1
Q
How are compounds named
A
Named according to the number of carbon atoms linked together in the longest chain of carbons
2
Q
What forms the root name
A
The number of carbons in the longest continuous chain
3
Q
How is a simple non branched Alkane named?
A
Named by the root (number of carbons) followed by the suffix “ane”
4
Q
How do you name branched Alkanes?
A
- Find the longest continuous chain of carbons - gives the root name
- Name the branch group using the root name for the number of carbons - To indicate that it is an “yl”
- The compound can be named by putting the three parts of the name together
(Branch + Root + Family)
The number for the location must be added at the beginning
5
Q
What do you do if there is more than one branch in an Alkane?
A
- Longest chain forms the root name of the main chain
- The branches are named according to the number of carbons
- The chains are numbered to give the lowest possible number combination for the branches
- Name the branches in alphabetical order
6
Q
What is there is more than one branch with the same number of carbons?
A
The terms di, tri are incorporated into the name followed by the position of each group
7
Q
What happens when a branch within a branch cannot be avoided?
A
- Label the branch according to the longest continuous carbon chain
- Label the branch off this as normal
- To avoid getting confused with the number of locates associated with the main chain it should be placed in brackets
8
Q
How do you name cycloalkanes?
A
- Named by the number of carbons in the ring followed by the prefix cyclo
- If the ring is the longest chain of carbons this is the root name
- if the ring is not the longest carbon chain the ring is treated as a branch
9
Q
What is a bicyclicalkane?
A
Have two rings sharing only one carbon are known as spiro compounds
10
Q
How do you name a Spiro compound?
A
- The prefix Spiro is added to the name
2. The root name is taken form the total number of carbons in both ring
11
Q
How do you distinguish between different Spiro carbons with the same total number of carbons but a different number in each ring?
A
The numbers in each ring (excluding the central carbon) is placed in square brackets with a dot between them
The numbers always go low to high
12
Q
How do you name a Spiro carbon if there are substitutes on the ring?
A
When there are substitutes in the ring you start the numbering in the small ring next to the ring junction then in to the larger ring
Go in the direction that will give the lowest number in each ring
13
Q
What is a bridgehead compound?
A
When two rings have two carbons in common. Carbons are known as bridgeheads.
14
Q
How do you name the bridgehead compounds?
A
- The compounds are given the prefix bicyclo.
- The root name is based on the total number of carbons in the bicycle
- The stereo chemistry is described in brackets
The three numbers depict the number of intervening carbons between the two bridgehead carbons ( in decreasing order)
15
Q
How do you number the carbons of the bridgehead rings?
A
- Start with one of the bridgehead carbons and label it
- Proceed around the longest chain of carbons to the second bridgehead
- Number the second bridgehead carbon and continue around the next longest chains of carbons back towards the first bridgehead carbon
- Pass over the first bridgehead carbon (as it is already labelled 1 ) along the final, shortest chain of carbons to the second bridgehead.
16
Q
How do you name the bridgehead compound when there are substitutes
A
- Name the branch and add
- yl to the end - Number the substitute according to the number carbon it is attached to
17
Q
What is difference when naming alkanes, alkenes and alkynes
A
They are named in similar ways except the a in “ane” is replaced by “e” for alkenes and by “y” for alkynes
18
Q
How do you show the position of the double or triple bonds?
A
The position is denoted by a number ( The number carbon that the double is on)
19
Q
What happens if there is more than one double or triple bond?
A
If more than one double or triple bond is present then the compound is named using di- or tri-
20
Q
What happens is the double or triple bond is not part of the longest carbon chain?
A
A change is made to the standard IUPAC rules
The whole double or triple bond must be in the chain used for the root name even if it is not the longest chain
21
Q
What are the three possible structural isomers substitutions called?
A
Ortho
Meta
Para
22
Q
What is the Ortho- substitution?
A
The substitutes are at carbons 1 and 2
23
Q
What is the Meta- substitution?
A
The substitutes are at carbons 1 and 3
24
Q
What is the para- substitution?
A
The substitutes are at carbons 1 and 4
25
What is the general rule for naming functional groups?
If there is a functional group present which can be named as a suffix then there must be a suffix in the name.
If several functional groups are present the higher priority group will be the suffix the others are added as prefixes.
One exception is the suffixes -ane -ene and -yne can have another suffix denoting another functional group added to the.
- Just remove the terminal e
26
What is an ether?
Two chains of carbons on either side of an oxygen atom
27
How do you name the either?
1. The longest carbon chain gives you the root name
2. The smaller carbon chain is named as alkoxy
- the "alk" describes the number of carbons in the shortest chain
28
What is an Ester?
Have two carbon chains separated by an oxygen
29
How is an ester named?
Both chains must be named separately in the full ester name
| - Takes the form alkyl alkanoate
30
What part is the Alkyl when naming an ester?
Name derived from the carbon chain directly attached to the oxygen
31
What part is the Alkanoate when naming an ester?
Name derived from the carbon chain containing the carbonyl group (C=O)
32
What is the suffix for a carboxylic acid?
- oic acid
33
What is important about carboxylic acids?
It is the highest priority functional group
34
How do you identify the carboxylic
Identified by the COOH group
35
What is an amide?
A derivative from a carboxylic acid
An amide is a functional group containing a carbonyl group linked to a nitrogen atom or any compound containing the amide functional group
36
How are amides named?
The terminal -e of the hydrocarbon name is dropped before the suffix is added.
37
What is the general formula for an amide?
RC(=O)NR′R″
38
What are the forms of an amide?
Primary
Secondary
Tertiary
39
What is a primary amide?
An amide in which the amido group is directly bonded to only one carbon
(the carbonyl group)
40
What is a secondary amide?
An amide in which the nitrogen is directly bonded to two carbons
(the carbonyl group plus one other carbon)
41
What is a tertiary amide?
An amide in which the nitrogen is directly bonded to three carbon atoms
(the carbonyl group plus two additional carbon groups)
42
What is an aldehyde?
A carbon atom shares a double bond with an oxygen atom
Shares a single bond with a hydrogen atom
Shares another single bond with a another atom or group of atoms
43
How is an aldehyde named?
Suffix: -al
Prefix: oxo
naming of simple aldehydes is usually obtained by replacing the ending -e of the hydrocarbon by the suffix.
- Butanal
if a higher priority group is present it is named using the prefix
- 4-Oxo-butanoic acid
44
What is a ketone?
Contain the carbonyl group bonded to two carbons
contain the functional group C=O
45
How do you name a ketone?
Suffix : -one
Prefix: oxo
The name of a simple aldehyde is usually obtained by removing the ending -e and replacing it with the suffix
If a higher priority group is present it is named using the prefix
46
How do you name alcohols and phenol's?
Suffix: - ol or phenol
Prefix: Hydroxy
The terminal -e is removed and the apporpriate suffix is used
If the compound has more than one hydroxy group they are named using Di, Tri ect
The parent -e of the parent Alkane is not removed
If another functional group is present of higher priority it will be name as the prefix
47
How do you name Thiols and Thiophenols?
Suffix : -thiol or thiophenol
| Prefix : Mercapto
48
How are Thiols classified?
Can be classified as
- Primary CH2SH
- Secondary CHRSH
- Tertiary CHRR'SH
49
What is an amine?
In amines the hydrogen atom int he ammonia have been replaces one at a time by the hydrocarbon groups
50
How do you name an amine?
Suffix : amine
Prefix : Amino
If more than one type of alkyl group is attached to the nitrogen, the largest alkyl group is considered to be the parent
any other alkyl groups are denoted by the N-alkyl prefix
51
What is a primary amide?
Amide group is directly attached to one carbon
| -NH2
52
What is a secondary amide?
Amide group is attached to two carbons
| -NH
53
What is a tertiary amide?
The amide group is attached to three carbons
| -N
54
What is stereo chemistry?
Is the study of isomers
Are compounds that have the same molecular formula but are chemically distinct from each other
Isomerism is broadly divided into two types
- Structural isomerism
- Stereo-isomerism
55
What is structural isomerism?
Compounds that have the same molecular formula but differ in the position that the atoms are connected to each
56
What is an effect of structural isomer?
Can have very different physical and chemical properties
57
What is stereoisomerism?
Compounds that have the same molecular formula and have their atoms bonded in the same order can differ in there 3D shape
58
What are the three types of stereo isomerism?
- Geometric Isomerism
- Optical Isomerism
- Conformational Isomerism
59
What are the three types of stereo isomerism?
- Geometric Isomerism
- Optical Isomerism
- Conformational Isomerism
60
What is Geometric Isomerism?
Rigidity in a molecule can lead to restricted rotation
Two common casses where this can arise
- Pi bonds
- cyclic structures
61
What happens in with Cis and Trans geometric isomers?
The double bond in alkenes restricts the free rotation of this bond at room temperature and atmospheric pressure.
This is because the pi bond would have to be broke to allow rotation
62
When can Cis and Trans geometric isomerism not occur?
If the atoms are bonded to one edge on the double bond are the same.
This is because the structures are flat and therefore by turning the molecule over (not breaking the bonds) you will have the same molecule
63
When to use E/Z or Cis/Trans
It is more common to use E/Z when there is more than two different groups attached to the alkene double bonds
64
How do you decide on E/Z isomers?
Prioritise the groups on either side of the double bond and label them
- 1 (Top priority)
- 2 (Lower priority)
If the two top priority are on the same side this is known as Z isomer (similar to cis)
If they are on opposite side then this is known as the E isomer (similar to trans)
65
How do you determine priority for isomerism?
1. Look at the atom directly attached to the double bond. The higher its molecular mass the greater its priority
I > Br > Cl > O > N > C
2. With isotopes the higher mass isotopes has priority
Cl37 > Cl35
H3 > H1
3. If the two atoms bound to the double bound are the same look one bond away and find out which one has the highest mass atom. Continue to move another bond away until you can distinguish the higher priority
4. Multiply bonded groups, C=O, C=C are counted as almost twice (double bond) or three times (triple bond)
It is important to note the two single bonded atoms have greater priority than a double bonded atom
66
How do cyclic compounds exhibit geometric isomerism?
The atoms of the ring are not able to freely rotate around their sigma bonds since it would require breakage of the ring.
Also classified using the cis/trans or E/Z terminology
67
What are the general properties and biological significance of geometric isomers?
Physical properties of geometric isomers are usually very different.
- usually makes them easy to separate when there is a mixture
Trans isomers tend to be more stable than Cis isomers
- shown by there higher boiling points and melting points
Normal room temp and pressure dose not usually provide enough energy to convert between Cis and Trans (break the pi bond)
- With elevated temperature, additional sources of energy (light) or the use of a catalyst
- > inter conversion between Cis and Trans becomes possible
68
Biological application of geometric isomers
| - Rhodospin
Rhodospin
- is a light sensitive substance formed in the rod cells of the eye
- Light converts rhodospin from its Cis configuration into its more stable Trans counterpart metarhodopsin II
- results in a nerve impulse to the brain -> causes the effect of sight
^ Example of the different effects in the body
69
What can some geometric isomers be sensitive to?
What does this mean ?
- Heat
- Light
- UV radiation
Must be stored at or below room temperature in lightproof containers
Important that prescriptions containing these compounds are dispensed in the appropriate container
70
What is conformational isomerism?
In saturated open chain compounds free rotation can occur about the sigma bonds
Groups attached to the appropriate carbon atom may have an infinite number of positions in space relative to each other
- These are called conformers
71
How can conformers be shown?
With the Newman Projections
72
How does the energy of the conformer change?
The bonds can be maximally spaced out (Staggered) or all of the bonds can be minimally spaced out (Eclipsed).
Eclipsed - requires more energy due to the close proximity of the electrons of the hydrogen's.
73
Is the energy of all conformers the same?
Not all of the staggered and eclipsed conformers have the same energy.
The bigger the atoms or groups the more they tend to repel each other and the more energy is required for the molecule to exist in that conformation
74
On the Newman projection which parts are Eclipsed and staggered?
Peak is Eclipsed
Trough is Staggered
75
What are the general properties and biological significance of conformers?
Energy required to freely rotate most sigma bonds through their different conformations is usually low enough so that rotation can happen freely at room temperature and pressure
- Separating conformers is therefore not usually possible under normal conditions
76
Where is conformation important?
Very important in biological systems
When drug molecule causes a biological response by binding to biological molecules in the body such as enzymes and receptors
- often are required to adopt a certain shape
There is a vast area of drug discovery research that utilises computers to calculate stable conformations of drug molecules
77
What is optical isomerism?
Any compound that cannot be superimposed onto its mirror image is said to be Chiral.
The two mirror image forms are optical isomers of each other and are called Enantiomers
78
Common cause of chirality?
Is an asymmetric carbon atom or chiral centre
This is a carbon with four different groups bonded on to it
79
What properties are Similar or different for a single pair of enantiomers?
Similarities
Almost all of their physical and chemical properties are the same
- Melting point
- Boiling point
Differences
1. Interactions with other Chiral substances
(important to remember since the body is full of chiral molecules)
2. Interactions with plane polarised light
80
How does ordinary light travel?
Travels in waves that are at right angles to the direction of travel
81
What is R and S configuration of Chiral compounds?
Tells you about the positions of groups around the chiral centre
82
Rules for assigning R and S nomenculture to an enantiomer
1. Rank the four groups surrounding the chiral centre according to priority
- 1 for the highest and 4 for the lowest
2. Rotate the compound so that the lowest priority group faces away from you
3.
- If the priority numbers increase in a clockwise direction then this is the R enantiomer
- If the priority numbers increase in an anticlockwise direction than this is the S enantiomer
83
What happens with more than one chiral centre?
A molecule can have more than one chiral centre
Each of the centres could be R or S, so there are four different stereo isomers possible
84
How do you assign R and S configuration to two chiral centres?
Consider each chiral centre in turn
When a molecule has more than one chiral carbon not all of the optical isomers are enantiomers
(mirror images of each other)
85
What are diasteroisomers?
Are chemically and physically different
- Have different melting points
- Different boiling points
- Different solubility's
86
What is a meso compound?
When a molecule with chiral centres doesn't have a mirror image
87
What is the Fisher projections + Rules to use them?
When it is to time consuming to to show all of the stereochemisty with dashed and wedges
The Fisher Projections are often used
1. All Carbons must be drawn in vertical orientation
2. Vertical lines represent 3D bonds that lie in the plane of paper or behind
3. Horizontal bonds represent 3D bonds that lie out of the plane
Pharmaceutical Chemistry
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