1 Indentifying Unknown #M20 via Infrared Spectroscopy, Mass Spectrometry and 13Carbon
Nuclear Magnetic Resonance Spectroscopy
Monica DiFiori
November 8, 2013
Elementary Organic Chemistry 211
Prof. Rau
2 Abstract
The objective of the experiment described below was to identify an unknown, #M20, via
infrared spectroscopy, mass spectrometry and 13C NMR spectroscopy. The infrared spectrum
suggested a ketone functional group was present. Combining that information with the identified
molecular weight from the mass spectrum, the molecular formula, C6H10O was determined.
Collectively analyzing the data presented in all three 13C NMR spectra, the symmetry and
bonding environments of the carbon atoms within the compound lead to the final structure
consisting of a six-carbon ring with a double-bonded oxygen.
Introduction
The purpose of the experiment was to use infrared spectroscopy, mass spectroscopy, and
13
C NMR spectroscopy to identify an unknown compound. Each technique suggests key
information such as functional group, molecular weight, symmetry and bonding environments
helpful for determining the molecular formula and structure of the unknown.
Determining the functional group present in an unknown compound is important because
that information is also used to determine the molecular weight and the architecture of the
compound. Covalent bonds absorb infrared radiation differently, depending on the masses of
incorporated atoms and the strength and polarity of the bonds involved (Rau, 2013). Thus,
running infrared radiation on the unknown compound and measuring the absorbance at different
wavelengths sheds light on the various bonds between atoms within the compound. Because
bonds elicit different absorbance, the functional group can be determined. The spectrum
produced is relative absorbance versus wavelength. This, in addition to mass spectrometry help
determine the unknown compound’s molecular formula and structure.
Mass spectrometry is used to determine the molecular weight of a molecule and elements
of its structure. First the compound is flash vaporized via gas chromatography to separate
impurities. The evaporated compound is bombarded with high-energy particles, forcing the once
neutral molecules to gain a charge. Next, the now ions are accelerated via an external electric
3 field and sorted by mass and charge, using the relationships between force, mass, and velocity to
classify the ions. Because the acceleration reached by an object is inversely related to it’s mass, a
heavier ion will travel slower than lighter ion (Rau, 2013). The spectrum created shows the
relative abundance of ions versus the mass/charge ratio (which is also equivalent to grams per
mole). The molecular ion peak represents the molecular weight of the molecule.
13
C nuclear magnetic resonance spectroscopy (NMR) determines the specific
arrangement of carbon atoms in a molecule. 13C NMR specifically involves interactions of
electromagnetic radiation and magnetic fields with atomic nuclei of 13C isotopes. All NMRactive nuclei have an odd number of nuclear particles because the uneven number of particles
means uneven pairing of spin. Because there’s one unmatched particle, the entire nucleus has a
spin. A nucleus that has a spin also has a small magnetic field. When in the presence of another
magnetic field, more 13C nuclei adopt to a lower energy spin state because the nucleus’s small
magnetic field is opposite of the stronger magnetic field (Rau, 2013). Energy in the form of
radiation is added to induce the change from lower energy spin states to higher energy spins
states. Molecules with 13C atoms absorb radio wave energy varying with the bonding
environment of each carbon (Rau, 2013). Thus, the NMR spectrum is a graph of the amount of
radiation a nucleus needs to undergo the transition versus the wavelength of radiation. The
spectrum indicates chemical shift values that determine each unique carbon’s bonding
environment. Knowing the carbons’ bonding environment helps determine the specific
arrangement of carbons within the molecule. In addition, knowing the number of different
carbons indicates the level of symmetry in the compound.
Combining all the information provided from all three techniques, the molecular formula
and structure can be determined. Applying the information gathered from the IR spectrum to the
4 information gathered from the mass spectrometry, the molecular formula can be calculated. In
addition to discovering the unknown molecule’s formula, the degrees of unsaturation can also be
determined by analyzing the information presented in the mass spectrum. By comparing the
determined formula to the fully saturated version of the formula, the degrees of unsaturation can
de calculated and will shed light on the number of double and/or triple bonds and the possibility
of a ringed structure. Once the molecular formula is determined based on the information
presented in both the IR and mass spectra, the 13C NMR contributes by determining symmetry
and carbon bonding environments.
Three spectra are created from 13C NMR: carbon-proton decoupled (CPD), distortionless
enhancement bi-polarization transfer (DEPT), and attached-proton test (APT). The CPD
spectrum denotes each unique carbon bonding environment with single peaks. The number peaks
demarcated in the spectrum compared to the number of carbons in the molecule reveals the level
of symmetry within the molecule. The DEPT spectrum denotes all carbons bonded to one
hydrogen and three hydrogen as positive peaks, all carbons bonded to two hydrogen as negative
peaks and does not display single carbons (carbons with no bonds to hydrogens). The final
spectrum, APT denotes carbons bonded to one or three hydrogen as positive peaks as in the
DEPT and denotes carbons bonded to no hydrogens or two hydrogens as negative peaks. By
comparing data between the three structures, the number of hydrogens bonded to each specific
carbon can be determined. Pooling all the information gathered from all the spectra generated,
the molecule’s molecular formula and structure is eventually identified.
5 Experimental
A vial of unknown liquid, #M20, was obtained and was first run through IR
spectroscopy. After cleaning the ATR sampler with acetone and a kim-wipe, one drop of the
unknown liquid was placed on the ATR sampler. The program was run and it generated an IR
spectrum.
Next, the unknown compound was prepped for mass spectrometry. First, one drop of the
unknown sample was placed in a 50 mL Erlenmeyer flask. Next, 5.0 mL of acetone was added to
flask. After swirling the flask to ensure that the sample solution was evenly mixed, 1-1.5 mL was
used to wash out the mass spectrometry vial. Rinsing out the vial in this manner ensures that the
sample solution has no impurities. When thoroughly rinsed, the vile was filled to the third line
with the sample solution, capped and labeled appropriately. After running the sample through
mass spectrometry, a spectrum revealing the molecular weight was generated.
The final part to the procedure was preparation of the unknown for 13C NMR. Before
measuring and recording the exact mass of the unknown compound used for 13C NMR, an
Erlenmeyer flask with an empty test tube inside was placed on the scale. Then, re-zeroing the
scale, the unknown was added drop by drop until a sample with a mass of 2.5-3.5 g was reached.
Next, 0.75 mL of CDCl3 was added to the test tube. Once the test tube was swirled, the sample
solution was transferred to an NMR tube, which was capped and labeled appropriately. The
sample was run and three spectra were produced.
6 Results
Figure 1: Infrared Spectroscopy of Unknown Compound
C:\Xcalibur\...\Ex3 C13 NMR\Ex350
DiFiori W23
A
9/24/2013 1:59:31 PM
RT: 0.00 - 11.52
NL:
1.69E7
TIC F: MS
Ex350
4.32
100
90
Relative Abundance
80
70
60
50
40
Figure 1:30The spectrum depicted above suggests a ketone functional group is present in the unknown molecule
because the very intense peak (A) that appears at approximately 1704 wavenumbers represents the carbonyl bond. A
20
ketone functional
group was determined rather than an ester functional group due to the peak appearing below 1730
wavenumbers.
10
3.34 3.76
0
0
2
6.88
4.46 5.29
4
8.01
6
9.25 10.27 11.28
8
10
98.01
99.04
Relative Abundance
Figure 2: Mass Spectrometry of Unknown
Compound
Time (min)
#275 RT: 4.31 AV: 1 NL: 2.95E6
Ex350
T: + c Full ms [ 60.00-300.00]
100
90
M+1
80.12
80
70
60
50
83.17
40
69.05
79.13
30
20
70.04
81.12
10
65.13
84.18 88.98
77.13
63.15
71.10
0
65
70
75
80
m/z
85
97.10
91.17
90
96.25
95
100
Figure 2: The spectrum produced from mass spectroscopy, pictured above, suggests the molecular weight of the
unknown. The molecular ion peak (M+1), appearing on the far right, indicates a molecular weight of 98 g/mol.
Calculations:
To find molecular formula with determined weight of 98 g/mol (Figure 2):
Mwt. of molecule – Mwt. of functional group = Mwt. of hydrocarbon structure
(Mwt. of hydrocarbons ÷ amu of Carbon) = probable number of Carbons in molecule
(probable number of Carbons)(amu of Carbon) = Mwt. of carbon within molecule
mwt. of hydrocarbons – Mwt. of carbon within molecule = probable number of Hydrogens
number of Carbons + number of Hydrogens = Hydrocarbon formula
hydrocarbon formula + functional group formula = entire molecular formula
98 g/mol – 28 g/mol = 70 g/mol
(70 g/mol ÷ 12 g/mol) ≈ 5 Carbons
(5)(12 g/mol) = 60 g/mol Carbon
70 g/mol – 60 g/mol = 10 Hydrogens
5 Carbons + 10 Hydrogens = C5H10
deduced hydrocarbon molecular formula: C5H10
C5H10 + CO = C6H10O
deduced molecular formula = C6H10O
To find possible structures:
Compare molecule to fully saturated molecule and subtract the number hydrogens in deduced
molecule from the fully saturated molecule, then dividing by two to get degrees of unsaturation.
7 8 compare C6H10 to C6H14
14 - 10 = 4
4÷2=2
deduced degrees of unsaturation: 2°
possible structures:
1)
2)
3)
Figure 3: 13C NMR Spectroscopy CPD of Unknown Compound
C
D
B
E
A
Figure 3: The above spectrum indicates four unique carbon-bonding environments. The small peak (B), at
approximately 77 ppm, is the solvent that is used in the sample preparation and therefor dismissed.
9 Figure 4: 13C NMR Spectroscopy DEPT of Unknown Compound C
E
D
Figure 4: The DEPT spectrum shown above depicts three unique carbons-bonding environments occupied by
carbons attached to two hydrogens represented by the three negative peaks (A, B, C). Also note that the solvent peak
and the small peak that appeared around 210 ppm in the CPD are not present because single carbons are not shown
in DEPT.
Figure 5: 13C NMR Spectroscopy APT of Unknown Compound
B
A
E
D
Figure 5: The spectrum depicted above suggests four uniquely bonded carbons when negating the solvent peak (B).
Because the spectrum only indicates negative absorbance peaks, it suggests that all carbons present in the unknown
are single carbons or carbons bonded to two hydrogens.
C
10 Table 1: Carbon Signals within 13C NMR Spectra
Peak Label Within
Spectra
A
B
C
D
E
Chemical Shift Value (ppm)
210
77
41
26
24
Number of Carbon Atoms
in Compound
1
0
2
2
1
Discussion
In order to achieve the goal of determining the molecular formula and eventually the
structure of an unknown compound, three different techniques are utilized. In order to discover
the functional group within the unknown molecule, IR spectroscopy was used. Because all bonds
absorb infrared light uniquely, the nature of the bonding within the unknown is revealed through
measurements during radiation. Then, mass spectrometry is performed to further identify the
molecular weight and formula. After gas chromatography, which flash vaporizes the molecule to
ensuring purity, the evaporated compound is hit with it with high-energy particles and then put
through an acceleration phase, which classifies the ions based on their mass to charge ratio. In
addition to the produced IR and mass spectra, 13C NMR spectroscopy indicates the details of
carbon bonding. The radiation of unevenly paired spins in NMR active nuclei, induces a
transition from a lower energy spin state to a higher energy spin state. The spectra yielded
illustrate chemical shift values and the number of differently bonded carbons, including their
relationships with hydrogen.
By collectively analyzing all spectra produced from the three techniques, the unknown
can be identified. The first piece of the puzzle, the functional group was determined to be a
ketone due to the carbonyl peak (A in Figure 1) at approximately 1704 wavenumbers.
Combining that information with the information presented in the mass spectra, the molecular
11 formula was discovered. When looking at the mass spectra (Figure 2) the molecular ion peak (A
in Figure 2), which was determined to be an even numbered value because the unknown was
determined to have no nitrogen atoms, appears at approximately 98 g/mol. To calculate the
molecular formula, the molecular weight of the functional group is subtracted from the total
molecular weight. To help determine the structure, the degrees of unsaturation, which indicate
double and/or triple bonds and ring formation, is determined by comparing the molecular
formula, C6H10O, to the fully saturated version of the molecular formula, C6H14. The resulting
two degrees of unsaturation indicates a double bond, due to the ketone functional group and an
additional double bond or a ring formation. Additionally, to help identify the structure, the
spectra yielded from 13C NMR is analyzed to determine the carbons in unique bonding
environments, and symmetry within the molecule. The first spectrum, CPD (Figure 3) illustrates
all different carbons within the molecule and suggests that the unknown molecule has four
distinctive carbons out of a total of six carbons. As demonstrated in Table 1, the carbon signal
labeled B is negated because it is a result of the solvent. Peak A, (Table 1) has a chemical shift
value that suggests a carbonyl bond because electronegative bonds appear to the far left of the
spectrum. This also confirms the functional group suggested by the IR spectrum. The peaks on
the right side of the spectrum (C, D, E in Table 1) have chemical shift values that suggest a ring
formation. Next, looking at the DEPT spectrum (Figure 4) the presence of the single carbon
double bonded to an oxygen atom and thus the ketone functional group is confirmed again
because there is no peak present above 200 ppm as in the CPD spectrum. Moreover, because all
peaks (A, B, C in Figure 4) are negative, the three carbons indicated have two attached
hydrogens. To confirm, the APT spectrum depicts only negative peaks (A, B, C, D, E,) as well.
12 The single carbons appear again at approximately 210 ppm (peak A in Figure 5) and at
approximately 77 ppm (peak B in Figure 5).
In order to determine the final correct structure, the proposed structures are tested against
the information presented in the 13C NMR spectra. The second proposed structures fits the
spectra, while the other two proposed structures do not. The ring of single bonded carbons
contains four different carbon-bonding environments the first of which is represented as peak A
throughout all 13C NMR spectra and as carbon A in Figure 6 (see below) and is the most
electronegative carbon in the compound. The second carbon-bonding environment is represented
as peak C, encompassing two similar carbons. These similar carbons are represented as C1 and
C2 in Figure 6. Moving from more electronegative to less electronegative, the next carbonbonding environment represented in the 13C NMR spectra is peak D, shown as D1 and D2 in
Figure 6 because two carbons occupy that same bonding environment. The last carbon in the
compound is referred to as peak E in the 13C NMR spectra and carbon E in Figure 6.
Figure 6: Detailed Carbon Labeling of Determined Final Structure
C1
D1
E
D2
A
C2
Conclusion
The goal of the experiment was to correctly identify various elements of an unknown
compound using IR spectroscopy, mass spectrometry, and 13C NMR. First by analyzing the IR
13 spectrum, a ketone functional group was determined. The molecular ion peak found at 98 g/mol
shown in the mass spectrum was used to determine the molecular weight, formula and ultimately
the degree of unsaturation. Lastly, the spectra presented through the 13C NMR revealed a
carbonyl peak at approximately 210 ppm and three other unique carbons with chemical shift
values that suggests a ring structure. In combination with the APT, the DEPT spectrum indicated
one single carbon and three carbons with two hydrogens attached to each. The only structure
that satisfies all information presented from the respective spectra is a monosubstituted sixcarbon ring, with a double bonded oxygen, representing the ketone functional group.
14 References
Rau, D. Elementary Organic Chemistry 1 Lab Manual. 2013