Spectroscopy Flashcards

1
Q

What do the following types of energy involve?

  1. Nuclear
  2. electronic
  3. vibrational
  4. rotational
  5. translational
A
  1. Nuclear: protons and neurtrons within the nucleus
  2. Electronic: Electrons between a few atoms
  3. Vibrational: Few atoms
  4. Rotational: Whole molecule
  5. Translational: Whole molecule moving large distance
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2
Q

Whats the formula for the Boltzmann distribution of molecules over energy levels?

What makes molecules move up into a higher energy level?

A

As temperature increases, the moelcules inhibit higher energy levels

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3
Q

What is electromagnetic radiation?

What is the energy for a given frequency described as?

A

Electromagnetic radiation has an electric and magnetic component. where the electric component is oscillating and the magnetic component is rotating from north and south

Energy (E) for a given frequency (u) is

E= hu

where h is the Planks constant (6.626x10-34 J s)

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4
Q

Whats the order of the electromagnetic spectrum from the smallest frequency to the largest?

A
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5
Q

What are the conditions in order for the electromagnetic radiation to be absorbed?

A
  • must be two or more energy levels
  • Charge displacement must occur:

a. Linear displacement: electric transition dipole
b. Rotation of charge: magnetic transition dipole
* ∆E= hu (must be between the ground and excited state)

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6
Q

Once the incident radiation, I0, is absorbed what are the types of radiation you can get from this?

A
  1. Transmitted radiation, It
  2. Emitted radiation, Ie
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7
Q

What are the characteristics of a spectrum?

A
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8
Q

What does the intensity depend on?

A

The number of moelcules that can be excited from ground state

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9
Q

What determines if population different is small and therefore sensitivity to be low?

A

∆E is roughly kT

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10
Q

Name 3 types of spectroscopy and which one sees more absorption of the electromagnetic radiation?

A
  1. NMR
  2. rotational
  3. electronic (sees more absorption)
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11
Q

What is absorption dependent on?

What equation describes this?

What does each part of the equation represent? Units?

A

The concentration of absorbing species

The Beer Lambert law:

Log10(I0/ It) = OD = ecl

e= the extinction coefficient (absorbing power of a species at a particular wavelength)

C= the concentration of absorbing species (mol dm-3)

l= length of solution of light passes through (cm)

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12
Q

In the Beer Lambert law, when OD >1 what does this mean?

A

It is no longer linear–> not accurate

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13
Q

What is the Beer Lambert law?

A

Its combined of 2 laws and each are correlates which state that, the absorbance of light is proportional to the thickness of the sample or absorbance is proportional to the concentration of the sample

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14
Q

When is maximum absorbance seen in intensity?

A

When the transition dipole is aligned with the polarised light

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15
Q

The orientations of light leads to differential…

A

absorption

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16
Q

What is natural linewidth determine by?

A

Lifetime of excited state (t)

17
Q

Whats the Heissenberg uncertainty principle?

A

it states that its impossible to know simultaneously the exact position and momentum of a particle

That is, the more exactly the position is determines, the less known the momentum and vice versa

18
Q

How does decay from an excited state occur?

A
  • stimulated emission: through application of external field
  • conversion to other excited state
  • non-radiative loss to environment
  • resonance energy transferred to nearby molecule
  • chemical reactions
19
Q

Why is spectroscopy important?

A
  1. Study conformation of molecules
  • Structure of molecules
  • Reports on their environment
  1. Quantitation
  • Protein/ DNA concentration determination
  • Biochemical assays
  1. Detection
  • DNA sequencing
  • Microscopy
  • Cytometry
20
Q

Learn absorbance/ emittence

A
21
Q

Coupling to vibrational states

A
22
Q

What are the types of electronic transitions?

A

1. Transition involving p, s and n electrons

Organic compounds:

  • Saturated (σ –> σ (< 150 nm)*, n –> σ*(<250 nm))

leads to displacement of charge when σ –> σ*

  • unsaturated (π- π*, n–> π* (200-700nm))

2. Transitions involving charge transfer

  • electrons move from ligand donor to metal acceptor

3. Transitions involving d and f electrons

  • transitions between d orbitals split by the presence of a ligand
23
Q

Whats determines

A
  1. Dependent on molecular structure
  2. No easy rule for assignment, however:
  • Presence of resonance >300 nm suggests presence of conjugated polyene chain/ polycyclic aromatic
  • Conjugated systems typically have larger extinction coefficients
  1. Refer to databases (as above doesn’t give much detail)
24
Q

What are the changes that can occur in a UV/ visible spectra?

A
25
Q

Name the chromophores found in biology?

A
  1. Proteins
  2. Nucleic acids
  3. ​Metal ions
26
Q

Whats the most common protein chromophore?

A

Peptide bonds

27
Q

How many transition states are associated with this molecule?

A

2

28
Q

In proteins sidechains are there transition dipoles and conjugates bonds present?

What determines a higher extinction coeffient in a sidechain?

A

yes

The number of delocalised electrons

29
Q

What can influence energy levels? and how?

A

Solvent polarity by stabilising or destabilising the excited state

30
Q

How does changing the exposure to light influence the wavelength in prosthetic groups?

A

When in dakr conditions and then exposed to light, the wavelength can decrease

31
Q

Do nucleic acids have more transition dipoles then protens?

A

Yes

32
Q

How does nucleic acid transition coupling effect the excited state?

What does coupling depend on?

A

When two transition dipoles are coupled, they interact, splitting the energy levels (excitation coupling)

The coupling depends on relative orientation

33
Q
  1. When the transition dipole is parallel to the induced dipole what occurs?
  2. When the transition dipole os collinearl to the induced dipole what occurs?
A
  1. Hypochromism
  2. Hyperchromism
34
Q
  1. What effect does structured DNA cause
  2. What effect does unstructured DNA cause
A
  1. Structured DNA –> parallel dipoles Hypochomism
  2. Unstructured DNA –> Dipole unaligned hyperchromic shift