FOUNDATIONS OF PMC EXAM 1 OBJECTIVES
What 2 fields is medicinal chemistry a combination of? - Answers :-Pharmacology
-Organic chemistry
How many bonds does carbon want to make? - Answers :-4 bonds
How many bonds does oxygen want to make? How many lone pairs of electrons does it
have? - Answers :-2 bonds
-2 lone pairs of electrons
How many bonds does nitrogen want to make? How many lone pairs of electrons does
it have? - Answers :-3 bonds
-1 lone pair of electrons
Give the definition for the term "functional group" - Answers :-Specific groups of atoms
attached to a hydrocarbon skeleton have specific chemical properties
>they provide some specific chemical properties to the molecules they are attached to
What are some of the chemical properties that functional groups confer on the
molecules they are attached to? - Answers :-Charge
-Acidity/basicity
-Polarization
-Lipophilicity
-Size
-Reactivity
Identify methyl, ethyl, propyl, butyl, pentyl, and hexyl functional groups. Are they polar or
nonpolar? - Answers :-Nonpolar
What is the general term used to describe an aromatic functional group? - Answers :-
"Aryl group" or arene
Are aromatic hydrocarbons just basically cyclic alkenes? What 2 things makes them
different from cyclic alkenes? - Answers :-Aromatic hydrocarbons are NOT just cyclic
alkenes
-Have special properties due to:
>delocalization of electrons across a conjugated system of double bonds in a ring
What is meant by the term "electron delocalization"? Know that delocalization results in
a cloud of electrons above and below the plane of the ring carbon atoms - Answers :-
They have delocalized electrons
-Due to the cloud of electrons above/below the ring, aromatic rings often bind well with
drug-receptor targets due to Van der Waals forces
,Compare conformational isomers to geometric isomers, which can interconvert? -
Answers :CONFIRMATIONAL:
-Flexible molecules can exist in multiple conformations, due to rotation around single
bonds
>these can interconvert
GEOMETRIC:
-Rotation around a double bond
What do the terms "conformation", "conformational isomers", and "conformers"?
Understand that these terms are referring to the same thing - Answers :-Different spatial
relationships of atoms in a molecule resulting from rotation around single bonds
Regarding alcohols, can you define one (if shown structure) as primary, secondary, or
tertiary? - Answers :-Primary, secondary, and tertiary are define by branching (number
of carbons attached to -OH carbon)
What does the -OH group do to a molecule it is attached to, in terms of water solubility?
- Answers :-An -OH group can hydrogen bond with water, increasing solubility
-Solubility decreases with increase in chain length (increase in lipophilicity)
-A 2nd -OH increases solubility
Can you recognize a primary, secondary, tertiary, or aromatic amines? - Answers :-
Primary, secondary, and tertiary are define by branching (number of carbons attached
to -NH2 carbon)
-Aromatic has a ring attached to the amine
What effect does the amino functional group have on a molecule's water solubility? -
Answers :-They can increase the solubility of a drug
What is the result of the reaction of an amine with an acid? - Answers :-Formation of
salts, which can increase the solubility of a drug
Compare the salt of an amine to the parent "free base". Which one is more water
soluble? - Answers :-A "free base" molecule is insoluble in water, so the salt form is
more water soluble
-"Free base" means an amine that is NOT in a salt form
Are amines acid, basic, or neutral? - Answers :-Amine are basic groups
What are the 2 simple definitions of "basic"? - Answers :-Basicity depends on ability to
donate electron pairs
>i.e. accept a proton
Compare aromatic amine to alkyl amines, which is more basic? - Answers :-Aromatic
amines are much LESS basic than alkyl amines
, Can you recognize the "free base". Could you identify it as a salt formation - Answers :-
Salt formation has the acid and usually has a charge
-"Free base" contains the -NH2
Can you recognize an aldehyde? - Answers :-A carbonyl carbon connected to a carbon
on one side and a hydrogen on the other
Can you recognize a ketone? - Answers :-A carbonyl carbon is bound to 2 other
carbons
Can you recognize an ester? - Answers :
What is the broad term for this kind of functional group (methyl, ethyl, etc.)? - Answers :-
Corresponds to methyl, ethyl, and propyl functional groups (these are alkyl or aliphatic
groups)
Describe the solubility in water and nonpolar (lipid) organic solvents of alkanes and alkyl
functional groups - Answers :-Nonpolar
-Insoluble in water (which is polar)
-Soluble in lipid solvents (nonpolar)
What is the main function of alkenes? - Answers :-The suffix "-ene" indicated a double
bond
Describe the geometry around the double bond for alkenes (know that all 4 atoms
attached to a double bond are planar) - Answers :-Coplanar (flat)
-Rigid molecule
>cannot rotate around double bond
>presence of double bond raises possibility of geometric isomers
Describe their (alkenes) lipophilicity (relatively polar or nonpolar compared to amines or
alcohol groups) - Answers :-Lipophilic
>like alkanes
-Insoluble in water
-Soluble in lipids
What is meant by "unsaturation"? Be able to identify, given a structure, if a molecule is
saturated or unsaturated - Answers :-A fully saturated compound in one where there are
NO double bonds
>it has been "saturated" with hydrogens
-Unsaturated means double bonds are present
Describe what is meant by a conjugated or nonconjugated double bonds. Be able to
identify whether a structure is conjugated or unconjugated - Answers :CONJUGATED:
-Alkenes with MORE than 1 double bond
What 2 fields is medicinal chemistry a combination of? - Answers :-Pharmacology
-Organic chemistry
How many bonds does carbon want to make? - Answers :-4 bonds
How many bonds does oxygen want to make? How many lone pairs of electrons does it
have? - Answers :-2 bonds
-2 lone pairs of electrons
How many bonds does nitrogen want to make? How many lone pairs of electrons does
it have? - Answers :-3 bonds
-1 lone pair of electrons
Give the definition for the term "functional group" - Answers :-Specific groups of atoms
attached to a hydrocarbon skeleton have specific chemical properties
>they provide some specific chemical properties to the molecules they are attached to
What are some of the chemical properties that functional groups confer on the
molecules they are attached to? - Answers :-Charge
-Acidity/basicity
-Polarization
-Lipophilicity
-Size
-Reactivity
Identify methyl, ethyl, propyl, butyl, pentyl, and hexyl functional groups. Are they polar or
nonpolar? - Answers :-Nonpolar
What is the general term used to describe an aromatic functional group? - Answers :-
"Aryl group" or arene
Are aromatic hydrocarbons just basically cyclic alkenes? What 2 things makes them
different from cyclic alkenes? - Answers :-Aromatic hydrocarbons are NOT just cyclic
alkenes
-Have special properties due to:
>delocalization of electrons across a conjugated system of double bonds in a ring
What is meant by the term "electron delocalization"? Know that delocalization results in
a cloud of electrons above and below the plane of the ring carbon atoms - Answers :-
They have delocalized electrons
-Due to the cloud of electrons above/below the ring, aromatic rings often bind well with
drug-receptor targets due to Van der Waals forces
,Compare conformational isomers to geometric isomers, which can interconvert? -
Answers :CONFIRMATIONAL:
-Flexible molecules can exist in multiple conformations, due to rotation around single
bonds
>these can interconvert
GEOMETRIC:
-Rotation around a double bond
What do the terms "conformation", "conformational isomers", and "conformers"?
Understand that these terms are referring to the same thing - Answers :-Different spatial
relationships of atoms in a molecule resulting from rotation around single bonds
Regarding alcohols, can you define one (if shown structure) as primary, secondary, or
tertiary? - Answers :-Primary, secondary, and tertiary are define by branching (number
of carbons attached to -OH carbon)
What does the -OH group do to a molecule it is attached to, in terms of water solubility?
- Answers :-An -OH group can hydrogen bond with water, increasing solubility
-Solubility decreases with increase in chain length (increase in lipophilicity)
-A 2nd -OH increases solubility
Can you recognize a primary, secondary, tertiary, or aromatic amines? - Answers :-
Primary, secondary, and tertiary are define by branching (number of carbons attached
to -NH2 carbon)
-Aromatic has a ring attached to the amine
What effect does the amino functional group have on a molecule's water solubility? -
Answers :-They can increase the solubility of a drug
What is the result of the reaction of an amine with an acid? - Answers :-Formation of
salts, which can increase the solubility of a drug
Compare the salt of an amine to the parent "free base". Which one is more water
soluble? - Answers :-A "free base" molecule is insoluble in water, so the salt form is
more water soluble
-"Free base" means an amine that is NOT in a salt form
Are amines acid, basic, or neutral? - Answers :-Amine are basic groups
What are the 2 simple definitions of "basic"? - Answers :-Basicity depends on ability to
donate electron pairs
>i.e. accept a proton
Compare aromatic amine to alkyl amines, which is more basic? - Answers :-Aromatic
amines are much LESS basic than alkyl amines
, Can you recognize the "free base". Could you identify it as a salt formation - Answers :-
Salt formation has the acid and usually has a charge
-"Free base" contains the -NH2
Can you recognize an aldehyde? - Answers :-A carbonyl carbon connected to a carbon
on one side and a hydrogen on the other
Can you recognize a ketone? - Answers :-A carbonyl carbon is bound to 2 other
carbons
Can you recognize an ester? - Answers :
What is the broad term for this kind of functional group (methyl, ethyl, etc.)? - Answers :-
Corresponds to methyl, ethyl, and propyl functional groups (these are alkyl or aliphatic
groups)
Describe the solubility in water and nonpolar (lipid) organic solvents of alkanes and alkyl
functional groups - Answers :-Nonpolar
-Insoluble in water (which is polar)
-Soluble in lipid solvents (nonpolar)
What is the main function of alkenes? - Answers :-The suffix "-ene" indicated a double
bond
Describe the geometry around the double bond for alkenes (know that all 4 atoms
attached to a double bond are planar) - Answers :-Coplanar (flat)
-Rigid molecule
>cannot rotate around double bond
>presence of double bond raises possibility of geometric isomers
Describe their (alkenes) lipophilicity (relatively polar or nonpolar compared to amines or
alcohol groups) - Answers :-Lipophilic
>like alkanes
-Insoluble in water
-Soluble in lipids
What is meant by "unsaturation"? Be able to identify, given a structure, if a molecule is
saturated or unsaturated - Answers :-A fully saturated compound in one where there are
NO double bonds
>it has been "saturated" with hydrogens
-Unsaturated means double bonds are present
Describe what is meant by a conjugated or nonconjugated double bonds. Be able to
identify whether a structure is conjugated or unconjugated - Answers :CONJUGATED:
-Alkenes with MORE than 1 double bond
