Tomado con fines académicos de: Atkins and De Paula, 10 ed.

Molecular Modeling

Structure and Vibrational Spectra

1. Using Vibrational Frequencies to Verify an Equilibrium also presumably to bond lengthening. This in turn suggests
Structure. that Hartree-Fock bond distances are too short.
Each of the frequencies that make up the vibrational
(infrared/Raman) spectrum of a molecule is proportional to Compare the experimental bond length for hydrogen fluoride
the square root of the ratio of the curvature of the potential (0,917Ǻ) with that obtained from the Hartree-Fock model
surface in the vicinity of the structure (the second derivative of using the cc-pVTZ basis set. This is a sufficiently large basis set
the energy) and a mass. As mass is positive, this means that the to approximate the limit of the Hartree-Fock model for
resulting frequency will be a real number only if the surface equilibrium geometries. Is the calculated distance shorter than
curves upward (the second derivative is positive). Therefore, the experimental value?
the presence of one or more imaginary frequencies in a Repeat your calculations for lithium hydride (the experimental
calculated spectrum indicates that the structure is not an bond length is 1.596Ǻ). Is the Hartree-Fock distance shorter
energy minimum. than the experimental length? If it is not, provide an
explanation why not. Hint: examine both highest-occupied and
Use the HF/6-311G** model to obtain equilibrium geometries lowest-unoccupied molecular orbitals.
and vibrational spectra for the chair and boat forms of
cyclohexane. Are all frequencies real for both molecules? 4. Bond Lengths in Cyclopropane and Cyclobutane.
Which if either molecule is not a minima on the energy Use the Hartree-Fock model with the 6-31G* basis set to
surface? Elaborate. obtain equilibrium geometries for propane and cyclobutane.
Are the carbon-carbon bond lengths in the cycloalkane
2. Equilibrium Geometry of Disilylene (H2Si=SiH2). shorter, longer or about the same as those in propane (the
As discussed in the previous problem, a structure that gives “standard)? Is what you find consistent with the fact that CH
rise to a vibrational spectrum with an imaginary frequency is bonds on adjacent CH2 groups nearly eclipse each other
not an energy minimum. However, a minimum energy leading to an increase in non-bonded repulsion? Elaborate.
structure can be located from such a structure by “walking Given your result for cyclobutane, what you expect the carbon-
along” the geometrical coordinate associated with the carbon bond lengths in cyclopropane to be? Is your
imaginary frequency. expectation supported by the calculated equilibrium
structrure? If it is not, provide a plausible explanation as to why
Use the B3LYP/6-311G** model to obtain the equilibrium not.
geometry of planar (like ethylene) disilylene, the simplest
molecule with a silicon-silicon double bond, and calculate the 5. Water Dimer.
vibrational spectrum. Are all frequencies real numbers? If they The water dimer exhibits a structure with a single hydrogen
are not, perform the following operations: First, animate any bond. While the H --- O distance is not known experimentally,
imaginary frequencies to see how disilylene wants to distort to the distance between the two oxygen atoms has been
move it toward an energy minimum. Next, distort your measured as 2.98Ǻ.
structure accordingly. Finally, reoptimize the geometry (of the
distorted molecule) and again calculate vibrational
frequencies. Is it now an energy minimum? If not, repeat the
process until you get a minimum energy structure. Describe
the equilibrium geometry of disilylene.
The Hartree-Fock model with the very large cc-pVQZ basis set
3. Limiting Hartree-Fock Bond Lengths. shows a similar overall geometry but with an OO distance that
The Hartree-Fock model almost always yields bond lengths is 0.05Ǻ longer than the experimental value. This suggests that
that are shorter than experimental distances. This may be electron correlation shortens the hydrogen bond, the opposite
explained by noting that improvements to the Hartree-Fock of what is normally observed for covalent bonds. To model the
model involve promotion of electrons from molecular orbitals effect of correlation on the geometry of water dimer, consider
that are occupied to orbitals that are unoccupied. Occupied the consequences of promoting electrons from filled to empty
orbitals are typically either bonding or non-bonding whereas molecular orbitals, most simply from the highest-occupied to
unoccupied orbitals are typically antibonding. Therefore, the lowest-unoccupied molecular orbital.
electron promotion not only leads to a better description but
Obtain the geometry of water dimer using the Hartree-Fock/6-
31G* model, and display the highest-occupied and lowest-
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unoccupied molecular orbitals. Is the HOMO bonding, larger dimerization energy also that with exhibits the larger
antibonding or non-bonding with respect to the H --- O changes in structure?
hydrogen bond? Would loss of an electron lead to shortening
or lengthening of the hydrogen bond or would it be expected 8. Infrared Spectrum of Acetic Acid Dimer.
to have little effect? Is the LUMO bonding, antibonding or non- Use the B3LYP/6-31G* model to calculate infrared spectra for
bonding with respect to the H --- O hydrogen bond? Would acetic acid and its dimer. (You already have equilibrium
gain of an electron lead to shortening or lengthening of the structures if you completed the previous problem.)
hydrogen bond or would it be expected to have little effect?
Overall, would you expect the limiting Hartree-Fock hydrogen
bond distance in water dimer to be shorter or longer than or
unchanged from the experimental value?

6. Alternative Structure of the Water Dimer. Point out and rationalize any significant differences between
As detailed in the previous problem, water forms a dimer with the frequencies and/or intensities associated with the (two)
a single hydrogen bond. However, because water incorporates OH stretching motions in the dimer and the OH stretching
two electron pairs that may act as hydrogen bond acceptors frequency in acetic acid.
and two OH bonds that may act as hydrogen-bond donors, it
should be possible to construct an alternative dimer with two 9. Radical Cation of Diborane.
hydrogen bonds. Does such a structure actually exist? One of the valence molecular orbitals of diborane closely
resembles the π orbital in ethylene.

Attempt to obtain an equilibrium geometry for the doubly

hydrogen-bonded structure of water dimer. Use the B3LYP/6-
31G* model. If you find such a structure, confirm that it is or is
not an energy minimum. If it is an energy minimum, calculate
the room-temperature Boltzmann distribution of the two Removal of an electron from this orbital should increase the
different forms of water dimer.
separation of the boron atoms, just as removal of an electron
from the π orbital in ethylene should lengthen the CC bond.
7. Acetic Acid Dimer.
Acetic acid forms a dimer with two equivalent hydrogen- Use the B3LYP/6-31G* model to obtain geometries for
bonds. Has the geometry of acetic acid remained largely
diborane and its radical cation. Make certain that you start
unaffected by hydrogen bonding (as suggested in the drawing with a distorted (C1 summetry) structure for the radical cation.
below), or have significant structural changes occurred? Also, obtain vibrational frequencies (infrared spectrum) for the
radical cation to be certain that it is an energy minimum. Does
ionization lead to the “anticipated” increase in distance
between the two boron atoms? If it does not, then explain why
not. Hint: Is the molecular orbital in diborane that resembles
the π orbital in ethylene the HOMO?
Use the B3LYP/6-31G* model to calculate equilibrium
structures for acetic acid and its dimer. Point out any
10. Limitations of VSEPR Theory.
significant changes in bond lengths between the two. Does the
VSEPR (Valence State Electron Pair Repulsion) theory uses two
dimer incorporate distinct CO single and double bonds? Have
simple rules to assign geometry. First, the geometry about an
the hydrogen atoms involved in the hydrogen bonds moved to
atom follows by insisting that electron pairs (bonds or lone
positions halfway between the oxygen atoms, or has each
pairs) are as far apart as possible. Second, it is more important
hydrogen atom remained with a single oxygen atom? Do the
to separate two lone pairs than it is to separate a lone pair
structural changes (or lack of structural changes) suggest that
from a bond than it is to separate two bonds. Taken together,
hydrogen bonds are comparable in strength to
these two rules properly account for the observed “see-saw”
normal(covalent) bonds or that they are weaker? Elaborate.
structure of sulfur tetrafluoride, SF4. Sulfur atom surrounded
by five electron pairs (four bonds and a lone pair) assumes a
Repeat your calculations for trifluoroacetic acid and its dimer.
trigonal bipyramidal geometry, and the lone pair prefers an
Are geometry changes smaller, larger or about the same as
equatorial position. What VSEPR theory does not tell us is
those seen for acetic acid? Is the dimerization energy for
whether this is the only structure of SF4, in particular, whether
trifluoroacetic acid smaller, larger or about the same as that
a trigonal pyramid structure (which obeys the first rule but
for acetic acid? If the two are different, is the acid with the
violates the second) might also be an energy minimum.

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 ethylene. Do both structures appear to be minima on the C2H5+
potential surface or does one of the structures “collapse” to
the other? Elaborate. If there is only one energy minimum, is it
open or bridged?

14. Protonated Methane.

The structure of the ion resulting from protonation of a
Use the HF/6-31G* model to obtain geometries for both forms
molecule with a non-bonded electron pair should be similar to
of SF4. Start with C2v symmetry for the see-saw structure and
the structure of the corresponding isoelectronic neutral
C3v symmetry for the trigonal pyramid structure. Are both
molecule, that is, the neutral molecule with the same number
structures energy minima or is there only one structure? Detail
of electrons. For example, protonated ammonia should be
your reasoning. If there is only one structure, is it the observed
tetrahedral by analogy with methane. There are, however, no
structure? If there are two structures, is the observed
known (characterized) neutral analogues of ions resulting from
structure favored? Is the higher-energy structure likely to be
protonation of alkanes. Here, all the valence electrons are
observed at room temperature? (Assume that it must make up
already tied up in σ bonds, and any new bonds must be made
at least 5% of the mixture to be detected.)
at the expense of these existing bonds. Nevertheless,
protonated alkanes are observed by mass spectrometry. What
11. Failures of VSEPR Theory.
do they look like?
The crystal structure of CaF2 shows that the molecule is bent,
at odds with the prediction of VSEPR theory which assigns a
Use the B3LYP/6-31G* model to explore possible structures for
linear geometry. Is this a failure of VSEPR theory or is it due to
protonated methane (CH5+). Calculate vibrational frequencies
crystal packing? Use the B3LYP/6-31G* model to obtain the
for whatever you uncover to verify it is actually and energy
equilibrium geometry of CaF2. Start with a bent structure, Does
minimum. Describe the bonding in terms of a weak complex or
this collapse to linear geometry or does the molecule remain
a molecule with a pentavalent carbon. If it is a complex,
bent?
identify the components and calculate the binding energy. The
If "free" CaF2 is linear, calculate the geometry for a molecule
gas-phase proton affinity of methane is 544 kJ/mol, which is
with a FCaF bond angle constrained to 140o, and compare its
significantly less than the proton affinity of water (691 kJ/mol),
energy to that of linear CaF2. What does the energy difference
but larger than the proton affinity of N2 (494 kJ/mol). What is
tell you about the magnitude of the crystal packing energy? If
the calculated proton affinity? (Note that the energy of a
on the other hand, "free" CaF2 is bent, calculate the geometry
proton is 0.)
of "linear" CaF2 and compare its energy to that of the bent
molecule.
Repeat you calculations and analysis for protonated ethane
(C2H7+).
12. Geometry Changes with Change in the Number of
Electrons.
15. Structure of Diazomethane.
The geometry of a molecule depends not only on the
Is there a single Lewis structure for diazomethane or is a
constituent atoms, but also on the total number of electrons.
composite of two structures required for proper description?
Use the HF/6-31G* model to obtain equilibrium geometry for
2-methyl-2- propyl cation (tert-butyl cation), as well as those
for the corresponding radical (with one additional electron)
and the anion (with two additional electrons). Describe any
changes to the geometry of the central carbon with increasing To decide, compare the geometry of diazomethane obtained
number of valence electrons, and speculate on the origin of from the HF/6-31G* model with those of methylamine,
these changes. Hint: examine the lowest-unoccupied CH3NH2, and methyleneimine, H2C=NH, molecules
molecular orbital (the next orbital to be occupied) in tert-butyl incorporating normal CN single and double bonds,
cation. respectively, and those of trans diimide, HN=NH, and nitrogen,
N N, molecules incorporating normal NN double and triple
13. Protonated Ethylene. bonds, respectively. If two Lewis structures are required,
What is the geometry of protonated ethylene? Is the proton which appears to be the more important?
primarily associated with a single carbon does it “bridge” both
carbons? 16. Structure of Ozone.
Ozone, O3, leads a proverbial double life. In the upper
atmosphere, it protects the earth and its inhabitants from
harmful UV radiation, while nearer to the surface it is a serious
pollutant contributing to respiratory problems. Draw two
Use the B3LYP/6-31G* model to calculate equilibrium different Lewis structures for ozone, one or both of which may
geometries for both open and bridged forms of protonated require non-zero formal charges. Attempt to obtain
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equilibrium geometries corresponding to both structures using gaseous atmosphere. This in turn means that the earth is
the B3LYP/6-31G* model. Verify your results by obtaining actually warmer than it would be were it not to have an
infrared spectra. If you do obtain two different structures, atmosphere. This warming is known as the greenhouse effect,
identify which structure is lower in energy. Is it in accord with to make the analogy between the earth’s atmosphere and the
the experimentally known equilibrium geometry? If the glass of a greenhouse. Both allow energy in and both impede
preferred structure has more than one distinct oxygen atom, its release. The actual distribution of radiated energy as
which is most positively charged? Most negatively charged? Is measured from outside the earth’s atmosphere in the range of
your result based on electrostatic charges consistent with that 500- 1500 cm-1 is given below. The overall profile matches that
based on formal charges (in the Lewis structure)? for a blackbody, but the curve is peppered with holes.

17. Hydrated Hydronuim Cation.

Use the B3LYP/6-31G* model to calculate the equilibrium
geometry of hydronium cation, H3O+. Next, calculate the
structure of a complex between H3O+ and four water
molecules. Point out any significant changes that have
occurred to the cation a result of interaction with water. In
particular, is there evidence for “sharing” the proton? Has the
positive charge remained localized on the hydronium cation or
has it spread out to the surrounding water molecules?

18. Hydrated Chloride Anion.

Use the B3LYP/6-31G* model to calculate the equilibrium
geometry for chloride anion surrounded by four water Neither nitrogen nor oxygen, which together comprise 99% of
molecules. Has the negative charge remained on the chlorine the earth’s atmosphere absorbs in the infrared and causes the
or has it spread out to the water molecules? “holes”. However, several “minor” atmospheric components,
carbon dioxide most important among them, absorb in the
19. Borane Carbonyl. infrared and contribute directly to greenhouse warming. Its
Borane carbonyl, BH3CO, results from interaction of the infrared spectrum shows a strong absorption in the region
nonbonded electron pair (on carbon) in carbon monoxide and centering 670 cm-1, the location of the most conspicuous hole
an empty p-type orbital in borane. in the blackbody radiation profile.

Unlike transition-metal carbonyl complexes (see following

problem), there is little possibility for significant back bonding,
that is, interaction of a high-energy filled molecular orbital on
borane with an empty π* orbital on carbon monoxide. This
suggests that neither the CO bond length nor the vibrational
frequency of carbon monoxide is likely to change significantly
as a result of complexion.

Use the B3LYP/6-31G* model to obtain equilibrium geometries

and infrared spectra for both carbon monoxide and borane
carbonyl. Is there a significant change in CO bond length?
Identify the frequency in borane carbonyl corresponding to the
CO stretch. Is it smaller, larger or about the same as that in free
carbon monoxide?

20. Greenhouse Gases.

In order to dissipate the energy that falls on it due to the sun,
the earth “radiates” as a so-called “blackbody” into the
universe. The “theoretical curve” is a smooth distribution Identify three of the top ten chemicals manufactured
peaking around 900 cm-1 and decaying to nearly zero around worldwide. Use the B3LYP/6-31G* model to calculate the
1500 cm-1. This is in the infrared, meaning that some of the infrared spectra for each and comment whether or not you
radiation will be intercepted by molecules in the earth’s would expect it to be a significant greenhouse gas.

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21. Comparison of Measured and Calculated Frequencies. 23. Lithium Aluminum Hydride.
Frequencies routinely obtained from quantum chemical Lithium aluminum hydride (LiAlH4) is among the most
calculations assume that the potential in the vicinity of the important reducing agents, that is, source of “hydride”. Is it
minimum is a quadratic function. This means that they are best described as an ion pair between lithium cation and
generally larger than measured frequencies. (The correct aluminum hydride anion (AlH4— ), a weak complex between
potential for say a bond stretching motion goes to zero lithium hydride (LiH) and aluminum hydride (AlH 3), or are one
whereas a quadratic potential goes to ∞. It is possible to or more hydrogen atoms “shared” by the two metals? To
correct calculated frequencies for cubic and higher-order decide, obtain the equilibrium geometry using the B3LYP/6-
terms, but this is generally prohibitive in terms of computer 31G* model. Are the calculated atomic charges consistent with
time. It is also possible to correct measured frequencies for your geometry? Elaborate. Is there more than one stable
anharmonic behavior, leading so-called “harmonic structure for lithium aluminum hydride? Start from one or
frequencies”. These exist only for diatomic and very small more structures that are different from what you have found
polyatomic molecules, and include: LiF, 914; CO, 2170; N 2, and see if you get a different result.
2360 and F2, 923 (all in cm-1).
24. Sodium Cyclopentadienide:
Use the HF/6-311+G** model to calculate equilibrium Is sodium cyclopentadienide accurately represnted in terms of
geometries and vibrational frequencies for LiF (914), CO a structure in which sodium cation associates with
(2170), N2 (2360) and F2 (923). (Harmonic frequencies in cm-1 cyclopentadienyl anion?
are given in parentheses.) What is the average percentage
error between calculated and measured (harmonic)
frequencies? Are calculated frequencies uniformly too small or
too large?

Repeat your calculations using the B3LYP/6-311+G** model. Obtain the equilibrium geometry of sodium cyclopentadienide
What is the average percentage error between calculated and using the B3LYP/6-31G* model. Is the charge on sodium close
measured (harmonic) frequencies? Is this smaller than the to unity? Calculate the equilibrium geometry of
average error for Hartree-Fock calculations? Are calculated cyclopentadienyl anion and compare it with the
frequencies uniformly too small or too large? cyclopentadienyl fragment in sodium cyclopentadide. Is what
you find indicative of a weak complex? Elaborate. Calculate the
22. Methyl Lithium: energy of dissociation to cyclopentadienyl anion and sodium
The structure of methyl lithium appears to be “normal” insofar cation (you need to obtain the energy for sodium cation). Is the
as it incorporates a carbon with a roughly tetrahedral binding energy weak (< 100 kJ/mol), comparable to that of a
geometry. This could either mean that the C-Li bond is normal covalent bond (~400 kJ/mol) or somewhere in
covalent, or that lithium cation is loosely associated with between? Is your result consistent with the calculated charges
methyl anion (which also incorporates a tetrahedral carbon). and geometries?
Which of these descriptions is more consistent with atomic
charges obtained from the HF/6-31G* model? Elaborate. 25. Proton NMR Spectrum of Cyclohexane.
At very low temperatures, the proton NMR spectrum of
Experimentally, methyl lithium exists most simply as a cyclohexane shows two equal intensity lines at 1,12 and 1,60
tetramer with the four lithium atoms and four methyl groups ppm. Use the HF/6-31G* model to obtain the equilibrium
at the corners of a cube. geometry and the proton chemical shifts. Which line
corresponds to the equatorial protons and which corresponds
to the axial protons?

Use the HF/6-31G* model to calculate the geometry of methyl

lithium tetramer. Does the conclusion you reached about the
nature of the bonding in methyl lithium maintain?
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