Calculation of IR & NMR Spectra

Measuring nuclear vibrations and spins

Computational Chemistry Lab

Inbal Oz
2018
Lecture Outline
• EM spectrum

• IR – vibrations of nuclei on the electronic PES

• Review of theory
• Calculation scheme
• Calculations vs. experiment

• NMR – effect of electronic environment on nuclear spin transitions

• Review of theory
• Calculation of shielding tensor
• Worked example (calculation vs. experiment)
The Electromagnetic Spectrum
Electromagnetic (EM) Spectrum
• Frequency and wavelength are inversely
proportional,
𝑐 = 𝜆𝜈,
where 𝑐 is the speed of light.
• Plank’s relation:
ℎ𝑐
𝐸 = ℎ𝜈 = ,
𝜆
where ℎ is Plank’s constant. Max Plank
1858 –1947
Lecture Outline
• EM spectrum

• IR – vibrations of nuclei on the electronic PES

• Review of theory
• Calculation scheme
• Calculations vs. experiment

• NMR – effect of electronic environment on nuclear spin

transitions
• Review of theory
• Calculation of shielding tensor
• Worked example (calculation vs. experiment)
Infrared Radiation
• Infrared radiation is emitted or absorbed by molecules when they
change their rotational-vibrational movements.
• It excites vibrational modes in a molecule through a change in the
dipole moment.
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different [Link] Wildlife Trust/LJMU
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Review of Theory
Infrared (IR) spectroscopy measures the bond vibration
frequencies in a molecule.

→used to determine the functional group and to confirm

molecule-wide structure (“fingerprint”).
Lecture Outline
• EM spectrum

• IR – vibrations of nuclei on the electronic PES

• Review of theory
• Calculation scheme
• Calculations vs. experiment

• NMR – effect of electronic environment on nuclear spin

transitions
• Review of theory
• Calculation of shielding tensor
• Worked example (calculation vs. experiment)
Review of Theory
Born-Oppenheimer calculation of the PES:
Review of Theory
Born-Oppenheimer calculation of the PES:
Harmonic oscillator
Extracting the Resonant Frequency
Extracting the Vibrational Frequencies

Calculate the
potential energy
surface.
Normal modes
Example: Water Molecule
• Number of atoms: 𝑁 = 3.
• Linear?
→No.
• Number of normal modes: 𝑁 = 3𝑁 − 6 = 9 − 3 = 3.
Normal Mode Calculation

Solve the BO electronic Hamiltonian at each

nuclear configuration to get the PES
PES

Create the force constant (k) matrix, which is the

matrix of second-order derivatives:   2V 
 
K matrix  Ri R j eq.

k 1   2V 
Mass weighted:  =    = H ij
2

m mi m j  Ri R j eq.
Hessian
Normal Mode Calculation

Diagonalize the Hessian to get eigenvalues,

λk, and eigenvectors, ljk:
 (H −  ij k ) l jk = 0
3N

Eigenvalues i , j =1
ij

Six (five) of the roots should be zero, and the

rest are vibrational modes.
k k
Roots k = =
2 2
Normal Mode Calculation
• What would it mean if we got too few non-zero roots?
→ Calculation hasn’t converged.
• Too many?
→ It is actually non-zero, but very small. (we may use more iterations or a
different method)

• When would we get one negative eigenvalue of the Hessian?

→ Saddle point.

• What does a complex eigenvalue of the Hessian?

→ Our calculation hasn’t converged.
General Trends
•
Summary of IR Absorptions
Example: Water
Final Notes
• IR alone cannot determine a structure.

• Functional groups are usually indicated.

• The absence of a signal is definite proof that the functional group

is absent.

• Correspondence with a known sample’s IR spectrum confirms the

identity of the compound.
Lecture Outline
• EM spectrum

• IR – vibrations of nuclei on the electronic PES

• Review of theory
• Calculation scheme
• Calculations vs. experiment

• NMR – effect of electronic environment on nuclear spin transitions

• Review of theory
• Calculation of shielding tensor
• Worked example (calculation vs. experiment)
Lecture Outline
• EM spectrum

• IR – vibrations of nuclei on the electronic PES

• Review of theory
• Calculation scheme
• Calculations vs. experiment

• NMR – effect of electronic environment on nuclear spin transitions

• Review of theory
• Calculation of shielding tensor
• Worked example (calculation vs. experiment)
Review of theory
N
Any moving
charge creates a
magnetic field.

S
Shielding
Any moving charge creates a magnetic field.

→ Shielding of proton.
Terminology
1 3 5
• 𝑠 – total spin. Fermions: , , , …, Bosons: 0,1,2, …
2 2 2
• 𝜇𝑛 - the magnetic moment represents the magnetic strength of a
given magnet.
• The magnetic moment is related to the angular momentum
through the gyromagnetic ratio,

• 𝑆 – spin angular momentum.

Terminology
• In the presence of a magnetic field, 𝐸 = −𝜇𝑛 𝐵.

𝜇𝑛 = 𝛾𝑛 𝑆
𝑆 = ℏ 𝑠 𝑠 + 1 , −𝑠, … , 𝑠

→ 2𝑠 + 1 energy values.
Two Energy States
Shielding and Resonance Frequency
Shielding and Resonance Frequency
• Shielding effects can be taken into account by the expression:
B = B0 −  i B0

where B0 is the applied magnetic field strength and σi is the shielding

factor.

• The effective shift is then:

B
  i = 0 (1 −  i ) [nucleus i ]
2
 B0
 ref = (1 −  ref )
2
 B0
 i −  ref = ( ref −  i )
2
 −  ref  ref −  i
 i = = 10−6  i chemical shift in ppm
 ref 1 −  ref
NMR Signals
• The number of signals shows how many different kinds of
protons are present.

• The location of the signals shows how shielded or deshielded the

proton is.

• The intensity of the signal shows the number of protons of that

type.

• Signal splitting shows the number of protons on adjacent atoms.

Shielding and Resonance Frequency
• Shielding effects can be taken into account by the expression:
B = B0 −  i B0

where B0 is the applied magnetic field strength and σi is the shielding

factor.

• The effective shift is then:

B
  i = 0 (1 −  i ) [nucleus i ]
2
 B0
 ref = (1 −  ref )
2
 B0
 i −  ref = ( ref −  i )
2
 −  ref  ref −  i
 i = = 10−6  i chemical shift in ppm
 ref 1 −  ref
Calculation of the Shielding Tensor
Calculate zero-field SCF.

Choose gauge by which to enter the

magnetic vector potential.

Calculate new SCF for non-zero field.

Use the zero-field SCF results as the initial guess.

Calculate shielding tensor using the non-zero

field electron structure.
 Worked Example
• NMR spectra, and particularly spin-spin coupling constants, are
sensitive functions of molecular geometry.
• We start with the computed NMR spectrum of a single molecule
of ethanol.
• B3LYP/6-31+G(d,p) geometry optimization using a reasonable
initial guess geometry:

[Link]
 Worked Example
• We run the geometry optimization.
• Once complete, we use the computed optimized geometry and
set up a calculation with "Job Type" equal to "NMR". (default
GIAO method, calculate spin-spin couplings between all atoms).

[Link]
 Worked Example
• The predicted spectrum is indexed by the "number" of each
atom, which comes from their order in the original input file. Use
"View"=>"Labels" to see these numbers. (For example: the OH
hydrogen is atom number 9).

[Link]
Worked Example

NMR spectrum of ethanol dissolved in

chloroform at 89.56 MHz, taken from the SDBS.

• Experimental peaks have a certain width.

→The calculation does not take into account temperature or
solvent effects.
Worked Example

OH
OH

NMR spectrum of ethanol dissolved in

chloroform at 89.56 MHz, taken from the SDBS.

• OH hydrogen is more shielded than in the experiment.

• This is because our gas phase calculation does not account
for hydrogen bonding to solvent seen in this experiment.
Worked Example
CH3

NMR spectrum of ethanol dissolved in

chloroform at 89.56 MHz, taken from the SDBS.

• The CH3 group seen experimentally at δ=1.226 is split into peaks

at 1.35 and 0.98.
• The experiment can only measure the rotational average of the
three symmetry-nonunique CH3 hydrogens.
Worked Example

NMR spectrum of ethanol dissolved in

chloroform at 89.56 MHz, taken from the SDBS.

• No signal splitting.
Spin-Spin Coupling
Example: 1,1,2-trichloroethane
Spin-Spin Coupling
Spin-Spin Coupling
Worked Example

NMR spectrum of ethanol dissolved in

chloroform at 89.56 MHz, taken from the SDBS.

• Gaussian's "SpinSpin" option will calculate spin-spin couplings between

all atoms.
• While GaussView won't display the results directly, one can simply use
"Results"=>"Stream Output File" and search for "Total nuclear spin-spin
coupling J (Hz)
Calculation vs. Experiment
• Since the calculation is done on a static molecule, no bond
rotations are possible.

• The location of the signals is given relative to a reference

material calculated separately, at the same calculation level.

• Linewidths are zero (no solvent or temperature effects, T=0).

• Splitting is not shown be default.