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Unknown Compound 6

Natalie Duke, Michelle Jeu,


Fern Lawson, Morgan Renfro
Mass Spectroscopy

The compound given is C6H12O3. Using mass spectrometry, it was determined


that unknown compound 6 is more specifically 2,2-dimethyl-1,3-dioxolane-4-methanol.
Since mass spectrometry is a plot of ion abundance versus mass-to-charge ratio (m/e), a
list of known (m/e)s and their corresponding molecular compound combinations is
helpful in determining the structure of the compound. Since each peak at different (m/e)s
depicts different segments of the structure of the compound, and the compound is to be
thought of as being split into different ion groups, list is helpful.
This compound was discovered to be 2,2-dimethyl-1,3-dioxolane-4-methanol
based on four different peaks in the mass spectrometry plot. When looking at the peaks at
an m/e of 31 and 101, both segments together contain the total necessary carbons,
hydrogens and oxygens that make up the compound. The peak at (m/e) 31 corresponds to
the group CH2OH and the peak at (m/e) 101 corresponds to the group C4H9OCO.1Since
the segments are to be thought of as divisions of the compound’s structure, the
components of the segments must remain adjacent to each other in the structure, i.e. the
CH2 and the OH from the peak at (m/e) 31 must be adjacent to each other. Thus, the
segment at m/e 31 makes up one half, or side, of the compound and the segment at m/e
101 makes up the other half, or side, of the compound. Since (m/e) 31 is CH2OH, it is
known that the compound is an alcohol.
The other two peaks at (m/e) 43 and 15 both have a methyl group in them. The
peak at (m/e) 43 corresponds to CH3CO and the peak at (m/e) 15 corresponds to CH3.
This fact means that there are two methyl groups in the compound. Since the peak at
(m/e) 43 is the tallest peak, it is therefore the base peak.2 This fact means that whatever
segment is associated with this peak is the most abundant, or is present in multiple
different “splittings,” of the compound. Since there are two methyl groups in the
compound and the (m/e) at peak 43 is the most abundant and there are only two oxygens
in the compound, it is apparent that the two methyl groups are on the same carbon. After
comparing the oxygen components within this peak at (m/e) 43, and taking into account
that the components of the peak at (m/e) 43 are the most abundant, it is apparent that
there are two oxygens bonded to the carbon to which the two methyl groups are bonded.
After determining this aspect of the structure, it is then chemically impossible for there to
be a double bond between the carbon and either of the oxygens, since there are two
oxygens and two methyl groups on carbon resulting in four bonds on that carbon, this
thus means that the compound must be a ring in order for the structure to be chemically
possible. This in turn determines the rest of the structure, that the CH2OH segment is on
the side of the ring, and then yields the nomenclature of 2,2-dimethyl-1,3-dioxolane-4-
methanol.

IR Spectroscopy
1
Spectroscopy m/e and corresponding Ions handout, 240.
2
Pavia, D.L., Lampman, G.M., Kriz, G.S., and Engel, R.G. 2005. Introduction to Organic Laboratory
Techniques: A Small Scale Approach. 2nd Ed. Thomson Brooks/Cole, Belmont. 964-977.
Analysis of the infrared spectrum is useful in identifying the functional groups
present within a compound. IR does not tell scientists anything about connectivity, but it
does give them some clues about the structural components of an unknown compound.
No two molecules will have the same exact spectra. This is due to the fact that every
bond possesses a different type of frequency. These frequency vibrations appear within
an IR spectrum as specific peaks. When molecules absorb infrared radiation, an IR
spectrum can be produced and used for analysis. The IR spectroscopy of unknown
compound 6 revealed that the unknown was indeed 2, 2- dimethyl-1, 3-dioxolane-4-
methanol, a cyclic diester. 1
The first step in reading the IR spectrum for the compound with the molecular
formula C6H12O3 is to identify the main functional groups. A first glance at the
unknown’s IR spectrum reveals the presence of an OH group. This means the compound
is an alcohol. Alcohols show a peak to the left of 3000 cm-1. The presence of an OH group
is indicated by a sharp absorption peak between the range of 3650-3600 cm-1 if there is no
hydrogen bonding taking place. However, if hydrogen bonding is present, the alcohol’s
indicative peak will be shifted to the right to 3500- 3200 cm-1. The peak will generally be
broader. One is given that the IR was in a neat solution. This usually means there is
hydrogen bonding present. Analysis of the IR spectrum reveals a somewhat broad peak of
medium strength at around 3500 cm-1 indicating the presence of a hydrogen bonded
alcohol within the unknown. A medium stretch within the range of 1300-1000 cm-1 shows
that the O in the OH group participates in a single bond with a C. 1
In addition, there appears to be a bend indicative of a CH2 group around 1450 cm-
1
. This bend mode of vibration suggests that the unknown compound is a ring structure.
Two peaks appear approximately in the 1300-1000 cm-1 indicating the presence of two
CH3 groups. Analysis of the IR also reveals that this compound is a cyclic diester having
two C-O bonds. It is evident that a single bond exists between the carbon and the oxygen.
There is no C=O bond present. C=O bonds are found in the 1800-1600 cm -1 region, and
this spectrum shows little to no absorption in this region of the IR. However, two bands,
one stronger than the other, appear in the relative range of 1300-1000 cm-1 indicating the
single C-O bonds. A peak slightly to the right of 3000 cm-1 reveals the aliphatic C-H
bonds that are present in the cyclic diester ring.1

1
Pavia, Donald L., Gary M. Lampman, George S. Criz, and Randall G. Engel. Introduction to Organic
Laboratory Techniques: A Small Scale Approach. Canada: Brooks/Cole, 2005
Carbon-13 NMR

Using Carbon-13 NMR spectra, the composition of the compounds produced can
be verified to ensure pure products and that the reaction proceeded to completion.
Analysis of
13
C-NMR provides direct information about the carbon skeleton of a molecule.
Deuterated chloroform is used most commonly to stabilize the field. In CNMR, the spins
of protons attached directly to 13C atoms interact with the spin of carbon which causes the
carbon signal to split according to the n + 1 rule of heteronuclear (carbon-hydrogen)
coupling (Pavia 946-58).1 From the analysis of the Infrared spectra, it is found that the
compound is most likely a cyclic diester alcohol since IR spectra is useful in identifying
the functional groups present in the compound and provides structural information.
Analysis of the Proton NMR and the molecular formular from a chemical data base
suggests that Unknown Compound 6 with the chemical formula of C6H12O3 is 2,2-
dimethyl-1,3-dioxlane-4-methanol.2
Based on this proton coupling, the top part of the spectra yields the proton
coupled spectra. The chemical shift will give the electronegativity of each group attached
to a carbon atom. Electronegativity plays a large part in that the carbon group in the most
electronegative environment is on the left and least electronegative is on the right. The
intense peak at 110 ppm does not have any neighbors and is most characteristic of the O-
C-O diester. It is shifted further downfield because the carbon atom is attached to two
electronegative oxygen atoms caused by deshielding effects and the hybridization of the
molecule. Medium peaks showing 3 spin-spin splittings is characteristic of a methylene
carbon –CH2 group that is most likely bonded to an –OH group which again shifts the
peak down field. Two methyl groups attached to the same carbon yield 4 spin split peaks
that denote equivalent CH3 groups at the same chemical shift at a range of 20-30 ppm.
This is found from analysis of the n + 1 neighboring groups at this shift range that signals
3 protons connected directly to a singular carbon atom. Medium peaks at around 5 ppm
have two spin-spin splits that indicate two neighboring carbons and the oxygen bonded to
it draws the methine group downfield. At a shift range of 60-70 ppm there appears to be a
5 peak split which is probably a methylene group attached to an electronegative oxygen
that affects the shielding of the carbon atom.1
Nuclear Overhauser enhancement affects the increase in intensity of the peaks.
The more protons attached to the carbon the higher the correlation that the peaks will be
higher as well. The bottom spectra shows proton decoupling which further verifies the
identity of the relative groups by obliterating all interactions between protons and 13C
nuclei. This causes only singlets to be observed in the decoupled spectra. This technique
simplifies the spectrum and avoids overlapping multiplets. Because of this, the peaks at
20-30 ppm are shown indeed to be two separate carbon equivalents. The other spectra are
affirmed in the same way revealing the diester alcohol. Any impurirties or interference in
the absorptions also yield small peaks that affect the spin-spin splitting as well, but not
enough to change the chemical composition.1
1
Pavia, D.L.. Lampman, G.M.; Kriz, G.S.; Engel, R.G. Introduction to Organic Laboratory Techniques: A
Small Scale Apporach. 2nd Ed. Brooks/ Cole-Thompson, Belmont
2
Integrated spectral DataBase System for Organic Compounds. National Institute of Materials and
Chemical Research. 7 March 2008. <http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi>
From the analysis of the graph, it can be concluded that the compound is 2,2-
dimethyl-1,3-dioxlane-4-methanol. First, it has to be an alcohol because of the –OH
group. Also, the compound matches up perfectly with chemical shift and spin-spin
splitting of the graph. Therefore, the 13C-NMR confirms this is the compound’s identity.

Hydrogen NMR

In analyzing the mass spectroscopy, IR, 1H NMR, and 13C NMR of the given
molecule, we have concluded that this data is derived from the 2,2-dimethyl-1,3-
dioxolane-4-methanol molecule. This conclusion is supported by the proton-NMR
spectroscopy. Each proton will demonstrate a chemical shift, integral rise, and spin-spin
splitting that help to identify the exact proton in the molecule. The first two peaks on the
1H NMR represent the protons of two different methyl groups. This is evident because
each peak is integrated to 3. This integrated number is derived from the area under each
peak, which is proportional to the number of hydrogens that generated the peak. One
important observation of these two methyl groups is the similarity in their chemical
shifts. The similarities in the shifts are a result of the similar chemical environments
surrounding the protons on each methyl group. However, the methyl protons do not show
up as a single peak integrated to six, because the five-membered ring that the protons are
attached to give the protons a very small difference in chemical shift due to slightly
different chemical environments. Another factor supporting the presence of these two
groups of methyl protons is the measure in ppm of the shifts. Chemical shifts of methyl
groups typically range from 0.7-1.3 ppm.1 Our molecule’s protons have a slightly higher
chemical shift than the typical shift as a result of only being two carbons away from the
electronegative atom, oxygen. Electronegative atoms attached to a carbon atom reduce
the valence electron density that shields the protons of that carbon from the applied
magnetic field. As a result, electronegative atoms are said to “deshield” the proton giving
it a greater chemical shift.1 Because the protons of the methyl groups are two carbons
away from the oxygen, the influence of the oxygen on the chemical shift is lessened but
still apparent. The third peak on the 1H NMR represents the single proton of an OH
group. The peak is integrated to 1. The chemical shift of –OH groups range from 0.5-5
ppm and are variable depending on the chemical environment in the molecule and on the
concentration, temperature, and solvent used in the experiment.1 The chemical shift of
the proton on the OH group is about 3.1 ppm. The 5 proton integral, more downfield can
be attributed to the remaining protons of the molecule. These remaining protons are alkyl
protons, which, based on the range in the spectrum, should be –CH2O or similar protons.
The typical range for protons like this is 3-5 ppm. 1

1
Pavia, D.L.. Lampman, G.M.; Kriz, G.S.; Engel, R.G. Introduction to Organic Laboratory Techniques: A
Small Scale Apporach. 2nd Ed. Brooks/ Cole-Thompson, Belmont