Chapter 2 – The Chemistry of Water and Acid-Base Chemistry

• Lessons of the past few years-life can survive just about any conditions (acidic/basic, hot (now at least 121 °C)/cold, oxidizing/reducing, high/low salt, relatively high radiation)

• Cannot survive without H2O, can’t metabolize without liquid H2O

• Water and its unique properties

compound boiling point (°C)

H2O 100

H2S -60

H2Se -40

H2Te -10

What’s necessary for H-bonding?

• General pattern:

– Where X,Y = N,O,F (usually)• Y (acceptor) must have free lone pair(s)

– i.e. nitrogen of a quaternary amine can’t accept an H-bond

• H-bonds vary in strength from ~5-20 (normal) kJ/mol (covalent bonds ~150 to 1075 kJ (CO triple bond))

-X-H Y-| | | | |donor

acceptor

H2O - 4 H-bonds max (reality ~3.5 in solution) – this means that very few species are as good at H-bonding as water, so water tends to want to associate wi/ itself

Distance usuallyreferred to (sinceH is “invisible” inmost proteinstructures)

• Bond distance is the major determinant of whether or not an H-bond has occurred

• H bond distances (distance between hetero atoms (X and Y), ignoring H) are in the range of 2.5-3.5 Å (covalent bonds are in the range of 1-2 Å and shorter)

• Linear (i.e. a straight line from the lone pair on Y to the X-H bond) tend to be stronger than “bent” H-bonds

SSHB or LBHB• SSHB “short, strong hydrogen bond”, also known as an LBHB

“low-barrier hydrogen bond,” occurs when the acceptor and donor share the H equally

• Water will wipe these out (must be isolated at an enzyme active site)

• Distances of ≤ 2.6 A, stronger than normal H-bond• pKas between donor/acceptor must be matched• Implicated in enzymatic catalysis (still controversial)

-X-H Y-| | | | |donor

acceptor

-X H Y- | | | | | |

SSHB or LBHB

Other hydrogen bonds (special cases-don’t write these on a test)• H can be attached to other atoms

• X/Y (in X-H||||Y pattern) can be sulfur (especially if Y is S-) or P

• The real determinant of an H bond is if an H is being shared (based on bond distances and strengths)

X-C-H Y | | | | |

where X is very e- withdrawing, Y isStill N, O or F

• The thermodynamics of hydrogen bonding (especially between water molecules) has a strong effect on almost everything that happens in biochemistry

• as an example, see the section in Chapter 2 regarding protein-bound water

X-ray crystal structure of hemoglobin, showing waters that are tightly bound to the protein (even in the solid state. Removal of these waters frequently results in loss of protein structure (and function). In most protein structure illustrations these waters are not shown – but they are there

Close up of water colored yellow in previous image – water hydrogen bonded to carbonyl oxygen of protein backbone (and also H-bonded to another water). Distances are in Å.

Relative strengths of intermolecular/atomic forces

Interaction Energy (to break)

London forces/dipole-dipole

Low –high (London forces vary greatly based on size)

H-bonding 8-40 kJ or greater

Ionic attraction(+/-) ~40 kJ

Ionic repulsion(+/+), (-/-)

~-20 kJ

Covalent bonds 150-1075 kJ

Hydrophobic vs. hydrophilic

• Hydrophilic compounds-dissolve in/are miscible with H2O– Hydrophilic compounds like water (and water likes

them) so this term is accurate• Hydrophibic compounds-do not dissolve in/are not

miscible with H2O• “the hydrophobic effect”- water tends to want to

associate with water, and exclude other compounds– Hydrophobic compounds don’t hate water, water hates

them (therefore the term hydrophobic is a misnomer)

Or facing head to tail as in a membrane

Water and “waters of hydration”

• Salts can dissolve in water because the H2O “hydrates” the charge

Behavior of buffers and charged compounds

• pKas – remember:– Ka = ([H+][A-])/[HA] or ([H+][B])/[BH+]– pKa = -logKa

– If pH of solution > pKa, species is mostly in the basic form

– If pH of solution < pKa, species is mostly in the acidic form

– What about pH = pKa?• How about pH = pKa± 1 unit? 2 units? 3 units?

• Know the pKa ranges of biologically relevant functional groups – carboxylic acids, amines, alcohols (aryl and alkyl), thiols

• Be able to recognize strong acids/bases– Why do strong acids that have very different pKas

(for example, HCl, HBr and HI) behave the same in water? How could you determine their pKas?

• Think about the difference between neutral acid/anionic base pair and a positive acid/neutral base pair– Example: ionization behavior of carboxylates vs.

amines

Alcohols ~ 14-16

Phenol ~ 9

H3O+ = -1.7

HI = -10, HBr = -9,HCl = -7

H2O = 15.7

Thiols ~ 8

Amines 9-12

Carboxylic acids 2-5

Cocaine and pH• Cocaine is a stimulant that exerts its effect by inhibiting the

reuptake of neurotransmitters (especially norepinephrin)• Also has other longer term effects

CC

CCC

C

C

O

O

C

O O

CH3

N+

CH3

H

H

HH

H

H

H

H

H

H

N+

R

'R

R''

H

ionizable groupH

cocaine tertiary aminepKa = 8.41

• If cocaine is smoked or otherwise inhaled, only the neutral form crosses membranes and enters the blood. Therefore only the base form (free base) is taken up efficiently

• Both “free base” cocaine and crack cocaine are cocaine in the neutral (free) base form

N+

R

'R

R''

H

acid form-also known as cocaine HCl

N

R

'R

R''

base form-also known as the "free base"

pKa = 8.41

Why would tobacco manufacturers add NH3 (ammonia) to their products?

• Nicotine acid base behavior – nicotine in the “free base” form will cross membranes

N

N

CH3N+

N+

CH3

H

H

pKa= 5

pKa=8 (?)

+ 2NH3 +2NH4+

charged, won't cross membranes easily neutral, will cross membranes easily

Absorption of aspirin• Aspirin is neutral in its acidic form, therefore it will only

cross membranes in its acid form• The pH of the intestine is 6- aspirin is in its –COO- form,

and can’t cross the membrane• The pH of the stomach is 1.5-aspirin is in its –COOH

form, and can cross the membrane

H3C

O

C

O

OH

aspirin

pKa=3.5

BBS system of blood

• Blood uses the bicarbonate buffer system, based on HCO3

-

• pKa of H2CO3 = 3.77, while blood is held precisely at pH 7.4 (pH 7.2-7.3 is acidosis, <7.1 is severe acidosis)

• How can this system work?

Keq ~ 10-3

catalyzed bycarbonic anhydrasepKeq~ 3

Ka~ 10-4

pKa ~ 4Koverall = KaKeq ~ 10-7

pKoverall ~ 7

• If acid is produced, breathing increases, CO2 is blown off, equilibrium shifts in a direction that decreases H+

• If base is produced, breathing decreases, dissolved CO2 increases, increasing H+, bringing the pH back down

• Respiratory acidosis – what causes it? What can be done about it?

• Respiratory alkalosis – what causes it? What is the simple solution?

• If blood is normally ~99-100% saturated with O2, why does deep breathing before a sprint or weight lifting improve performance?

pKa and structural factors affecting pKa

• Inductive effect – CH3-CO2H vs. CF3-CO2H

• Charge effect – through space (i.e. independent of above)– Amino acid -CO2H and –NH3

+ vs. N and C termini of proteins (sort of)

– Enzyme active sites (position of charged residues in 3 dimensional space)

• Resonance effect– R-OH vs. R-CO2H

• Atom size (bond strength) effect– HF vs. HCl vs. HBr vs. HI

Effect of solvent and environment on pKa

• Polar solvents/environments tend to favor charged species– Example - charged area (especially + charges) on an enzyme

might favor –CO2-, decreasing pKa of a –COOH group in that area

– The same region would decrease the pKa of an R-NH3+ group

• Non-polar solvents/environments tend to favor uncharged species – Example – nonpolar region of an enzyme might favor –COOH

form of a carboxylic acid, increasing pKa

– pKa of R-COOH would be increased, R-NH3+ decreased in ethanol

– Exception – aromatics can favor anionic species via pi bond/anionic interactions

pH behavior of buffers• Buffers have the best “buffering” effect at pHs within 1

unit of their pKa – why?

Solving buffer problems

• Three main types– Add in buffer in both acid and base forms in

proper ratios – Start with all of buffer in acid (or base) form

and titrate to proper pH with strong base (or acid)

– Starting with buffer of known pH, adjust pH to required pH with strong acid or base