Welcome to Chemistry 421

1
Welcome to Chemistry 421

• Use of Physical Methods to determine structures
  in Organic Chemistry
• Dr. Charles DeBrosse
• 232 Beury Hall (across from Dept. office)
• NMR lab 001 Beury Hall
• 215-204-1082

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Course Organization

• Lectures Tuesday evenings 6-9pm. Attendance is
  strongly encouraged. You should read the assigned
  material and do the homework problems prior to
  the lecture.
• Textbook, Organic Structural Spectroscopy, by
  Lambert, Shurvell, Lightner and Cooks
• Grade based on 3 In-class quizzes, homework sets
  and Final exam
• Course notes will be available on Blackboard
  generally the Monday before the lecture.
• I will reserve Monday 10-11am as office hour, and
  am accessible other times in my lab or office

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Spectroscopy in Organic Chemistry.

• The Chemists Eyes, Ears and Nose
• How do we know what we have?
• Read labels (sometimes labels lie)
• Whose word do we have to take on it?
• Check it out for yourself! (Get a spectrum!)
• A spectroscopist. (never the hero, just the
  heros best friend)

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Chemistry 421

• Goal of the course is to give you the tools to
  answer parts of these questions.
• Organic Structure determination by spectroscopic
  methods
• NMR (nuclear magnetic resonance spectroscopy)
• Mass Spectrometry (MS)
• Infrared Spectroscopy (IR and other vibrational
  classes like Near IR, Raman)
• Electronic Spectra (Ultraviolet and chiroptical
  methods)

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Structural Features we can address
Spectroscopically

• Molecular weight
• Chemical Formula
• Functional groups
• Skeletal Connectivity, structural isomers
• Spatial-geometric arrangements, stereoisomerism,
  symmetry
• Presence and location of chromophores
• Chirality issues
• Some of these are more central than others.
  Sometimes we can stop when the answer is fit to
  purpose.

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Techniques we will study in this Course

• NMR--looks atb atoms by means of their nuclei.
  Connectivity pathways, spatial arrangements of
  atoms and 11 correspondence between signals and
  atoms
• Mass Spec--measures molecular weight, most
  fundamentally useful for unknowns. Controlable
  fragmentation can distinguish among rival
  possibilities
• IR and Raman--Vibrations characteristic of bonds,
  particulary for functional group identification.
  Excellent fingerprint
• UV--reports on conjugation and multiple bonds.
  Provides entre to chiroptical probes to
  assymetric configurations

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Chemistry 421

• Goal is for you to gain a conversational level of
  knowledge
• Base level of theory, as pictoral as possible
  should help you realize the scope and limitations
  of these methods.
• Survey of representative data and how to
  interpret it.
• Applying the right tool to the right question

Integrating data from various tools and sources
(i.e. we should be able to explain all our
observations. Also we should be able to observe
features we predict, knowing our chemistry)
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Complementary Spectroscopies

• There are strengths and weaknesses in all the
  various spectroscopy methods
• Blind Spots (see story of three blind men
  describing an elephant)
• NMR e.g. has NMR silent nuclei fully
  substituted carbons as blocks blind to
  inorganics, nearly blind to polymeric mtls.
• IR e.g. robust for functional groups great if
  you have a compound match in a library
  (fingerprint) shaky on quantitative response,
  same spectrum might explain multiple compounds
  subject to selection rules governed by dipole
  moment in vibration (complement somewhat with
  Raman)
• UV needs chromophores
• Mass Spec compounds differ in ionizability.

A smart chemist will be attuned to possible blind
spots before making conclusions. Best solution
is to marry up complementary data. All the
data needs to agree or at least, not conflict
withing the various methods.
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Total Synthesis as a Structural Proof

• Use of all our knowledge
• Generally the product of a reaction is rationally
  related to the ingredients we have used.
• Non-ambiguous route from known compounds
• Oxidative degradation to known compounds and
  history of chemistry

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The Electromagnetic Spectrum

• Light comes in different colors
• No matter what part of range, there are some
  features in common, that you should know.

Amplitude
Photon?E h? ? is frequency, Hz, 1/sec ? c/?
c3x1010 cm/sec h Plancks constant 6.624
x10-34 Jsec ?/c 1/ ? wavenumber, cm-1
Propagation of e,b fields, time
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Chemical Properties as related to the different
colors of light
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What about Mass Spec?
The properties measured do not directly bear on
absorption of light More properly termed mass
spectrometry We do however in quadrupole mass
spectrometry scan an electric field that induced
different curve paths for different
masses Radiofrequency also does show up in FT
mass spec (ion cyclotron resonance)
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Sensitivity of the methods we will study

• NMR is worst, typically needing 10s of ?g to 10s
  of mg for 13C.
• Mass Spec is generally about 103-104 x more
  sensitive than NMR
• UV is about 100 x more sensitive than NMR

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Questions, Questions.

• Whats in this flask?
• What have you just synthesized?
• Did my reaction Work?
• What is present in that sample?
• How could this reaction have possibly Failed?
• Isolated materials?
• Purity? Mixture? What kind of mixture?
• Is this material suitable for the next step?
• Best to Ask Yourself these questions! (Better
  than making your Boss ask, or not to be able to
  answer a Customer

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Answers!

• Bad Answer because this always works in our
  lab
• Bad Answer 2 ..because my Professor (or some
  slightly older grad student, postdoc) said so..
• Slightly less Bad Answer 3 this was done in
  the literature
• Good Answer because all the spectral and other
  analytical data agree with me
• Analytical Chemistry. If you do it right, nobody
  has to take your word on the answers!

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Features in Common for all Spectroscopy
Measuring Scheme
Data
Some Physical Property
Analysis, Interpretation
A key for us here is, we use instruments to
Disperse energy across a scale appropriate to a
chemical property
Knowledge
Wisdom (or Progress)
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Therefore we have Precise Analytical Instruments
that can Disperse Energy

• Accurate, precise, reproducible
• Combine the energy dispersion scheme with a
  detection scheme.
• Generally the sample sits physically between the
  source and the detector.
• Detector provides selectivity in response,
  usually generates a voltage. We record voltage
  responses as DATA

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The dispersion is easy to achieve with ordinary
light
Monochromator rotates Prism or diffraction
grating Spacings on grating appropriate to
wavelength Schemes use slits to admit a select
region of spectrum Pretty ineffective for radio
waves
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Spectroscopy Spreads out Vision
All the techniques we will discuss have some
features in common Data will have a running
variable (x-axis) that is in some sense, a
energy scale. (not at least directly, a time
axis. Therefore a snapshot in time of a
molecule) The response variable (an absorption or
other intensity) is related to the chemical
preponderance of some feature that cause the
response.
The position informs us about some chemical
property in the sample The peak height informs us
about how much of that property is in the sample
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Fourier Transform MethodsAn alternative to
Energy Dispersive methods

• All modern NMR and IR is done this way
• Measures all frequencies at same time. More
  efficient at signal-gathering in a give time
  (better S/N)
• The frequencies present are deconvoluted (or
  dispersed) after data is collected.
• Fourier Analysis is the mathematical method for
  doing this. It is based on the theory that any
  complex periodic (repeats over time) wave can be
  decomposed into a linear combination of sinusoids

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To get the measurement, we collect a detector
response as a function of time
Lots of different frequencies present from the
sample Their voltages beat against each other
making interference pattern (interferogram) Interf
erence is periodic, because the frequencies are
constant w.r.t each other
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An Oscillating voltage is interpreted as a
Frequency
The process is similar to the way a sound wave is
digitized to make e.g. a music CD
Key to this is sampling at exactly equal time
intervals
This is a Frequency Axis. Think Hz!
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Interfering Sinusoids are Represented in a
decaying trace
Space is frequency 1
Space is beating of frequency 2 vs 1 (1 - 2)
A human being could compute this FT, counting
beats per time unit
Key to the process is a very precisely defined
time base (the x axis) that the FT algorithm uses
to count
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Interference patterns--Almost able to Transform
by Hand
Time(ms)
But its really the Fast Fourier Transforms and
fast computers that make this practical!
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Since the time-acquisition is fast and efficient
it is easy to Signal-Average
Adding accumulating scans from the detector into
memory of computer Signals are coherent and
adding the scans causes signal to grow linearly
with number of scans. Noise being random and
incoherent grows with vno.of scans From this,
the Signal-to-Noise ratio (S/N) grows
proportionally to the square root of number of
scans E.g., a spectrum acquired with 100 scans
will be 10x better than one with 1 scan only.
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Some Features common to all Spectra
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Noise, the curse of Science

• All measurements, especially those we carry out
  with instruments, generate Noise.
• Detectors of all sorts generate electrical noise
• Noise is bad. It is random and incoherent and
  does not possess information. We go to
  tremendous expense and effort to eliminate,
  suppress, and finesse our way past noise.
• Signals are good. They give us information.
• Noise limits our ability to even observe very
  weak signals or to quantify somewhat weak
  signals. The Signal-to-Noise Ratio is an
  important parameter is assessing our ability to
  interpret data.
• Noise is superimposed on top of peaks

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Signal-to-Noise (S/N) ratios
Measure height
Typical rule of thumb Limit of detection,
S/N3 Limit of Quantitation, S/N10
Noise(rms) is 0.707 x peak to peak
S/N6.3/20.707 4.45 So this peak is
reliably detectable, but not reliably
quantitatable
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Chemistry 421--Structure Determination

• Interpretable Connection between Structural
  Features and Spectroscopic signals
• We will interpret spectra to learn about
  structures.
• The Interpretation paradigm consists of
  charting

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A way of Thinking
Known compounds (verify structure) All predicted
signals present? Agreement with
literature? Impurities present? Fingerprint?
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A Strategy for Handling Unknown Structures

• Complementary 1H NMR, 13C NMR, Mass Spec, UV--any
  features stand out?
• Get the Molecuar Weight from MS
• Heavy Atoms? (ratio of M to M1, M2)
• If heavy atoms are identified, subtract from MW
• Consult various molecular formula DBs (Merck, CRC
  etc). Write out Molecular Formula
• Use the DBE (sites of unsaturation) rule
• Infrared-- Functional groups present? Identify as
  possibly subtract from formula (retain the need
  to incorporate at end)
• Inventory 13C NMR and classify the C,H groups
  present. Tabulate fragments of structure.
  Reconcile MS fragments.
• Assemble possible structures

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Molecular Weight and Molecular Formulas

• Absolutely critical to Stucture determination
• Centrality of Mass Spectrometry to modern
  Chemistry
• Molecular weight must agree with the structure.
  Note well, that a given nominal MW generally is
  consistent with several possible formulas.
• The nitrogen rule. A compound with an
  even-numbered molecular weight has 0, 2 or an
  even number of nitrogens.
• Very Important Learn the rule for sites of
  unsaturation (double-bond equivalents, DBE) as a
  predictive tool for multiple bonds and/or rings.
  These are based on the standard valencies for
  ordinary atoms.

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DBE Rules

• Aim to reduce a formula to CNH2N2
• Take formula and cross off Oxygen atoms
• Replace all halogen atoms with hydrogen
• Cross off all Nitrogen atoms, and for each N
  remove one H atom.
• Sulfur treat like Oxygen (? Use care if there are
  a lot of oxygens, possible OSO type groups,
  similar issues with Phosphorus)
• Subtract your newly reduced formula (looks like
  CxHx, from CxH2x2 number H (even
  number)
• Divide this answer by 2. Result is DBE.

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So some Decision-Tree thinking is possible
The NMR branch. Integrate at higher level with
other techniques
Data
Synthetic Product
1H NMR
Could it be what I want?
Quick Inventory of signals
NO
YES
Do I need more information?
Worth more spectroscopy?
What do I need to find out
Back to the Lab!
granularity of questions
Assess Purity
Carbon Survey
Proton coupling pattern
Need Assignments?
YES
NO
Correlations to protons
Separations methods, Feedback to synthesis.
Noe for stereochemistry
Information Content higher
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Nuclear Magnetic Resonance(NMR)
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Tonights Subjects

• How do the spectrometers work?
• The NMR measurable quantities

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What is NMR Spectroscopy?

• Nuclear Magnetic Resonance
• Radio Frequency Absorption Spectra of atomic
  nuclei in substances subjected to magnetic
  fields.
• Spectral Dispersion is Sensitive to the chemical
  environment via coupling to the electrons
  surrounding the nuclei.
• Interactions can be interpreted in terms of
  structure, bonding, reactivity

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The Fundamental NMR equations

• Spinning nuclei produce a magnetic field that is
  proportional to its magnetic moment ?. The
  proportionality constant is ? ? ?hI
• An active nucleus in a magnetic field B0 has an
  energy w.r.t. zero field of
• E ( h? h?) -? B0 where ? is the component
  of the magnetic moment colinear with B0
• This gives for IZ 1/2 E 1/2 (?h B0)
• ?E ?h B0 and in angular units ? ? B0

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Origin of the NMR Effect

• Nuclei with other than A(protonsneutrons) and
  Z(protons) both even numbers, possess net spin
  and associated angular momenta
• Reveals itself only in magnetic field. As usual,
  such momenta are quantized
• States have different energies, populated
  according to Boltzmann distribution
• States are 1/2, 3/2, 5/2for A odd number and
  integer if A even number and Z odd number
• Transitions of individual nuclei between spin
  states is possible (both directions) leading to
  an equilibrium of populations
• Number of states is 2I 1

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Pictoral View of Spin
Precession of nuclear magnet--Units of Torque
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Resonance--A general phenomenon for energy pumping
Imagine a kid on a swing The period (frequency
of the swing is determined (g, r(length),
?). Lets say the natural period is 3 seconds, or
the frequency is 0.33 If the Daddy gives a push
every 3 seconds, the kid will go higher and
energy will be absorbed. Every 2 seconds and
the motion will get stalled and interfered
with. Every 1.5 seconds and the energy will get
absorbed but not as efficiently. The Daddy will
get tired. This general principal applies in NMR
among other kinds of measurement, and holds
whether we scan through the applied frequency or
multiplex all at once
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NMR-What is it Good For?(absolutely everything!)

• Solving structures of compounds like synthetics,
  impurities, natural products
• Identifying metabolites
• Stereochemical determination
• Follow reactions
• Validating electronic theory trends within
  series of compds.
• Kinetics
• Extended structure, e.g. protein nmr
• Molecular interactions e.g. ligand binding
• Acid-base questions
• Purities
• Mechanisms, e.g. isotope distributions, other
  effects
• Questions about the solid state
• Imaging

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And Besides that

• You get your sample back!
• Not so for mass spec
• Try recovering your compound from a KBr pellet or
  nujol mull

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But on the other Hand

• NMR is one of the least sensitive analytical
  methods
• Characterized by long relaxation time constants,
  limiting experimental efficiency in real time
• Sometimes too much information. Can be demanding
  on interpretation skill
• Relatively Expensive compared with other
  analytical methods
• As with other methods NMR has blind spots and
  cannot serve as an analytical panacea

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What Do I Hope you will Learn?

• Enough theory to make you conversant in the
  area.
• NMR with respect to how the effects arise and can
  be predicted connection with experiments and
  limitations of these survey of how the
  instruments work.
• Basis of the experiments
• Data processing considerations, at level to
  appreciate what may have been done to give your
  result.
• A basic toolbox of experiments, what they do and
  how to use them in your work
• A working knowledge of organic chemical shifts
  and influence of symmetry on signal counting
• Spin coupling, coupling networks and
  connectivity, use of J-coupling constants in
  chemistry

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Why NMR?

• Unmatched versatility as an Analytical technique
• High on chemical information content
• Significant interpretability
• Interpretable at several levels of sophistication
• Response related to molar preponderance
• These attributes are true for solids, liquids,
  mixtures, and to a small extent, gas phase
• More than half the periodic table has at least
  one NMR active isotope

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What are the Measurables in NMR?

• Intensity (analytical parameter, proportional to
  molarity)
• Chemical Shift (the electronic surroundings)
• Couplings (scalar J and dipolar D bond paths,
  angles connectivity and distances)
• Relaxation parameters (motions, distances)

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How do we Generate, and Record NMR Spectra?

• Pulser
• Frequency generation
• Power Amplifier
• Oscillator

Host Workstation
transmitter
Acquisition computer
RF pulse
Timing control signals
signal
Probe in Magnet
NMR Acquisition commands
Phase locked loop
Network

• User interface
• Expt. Setup, control
• Data processing, plotting

receiver
PreAmp
signal

• Superheterodyne (beat-down to AF)
• Phase sensitive detection
• A/D convertor

Data file storage
FID with 90deg phase shift
Free Induction Decay
Block Diagram for Spectrometer
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• Radio Frequency Transmit-Receive system
• Finely controlled RF pulses
• Microsecond control
• Precise control of timing, e.g pulses and delays
• Other precisely delivered RF for decoupling,
  selective excitation
• Gradient amp and generator, shielded in probe to
  avoid eddy currents

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Modern Superconducting NMR Magnets
Older Magnets (1970s) had opposed pole faces.
High voltages and currents demanded heroic
temperature control. Field ran side to side
through sample
Note Special superconducting alloys
Niobium-Tantalum. Search goes on for higher
temperature superconductors.
Supercon magnets have much larger fields, better
homogeneity. Field runs up the axis of the sample.
New technology! Built in auxilliary magnet with
reversed current acts as active shield, partly
eliminating the projection into the room.
Lines of force project several feet into the
room. They concentrate at the top and bottom.
Magnets can grab iron objects and accelerate them.
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Whats the role of the magnet?

• Bigger the field strength, the better. This is
  both from a sensitivity and dispersion of signals
  point of view.
• Expressed in Hz, permits easiser math and trig as
  needed. Gauss would generate energies in ergs.

Remember the energy difference gives the
population excess. Roughly H7/4 increase
energy
?E h ? H0Iz
Field strength, H0
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The NMR Probe
Matching to Tx network
Sample goes inside here
Coil
Tuned Circuit
Usually there is a double tuned response for
Deuterium lock A second coil provides a
decoupling, gradient or other RF
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How Sensitive is NMR?
Nspins
The Rider site, referenced below gives
receptivity vs. 13C with clickable entries. These
reflect natural abundance, ?, etc.
http//arrhenius.rider.edu/nmr/NMR_tutor/periodic_
table/nmr_pt_frameset.html Another good site is
http//nmr.magnet.fsu.edu/resources/nuclei/table.h
tm
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The answer to that question is

• Not all that Sensitive!
• At any given time Mass spec is at least a 104
  times more sensitive
• Compare with UV, IR at least 102x sensitive
• This is tied to the fact that NMR detects only
  the tiny Boltzmann excess. Any old molecule can
  fragment in MS or absorb a IR photon. Lots of
  research in NMR aimed at the sensitivity problem

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Most Important Nuclei in NMR

• 1H, (also 2H, 3H)
• 13C
• 31P
• 15N especially when labeled into proteins
• 19F
• 29Si
• Some isotopes of Sn, Cd. Pb, Ag, Pt
• No coincidence that these are the I1/2 nuclei.
  Spin numbers higher possess nuclear quadrupole
  moment as well. This couples to, broadens and
  complicates the nuclear spin angular momentum.
  For the most part these are niche nuclei.
  Exception is 11B

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Quadrupolar Nuclei

• Spin 1
• Electric field at nucleus non-symmetrical
• Effective relaxation mechanism, promotes loss of
  NMR fine structure
• decouple from attached spins. Can even wipe out
  attached spin 1/2 signals.
• Lines are broad, very challenging NMR
• 35Cl, 11B, 17O, 14N, 7Li, etc.
• Some redeem themselves, deuterium, 6Li