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Flashcards in Exam 2 Deck (140):
1

Molecules

Have covalent bonds

2

Hybrid Molecules

Have both covalent and non-covalent bonding, the part of these hybrids that have the covalent bonds are molecules.

3

Covalent Bonds

Sharing of electrons, changes the energy diagrams by creating hybridized orbitals; ex) sp, sp2, sp3, etc.)

4

To cause an emission....

An electron must be excited to a higher energy state.

5

The stokes shift can be observed when.....

Fluorescence and adsorption are graphed on the same plot.

6

Beers Law

Demonstrates relationship between absorbance and concentration

7

Beers Law Formula

A = Ebc

A = absorbance
E = absorptivity constant
b = path length (length of cuvette, ~1 cm)
c = concentration

8

Transmittance Formula

A = -logT

A = absorbance
T = transmittance
(To find T, use 10^-A)

9

Percent Transmittance

%T = P/P0 x100

10

Absorbance System

Source —P0–> Sample —P—> Detector

11

Graph of Absorbance/Transmittance

Linear graph
Y=my+b , A=Ebc

Y = A
m = Eb
x = c

12

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.

13

IR Spectroscopy:
Infrared energy is absorbed so.......

It does NOT make it to the detector.

14

IR Spectroscopy:
In order for IR energy to be absorbed......

The dipole moment must be changed.

15

IR Spectroscopy:
The greater the dipole moment.....

The greater the peak.

16

IR Spectroscopy:
2 Factors of Peak Intensity:

1. Vibrations from stretching/bending (*stretching generally gives larger peaks*)
2. Electronegativity differences between atoms involved in the bond (*the larger the electronegativity difference, the larger the peak*)

17

IR Spectroscopy:
Strong Peak

Tall peak, low transmittence

18

IR Spectroscopy:
Weak Peak

Short peak, high transmittance

19

IR Spectroscopy:
Medium Peak

Peak is at mid-height

20

IR Spectroscopy:
Broad Peak

Very large peak base exists across many wavelengths; involves several energies and several bonds that are related.

21

Functional Groups:
Alcohol

R—OH

22

Functional Groups:
Ether

R—O—R

23

Functional Groups:
Aldehyde

R—C—H
II
O

24

Functional Groups:
Amine

R—NH2

25

Functional Groups:
Carboxylic Acid

R—C—OH
II
OH

26

Functional Groups:
Ester

R—C—O—R
II
O

27

Functional Groups:
Ketone

R—C—R
II
O

28

Functional Groups:
Amides

R—C—NH2
II
O

29

Larger bases indicate.....

ACIDS

30

IR Spectroscopy:
Location of Carbonyl Peak

~1700

31

IR Spectroscopy:
Location of Alcohols

~3300
- rounded peak

32

IR Spectroscopy:
Location of Alkanes

Slightly under 3000 cm-1

33

IR Spectroscopy:
Location of Carboxylic Acids

~3000 ish
- wide peak base with sharp peak point

34

IR Spectroscopy:
Location of Alkenes

Slightly above 3000 cm-1

35

IR Spectroscopy:
Location of Alkynes

~3300 cm-1

36

IR Spectroscopy:
Location of Aldehyde

Contains a carbonyl (C=O) at ~1700 cm-1

37

IR Spectroscopy:
Location of Ether

~1050 - 1300 cm-1

38

IR Spectroscopy:
Location of Ester

Contains carbonyl group (C=O) at ~1700 cm-1

39

IR Spectroscopy:
Location of Amine

Large, wide based, curved peak around 3000 and greater,
Contains many curved peaks

40

IR Spectroscopy:
Location of Amide

Multiple peaks with large base peaks (one larger than 3000, one ~1700)

41

IR Spectroscopy:
Location of Benzene Ring

Narrow, thin peaks
Three located at ~3000, ~1400, ~900

42

IR Spectroscopy:
Location of Ring
(Single bonds only)

Narrow, thin peaks
VERY LARGE peak at ~2900
Other peaks at ~1400, small peaks at ~900

43

Steps in NMR:

1. Align all of the nuclei
2. Blast them all with energy
3. See what happens

44

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)

45

How to generate NMR spectra (frequency vs. intensity) from FID:

Use Fourier transform to pull wave functions apart into frequency vs. intensity.

***FOURIER TRANSFORM***

46

What does information does FTIR give you?

FUNCTIONAL GROUPS

47

What information does H-NMR give you?

Types and number of equivalent protons and nearby protons

48

What information does C-NMR give you?

Types and number of equivalent carbons

49

What information does Mass Spec give you?

Molecular mass and groups that can fall from the larger structure

50

Peak splitting is dependent on.....

Nearby protons; only for H-NMR (proton) spectra

51

Duderated

All hydrogen’s are one mass unit greater

52

What does mass spectrometry measure?

Mass to charge ratio

53

Infrared Radiation (IR) causes.......

VIBRATIONAL STATE CHANGES
(IR is not strong enough to cause band gap jumps)

54

IR Active = ?
Raman Active = ?

IR Active = dipole moment change
Raman Active = NO dipole meant change

55

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

56

Harmonic Oscillator

How the energy of the vibrational mode can be seen

E = (v + 1/2) h Vm

57

Degrees of Freedom =

= 3N

58

Degrees of Freedom

How you can deduce the number and kind of vibrations in simple systems

59

How to Calculate Degrees of Freedom:

A molecule containing N atoms is said to have 3N degrees of freedom (3*N)

60

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

61

How to Calculate Vibrational Degrees of Freedom:

3N - 6

(3N - 5 for LINEAR molecules)

62

4 Things that give less Degrees of Freedom than expected:

1. No change in dipole moment (due to symmetry of molecules)
2. The energies of 2 or more vibrations are identical (or nearly identical)
3. The absorption intensity is so low that it is undetectable
4. The vibrational energy is in a wavelength region beyond the instrument’s range

63

Vibrations are not completely separate......

They interact with each other.

64

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.

65

Layout of FTIR:

- the laser is NOT the source; it is only a guide.
- interferometer is a critical piece.

66

Interferometer

Device that separates a beam of light by reflection, then recombines them causing interference; used to measure wavelength and index of refraction

67

NMR Spectroscopy

Nuclear Magnetic Resonance Spectroscopy

68

What frequency region does NMR use?

Radio frequency region

69

Example of NMR in practical use

MRI

70

4 Important Nuclei in NMR Spectroscopy:

H1
C13
F19
P31

71

Why does spinning matter in NMR Spectroscopy?

- nuclei are charged and spin
- charged stuff that spins generates a magnetic field
- gives magnetic quantum number

72

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)

73

Application of Radio Waves during NMR Spectroscopy:

Hitting system with radio waves of a particular frequency can cause the energy level to jump

74

Spin-Lattice Relaxation has to do with.....

PEAK LOCATION

75

Spin-Spin Relaxation has to do with.....

PEAK SPLITTING

76

Lattice

The entire collection of atoms that constitute a sample; atoms are constantly in motion which creates a magnetic field around the atoms

77

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)

78

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

79

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.

80

Chemical shift is due to.....

Spin-lattice coupling

81

Chemical Shift

The frequency of the resonance expressed with reference to a standard compound which is defined to be at 0 ppm

82

Screening

Detection of fragments from NMR, which can be used to determine the overall structure

83

Shielding

When a nucleus’s chemical shift has been decreased due to addition of electron density or change in magnetic field

84

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.

85

Necessary Parts of NMR instrument:

- magnets (need to be very cold)
- shimming coils (shims)
- homogeneity of the order of 10^-9

86

How the magnets in an NMR instrument cooled?

Liquid nitrogen and liquid helium

87

Phasing

The modification of a peak to increase resolution in NMR

88

Phasing can cause.....

Upside down peak in NMR spectra; can also get rid of inverted peaks as well

89

Goal of shimming coils (shims) in NMR instrument:

To create a homogenous magnetic field

90

Results of Shimming:

- impacts resolution (poorly shimmed = loss of resolution)

91

Mass Spectrometry is able to.....

1. Give elemental composition
2. Give structural info about the inorganic, organic, and biological molecules
3. Gives qualitative and quantitative info about complex mixtures
4. Gives structure and composition of solid surfaces
5. Gives isotope ratios of atoms in a sample

92

Mass Spec data output:

- x-axis is mass/charge
- y-axis is relative intensity; values depend on instrument parameters

93

Ions.....

Can be detected as either positive or negative

94

Important parts of Mass Spec:

1. Sample Inlet
2. Ion sources
3. Ion transfers
4. Mass Analyzers
5. Detector
6. Recorder

95

Mass Spec:
Generic function of Sample Inlet

Introduces the sample

96

Mass Spec:
Generic function of ion sources

Ionizes

97

Mass Spec:
Generic function of ion transfers

Transfers ions

98

Mass Spec:
Generic function of mass analyzers

Separates ion stream into something useful

99

Mass Spec:
Generic function of detector

Converts info to electrical domain

100

Mass Spec:
Generic function of recorder

Records infromation

101

Mass Spec:
Type of sample inlet is dependent on....

1. Sample phase (s/l/g)
2. Sample composition (pure/mixture)
3. Sample stability

102

Mass Spec:
Which type of sample is most convenient?

GAS SAMPLES

103

Mass Spec:
Which type is used to analyze gas samples?

GCMS
(Gas Chromatography Mass Spec)

104

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

105

Mass Spec:
What type is used to run liquid samples?

HPLC-MS
(High Pressure Liquid Concentration Mass Spec)

106

Mass Spec:
What type is used to analyze solid samples?

MALDI - most common
(Matrix Assisted Laser Desorption/Ionization)

ASAP (Atmospheric Solids Analysis Probe)

107

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*

108

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*

109

The larger the molecule..... the _______ the ionization technique required.

SOFTER

110

MALDI

Matrix Assisted Laser Desorption/Ionization
- soft technique
- mass spec used to analyze solid samples

111

Ion Source:
EI

Electron Impact (mass spec)
- hard ionization
- good for small molecules

112

Ion Source:
ESI

Electro spray Ionization (Mass Spec)
- soft ionization
- good for proteins

113

FAB

Fast Atom Bombard (mass spec)
- semi hard ionization
- good for proteins and sugars

114

Skimmers

*important part of mass spec.
- interface between vacuum chambers used to thin out solvent

115

3 Categories of Mass Analyzers

1. Quadripole
2. Time of Flight
3. Double Focusing/Magnetic Sector

116

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

117

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

118

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.

119

Double Focusing/Magnetic Sector

*Type of mass analyzer in mass spec.
- ions are accelerated down a curved flight tube, magnets deflect trajectory

120

Advantage and Disadvantage of Double Focusing:

Ad: easily reproduced
Dis: expensive

121

Advantage and Disadvantage of Time of Flight:

Ad: great for large molecules
Dis: low reproducibility

122

Advantage and Disadvantage of Traps:

Ad: multiple ms/ms/ms/ms on trapped ions
Dis: lose a lot of sample each time

123

Transduction

Detection process; converts domain

124

Faraday Cup

Transduction in Mass Spec
- blocks signals, making it easy to detect charge

125

Electron Multiplier

Transduction in Mass Spec.
- device that uses a series of dynodes
- cascade of electrons generates a measurable electrical current

126

Photocathode

Converts light to electricity

127

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

128

Mass Spec stands for

Mass Spectrometry

129

Tandem Techniques

Any technique that involves running MS followed by MS
- most common is the triple quad and QTOF

130

Ionization in Atomic vs. Molecular vs. Biomolecules Mass Spec.’s

Atomic MS = hard ionization
Molecular MS = hard, but softer than atomic
Biomolecule MS = soft

131

Ion Mobility Instruments

Separates ions based on their mobility

132

PTR-MS

Soft ionization; ionizes protons and allows them to interact with analyte

133

Ion Sources:
APCI

Atmospheric Pressure Chemical Ionization
- soft ionization
- used in trace analysis detection of steroids, pesticides, etc.

134

Ion Sources:
DESI

Desorption Electrospray Ionization
- used for chemical analysis of atmospheric conditions

135

Ion Source:
PI

Photoionization
- used to investigate chemistry of low pressure flames

136

Ion Source:
SIMS

Secondary Ion Mass Spectrometry
- determines the elemental composition of a surface, VERY SENSITIVE

137

Ion Source:
LD

Laser Desorption
- soft ionization

138

Ion Source:
DART

Direct Analysis in Real Time
- can be used to analyze solids, liquids, and gases

139

Ion Source:
LTP

Low Temperature Plasma

140

Deshielding

when a nucleus’s chemical shift has been increased due to the removal of electron density or change in magnetic field