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BioMedChem M2 > 20/21 - Spectroscopy > Flashcards

20/21 - Spectroscopy Flashcards

1
Q

Some uses of SPECTROSCOPY:

A

Mixture of compounds -> Chromatography -> single compound

Single Compound -> KNOWLEDGE OF STRUCTURE

Bio System + Compound –> Compound Localization / MoA / Protein-protein Interactions

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2
Q

What is SPECTROSCOPY?

A

Study of matter through its interaction w/ diff compounds of the EM spectrum,

interaction of energy with matter

understand how LIGHT interacts with MATTER

how to use it to learn about variety of properties in a molecule

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3
Q

4 First (smallest) Wavelength Regions

& what they measure

A

Gamma rays - n/a

X-Rays - core/inner level electrons

UV & Visible** = **valence / outer electrons

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4
Q

3 LAST (largest) Wavelength Regions

& what they measure

A

IR** **- molecular VIBRATIONS

Microwave - molecular ROTATIONS

Radio - NUCLEAR SPIN

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5
Q

What does a spectrum measure?

A

how the sample MODIFIES THE LIGHT interacting with it

  • Light source (EM wave) -> Sample
    • Change in Light
    • Change in Sample
      • =photochemistry
        • ​leads to DEGRADATION, typically irreversible
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6
Q

Typical process of “small molecule” structure ELUCIDATION

A

Compound ->

IR / UV-Vis / MS ->

1D NMR / 2DNMR ->

IDENTIFIED STRUCTURE

X-Ray Cytallography SKIPS all those steps

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7
Q

X-Ray Crystallography

Energy Interaction / Central Concept

A

DIFFRACTION = bending of light around an object

  • x-ray beam -> crystal of a SINGLE PURE crystal compound
    • bend/defract/scatter light in 3D space, 360 rotation
      • onto a detector, which is then computed
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8
Q

X-Ray Crystallography

Used for / Works on?

A

ribosome / how proteins fit together / antibiotic mechanism

has to be a PURE / SINGLE crystal

(has a HUGE number of PRECISELY ordered, IDENTICAL molecules)

Performed on both:

SMALL or LARGE

molecules 100-2k Da or >2k Da

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9
Q

X-Ray Crystallography

strengths & weaknesses

A
  • Strength:
  • Possible to determine entire structure** including **relative or absolute stereochemistry of small molecules

Good if you can get it to crystallize in the first place

  • Weakness:
  • Crystallization process is laborious; certain classes of molecules are difficult/nearly impossible to crystallize

•Crystallization is difficult to make

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10
Q

IR (infrared) Spectroscopy

Energy interaction / Central Concept

A

IR spectroscopy measure

MOLECULAR VIBRATIONS

  • X = Wave number (cm-1)
  • Y = % Transmittance, similar to absorbance but FLIPPED
  • Specific functional groups act in a
    • VERY SPECIFIC & CONSISTANT WAY
      • ​made a reference sheet for comparison
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11
Q

IR (infrared) Spectroscopy

Used for / Works For?

A

presence of FUNCTIONAL GROUPS

Bond Distance

Natural product elucidation, but NMR/MASS spectroscopy is better

need to compare to a reference / cheat sheet

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12
Q

IR (infrared) Spectroscopy

Strength / Weakness

A
  • Strength:
    • ​Indicates potential presence of FUNCTIONAL GROUPS
      • including bond distance
  • Weakness:
    • ​does NOT indicate CONNECTIVITY of functional groups
      • ​ex. we don’t know how 8 carbons + 10 hydrogens are bound,
        • dont know the actual molecule STRUCTUR
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13
Q

Atomic Absorption (aa) Spectroscopy

Energy Interaction / Central Concept

A

EMISSION SPECTRA of each element produces a unique fingerprint

Flame Test - similar to FP (Flame Photometry)

Flame converts metal ions -> atoms

measures Light Intensity

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14
Q

AA Spectroscopy

Works on / Common uses

A

Determination of METALS (Hg / Pb / etc)

from LIQUID** **(urine / plasma / serum)

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15
Q

AA Spectroscopy

Strengths / Weaknesses

A
  • Strength:
    • ​__used for Metals in Liquids/Solution
  • ​Weakness:
    • ​Low throughput, requires manual operation
      • ​_DESTRUCTIVE_
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16
Q

UV-Vis Spectroscopy

Energy Interaction / Central Concept

A
  • Spec of UV & Vis regions measures valence / outer electrons​
    • Molecules absorb EM radiation
      • as atoms pass from ground state -> Excited State
  • ​More effectively a molecule ABSORBS LIGHT (given wavelength,
    • –> GREATER the extent of light ABSORBANCE
  • views CHROMOPHORE
    • functional group that absorbs UV radiation
17
Q

Chromophore

A

Functional group that absorbs UV Radiation

views CONJUGATION

organic molecules between 190-800 nm

detected by UV / PDA Detectors

18
Q

Name the Process of rapidly identifying compounds that are

KNOWN CHEMICAL SCAFFOLDS

A

DEREPLICATION

used in UV/PDA

19
Q

UV / PDA Detectors

PhotoDiode Array

A

both view Light Absorption** of **Chromaphores

Photodiode Array (PDA) Detectors = pretty much the same as UV detection but with ALL WAVELENGTHS

IF DETECTABLE BY UV IT IS ALSO DETECTABLE BY PDA,

but not the other way around

20
Q

UV / PDA Spectroscopy

S / W

A
  • Strengths:
    • ​UV fingerprint may indicate the CLASS of a molecul
  • ​​Weakness:
    • ​does NOT distinguish between ISOMERS within a molecular class
      • ​if the structural change does not involve the CHROMOPHORE
    • ​Need an EXTENSIVE UV fingerprint
    • some classes do not absorb in UV regionn
21
Q

Common Chromophores

A

Blue box = solvent interference

chromophore wavelength OVERLAPS

w/ wavelength of solvent

22
Q

Chromophres with more complex conjugation

A

Complex conjugation = more DISTINCT UV Fingerprint

23
Q

UV / PDA Spectroscopy

Works on / Common uses

A

UV fingerprint is helpful for INDENTIFYING compound class if:

MOST of the structure contributes to the UV Chromophore

but we can link a chromophore to a reactive functional group

to make an UV-Active material

24
Q

ELSD

Evaporative Light Scattering Dector

Concept / Detects for?

A

Replacement or used in TANDEM w/ UV/PDA Detector

does not rely on spectroscopic qualities of molecule

only detects a PHYSICAL PRESENCE

of a compound, either SENSES or NOT,

needs physical blockage to be detected

25
Q

ELSD

Evaporative Light Scattering Dector

Steps / Method

A

DESTRUCTIVE DETECTION METHOD

detects for PHYSICAL PRESENCE

Solvent + Anyltes -> METAL NEBULIZER

Evaporated / carrier gas transports MIST through LASER

Gas condenses on tube after being removed from anylites

26
Q

ELSD Detection

Used For?

A

detects Physical Presence

useful for detecting molecules that do

NOT have any spectroscopic qualities

is destructive though

27
Q

Fluorescense vs Absorbance

A

You can’t have _fluorescence_ without absorbance

  • Absorbance
    • FIRST step in fluorescence.
      • electronic transition that promotes electron from ground state (LIGHT ENERGY)
  • Fluorescence
    • the light emitted by an atom or molecule
      • after absorbance of EM energy
28
Q

Fluoresence

A
  • Light Emitted by an atom or a molecule after
    • the absorbtion of EM energy
  • Need to Filter OUT excited light
    • remaining light is Fluorescent light
      • enables visualization of molecules / proteins
29
Q

Fluorophores

A
  • Molecules or Functional groups that have the
    • Capacity to exhibit flourescence
  • ​Structural characteristic of useful fluorophores:
    • Extended Conjugated Pi bonds
  • the MORE conj bonds
    • & lower the excited energy requirement
      • ​LONGER the wavelength (redder) the exciting light can be
  • ​​Ex. GFP, green fluorescent protein
30
Q

GFP Mechanism

A

Green fluoresent protein resulting in Fluorescence

  • Cyclization step to form 5-membrane ring
    • Gly-N –> attacks Ser amide carbonyl
  • Dehydration step
    • forms unsaturated imidazoline
  • ​DeHydrogenation of TYR carbons
    • by OXYGEN to from conjugated fluorophore which:
      • absorbs & emits light in th visible range

BioMedChem M2 (8 decks)

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