Exam 2 Flashcards
Molecules
Have covalent bonds
Hybrid Molecules
Have both covalent and non-covalent bonding, the part of these hybrids that have the covalent bonds are molecules.
Covalent Bonds
Sharing of electrons, changes the energy diagrams by creating hybridized orbitals; ex) sp, sp2, sp3, etc.)
To cause an emission….
An electron must be excited to a higher energy state.
The stokes shift can be observed when…..
Fluorescence and adsorption are graphed on the same plot.
Beers Law
Demonstrates relationship between absorbance and concentration
Beers Law Formula
A = Ebc
A = absorbance E = absorptivity constant b = path length (length of cuvette, ~1 cm) c = concentration
Transmittance Formula
A = -logT
A = absorbance
T = transmittance
To find T, use 10^-A
Percent Transmittance
%T = P/P0 x100
Absorbance System
Source —P0–> Sample —P—> Detector
Graph of Absorbance/Transmittance
Linear graph
Y=my+b , A=Ebc
Y = A m = Eb x = c
IR Spectroscopy:
Infrared radiation interraction with a molecule is………
NOT enough to excite an electron to a new energy state; however vibrational bands can be accessed.
IR Spectroscopy:
Infrared energy is absorbed so…….
It does NOT make it to the detector.
IR Spectroscopy:
In order for IR energy to be absorbed……
The dipole moment must be changed.
IR Spectroscopy:
The greater the dipole moment…..
The greater the peak.
IR Spectroscopy:
2 Factors of Peak Intensity:
- Vibrations from stretching/bending (stretching generally gives larger peaks)
- Electronegativity differences between atoms involved in the bond (the larger the electronegativity difference, the larger the peak)
IR Spectroscopy:
Strong Peak
Tall peak, low transmittence
IR Spectroscopy:
Weak Peak
Short peak, high transmittance
IR Spectroscopy:
Medium Peak
Peak is at mid-height
IR Spectroscopy:
Broad Peak
Very large peak base exists across many wavelengths; involves several energies and several bonds that are related.
Functional Groups:
Alcohol
R—OH
Functional Groups:
Ether
R—O—R
Functional Groups:
Aldehyde
R—C—H
II
O
Functional Groups:
Amine
R—NH2
Functional Groups:
Carboxylic Acid
R—C—OH
II
OH
Functional Groups:
Ester
R—C—O—R
II
O
Functional Groups:
Ketone
R—C—R
II
O
Functional Groups:
Amides
R—C—NH2
II
O
Larger bases indicate…..
ACIDS
IR Spectroscopy:
Location of Carbonyl Peak
~1700
IR Spectroscopy:
Location of Alcohols
~3300
- rounded peak
IR Spectroscopy:
Location of Alkanes
Slightly under 3000 cm-1
IR Spectroscopy:
Location of Carboxylic Acids
~3000 ish
- wide peak base with sharp peak point
IR Spectroscopy:
Location of Alkenes
Slightly above 3000 cm-1
IR Spectroscopy:
Location of Alkynes
~3300 cm-1
IR Spectroscopy:
Location of Aldehyde
Contains a carbonyl (C=O) at ~1700 cm-1
IR Spectroscopy:
Location of Ether
~1050 - 1300 cm-1
IR Spectroscopy:
Location of Ester
Contains carbonyl group (C=O) at ~1700 cm-1
IR Spectroscopy:
Location of Amine
Large, wide based, curved peak around 3000 and greater,
Contains many curved peaks
IR Spectroscopy:
Location of Amide
Multiple peaks with large base peaks (one larger than 3000, one ~1700)
IR Spectroscopy:
Location of Benzene Ring
Narrow, thin peaks
Three located at ~3000, ~1400, ~900
IR Spectroscopy:
Location of Ring
(Single bonds only)
Narrow, thin peaks
VERY LARGE peak at ~2900
Other peaks at ~1400, small peaks at ~900
Steps in NMR:
- Align all of the nuclei
- Blast them all with energy
- See what happens
FID
Free Induction Decay
Generated when nuclei return to their ground state
(Different nuclei will return to their ground states at different rates depending on its surroundings)
How to generate NMR spectra (frequency vs. intensity) from FID:
Use Fourier transform to pull wave functions apart into frequency vs. intensity.
FOURIER TRANSFORM
What does information does FTIR give you?
FUNCTIONAL GROUPS
What information does H-NMR give you?
Types and number of equivalent protons and nearby protons
What information does C-NMR give you?
Types and number of equivalent carbons
What information does Mass Spec give you?
Molecular mass and groups that can fall from the larger structure
Peak splitting is dependent on…..
Nearby protons; only for H-NMR (proton) spectra
Duderated
All hydrogen’s are one mass unit greater
What does mass spectrometry measure?
Mass to charge ratio
Infrared Radiation (IR) causes…….
VIBRATIONAL STATE CHANGES
IR is not strong enough to cause band gap jumps
IR Active = ?
Raman Active = ?
IR Active = dipole moment change
Raman Active = NO dipole meant change
KNOW THE VIBRATIONAL VARIATIONS
Bond Stretching and Bending
Stretching = symmetric vs. asymmetric
Bending = in-plane rocking vs. in-plane scissoring
= out-of-plane wagging vs. out-of-plane twisting
Harmonic Oscillator
How the energy of the vibrational mode can be seen
E = (v + 1/2) h Vm
Degrees of Freedom =
= 3N
Degrees of Freedom
How you can deduce the number and kind of vibrations in simple systems
How to Calculate Degrees of Freedom:
A molecule containing N atoms is said to have 3N degrees of freedom (3*N)
3 Different Types of Degrees of Freedom:
A. Translational - motion of the entire molecule thru space
B. Rotational - motion of entire molecule around its center of gravity
C. Vibrational - motion of each of its atoms to the other atoms
How to Calculate Vibrational Degrees of Freedom:
3N - 6
3N - 5 for LINEAR molecules
4 Things that give less Degrees of Freedom than expected:
- No change in dipole moment (due to symmetry of molecules)
- The energies of 2 or more vibrations are identical (or nearly identical)
- The absorption intensity is so low that it is undetectable
- The vibrational energy is in a wavelength region beyond the instrument’s range
Vibrations are not completely separate……
They interact with each other.
Rules of Vibrational Coupling:
A. Strong coupling between stretch vibrations occurs only when there is an atom common to the 2 vibrations.
B. Interaction between bending vibrations requires a common bond between the vibrating groups.
C. Coupling between a stretching and bending vibration can occur if the stretching bond forms one side of the angle that varies in the bending vibration.
D. Interaction is greatest when the coupled groups have individual energies that are nearly equal.
E. Little or no interaction is observed between groups separated by 2 or more bonds.
F. Coupling requires that the vibrations be of the same symm. species.
Layout of FTIR:
- the laser is NOT the source; it is only a guide.
- interferometer is a critical piece.
Interferometer
Device that separates a beam of light by reflection, then recombines them causing interference; used to measure wavelength and index of refraction
NMR Spectroscopy
Nuclear Magnetic Resonance Spectroscopy
What frequency region does NMR use?
Radio frequency region
Example of NMR in practical use
MRI
4 Important Nuclei in NMR Spectroscopy:
H1
C13
F19
P31
Why does spinning matter in NMR Spectroscopy?
- nuclei are charged and spin
- charged stuff that spins generates a magnetic field
- gives magnetic quantum number
Bolzmann’s Distribution of States
Statistical probability for the population of each of the states
Nj/No = exp (-deltaE / KT)
(Delta E is the energy levels generated by the magnetic moment; magnet dependent)
Application of Radio Waves during NMR Spectroscopy:
Hitting system with radio waves of a particular frequency can cause the energy level to jump
Spin-Lattice Relaxation has to do with…..
PEAK LOCATION
Spin-Spin Relaxation has to do with…..
PEAK SPLITTING
Lattice
The entire collection of atoms that constitute a sample; atoms are constantly in motion which creates a magnetic field around the atoms
Spin-Lattice Relaxation:
All magnetic field interact and will convert almost anything into minuscule temperature adjustments
(1st order exponential decay characterized by a relaxation time, T1)
Spin-Spin Relaxation
When 2 neighboring nuclei of the same kind have identical relaxation rates but are in different magnetic quantum states, the magnetic fields of each can interact to cause an interchange of states
Resolution in NMR:
- spin-lattice can be impacted to spread peaks further apart; peaks shifter further apart at a better resolution
- spin-spin is NOT affected.
Chemical shift is due to…..
Spin-lattice coupling
Chemical Shift
The frequency of the resonance expressed with reference to a standard compound which is defined to be at 0 ppm
Screening
Detection of fragments from NMR, which can be used to determine the overall structure
Shielding
When a nucleus’s chemical shift has been decreased due to addition of electron density or change in magnetic field
Splitting
Occurs as the magnetic field of 2 adjacent nuclei interact, which pushes electrons around the structure. The movement of electrons produces changes in the magnetic field.
Necessary Parts of NMR instrument:
- magnets (need to be very cold)
- shimming coils (shims)
- homogeneity of the order of 10^-9
How the magnets in an NMR instrument cooled?
Liquid nitrogen and liquid helium
Phasing
The modification of a peak to increase resolution in NMR
Phasing can cause…..
Upside down peak in NMR spectra; can also get rid of inverted peaks as well
Goal of shimming coils (shims) in NMR instrument:
To create a homogenous magnetic field
Results of Shimming:
- impacts resolution (poorly shimmed = loss of resolution)
Mass Spectrometry is able to…..
- Give elemental composition
- Give structural info about the inorganic, organic, and biological molecules
- Gives qualitative and quantitative info about complex mixtures
- Gives structure and composition of solid surfaces
- Gives isotope ratios of atoms in a sample
Mass Spec data output:
- x-axis is mass/charge
- y-axis is relative intensity; values depend on instrument parameters
Ions…..
Can be detected as either positive or negative
Important parts of Mass Spec:
- Sample Inlet
- Ion sources
- Ion transfers
- Mass Analyzers
- Detector
- Recorder
Mass Spec:
Generic function of Sample Inlet
Introduces the sample
Mass Spec:
Generic function of ion sources
Ionizes
Mass Spec:
Generic function of ion transfers
Transfers ions
Mass Spec:
Generic function of mass analyzers
Separates ion stream into something useful
Mass Spec:
Generic function of detector
Converts info to electrical domain
Mass Spec:
Generic function of recorder
Records infromation
Mass Spec:
Type of sample inlet is dependent on….
- Sample phase (s/l/g)
- Sample composition (pure/mixture)
- Sample stability
Mass Spec:
Which type of sample is most convenient?
GAS SAMPLES
Mass Spec:
Which type is used to analyze gas samples?
GCMS
Gas Chromatography Mass Spec
Mass Spec:
How are liquids analyzed?
Nebulization is used as an ion source since the molecules in a liquid are closer together, therefore there are more of them
Mass Spec:
What type is used to run liquid samples?
HPLC-MS
High Pressure Liquid Concentration Mass Spec
Mass Spec:
What type is used to analyze solid samples?
MALDI - most common
(Matrix Assisted Laser Desorption/Ionization)
ASAP (Atmospheric Solids Analysis Probe)
Hard Ion Source
Something that applies a lot of energy to a system fast; leaves a large amount of energy in the molecules
INCREASES FRAGMENTATION
Soft Ion Source
Something that gently applies energy to a system; puts just enough energy into a molecules to attach a charge
INCREASES STABILITY OF IONIZED SPECIES
The larger the molecule….. the _______ the ionization technique required.
SOFTER
MALDI
Matrix Assisted Laser Desorption/Ionization
- soft technique
- mass spec used to analyze solid samples
Ion Source:
EI
Electron Impact (mass spec)
- hard ionization
- good for small molecules
Ion Source:
ESI
Electro spray Ionization (Mass Spec)
- soft ionization
- good for proteins
FAB
Fast Atom Bombard (mass spec)
- semi hard ionization
- good for proteins and sugars
Skimmers
- important part of mass spec.
- interface between vacuum chambers used to thin out solvent
3 Categories of Mass Analyzers
- Quadripole
- Time of Flight
- Double Focusing/Magnetic Sector
Quadripole
- type of mass analyzer in mass spec
- design: linear, allows only ions you want to pass thru
- combination of DC current and RF frequency to alter trajectories of ions
- advantages: fast, small, able to use multiple sources
Traps
Mass analyzer in mass spec.
- traps desired ions in center of electromagnetic field
- advantage: can do multiple MS/MS
- disadvantage: lose a lot of sample
Time of Flight
- type of mass analyzer
- time it takes for an ion to migrate a set distance
- ions are formed, then spread are arrive at the detector at different times due to differing velocities.
Double Focusing/Magnetic Sector
- Type of mass analyzer in mass spec.
- ions are accelerated down a curved flight tube, magnets deflect trajectory
Advantage and Disadvantage of Double Focusing:
Ad: easily reproduced
Dis: expensive
Advantage and Disadvantage of Time of Flight:
Ad: great for large molecules
Dis: low reproducibility
Advantage and Disadvantage of Traps:
Ad: multiple ms/ms/ms/ms on trapped ions
Dis: lose a lot of sample each time
Transduction
Detection process; converts domain
Faraday Cup
Transduction in Mass Spec
- blocks signals, making it easy to detect charge
Electron Multiplier
Transduction in Mass Spec.
- device that uses a series of dynodes
- cascade of electrons generates a measurable electrical current
Photocathode
Converts light to electricity
Array Transducers
Transduction in Mass Spec.
- used to detect multiple ions that have been separated spatially
- works on time of flight and double focusing instruments
- includes micro channel plates, microfaraday array
Mass Spec stands for
Mass Spectrometry
Tandem Techniques
Any technique that involves running MS followed by MS
- most common is the triple quad and QTOF
Ionization in Atomic vs. Molecular vs. Biomolecules Mass Spec.’s
Atomic MS = hard ionization
Molecular MS = hard, but softer than atomic
Biomolecule MS = soft
Ion Mobility Instruments
Separates ions based on their mobility
PTR-MS
Soft ionization; ionizes protons and allows them to interact with analyte
Ion Sources:
APCI
Atmospheric Pressure Chemical Ionization
- soft ionization
- used in trace analysis detection of steroids, pesticides, etc.
Ion Sources:
DESI
Desorption Electrospray Ionization
- used for chemical analysis of atmospheric conditions
Ion Source:
PI
Photoionization
- used to investigate chemistry of low pressure flames
Ion Source:
SIMS
Secondary Ion Mass Spectrometry
- determines the elemental composition of a surface, VERY SENSITIVE
Ion Source:
LD
Laser Desorption
- soft ionization
Ion Source:
DART
Direct Analysis in Real Time
- can be used to analyze solids, liquids, and gases
Ion Source:
LTP
Low Temperature Plasma
Deshielding
when a nucleus’s chemical shift has been increased due to the removal of electron density or change in magnetic field
