Periodic Table 8/3/2006 MEDC 501 Fall 2006 1
rbitals Shapes of rbitals s - orbital p -orbital 8/3/2006 MEDC 501 Fall 2006 2
Ionic Bond - acl Electronic Structure 11 a :: 1s 2 2s 2 2p x2 2p y2 2p z2 3s 1 11 a + :: 1s 2 2s 2 2p x2 2p y2 2p z2 3s 0 = 10 e 17 Cl - :: 1s 2 2s 2 2p x2 2p y2 2p z2 3s 1 3p x2 3p y2 3p z 2 = 18 Ar 17 Cl :: 1s 2 2s 2 2p x2 2p y2 2p z2 3s 1 3p x2 3p y2 3p z 1 8/3/2006 MEDC 501 Fall 2006 3
Electronic Structure Can 6 C form ionic bonds? 6 C :: 1s 2 2s 2 2p x1 2p y 1 8/3/2006 MEDC 501 Fall 2006 4
s -orbital ybridization + sp -orbital p -orbital n A give n 8/3/2006 MEDC 501 Fall 2006 5
ybridization in Carbon sp 3 hybridization C 4 6 C :: 1s 2 2s 2 2p x1 2p y 1 6 C :: 1s 2 2s 1 2p x1 2p y1 2p z 1 1 :: 1s 1 6 C :: 1s 2 2sp x2 2sp y2 2sp z 2 8/3/2006 MEDC 501 Fall 2006 6
ybridization in Carbon sp 2 hybridization C 2 =C 2 6 C :: 1s 2 2s 2 2p x1 2p y 1 6 C :: 1s 2 2s 1 2p x1 2p y1 2p z 1 8/3/2006 MEDC 501 Fall 2006 7
ybridization in Carbon sp 2 hybridization C 2 =C 2 8/3/2006 MEDC 501 Fall 2006 8
ybridization in Carbon sp hybridization C=C 6 C :: 1s 2 2s 2 2p x1 2p y 1 6 C :: 1s 2 2s 1 2p x1 2p y1 2p z 1 sp hybrid orbital π orbitals σ orbitals p orbitals 8/3/2006 MEDC 501 Fall 2006 9
ybridization in Carbon sp 2 hybridization benzene C 6 6 8/3/2006 MEDC 501 Fall 2006 10
Are all bonds same? Bond Polarity 3 C C 3 versus 3 C 8/3/2006 MEDC 501 Fall 2006 11
Electronegativity Electronegativity: The ability of certain atoms to draw sigma electrons to themselves 8/3/2006 MEDC 501 Fall 2006 12
Quantitative Measure of Electronegativity Sanderson Scale F 4.000, Cl 3.475, Br 3.219, I 2.778 3.654, 3.194, S 2.957 C 2.746, 2.592 Pauling Scale F 4.0, Cl 3.0, Br 2.8, I 2.5 3.5, 3.0, S 2.5 C 2.5, 2.1 Kier-all Scale χ = (column # - # of σ bonds) (row #) 2 8/3/2006 MEDC 501 Fall 2006 13
Calculating Kier-all Electronegativity χ = b a (column # - # of σ bonds) (row #) 2 c d Cl e f g h 4 5 6 7 2 6 C 7 8 9 F 3 15 P 16 S 17 Cl 4 34 Se 35 Br 5 53 I 8/3/2006 MEDC 501 Fall 2006 14
Dipolar Bonding Consequences of Bond Polarity C 3 3 C C 3 3 C 3 C 3 C C 3 3 C 3 C C C 3 2 C C 3 C 3 2 C C 3 MW 72 72 bp 28 C 80 C 8/3/2006 MEDC 501 Fall 2006 15
Consequences of Bond Polarity ydrogen Bonding 2 2 S MW 18 34 bp 100 C -60 C χ = (6-2)/4 = 1.0 χ S = (6-2)/9 = 0.44 8/3/2006 MEDC 501 Fall 2006 16 S........................
Consequences of Bond Polarity ydrogen Bonding Each in a hydrogen-bond is shared by two e atoms Linear arrangement of three atoms ( plus 2 e) is strongest Each linear arrangement is ~ 4-5 kcal/mol Typically form -bond -.- -.= -.F- Typically do not form -bond S- - P- = - Cl- 8/3/2006 MEDC 501 Fall 2006 17
Consequences of Bond Polarity ydrogen Bonding - Alcohols C 3 C 2 C 3 C 3 C 2 C 2 MW 44 46 bp -45 C 78 C.... 8/3/2006 MEDC 501 Fall 2006 18
Consequences of Bond Polarity ydrogen Bonding - Acids C C C MW 138 138 138 mp 159 201 214 C............ 8/3/2006 MEDC 501 Fall 2006 19
Consequences of Bond Polarity ydrogen Bonding - Structure of Proteins and ucleic Acids R1 R9. R2. R10 R3 R11. R4. R12 R5 R13. R6. R14 R7 R15. R8. R16 ydrogen Bonding in β-strands (3D structure) 8/3/2006 MEDC 501 Fall 2006 20
Inductive Effect Consequences of Bond Polarity the transfer of electronegative effect of polar σ bonds to neighboring σ bonds, causing them to be more or less polarized. 8/3/2006 MEDC 501 Fall 2006 21
Consequences of Bond Polarity Change in Acidity or Basicity of Groups C 3 C 3 a carboxylic acid an alcohol C 3 F 3 C a carboxylic acid a trifluoro-carboxylic acid 8/3/2006 MEDC 501 Fall 2006 22
Consequences of Bond Polarity Inductive Effect - Influence on pka 1.25 C 3 3 C 1.0 1.0 pka 4.5 16.5 8/3/2006 MEDC 501 Fall 2006 23
Chemical Equilibrium pk A and Ions in Solution k 1 A + B C + D k 2 At equilibrium, k 1 [A] [B] = k 2 [C] [D] k k 1 2 = [ C][ D] [ A][ B] = K E Le Chatelier s Principle: When a stress is applied on a system at equilibrium, the system will re-adjust to diminish the stress or counteract the change. 8/3/2006 MEDC 501 Fall 2006 24
2 Equilibrium pk A and Ions in Solution k 1 + _ 2 + k 2 + [ ][ [ ] 2 ] = K E [ + ][ ] = KE W log[ [ 2] = KE 55.5 = K = 10 + ][ ] = log10 14 14 log[ + ] + log[ ] = 14 + log[ ] log[ ] = 14 p + p =14 8/3/2006 MEDC 501 Fall 2006 25
pk A and Ions in Solution Acidity, basicity and neutrality and p conditions 8/3/2006 MEDC 501 Fall 2006 26
pk A and Ions in Solution Ionization and Strength of Acids and Bases Property of Ionization: The degree of ionization of a particular compound in water is dependent on its structure and is characteristic for that compound. 8/3/2006 MEDC 501 Fall 2006 27
pk A and Ions in Solution Ionization of a weak acid C 3 C + 2 3 + + C 3 C - K E log pk A = p [ K A K E 2 [ = [ ] = K 3 ][ C3C ] ][ C C ] 2 A = log[ [ C log [ C 3 + [ = 3 3 3 + ] + ][ C3C [ C C ] 3 [ C log [ C 3 ] C ] C ] C ] [ conj. base] = p log C ] [ acid] 3 [ conj. base] log [ acid] 3 = p pk A enderson-aselbach Equation 8/3/2006 MEDC 501 Fall 2006 28
Consequences of Bond Polarity Inductive Effect - Influence on pka C 3 F 3 C pka 4.5 0.23 C 3 C ClC 2 C pka 4.5 2.9 8/3/2006 MEDC 501 Fall 2006 29
Consequences of Bond Polarity Inductive Effect - Additive Property pka C 3 C 4.5 ClC 2 C 2.9 Cl 2 CC 1.3 Cl 3 CC 0.7 8/3/2006 MEDC 501 Fall 2006 30
Consequences of Bond Polarity Inductive Effect - Distance Dependent Property pka C 3 C 2 C 2 C 4.8 ClC 2 C 2 C 2 C 4.5 C 3 CClC 2 C 4.1 C 3 C 2 ClC 2 C 2.8 8/3/2006 MEDC 501 Fall 2006 31
Consequences of Bond Polarity Inductive Effect - Group Electronegativities Electron-withdrawing groups χ -C= 0.5+1.0 = 1.5 -C 0.25+1.25+1.0+0 = 2.5 -C 0.25+1.25+0 = 1.5-2 0.5+1.25+1.25 = 3.0 pka 2 C 2 C 1.7 ClC 2 C 2.9 CC 2 C 2.8 CC 2 C 3.5 8/3/2006 MEDC 501 Fall 2006 32
Consequences of Bond Polarity Inductive Effect Multiple pk A values A molecule may have more than one pk A value!! pk A = 2.8 pk A = 5.7 _ + pk A = 2.35 + pk A = 9.78 3 _ 3 _ 2 8/3/2006 MEDC 501 Fall 2006 33
Consequences of Bond Polarity Influence on pka. through space effect Cl Cl C Cl Cl C pka 6.1 5.7 8/3/2006 MEDC 501 Fall 2006 34
Consequences of Bond Polarity atural Amino Acids Structure and pk A R C 2 Structure of Amino Acid Residues All L-configuration or R geometry (except for glycine) on-polar R = -Bonding R = Glycine Serine C 2 Alanine C 3 Threonine C 3 C() Valine (C 3 ) 2 C Cysteine SC 2 Leucine (C 3 ) 2 C 2 C Tyrosine C 6 4 C 2 Isoleucine C 3 C 2 C(C 3 ) Asparagine 2 C()C 2 Phenyalanine PhC 2 Glutamine 2 C()C 2 C 2 Methionine 3 CSC 2 C 2 Tryptophan C 2 8/3/2006 MEDC 501 Fall 2006 35
Consequences of Bond Polarity atural Amino Acids Structure and pk A R C 2 Structure of Amino Acid Residues All L-configuration or R geometry (except for glycine) Acidic R = Basic R = Aspartic Acid CC 2 Lysine 2 (C 2 ) 4 Glutamic Acid CC 2 C 2 Arginine 2 C()(C 2 ) 3 istidine 2 C 8/3/2006 MEDC 501 Fall 2006 36
Consequences of Bond Polarity Residues pk A 1 pk A Side-Chain pk A (group identification) on-polar Glycine 2.35 9.78 Alanine 2.35 9.87 Valine 2.29 9.74 Leucine 2.33 9.74 Isoleucine 2.32 9.76 Phenyalanine 2.16 9.18 Methionine 2.13 9.28 Tryptophan 2.43 9.44 ydrogen-bonding Serine 2.19 9.21 Threonine 2.09 9.10 Cysteine 1.92 10.78 8.33 (thiol group) Tyrosine 2.20 9.11 10.13 (phenol group) Asparagine 2.10 8.84 Glutamine 2.17 9.13 Acidic Aspartic Acid 1.99 9.90 3.90 (γ-c group) Glutamic Acid 2.10 9.47 4.07 (γ-c group) Basic Lysine 2.16 9.18 10.79 (ε-amino group) Arginine 1.82 8.99 12.48 (guanidino group) istidine 1.80 9.33 6.04 (imidazole group) 8/3/2006 MEDC 501 Fall 2006 37
pka and bases Consequences of Bond Polarity R 3+ + 2 3 + + R 2 pk A = p - log [R 2 ] [R 3+ ] Rank the following amines according to their pk A values. Use 1 for lowest pk A and 3 for highest. C 3 C 2 2 FC 2 C 2 2 C 3 FC 2 Rank the above amines according to their basicity. Use 1 for least basic and 3 for most basic. 8/3/2006 MEDC 501 Fall 2006 38
Inductive Effect Consequences of Bond Polarity depend on the ew atom or e atom is distance dependent may be re-inforced or cancelled is additive can affect the acidity or basicity of molecules can affect the physical properties of molecules 8/3/2006 MEDC 501 Fall 2006 39
Resonance Effect Consequences of Bond Polarity 2 2 pk A 8-11 3-5 3 + 2 + 2 + 3 + 3 + 2 + 2 + 3 + 8/3/2006 MEDC 501 Fall 2006 40
Consequences of Bond Polarity Resonance Effect C C C 2 Me pka 4.2 3.4 4.5 _ + 2 + 3 + + + _ + 2 + 3 + Me Me 8/3/2006 MEDC 501 Fall 2006 41
Resonance Effect Consequences of Bond Polarity Electron-donating groups., Me,, 2, C 3, Cl, F, Br, I Electron-withdrawing groups. 2, C, C, C, S 3, S 2 2, S 2 Cl 8/3/2006 MEDC 501 Fall 2006 42