Chapter 13 Structure Determination

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Chapter 13 Structure Determination

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Four of the most useful techniques

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13.1 Electromagnetic Radiation A Common
Probe of Structure
FIGURE 13.1 The electromagnetic spectrum.
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Chapter 13. Structure Determination
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FIGURE 13.2 (a) Wavelength (?) is the distance
between two successive wave maxima. Amplitude is
the height of the wave measured from the center.
(b)(c) What we perceive as different kinds of
electromagnetic radiation are simply waves with
different wavelengths and frequencies.
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Chapter 13. Structure Determination
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13.2 X-Ray Crystallography
FIGURE 13.3 The structure of arachidonic acid
and cyclooxyge-nase as determined from X-ray
crystallography. (Dr. Lisa M. Perez, Texas AM
University. Used with permission.)
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FIGURE 13.4 The steps required to perform a
structure determina-tion using X-ray
crystallography include obtaining crystals,
collecting D-ray diffraction data, solving the
data set to generate an electron density map, and
interpreting the electron density map.
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13.3 Mass Spectrometry
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PRACTICE PROBLEM 13.3
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Mass Spectral Fragmentation of Hexane
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IR Spectrum
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UV-Vis Spectrum
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NMR Spectrum
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Electromagnetic spectrum

• e hu
• a.IR
• b.UV
• c.NMR

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IR absorption spectrum
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Infrared region
The infrared (IR) region of the electromagnetic
spectrum extends from 7.810-7 m to 10-4 m.   
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13.2 IR Spectroscopy of Organic Molecules

• Why does an organic molecule absorb some
  wavelength of IR radiation but not others?
• a. molecular vibration
• .stretching
• .bending
• b. absorb quantized energy

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Kinds of allowed Vibrations

• CH4

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Information from IR

• IR spectrum
• ?
• What molecular motions?
• ?
• What functional groups?

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Interpreting Infrared Spectra

• Most functional groups have characteristic IR
  absorption bands that dont change from one
  compound to another.
• Characteristic IR absorptions of some functional
  groups. (Table 13.1)

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Table 13-1
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Infrared spectra of compounds
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Significant regions of IR
The useful range of IR radiation is 4000 cm-1
400 cm-1 this corresponds to energies of 48.0
kJ/mol 4.8 kJ/mol.
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13.3 Absorption Spectroscopy

• The ultraviolet region of interest 200 nm and
  400 nm
• The energy absorbed is used to promote a p
  electron in a conjugated system from one orbital
  to another.
• A UV spectrum is a plot of absorbance vs.
  wavelength.
• UV spectra usually constant of a single broad
  peak, whose maximum is ?max. (Figure13.8 )
• ?max increase with the degree of conjugation of a
  molecule.  

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Fig 13.7 The region
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MO

• 1,4-butadiene has four ? molecular orbitals
• HOMO ? LUMO at 217 nm

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Fig13.8
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Table 13.2

• ?max increases as conjugation increases (lower
  energy)

Practice 13.5
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13.5 NMR Spectroscopy

• Theory of NMR spectroscopy
• (1) Many nuclei behave as if they were spinning
  about an axis.
• The positively charged nuclei produce a magnetic
  field that can interact with an externally
  applied magnetic field (B0).
• The 13C nucleus and the 1H nucleus behave in
  this manner.
• In the absence of an external magnetic field the
  spins of magnetic nuclei are randomly oriented.

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(2) Nuclear spin when a sample containing
these nuclei is placed between the poles of a
strong magnet (B0), the nuclei align themselves
either with the applied field or against the
applied field.
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(3) The energy difference ?E between nuclear spin
state
The parallel orientation is slightly lower in
energy and is slightly favored.
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(4) Nuclear magnetic resonance

• If the sample is irradiation with radio frequency
  (rf) energy of the correct frequency, the nuclei
  of lower energy absorb energy and spin-flip to
  the higher energy state.
• The frequency of the rf radiation depends on the
  magnetic field strength and on the magnetic
  nuclei.
• At a magnetic field strength of 2.62T, rf energy
  of 100 MHz is needed to bring a 1H nucleus into
  resonance, and energy of 25 MHz is needed for
  13C.
• All nuclei with an odd number of protons (1H, 2H,
  19F, 31P) and neutrons (13C) NMR
• even number of both protons neutrons (12C,
  16O) No NMR

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schematic operation of an NMR spectrometer
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13.6 The nature of NMR absorptions

• (1) Not all 13C nuclei and not all 1H nuclei
  absorb at the same frequency.
• Each magnetic nucleus is surrounded by electrons
  that set up their own magnetic fields.
• These little fields oppose the applied field and
  shield the magnetic nuclei
• BeffectiveBapplied-Blocal
• These shielded nuclei adsorb at slightly
  different values of magnetic field strength.
• NMR spectra can be used to map the
  carbon-hydrogen framework of a molecule.

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(2) NMR spectra

• The horizontal axis shows effective field
  strength, and the vertical axis shows intensity
  of absorption.
• Each peak corresponds to a chemically distinct
  nucleus.

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1H NMR spectrum
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13C NMR spectrum
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13.7 Chemical Shifts

• (1) TMS is used as a reference point
• The TMS absorption occurs upfield of other
  adsorptions, and is set as the zero point.

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• (2) Field strength increases from left
  (downfield) to right (upfield).
• Nuclei that adsorb downfield require a lower
  field strength for resonance and are deshielded.
• Nuclei that adsorb upfield require a higher field
  strength and are shielded.

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• (3) The chemical shift is the position on the
  chart where a nucleus absorbs.
• (4) NMR charts are calibrated by using an
  arbitrary scale - the delta scale (ppm).

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1H NMR spectroscopy

• (1) Chemical shifts (13.8)
• Chemical shifts are determined by the local
  magnetic fields surrounding magnetic nuclei.
• Most 1H NMR chemical shifts are in the range 0
  10d.
• H (sp3) adsorb at higher field strength.
• H (sp2) adsorb at lower field strength.
• Protons on carbons that are bonded to
  electronegative atoms absorb at lower field
  strength.
• The 1H NMR spectrum can be divided into 5
  regions
• See Table 13.3

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(2) Integration of 1H NMR spectra proton
counting (13.9)

• The area of a peak is proportional to the number
  of protons.
• To compare two peaks, measure the relative
  heights of the peak areas.

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(3) Spin-spin splitting (13.10)

• The tiny magnetic field produced by one nucleus
  can affect the magnetic field felt by other
  nuclei.
• Protons that have n equivalent neighboring
  protons show a peak in their 1H NMR spectrum that
  is split into n1 smaller peaks (a multiplet).
• This splitting is caused by the coupling of spins
  of neighboring nuclei.
• The distance between peaks in a multiplet is
  called the constant (J).

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• Chemically identical protons dont show spin-spin
  splitting.
• The signal of a proton with n equivalent
  neighboring protons is split into a multiplet of
  n1 peaks with coupling constant J.
• Two groups of coupled protons have the same value
  of J.

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13.11 Uses of 1H NMR spectroscopy
1H NMR can be used to identity the products of
reactions.
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13.12 13C NMR spectroscopy
13C NMR spectroscopy can show the number of
nonequivalent carbons in a molecule and can
identify symmetry in a molecule.
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13.57
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13.58