Download Testing Lewis Formulas and VSEPR Models with Quantum Theory

Testing Lewis Formulas and VSEPR Models with Quantum Theory
VI. Advanced Option. Analyzing molecular geometry and dipole moment
1. Actual bond angles. Only in certain symmetric molecules do the bond angles equal the
exact nominal value. More commonly, the different effective sizes of lone pairs, double
bonds, and single bonds cause variations in bond angles of up to about ± 5° from the nominal
values. The effective sizes of different bonds and lone pairs decrease in the order: lone pair >
double bond > single bond. Lone pairs are large and diffuse because there is only one nucleus
to attract the electron pair. Double bonds are larger than single because they contain four
electrons rather than two.
Electron Pair # Lone
Nominal Bond Actual Bond
Molecular shape
Geometry
Pairs
Angle (°)
Angle (°)
Linear
0
Linear
180
180
Trigonal planar
1
Bent
120
< 120
0
Trigonal planar
120
>, =, or < 120
Tetrahedral
2
Bent
109
< 109
1
Trigonal pyramidal
109
< 109
0
Tetrahedral
109
>, =, or < 109
Trigonal
Linear
3
180
180
bipyramidal*
2
See-saw
90, 120
< 90, < 120
1
T-shaped
90
< 90
0
Trigonal bipyramidal
90, 120
>, =, or < 90, 120
Octahedral*
2
Square pyramidal
90
>, =, or < 90
1
Square planar
90
>, =, or < 90
0
Octahedral
90
>, =, or < 90
*Only nearest neighbor bond angles are included here.
Choose a nonlinear molecule or ion from Part I and open the WebMO job
for the correct molecular geometry. Measure several bond angles, print out the
structure, or make a drawing, and label the various angles. List the bond angles,
and tell how they differ from the nominal values, and discuss how any
differences are (or are not) consistent with the orbital size requirements
mentioned above.
2. Molecular dipole. The unequal distribution of electrons within an ion or
molecule sets up an electric field called the molecular dipole. This can be
thought of as the vector sum of bond dipoles, which in turn arise from partial
charge differences between bonded atoms. A lone pair can also be assigned its
local dipole. In the Part 1 WebMO page, click the magifying glass icon inside the
Partial Charges box. Print, or make a drawing of, the partial charges. Draw in
estimated bond dipoles, and “eye-ball” the vector sum of these. Finally, in
WebMO, click the icon next to Dipole Moment to display the PM3-calculated
dipole moment. Print or draw this.
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Example
Thioformate (PM3)
S-C-O: 131.73°
H-C-S: 114.11°
H-C-O: 114.16°
The C-S bond is rather
large due to the large
size of S. The C-S
bond results from
overlap of S 2s with C
1s.
Testing Lewis Formulas and VSEPR Models with Quantum Theory
VI. Use the Internet to track down occurences of trigonal bipyramidal or
octahedral atoms in nature
Molecules with the trigonal bipyramidal or octahedral molecular geometry seem rather exotic
at first glance. However, these bonding patterns are surprisingly common in nature and in
manufactured substances, and atoms like this ultimately play important roles in many natural
chemical processes.
Using an Internet search engine, enter in the search box “trigonal bipyramidal” or
“octahedral”, plus “enzyme”, “drug”, “gene”, “cancer”, “ore”, or “catalyst”, or other term
related to your scientific or engineering interests that may have a chemistry connection. In
the resulting hit list, locate a scientific article or webpage (not Wikipedia) that describes a
molecule, ion, or complex material containing a bonded atom with (approximate or exact)
trigonal bipyramidal (or octahedral) molecular geometry. You may use other linked web
sources to find out more about the terms, concepts, or background on this substance.
Write a one-page report including the following:








Your name, date, lab section, teaching assistant
Name and description of the compound or substance, including the atoms or groups
occupying the five (or six) positions around the central atom.
Geometric parameters, such as actual bond angles and bond distances.
Optional: To better understand the molecule’s geometry and bonding, you may wish
to build and optimize it using WebMO with PM3 method, or Import the XYZ
coordinates if you can find them. Other molecular modeling software that may be
available to you could be used as well.
Picture of molecule.
Function of the molecule or substance: what does it do? Why is it useful or important?
Names and affliations (university or manufacturing company) of scientists or engineers
who discovered, synthesized, or studied the molecule.
List the URLs and other bibliographic information for the sources that you used, such
as an article’s author(s), title, journal, pages, and year.
Example. Entering the terms “octahedral gene” in Google
Chrome search box, the 8th hit was “Trans- and Cis-Water
Reactivities in d6 Octahedral Ruthenium..”
http://tinyurl.com/pc3c9no. I noticed that on this page, there is
a list of Citing Articles, that is, more recent articles that cite this
as a footnote. Of particular interest from a medical point of view
was a 2008 article in the Journal of Physical Chemistry by Besker
et al. entitled “Aquation of the Ruthenium-Based Anticancer
Drug NAMI-A” http://tinyurl.com/pumplhx
Figure. (L) From Besker et al. (R)
optimized by PM6 with WebMO.
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