CHMBD 449 Organic Spectral Analysis

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Fall 2005

• Chapter 1 Molecular Formulas
• Elemental Analysis
• Molecular Mass Determination
• Molecular Formulas
• Structural inference from
• Rule of Thirteen
• Preview of HRMS

CHMBD 449 Organic Spectral Analysis
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• Three Objectives for Organic Spectral Analysis
• For every method we cover in this course, our
  approach must differ depending on the type of
  work we are performing.
• We will divide these approaches into three types
• Cold analysis the unknown organic is a
  complete unknown
• Forensic chemistry
• EPA methods and related analyses
• Natural products taxonomy
• In these cases, little if anything is known about
  the individual compounds detective work must
  recreate the entire structure
• Results of a synthetic experiment
• In this case, the majority of the structure
  should be maintained, the goal is to analyze for
  and confirm changes
• Characterization for the chemical literature
• The analysis here is to confirm the authors
  findings and serve as a benchmark for further
  work on the compound

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• Molecular Formulas What can be learned from
  them
• Importance
• Organic molecules exist as discrete sets of
  covalent bonds based on the valence of the
  elements that comprise them
• i.e. hydrogen is monovalent, oxygen divalent and
  carbon tetravalent
• If a molecular formula is known
• Functional groups can be implied or ruled out
• Obvious, but often overlooked tool
• The number of times valence rules for elements
  are violated is implied
• Most commonly for carbon, which is called the
  index of unsaturation or hydrogen deficiency
  index (HDI), less commonly for elements such as
  oxygen and nitrogen that may be involved in
  acid-base chemistry

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Molecular Formulas What can be learned from
them Hydrogen Deficiency Index For simple
straight chain or branched hydrocarbons, there is
always a certain ratio of hydrogen to carbon
necessary to make the entire structure saturated
We say these molecules are not hydrogen
deficient, and set the index at zero
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Molecular Formulas What can be learned from
them Hydrogen Deficiency Index If we add a
double bond anywhere in the structure, two
hydrogens must be removed for each double bond
We say these molecules are hydrogen deficient,
and the index increases by one for each double
bond added, for the first structure, the index is
one, for the second the index is two
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Molecular Formulas What can be learned from
them Hydrogen Deficiency Index A ring closure,
like a double bond requires the sacrifice of
two hydrogens from the formula, increasing the
index by one for each closed ring in the compound
Triple bonds act as two double bonds increasing
the index by two for each one in a
molecule Hence, the first structure has an index
of one, the second an index of two
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Molecular Formulas What can be learned from
them Hydrogen Deficiency Index other
elements Nitrogen (for the azaphobics) is usually
assumed to be trivalent obviously ammonium salts
and nitro compounds violate this. When working
cold, assume nitrogen is trivalent, and
therefore, for every nitrogen in a structure, one
less hydrogen is needed to fill its valence
requirement than carbon
Halogens (normally monovalent) merely replace
hydrogen in a like-indexed formula
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Molecular Formulas What can be learned from
them Hydrogen Deficiency Index the
equation! Elements such as carbon and hydrogen
never violate their index rules Elements such as
oxygen rarely violate their index rules Elements
such as nitrogen and the halogens may violate
their index rules Higher elements, found
commonly in biologically interesting organic
compounds, such as sulfur and phosphorus exist in
almost equal populations in the various valences
they are capable of and are typically not
considered by this method directly Furthermore,
it is tedious to go through a structural analysis
to get the index of unsaturation. It can be
algebraically expressed by combining the effects
of each of the common elements. For an organic
compound of formula CxHyNzO the index of hydrogen
deficiency becomes HDI x - y/2 z/2
1 Remember to count halogens in the number of
hydrogens and to omit oxygen
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Molecular Formulas What can be learned from
them Hydrogen Deficiency Index Lets test the
equation HDI x - y/2 z/2 1
C7H12
C5H5N
C14H10
C60
C6H12O6
C6H8O
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Molecular Formulas What can be learned from
them Hydrogen Deficiency Index Lets test the
equation HDI x - y/2 z/2 1
C7H12
C5H5N
C14H10
C60
C6H12O6
C6H8O
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Molecular Formulas What can be learned from
them The Rule of Thirteen Molecular Formulas
from Molecular Mass For the formula connoisseur
there is another algebraic treatment of molecular
mass that can lead to possible molecular formulas
When a molecular mass, M, is known, a base
formula can be generated from the following
equation M n r 13
13 the base formula being CnHn
r For this formula, the HDI can be calculated
from the following formula HDI ( n
r 2 ) 2
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Molecular Formulas What can be learned from
them The Rule of Thirteen When a formula
containing other elements than carbon and
hydrogen are considered, the appropriate
adjustment must be made. If we wish to
consider that the base formula also includes
oxygen, with atomic mass 16, one carbon (12) and
four hydrogens (4 x 1) must be removed to give
the same molecular mass Likewise, an adjustment
to hydrogen deficiency must be made. The
following table gives the carbon-hydrogen
equivalents and change in HDI for elements also
commonly found in organic compounds
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Molecular Formulas What can be learned from
them The Rule of Thirteen Possible molecular
weights can only generate real formulas if the
assumption you made is incorrect fractional
elements or HDI indices appear, or sub-zero
HDI. Some examples We experimentally determine
the molecular mass to be 98 From the rule of
thirteen a base formula is generated
98 / 13 n r / 13 7
7 / 13 Base formula C7 H7 7
C7H14 and HDI (U) (7 7 2)/2
1 Remember, this is only the first of several
possible formulas that give a molecular mass of
98!
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Molecular Formulas What can be learned from
them The Rule of Thirteen From this starting
point, we can infer the isomeric alkenes (HDI
1) of molecular formula C7H14
Or we can infer the various aliphatic ring
compounds, C7H14
Observe how, with the knowledge of molecular
mass, we can whittle the infinity of possible
organic compounds to two families of closely
related isomers, and even begin to know something
about the chemistry of the unknown Remember, off
of the base formula we can begin to add other
elements to see what other possibilities give a
molecular mass of 98
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Molecular Formulas What can be learned from
them The Rule of Thirteen If we now assume the
unknown has a single oxygen Base
formula C7H14 Add oxygen C7H14O (mol. mass
now 114) Subtract CH4 C6H10O (mol. mass now
correct at 98) HDI correction 1 1
2 (originally 1, add one for O) (you can check
the HDI vs. the new formula as well) We can now
picture compounds that have the formula C6H10O
with a HDI of 2
Quickly, we can add other elements, such as
nitrogen, halogen and sulfur. See how for a low
molecular mass the inference of big elements
greatly simplifies the number of possible
structures
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Molecular Formulas What can be learned from
them The Rule of Thirteen Quickly, we can add
other elements, such as nitrogen, halogen and
sulfur. See how for a low molecular mass the
inference of big elements greatly simplifies the
number of possible structures Base formula
C7H14 Add Nitrogen C6H12N (sub. CH2) HDI
1.5 Probably an incorrect formula, it is
unlikely this compound has nitrogen Base
formula C7H14 Add Sulfur C5H6S (sub.
C2H8) HDI 3 Very few possibilities
with only 6 hydrogens and an HDI of 3 Base
formula C7H14 Add Bromine CH7Br (sub.
C6H7) HDI -2 Impossible structure
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Molecular Formulas Where we are Importance of
Molecular Formula in Structure Determination
HDI
HDI calc.
HDI calc.
Molecular Formula
Functional group inference
Molecular Mass
Rule of 13
Now we see the experimental need to get this
information
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• Molecular Formula and Mass Determination
• Determination of Molecular Formula
• The most often used approach involves three steps
  with a cold unknown
• Qualitative elemental analysis
• What elements are present in the unknown?
• Quantitative elemental analysis
• How much of each element is in the unknown?
• Molecular mass determination
• By combining the relative amount of each element
  to give a determined mass an exact formula can be
  obtained

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• Molecular Formula and Mass Determination
• Determination of Molecular Formula
• Qualitative elemental analysis
• We can assume that almost all organic compounds
  contain carbon and hydrogen
• If in doubt burn in presence of O2
• if CO2 is detected there must be carbon
• if H2O is detected there must be hydrogen
• Even in 2005, there is no routine qualitative
  test for the presence of oxygen
• Nitrogen, sulfur, and the halogens are
  qualitatively determined by the dreaded sodium
  fusion test (in sophomore organic lab texts)
• When an organic compound containing these
  elements is fused with molten sodium metal,
  reductive decomposition occurs to give the
  corresponding inorganic sodium salts
• R-N, R-S, R-X ? NaCN, Na2S, NaX
  decomposed R-
• A series of wet chemical qual tests for these
  ions infers the presence of each element

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• Molecular Formula and Mass Determination
• Determination of Molecular Formula
• Quantitative elemental analysis
• Commercial laboratories perform these analyses on
  a routine basis for reasearch and industry
• Midwest Microlabs
• Intertek
• Galbraith Laboratories
• A small (10-50 mg) sample of the pure material is
  submitted
• Carbon and hydrogen are determined by
  quantitative analysis of CO2 and H2O production
  from the pyrolysis of the sample in an O2 chamber

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• Molecular Formula and Mass Determination
• Determination of Molecular Formula
• Quantitative elemental analysis
• From the combustion analysis for a given sample
  mass, the percentage of each element can be
  derived
• Example is in text, as Table 1.1
• From these percentages, an empirical formula can
  be calculated, as in Table 1.2
• Remember, empirical formulas give the simplest
  integer ratios of each element, the compound may
  actually be a multiple of this
• Please review these calculations!

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• Molecular Formula and Mass Determination
• Determination of Molecular Formula
• Determination of molecular mass
• The weight of one mole of a substance in
  conjunction with the empirical formula will give
  the true overall molecular formula
• Old methods these methods are based on
  colligative properties, you may have done them in
  a general chemistry laboratory course
• Vapor Density Method material is vaporized and
  weighed, and after converting the volume to
  standard temperature and pressure, the exact
  fraction of a mole the sample represents would be
  known (PV n RT)
• Cryoscopic Method (freezing point depression)
  the material is dissolved in a solvent of a known
  freezing point, the amount of deviation of the
  freezing point of the resulting solution from the
  pure solvent gives the molal concentration of the
  solute (DT kf m, where m is moles per Kg of
  solvent)
• Vapor Pressure Osmometry (related to boiling
  point elevation) the change in vapor pressure
  of a pure solvent by adding a known weight of
  solute gives the molal concentration of the
  solute
• Titration of an unknown acid titration of a
  known weight of the unknown with standardized
  base gives the molecular weight

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• Molecular Formula and Mass Determination
• Determination of Molecular Formula
• Determination of molecular mass
• New method HRMS High Resolution Mass
  Spectroscopy
• Mass spectroscopy works on the principle of
  punching an electron out of a sample molecule
  and determining the mass of the ion fragments
  produced (which we will study in detail later)
• The largest fragment is one that differs in mass
  from the original molecule by the weight of a
  single electron (negligible, even by molecular
  standards)
• From our study of molecular formulas, we see a
  limited subset of possible formulas gives a crude
  molecular mass
• If we take the isotopic weights of each
  naturally occuring element into account (i.e. C
  is 12.011 not 12 H is 1.0079 not 1, O is 15.9994
  not 16) the subset of possible combinations
  falls dramatically
• HRMS can give the molecular mass (from the
  molecular ion) to a precision of 6-8 significant
  figures

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• Molecular Formula and Mass Determination
• Determination of Molecular Formula
• Determination of molecular mass
• New method HRMS High Resolution Mass
  Spectroscopy
• From tables of combinations of formula masses
  with the natural isotopic weights of each
  element, it is often possible to find an exact
  molecular formula from HRMS
• Example HRMS gives you a molecular ion of
  98.0372
• From a table of mass 98 data
• C3H4N3O 98.0355
• C3H6N4 98.0594
• C4H4NO2 98.0242
• C4H6N2O 98.0480
• C4H8N3 98.0719
• C5H6O2 98.0368 ? gives us the exact formula
• C5H8NO 98.0606
• C5H10N2 98.0845

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Molecular Formulas Complete picture of Chapter 1
HDI
HDI calc.
HDI calc.
Molecular Formula
Functional group inference
Molecular Mass
Rule of 13
HRMS Legacy methods

• Qualitative elemental analysis
• Quantitative elemental analysis
• Determination of Molecular Formula