituted benzenes include: styrene (vinyl sub.), acetophenone (acetyl sub.), phenol (hydroxy sub.), anisole (methoxy sub.), and aniline (amine sub.)


Download ppt "Biomass Fundamentals Modules 3-5: Fundamental Concepts of Organic Chemistry A capstone course for BioSUCCEED: Bio products S ustainability: a U niversity."

Similar presentations


Ads by Google