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IDM > TBL 2 - STRUCTURE OF ORGANIC DRUGS > Flashcards

TBL 2 - STRUCTURE OF ORGANIC DRUGS Flashcards

1
Q

Why do atoms hybridise or mix their orbitals?

A

Atoms hybridize or ‘mix’ their atomic orbitals in order to optimize the geometry and minimize energy of the molecules in which they are included.

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2
Q

Which period has orbital s and p type orbitals available?

A

2nd period elements (like C, N and O) only s and p types of orbital are available.

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3
Q

What type of hybridised states are there?

A

Hybridization states can be sp3, sp2 and sp

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4
Q

A hybridisation state of an atom can be sp(3-n) what does the n stand for?

A

Hybridization state of such atom given as sp(3-n) where n = the number of pi bonds associated with that atom.

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5
Q

What can be contained in hybrid orbital - in reference to bonding?

A

Hydride orbitals may contain bonding or non-bonding pairs of electrons

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6
Q

Which element has the lowest energy arrangement?

A

Carbon has electronic configuration of 1s^2 , 2s^2, 2p^2 ( 6 electrons in total). This arrangement is only the lowest energy arrangement for isolated C atoms.

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7
Q

How does bonding occur in carbon?

A
  • Bonding occurs using outer 2s^2 and 2p^2 electrons (4 electrons needed for 4 bonds)
  • Sharing with 4 outside electrons produces 4 bonding pairs
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8
Q

How do you form equivalent bonds?

A

There’s a mismatch in energy between the s and p electronic levels. In order to form equivalent bonds, equivalent energy levels are needed so the s and p orbitals combine or hybridize to produce orbitals which have the same energy levels.

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9
Q

What shape will be given is S orbital combines with 3p orbitals?

A

When s orbital combines 3 p orbitals it gives rise to 4 sp3 orbitals, these combine to give a tetrahedral shape.

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10
Q

What does the tetrahedral shape allow for in terms of orbitals?

A

This shape allows the orbitals to be as far apart from each other as possible and have lowest possible energy.

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11
Q

How much capacity is there for 4 sp3 orbitals?

A
  • 4 sp3 hybrid orbitals have the capacity for up to 2 electrons each (8 in all)
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12
Q

What are the characteristics of an Sp3 hybridisation?
- How many S and P orbitals?
- Shape of Sp3 hybridisation?
- Bond angle of Sp3 hybridisation?
- How many S and P character are there is Sp3 hybridisation?
- What are the 2 lobes involved in Sp3 hybridisation?
- Does rotation occur?

A
  • 1s and 3p orbitals = sp3
    • Tetrahedral shape
    • Bond angle = 109.5
    • Large front lobe for bonding. Back lobe. Nucleus in the middle.
  • 25% S character, 75% P character
  • Yes rotation occur as its a single bond
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13
Q

What are the characteristics of an Sp2 hybridisation?
- How many S and P orbitals?
- Shape of Sp2 hybridisation?
- Bond angle of Sp2 hybridisation?
- How many S and P character are there is Sp2 hybridisation?
- Does rotation occur?

A
  • 33 1/3 % S and 66 2/5% P
    • 1 S orbital/2 P orbital
    • Equal size, shape and energy
    • Tetrahedral geometry
    • Bond angle = 120
  • No rotation around bond

Gives flat (or triangular) arrangement of 3 sp2 orbitals, with perpendicular p-orbital.

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14
Q

What are the characteristics of an Sp hybridisation?
- How many S and P orbitals?
- Shape of Sp hybridisation?
- Does rotation occur?

A
  • Gives 2 sp orbitals which has a linear arrangement.
  • 2 unhybridized p orbitals fill the perpendicular space on both the y and z axis.
    -No rotation around the bond.
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15
Q

Example of Sp3 hybirdise….

A
  • Methane
  • Sp3 orbitals of C can form bonds with the s orbital of H, results in formation of methane (CH4) which has sigma bonds between C and H atoms. The sigma bonds (single bonds) are free to rotate.
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16
Q

Example of Sp2 hybirdisation….

A
  • In ethane (CH2CH2) the bonding between the sp2 orbitals is flat
  • Perpendicular p orbitals align to produce a pi bond which results in the formation of a double bone (sigma + pi)
  • Pi character above and below bond holds it rigid, so unlike single bonds is not free to rotate.
  • 3 type of hybridization occurs when an s and p orbital combine to form 2 sp orbitals.
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17
Q

Example of Sp hybridisation….

A
  • In ethyne these p orbitals align to produce 2 pi bonds and result in a triple bond overall (sigma + 2 pi)
  • No rotation around the bond.
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18
Q

What does the benzene orbital diagram look like?

A
  • Benzene 6 membered ring.
  • Bond line representation shows 3 double bonds and 3 single bonds each carbon is sp2 hybridized.
  • Six p orbitals, sit above and below three ring delocalize giving a pi system which covers all 6 carbons.
  • Gives flat hexagonal shape where each bond in the same length
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19
Q

What hybridisation for benzene?

A
  • C6H6
  • Sp hybridization
  • Delocalized orbitals - electrons free to move around.
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20
Q

What is the Valence shell electrons pair repulsion theory (VSEPR theory)?

A
  • Theory relies on understanding that the valence electrons (which are found on the outer shell of an atom) which combined with other atoms to form molecules repel each other.
  • Resulting geometries ensure the electrons (and lone pairs of electrons) are far apart from each other as possible.

ELECTRONS REPEL EACH OTHER

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21
Q

What are the example of tetrahedral shape and what is the bond angle for the tetrahedral shape and what groups produce tetrahedral?

A

Tetrahedral:
- CF4, CH4, SiF4
- Bond angle = 109.5
- Group 4/14

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22
Q

What is the exception of the trigonal planer shape, what is the bond angle of the trigonal planer and what groups produce a trigonal planer?

A

Trigonal planer:
- BF3 (exception no unshared electron pair), - Bond angle = 120
- group 3/13

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23
Q

What is the example of the trigonal pyramidal shape, what is the bond angle of the trigonal pyramidal and what groups produce a trigonal pyramidal?

A

Trigonal pyramidal:
- NF3, PF3
- Bond angle = 107
- group 5/15 - unshared pair of electron repel each other, electrons downwards/away

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24
Q

What is the example of the trigonal pyramidal shape, what is the bond angle of the trigonal pyramidal and what groups produce a trigonal pyramidal?

A

Trigonal pyramidal:
- NF3, PF3
- Bond angle = 107
- group 5/15 - unshared pair of electron repel each other, electrons downwards/away

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25
Q

What is the example of the bent shape, what is the bond angle of the bent shape and what groups produce a bent shape?

A

Bent:
- H2O/H2S
- Bond angle = 104.5 (for H2O)/109.5, unshared pair of electrons repel clockwise.

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26
Q

What is the example of the linear shape, what is the bond angle of the linear shape and what groups produce a linear shape?

A

Linear:
- CO2
- Bond angle = 180
- no unshared pair of electrons

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27
Q

What is the difference between the trigonal planer and trigonal pyramidal?

A

Trigonal planer:
- No unshared pairs of electrons

Trigonal pyramidal:
- Unshared pair of electrons

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28
Q

What happens to the bond when it contains for pi character?

A

Bond length deceases as the bond contains more pi character

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29
Q

What are the bond length and bond energy for a single, double and triple bond?

A

C - C (single bond)
Bond length =1.54
Bond energy = 347

C = C (double bond)
Bond length = 1.34
Bond energy = 611

C— C (triple bond)
Bond length = 1.20
Bond energy = 837

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30
Q

What is the meaning of bond order?

A
  • Number of formal bonds between any 2 atoms is known as the bond order.
  • Varies between 1 and 3 and doesn’t have an integer
    C - C bond distance in benzene is 1.40 x 10^-10 m
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31
Q

Which bond exerts more repulsion?

A

Double bonds exert a greater repulsion than single bond.

32
Q

What are structural isomers?

A

Are different compounds that share the same molecular formula e.g ethanol and dimethyl ether share formula C2H6O
Constitutional isomers can be inter-converted by breaking and reforming chemical bonds - a process that requires a lot of energy.

33
Q

What is a cis/trans isomer?

A
  • Double bonds cant rotate due to pi character.
  • Same side on double bond is cis, opposite sides = trans
34
Q

What is optical isomer?

A
  • Stereoisomers are distinguable by having observable but different interactions with plane-polarised light.
35
Q

What are stereoisomers?

A

Defined as isomers that are different from each other only in the way of atoms are oriented in space.

36
Q

How does optical isomer arise?

A

Optical isomers these differences arises from chirally and no other forms of isomerism such as positional, functional group etc.

37
Q

What are 2 types of stereoisomers?

A

2 types of stereoisomers are enantiomers and diastereomers.

38
Q

What are enantiomers?

A

Non-superimposable mirror image stereoisomers referred to as enantiomers.

39
Q

What is absolute configuration?

A

Order of arrangement of 4 groups around a chiral carbon atom called absolute configuration.

40
Q

What are racemic mixtures?

A
  • Contains 50% of each enantiomers
    • Mixtures are optically inactive.
41
Q

What do individual enantiomers have compared to their mirror images?

A

Individual enantiomers have identical physical and chemical properties when compare to their mirror images except for their ability to rotate the plane of polarised light PPL (in different directions) and their reaction/interaction with other enantiomeric compounds.

42
Q

What is optically active enantiomers?

A

enantiomers can rotate the plane of polarised light they are referred to a optically active as such are optical isomers.

43
Q

What is the plane polarised light (PPL) when rotated clockwise and anti-clockwise?

A
  • PPL ROTATED CLOCKWISE = (+ FORM) (d)
  • PPL ROTATED ANTI-CLOCKWISE (- FORM) (l)
44
Q

What is the specific rotation equation?

A

Specific rotation [a]^T = a obs / cl
- a obs = observed rotation in degrees
- C = conc (g/ml)
l = cell path length (dm)

45
Q

What would a sample containing one enantiomer be called?

A

Sample contains only ONE enantiomer is said to be enantiomerically pure or homochirality.

46
Q

What is the equation for Enantiomeric excess (ee)?

A

ee = % of one enantiomer - % of other enantiomer
For example: 99% 1 enantiomer, 1% for another enantiomer so ee is 98% (99-1 = 98 )

47
Q

When can molecules exist as a single conformer?

A
  • Continually inter-converting by using thermal energy to rotate the single bonds in the molecules. Molecules may exist as a single conformer if there is an sufficiently large energy barrier to rotation.
  • Configuration only be changed by breaking covalent bonds.
48
Q

What does conformation occur?

A
  • Conformation simply involves rotation of bonds.
49
Q

How are conformers visualised as?

A

Visualize conformer’s represent molecules as Newman projections.

50
Q

Example of conformation using acetylcholine….

A

An example where conformation produces significant differences is in the action of the neurotransmitter acetylcholine:
1) Acetylcholine acts 2 different receptors.
2) One is the nicotinic receptor (nicotine is an agonist)
3) Other is the muscarinic receptor (muscarine is an agonist)
These are found of nerve tissue and trigger impulses in various types of nerves and target organs.

51
Q

Where can muscarine be found?

A

Muscarine found in ‘fly agaric’ toadstool (amanita muscaria)

52
Q

What is nicotine an active ingredient in?

A

Nicotine is an active ingredient in tobacco

53
Q

What does acetylcholine have the ability to do?

A

Acetylcholine has the ability to mimic both muscarine and nicotine and then its postulated that in order to do both, different conformers were important at each receptor.

54
Q

Hypothesis tested by synthesising the cyclo-propyl analogues of acetylcholine (3 things):

A
  • Armstrong study showed that the trans-isomer was the best agonist for muscarinic receptors.
  • A dihedral angle of 137 was determined between the trans-substituents
  • A different conformer of acetylcholine is required to optimally bind to a nicotinic receptor.
55
Q

How does ring flipping occur?

A

Position of axial and equatorial hydrogens in chair form
Equatorial can interchange within chair conformer by process called ring flipping

56
Q

What happens with Fischer plane projection?

A

Arrange molecule so that longest carbon chain is vertical with the highest priority group at the top. (priority given to most oxidised carbon)
Arrange the carbon chain so that each carbon atom goes away from the observer

57
Q

When is a Fischer convention dextrorotation (d) and when is the Fischer convention laevorotation (l)?

A

Fischer convention an isomer is said to be (d) but if the OH group (of glyceraldehyde) is on the RHS. Enantiomer said to be (l).

58
Q

What does D and L mean in Fischer convention?

A

D = Dextrorotation, L = laevorotation

59
Q

How to figure out Fischer convention?

A

1) No. carbons
2) Identify r/s
3) Draw rough fisher
4) Figure out r/s on Fischer projection so correct

60
Q

What does laevorotation (D) mean?

A

D - amino acids are rare and only found in proteins produced by enzyme posttranslational modifications.

61
Q

What does laevorotation (L) mean?

A

L - amino acids are considered to naturally occurring and are present in proteins which formed during translation in the ribosome.

62
Q

Examples of prescribed medicines which have laevorotation - 3 of the most common include:

A

1) Levocetirizine (antihistamine)
2) Levothyroxine (for treating hypothyroidism)
3)Levonorgestrel (a progesterone)

63
Q

What are the 3 sequence rule (Cahn, Ingold, Prelog rules):

A

The sequence rule (Cahn, Ingold, Prelog rules):
Sequence 1:
If the 4 atoms attached to the chiral centre are all different then the priority depends upon atomic number with atom of the highest atomic number getting highest priority. With isotope of the same element the heavier isotope takes priority.

Sequence 2:
If sequence rule 1 fails to establish priority cus 2 atoms attached to the chiral centre are the same , then compare the atoms attached to each of these , work outwards until 1st point of difference is found.

Sequence 3:
Both atoms are regarded are duplicated or triplicated when double bonds or triple bonds exist between them:

64
Q

If the configuration is clockwise is it R or S?

A

If the remaining 3 groups go clockwise in order of decreasing precedence the configuration is said to be R (rectus) - clockwise = R

65
Q

If the configuration is anti-clockwise is it R or S?

A

If the remaining 3 groups go anti-clockwise in order of decreasing precedence the configuration is said to be S (sinister) - anti-clockwise = S

66
Q

What are diastereomers?

A

stereoisomers which are not enantiomers are described as diastereoisomers and, unlike enantiomers, they differ in physical properties

67
Q

What is the difference between the diastereoisomers and enantiomers?

A

The key is that in diastereoisomers the object to mirror image relationship is different, but in enantiomers it is the same.

67
Q

What is the difference between the diastereoisomers and enantiomers?

A

The key is that in diastereoisomers the object to mirror image relationship is different, but in enantiomers it is the same.

68
Q

What isomers grouped into?

A
  • 2 pairs of enantiomers
  • 4 pairs of diastereoisomers
69
Q

What is a meso compound?

A
  • Rotation of plane polarised light caused by one half of the molecule cancelled by an equal and opposite rotation caused by mirror image other half.
  • Compound with n chiral carbon atoms may have a max of 2n stereoisomers but it may less
  • Compound contains 2 chiral centers also contains an internal plane of symmetry
70
Q

Why is the shape and chirality of a molecule important for pharmacists?

A

It is simply because we are all chiral:
- Our proteins are made up of amino acids
- These occur naturally as single enantiomers.
- DNA is also chiral as the twist only goes in one direction (right handed).

  • The drugs we make and use need to interact with chiral molecules in the body to elicit an effect, sometimes different enantiomers have different or opposing affects.
71
Q

What was thalidomide being sold as involving enantiomers and what did it lead to?

A

The drug was being sold as a racemic mixture of the two enantiomers, which accounts for the unwanted effects.

72
Q

What was discovered to show that thalidomide was unsafe for pregnant women?

A

It was later discovered that the enantiomers inter-convert under physiological conditions and the drug was therefore unsafe (for pregnant women) even if used as a single enantiomer.

73
Q

What condition is thalidomide used treat now?

A
  • thalidomide has made a comeback for use in men and post-menopausal women.
  • used in combination with melphalan and prednisolone as first-line treatment for untreated multiple myeloma, in patients aged 65 years and over, or for those not eligible for high-dose chemotherapy (for example, patients with significant co-morbidity such as cardiac risk factors).
74
Q

What drugs were first licensed as racemic mixture and then its S-enantiomers were launched?

A

There are other drugs which were first licensed in the UK as racemic mixtures, and then the S-enantiomers were subsequently launched. These include omeprazole (a proton pump inhibitor), which was remarked as the single enantiomer esomeprazole, and citalopram (SSRI antidepressant), subsequently marketed as escitalopram

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