Download Line-Angle Notation for Depicting Chemical

Line-Angle Notation for Depicting Chemical Structures
A shorthand notation for drawing chemical structures involves the
use of lines to depict bonds and angles to depict atoms. By
convention, hydrogen atoms are not indicated. Therefore, the
line-angle notation for butane, CH3CH2CH2CH3 would be:
Organic Functional Groups
H
O
H
H
R=
alkane
-H
H
C
C
alkene
C
C
alkyne
aromatic
H
-CHO
R=
aldehyde
H
H
H
H
O
R 2C
O
ketone
O
RCO2 H
carboxylic acid
OH
many different kinds
X
NC
-C
N
H
nitrile
H
H
alkyl halide
-X
H
H
H
H
(chloride, bromide, iodide)
H
H
HO
H
H
H
alcohol
-OH
O
H
H
RCONR2
NH2
O
H
RCOOR
OH
phenol
many different kinds
RO
-OR
ester
OR
H
O
H
ether
RCOOCOR
H
H
R2N
-NR2
amide
H
acid anhydride
O
H
H
O
H
amine
RCOCl
H
H
O
acid chloride
Cl
Exercise:
Circle all the functional groups in the antitumor antibiotic, Dynemicin A
sp3 hybridization
tetrahedral
geometry
bond angle =
sp3 hybridization of carbon in methane
tetrahedral
geometry
sp2 hybridization
trigonal
geometry
sp2 hybridization of carbon in ethylene (a.k.a. ethene)
trigonal
geometry
sp hybridization of carbon in acetylene (a.k.a. ethyne)
Buffer Effect
Henderson-Hasselbalch Equation:
pH = pKa + log
[A-]
[HA]
The Henderson-Hasselbalch equation describes how the pH of a solution is governed by the pKa of the acid present and the logarithm of
the ratio of the concentrations of the conjugate base and protonated form of the acid. If the pH is greater than the pKa of the acid, it will
predominantly exist in it’s conjugate base form. If the pH is less than the pKa, the acid will exist predominantly in it’s protonated form.
Buffer Effect: The ability of a solution to resist a change in pH as H+ or HO- are
added to it.
Buffer Capacity: The amount of H+ or HO- that can be absorbed before the pH
begins to shift significantly. The buffer capacity of a solution is related to the total
concentration of HA & A- in solution as well as the magnitude of the separation
between the pH & pKa.
Of the many species capable of buffer action in biological systems, the most
important biological buffers are H2PO4- (phosphate) and H2CO3/HCO3(carbonate) due to their higher relative concentrations (i.e., greater buffer capacity).
→ H2CO3 ←
→ HCO3- + H+
Carbonate: CO2 + H2O ←
→ H2PO4- + H+ ←
→ HPO42- + H+ ←
→ PO43- + H+
Phosphate: H3PO4 ←
Buffer Effect
Phosphate Titration Curve
PO43-
Acetate Titration Curve
→
HPO42- ←
3PO4 + H+
→ CH CO - + H+
CH3CO2H ←
3
2
HPO42-
→
H2PO4- ←
HPO42- + H+
H2PO4-
→
H3PO4 ←
H2PO4 + H+
H3PO4
pKa’s of Some Amino Acids
Titration Curve for the
Amino Acid Histidine
Effect of Electronegativity Differences in Bonded Partners:
Polar Covalent Bonds & Their Effect on Molecular Properties
insoluble
in water
highly soluble
in water
Cartoon of Dipole-Dipole Association
Cartoon of Van der Waals (induced dipole) Association
Hydrogen Bonding
Hydrogen bonds occur when a hydrogen that is bonded to a strongly
electronegative element encounters the lone pair electrons of a second
strongly electronegative element.
Like dissolves like:
polar and/or charged species easily dissolve in a polar solvent like water
Dipole of water
(negative pole at the
center of the oxygen
atom; positive pole
centered between the
hydrogen atoms)
Polar species are insoluble in nonpolar solvents
Like dissolves like:
nonpolar species easily dissolve in nonpolar solvents
The dielectric constant of a
solvent is one way to estimate
it’s capacity to dissolve a polar
compound relative to it’s
behavior in a solvent of known
dielectric constant
Nonpolar species are insoluble in polar solvents
This is also called the “hydrophobic effect” and is the underlying reason why
nonpolar species like lipids, fats & membrane proteins are sequestered away
from water in structures called cell membranes--this is a major organizing
principle in biological systems!
Structural Isomers:
compounds having the same molecular formula, but with different connectivity
Structural isomers of butane, C4H10:
Structural isomers of pentane, C5H12:
Conformational Isomers:
compounds differing only by the rotation about a single bond in the molecule
rotation about the central C-C bond
conformational analysis of butane, CH3-CH2-CH2-CH3
Geometric Isomers:
compounds of the same molecular formula and connectivity, but differing in
their spatial orientation of substituents
Stereoisomers:
compounds of the same molecular formula and connectivity, but differing by
a mirror image relationship in their spatial orientation of substituents
Biological systems usually display a preference for one
stereoisomer over the other