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William F. Coleman Wellesley College Wellesley, MA 02481
Molecular Models of Alkyl Carboxylic Acids and Amines William F. Coleman Department of Chemistry, Wellesley College, Wellesley, Massachusetts 02481
[email protected]. w This paper contains enhanced objects available on the Internet at http://pubs.acs.org/jchemeduc. n
JCE Featured Molecules for April 2010 In their paper describing a colorful overhead projector demonstration, Sally Solomon and Susan Rutkowsky make use of three medium chain length carboxylic acids and the corresponding amines (1). These molecules can be used to illustrate a number of chemical principles in addition to their acid-base behavior. All of these molecules (butanoic acid, hexanoic acid, octanoic acid, butylamine, hexylamine, and octylamine) have been added to the collection (2) and 3D rotatable images in MOL format are available in the HTML version of this paper. Table 1 shows some computed Mulliken charges and bond lengths on the three acids using three different computational methods: PM6; HF-631G(d); and DFT-B3LYP-631G(d). This is a good opportunity to discuss the difficulties of calculating partial atomic charges (3). It is interesting to note that the Table 1. Computed Mulliken Charges and Bond Lengths Computational Methods Carboxylic Acid
PM6
HF
changes in the alkyl substituents on the carboxyl group have minimal effect on the computed properties in that group. Students could perform similar calculations on other acids to examine the effect of the nature of the substituent; a good example would be the chloro-substituted acetic or propionic acids. The acids that are in the collection show straight chain alkyl groups for the optimized structures. Students attempting to model,
Figure 1. n w Butanoic acid. The left image shows a straight chain alkyl group for the optimized structure. The right image shows the optimization converging to a structure with a bent alkyl chain. Web enhanced images of the panels in Figure 1 can be found in the HTML version of this paper.
DFT
Butanoic Acid H in OH
0.324
0.463
0.407
O in OH
-0.540
-0.704
-0.569
C in COOH
0.650
0.789
0.606
-0.440
-0.528
-0.436
r CdO
1.201
1.181
1.204
r C-O
1.388
1.338
1.364
O in CdO
Figure 2. Dihedral angles of butanoic acid varied to produce the graph in Figure 3.
Hexanoic Acid H in OH
0.324
0.463
0.407
O in OH
-0.540
-0.705
-0.570
0.651
0.792
0.609 -0.437
C in COOH
-0.439
-0.528
r CdO
1.201
1.181
1.204
r C-O
1.388
1.338
1.365
O in CdO
Octanoic Acid H in OH
0.324
0.463
0.407
O in OH
-0.540
-0.705
-0.570
C in COOH
0.651
0.792
0.609
-0.439
-0.528
-0.437
r CdO
1.201
1.181
1.204
r C-O
1.388
1.338
1.365
O in CdO
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Figure 3. Two dihedral angles, shown in Figure 2, were varied to produce the result of 1044 HF-631G(d) calculations on butanoic acid.
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r 2010 American Chemical Society and Division of Chemical Education, Inc. pubs.acs.org/jchemeduc Vol. 87 No. 4 April 2010 10.1021/ed1001224 Published on Web 03/09/2010
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Journal of Chemical Education
457
On the Web
for example, butanoic acid, might well find their optimization converging to a structure with a bent alkyl chain. This presents a good opportunity to discuss global versus local minima, the importance of starting optimizations from several different geometries, and the concept of conformational analysis. These two structures are shown in Figure 1, and both are included in the molecule collection. Two dihedral angles, shown in Figure 2, were varied to produce the result of 1044 HF-631G(d) calculations on butanoic acid shown in Figure 3. Dihedral angle 1 was scanned from 0 to 360 degrees in 10-degree increments, and dihedral angle 2 from 0 to 270 degrees. It is clear that there are a number of local minima, all lying with a few kcal/mol of the global minimum. The entire spread of the energies shown in the graph is about 11 kcal/mol.
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Journal of Chemical Education
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Vol. 87 No. 4 April 2010
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Literature Cited 1. Solomon, S. D.; Rutkowsky, S. A. J. Chem. Educ. 2010, 87, DOI: 10.1021/ed800122y. 2. Molecular Models of Alkyl Carboxylic Acids and Amines; available at the JCE Digital Library, http://www.jce.divched.org/JCEWWW/ Features/MonthlyMolecules/2010/Apr (accessed Feb 2010). 3. More details of the difficulties in calculating partial atomic charges can be found in many texts on computational chemistry, including Cramer, C. J. Essentials of Computational Chemistry: Theories and Models, 2nd ed.; Wiley: Chichester, West Sussex, England, 2004 and Hehre, W. J. A Guide To Molecular Mechanics and Quantum Chemical Calculations; Wavefunction, Inc.: Irvine, CA, 2003.
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r 2010 American Chemical Society and Division of Chemical Education, Inc.
