Table of Contents
1
PAGE NO.
Table of Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
Inherent Strengths . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Connectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Notes on Particular Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Assembling CPK® Atomic Midels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Linear Alkanes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Linear Alkenes (Dienes and Trienes) . . . . . . . . . . . . . . . . . . . . . . . . 11
Linear Alkynes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Cyclic Alkynes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Cyclic Alkynes, Dienes, and Trienes . . . . . . . . . . . . . . . . . . . . . . . . 12
Alcohos, Aldehydes, and Ketones . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Organic (Carboxylic) Acid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Saturated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Unsaturated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Amino Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Aliphatic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Aromatic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Sulfur-Containings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Imino Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Dicatboxylic Amino Acids and Their Amide Derivatives . . . . . . 88
Basic Amino Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Modified Amono Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . .88
Penta- and Decapeptides. . . . . . . . . . . . . . . . . . . . . . . . . . . .88
Amino Acid Stereoisomerism . . . . . . . . . . . . . . . . . . . . . . . . . 88
Purines & Pyrimidines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Nucleic Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .88
Vitamins & Enzyme Cofactors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Ring Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
SUBJECT
Revision 6
List of Figures
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
2
Publication 5381-001
FIGURES
Figure
Figure
Figure
Figure
Figure
Figure
1.
2.
3.
4.
5.
6.
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
PAGE NO.
Connector Link, Standard
Connector Link, Short
Connector Link, Long
Connector Link, Locking
Connector Link, Carbon
Link
For Metal Hook
Hydrogen Bond Connector
Connector Link, Bayonet H-Bond Replacement
Connector Link For Amine Cap
Connector Link, Gluing
Socket
H-Bond Spacer
Metal Atom Connector Link
Screw For Amine Cap
Carbon Acetylenic Triple Bond
Carbon Amine
Carbon Aromatic-5
Carbon Aromatic-6
Carbon Ethylenic Double Bond
Carbon Fused 5-6 Rings
Carbon Fused 6-6 Rings
Carbon Fused 5-5 Rings
Carbon Tetrahedral
Carbon Tetrahedarl-4
Carbon Trigonal-4
Oxygen Single Bond
Oxygen Double Bond
Oxygen Indented Double Bond
Nitrogen Amide
N-Nitrile Triple Bond
Nitrogen Aromatic-5
Nitrogen Aromatic-6
Nitrogen Tetrahedral
Nitrogen Tetrahedral-4
(67-7005)
(67-7013)
(67-7021)
(67-7039)
(67-7047)
(67-7211)
(67-7203)
(67-6726)
(67-7062)
(67-7112)
(67-7054)
(67-7088)
(67-7096)
(67-7161)
(67-8187)
(67-6593)
(67-6536)
(67-6551)
(67-6569)
(67-6585)
(67-6601)
(67-6619)
(67-6600)
(67-6577)
(67-6528)
(67-6544)
(67-6874)
(67-6890)
(67-6916)
(67-6791)
(67-6792)
(67-6825)
(67-6833)
(67-6841)
(67-6858)
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
List of Figures (Contd)
3
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
44.
45.
46.
47.
48.
49.
50.
51.
Figure 52.
PAGE NO.
Nitrogen Trigonal-4
H-Bond Bayonet Type, Hydrogen
H-Bond Hook Type, Hydrogen
Hydrogen
Bromide
Chloride
Fluoride
Iodide
Sulfur, Digonal
Sulfur, Tetrahedral
Same as Phosphorus Tetrahedral
Phosphorus, Tettrahedral
Metal, Ionic
Metal, Covalent
Metal, All Purpose
Amine Cap
CPK* Construction Tool
Hydrogen Wrench
Calipers With Angstrom Unit Scale
For CPK* Models
Methane
Figure 53. Ethane
Figure 54. N-Propane
Figure 55. (A.) N-Butane
(B.) N-Octane
Figure 56. (A.) Methyl
(B.) Ethyl
(C.) N-Propyl
(D.) N-Butyl
(E.) N-Octyl Radicals
Figure 57. Isomers of
(A.) N-Propyl
(B.) N-Butyl
(C.) N-Octyl
Figure 58. Propene
(67-6866)
(67-6684)
(67-6726)
(67-6692)
(67-6510)
(67-6650)
(67-6676)
(67-6734)
(67-6957)
(67-6924)
88
88
88
88
88
88
88
88
88
88
(67-6924)
(67-6981)
(67-6973)
(67-6999)
(67-7112)
(67-7120)
(67-7138)
(00-0000)
88
88
88
88
88
88
88
88
(67-0407)
88
(67-0408)
(67-0409)
(67-0410)
(67-0414)
(67-8128)
(00-0000)
(00-0000)
(00-0000)
(00-0000)
88
88
88
88
88
88
88
88
88
(00-0000)
(00-0000)
(00-0000)
(67-0427)
88
88
88
88
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
FIGURES
Revision 6
List of Figures (Contd)
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
4
FIGURES
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
59.
60.
61.
62.
63.
64.
65.
66.
67.
68.
69.
Figure
Figure
Figure
Figure
70.
71.
72.
73.
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
74.
75.
76.
77.
78.
79.
80.
81.
Figure 82.
Figure 83.
Figure 84.
Figure 85.
Publication 5381-001
PAGE NO.
TRANS-2-Butene
CIS-2-Butene
TRANS-3-Hexene
CIS-3-Hexene
Carbon Chain Conjugation
1,3-Butadiene
1,3-Pentadience Carbon Skeleton
TRANS-1,3-Pentadiene
Hexatriene Carbon Skeleton
TRANS-1,3,5-Hexatriene
(A.) TRANS-2,4,6-Octatriene
(B.) CIS-2,4,6-Octatriene
Ethyne
Propyne
1-Butyne and 2-Butyne
(A.) 1-Hexyne
(B.) 2-Hexyne
(C.) 3-Hexyne
Cyclobutane
Cyclopentane
Cyclohexane
TRANS-1-Cyclopentene
TRANS-1,3-Cyclohexadiene
TRANS-1,3,5-Cyclohexatriene
The Hydroxy Unit
(A.) Methanol
(B.) Ethanol
(C.) N-Propanol
(D.) 1-Butanol
(A.) N-Propanol
(B.) 2-Propanol
(A.) 1-Butanol or Butyl Alcohol
(B.) 2-Butanol or Isobutyl Alcohol
Tert-Butyl Alcohol
(A.) Cyclobutanol
(67-0419)
(67-0420)
(67-0432)
(00-0000)
(00-0000)
(67-0452)
(00-0000)
(67-0453)
(00-0000)
(00-0000)
(00-0000)
(00-0000)
(67-0439)
(67-0440)
(00-0000)
(00-0000)
(00-0000)
(00-0000)
(67-0400)
(67-0401)
(67-0402)
(67-0457)
(67-0458)
(00-0000)
(67-8193)
(67-0350)
(67-0351)
(67-0352)
(67-0354)
(67-0353)
(67-0353)
(67-0354)
(00-0000)
(00-0000)
(00-0000)
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
List of Figures (Contd)
5
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
PAGE NO.
(B.) Cyclopentanol
1,2-Propanediol
1,2, 3-Propanetriol (Glycerine)
Aldehyde Family Empirical Formula
(A.) Methanal
(B.) Ethanal
(00-0000)
(00-0000)
(00-0000)
(00-0000)
(67-0331)
(67-0332)
88
88
88
88
88
88
(C.) Propanal
90. Ketone Family Empirical Formula
91. Propanone
92. Butanone
93. Methyl
Propyl “R” Groups For 2-Pentanone
94. 2-Pentanone
95. Ethyl “R” Group
96. 3-Pentanone
97. Carboxyl (Carboxylate) Functional Group
98. Alternataive Forms of the
Carboxyl Functional Group
99. Empirical Formula For Carboxylic Acids
100. Formic Acid
101. Ethanoic (Acetic) Acid
102. N-Propanoic (Propionic) Acid
103. “R” Group Carbon Skeleton of
(A.) N-Butanoic
(B.) N-Pentanoic
(C.) N-Decanoic Acid
104. (A.) N-Butanoic Acid
(B.) N-Pentanoic Acid
(67-0333)
(00-0000)
(67-0340)
(67-0341)
(67-8128)
(00-0000)
(67-0343)
(00-0000)
(67-0343)
(67-8144)
(00-0000)
88
88
88
88
88
88
88
88
88
88
88
(00-0000)
(67-0200)
(67-0201)
(67-0202)
88
88
88
88
(67-0203)
(67-0204)
(67-0039)
(67-0203)
(67-0204)
88
88
88
88
88
(67-0039)
88
(67-0040)
(67-0041)
(67-0042)
(67-0043)
(67-0044)
88
88
88
88
88
86.
87.
88.
89.
(C.) N-Decanoic Acid
Figure 105. “R” Group Carbon Skeleton of
(A.) N-Docecanoic
(B.) N-Tetradecanoic
(C.) N-Hexadecanoic
(D.) N-Octadecanoic
(E.) N-Eicosanoic Acid
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
FIGURES
Revision 6
List of Figures (Contd)
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
6
Publication 5381-001
FIGURES
Figure 106. (A.) N-Dodecanoic Acid
(B.) N-Tetradecanoic Acid
(C.) N-Hexadecanoic Acid
(D.) N-Octadecanoic Acid
(E.) N-Eicosanoic Acid
Figure 107. 9-CIS-Hexadecenoic (Palmitoleic Acid)
Carbon Skeleton
Figure 108. Hydrogenated (i.e. “hydrogen added”)
9-CIS-Hexadecenoic (Palmitoleic) Acid
Carbon Skeleton
Figure 109. Condensed Formula For
9-CIS-Hexadecenoic (Palmitoleic) Acid
Carbon Skeleton
Figure 110. 9-CIS-Hexadecenoic (Palmitoleic) Acid
Figure 111. Carbon Atom Skeletons For Five and Seven
Carbon Atom Alkane Units With Hydrogen
Figure 112. Condensed Structural Formula
For 9-CIS-Octadecenoic (Oleic) Acid
Carbon Skeleton
Figure 113. 9-CIS-Octadecenoic (Oleic Acid)
Figure 114. 9, 12-CIS, CIS-Octadecedienoic (Linoleic) Acid
Carbon Skeleton
Figure 115. Hydrogenated Condensed Carbon Skeleton of
9, 12-CIS, CIS-Octadecedienoic (Linoleic) Acid
Figure 116. 9, 12-CIS, CIS-Octadecedienoic (Linoleic) Acid
Figure 117. Condensed, Hydrogenated Carbon Skeleton of
6, 9, 12-CIS, CIS, CIS-Octadecetrienoic
(Linolenic) Acid
Figure 118. 6, 9, 12-CIS, CIS, CIS-Octadecetrienoic
(Lenolenic) Acid
Figure 119. Condensed Hydrogenated Carbon Skeleton of
5, 8, 11, 14-CIS, CIS, CIS, CIS-Eicosatetraenoic
(Arachidonic) Acid
Figure 120. 5, 8, 11, 14-CIS, CIS, CIS, CIS-Eicosatetraenoic
(Arachidonic) Acid
Figure 121. L-Amino Acid Backbone
Figure 122. Diagram of Glycine
Figure 123. Glycine
Figure 124. Diagram of L-Alanine
PAGE NO.
(67-0040)
(67-0041)
(67-0042)
(67-0043)
(67-0044)
(67-0045)
88
88
88
88
88
88
(67-0045)
88
(67-0045)
88
(67-0045)
(67-6692)
88
88
(67-0046)
88
(67-0046)
(67-0047)
88
88
(67-0047)
88
(67-0047)
(67-0048)
88
88
(67-0048)
88
(67-0049)
88
(67-0049)
88
(00-0000)
(67-3772)
(67-3772)
(67-3707)
88
88
88
88
List of Figures (Contd)
7
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
125. L-Alanine
126. Diagram of L-Valine
127. L-Valine
128. Diagram of L-Leucine
129. L-Leucine
130. Diagram of L-Isoleucine
131. L-Isoleucine
132. (A.) L-Seryl
(B.) L-Threonyl
133. L-Serine
134. L-Threonine
135. (A.) L-Phenylalanyl
(B.) L-Tyrosyl
(C.) L-Tryptophanyl
136. L-Phenylalanine
137. L-Tyrosine
138. L-Tryptophanyl
139. L-Tryptophan
140. (A.) L-Cystinyl
(B.) L-Cystine (Diagram)
141. L-Cystine (Structure)
142. L-Cysteine Formation
143. (A.) L-Cysteinly
(B.) L-Cysteine
144. L-Methionyl
145. (A.) L-Methionyl
(B.) L-Methionine
146. The Pyrolidine-2-Carboxylic Acid Ring
System For IMINO ACIDS
147. L-Proline
Insertion into Amino Acid Chain
148. Parts Arrangement For
(A.) L-Prolyl
(B.) L-Proline
149. L-Proline
PAGE NO.
(67-3707)
(67-3897)
(67-3897)
(67-3806)
(67-3806)
(67-3798)
(67-3798)
(67-3856)
(67-3864)
(67-3855)
(67-3863)
(67-3831)
(67-3890)
(67-8102)
(67-3830)
(67-3889)
(67-8102)
(67-3871)
(00-0000)
(00-0000)
(00-0000)
(67-3749)
(67-3750)
(67-3749)
(67-3823)
(67-3823)
(67-3822)
(00-0000)
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
(67-3848)
88
(67-8094)
(67-3848)
(67-3848)
88
88
88
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
FIGURES
Revision 6
List of Figures (Contd)
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
8
Publication 5381-001
FIGURES
PAGE NO.
Figure 150. (A.) 3-Hydroxyproline
(B.) 4-Hydroxyproline
Figure 151. (A.) L-Aspartyl
(B.) L-Aspartic Acid
Figure 152. Parts Arrangement For
(A.) L-Aspartyl
(B.) L-Aspartic Acid
Figure 153. (A.) L-Glutamyl
(B.) L-Glutamic Acid
Figure 154. (A.) L-Asparaginyl
(B.) L-Asparagine
Figure 155. L-Asparagine
Figure 156. (A.) L-Glutaminly
(B.) L-Glutamine
Figure 157. L-Glutamine
Figure 158. (A.) L-Histidyl
(B.) L-Histidine
Figure 159. Arrangement of Parts For L-Histidine
Figure 160. (A.) L-Arginyl
(B.) L-Arginine
Figure 161. Arrangement of Parts For L-Arginine
Figure 162. L-Arginine
(00-0000)
(00-0000)
(67-3724)
(67-3723)
88
88
88
88
(67-3724)
(67-3723)
(67-3757)
(67-3756)
(67-3732)
(67-3731)
(67-3731)
(67-3765)
(67-3764)
(67-3764)
(67-8086)
(67-3870)
(67-8089)
(67-3716)
(67-3715)
(67-3715)
(67-3715)
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
Figure 163. (A.) L-Lysyl
(B.) L-Lysine
Figure 164. Arrangement of Parts For L-Lysine
(67-3815)
(67-3814)
(67-3814)
88
88
88
Figure 165. L-Lysine
(00-0000)
88
Figure 166. 5-Hydroxylysine
(00-0000)
88
Figure 167. B-Alanine
(00-0000)
88
Figure 168. L-Ornithine
(00-0000)
88
Figure 169. L-Thyronine
(00-0000)
88
Figure 170. (A.) 3, 5, 3'-Triiodothyronine
(B.) 3, 5, 3', 5'-Tetraiodothyronine
(67-0150)
(00-0000)
88
88
Figure 171. (A.) Pentapeptide Chain Unit
(B.) Decapeptide H-Bonding Unit
(67-8011)
(67-8045)
88
88
List of Figures (Contd)
9
PAGE NO.
Figure 172. Finished Structures for
(A.) Pentapeptide Chain Unit
(67-8011)
(B.) Decapeptide H-Bonding Unit
(67-8045)
Figure 173. Repeating Unit For
(A.) Pentapeptide Chain Unit
(67-8011)
(B.) Decapeptide H-Bonding Unit
(67-8045)
Figure 174. Pentapeptide Alanyl- Glycyl- Tryptophanyl- Arginyl- Histidyl
Figure 175. Diagrammatic Representations of
(A.) D-Amino Acid
(00-0000)
(B.) L-Amino Acid Configurations
(00-0000)
Figure 176. The Purine Ring System
(67-8262)
Figure 177. The Purine Ring System
(67-8262)
Figure 178. (A.) Adenine
(67-8202)
(B.) Guanine
(67-8203)
(C.) Hypoxanthine
(67-8204)
Figure 179. (A.) Adenine
(67-8202)
(B.) Guanine
(67-8203)
(C.) Hypoxanthine
(67-8204)
Figure 180. (A.) Adenosine
(67-8214)
(B.) Guanosine
(67-8215)
(C.) Inosine
(67-8216)
Figure 181. (A.) Adenosine
(67-8214)
(B.) Guanosine
(67-8215)
(C.) Inosine
(67-8216)
Figure 182. (A.) Adenosine-5'-Monophosphate
(67-8207)
(B.) Guanosine-5'-Monophosphate
(6708210)
(C.) Inosine-5'-Monophosphate
(67-8213)
Figure 183. (A.) Adenosine-5'-Monophosphate
(67-8207)
(B.) Guanosine-5'-Monophosphate
(67-8210)
(C.) Inosine-5'-Monophosphate
(67-8213)
Figure 184. (A.) Adenosine-5'-Diphosphate
(67-8206)
(B.) Guanosine-5'-Diphosphate
(67-8209)
(C.) Inosine-5'-Diphosphate
(67-8212)
Figure 184. (A.) Adenosine-5'-Diphosphate
(67-8206)
(B.) Guanosine-5'-Diphosphate
(67-8209)
(C.) Inosine-5'-Diphosphate
(67-8212)
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
FIGURES
Revision 6
List of Figures (Contd)
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
10
FIGURES
PAGE NO.
Figure 185. (A.) Adenosine-5'-Diphosphate
(B.) Guanosine-5'-Diphosphate
(C.) Inosine-5'-Diphosphate
Figure 186. (A.) Adenosine-5'-Triphosphate
(B.) Guanosine-5'-Triphosphate
(C.) Inosine-5'-Triphosphate
Figure 187. (A.) Adenosine-5'-Triphosphate
(B.) Guanosine-5'-Triphosphate
(C.) Inosine-5'-Triphosphate
Figure 188. (A.) Xanthine (2,6-Dioxypurine)
(B.) Caffeine (1,3,7-Trimethylxanthine)
(C.) 2,6,8-Trioxypurine
Figure 189. Pyrimidine Ring System
Figure 190. Pyrimidine Ring System
Figure 191. (A.) Thymine
(B.) Cytosine
(C.) Uracil
(D.) 5-Methylcytosine
(D.) 5-Hydroxymethylcytosine
Figure 192. (A.) Thymine
(B.) Cytosine
(C.) Uracil
Figure 193. (A.) Thymidine
(B.) Cytidine
(C.) Uridine
Figure 194. (A.) Thymidine
(B.) Cytidine
(C.) Uridine
Figure 195. (A.) Thymidine-5'-Monophosphate
(B.) Cytidine-5'-Monophosphate
(C.)
Figure 196. (A.)
(B.)
(C.)
Publication 5381-001
Uridine-5'-Monophosphate
Thymidine-5'-Diphosphate
Cytidine-5'-Diphosphate
Uridine-5'-Diphosphate
(67-8206)
(67-8209)
(67-8212)
(67-8205)
(67-8208)
(67-8211)
(67-8205)
(67-8208)
(67-8211)
(00-0000)
(00-0000)
(00-0000)
(67-8263)
(67-8263)
(67-8220)
(67-8221)
(67-8222)
(67-8239)
(67-8240)
(67-8220)
(67-8221)
(67-8222)
(67-8232)
(67-8233)
(67-8234)
(67-8232)
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
88
(67-8233)
88
(67-8234)
(67-8225)
88
88
(67-8228)
88
(67-8231)
(67-8224)
(67-8200)
(67-8230)
88
88
88
88
List of Figures (Contd)
11
Figure 197. (A.)
(B.)
(C.)
Figure 198. (A.)
(B.)
(C.)
Figure 199. (A.)
(B.)
(C.)
Figure 200. (A.)
(B.)
(C.)
Figure 201. (A.)
PAGE NO.
Thymidine-5'-Triphosphate
Cytidine-5'-Triphosphate
Uridine-5'-Triphosphate
Thymidine-5'-Monophosphate
Cytidine-5'-Monophosphate
Uridine-5'-Monophosphate
Thymidine-5'-Diphosphate
Cytidine-5'-Diphosphate
Uridine-5'-Diphosphate
Thymidine-5'-Triphosphate
Cytidine-5'-Triphosphate
Uridine-5'-Triphosphate
Adenine-Thymine Base Pair
(B.) Guanine-Cytosine Base
Figure 202. (A.) Adenine-Thymine Base
(B.) Guanine-Cytosine Base
Figure 203. 2-Deoxy-D-Ribosephosphate
Pair
Pair
Pair
Chain Unit
(67-8223)
(67-8226)
(67-8229)
(67-8225)
(67-8228)
(67-8231)
(67-8224)
(67-8200)
(67-8230)
(67-8223)
(67-8226)
(67-8229)
(67-8318)
88
88
88
88
88
88
88
88
88
88
88
88
88
(67-8326)
(67-8318)
(67-8326)
(67-8300)
88
88
88
88
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
FIGURES
Revision 6
Specifications
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
12
Specifications
Accuracy
+/- 0 degrees 30’, covalent radii +/- 0.01 A (Angstrom), van der Waals radii +/- 0.03 A, with
respect to the nominal values chosen for each specie. These are as they occur in most biomolecular structures, and these data agree generally with those published by Corey and
Pauling.
Density
< 1.0 for assembled molecules. Models weigh about 1/3 as much as the original CoreyPauling models. For maximum strength with minimal weight, the atoms ar hollow. With the
exception of the Hydrogen atom (67-6692), they are injection-molded Implex, a hard and
durable modified acrylic polyester. Hydrogen (67-6692) has an elastically compressible polyethylene shell.
Scale
1.25 cm/A (slightly < 2% smaller than the 1/2”/A of the Corey-Pauling models). This scale
is large enough to maintain high accuracy, yet sufficiently small so that macromolecules are
not unwieldly. For example, a model 20 x 40 x 100 A (25 x 50 x 125 cm) can be built on a
table top.
Finish (surface)
All molds are vapor-honed to provide a dull surface finish on the models. Furthermore, atom
surfaces are satin-finished so that they can be lighted easily for vivid photography to illustrate journal articles. Thus, they may be photographed without distracting highlight.
Excellent color pictures have been taken with a variety of readily available color film types.
All components are color-coded according to the IUPAC (International Union of Pure and
Applied Chemistry) Nomenclature.
Color
Atoms and connectors are easily identified since each component is color coded. The color
cannot be worn away since it is an integral part of the plastic.
Publication 5381-001
Background
13
The National Institutes of Health (NIH), Washington, D.C., formed an Atomic Models Subcommittee
of the Biophysics and Biophysical Chemistry Study Section which coordinated the work of more
than 40 scientists from more than two dozen research centers in the development of these improved
versions of the Corey-Pauling Models They were originally designed at the California Institute of
Technology in the late 1940’s with the new connectors by Dr. Walter Koltun...hence, the name CPK*
Atomic Models.
The United States National Science Foundation (USNSF) provided financial support for the
American Society of Biological Chemists to put the models into manufacture. The American Society
For Biochemistry and Molecular Biology selected Harvard Apparatus, Inc. to distribute the models
worldwide. CPK* is a registered trademark of Harvard Apparatus, Inc.
Inherent Strength
Limitations in the technology of graphic arts impose upon the scientist the practical necessity of
studying and communicating most of his/her ideas about the three-dimensional world of molecules
in words alone or in two-dimensional graphics.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
Background
The relative sizes of the constituent groups, constraints to free rotation, steric hinderance (crowding), interchangeability of groups, just to mention a few, cannot be entirely or adequately represented in this manner. Consequently, numerous systems of molecular models have been devised
and used for such studies.
Good models are by far the most effective way of making vivid to students and researchers the fact
that our three-dimensional world does extend to the molecular and atomic levels and that the planar representations frequently give misleading impressions much in the same manner a two-dimenional map would in studying terrain features.
Alternative methods for driving home these concepts are available in the forms of stereoscopic
drawings and three-dimensional photographs (xographs). These may be used as substanstially satisfactory substitutes for models for some purposes, although none really takes the place of the
model itself. Models are used principally for two purposes, that is, for teaching and research. The
development of moderm chemical concepts rests heavily upon a three-dimensional concept.
For example, the entire realm of stereochemistry would have no foundation were it not for the idea
that molecular structures project in three-dimensions. We would be hardpressed to explain such
things as mirror-image isomers, bond angles, enzyme specificity, chelation and the like were it not
for the simple idea that ours is a three-dimensional world, and right down to the atomic level.
Further, accurate representation of currently accepted atomic parameters such as bond distance and
van der Waals radius is especially crucial if the construction of hypothesized structures and conformations (i.e. three-dimensional shapes) is to lead to suggestions for future studies and further experiments.
However, measurements of bond length and bond angle of an atom in a particular configuration
vary somewhat not only from compound to compound, but also as the configuration occurs within a compound. Designers of model systems are, therefore, constrained by practical consideratons
to choose a singular value
Revision 6
Connectors
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
14
For example, the bond angles reported between adjacent atoms in the Pyridine Ring system (678255) range from 116 degrees 50’ to 123 degrees 53’. Dictates of simplicity and economy might well
lead to a choice of a uniform bond angle of 120 degrees. This, of course, is not an unreasonable
compromise, but, nonetheless, a compormise and one based upon practicality.
Once these compromise parameters are selected for the several atomic species within a system, the
units put into production, changes to correspond new data are costly and trivial revisions cannot
be tolerated.
Moreover, the experimental data to be reproduced by the model are only too fallible. The uncertainties inherent in data collection for any particular molecule are well known. They mirror both
the difficulties of sample preparation, problems of isomorphic replacement, product purity and the
like, and the errors of measurement which involve equipment, calibration, and operation, just to
mention a few limitations.
This write-up is concerned with the effective use of CPK* space filling Atomic Models. Preliminary
designs of these essentially improved versions of the well-known Corey-Pauling models were developed during 1960-62 under the auspices of the Biophysics and Biophysical Chemistry Study Section
of the NIH.
They were made available to the American Society of Biological Chemists which,with the support
of the NSF and under the guidance of an expert committee, made the important modifications
which were essential for their development, critical evaluation, and economical production.
Connectors
The marked superiority of the CPK* Atomic Models derives largely from Dr. Koltun’s connector
links. His analysis of the engineering problems involved led him to novel plastic materials in combination with new link configurations which satisfy four critical requirements simultaneously:
A. Hold atoms together with great tenacity. A force of 5-7 kg is required to separate them. This
force is readily furnished by the levering blade of the CPK* Construction Tool (67-7120).
B. Permit distortions of bond angles to vary up to +/- 8 degrees with negligible loss in bond
strength.
C. Develop sufficient rotational friction to assure that large, extended side chains, frequently
attached by a single bond, will remain indefinitely in proper steric orientation.
D. Allow bond distances to be shortened or lengthened. The connectors are made of Texin, a hard
rubber-like elastomer which is strong albeit resilient and flexible.
E. Enable bond distances to be incrementally shortened (by 0.05 A) or lengthened (by 0.08 A).
F.
Enable units to be cemented together permanently.
G. The concept of rotational potential can be simulated in bonds between, for example, tetrahedral carbons (Catalogue Number 67-6577).
H. HYDROGEN BOND May be simulated with -N-H—0- distance options ranging from 2.69-3.09
A in 0.20 A steps, yielding substantially rigid configurations over a wide range of bond angles.
Publication 5381-001
CPK Components
15
Natural
Provides Standard Bond Distance
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 2. Connector Link, Short (67-7013)
Blue
Shortens Bond Distances by 0.05 A
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
FIGURE 1. Connector Link, Standard (67-7005)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 3. Connector Link, Long (67-7021)
Red
Lengthens Bond Distances by 0.08 A
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
Figure 4. Connector Link, Locking (67-7039)
Grey
Provides Standard Bond Distance and Aligned Keys for Hindered
Rotation about a single Bond
Revision 6
CPK Components
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
16
FIGURE 5. Connector Link, Carbon (67-7047)
Black
Provides Standard Bond Distanceand Restricted Rotation of the
Tetrahedral Carbon (67-6577)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 6. Link (67-7211), For Metal Hook (67-7203) and
Hydrogen Bond Connector (67-6726)
CREATE
TRANS.
White
Standard Length, Keyed On One Side For H-Bond Hydrogen
Body To Accept Metal Hook (67-7203)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 7. Link with Hydrogen Bond Connector (67-7062)
Commonly referred to as Connector Link, Bayonet H-Bond
Replacement
White
Standard Length, keyed on one side with Barbed Extension on
same side for H-Bond Hydrogen Bond
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 8. Link, Nitrogen, Commonly referred to as an Amine
Cap (67-7112)
Blue
Special Connector for Amine Cap to Accommodate the
Hydrogen Bond Barb (67-7062). Or the Hook (67-7203) of 676726. Note that the Amine Cap (67-7112) is Mated to H-Bond
Connector Hook Type Hydrogen (67-6726). When the Hook (677203) is removed by means of a Screw (67-7187)
Publication 5381-001
CPK Components
17
Black
For Permanently Connecting Atoms At Standard Bond Distance
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 10. Socket (67-7088)
White
Standard, Slotted Female Socket to Be Mounted on Models
Fabricated By The User
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
FIGURE 9. Connector Link, Gluing (67-7054)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 11. H-Bond Spacer (67-7096)
White
For Use With the H-Bond Hook Type Connector (67-6726). One
Or More Of These Spacers Can Be Slipped Over the Hook Of the
67-6726 to Increase the Bond Distance By 0.2 A For Each Spacer
Used
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 12. Metal Atom Connector Link (67-7161)
White
Supplied With One Self-Tapping Screw For Use With Metal, All
Purpose (67-6999). Two Of These Connectors Are Supplied With
Each Metal All Purpose.
Revision 6
CPK Components
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
18
Publication 5381-001
FIGURE 13. Screw For Amine Cap (67-8187)
Silver
This Screw Is Used to Connect the Amine Cap (67-7112) to the
H-Bond Hook Type, Hydrogen (67-6726) When the Hook (677203) Is Removed
Notes on Particular CPK Components
19
Carbon Acetylenic Triple Bond (67-6593):
This component is used to construct Carbon triple bonds as
in acetylene (Ethyne/IUPAC) and its derivatives. It is
used with a Connector Link, Locking (67-7039) to demonstrate hindered rotation characteristic of a triple bond.
The covalent radius 0.60 A along the triple bond which is
marked with a “carbon triple bond.” The second socket is
notched to accept the Connector Link, Locking (67-7039) for
restricted rotation. The unit has a covalent radius of 0.70 A
along the single bond.
FIGURE 14. Carbon Acetylenic Triple Bond (67-6593)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
2. Carbon Amine (67-6536):
This component is used in the construction of peptide
bonds
and also serves as a general planar carbon (i.e.
“C=O”) for carbonyl group formation. It is used with a
Connector Link,
Locking (67-7039) to demonstrate hindered rotation characteristic of a double bond.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
1.
The covalent radius is stamped on each face of this unit: 0.72
A for the Nitrogen Amide (67-6791), 0.67 A to Oxygen
Double Bond (67-6890) or Oxygen Indented Double Bond
(67-6919), and 0.75 A to Carbon Tetrahedral (67-6577).
The bond angle between the Nitrogen Amide (67-6791) and
Carbon Tetrahedral (67-6577) is 115 degrees; 120 degrees
between Carbon Tetrahedral (67-6577) and Oxygen Double
Bond (67-6890) and Oxygen Indented Double Bond (676919); and 125 degrees between Nitrogen Amide (67-6791)
and Oxygen Double Bond (67-6890) and Oxygen Indented
Double Bond (67-6919).
FIGURE 15. Carbon Amine (67-6536)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
3. Carbon Aromatic-5 (67-6551):
This component is intended for use in unsaturated or aromatic 5-member ring structures such as the Imidazole Ring
System (67-8266), Pyrazole (67-8272), Purine (67-8262), and
Pyrrole (67-8261). This unit has a covalent radius of 0.68 A
to atoms within the ring and 0.72 A to atoms attached to the
ring.
The bond angle is 126 degrees within the ring and 126
degrees between single-bonded atoms attached to the ring
Revision 6
Notes on Particular Components
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
20
system and double-bonded ring members. The symbol “5” is
stamped on one inner face.
Partial double-bond sockets are notched to accept restricted
rotation connectors like the Connector Link Locking (677039). This unit is the same as the Nitrogen Aromatic-5 (676825) listed below except for the color.
FIGURE 16. Carbon Aromatic-5 (67-6551)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
4. Carbon Aromatic-6 (67-6569):
This unit is intended for used in unsaturated or aromatic 6member rings compounds such as Benzene Ring System (676850), Pyridine (67-8255), and Pyrimidine (67-8263).
The covalent radius within the ring system is 0.69 A and 0.73
A to singular atoms attached to or outside the ring system.
The symbol “6” is stamped on one inner face. This unit is the
same as the Nitrogen Aromatic-6 (67-6833) listed below
except for the color. Partial double bond sockets are notched
to accept restriced rotation connectors like the Connector
Link, Locking (67-7039).
FIGURE 17. Carbon Aromatic-6 (67-6569)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
5. Carbon Ethylenic Double Bond (67-6585):
This component is used to construct “C=C” or the planar carbon-to-carbon double bond structure as in ethylene
(Ethene/IUPAC) derivatives. This component should be used
with the Connector Link, Locking (67-7039).
This unit has a covalent radius of 0.67 A along the double
bond. This face is stamped with the symbol “C=”, and the
connector socket is notched to accept restricted rotation
connectors such as the Connector Link, Locking (67-7039).
The covalent radius is 0.73 A along the single bonds. The
bond angle is 125 degrees 15’ between the double and single bonds and 109 degrees 30’ between single bonds.
FIGURE 18. Carbon Ethylenic Double Bond (67-6585)
Publication 5381-001
Notes on Particular Components
21
Carbon Fused 5-6 Rings (67-6601):
This “fused” component is specifically designed to symbolize the aromatic carbon atoms common to joined 5- and 6membered aromatic rings such as Purine (67-8262) and
Indole (67-8291). The 120 degrees face bonds in the 6member ring, and the 108 degrees face bonds in the 5member ring. The unit is stamped with the symbol “5-6” for
ease of indentification.
FIGURE 19. Carbon Fused 5-6 Rings (67-6601)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
7. Carbon Fused 6-6 Rings (67-6619):
This “fused” component is designed to symbolize the aromatic carbon atoms common to two joined 6-membered
aromatic ring systems such as Anthracene (67-8252),
Phenanthrene (67-8253), and Naphthalene (67-8251). Also,
this unit is stamped with the symbol “6-6” to differentiate it
quickly from the Carbon Fused 5-6 (67-6601) unit above.
ºH a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
6.
FIGURE 20. Carbon Fused 6-6 Rings (67-6619)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
8. Carbon Fused 5-5 Rings (67-6600):
This “fused” component is a special double-atom unit representing the carbons common to two 5-member rings. The
108 degrees face bonds in the two 5-member rings of such
compounds as the pentalenes.
FIGURE 21. Carbon Fused 5-5 Rings (67-6600)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
9. Carbon Tetrahedral (67-6577):
This unit symbolizes the classical carbon tetrahedral component with four bond angles of 109 degrees 30’ each and
corresponding bond distances of 0.77 A. When these units
are bonded adjacently, you must use the Connector Link,
Carbon (67-7047, see Table 1) which gives a standard bond
distance and simulates restricted rotation.
FIGURE 22. Carbon Tetrahedral (67-6577)
Revision 6
Notes on Particular Components
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
22
10. Carbon Tetrahedral-4 (67-6528):
This component is used for constructing 4-membered rings
systems such as the Beta-Lactams and Cyclobutane (670400). The covalent radius is 0.77 A to atoms within the ring
system and 0.76 A to atoms attached to or outside the ring
system. Each face of the unit is marked with the appropriate
covalent radius, The intraring bond angle is 88 degrees.
FIGURE 23. Carbon Tetrahedarl-4 (67-6528)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
11. Carbon Trigonal-4 (67-6544):
This unit is used to assemble 4-member ring systems. The
Intraring covalent radii of 0.73 A is stamped on one face. A
permanent or integral connector is molded into the other
intraring surface and provides the same bond length as the
Connector Link, Standard (67-7005).
The external cyclic face is stamped with the covalent radius
of 0.65 A. The bond angle between two intraring bond axes
is 92 degrees. The bond angle is 134 degrees between the
intraring bond axis and the axis of the atom outside or connected to the ring.
FIGURE 24. Carbon Trigonal-4 (67-6544)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
12. Oxygen Single Bond (67-6874):
This unit is triple-slotted to accept the H-Bond Bayonet Type
(67-6684), Hydrogen (67-6692), and the H-Bond Hook Type
Hydrogen (67-6726) for hydrogen bonding.
The center slot extends +/- 48 degrees. The side slots extend
+/- 35 degrees at +/- 15 degrees displacement from the center line. The covalent radius is 0.66 A, and the bond angle is
110 degrees.
FIGURE 25. Oxygen Single Bond (67-6874)
Publication 5381-001
Notes on Particular Components
23
FIGURE 26. Oxygen Double Bond (67-6890)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
14. Oxygen Indented Double Bond (67-6916):
This unit has indented sides with radii of 1.15 A from centers that are laterally spaced. Three slots on the surface of the
unit are parallel to the longitudinal axis of the indentations
and accept H-Bond Bayonet Type (67-6684), Hydrogen (676692), and H-Bond Hook Type, Hydrogen (67-6726) for
hydrogen bonding.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
13. Oxygen Double Bond (67-6890):
This component also serves as a partially negatively-charged
(i.e. “delta” charge) Oxygen and has a covalent radius of
0.57 A.
All three slots extend +/- 48 degrees, and the side slots are
displaced +/- 15 degrees from the center line. The connector socket is notched to accept restricted rotation connectors
such as the Connector Link, Locking (67-7039). The covalent
radius is 0.57 A.
FIGURE 27. Oxygen Indented Double Bond (67-6916)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
15. Nitrogen Amide (67-6791):
This component is stamped on each face with the following
covalent radii: 0.60 A to the Carbon Amine (67-6536), 0.70 A
to the H-Bond Bayonet Type (67-6684) or H-Bond Hook
Type (67-6726) for hydrogen bonding, and 0.70 A to chain
carbon, be it Carbon Amine (67-6536) or Carbon Tetrahedral
(67-6577).
The bond angle between Carbon Amine (67-6536) and HBond Bayonet Type (67-6684) or H-Bond Hook Type (676726) is 123 degrees; 114 degrees between chain carbon
(Carbon Amine or Carbon Tetrahedral and the H-Bond
Hydrogen, Bayonet or Hook Type.
One face has the symbol “H” stamped on it to facilitate construction of transpeptide linkages such as would be found in
polymers as Collagen (67-7997), Pleated Sheets of Poly-LAlanine (67-7963), Poly-L-Alanine (67-8003), Poly-L-Serine
(67-8029), Poly-L-Valine (67-8037), and Poly-L-Phenylalanine
(67-8052)
Revision 6
Notes on Particular Components
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
24
This unit can also be used in the construction of general planar trigonal nitrogen and the the Amine Cap (67-7112) as in
azo nitrogen.
FIGURE 28. Nitrogen Amide (67-6791)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
16. N-Nitrile Triple Bond (67-6792):
This unit has a covalent radius os 0.60 A along the triple
bond for the formation of nitriles of “cyano” compounds.
The second socket is notched to accept restricted rotation
connectors such as the Connector Link, Locking (67-7039).
The covalent radius is 0.70 A along the single bond.
FIGURE 29. N-Nitrile Triple Bond (67-6792)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
17. Nitrogen Aromatic-5 (67-6825):
This component is used in 5-membered ring systems such as
Imidazole (67-8266) or in the 7 and 9 positions of Purine (678262). There is a covalent radius of 0.68 A to atoms within
the ring and 0.73 A to atoms outside or attached to the ring
sytem.
The bond angle is 108 degrees between atoms within the
ring and 126 degrees between single-bonded atoms outside
the ring and double-bonded ring atoms. The symbol “5” is
stamped on one inner face. The Amine Cap (67-7112) converts the Nitrogen Aromatic-5 (67-6825) to azo nitrogen. See
Amine Cap (67-7112) for additional nitrogen conversion
details.
FIGURE 30. Nitrogen Aromatic-5 (67-6825)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
18. Nitrogen Aromatic-6 (67-6833):
This unit is for use in 6-membered ring systems such as
Pyridine (67-8255) and Pyrimidine (67-8263). There is a
covalent radius of 0.69 A within the ring system and a covalent radius of 0.72 A to single atoms outside the ring.
The symbol “6” is stamped on one inner face. The Amine
Cap (67-7112) converts the Nitrogen Aromatic-6 (67-6833) to
a nitrogen. As with the Nitrogen Aromatic-5 (67-6825), see
Amine Cap (67-7112) for details of nitrogen conversion.
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FIGURE 31. Nitrogen Aromatic-6 (67-6833)
Notes on Particular Components
25
FIGURE 32. Nitrogen Tetrahedral (67-6841)
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20. Nitrogen Tetrahedral-4 (67-6858):
This component is used for constructing 4-membered ring
systems. It is identical to the Carbon Tetrahedral-4 (67-6528)
except for color. With the Amine Cap (67-7112), it is converted to a trivalent (triple-bonded) nitrogen atom for use in
Beta-Lactam rings structures as found in the antibiotic penicillin.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
19. Nitrogen Tetrahedral (67-6841):
This unit has connector sockets that are notched for simulation of restricted rotation. The covalent radius is 0.70 A, and
the bond angle is 109 degrees 30’. The Amine Cap (67-7112)
converts the Nitrogen Tetrahedral (67-6841) to an amine
nitrogen.
FIGURE 33. Nitrogen Tetrahedral-4 (67-6858)
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21. Nitrogen Trigonal-4 (67-6866):
This unit is used to assemble 4-membered ring systems such
as Beta-Lactams and is identical to Carbon Trigonal-4 (676544) except for color.
FIGURE 34. Nitrogen Trigonal-4 (67-6866)
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22. H-Bond Bayonet Type, Hydrogen (67-6684):
This component fits the slot atop the Amine Cap (67-7112),
the slots of the Oxygen Single Bond (67-6874), and the slots
of the Oxygen Indented Double Bond (67-6916). If the bayonet component breaks, reparation is a simple matter of
replacing the Connector Link, Bayonet H-Bond Replacement
(67-7062). See Table 1 above.
This unit has an indentation radius of 1.35 A about its center and 1.66 A from the spherical center of the hydrogen
atom. By using the upper sets of barbs on the shank, one
can lengthen hydrogen bonds by 0.20 or 0.40 A.
FIGURE 35. H-Bond Bayonet Type, Hydrogen (67-6684)
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26
23. H-Bond Hook Type, Hydrogen (67-6726):
This hook type hydrogen is designed to impart appreciable
structural strength to the hydrogen bonding system. This unit
has an indentation radius of 1.35 A about its center and 1.66
A from the spherical center of the hydrogen atom. See Table
1 above.
The Oxygen Single Bond (67-6874) and Oxygen Indented
Double Bond (67-6916) have strong ribs to accept the Metal
Hook (67-7203) of the H-Bond Hook Type, Hydrogen (676726).
When the Metal Hook (67-7203) is placed over the ribe of
either of these oxygen types, the Hydrogen Wrench (677138) then fits over the hexagon sided base (67-7195) of the
hydrogen body. The wrench is then turned clockwise until
the hook is brought ro rest securely against the oxygen
atom, thus completing the hydrogen bonding structure.
One or more H-Bond Spacers (67-7096) can be placed over
the hook to increase the bond distance by 0.20 A for each
spacer used. See Table 1 above.
FIGURE 36. H-Bond Hook Type, Hydrogen (676726)
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24. Hydrogen (67-6682):
This unit has a single bond and is a shell that is elastically
compressible. The connector link is incorporated.
FIGURE 37. Hydrogen (67-6692)
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25. Bromide (67-6510):
This component is single-bonded and has the symbol “Br”
stamped near the socket. The covalent radius is 1.14 A.
FIGURE 38. Bromide (67-6510)
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Notes on Particular Components
27
FIGURE 39. Chloride (67-6650)
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27. Fluoride (67-6676):
This unit is single-bonded, and the covalent radius is 0.57 A
along the single bond. The symbol “F” is stamped near the
socket.
FIGURE 40. Fluoride (67-6676)
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26. Chloride (67-6650):
This unit is single-bonded and has the symbol “Cl” stamped
near the socket. The covalent radius is 0.99 A.
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28. Iodide (67-6734):
The symbol “I” is stamped near the socket. The covalent
radius is 1.35 A along the single bond.
FIGURE 41. Iodide (67-6734)
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29. Sulfur, Digonal (67-6957):
This component has notches every 90 degrees in sockets.
The covalent radius is 1.04 A, and the bond angle is 104
degrees.
FIGURE 42. Sulfur, Digonal (67-6957)
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30. Sulfur, Tetrahedral:
This unit is represented by Phosphorus, Tetrahedral (676924) when it is used with the Connector Link, Long (677021). This combination results in a covalent radius of 1.04
A. The double-bonded face in this instance is not differentiated. Thus, to receive a Sulfur, Tetrahedral (67-6924), order
one Phosphorus, Tetrahedral (67-6924) and four Connector
Links, Long (67-7021).
FIGURE 43. Sulfur, Tetrahedral
Phosphorus Tetrahedral
(67-6924)/Same
as
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31. Phosphorus, Tetrahedral (67-6924):
The covalent radius is 0.96 A, and the bond angle is 109
degrees 30 min.
FIGURE 44. Phosphorus, Tetrahedral (67-6924)
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32. Metal, Ionic (67-6981):
This unit is used for ionic octahedral bonds, or it can be used
for planar configurations. The covalent radius is 1.32 A, and
the van der Waals radius is 1.46 A. The bond angle is 90
degrees.
FIGURE 45. Metal, Ionic (67-6981)
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33. Metal, Covalent (67-6973):
This unit is specifically for chelate-type compounds such as
Fe, Co, Ni, or Cu or for covalent octahedral bonds. The component can also be used for planar configurations or shapes.
The covalent radius is 1.32 A, the bond angle is 90 degrees,
and the van der Waals radius is 1.70 A.
FIGURE 46. Metal, Covalent (67-6973)
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29
The Metal, All Purpose (67-6999) has a special connector, Metal Atom Connector Link (67-7161, see Table 1 above)
which consists of a connector link one-half the length of a
normal link (Connector Link, Standard, 67-7005) with a selftapping screw. A 1/16 in. (1.6 mm) hole must be drilled in
the sphere in order to accommodate the self-tapping screw.
Two Metal Atom Connector Links (67-7161) are supplied
with each Metal Atom, All Purpose (67-6999).
FIGURE 47. Metal, All Purpose (67-6999)
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34. Metal, All Purpose (67-6999):
This unit is a sphere with a diameter corresponding to
a distance of 2.7 A. The lines of longitude and latitude are
raised at 30 degree intervals. There is also an indentation at
one of the poles of the sphere. With the aid of the lines of
longitude and latitude, you may orient the sphere in any
direction required by a particular situation.
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35. Amine Cap (67-7112):
This unit is hemispherical in contour with a hollow, blue
connector link inserted into the bottom or flat face with a
liner slot in the contoured cap. The slot in the top of the
Amine Cap (67-7112) accepts the bayonet portion of the HBond Bayonet Type, Hydrogen (67-6684) for temporary connections and the H-Bond Hook Type, Hydrogen (67-6726)
after the Hook (67-7203) has been removed and replaced
with a Screw For Amine Cap (67-7187) for more permanent
connections.
The Amine Cap (67-7112) is also used with the Nitrogen
Amide (67-6791), Nitrogen Aromatic-5 (67-6825), and the
Nitrogen Aromatic-6 (67-6833) to convert them to azo nitrogens; with the Nitrogen Tetrahedral (67-6841) to convert it to
an amino nitrogen; and with the Nitrogen Tetrahedral-4 (676858) to convert it to a trivalent nitrogen.
FIGURE 48. Amine Cap (67-7112)
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36. CPK* Construction Tool (67-7120):
This tool is used to assemble/disassemble the models. To
assemble, a connector link is placed in the well on the end
of the handle of this construction tool and then pressed
into the female socket of the atom. The second atom is
simple pressed onto the first with a slight twisting action,
and the bond is completed.
To separate the atoms or disassemble the molecule, place
the U-notched end of the lever blade between the atoms at
the point of the connector and simply pry them apart. The
connector link may be completely removed by slipping the
U-notch around the exposed, grooved portion of the connector and prying it from the female socket of the atom.
FIGURE 49, CPK* Construction Tool (67-7120)
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37. Hydrogen Wrench (67-7138):
This wrench is used with the H-Bond Hook Type,
Hydrogen (67-6726) to secure the Hook (67-7203) connec
tion between the Base (67-7195) of 67-6726 and Oxygen
Indented Double Bond (67-6916) or Oxygen Single Bond
(67-6874).
When the Hook (67-7203) of 67-6726 is placed in the slot of
either 67-6916 or 67-6874,, the wrench fits over the eightsided face of the Base (67-7195), and the Base is turned until
the hook is brought to rest securely against the oxygen atom
component.
FIGURE 50. Hydrogen Wrench (67-7138)
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38. Calipers With Angstrom Unit Scale 67-7146):
This unit is calibrated at 1.25 cm/A, which is the scale of the
CPK* models. It offers a convenient mode of direct measurement of CPK* in unit of Angstroms (A). The range is 030 A, graduated in 0.1 A units with each one numbered for
convenient reference.
The sturdy bar is engraved with blackened graduations upon
a white background. Accurate, reproducible measurement is
obtained by two spring-loaded cursors with long transparent, plastic jaws. One cursor is reversible to make internal
and external measurements. The overall length of the
Caliper is 25 in. (64 cm).
FIGURE 51. Calipers With Angstrom Unit Scale For CPK*
Models (67-7146)
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1.
LINEAR ALKANES:
Let’s begin our assembly with the simplest of organic molecules, (A.) Methane (67-0407), symbolic of the alkane family, with the formula C(n) H(2n+2) and the presence solely of “C-C” single bonds. Select one Tetrahedral Carbon (67-6577) and four Hydrogens (67-6692) as components.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
ASSEMBLING CPK* ATOMIC MODELS:
The assembly of CPK* Atomic Models is a very simple matter involving for the most part the use
of the CPK* Construction Tool (67-7120) and the appropriate pieces. Recall that the construction
tool has dual uses, assembly and disassembly, depending upon the end of the tool chosen. The Unotched end of the lever blade is used to separate pieces or disassembly, and the well at the end
of the black handle is used to press connectors into the sockets of the individual plastic pieces for
assembly.
AA
Notice that each of the hydrogen atoms has its own connector incorporated and that the tetrahedreal carbon has four equivalent sockets. Now, without the use of the construction tool, simply press one hydrogen atom into each of the tetrahedral carbon sockets using your thumb and
forefinger. The finished product is shown at right:
FIGURE 52. (A.) Methane (67-0407).
Next, let’s make Ethane (67-0408). For this structure, select for the components two of the tetrahedral carbons, six of the hydrogens, and one Connector Link, Carbon (67-7047) for restricted
rotation about a C-C single bond. First, using the construction tool well, press the connector
link into a socket on one of the tetrahedral carbons as shown above:
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Now, take the other tetrahedral carbon and press it onto the other end of the connector link.
Finish up simply by filling all vacant sockets on the two coupled tetrahedral carbons with a
hydrogen atom. The finished product will appear like the structure above:
FIGURE 53. (B.) Ethane (67-0408).
Building N-Propane (67-0409) is simply a matter of continuing the growth of the alkane chain.
The “N” prefix of N-Propane signifies “Normal” or unbranched and straight-chain. Now, connect three tetrahedral carbons in a line, joining each with a Connector Link, Carbon (67-7047)
and filling each vacant carbon socket with a hydrogen atom until you have the structure shown
in FIGURE 53. N-Propane (67-0409).
FIGURE 54. (C.) N-Propane (67-0409)
Next, try your hand at more complex alkane structure, such as N-Butane (67-0410), N-Octane
(67-0414), etc. Take care as the alkane chain grows to alternate or stagger adjacent hydrogen
atoms. See FIGURE 55.
FIGURE 55. (D.) N-Butane (67-0410) & (E.) N-Octane (67-0414)
Note that you can assemble the radical version of each of these alkanes simply by
leaving off a terminal (i.e. “N-” position)
hydrogen atom and in its place inserting a
connector link. For example, you can
assemble the Methyl (67-8128), Ethyl, NPropyl, N-Butyl, and N-Octyl radicals as
pictured in FIGURE 56.
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FIGURE 56. (A) Methyl (67-8128), (B)
Ethyl, (C) N-Propyl, (D) N-Butyl, and (E) NOctyl Radicals.
You can construct simple isomers especially with the radicals by selecting different points along
the carbon chain to remove a hydrogen atom and inserting a connector link. For example, the
Propyl radical can be N-Propyl if a terminal hydrogen is missing or Iso-propyl (2-Propyl) is one
of the two middle hydrogens is missing.
In like maner, the Butyl radical can be NButyl if a terminal hydrogen is missing or
Isobutyl (2-Butyl) if one of the number two
hydrogens is missing. You can also have
Tert-butyl (i.e. Tertiary Butyl) isomer, but
we are getting a little ahead of ourselves.
Octyl can have several radical isomers such
as N-Octyl, 2-Octyl, 3-Octyl, or 4-Octyl.
FIGURE 57. Isomers of (A.) N-Propyl-, (B.)
N-Butyl, and (C.) N-Octyl-Radicals.
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LINEAR ALKENES (DIENES AND TRIENES):
Now, let’s move on the the alkene structures, the simplest of which is ethylene or Ethene (670426). Recall that these structures are characterized by the presence of one double bond and
have the formula C(n)H(2n). Alkenes with two carbon-to-carbon double bonds (i.e. “C=C”) are
known as “Dienes” and those with three are “Trienes.”
However, for now, we will concern ourselves solely with simple alkenes with but one double
bond. Select for Ethene(67-0426) two of the Carbon Ethylenic Double Bond (67-6585) atoms,
one Connector Link, Locking (67-7039), and four Hydrogen atoms (67-6692).
First, using the well end of the construction tool handle, press the gray Connector Link, Locking
(67-7039) into the face of the Ethylenic Double Bond (67-6585) atom marked “C=”. Next, presss
onto the open end of the connector the other carbon atom at its corresponding face marked
“C=”.
Now, you have a “C=C” complex with four open valence sockets available for hydrogen atom
insertion. The gray connector link simulates a double bond and the accompanying hindered
rotation. The next step is to insert all four hydrogens into the open sockets. Notice that the
Ethene (67-0426) is planar as it should be.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
2.
The next structure in the alkene family is propylene or Propene (67-0427) which consists of
two Ethylenic Double Bond (67-6585) atoms, one Carbon Tetrahedral (67-6577) atom, one
Connector Link, Locking (67-7039), one Connector Link, Carbon (67-7047), and six Hydrogen
(67-6692) atoms.
BB
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As before, using the construction tool, join the two Carbon Ethylenic Double Bond (67-6585)
atoms with the gray Connector Link, Locking (67-7039) along their respective “C=” faces. Next,
connect the Carbon Tetrahedral (67-6577) atom to any one of the four vacant sockets of the
“C=C” complex and follow up by connecting the six hydrogens. The Propene (67-0427) should
appear as in FIGURE 58. Propene (67-0427).
FIGURE 58. Propene (67-0427)
Next, let’s build the butene molecule of which there are several isomers. For the components,
you will need two of the Carbon Ethylenic Double Bond (67-6585) atoms, two of the Carbon
Tetrahedral (67-6577) atoms, one Connector Link, Locking (67-7039), two Connector Link,
Carbon (67-7047), and eight Hydrogen (67-6692) atoms.
Recall how to build the “C=C” complex using the Construction Tool (67-7120) well to join the
two ethylenic double bond atoms along their respective faces marked “C” with the Connector
Link, Locking (67-7039).
Now, join the two tetrahedral carbon atoms with one of the Connector Link, Carbon (67-7047)
components, and with the other connector link, carbon join the two-tetrahedral carbon unit to
any one of the vacant sockets on the “C=C” complex. You now have the butene carbon skeleton.
Next, fill in the remaining vacant sockets with hydrogen atoms. You now have an isomer of
butene known as 1-Butene in which case the “C=C” complex appears at the end of the molecule. The numerical prefix “1” comes from IUPAC Nomenclature rules.
Simply stated, the rules call for using the least whole number to indicate the location
of the C=C beginning with the first carbon atom. That is, 1-Butene would not be called
4-Butene since 4 > 1. Again, the rule calls for using the least whole number.
The more stable form of the isomer is 2-Butene wherein the “C=C” appears in the middle of
the carbon chain. Again, according to IUPAC Nomenclaure, the numerical prefix indicates the location of the C=C using the number of the carbon atom first encountered
that contains the C=C using the least whole number possible.
An even more stable form of the isomer 2-Butene is Trans-2-Butene. In this case, hydrogen
atoms of the “C=C” are located on opposite sides of the C=C (i.e “TRANS”) as shown in FIGURE 59. TRANS-2-Butene. (67-0419).
FIGURE 59. TRANS-2-Butene (67-0419)
Should the “C=C” hydrogens appear on the same side of the molecular axis, the isomer
becomes less stable than the “TRANS” version and is known as CIS-2-Butene (67-0420) as pictured in FIGURE 60. CIS-2-Butene (67-0420).
FIGURE 60. CIS-2-Butene (67-0420)
Next, let’s try the hexene molecule for which you will need four Carbon Tetrahedral (67-6577)
atoms, two Carbon Ethylenic Double Bond (67-6585) atoms, 12 Hydrogen (67-6692) atoms,
four Connector Link, Carbon (67-7047) units, and one Connector Link, Locking (67-7039).
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FIGURE 61. TRANS-3-Hexene (67-0432)
Next, using the well end of the construction tool, join the carbon tetrahedral pieces into two
two-carbon units using the Connector Link, Carbon (67-7047) and, in turn, connect them to the
opposite ends of the “C=C” complex using the other two connector link, carbon components.
You now have a TRANS-3-Hexene carbon skeleton with the “C=C” in the center.
Now, fill in all vacant sockets with the 12
Hydrogen (67-6692) atoms making sure to
place the “C=C” complex hydrogens opposite one another (i.e. “TRANS”) so as to cut
across the carbon-chain axis. Were these
same two hydrogens to be placed adjacent
to one another, you would have the less
stable form of the isomer, CIS-3-Hexene as
shown in picture 62.
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H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
As before, use the Constructon Tool (67-7120) to construct the “C=C” complex with the two
carbon ethylenic double bond pieces and the gray Connector Link, Locking (67-7039). From
here, we will proceed to build the most stable isomeric form of hexene, TRANS-3-Hexene (670432) as pictured in FIGURE 61. TRANS-3-Hexene (67-0432).
FIGURE 62. CIS-3-Hexene
You can construct additional isomeric forms of hexene such as 1-Hexene, 2-Hexene, “TRANS”
and “CIS” forms?
Now, let’s take up alkenes of a somewhat more complex nature, the “dienes” and “trienes”, or
those consisting of two and three “C=C” complexes, respectively. The formula for a diene structure is C(n)H(2n-2), and triene is C(n)H(2n-4).
Also, as in the case of the LINEAR ALKENES, the initial recommendation is to construct the
“C=C” complex since all the structures of current concern revolve around this keystone configuration.
The simplest “diene” is 1,3-Butadiene (67-0452), but before we continue further, let’s review a
few fundamentals regarding alkenes in general. Recall as in the case of the LINEAR ALKENES
the tendency for the “C=C” structure to “seek” the middle of the molecule as it were.
This is in keeping with Thermodynamic Principles, that is, to “seek” the lowest possible energy state (i.e. entropy)or maximize stability. This is true of all alkene isomers. Now, in the case
of the dienes and trienes, there is a tendency for the “C=C” structures to conjugate themselves,
and this is the second rule of thumb to remember when building these structure. Conjugation
involves simply alternating the carbon-to-carbon double bond (C=C) with a carbon-to-carbon
single bond (C-C).
An additional rule of thumb to keep in mind is the CIS/TRANS configuration about the “C=C”
structure alluded to just prior to FIGURE 59. Recall that the TRANS configuration is more stable than the isomer CIS form. Keep these three principles in the forefront as we move on.
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In the case of Cyclic Dienes and Trienes there is no “middle of the molecule” per sae , but the
conjugation rule still applies.
This, too, lends itself to enhanced stability among a family of isomers. See FIGURE 63. Carbon
Chain Conjugation. Also, the CIS/TRANS rule applies to the dienes and trienes just as it did for
the LINEAR ALKENES.
C
C
C
C
C
C
FIGURE 63. Carbon Chain Conjugation.
Now, build 1,3-Butadiene. This will require four of the Ethylenic Double Bond (67-6585) units,
two Connector Link, Locking (67-7039) components, one Connector Link, Standard (67-7005),
and six Hydrogens (67-6692).
First of all, assemble the two “C=C” complexes. Recall that this involves joining two of the carbon ethylenic double bond units along their respective faces stamped with the “C=” symbol
with a gray connector link, locking. Again, use the well end of the construction tool to insert
the ends of the connector.
CC
For 1,3-Butadiene (67-0452) make up two of these “C=C” complexes. Now, using the connector link, standard, join these two complexes along their respective faces marked with the “0.73
A” symbol. You now have a 1,3-Butadiene carbon skeleton. Next, fill all vacant sockets with
hydrogens so that the structure looks like the one shown in FIGURE. 64.
FIGURE 64. 1,3-Butadine (67-0452).
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C
C
C
C
C
FIGURE 65. 1,3-Pentadience Carbon Skeleton.
Next, fill all vacant sockets with hydrogen atoms, such that the finished product will appear as
the structure in FIGURE 66. Check the conformation of the singular hydrogens on carbon atoms
no. 3 and 4 to assure they are in the TRANS configuration, the more stable of the two isomers.
IGURE 66. Trans-1,3-Pentadiene (67-0453)
You can construct higher order dienes, remembering the rule that carbon-to-carbon double
bonds (i.e. “C=C”) tend to seek the middle of the chain (assuming an even number of carbon
atoms in the chain) and conjugate themselves to “satisfy” stability demands..
Next, let’s build a triene, the simplest of which is 1,3,5-Hexatriene. First, construct three “C=C”
complexes. Remember, central tendency of “C=C” complexes, conjugation, and “TRANS” conformation. With these in mind, let’s begin.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
Next, build 1,3-Pentadiene (67-0453) which should have a carbron skeleton as shown in FIGURE 65.
Build three of the “C=C” groups using six Carbon Ethylenic Double Bond (67-6585) units, connecting the respective faces marked with the “C” symbol with a gray Connector Link, Locking
(67-7030) with the well end of the construction tool.
In turn, connect each of the complexes with each other with the Connector Links, Standard
(67-7005) along the faces marked with the “0.73A” symbol. You now have a 1,3,5-Hexatriene
carbon skeleton as shown below in FIGURE 67 Hexatriene Carbon Skeleton. Make sure that
the hydrogens on carbon atoms number 3 and 4 are going to be in the “TRANS” conformation.
C
C
C
C
C
C
FIGURE 67. Hexatriene Carbon Skeleton.
Note also that the “C=C” complexes are
conjugated. Now fill in all vacant sockets
with hydrogens until you have the structure shown in FIGURE 68. TRANS-1,3,5Hexatriene.
FIGURE 68. TRANS-1,3,5-Hexatriene.
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You can assemble the “TRANS” and “CIS”
isomer of octatriene, TRANS-2,4,6Octatriene and CIS-2,4,6-Octatriene and
shown in FIGURE 69.
FIGURE 69. (A.) TRANS-2,4,6-Octatriene
and (B.) CIS-2,4,6-Octatriene isomers.
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3. LINEAR ALKYNES:
These hydrocarbons are characterized by the presence of the carbon-to-carbon triple bond and
the formula C(n)H(2n-2), the simplest being Ethyne (67-0439) or simply acetylene. It is composed of two of the Acetylenic Triple Bond (67-6593) units, one Connector Link, Locking (677039), and two Hydrogen (67-6692) atoms.
Using the construction tool, insert one end of the connector link, locking into one of the
acetylenic triple bond pieces at the notched socket opposite the side marked with a triple-bond
symbol. Now, connect the other acetylenic triple bond unit by placing the vacant notched socket over the exposed end of the connector link, locking and pressing it until the connection is
complete.
DD
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FIGURE 70. Ethyne (67-0439)
Next, let’s examine Propyne (67-0440). Again, the keystone structure is the carbon-to-carbon
triple bond structure composed of two Carbon, Acetylenic Triple Bond (67-6593) pieces joined
along their respective notched sockets by means of a gray Connector Link, Locking (67-7039)
unit. To finish the structure, simple place a hydrogen atom in one of the vacant sockets and a
Methyl (67-8128) radical (see FIGURE 56) in the other vacant socket. The Propyne (67-0440)
structure is now complete.
FIGURE 71. Propyne (67-0440)
You can easily assemble isomers of Butyne such as 1-Butyne (67-0441) or 2-Butyne (67-0442).
Which isomer do you think is the more stable of the two (remember, the key is the location
along the carbon chain of the triple bond...the closer it gets to the center of the carbon chain,
the greater the stability)?
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You now have an acetylenic triple bond carbon skeleton. Next insert the two hydrogen atoms,
one into each of the vacant carbon sockets marked with the carbon-to-carbon triple bond symbol. You now have Ethyne (67-0439) as shown in FIGURE 70 Ethyne (67-0439).
FIGURE 72. (A.) 1-Butyne (67-0440) and (B.) 2-Butyne (67-0442)
Next, build the isomers of hexyne, that is 1-Hexyne (67-0445), 2-Hexyne (67-0446), and 3Hexyne (67-0447). Again, which is the most stable? least stable and why?
FIGURE 73. (A.) 1-Hexyne (67-0445), (B.) 2-Hexyne (67-0446), and (C.) 3-Hexyne (67-0447).
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4. CYCLIC ALKANES:
The simplest of the cyclic (i.e. circular) alkanes is Cyclobutane (67-0400) which consists of four
Carbon Tetrahedral-4 (67-6528) units, four of the Connector Link, Standard (67-7005) units, and
eight Hydrogen (67-6692) atoms.
Recall that the formula for the Linear Akene family was C(n)H(2n), and the same holds for the
Cyclic Alkanes. Note that with the Cyclic Alkanes you can use the less expensive Connector
Link, Standard (67-7005) as hindered rotation, something simulated with the Connector Link,
Carbon (67-7047), is inherent in the cyclic ring.
To build Cyclobutane (67-0400), use the construction tool to join the Carbon Tetrahedral-4 (676528) units along their respective faces stamped with the “0.77 A” with the four Connector Link,
Standard (67-7005) pieces. Make sure that carbon faces bearing the “0.76 A” symbol are located outside the ring.
Next, fill in the vacant carbon socket with the Hydrogen (67-6692) atoms. Note that the Carbon
Tetrahedral-4 (67-6528) was specifically designed to build 4-member rings structures. See
NOTES ON PARTICULAR COMPONENTS, Paragraph 10.
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EE
FIGURE 74. Cyclobutane (67-0400)
Now, we are ready to go to the higher order cyclic alkanes, that is, Cyclopentane (67-0401) and
above, which will require the use of Carbon Tetrahedral (67-6577) in lieu of Carbon
Tetrahedral-4 (67-6528).
This assembly will be a rather simple matter as all the faces of the Carbon Tetrahedral (67-6577)
are equal. Using the construction tool and the Connector Links Standard (67-7005), join the carbon tetrahedrals in a 5-membered ring and fill all vacant sockets with hydrogens. The finished
structure is Cyclopentane (67-0401).
FIGURE 75. Cyclopentane (67-0401)
Next, try Cyclohexane (67-0402). Again, join six Carbon Tetrahedarl (67-6577) units using the
construction tool and Connector Links Standard (67-7005). At this point observe that what you
have is a cyclohexane carbon skeleton. Now, fill in all carbon sockets with hydrogen, and the
finished product will look like the Cyclohexane (67-0402) structure in FIGURE 76. Cyclohexane
(67-0402).
FIGURE 76. Cyclohexane (67-0402)
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CYCLIC ALKENES AND DIENES:
Now we come to the cyclic versions of the alkenes, dienes, and trienes. See LINEAR ALKENES
(DIENES AND TRIENES). The formula for Cyclic Alkenes is C(n)H(2n-2), Cyclic Dienes is
C(n)H(2n-4), and Cyclic Trienes is C(n)H(2n-6).
We will begin with a simple cyclic alkene, say 1-Cyclopentene (67-0457,) for example. This
structure consists of two Carbon Ethylenic Double Bond (67-6585) units, three Carbon
Tetrahedrals (67-6577), one Connector Link, Locking (67-7039), four Connector Links, Standard
(67-7005), and eight Hydrogens (67-6692)
As before, the initial task is to construct the “C=C” complex as everything in the molecular structure revolves around this structure to include the nomenclature. Join two of the Carbon
Ethylenic Double Bond (67-6585) units along their respective faces marked with the “C=” symbol with the Connector Link , Locking (67-7039) using the Construction Tool (67-7120).
Next, joint the three Carbon Tetrahedrals (67-6577) with the Connector Links, Standard (677005) along any of their faces as they are all equivalent. Now, join the three-carbon tetrahedral
carbon unit with the “C=C” complex using the remaining two connector links, standard.
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5.
FF
You should now have a 5-member ring system (i.e. pentagon). Next, fill in the vacant carbon
atom sockets with hydrogen atoms and make sure that the two hydrogens attached to the
“C=C” are in the “TRANS” conformation. You now have TRANS-1-Cyclopentene (67-0457).
FIGURE 77. TRANS-1-Cyclopentene (67-0457)
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Next, let’s try the diene TRANS-1,3-Cyclohexadiene (67-0458) and follow up with TRANS-1,3,5Cyclohexatriene. Obviously, for the diene structure, you will need two “C=C” complexes.
In addition, you will need two Carbon Tetrahedrals (67-6577), two gray Connector Links,
Locking (67-7039), four Connector Links, Standard (67-7005), and finally eight Hydrogens (676692). Remember to construct each of the “C=C” complexes, join the carbon ethylenic double
bond units along their faces marked with the “C=” symbol with a gray connector link, locking.
Join the carbon tetrahedrals along any of their equivalent faces with the connector links, standard. Next join the two “C=C” complexes along their faces marked with the symbol, “0.73 A”
with a connector link, standard.
Now, join all carbon units into a 6.-member ring such that you now have a hexagon carbon
skeleton. Note, that the two “C=C” complexes are conjugated (i.e. separated by a “C-C”) and
that the hydrogens of the “C=C” will end up in the “TRANS” conformation.
Fill in all vacant sockets with hydrogen atoms so that the structure appears as the one pictured
in FIGURE 78. TRANS-1,3-Cyclohexadiene (67-0458).
FIGURE 78. TRANS-1,3-Cyclohexadiene (67-0458)
Next, let’s build a triene structure, say, for example, TRANS-1,3,5-Cyclohexatriene, a structure
just somewhat more complex than the previous diene version. In stead of two of the “C=C”
complexes, this time we will need three, all to be connected one to another by Conector Links,
Standard (67-7005).
Note on the hexagon carbon skeleton that
the “C-C” complexes are conjugated and
that the hydrogens to be attached to these
complexes will be in the “TRANS” conformation. Next, attatch hydrogen atoms to all
vacant sockets. The structure shown in
FIGURE 79 is TRANS-1,3,5-Hexatriene, a
component found in one of the Vitamin A
isomers, Retinal. See section on VITAMINS
AND ENZYME COFACTORS.
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FIGURE 79. TRANS-1,3,5-Cyclohexatriene
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6. ALCOHOLS, ALDEHYDES, AND KETONES:
This section groups together the Alcohols, Aldehydes, and Ketones since they are merely short
oxidation or reduction steps away from one another, so to speak, and, therefore, closely related.
The Alcohols are characterized by the presence of the “hydroxyl” or “hydroxy” group, -OH,
which consists one each of a Connector Link, Standard (67-7005), Hydrogen (67-6692), and
Oxygen Single Bond (67-6874) as shown in FIGURE 80. The Hydroxy Unit (67-8193).
FIGURE 80. The Hydroxy Unit (67-8193)
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For example, the alcohol derivative of
Methane (67-0407) would be Methyl
Alcohol or Methanol. The alchohol derivative of Ethane (67-0408) would be Ethyl
Alcohol or Ethanol. Propane (67-0409)
would be Propyl Alcohol or Propanol, and
Butane (67-0410) would be Butyl Alcohol
or Butanol.
Photo in
1981 Blue
Cataloge
Isomeric forms of the alcohols will be dealt with later. See FIGURE 81. Methanol (67-0350),
Ethanol (67-0351), Propanol (67-0352), and Butanol (67-0354).
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Alcohols are named simply by using the
alkane radical prefix followed by the word
“alcohol.” or by replacing the “e” ending of
the alkane name with the suffix”ol””
GG
FIGURE 81. (A.) Methanol (67-0350), (B.) Ethanol (67-0351), (C.) N-Propanol (67-0352), and
(D.) 1-Butanol (67-0354)
Alcohol isomers begin with the Propane derivative. You can have N-Propanol (67-0352) in
which case the -OH radical is attached at the end of the carbon skeleton or Isopropyl Alcohol
(67-0353) or 2-Propanol in which case the -OH is attached to the middle carbon atom of the
skeleton.
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IUPAC Nomenclature Rule for naming alcohols are much like those for Alkenes. That
is, use the least possible whole number prefix to indicate the location of the hydroxyl
group (-OH) along the carbon chain.
FIGURE 82. (A.) N-Propanol (67-0352) and (B.) 2-Propanol (67-0353)
Isomers of Butanol (67-0354) are somewhat more complex since not only can the hydroxyl
group be located on different carbon atoms but the carbon skeleton itself can be isomerically
configured as alluded to under ALKANES.
For example, with a linear carbon skeleton, you can have two isomeric alcohol forms of
Butane, one with the -OH group on the end of the carbon skeleton (1-Butanol or Butyl
Alcohol) and one with the -OH group on the number two carbon atom (2-Butanol or Isobutyl
Alcohol).
FIGURE 83. (A.) 1-Butanol or Butyl Alcohol(67-0354) and (B.) 2-Butanol or Isobutyl Alcohol
A third form of Butanol results from the isomerization of the carbon skeleton as shown in
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Fig.
Fig.
Fig.
84
85
86
87
FIGURE 84 to give the “Tertiary” or Tert-Butyl Alcohol (2-Hydroxymethylpropane) form of the
original parent structure, Butane (67-0410).
FIGURE 84. Tert-Butyl Alcohol
You can also build alcohols of cyclic alkanes such as Cyclobutanol and Cyclopentanol as shown
in FIGURE 85. A. Cyclobutanol and B. Cyclopentanol simply by building the cyclic alkane version and replacing one hydrogen atom with a hydroxy group (See CYCLIC ALKANES)
FIGURE 85. (A.) Cyclobutanol and (B.) Cyclopentanol
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Alcohols with two or three -OH groups, linear or cyclic, are named simply by adding the suf-
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FIGURE 86. 1,2-Propanediol.
An example of a “trihydroxy” alcohol is 1,2,3-Propanetriol or what is commonly referred to as
glycerine.
FIGURE 87. 1,2,3-Propanetriol (Glycerine)
Aldehydes are essentially oxidized alcohols characterized by the empirical formula :
H
R
C
O
FIGURE 88. Aldehyde Family Empirical Formula
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fix “diol” for two hydroxyl (“dihydroxy”) groups and “triol” for three hydroxyl groups. For
example, 1,2-Propanediol has two hydroxyl groups, one each on carbon atoms number one
and two respectively as shown in FIGURE 86. 1,2-Propanediol.
The “R” symbolizes a “Radical” group (i.e. Methyl, Ethyl, Propyl, etc.), “C=O” symbolizes the
carbonyl group, and “H” of course is Hydrogen (67-6692). The “C=O” group consists of one
each of Carbon Amine (67-6536), Oxygen Double Bond (67-6890), and Connector Link,
Locking (67-7039).
Notice that the “common denominator” for the aldehyde family is the carbonyl group with an
attached hydrogen (H-C=O) When assembling this complex, make sure that the Oxygen
Double Bond (67-6890) is attached to the Carbon Amine (67-6536) by means of a Connector
Link, Locking (67-7039) at the carbon amine socket marked “0.67 A”, hydrogen at the socket
marked 0.72 A, and the radical at the carbon amine socket marked 0.75 A.
IUPAC Nomenclature Rules for naming Aldehydes assumes that the Corbonly carbon is
carbon atom number one and that the other carbon atoms are numbered consecutively thereafter.
One names the aldehydes simply by removing the final “e” from the name of the parent alkane and adding the suffix “al”. For example, the simplest aldehyde is Methanal (67-0331)
(Methane - “e” + “al”) or Formaldehyde.
The aldehyde derivative of Ethane (67-0408) is Ethanal (67-0332) (Ethane - “e” +”al”) or
Acetaldehyde, and Propane (67-0409) is Propanal (67-0333) (Propane - “e” + “al”) or
Propionaldehyde.
FIGURE 89. (A.) Methanal (67-0331), (B.) Ethanal (67-0332), and (C.) Propanal (67-0333)
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II
Notice that the “R” group for Methanal is Methyl, Ethanal is Ethyl, and Propanal is Propyl. This
is most typical for the aldehyde family. In addition, you could have, from Butane (67-0410),
Butanal (67-0334) (Butane - “e” + “al”).
The ketones, like the aldehydes, contain the Carbonyl (“C=O”) complex, and it is flanked (i.e.
on each side), so to speak, by “R” groups or radicals. The “R” groups may be indentical or dissimilar.*
R
C
O
R
* May be identical or unique
FIGURE 90. Ketone Family Empirical Formula
Again, the Carbonyl complex is assembled simply by connecting the Carbon Amine (67-6536)
along the socket marked 0.67 A to the Oxygen Double Bond (67-6890) with a gray Connector
Link, Locking (67-7039).
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The ketones are named, like the aldehydes, from the parent alkane by dropping the final “e”
and adding the suffix “one” (pronounced either “on” or “own”). For example, the simplest of
the ketones is derived from the parent alkane N-Propane (67-0409) (Propane - “e” + “one”) to
give Propanone (67-0340), more commonly known as acetone or dimethylketone. Any of these
three names is appropriate. For this last term, you name the two “R” groups in ascending order
of complexity and add the word “ketone.”
FIGURE 91. Propanone (67-0340)
Plate 10
Ketones
(A)
N-Dodecanoic (Lauric) Acid
(67-0040)
(B)
N-Tetradecanoic (Myristic) Acid
(67-0041)
(C)
N-Hexadecanoic (Palmitic) Acid
(67-0042)
(D)
N-Octadecanoic (Stearic) Acid
(67-0043)
(E)
N-Eicosanoic (Arachidic) Acid
(67-0044)
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The remaining vacant sockets on the carbon amine are then filled with one each Connector
Link, Carbon (67-7047) in anticipation of receiving an “R” complex composed of chains of
Carbon Tetrahedral (67-6755).
JJ
The next ketone member is Butanone (67-0341) or what is commonly known as methylethylketone. Again, the parent alkane is N-Butane (67-0410). To name the ketone derivative, drop the
final “e” from the name “butane” leaving “butan-”. Add “one” to the root word “butan-” , and
the result is “butanone”.
FIGURE 92. Butanone (67-0341)
The next ketone is Pentanone and is the first to show isomerization, 2-, or 3-Pentanone. (670343) It is, however, usually found in the 3-Pentanone (67-0343) as this is the more stable form
(i.e. the Carbonyl functional group is located in the middle of the carbon chain as was the case
for the C=C complex for the alkenes).
As was the case for Alkenes and Alcohols, IUPAC Nomenclature Rules call for using the
least whole number prefix in the name of any kentone to indicate the location along
the carbon chain of the Carbonyl carbon (C=O).
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The ketone 2-Pentanone has the common name Methylproplyketone. Notice that the “R”
groups are named in the order of increasing (i.e. ascending) complexity. That is, in the name
“Methyethylketone”, the appropriate order of ascending complexity is “methyl” before “ethyl”,
and it would be inappropriate to use the name “Ethylmethylketone.”
The Methyl group (67-8128) is assembled by inserting a Connector Link, Carbon (67-7047) into
any one of the sockets of a Carbon Tetrahedral (67-6577) unit using the construction tool and
filling the remaining sockets with Hydrogen (67-6692) atoms.
The Propyl “R” group is assembled by joining three carbon tetrahedrals using connector link,
carbons along any of the equal sockets of the carbon atoms and then filling in the remaining
sockets with hydrogens. The two “R” groups are shown in FIGURE 93.
FIGURE 93. Methyl (67-8128) and Propyl “R” Groups for 2-Pentanone
Completion of 2-Pentanone assembly is simply a matter of inserting the two “R” groups one
each into the remaining vacant sockets of the carbon atom of the carbonyl complex. In this
instance, the propyl group goes into the socket marked “0.75A”, and the methyl into “0.72 A”.
2-Pentanone is shown in FIGURE 94.
FIGURE 94. 2- Pentanone
As alluded to, the more stable isomer is 3-Pentanone (67-0343). In this instance, the two “R”
groups are equivalent, ethyl units, each assembled with two Carbon Tetrahedrals (67-6577), two
Plate 11
Saturated Carboylic Acids
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fig. 95
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FIGURE 95. Ethyl “R” Group
To complete the assembly of 3-Pentanone (67-0343), merely join the two ethyl groups to the
amine carbon of the carbonyl group (C=O) without regard to socket markings.
FIGURE 96. 3-Pentanone (67-0343)
Next, assemble the isomers of Hexanone, the next member in the family of ketones.
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7. ORGANIC (CARBOXYLIC) ACIDS:
The Organic Acids are commonly referred to as “Carboxylic Acids” as they are characterized by
the Carboxyl (Carboxylate) functional group (67-8144) which is typically the most common
form (i.e. R-COO-, ionic) found in an aqueous environment at prevailing physiological pH conditions (i.e. 7.39-7.41).
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Connector Links, Carbon (67-7047) joining the carbons along any of their equivalent sockets,
and the remainder of the vacant carbon sockets occupied by hydrogens. A typical ethyl unit is
shown in FIGURE 95. Ethyl “R” Group.
The Carboxylate Unit (67-8144) consists of one each Carbon Amine (67-6536), Oxygen Double
Bond (67-6890), and Oxygen Indented Double Bond (67-6916).
The Oxygen Double Bond(67-6890) joins to the Carbon Amine (67-6536) along carbon atom
face marked “0.67A C=” and the Oxygen Indented Double Bond (67-6916) at the face marked
“0.72A”, each using a Connector Link, Locking (67-7039).
In turn, the Carboxylate Unit (67-8144) connects to the remainder or the molecular structure
using an additional Connector Link, Carbon (67-7047).
?
O
O
or
C
O
–
C
O
?
FIGURE 97. Carboxyl (Carboxylate) Functional Group (67-8144)
Alternatively, the carboxyl functional group, in general, may also be represented as shown in
FIGURE 98. (A ) and (B.)
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?
O
O
R
or
C
R
O
–
FIGURE 98
C
O
?
FIGURE 98. Alternative Forms of the Carboxyl Functional Group.
The empirical formula for Carboxylic Acids is shown in FIGURE 99.
FIGURE 98
FIGURE 99. Empirical Formula For Carboxylic Acids.
For the most part, Organic or Carboxylic Acids are Linear Alkanes or Alkenes with a terminal carboxylate functional group. The Linear Alkane “R” Group forms of Organic Acid are
referred to as “saturated” since all C-C bonds are single and maximum hydrogen is present (i.e.
saturated). Otherwise, the presence of carbon-to-carbon double and/or triple bonds indicates
an “unsaturated” condition.
When the alkane or alkene “R” group is extensive (i.e. a skeleton of, say, 12-24 carbon atoms),
the acids are referred to as “fatty acids”. For the time being, we will discuss only the Carboxylic
Acids whose “R” Group is of the Linear Alkane or Alkene variety.
As in the case of the alcohols, aldehydes, and ketones, the “R” groups stands for “Radical“ and
can be anything from a singular hydrogen atom to an extended linear alkane or alkene.
For now, we will discuss what are “mono-carboxylic” acids, or those bearing a singular “carboxyl” group. Later, we will address the structure of “di-carboxylic” and “tri-carboxylic” acids,
those with two and three “carboxylic” groups, respectively.
SATURATED CARBOYLIC ACIDS:
The simplest Carboxylic Acid is Formic Acid (67-0200), a compound synthesized by ants and
produces a painful, stinging sensation in man when “bitten”. The structure of Formic Acid (670200) is shown in FIGURE 100. Formic Acid (67-0200).
FIGURE 100
FIGURE 100. Formic Acid (67-0200)
Notice in Formic Acid (67-0200) the “R” group is a Hydrogen atom (67-6692). The IUPAC
equivalent for Formic Acid is Methanoic Acid, so named by taking the parent compound, Methane (67-0407), dropping the suffix “e” and adding “oic” + Acid. This pattern works the same for all Organic or Carboxylic Acids.
The next in the series of Organic Acids is Acetic or Ethanoic Acid (67-0201), again so named
by taking the parent compound, Ethane (67-0408), dropping the “e” suffix, and adding
in its place “oic” + Acid.
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FIGURE 101
FIGURE 101. Ethanoic (Acetic) Acid (67-0201)
Predictably, the next Organic Acid is N-Propanoic (Propionic) Acid (67-0202) in which case the
“R” group is N-Propyl (see page), a Linear Alkane consisting of three Carbon Tetrahedrals (676577), two Connector Link, Carbon (67-7047), and seven Hydrogen atoms (67-6692).
The vacant socket will be located at the very end of the N-Propyl structure to receive the
Carboxlyl Group (67-8144, see page). The structure for N-Propanoic (Propionic) Acid (67-0202)
is shown in FIGURE 102.
FIGURE 102
FIGURE 102. N-Propanoic (Propionic) Acid (67-0202)
Plate 12
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Acetic Acid (67-0201) is a common household liquid used as an antiseptic (1:30 dilution) and
cooking ingredient and known as “vinegar”. Note in FIGURE 101 that the “R” group is the
Methyl Group (67-8128), consisting of one each Carbon Tetrahedral (67-6577) and Connector
Link, Standard (67-7005) and three Hydrogen Atoms (67-6692).
Saturated Carboylic Acids
LL
(A)
N-Dodecanoic (Lauric) Acid
(67-0040)
(B)
N-Tetradecanoic (Myristic) Acid
(67-0041)
(C)
N-Hexadecanoic (Palmitic) Acid
(67-0042)
(D)
N-Octadecanoic (Stearic) Acid
(67-0043)
(E)
N-Eicosanoic (Arachidic) Acid
(67-0044)
Additional common Carboxylic Acids include N-Butanoic (67-0203), N-Pentanoic (67-0204), and
N-Decanoic (67-0039) Acid. These examples, too, have Linear Alkanes for their respective “R”
Groups as diagrammatically shown in FIGURE 103.
C
C
C
C
(A.) N-Butanoic (Butyric) Acid (67-0203) Carbon Skeleton
C
C
C
C
C
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(B.) N-Pentanoic (Valeric) Acid (67-0204) Carbon Skeleton
C
C
C
C
C
C
C
C
C
C
(C.) N-Decanoic (Capric) Acid (67-0039) Carbon Skeleton
FIGURE 103. “R” Group Carbon Skeleton of (A.) N-Butanoic (67-0203), (B.) N-Pentanoic (670204), and (C.) N-Decanoic (67-0039) Acid
Obviously, the parent compound for Butanoic Acid (67-0203) is N-Butane (67-0410), NPentanoic Acid (67-0204) is N-Pentane , and N-Decanoic Acid (67-0039) is N-Decane.
The IUPAC nomenclature follows the same pattern as before. Drop the final “e” from
the parent compound name and add the suffix “oic” + Acid. All the skeletons consist of
Carbon Tetrahedrals (67-6577) joined by Connector Links, Standard (67-7005), and all vacant
sockets save one on the terminal carbon filled with Hydrogen atoms (67-6692). To this final,
terminal vacant socket, add the Carboxyl unit or functional group (67-8144).
FIGURE 104. (A.) N-Butanoic Acid (67-0203), (B.) N-Pentanoic Acid (67-0204), and C.) NDecanoic Acid (67-0039)
We will now finish our discussion of Saturated Monocarboxylic Acids whose “R” Groups are
Linear Alkanes with Lauric, Myristic, Palmitic, Stearic, and Arachidic Acid. Their respective
IUPAC names are N-Dodecanoic (67-0040), N-Tetradecanoic (67-0041), N-Hexadecanoic (670042), N-Octadecanoic (67-0043), and N-Eicosanoic (67-0044) Acid.
Recall that those Carboxylic Acids with rather lengthy or extensive “R” groups, say approximately 12 carbon atoms or greater, are commonly known as “Fatty Acids.” The following five
Carboxylic Acids are prime examples of “Fatty Acids”.
In addition, being Linear Alkanes, their carbon skeletons consist of Carbon Tetrahedrals (676577) joined by Connector Links, Carbon (67-7047) and with all save the final vacant terminal
carbon socket (available for connection to the Carboxyl functional group) filled with Hydrogen
atoms (67-6692). Their respective carbon skeletons are depicted in FIGURE 104.
C
C
C
C
C
C
C
C
C
C
C
C
(A.) N-Dodecanoic (Lauric) Acid (67-0040) Carbon Skeleton
C
C
C
C
C
C
C
C
C
C
C
C
C
C
(B.) N-Tetradecanoic (Myristic) Acid (67-0041) Carbon Skeleton
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
(C.) N-Hexadecanoic (Palmitic) Acid (67-0042) Carbon Skelton
C
Publication 5381-001
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
(D.) N-Octadecanoic (Stearic) Acid (67-0043) Carbon Skeleton
C
Assembling CPK Atomic Models
53
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
C
C
(E.) N-Eicosanoic (Arachidic) Acid (67-0044) Carbon Skeleton
FIGURE 105.“R” Group Carbon Skeleton of (A.) N-Dodecanoic (67-0040), (B.) N-Tetradecanoic
(67-0041), (C.) N-Hexadecanoic (67-0042), (D.) N-Octadecanoic (67-0043), and (E.) NEicosanoic (67-0044) Acid.
The finished structures for the above Carboxylic Acids are shown in FIGURE 105.
FIGURE 106. (A.) N-Dodecanoic (Lauric) Acid (67-0040), (B.) N-Tetradecanoic (Myristic) Acid
(67-0041), (C.) N-Hexadecanoic (Palmitic) Acid (67-0042), (D.) N-Octadecanoic (Stearic) Acid
(67-0043), and (E.) N-Eicosanoic (Arachidic) Acid (67-0044)
UNSATURATED CARBOXLIC ACIDS:
Now, we are ready to focus our discussion upon Unsaturated Carboxylic Acids, or those with
FIGURE 106
(A)
N-Dodecanoic (Lauric) Acid
(67-0040)
(B)
N-Tetradecanoic (Myristic) Acid
(67-0041)
(C)
N-Hexadecanoic (Palmitic) Acid
(67-0042)
(D)
N-Octadecanoic (Stearic) Acid
(67-0043)
(E)
N-Eicosanoic (Arachidic) Acid
(67-0044)
“R” groups that are Linear Alkenes. As alluded to previously, these Carboxylic Acids are called
“unsaturated” because they do not have a maximum amount of Hydrogen atoms (67-6692) in
their structures. The examples cited will have one (“monoenoic”), two (“dienoic”), or three
(“trienoic”) carbon-to-carbon double bond (C=C) units.
Recall from the section on Alkenes that the C=C unit consists of two Ethylenic Double Bond
(67-6585) carbon atoms joined by a Connector Link, Locking (67-7039) to simulate hindered
rotation about a C=C double bond. Of course, the remainer of the carbon skeleton consists
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H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
Carbon Tetrahedrals (67-6577) joined by Connector Links, Carbon (67-7047).
As before, the vacant carbon atom sockets will all be filled with Hydrogen atoms (67-6692)
except the final terminal one which will accept the Carboxylate unit (67-8144). The Hydrogen
atoms attached to the C=C unit are in the CIS conformation if on the same side of the C=C as
opposed to the TRANS conformation, placing them diagonally across from one another.
Let’s begin our discussion of Unsaturated Fatty Acids with 9-CIS-Hexadecenoic (Palmitoleic)
Acid (67-0045), one with but a single C=C unit (i.e. a “monoenoic” acid). The carbon skeleton
is depicted in FIGURE 107.
16
12
C
C
C
14
C
9
C
C
C
10
6
C
C
C
2
C
C
8
C
C
C
*
4
*Location of the Carboxylate unit (67-8144)
FIGURE 107. 9-CIS-Hexadecenoic (Palmitoleic) Acid (67-0045) Carbon Skeleton.
Obviously, in the case of 9-CIS-Hexadecenoic (Palmitoleic) Acid (67-0045), the parent compound is Hexadecane where carbon atom number one is the Carboxylate carbon. Notice, too,
as in the case of Saturated Carboxylic Acids, that you drop the final “e” of the parent compound (i.e. Hexadcane) and add “oic” + “Acid.”
That is,
Hexadecane - final “e” + “oic” + Acid yields Hexadecanoic Acid.
FIGURE 107
One additional change in the parent compound name is in order here, that is, change the “a”
in “decanoic” to “e” to give “decenoic”.
That is,
Hexadecanoic Acid -”decanoic” + “decenoic” yields Hexadecenoic Acid
According to FIGURE 106, IUPAC Nomenclature rules call for numbering the carbon
atoms consecutively in the skeleton from right-to-left beginning with the Carboxylate
carbon which is understood to be carbon atom number one. Notice that the above carbon skeleton has 16 carbon atoms (Carboxylate carbon atom understood to be present in the
number one position as indicated by the asterisk).
Secondly, the location of the carbon-to-carbon double bond will be indicated in the
nomenclature by the number of the carbon atom in which the double bond initially
occurs, that is, carbon atom number nine.
That is,
Hexadecenoic Acid becomes 9-Hexadecenoic Acid
In addition, the Hydrogen atoms (67-6692) attached to the C=C unit are in the CIS conformation, and thus...
9-Hexadecenoic Acid becomes 9-CIS-Hexadecenoic Acid
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CH3
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
*
*Location of the Carboxylate Unit (67-8144)
FIGURE 108. Hydrogenated (i.e. “hydrogen added”) 9-CIS-Hexadecenoic (Palmitoleic) Acid (67004) Carbon Skeleton.
Notice in FIGURE 108 the frequent appearance of the Methylene (67-8110) group (-CH2) which
consists one each of a Carbon Tetrahedral (67-6577) and Connector Link, Carbon (67-7047),
and, finally, two Hydrogen atoms (67-6692).
Factoring (i.e. condensing) the above carbon skeleton gives the structure shown in FIGURE
109.
CH3
(CH2)5
CH
(CH2)7
CH
*
*Location of Carboxylate Unit (67-8144)
FIGURE 108
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
Adding Hydrogen atoms (67-6692) to the carbon skeleton gives us the structure in FIGURE 107.
FIGURE 109. Condensed Structural
Formula
For
9-CIS-Hexadecenoic
(Palmitoleic ) Acid (67-0045) Carbon
Skeleton.
The finished structure of 9-CISHexadecenoic (Palmitoleic) Acid (67-0045)
is shown in FIGURE 110.
FIGURE 110. 9-CIS-Hexadecenoic
(Palmitoleic) Acid (67-0045)
Assembling this Unsaturated Carboxylic
Acid follow several easy steps (consult
FIGURE 109 throughout). First, construct
two alkane chains consisting of five and seven Carbon Tetrahedrals (67-6577) respectively using
the CPK* Construction Tool (67-7120).
Fill all vacant sockets with Hydrogens (67-6692) leaving one unfilled at each end of each alkane chain. The carbon atoms are joined by Connector Links, Carbon (67-7047). When finished,
you should have the following:
*
*
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
FIGURE 109
FIGURE 110
*
CH2
*
*Location of One Each Vacant Carbon Atom Sockets
FIGURE 111. Carbon Atom Skeletons For Five and Seven Carbon Alkane Units With Hydrogens
(67-6692)
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Next, build one Methyl Unit (67-8128, see page ) consisting of one each Carbon Tetrahedral
(67-6577) and Connector Link, Carbon (67-7047) and three Hydrogen atoms (67-6692). FIGURE
109 above indicates that we will also need one each C=C and Carboxylate Unit (67-8144).
The C=C unit consists of two each Carbon Ethylenic Double Bond atoms (67-6585) joined by
one Connector Links, Locking (67-7039) along each face of the carbon atom marked with
“0.67A C=” symbol. One each of the empty sockets of the C=C should be filled with Hydrogen
atoms (67-6692) on the same side of the double bond, giving the CIS conformation.
Next comes the Carboxylate Unit (67-8144) consisting one each of a Carbon Amine (67-6536),
Oxygen Double Bond (67-6890), and Oxygen Indented Double Bond (67-6916). The oxygen
atoms should be joined to the Carbon Amine (67-6536) with Connector Links, Locking (677039) to simulate a double bond.
Recall (see para. 7 Organic (Carboxylic) Acids above) that one should use the following pattern to join the Carboxylate Unit (67-8144) components: join the Oxygen Double Bond (676890) to the Carbon Amine (67-6536) face marked “0.67A” and the Oxygen Indented Double
Bond (67-6916) to the Carbon Amine (67-6536) face marked “0.72A”.
Again, consulting FIGURE 109, join the Methyl Unit (67-8128) to the five carbon alkane chain
unit using a Connector Link, Carbon (67-7047), and continue down the chain connecting the
C=C unit, the seven carbon alkane unit, and finally the Carboxylate Unit (67-8144), all joined
with Connector Links, Carbon (67-7047).
Another concept useful in describing complex Unsaturated Carboxylic Acid (i.e. carbon skeleton mapping) is the Abbreviated Formula which denotes (A.) the number of carbon atoms in
the carbon skeleton, (B.) the number of C=C units present, and the precise location of each
along the length of the carbon skeleton, and, for Unsatuated Carboxylic Acids, (C.) the CIS or
TRANS orientation of the Hydrogen atoms (67-6692) associated with each C=C unit.
Again, the IUPAC rule is to take the Carboxylate carbon as carbon number one, count
consecutively along the chain from right-to-left, and use the number of the first carbon
atom encountered in the C=C unit at the location of the carbon-to-carbon double bond
unit (C=C).
For example, the Abbreviated Formula for 9-CIS-Hexadecenoic (Palmitoleic) Acid (67-0045) is
9-C16:1(9 CIS) According to this formula, 9-CIS-Hexadecenoic (Palmitoleic) Acid (67-0045) has
16 carbon atoms in the carbon skeleton.
In addition, there is but one carbon-to-carbon double bond (C=C) present (“monoenoic”), and
it begins with carbon atom number 9 (i.e. it is located between carbon atoms number 9 and
10). Finally, the Hydrogens (67-6692) located at the C=C are in the CIS conformation. See FIGURES 107-109.
Let’s try one we have yet to examine pictorially.
9
C 18:1(9 CIS)
This particular Unsaturated Fatty Acid , as yet unnamed, has a total of 18 carbon atoms in its
carbon skeleton and one C=C (“monoenoic”) beginning with carbon atom number 9. In addiPublication 5381-001
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This Abbreviated Formula describes 9-CIS-Octadecanoic (Oleic) Acid (67-0046), a derivative of
the parent compound Octadecane. The condensed carbon skeleton is shown in FIGURE 112.
CH3
(CH2)7
CH
CH
(CH2)7
*
*Location of the Carboxylate Group (67-8144)
FIGURE 112. Condensed Structural Formula For 9-CIS-Octadecenoic (Oleic)VAcid (67-0046)
Carbon Skeleton
IUPAC nomenclature calls changing the “a” in the “ane” suffix to and “e” to give the modified
suffix “ene”, dropping the final “e” in “ene”, and adding “oic” + Acid. This gives the name
Octadecenoic Acid.
Using FIGURE 112 as a pattern, note that the assembly of 9-CIS-Octadecenoic (Oleic) Acid (670046) requires the following subassemblies: (A.) two alkane chain units of seven carbon atoms
each and (B.) one each of a Methyl Unit (67-8128), C=C, and a Carboxylate Unit (67-8144).
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
tion, the Hydrogen atoms (67-6692) at the C=C are in the CIS conformation. Remember the
IUPAC numbering rules above.
As before, the alkane chain units consist of Carbon Tetrahedrals (67-6577) joined by Connector
Links, Carbon (67-7047) with all but a single vacant carbon socket at each end of the alkane
chain units filled with Hydrogen atoms (67-6692).
The C=C units each, as before, consist of two Ethylenic Double Bond (67-6585) joned by a
Connector Link, Locking (67-0039) along the carbon atom face marked “0.67A C=”.
The Methylene Unit (67-8110) consists of a single Carbon Tetrahedral (67-6577), two Connector
Links, Carbon (67-7047), and two Hydrogen atoms (67-6692). The Carboxylate Unit is assembled as described above, and all subassemblies are joined in the order prescribed in FIGURE
112 by Connector Links, Carbon (67-0047).
Note carefully the similarity between the Condensed Structural Formulae of 9-Hexadecenoic
(Palmitoleic) Acid (67-0045) in FIGURE 109 and 9-CIS-Octadecenoic (Oleic) Acid (67-0046) in
FIGURE 112, two additional Methyl units (67-8128) in 9-CIS-Octadecenoic (Oleic) Acid. The finished structure for 9-CIS-Octadecenoic (Oleic) Acid (67-0046) is shown in FIGURE 113.
FIGURE 113. 9-CIS-Octadecenoic (Oleic) Acid (67-0046)
Next, let’s investigate a “dienoic” Carboxylic Acid, or one whose carbon skeleton bears two C=C
unit, beginning with the Abbreviated Formula 9,12-C18:2(9 CIS, 12 CIS). Again, the above formula tells us that we are dealing with a Carboxylic Acid with 18 carbon atoms in the skeleton,
or a derivative of the parent compound Octadecane.
There are two C=C double bond units, one beginning at carbon atom number 9 and the other
at number 12. Furthermore, the Hydrogens atoms (67-6692) attached to the C=C units are in
the CIS conformation in both instances.
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As before, modifying the name of the parent compound is simply a matter of replacing the “a”
in the suffix “ane” with the letter “e” to give “ene”, dropping the final “e” and adding “oic”+
Acid to give “enoic” Acid.
However, recall that this is a “dienoic” acid. Thus, the modified name is Octadecedienoic Acid,
and after addition of all final modifications, we have 9,12-CIS,CIS-Octadecedienoic (Linoleic)
Acid. (67-0047). The carbon skeleton for 9,12-CIS, CIS-Octadecedienoic Acid is show in FIGURE 114.
12
9
C-C-C-C-C-C=C-C-C=C-C-C-C-C-C-C-C-*
*Location of the Carboxylate Unit (67-8144)
FIGURE 114. 9,12-CIS,CIS-Octadecedienoic (Linoleic) Acid (67-0047) Carbon Skeleton
Notice in the above carbon skeleton, the beginning of the C=C unit at carbon atoms number 9
and 12 (the Carboxylate Unit carbon is number one) as specified in the Abbreviated Formula
9, 12-C18:2(9 CIS, 12 CIS) The hydrogenated condensed carbon skeleton for this “dienoic”
Carboxylic Acid is shown in FIGURE 115.
CH3-(CH2)4-CH=CH-CH2-CH=CH-(CH2)7-*
*Location of the Carboxylate Unit (67-8144)
FIGURE 115. Hydrogenated Condensed Carbon Skeleton of 9,12-CIS,CIS-Octadecedienoic
(Linoleic) Acid (67-0047)
Assembling this molecular structure is similar to that of 9-CIS-Octadecenoic (Oleic) Acid (670046) before it, using FIGURE 115 as a “blueprint”.
The components consist of two alkane chain units of four and seven carbon atoms, respectively, a Methyl unit (67-8128), two C=C units (CIS conformation) joined by a Methylene unit
(67-8110) at carbon atom number 11, and a singular Carboxylate Unit (67-8144). That accounts
for all 18 carbon atoms. The finished structure is shown in FIGURE 116.
FIGURE 116. 9,12-CIS,CIS-Octadecedienoic (Linoleic) Acid (67-0047)
The next Unsaturated Carboxylic Acid is a “trienoic” type. Recall, “trienoic” indicates the presence in the carbon chain of three C=C structures. It is 6,9,12-CIS,CIS,CIS-Octadecetrienoic
(Linolenic) Acid (67-0048).
The condensed, hydrogenated carbon skeleton is shown in FIGURE 117
12
9
6
CH3-(CH2)4-CH=CH-CH2-CH=CH-CH2-CH=CH-(CH2)4*
*Location of the Carboxylate Unit (67-8144)
FIGURE 117. Condensed, Hydrogenated
Octadecetrienoic (Lenolenic) Acid (67-0048)
Publication 5381-001
Carbon
Skeleton
of
6,9,12-CIS,CIS,CIS-
Assembling CPK Atomic Models
59
6,9,12-C18:3(6 CIS,9 CIS,12 CIS)
The completed structure of Linolenic Acid (67-0048) is shown in FIGURE 118.
FIGURE 118. 6,9,12-CIS, CIS, CIS-Octadecetrienoic (Linolenic) Acid (67-0048)
Notice how the reapeated CIS conformaton about the C=C units leads to a coiled appearance
in these “fatty acid” which is even more apparent in our next and final example, Arachidonic
Acid (67-0049), a “tetraenoic” acid. The Abbreviated Formula for this structure is
5,8,11,14-C20:4(5 CIS,8 CIS,11 CIS,12 CIS)
The condensed hydrogenated carbon skeleton of Arachidonic Acid (67-0049) is shown in FIGURE 119.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
Notice the three C=C units beginning at carbon atoms 6, 9, and 12. The Abbreviated Formula
for this structure is
CH3-(CH2)4-(CH=CH-CH2)4-(CH2)2*
*Location of the Carboxylate Unit (67-8144)
FIGURE 119. Condensed Hydrogenated Carbon Skeleton of 5,8,11,14-CIS,CIS, CIS,CISEicosatetraenoic (Arachidoic) Acid (67-0049)
The Abbreviated Formula for this example indicates, first of all, the presence of four C=C units,
beginning at carbon atoms number 5, 8, 11, and 14, and that the hydrogen atoms of these units
are all in the CIS conformation. Recall from previous instruction that carbon atoms are
numbered consecutivelybeginning with the Carboxylate carbon as carbon atom number one and counting down the carbon chain.
At first glance, this 20-carbon fatty acid may seem to have a very complicated structure, but like
anything complex, the secret is to attack the structure “one brick at a time.” Clearly, the condensed hydrogenated carbon skeleton in FIGURE 119 indicates the presence of a small number of very simple structures.
For example, there is one Carboxylate (67-8144) and one Methyl Unit (67-8128). Secondly,
there are four, (CH2)4, + two, (CH2)2, Methylene Units (67-8110) for a total of six. Thus far, we
have accounted for eight carbon atoms with 12 remaining. The final, simple structure is
Propene (67-0427) of which there are four, (CH=CH-CH2)4, each with three carbon atoms for
a total of 12 and a grand total of 20.
This completes the audit! Remember, the Carbon Tetrahedrals (67-6577) in the carbon chain are
joined by Connector Links, Carbon (67-7047), and the Carbons Ethylenic Double Bond (676585) are each joined by Connector Links, Locking (67-7039) which emulate restricted rotation
about a carbon-to-carbon double bond (C=C).
You should now be ready to assemble Arachidonic Acid (67-0049). Let’s move from left-to-right
using the “blueprint” of FIGURE 119.
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Start with the Methyl Unit (67-8128) and join it to four consecutive Methylene Units (67-8110)
to give the following structure:
CH3-(CH2)4Next come the four consecutive Propene Units (67-0427) to give the following 17-carbon atom
skeleton:
CH3-(CH2)4-(CH=CH-CH2)4Next come the final two consecutive Methylene Units (67-8110). The final structure, as follows,
should duplicate the condensed hydrogenated carbon skeleton shown in FIGURE 119. As the
final step, add the Carboxylate Unit (67-8144) to give the completed structure of Arachidonic
Acid (67-0049) as shown in FIGURE 120.
FIGURE 120. 5,8,11,14-CIS,CIS,CIS,CIS-Eicosatetraenoic (Arachidonic) Acid (67-0049)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
8. AMINO ACIDS:
In this section, we will work with the 20 essential Amino Acids as well as a few additonal types.
Further, we will address only the so-called “L-Amino Acids” (Levorotary) or those occurring naturally. The “L” prefix is used to indicate optically active Amino Acids that rotate polarized light
to the left.
Otherwise, the Amino Acids are of the “D” (Dextrorotary) variety (i.e. their optical isomer counterparts) that rotate polarized light to the right. There is a singular exception to this rule, an
Amino Acid called Glycine (67-3772). It has no optically active properties, and, therefore, there
is no “L” or “D” type. The subject of optical activity will be addressed subsequently (See
AMINO ACID STEREOISOMERISM, Pp.).
We will begin with the Amino Acid Functional Groups or “Radicals” since these set Amino Acids
apart from each other or give them their unique properties, their so-called “fingerprints.”
Otherwise, the basic foundation or backbone of individual Amino Acids is identical as show in
FIGURE 121.
H
H2N
C
R
O
C
O
–
*R is the “Radical” or Functional Group (Amino Acid “Fingerprint”)
FIGURE 121. L-Amino Acid Backbone .
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61
To join the Carbon Amine (67-6536) and the oxygen atoms, see Carboxyl (67-8144) or
Carboxylate Group under ORGANIC (CARBOXYLIC) ACIDS on page , and see FIGURE 97
on page . Next, using the well end of the CPK* Construction Tool (67-7120). join the Carbon
Tetrahedral (67-6577) to the sole vacant socket of the Carbon Amine (67-6539) with the
Connector Link, Carbon (67-7047).
Now, join the Nitrogen Tetrahedral to any of the vacant sockets of the Carbon Tetrahedarl (676577) with the Connector Link, Standard (67-7005), again, using the construction tool.
ALIPHATIC AMINO ACIDS:
The next logical step is to examine each of the Amino Acid Functional Groups followed, in
each case, by the finished L-Amino Acid. The first group is of the ALIPHATIC type as listed
below.
Glycine (67-3772)
L-Alanine (67-3707)
L-Valine (67-3897)
L-Leucine (67-3806)
L-Isoleucine (67-3798)
L-Serine (67-3855)
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
This structure consists of four Hydrogens (67-6692), one Nitrogen Tetrahedral (67-6841), one
Oxygen Double Bond (67-6890), one Indented Oxygen Double Bond (67-6916), one Carbon
Amine (67-6536), one Carbon Tetrahedral (67-6577), two Connector Links, Locking (67-7039),
one Connector Link, Carbon (67-7047), and one Connector Link, Standard (67-7005).
L-Threonine (67-3863)
The simplest is the Hydrogen (67-6692) atom or Glycyl Group (See FIGURE 37, page ). Note
that Glycyl is the sole Functional Group without an “L” or “D” (Dextrorotary) prefix. Glycine
(67-3772) is diagramatically depicted in FIGURE 122. The Functional Group. Hydrogen (676692), is simply connected to the vacant socket of the Carbon Tetrehedral (67-6577) of the LAmino Acid backbone to make Glycine (67-3772).
H
H2N
C
H
O
C
O
–
FIGURE 122. Diagram of Glycine (67-3772)
The finished model of Glycine (67-3772) is in FIGURE 123.
FIGURE 123. Glycine (67-3772)
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The next Functional Group is a familiar one, the Methyl Group (67-8128), but as it applies to
Amino Acids, it is called L-Alanyl (67-8128). See FIGURE 56, page . L-Alanine (67-3707) is
shown diagrammatically in FIGURE 124.
Recall that building the Methyl Group (67-8128) is simply a matter of connecting three
Hydrogens (67-6692) to a Carbon Tetrahedral and filling the final, fourth socket of the carbon
atom with a Connector Link, Carbon (67-7047). The finished model in FIGURE 125.
H
H2N
O
C
C
O
–
CH3
FIGURE 124. Diagram of L-Alanine (67-3707)
FIGURE 125. L-Alanine (67-3707)
L-Valine (67-3897). too, has a familiar Functional Group, the Isopropyl or 2-Propyl Group (See
FIGURE 57, page ). Notice that the L-Valine Functional Group, L-Valyl (67-3898), is a straightchain of three Carbons Tetrahedral (67-6577) with carbon atoms number one and three completely filled with Hydrogens (67-6692) and a singular Hydrogen (67-6692) on the middle carbon.
The sole vacant socket on the middle Hydrogen (67-6692) takes a Connector Link, Carbon (677047). A diagram of L-Valine (67-3897) is shown in FIGURE 126, and the finished product is in
FIGURE 127.
H
H2N
C
C
H3C
C
CH3
H
FIGURE 126. Diagram of L-Valine (67-3897).
FIGURE 127. L-Valine (67-3897)
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O
–
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H
O
C
C
H2N
O
CH2
H3C
–
CH
CH3
FIGURE 128. Diagram of L-Leucyl (67-3807)
Notice in FIGURE 128 that L-Leucyl (67-3807) consists of threee Carbons Tetrahedral (67-6577)
in a straight-chain configuration with a Methyl Group (67-8128) attached to the middle carbon.
All carbon atoms in this Functional Group must be connected using the Connector Link, Carbon
(67-7047). The completed assembly of L-Leucine (67-3806) is in FIGURE 129.
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The next Amino Acid, L-Leucine (67-3806), has a Functional Group, L-Leucyl (67-3807), that is
an isomer of N-Butane (67-0410). L-Leucyl (67-3807) is shown diagrammatically in FIGURE 128.
FIGURE 129. L-Leucine (67-3806)
The next ALIPHATIC AMINO ACID is L-Isoleucine (67-3798). The Functional Group, LIsoleucyl (67-3799), is the radical Isobutyl or 2-Butyl (See FIGURE 57, page ).
H
H2N
C
H3C
CH
O
C
O
–
CH2
CH3
FIGURE 130. Diagram of L-Isoleucine (67-3798).
FIGURE 131. L-Isoleucine (67-3798)
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The final two ALIPHATIC AMINO ACIDS, L-Serine (67-3855) and L-Threonine (67-3863), have
the respective Functional Groups L-Seryl (67-3856) and L-Threonyl (67-3864). L-Seryl (67-3856)
is the same as Hydroxymethyl, and L-Threonyl (67-3864) is Hydroxyethyl. Both are depicted
diagrammatically is FIGURE 132.
H
OH
CH2
H3C
C
OH
FIGURE 132. (A. ) L-Seryl (67-3856) and (B.) L-Threonyl (67-3864)
Note that the Hydroxymethyl L-Serine (67-3855) Functional Group consists of one Carbon
Tetrahedral (67-6577) atom, one Hydroxy Unit (67-8193), two Hydrogens (67-6692), one
Connector Link, Standard (67-7005), and one Connector Link, Carbon (67-7047).
The Connector Link, Standard (67-7005) joins the Oxygen Single Bond (67-6874) to the Carbon
Tetrahedral (67-6577), and the Connector Link, Carbon (67-7047) joins the two Carbons
Tetrahedral (67-6577)
The Hydroxethyl Functional Group of L-Threonine (67-3863) consists of two Carbons
Tetrahedral (67-6577), four Hydrogens (67-6692), two Connector Links, Carbon (67-7047), and
one Hydroxy Group (67-8193).
In short, the Hydroxyethyl Functional Group is really an Ethanol Radical of the alcohol Ethanol
(67-0351) with a singular Hydrogen (67-6692) replaced with one Connector Link, Carbon (677047)
A finished structure of L-Serine (67-3855) is shown in FIGURE 133 and L-Threonine (67-3863)
in FIGURE 134.
FIGURE 133. L-Serine (67-3855)
FIGURE 134. L-Threonine (67-3863)
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AROMATIC AMINO ACIDS:
The AROMATIC AMINO ACIDS are shown below.
L-Phenylalanine
(67-3830)
L-Tyrosine
(67-3889)
L-Tryptophan
(67-3871)
The Functional Groups for these Amino Acids are shown diagrammatically in FIGURE 135.
H
H
C
H
C
C
H
C
CH2
C
C
H
H
C
C
C
HO
C
C
H
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This completes the ALIPHATIC AMINO ACIDS. The next group of Amino Acids are the AROMATIC type, so named for the presence of the Benzene Ring System (67-8250) or a derivative
thereof, i.e. Benzimidazole Ring System for Tryptophan (67-3871).
CH2
C
H
H
H
CH2
H
C
C
C
C
C
C
C
H
C
H
H
N
H
FIGURE 135. (A.) L-Phenylalanyl (67-3831), (B.) L-Tyrosyl (67-3890), and (C.) L-Tryptophanyl
(67-8102)
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L-Phenylalanyl (67-3831) is a hydrogenated Benzene Ring System (67-8250) joined to the
Amino Acid Backbone through a Methylene Unit (67-8110). The Benzene Ring System consists
of six Carbons Aromatic-6 (67-6569) joined by six Connector Links, Standard (67-7005), and
with five of the six positions containing Hydrogen atoms (67-6692).
The hydrogenated Benzene Ring System (67-8250) is then joined to the Methylene Unit (678110) using a Connector Link, Carbon (67-7047) which is, in turn, joined to the Amino Acid
Backbone structure, again, using another Connector Link, Carbon (67-7047). The finished structure of L-Phenylalanine (67-3830) appears in FIGURE 136.
FIGURE 136. L-Phenylalanine (67-3830)
L-Tyrosyl (67-3890) is almost identical to L-Phenylalanyl (67-3830) with the exception that the
number four Hydrogen (67-6692) is replaced by a Hydroxy Unit (67-8193) in L-Tyrosyl (673890).
FIGURE 137. L-Tyrosine (67-3889)
L-Tryptophan (67-3871) is characterized by the presence of the modified Benzimidazole Ring
System as L-Tryptophanyl (67-8102) as depicted in FIGURE 138.
FIGURE 138. L-Tryptophanyl (67-8102)
The L-Tryptophanyl (67-8102) consists of one C-Fused 5-6 Rings (67-6601), four C-Aromatic-6
Carbons (67-6569), two C-Aromatic -5 Carbons (67-6551), one N-Aromatic-5 Nitrogen (676825), one Carbon Tetrahedral unit (67-6577), eight Hydrogen atoms (67-6692), ten Connector
Links, Standard (67-7005), and one Connector Link, Carbon (67-7047).
Note that the singular Connector Link, Carbon (67-7047) is used to join the L-Tryptophanyl (678102) Functional Group to the Carbon Tetrahedral (67-6577) of the Amino Acid Backbone.
The finished structure for L-Tryptophan (67-3871) is shown in FIGURE 139.
FIGURE 139. L-Tryptophan (67-3871)
This concludes the AROMATIC AMINO ACIDS.
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L-Cystine
L-Cysteine
(67-3749)
L-Methionine
(67-3822)
Cystinyl, the Functinal Group, and L-Cystine are depicted diagrammatically in FIGURE 140.
CH2
S
CH2
H
H
O
C
O
–
S
C
CH2
S
NH2
S
CH2
C
NH2
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SULFUR-CONTAINING AMINO ACIDS
O
C
O
–
FIGURE 140. (A.) L-Cystinly and (B.) L-Cystine
Notice that it is really two Amino Acids in a mirror image arrangement on either side of the
dashed vertical line. Note also that it is two L-Alanine (67-3707) molecules (one inside each rectangle) joined by what is called a “Sulfhydryl bridge” (-S-S-).
Assembling the L-Cystine structure is simply a matter of constructing two L-Alanine (67-3703)
Amino Acids with one Hydrogen atom (67-6692) missing from each of the two L-Alanyl
Functional Groups (67-8128) and joining the two Amino Acids with the “Sulfhydryl bridge.”
The bridge consists of two Sulfur, Digonal units (67-6957) and three Connector Links, Standard
(67-7005). The dashes in the “Sulfhydryl bridge” symbolize each of the Connector Links,
Standard (67-7005). The finished structure for L-Cystine is shown in FIGURE 141.
FIGURE 141. L-Cystine
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The next Amino Acid is L-Cysteine (67-3749). Note carefully the difference in the spelling of LCystine and L-Cysteine (67-3749). L-Cysteine (67-3749) is and L-Cystine molecule that has been
reduced by the introduction of two Hydrogen atoms (67-6692) which breaks the “Sulfhydryl
bridge”. See FIGURE 142 below for this process for the formation of L-Cysteine (67-3749).
H
H
O
C
C
O
–
CH2
CH2
S
S
C
O
C
NH2
NH2
O
–
H2
H
O
2X
C
O
–
C
CH2
SH
NH2
FIGURE 142. L-Cysteine (67-3749) Formation
Note that the Functional Group for L-Cysteine (67-3749), called Cysteinyl (67-3750), consists of
one Carbon Tetrahedarl (6706577), one Sulfur, Digonal (67-6957), three Hydrogen atoms (676692), one Connector Link, Standard (67-7005), and one Connector Link, Carbon (67-7047).
During the assembly of L-Cysteine (67-3749) take care that the Connector Link, Carbon (677047) joins the Carbon Tetrahedral (67-6577) of the Functional Group (L-Cysteinyl) to the
Carbon Tetrahedral (67-6577) of the Amino Acid backbone. The assembled structure for LCysteinyl (67-3750), the Functional Group, andL-Cysteine (67-3749) are in FIGURE 143.
FIGURE 143. (A.) L-Cysteinyl (67-3750) and (B.) L-Cysteine (67-3749)
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CH2
S
H3C
CH2
FIGURE 144. L-Methionyl (67-3823)
L-Methionyl (67-3823) consists of three Carbons, Tetrahedral (67-6577), one Sulfur, Digonals
(67-6957), two each of Connector Link, Standard (67-7005) and Connector Links, Carbon (677047), and seven Hydrogen atoms (67-6692).
Again, as with L-Cysteine (67-3749) take care to join all adjacent Carbons, Tetrahedral (67-6577)
with Connector Link, Carbon (67-7047). Otherwise, use Connector Links, Standard (67-7005).
The finished assembly for L-Methionyl (67-3823) and L-Methionine (67-3822) in FIGURE 145.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
The final SULFUR-CONTAINING AMINO ACID is L-Methionine (67-3822) whose Functional
Group, L-Methionyl (67-3823), is depicted in FIGURE 144.
FIGURE 145. (A.) L-Methionyl (67-3823) and (B.) L-Methionine (67-3822)
This completes the SULFUR-CONTAINiNG AMINO ACIDS.
IMINO ACIDS:
L-Proline
(67-3848)
L-4-Hyroxyproline
L-3-Hydroxyproline
The IMINO ACIDS all have the same ring system structure, the Pyrrolidine-2-Carboxylic Acid
system, shown in FIGURE 146.
H2C
H2C
CH2
C
N
H
H
O
C
O
+
FIGURE 146. The Pyrrolidine-2-Carboxylic Acid Ring System For Imino Acids
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In addition, the inclusion of any IMINO ACID type along the chain of a protein structure causes the chain to make a 90 degree turn or literally place a “fold” or “crease” in the chain, as
reflected in FIGURE 146. Another peculiarity of the IMINO ACID group is the inclusion of the
entire Amino Acid structure into the Amino Acid chain instead of just the Functional Group.
As reflected in FIGURE 147, attachment is at positions number 1 and 2. Further, if positions
number 3 and/or 4 are hydroxylated, attack of either or both of these positions lends itself to
additional modification.
H2C
H2C
CH2
O
2
C
3
4
5
C
1
N
H
FIGURE 147. L-Proline (67-3848) Insertion into Amino Acid Chain
The simplest of the IMINO ACIDS, L-Proline (67-3848), consists of four Carbons Tetrahedral
(67-6577), one each of Nitrogen Amide (67-6791), Carbon Amine (67-6536), Oxygen Indented
Double Bond (67-6916), and Oxygen Double Bond (67-6890) eight Hydrogen atoms (67-6692),
four Connector Links, Carbon (67-7047), two Connector Links, Locking (67-7039), and two
Connector Links, Standard (67-7005). The parts for L-Proyly (67-8094), the Functional Group,
and L-Proline (67-3848) are joined as indicted in FIGURE 148.
H
H
C
C
H
H
C
H
H
C
C
H
H
C
C
C
H
C
H
N
H
O
N
H
O
–
FIGURE 148. Parts Arrangement For (A.) L-Prolyl (67-8094) and (B.) L-Proline (67-3848)
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FIGURE 149. L-Proline (67-3848)
The additional two modified versions (positions 3 and 4 hydroxyled) of L-Proline (67-3848) are
illustrated in FIGURE 150.
H
OH
C
C
H
H
H
H
C
C
H
H
H
O
–
H
H
O
C
C
C
N
H
H
O
C
C
OH
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The finished structure for L-Proline (67-3848) is in FIGURE 149.
C
N
H
O
–
H
FIGURE 150. (A.) 3-Hydroxyproline and (B.) 4-Hydroxyproline
This completes the IMINO ACIDS section.
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DICARBOXYLIC ACIDS AND THEIR AMIDE DERIVATIVES:
L-Aspartic Acid (67-3723)
L-Glutamic Acid (67-3756)
L-Asparagine (67-3731)
L-Glutamine (67-3764)
L-Aspartyl (67-3724), the Functional Group, and L-Aspartic Acid (67-3723) are illustrated in FIGURE 151.
H
O
H2N
C
H2C
C
O
C
O
–
CH2
O
–
C
O
–
O
FIGURE 151. (A.) L-Aspartyl (67-3724) and (B.) L-Aspartic Acid (67-3723)
L-Aspartic Acid (67-3723) consists of two each of Carbons Tetrahedral (67-6577), Carbons
Amine (67-6536), Oxygen Double Bond (67-6890), and Oxygen Indented Double Bond (676916), one Nitrogen Amide (67-6791), six Hydrogens (67-6692), three Connector Links,
Standard (67-7005), four Connector Links, Locking (67-7039), and one Connector Link, Carbon
(67-7047). The parts arrangement for L-Aspartyl (67-3724) and L-Aspartic Acid (67-3723) shown
in FIGURE 152.
H
H
H
O
N
C
O
–
O
C
H
C
C
O
–
C
H
C
O
–
O
FIGURE 152. Parts Arrangement For (A.) L-Aspartyl (67-3724) and (B.) L-Aspartic Acid (67-3723)
L-Glutamic Acid (67-3756) is depicted in FIGURE 153. Notice that the only difference between
L-Aspartic Acid (67-3723) and L-Glutamic Acid (67-3756) is the insertion of a Methylene Unit
(67-8110) minus the accompanying Connector Link, Standard replaced by a Connector Link,
Carbon (67-7047). Note the insertion point of the Methylene Unit (67-8110) in FIGURE 152.
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FIGURE 153. (A.) L-Glutamyl (67-3757) and (B.) L-Glutamic Acid (67-3756)
Next are the AMIDE DERIVATIVES L-Aspartic (67-3723) and L-Glutamic Acids (67-3756). LAsparagine (67-3731), the AMIDE DERIVATIVE of L-Aspartic Acid (67-3723) is illustrated in
FIGURE 154 along with the Functional Group, L-Asparaginyl (67-3732).
H
H2N
O
C
CH2
C
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
The finished structure for L-Glutamyl (67-3757), the Functional Group, and L-Glutamic Acid (673756) are shown in FIGURE 153.
O
C
O
–
CH2
H2N
C
O
–
NH2
FIGURE 154. (A.) L-Asparaginyl (67-3732) and (B.) L-Asparagine (67-3731)
Note in FIGURE 154 that the only difference between L-Aspartic Acid (67-3723) and LAsparagine (67-3731) is the presence of the Amide Group in exchange for a singular Oxygen
Indented Double Bond (67-6916) in the B-Carboxyl (“Beta-Carboxyl”) Group. Otherwise, the
parts for L-Asparagine (67-3731) are identical to those L-Aspartic Acid (67-3723) as shown in
FIGURE 152. The completed structure for L-Asparagine (67-3731) is shown in FIGURE 155.
FIGURE 155. L-Asparagine (67-3731)
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L-Glutamine (67-3764), like L-Asparagine (67-3731), has a single Oxygen Indented Double
Bond (67-6916) replaced by an Amide Group in the B-Carboxyl Group as illustrated in FIGURE
156 along with the Functional Group, L-Glutaminly (67-3765).
H
H2N
C
O
C
O
C
CH2
O
–
CH2
CH2
CH2
H2N
C
H2N
O
FIGURE 156. (A.) L-Glutaminyl (67-3765) and (B.)L-Glutamine (67-3764)
The finished structure for L-Glutamine (67-3764) is shown in FIGURE 157.
FIGURE 157. L-Glutamine (67-3764)
This concludes the discussion of the DICARBOXYLIC AMINO ACIDS AND THEIR AMIDE
DERIVATIVES.
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L-Histidine (67-3870)
L-Arginine (67-3715)
L-Lysine (67-3814)
L-Hydroxylysine
L-Histidine (67-3870) and L-Histidyl (67-8086), the Functinal Group, contain the Imidazole Ring
System as illustrated in FIGURE 158.
H
H
CH
+ N
C
C
+ N
N
O
–
CH2
C
C
C
C
H2N
H
O
N
H
H
C
C
H
H
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
BASIC AMINO ACIDS:
FIGURE 158. (A.) L-Histidyl (67-8086) and (B.) L-Histidine (67-3870)
L-Histidine (67-3870) contains two each of Carbons Tetrahedral (67-6577) and Nitrogens
Aromatic-5 (67-6825), three Carbons Aromatic-5 (67-6551), one each of Nitrogen Amide (676791), Oxygen Double Bond (67-6890), Oxygen Indented Double Bond (67-6916), Amine Cap
(67-7112), and Carbon Amine (67-6536), eight Hydrogen atoms (67-6692), eight Connector
Links, Standard (67-7005), two Connector Links, Locking (67-7039), and one Connector Link,
Carbon (67-7047).
The arrangement of the parts for L-Histidine (67-8086) is shown in FIGURE 159.
H
+
C
H
HN2
C
C
H
H
O
N
C
C
C
N
H
O
–
H
FIGURE 159. Arrangement of Parts For L-Histidine (67-8086)
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L-Arginyl (67-3716), the Functional Group, and L-Arginine (67-3715) are shown diagrammatically in FIGURE 160. Note the highly basic Guanidino Group contained within the Functional
Group, L-Arginyl (67-3716).
H
H2N
C
N
CH2
CH2
CH2
NH
H
H
C
H2N
N
CH2
H2N
C
CH2
CH2
O
C
O
–
NH
FIGURE 160. (A.) L-Arginyl (67-3716) and (B.) L-Arginine (67-3715)
L-Arginine (67-3715) consists of four each of Carbons Tetrahedral (67-6577) and Nitrogens
Amide (67-6791), two Carbons Amine (67-6536), one each of Oxygen Double Bond (67-6890)
and Oxygen Indented Double Bond (67-6916), fourteen Hydrogen atoms (67-6692), six
Connector Links, Standard (67-7005), three Connector Links, Carbon (67-7047), and two
Connector Links, Locking (67-7039).
The arrangement of the parts for L-Arginine (67-3715) is shown in FIGURE 161.
H
N
H
C
N
H
H
H
H
N
C
C
C
H
H
H
H
FIGURE 161. Arrangement of Parts For L-Arginine (67-3715)
The finished assembly for L-Arginine (67-3715) is shown in FIGURE 162.
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L-Lysyl (67-3815) and L-Lysine (67-3814) are shown diagrammatically in FIGURE 162. Note the
similarity between the structure of L-Arginine (67-3715) as shown in FIGURES 161 and 162 and
L-Lysine (67-3814).
H2N
CH2
CH2
CH2
CH2
H
H2N
CH2
CH2
H2N
C
CH2
CH2
O
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FIGURE 162. L-Arginine (67-3715)
C
O
–
FIGURE 163. (A.) L-Lysyl (67-3815) and (B.) L-Lysine (67-3814)
L-Lysine (67-3814) consists of five Carbons Tetrahedral (67-6577), two Nitrogen Amides (676791), one each of Carbon Amine (67-6536), Oxygen Double Bond (67-6890), and Oxygen
Indented Double Bond (67-6916), thirteen Hydrogen atoms (67-6692), four Connector Links,
Carbon (67-7047), three Connector Links, Standard (67-7005), and two Connector Links,
Locking (67-7039). The arrangement of the parts for L-Lysine (67-6738) is shown in FIGURE
164.
H
N
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
N
H
O
C
O
–
H
FIGURE 164. Arrangement of Parts For L-Lysine (67-3814)
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The completed structure for L-Lysine (67-3814) is shown in FIGURE 165.
FIGURE 165. L-Lysine (67-3814)
A modified L-Lysine (67-3814) structure, Delta-Hydroxylysine or 5-Hydroxylysine is illustrated
in FIGURE 166. Notice the difference between L-Lysine (67-3814) and 5-Hydroxylysine is the
presence of a Hydroxy Unit (67-8193) at position number 5.
H
N
H
H
H
H
H
H
C
C
C
C
C
H
OH
H
H
N
H
FIGURE 166. 5-Hydroxylysine
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C
O
–
H
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In addition to those MODIFIED AMINO ACIDS already mentioned (i.e. Cystine, 3- and 4Hydroxyproline, 5-Hydroxylysine), there are several others of particular physiological significance. For example, B-Alanine (“Beta-Alanine”) illustrated below in FIGURE 167, is found in
the vitamin Pantothenic Acid (67-0027).
H
H
H
C
C
H2N
H
O
C
O
–
FIGURE 167. B-Alanine
L-Ornithine, shown diagrammatically in FIGURE 168, has one less Methylene Unit (-CH2-, 678110) than its structural homologue, L-Lysine (67-3814). Note the name L-Ornithine. This
Amino Acid was originally discovered in bird, the study of which is Ornithology.
NH2
CH2
CH2
CH2
H2N
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MODIFIED AMINO ACIDS:
O
C
C
O
–
H
FIGURE 168. L-Ornithine
One additional modified Amino Acid is L-Thyronine shown diagrammatically in FIGURE 169.
The tri- (FIGURE 170A.) and tetra-iodinated (FIGURE 170B.) forms of this Amino Acis are know
as Thyroxine or 3,5,3'-Triiodothyronine (67-0150) and 3,5,3',5'-Tetraiodothyronine (67-0151),
respectively.
H
C
H
H
H
C
C
C
C
C
H
H
O
C
C
C
C
H
H
NH2
C
C
CH2
C
H
O
C
O
–
H
FIGURE 169. L-Thyronine
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I
C
H
C
H
C
C
C
C
O
C
C
C
C
NH2
C
H
I
H
I
H
I
H
C
C
C
C
I
C
O
C
C
H
C
C
C
I
CH2
C
H
C
H
I
H
C
CH2
C
O
C
H
O
–
NH2
O
C
H
C
O
–
H
FIGURE 170. (A.) 3,5,3'-Triiodothyronine (67-0150) and (B.) 3,5,3',5'-Tetraiodothyronine (670151)
This discussion of MODIFIED AMINO ACIDS concludes the Amino Acids and their respective
Functional Groups.
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Harvard Apparatus, Inc. offers two CPK* products to accommodate the construction of
polypeptides and alpha-helix formation as well as pleated sheets for the more complex proteins.
These are the Pentapeptide Chain Unit (67-8011) and the Decapeptide H-Bonding Unit (678045), and they add a dimension of flexibility and uniqueness to the entire Amino Acid product line. Both structures are shown diagrammatically, and the parts are labelled in FIGURE 171.
H
NH
R
C
H
NH
O
C
R
C
O
C
H
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PENTA- AND DECAPEPTIDES:
*C-terminus for Carboxyl end and N-terminus for Nitrogen end
FIGURE 171. (A.) Pentapeptide Chain Unit (67-8011) and (B.) Decapeptide H-Bonding Unit (678045)
Note the alternating nature of vacant sockets on the Carbons Tetrahedral (67-6577) of either of
these two structures. Note also that even though these structures come in five and 10 segment
units, respectively, several tandum units can be joined to make polypeptides of considerable
length, i.e. three consecutive Decapeptide H-Bonding Units (67-8045) to make a tridecapeptide.
The finished structures for the Pentapeptide Chain Unit (67-8011) and Decapeptide H-Bonding
Unit (67-8045) are shown in FIGURE 172. Harvard Apparatus, Inc., on special order, can make
these units in any length desired including those less than five or 10 units, respectively.
FIGURE 172. (A.) Pentapeptide Chain Unit (67-8011) and (B.) Decapeptide H-Bonding Unit (678045)
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The Pentapeptide Chain Unit (67-8011) and the Decapeptide H-Bonding Unit (67-8045) are
repeating units of the structures depicted diagrammatically in FIGURE 173 (A.) and (B.), respectively.
FIGURE 173. (A.) Repeating Unit For the Pentapeptide Chain Unit (67-8011) and the (B.)
Decapeptide H-Bonding Unit (67-8045)
The alternating vacant sockets on these units accommodate the Amino Acid Functional Groups
previously mentioned, i.e. Glycyl (67-67-6692), L-Alanyl (67-8128), L-Arginyl (67-3716), etc. By
convention, when the Functional Groups are added to the polypeptide backbone structures,
they are done so beginning with the “C-terminus” and ending with the “N-terminus” (See FIGURE 171).
For example, Alanyl-Glycyl-Tryptophanyl-Arginyl-Histidyl is a pentapeptide unit that has the
Amino Acid Functional Groups, from C- to N-terminus, L-Alanyl (67-8128), Glycyl (67-6692), LTryptophanyl (67-8102), L-Arginyl (67-3716), and L-Histidyl (67-8086) along the polypeptide
backbone unit. See FIGURE 174 for the diagram of this structure.
FIGURE 174. The Pentapeptide Alanyl-Glycyl-Tryptophanyl-Arginyl-Histidyl
Many “man-made” or synthetic polypeptides are composed of identical repeating units such as
Polyalanyl or Polyglycyl. In fact, many such “Homopeptides” have been employed to “unlock”
or decipher the genetic code.
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As alluded to (See AMINO ACIDS heading, P. ), Amino Acids have two different isomeric
forms. These are the “L” forms (Levorotary) or those that rotate polarized light to the left, and
the “D” forms (Dextrorotary) or those that rotate polarized light to the right. In short, these are
examples of stereoisomerism or isomers that are mirror images of ea ch other. The singular
exception is the Amino Acid Glycine (67-3772).
The center of optical activity within these stereoisomers is carbon atom number two or the
“Alpha-Carbon” which is the tetrahedral carbon immediately adjacent to the Carbon Amine (676536).
What is more, some Amino Acids have more than one center of optical activity, such as D- or
L-Isoleucine (67-3798), D- or L-Threonine (67-3863), and D- or L-Hydroxylysine (3- or 4Hydroxylysine). The key is whether or not the “Alpha-Carbon” has four unique groups attached
to it. If so, it is in all likelihood a center of optical activity.
To construct models of the correct “D-” and “L-” configureations, the following guidelines are
offered:
1.
Join one Hydrogen atom (67-6692) into one socket of a Carbon Tetrahedral (67-6577). Note
that it makes no difference which vacant socket is selected as they are all equal.
2.
Hold the structure with the Hydrogen atom (67-6692) pointing upward.
3.
Next, attach the Carboxyl, Functional (“R”), and Amino Groups in a clockwise order looking downward upon the Hydrogen atom (67-6692). This will give the “L-” configuration.
Reversing the order of attachment of the Carboxyl and Amino Groups gives the “D-” configuration, that is, in a counter-clockwise fashion as shown diagrammatically in FIGURE
175.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
AMINO ACID STEREOISOMERISM:
FIGURE 175. Diagrammatic Representations of (A.) D-Amino Acid and (B.) L-Amino Acid
Configurations
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9.
PURINE AND PYRIMIDINES:
This section of the Operating Guide specifically addresses the fundamental building block of
the genetic acids DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid). We will confine
our discussion to Adenine (67-8202), Guanine (67-8203), Cytosine (67-8221), Thymine (678220), Uracil (67-8222), and the mono-, di, and triphosorylated derivataives of each.
PURINES:
The Purine Ring System (67-8262) is shown diagrammatically in FIGURE 176 with each position within the Ring System numbered and each part within the structure labelled with its part
number. Notice that the Purine Ring System (67-8262) is an aromatic or unsaturated ring structure.
H
+
N
+
N
C
6
1
5
2
4
C
7
8
C
H
3
N
+
C
C
H
9
N
H
FIGURE 176. The Purine Ring System (67-8262)
The finished structure for the Purine Ring System (67-8262) is hown in FIGURE 177.
FIGURE 177. The Purine Ring System (67-8262)
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NH2
+
N
+
N
C
C
C
H
C
H
C
H
N
N
+
H
C
C
H
O
H
+
N
C
N
C
C
C
N
N
+
H2N
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
The most common of the Purine Ring System structures is Adenine (67-8202) or more appropriately, 6-Amino Purine. Adenine (67-8202) is shown diagrammatically in FIGURE 178 (A.)
and the finished structure in FIGURE 179 (A.).
H
O
H
H
+
N
C
N
C
C
C
N
+
N
H
FIGURE 178. (A.) Adenine (67-8202), (B.) Guanine (67-8203), and (C.) Hypoxanthine (67-8204)
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FIGURE 179. (A.) Adenine (67-8202), (B.) Guanine (67-8203), and (C.) Hypoxanthine (67-8204)
Two other well-known purine compounds are Guanine (67-8203) and Hypoxanthine (67-8204),
shown diagrammatically in FIGURE 178 (B.) and (C.), respectively. The IUPAC name for
Guanine (67-8203) is 2-Amino-6-Oxypurine, and Hypoxanthine (67-8204) is 6-Oxypurine. The
final finished structures for Guanine (67-8203) and Hypoxanthine (67-8204) are shown in FIGURE 179 (B.) and (C.), respectively.
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NH2
+
N
O
+
N
C
H
H
C
C
C
H2C
H H
OH
O
C
H
C
C
C
H
N
N
+
H2N
O
H
C
C
N
N
+
N
H
C
C
C
+
N
C
C
H2C
H H
OH
C
C
H
C
H
H
H
OH
OH
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
The nucleoside (nitrogen base + sugar moiety) versions of Adenine (67-8202), Guanine (678203), and Hypoxanthine (67-8204) are shown diagrammatically in FIGURE 180. (A.), (B.), and
(C.), respectively. These are Adenosine (67-8214), Guanosine (67-8215), and Inosine (67-8216).
Note that for each structure, the sugar moiety, 2-Deoxy-D-Ribose (67-0118), is attached to ea
ch purine structure at the number 9 position.
O
H
+
N
C
N
C
C
C
H
C
H
N
N
+
O
C
H
H2C
H H
OH
C
C
C
H
H
OH
FIGURE 180. (A.) Adenosine (67-8214), (B.) Guanosine (67-8215), and (C.) Inosine (67-8216)
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The final finished structure for each nucleoside is shown in FIGURE 181. (A.), (B.), and (C.),
respectively.
FIGURE 181. (A.) Adenosine (67-8214), (B.) Guanosine (67-8215), (C.) Inosine (67-8216)
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NH2
+
N
+
N
C
C
H
C
O
C
C
N
N
+
H
O
C
H2C
H H
H
O
C
P
OH
O
C
H
C
H
OH
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The monophosphorylated version of each of these nucleosides is shown diagrammatically in
FIGURE 182. (A.), (B.), and (C.), respectively.
O
H
+
N
C
N
C
C
C
H
C
O
N
N
+
H2N
O
C
H2C
H H
H
O
C
P
OH
O
C
H
C
H
OH
O
H
+
N
C
N
C
C
C
H
C
H
O
N
N
+
O
C
H
H2C
H H
C
O
P
OH
O
C
C
H
H
OH
FIGURE 182. (A.) Adenosine-5'-Monophosphate (67-8207), (B.) Guanosine-5'- Monophosphate
(67-8210), (C.) Inosine-5'-Monophosphate (67-8213)
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The final finished structures for each of these monophosphorylated compounds are shown in
FIGURE 183. (A.), (B.), and (C.), respectively.
FIGURE 183. (A.) Adenosine-5'-Monophosphate (67-8207), (B.) Guanosine-5'- Monophosphate
(67-8210), (C.) Inosine-5'-Monophosphate (67-8213)
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NH2
+
N
+
N
C
C
H
C
N
N
+
H
O
O
C
C
O
C
H2C
H H
H
O
C
P
O
P
O
O
O
O
OH
C
H
C
H
OH
O
H
+
N
C
N
C
C
C
H
C
N
N
+
H2N
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
The diphosphorylated versions of these purine structures are shown diagrammatically in FIGURE 184. (A.), (B.), and (C.), respectively. The final finished diphosphorylated structures are
shown in FIGURE 185.
O
C
H2C
H H
H
O
C
P
O
P
O
O
O
O
OH
C
H
C
H
OH
O
H
+
N
C
N
C
C
C
H
C
H
N
N
+
O
C
H
H2C
H H
C
O
P
O
O
P
OH
O
C
C
H
H
OH
FIGURE 184. (A.) Adenosine-5'-Diphosphate (67-8206), (B.) Guanosine-5'-Diphosphate (678209), (C.) Inosine-5'-Diphosphate (67-8212)
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FIGURE 185. (A.) Adenosine-5'-Diphosphate (67-8206), (B.) Guanosine-5'-Diphosphate (678209), (C.) Inosine-5'-Diphosphate (67-8212)
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NH2
+
N
O
+
N
C
O
C
C
C
H H
O
P
OH
C
C
O
P
O
O
N
N
+
H2C
H
C
H
O
OH
P
OH
OH
H
C
H
C
OH
OH
O
H
+
N
C
N
C
C
C
H
C
O
O
O
N
N
+
H2N
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
The triphoshorylated versions of these purine structures are depicted diagrammatically in FIGURE 186. (A.), (B.), and (C.), respectively. The final finished structures for each of these compound are shown in FIGURE 187.
O
C
H2C
H H
H
O
C
P
O
P
O
P
O
O
O
O
O
O
OH
C
H
C
H
OH
O
H
+
N
C
N
C
C
C
H
C
H
N
N
+
O
C
H
H2C
H H
C
O
P
O
O
P
O
O
P
OH
O
C
C
H
H
OH
FIGURE 186. (A.) Adenosine-5'-Triphosphate (67-8205), (B.) Guanosine-5'-Triphosphate (678208), (C.) Inosine-5'-Triphosphate (67-8211)
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FIGURE 187. (A.) Adenosine-5'-Triphosphate (67-8205), (B.) Guanosine-5'-Triphosphate (678208), (C.) Inosine-5'-Triphosphate (67-8211)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
Three other minor purines are Xanthine, Caffeine, and Uric Acid. They are shown diagrammatically in FIGURE 188.
FIGURE 188. (A.) Xanthine (2,6-Dioxypurine), (B.) Caffeine (1,3,7-Trimethylxanthine), and (C.)
Uric Acid (2,6,8-Trioxypurine)
PYRIMIDINES:
The Pyrimidine Ring System (67-8263), shown diagrammatically in FIGURE 189, like its purine
counterpart, is aromatic. Note, however, that pyrimidine is numbered clockwise beginning with
the vertix nitrogen located at “six o’clock.”
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–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
The final finished structure for the Pyrimidine Ring System is shown in FIGURE 190.
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
FIGURE 189. Pyrimidine Ring System (67-8263)
FIGURE 190. Pyrimidine Ring System (67-8263)
The principal pyrimidines are Thymine (67-8220), Cytosine (67-8221), and Uracil (67-8222) as
well as two derivatives of Cytosine (67-8221), that is, 5-Methylcytosine (67-8239) and 5Hydroxymethylcytosine (67-8240). The IUPAC name for Thymine )67-8220) is 5-Methyl-2,4Dioxypyrimidine; Cytosine (67-8221) is 2-Oxy-4-Aminopyrimidine; and Uracil (67-8222) is 2,4Dioxypyrimidine.
Obviously, the 5-Methyl- and 5-Hydroxymethyl- derivatives of Cytosine (67-8221) have the
same IUPAC name as for Cytosine (67-8221) with the respective prefix for the appropriate derivative.
Thymine (67-8220), Cytosine (67-8221), Uracil (67-8222), 5-Methylcytosine (67-8239), and 5Hydroxymethylcytosine (67-8240) are shown diagrammatically in FIGURE 191 (A.)-(E.), respectively.
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FIGURE 191. (A.) Thymine (67-8220), (B.) Cytosine (67-8221), (C.) Uracil (67-822), (D.) 5Methylcytosine (67-8239), (E.) 5-Hydroxymethylcytosine (67-8240)
The final finished structures of the primary pyrimidines, Thymine (67-8220), Cytosine (67-8221),
and Uracil (67-8222), are shown in FIGURE 192.
FIGURE 192. (A.) Thymine (67-8220), (B.) Cytosine (67-8221), and (C.) Uracil (67-8222)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
The nucleoside (nitrogen base + sugar moiety combination) versions of these three pyrimidine
compounds are shown diagrammatically in FIGURE 193. Note that the sugar moiety for the
pyrimidine compound is the same as for the purine compound, that is, 2-Deoxy-D-Ribose (670118) with the exception of Uracil (67-8222) in which case the sugar compound is D-Ribose
(67-0117).
Note also that for all the pyrimidine compounds, the sugar group, whatever it may be, is
attached to position number 1 of the Pyrimidine Ring System (67-8263).
FIGURE 193. (A.) Thymidine (67-8232), (B.) Cytidine (67-8233), and (C.) Uridine (67-8234)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
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FIGURE 194. (A.) Thymidine (67-8232), (B.) Cytidine (67-8233), and (C.) Uridine (67-8234)
The mono-, di-, and triphosphorylated versions of these pyrimidine nucleosides are depicted
diagrammatically in FIGURES 195-197, respectively.
FIGURE 195. (A.) Thymidine-5'-Monophosphate (67-8225), (B.) Cytidine-5'-Monophosphate
(67-8228), and (C.) Uridine-5'-Monophosphate (67-8231)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 196. (A.) Thymidine-5'-Diphosphate (67-8224), (B.) Cytidine-5'-Diphosphate (67-8200),
and (C.) Uridine-5'-Diphosphate (67-8230)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
The final finished structure of each of these nucleoside compounds is shown in FIGURE 194.
FIGURE 197. (A.) Thymidine-5'-Triphosphate (67-8223), (B.) Cytidine-5'-Triphosphate (678226), and (C.) Uridine-5'-Triphosphate (67-8229)
The final finished structures of these phosphorylated pyrimidine nucleosides are shown in FIGURES 198-200, respectively.
FIGURE 198. (A.) Thymidine5'-Monophosphate (67-8225),
(67-8228), and (C.) Uridine-5'-Monophosphate (67-8231)
(B.) Cytidine-5'-Monophosphate
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 199. (A.) Thymidine-5'-Diphosphate (67-8224), (B.) Cytidine-5'-Diphosphate (67-8200),
and (C.) Uridine5'-Diphosphate (67-8230)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
FIGURE 200. (A.) Thymidine-5'-Triphosphate (67-8223), (B.) Cytidine-5'-Triphosphate (678226), and (C.) Uridine-5'-Triphosphate (67-8229)
This concludes the discussion of the nitrogen base compounds better known as the PURINES
AND PYRIMIDINES. From here, we will take what we have learned and apply it to the construction of NUCLEIC ACIDS or DNA (i.e. Deoxyribonucleic Acid) and RNA (i.e. Ribonucleic
Acid).
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10. NUCLEIC ACIDS:
These are the “building blocks” of the genes and are represented by DNA and RNA.
DNA:
In our discussion of Deoxyribonucleic Acids, we shall concern ourselves principally with what
we will refer to as the “base pairs” or Adenine-Thymine (67-8318) or A-T and Guanine-Cytosine
(67-8326) or G-C as well as the sugar moiety 2-Deoxy-D-Ribosephosphate Chain Unit (67-8300).
Also, in our discussion of DNA, we will confine our comments to the monophosphorylated versions of the respective nucleosides, i.e. Adenosine-, Guanidine-, Thymidine-, and Cytidinemonophosphate. The paired bases (i.e. A-T and G-C) are shown diagrammatically in FIGURE
201.
FIGURE 201. (A.) Adenine-Thymine Base Pair (67-8318) and (B.) Guanine-Cytosine Base Pair
(67-8326)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
First, note the hydrogen bonding between each of the base pairs, two in A-T and three in GC. Also, note the locations of the monophosphorylated sugar moieties (*), position number one
in the pyrimidines and number nine in the purines.
The final finished structures of these base pairs are shown in FIGURE 202.
FIGURE 202. (A.) Adenine-Thymine Base Pair (67-8318) and (B.) Guanine-Cytosine Base Pair
(67-8326)
The monophosphorylated sugar moiety is illustrated in FIGURE 203.
FIGURE 203. 2-Deoxy-D-Ribosephosphate Chain Unit (67-8300)
–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
To construct DNA, consult TABLE 2 for choices of components and sizes (i.e. the number of
turns about the central axis).
TABLE 2. DNA Molecular Size and Components.
QUANTITY
1.0 TURN
COMPONENTS
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Adenine-Thymine
Base Pair
(67-8318)
22
5
32
8
42
10
H a r v a r d A p p a r a t u s C P K® A t o m i c M o d e l s
2-Deoxy-D-Ribose
phosphate Chain Unit
(67-8300)
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