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Periodic Table

Periodic Table. s - orbital p - orbital. Orbitals. Shapes of Orbitals. Electronic Structure. Ionic Bond - NaCl. Electronic Structure. Can 6 C form ionic bonds?. 6 C :: 1s 2 2s 2 2p x 1 2p y 1. s -orbital. sp - orbital. p -orbital.

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Periodic Table

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  1. Periodic Table MEDC 501 Fall 2007

  2. s - orbital p - orbital Orbitals Shapes of Orbitals MEDC 501 Fall 2007

  3. Electronic Structure Ionic Bond - NaCl MEDC 501 Fall 2007

  4. Electronic Structure Can 6C form ionic bonds? 6C :: 1s22s22px12py1 MEDC 501 Fall 2007

  5. s -orbital sp - orbital p -orbital ‘n’ atomic orbitals give ‘n’ hybrid orbitals Hybridization + MEDC 501 Fall 2007

  6. 6C :: 1s22s12px12py12pz1 sp3 orbitals 6C :: 1s2(2sp3)1 (2sp3)1 (2sp3)1 (2sp3)1 4 1H :: 1s1 CH4 :: 1s2(2sp3)2 (2sp3)2 (2sp3)2 (2sp3)2 Hybridization in Carbon sp3 hybridization …… CH4 6C :: 1s22s22px12py1 MEDC 501 Fall 2007

  7. 6C :: 1s22s12px12py12pz1 Hybridization in Carbon sp2 hybridization …… CH2=CH2 6C :: 1s22s22px12py1 6C :: 1s2(2sp2)1 (2sp2)1 (2sp2)1 2pz1 MEDC 501 Fall 2007

  8. Hybridization in Carbon sp2 hybridization …… CH2=CH2 MEDC 501 Fall 2007

  9. sp hybridization …… CH=CH 6C :: 1s22s12px12py12pz1 p orbitals s orbitals p orbitals Hybridization in Carbon 6C :: 1s22s22px12py1 sp hybrid orbital MEDC 501 Fall 2007

  10. Hybridization in Carbon sp2 hybridization …… benzene C6H6 MEDC 501 Fall 2007

  11. Bond Polarity MEDC 501 Fall 2007

  12. Electronegativity MEDC 501 Fall 2007

  13. Sanderson Scale F 4.000, Cl 3.475, Br 3.219, I 2.778 O 3.654, N 3.194, S 2.957 C 2.746, H 2.592 Pauling Scale F 4.0, Cl 3.0, Br 2.8, I 2.5 O 3.5, N 3.0, S 2.5 C 2.5, H 2.1 (column # - # of s bonds) (row #)2  = Kier-Hall Scale Quantitative Measure of Electronegativity MEDC 501 Fall 2007

  14. 4 5 6 7 26C 7N 8O 9F 315P 16S 17Cl 434Se 35Br 553I (column # - # of s bonds) (row #)2  = Calculating Kier-Hall Electronegativity i f h h e c d a b g MEDC 501 Fall 2007

  15. Consequences of Bond Polarity Dipolar Bonding MW 72 72 bp 28 OC 80 OC MEDC 501 Fall 2007

  16. O = (6-2)/4 = 1.0 S = (6-2)/9 = 0.44 ... ... ... ... ... ... ... ... Consequences of Bond Polarity Hydrogen Bonding H2O H2S MW 18 34 bp 100 OC -60 OC MEDC 501 Fall 2007

  17. Consequences of Bond Polarity Hydrogen Bonding • Each H in a hydrogen-bond is shared by two eN atoms • Linear arrangement of three atoms (H plus 2 eN) is strongest • Each linear arrangement is ~ 4 -5 kcal/mol Typically do not form H-bond S-H O- P-H N= O-H Cl- Typically form H-bond N-H….O- O-H….N= O-H….F- MEDC 501 Fall 2007

  18. …. …. …. …. Consequences of Bond Polarity Hydrogen Bonding - Alcohols MW 44 46 bp -45 OC 78 OC MEDC 501 Fall 2007

  19. MW 138 138 138 mp 159 201 214 OC ... ... ... ... Consequences of Bond Polarity Hydrogen Bonding - Acids MEDC 501 Fall 2007

  20. …. …. …. …. …. …. …. …. Consequences of Bond Polarity Hydrogen Bonding - Structure of Proteins and Nucleic Acids Hydrogen Bonding in b-strands (3D structure) MEDC 501 Fall 2007

  21. Consequences of Bond Polarity Inductive Effect …the transfer of electronegative effect of polar s bonds to neighboring s bonds, causing them to be more or less polarized. MEDC 501 Fall 2007

  22. Consequences of Bond Polarity Change in Acidity or Basicity of Groups a carboxylic acid an alcohol a carboxylic acid a trifluoro-carboxylic acid MEDC 501 Fall 2007

  23. 1.25 1.0 1.0 Consequences of Bond Polarity Inductive Effect - Influence on pKa pKa 4.5 16.5 MEDC 501 Fall 2007

  24. k1 A + B C + D k2 pKA and Ions in Solution Chemical Equilibrium At equilibrium, k1 [A] [B] = k2 [C] [D] 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. MEDC 501 Fall 2007

  25. _ k1 + H2O H + OH k2 pKA and Ions in Solution H2O Equilibrium      MEDC 501 Fall 2007

  26. pKA and Ions in Solution Acidity, basicity and neutrality and pH conditions MEDC 501 Fall 2007

  27. Phenobarbital Warfarin pKA 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. MEDC 501 Fall 2007

  28. pKA and Ions in Solution Ionization of a weak acid CH3COOH + H2O H3O+ + CH3COO-     Henderson-Haselbach Equation MEDC 501 Fall 2007

  29. pKA and Ions in Solution What is the physical meaning of pKA? [Unionized Acid1] = [Unionized Acid2] If pKA1 = 4 and pKA2 = 1 …. MEDC 501 Fall 2007

  30. Consequences of Bond Polarity Inductive Effect - Influence on pKa pKa 4.5 0.23 CH3COOH ClCH2COOH pKa 4.5 2.9 MEDC 501 Fall 2007

  31. Consequences of Bond Polarity Inductive Effect - Additive Property pKa CH3COOH 4.5 ClCH2COOH 2.9 Cl2CHCOOH 1.3 Cl3CCOOH 0.7 MEDC 501 Fall 2007

  32. Consequences of Bond Polarity Inductive Effect - Distance Dependent Property pKa CH3CH2CH2COOH 4.8 ClCH2CH2CH2COOH 4.5 CH3CHClCH2COOH 4.1 CH3CH2ClCH2COOH 2.8 MEDC 501 Fall 2007

  33. Consequences of Bond Polarity Inductive Effect - Group Electronegativities Electron-withdrawing groups  -C=N 0.5+1.0 = 1.5 -COOH 0.25+1.25+1.0+0 = 2.5 -CHO 0.25+1.25+0 = 1.5 -NO2 0.5+1.25+1.25 = 3.0 pKa NO2CH2COOH 1.7 ClCH2COOH 2.9 COOHCH2COOH 2.8 CNCH2COOH 3.5 MEDC 501 Fall 2007

  34. Consequences of Bond Polarity Influence on pKa …. through space effect pKa 6.1 5.7 MEDC 501 Fall 2007

  35. pKA and Solubility in Water MEDC 501 Fall 2007

  36. pKA = 5.7 pKA = 2.8 _ _ _ pKA = 9.78 pKA = 2.35 + + _ _ Consequences of Bond Polarity Inductive Effect – Multiple pKA values A molecule may have more than one pKA value!! MEDC 501 Fall 2007

  37. Non-Polar R = Polar R = Glycine H— Serine HOCH2— Alanine CH3— Threonine CH3CH(OH)— Valine (CH3)2CH— Cysteine HSCH2— Leucine (CH3)2CH2CH— Tyrosine HOC6H4CH2— Isoleucine CH3CH2CH(CH3)— Asparagine H2NC(O)CH2— Phenyalanine PhCH2— Glutamine H2NC(O)CH2CH2— Methionine H3CSCH2CH2— Tryptophan __ Consequences of Bond Polarity Natural Amino Acids – Structure and pKA Structure of Amino Acid Residues All L-configuration or R geometry (except for glycine) MEDC 501 Fall 2007

  38. Consequences of Bond Polarity Natural Amino Acids – Structure and pKA Structure of Amino Acid Residues All L-configuration or R geometry (except for glycine) Acidic R = Basic R = Aspartic Acid HOOCCH2— Lysine H2N(CH2)4— Glutamic Acid HOOCCH2CH2— Arginine H2NC(NH)NH(CH2)3— Histidine __ MEDC 501 Fall 2007

  39. pKA Values of Natural Amino Acids Residues pKA1 pKA2 Side-Chain pKA (group identification) Non-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 Hydrogen-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 (g-COOH group) Glutamic Acid 2.10 9.47 4.07 (g-COOH group) Basic Lysine 2.16 9.18 10.79 (-amino group) Arginine 1.82 8.99 12.48 (guanidino group) Histidine 1.80 9.33 6.04 (imidazole group) MEDC 501 Fall 2007

  40. pKA Values of Natural Amino Acids and the Dominant Form Amino Acid pH 3.0 pH 7.0 pH 10.0 Serine Cysteine Tyrosine Asparagine Arginine Aspartic Acid MEDC 501 Fall 2007

  41. RNH3+ + H2O H3O+ + RNH2 [RNH2] [RNH3+] pKA = pH - log Consequences of Bond Polarity Influence on pKa of bases CH3CH2NH2 FCH2CH2NH2 MEDC 501 Fall 2007

  42. Consequences of Bond Polarity Inductive Effect • depend on the eW atom or eN 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 MEDC 501 Fall 2007

  43. Consequences of Bond Polarity Resonance Effect pKa 9-11 ~5 Resonance, Aromaticity & Conjugation MEDC 501 Fall 2007

  44. Consequences of Bond Polarity Resonance Effect pKa 9-11 ~5 + H2O + H3O+ + H2O + H3O+ MEDC 501 Fall 2007

  45. _ + H2O + H3O+ + + _ _ _ + H2O + H3O+ Consequences of Bond Polarity Resonance Effect pKa 4.2 3.4 4.5 MEDC 501 Fall 2007

  46. Consequences of Bond Polarity Resonance Effect Electron-donating groups …. OH, OMe, NH, NH2, NCH3 Electron-withdrawing groups …. NO2, COOH, CHO, CN, SO3H, SO2NH2, SO2Cl MEDC 501 Fall 2007

  47. pKA Values of Common Organic Functional Groups MEDC 501 Fall 2007

  48. [RNH2] [RNH2] [RNH2] [RNH2] [RNH3+] [RNH3+] [RNH3+] [RNH3+] [RNH2] [RNH3+] 100 100 (1+10-3) (1+10-7) Application of Henderson-Hasselbach Equation 1. Amphetamine has pKA of 9.8. What form will dominate at pH 2.8, 6.8, and 9.8? log = pH - pKA At pH 6.8 log = 6.8 – 9.8 = -3.0  = 10-3  [RNH2] = 10-3 [RNH3+]  % [RNH2] = 10-3   0.1 %  % [RNH3+] = 100 - 10-1  99.9 % RNH3+ is an ion, therefore % ionization of amphetamine is nearly 100% at pH 6.8 At pH 2.8 log = 2.8 – 9.8 = -7.0  = 10-7  [RNH2] = 10-7 [RNH3+]  % [RNH2] = 10-7   0.00001 %  % [RNH3+] = 100 - 10-5  99.99999 % RNH3+ is an ion, therefore % ionization of amphetamine is nearly 100% at pH 2.8 MEDC 501 Fall 2007

  49. [RNH2] [RNH2] [RNH3+] [RNH3+] [RNH2] [RNH3+] 100 (1+1) Application of Henderson-Hasselbach Equation 1. Amphetamine has pKA of 9.8. What form will dominate at pH 2.8, 6.8, and 9.8? log = pH - pKA At pH 9.8 log = 9.8 – 9.8 = 0.0  = 100 = 1  [RNH2] = 1[RNH3+]  % [RNH2] = 1  50 %  % [RNH3+] = 100 - 50 50 % RNH3+ is an ion, therefore % ionization of amphetamine is 50% at pH 9.8 MEDC 501 Fall 2007

  50. [RNH2] [RNH3+] [RNH2] [RNH3+] [RNH2] [RNH3+] Application of Henderson-Hasselbach Equation 2. Meperidine is a narcotic analgesic. Its pKA is 8.7. It needs to be injected (iv). What pH will you need to make the solution of meperidine? log = pH - pKA For meperidine to go into solution fully and easily, it should be fully ionized. Therefore, protonated species (the conjugate acid form, [A]), and not the base form {[B]} should dominate.  < 0.01 or 10-2  log < –2.0  pH – pKA < –2.0  pH – 8.7 < –2.0  pH < –2.0 + 8.7  pH < 6.7 MEDC 501 Fall 2007

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