Experiment 4

Experiment 4
Conformational Isomers of H2C=CH−OH(CH3). Theoretical Study

Introduction
Chemistry is, roughly speaking, the branch of the natural sciences investigating the
properties, composition, and transformation of matter. The computer-based molecular
modeling plays an increasingly important role in chemical studies and researches.
Nowadays, the computer-based molecular modeling is called Computational Chemistry.
Within computational chemistry, this is done not by observation, but by a mathematical
description of the physical system of interest. The constant improvement in the quality of
mathematical descriptions, combined with the enormous advancement of computer
technology in the past decades, has allowed the field of computational chemistry to
advance as well. Consequently, computational chemistry is becoming an essential adjunct
to experimental chemistry, whether it be organic synthesis, biochemistry, medicinal
chemistry, spectroscopy, or chromatography. Moreover, the main benefit of computational
modeling, though, is that it allows chemists to think more clearly about issues that are really
central to chemistry - structure, stability, and reactivity - than would be possible without
the use of a computer.
This experiment involves analysis of the conformational potential energy surface
of vinyl alcohol and methyl vinyl ether, Figure 1. The learning goals of this exercise are (i)
to familiarize students with the concept that different conformations of molecules relate to
energy minima and maxima, (ii) to highlight the relationship between the hybridization of
the O atom and its lone pairs, (iii) to illustrate that the p-hybridized lone pair of the O atom
is conjugated to the π-system of the vinyl part, and (iv) to show that conformational energy
minima and maxima of the molecules are related to the extent of conjugation of the p-
orbital lone pair.
(a) (b)
Figure 1. The structure of (a) Vinyl alcohol and (b) Methyl vinyl ether.
Experimental Part
All calculations in this experiment are provided at the B3LYP/3-21+G(d) level of
theory. Students examine a completed Coordinate Scan output to visualize rotation of the
C4−O6 bond defined by the C1−C4−O6−H7 and C1−C4−O6−C7 of the vinyl alcohol and
methyl vinyl ether, respectively, and the dihedral angle from 180° to 0° as depicted in
Figure 2, and use it to build the corresponding conformational potential energy plots of
dihedral angle (°) vs relative energies (kcal/mol) (Figure 2).
Figure 2. C1-C4-O6-C7(H7) dihedral angle of vinyl alcohol and methyl vinyl ether viewed
side-on and via Newman projection.
Steps:
1. Optimize the structures using
B3LYP/3-21+G* opt=calcfc freq gfinput pop=(full,nboread)
order in the input file. Name this job: compound name_opt1.
2. In the Coordinate output, scan, a new job, the dihedral angle from 180° to 0° as
shown in Figure 2. Use the following order:
%chk=C:\Users\GTS\Desktop\calculations\test\physical lab\vinyl
alcohol_scan.chk
# b3lyp/3-21+g(d) opt=modredundant nosymmetry
Title
0 1
Molecular Specification
Geometry connectivity #
D 1 4 6 7 S 18 10.0
Name this job: compound name_scan
●
3. Click on the film strip icon ( ) in the Coordinate Scan windows to view an
animation of the C4–O6 bond rotation explored in this experiment. You should
observe the 180 – 360° rotation of the C1–C4–O6–C7(H7) described by the dihedral
angle and the associated energy value in Hartrees displayed in the scan plot.
4. Save the data from the scan plot: choose plots then choose save data. Copy and
paste to excel. Convert all of these B3LYP energy values to relative B3LYP energy
values by following the steps below.
a. Find the conformer that has the lowest energy value, which will be
associated with the most stable conformer. This is now a column
of relative B3LYP energies, rather than B3LYP energies.
b. Relative energies are the energy value of a given structure compared to the
structure with the lowest energy. Thus, the lowest energy conformation will
have a relative energy of 0.0, while other conformations will have positive
energy values, allowing easy visual comparison of energies.
c. Generate the plot of energies as a function of C–C–O–C dihedral angle.
5. The geometries of the minimum and maximum energy structures are using the
following orders:
I. For the two minimum structures:
a. Optimization and frequency calculations:
# B3LYP/3-21+G(d) OPT FREQ
b. Get the optimized minimum structures from step 5.I.a then do the NBO
calculations:
# B3LYP/3-21+G(d) SP GFINPUT POP=(FULL,NBORead)
II. For the transition state structure that you got from the scanning step:
a. Optimization and frequency calculations:
# B3LYP/3-21+G(d) OPT=(TS,NoEigenTest,NewEstmFC) FREQ
b. Get the optimized transition state structure from step 5.II.a then do the NBO
calculations:
# B3LYP/3-21+G(d) SP GFINPUT POP=(FULL,NBORead)
6. Use these jobs to fill Tables 1 and 2 in the data sheet summarizing the key points
of the coordinate scan.
7. Examine the Natural Bond Orbitals (NBO) output for the lowest-energy
conformation(s). Using the check point file, then choose results from the bar menu,
click on the surfaces/contours to view each orbital. Starting from the highest
energy occupied molecular orbital (HOMO), then work your way to lower energy
molecular orbitals until you find π-bond. Place the images of these orbitals in your
report and describe which atoms participate in conjugation.
8. To understand the stability of the low energy conformation, investigate the
geometry and hybridization of the O−atom and its lone pairs.
9. Use the NBO computational output to view the Natural Hybrid Orbitals description
and image of each O−atom lone pair. Find the O−atom lone pairs (LP(1)O and
LP(2)O) and the O−atom bonding pairs (BD(1)O−(C4) and BD(1)O−(C7 and H7))
in the Natural Hybrid Orbitals list. Include an image of each orobital and state the
hybridization of each in your report using standard spx notation.
10. Click the tetrahedral angle, then click sequentially on the atoms defining the C−O–
C bond angle. Provide the measured angle in the data sheet, Tables 1 and 2.
11. Based upon all of the information available, state the approximate hybridization of
the O−atom in both compounds and justify your reasoning.
12. Explain how the O−atom lone pair hybridization relates to the conjugated π system
of both compounds. Include important molecular orbital depictions and/or
resonance structures.
13. Directly compare the lowest energy and highest energy conformations of both
compounds. State which isomer has:
a. The highest steric strain based upon measured atomic distances
b. The most effective π-conjugation based upon its lone pair hybridizations
and orientations
c. Based upon your answer, state whether steric strain or π-conjugation is most
important in determining the most stable conformation of both compounds.
d. Do your comparisons between the two compounds.
Report
Conformational Isomers of H2C=CH−OH(CH3). Theoretical Study
Hint: You can use extra sheets
Name: Partners’ Names:
Abstract
Introduction
Theoretical Details
Data Sheet
Table 1. The dihedral angles (o), the vibrational frequencies (cm-1) and the total B3LYP
energies (au) for the minimum and transition state structures of vinyl alcohol compound.
Vibrational frequency
C−C−O−H C−O−H tetrahedral B3LYP energy
(cm-1)
dihedral angle (o) angle (o) (au)
dihedral tetrahedral
Table 2. The dihedral angles (o), the vibrational frequencies (cm-1) and the total B3LYP
energies (au) for the minimum and transition state structures of methyl vinyl ether
compound.
Vibrational frequency
C−C−O−C C−O−C tetrahedral B3LYP energy
(cm-1)
dihedral angle (o) angle (o) (au)
dihedral tetrahedral
Calculations
Results and Discussion
Conclusion
References

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Conformational Isomers of H2C=CH−OH(CH3). Theoretical Study

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