DISSOCIATION OF A WEAK ELECTROLYTE Ostwald’s dilution law

Weak acetic acid: CH3COOH H+ + CH3COO- ; Kdis = = 1.75•10-5 H

H OOCH3C

OOCH3C

[ ]+ -[ ].

[ ]nondis

Dissociated molecules concentration is [H+]=[CH3COO-]=Cdis=α•C.

Concentration total is C=[CH3COOH]nondis+[H+] so [CH3COOH]nondis=C-[H+] and

[CH3COOH]nondis=C - α•C=C(1- α)

Inserting all these results we have: Kdis = = CC

C

22 2

1

Weak ammonium hydroxide base: NH4OH NH4+ + OH- ; Kdis = = 1.79•10-5

HONH4

ONH4

H

[ ]+ -[ ].

[ ]nondis

As week electrolyte dissociation degree tends to zero α =>0 and (1- α)=1 : Kdis = α2•C .

Ostwald’s dilution law α= is on 1886 in Riga proved discovery if concentration

C decreases dissociation degree α increases and remains pH=const .

Henderson Haselbalh buffer solution equation give that just on1908 as well 22 Years later .

C

Kdis

Ostwald dilution law side product is calculation pH for weak acid and weak base concentration:

Weak acid hydrogen ion concentration [H+]= = 10-pH Molarity ;

Weak base hydroxyl ion concentration [OH-]= = 10-pOH Molarity .

CKa

CKb

4th page : http://aris.gusc.lv/BioThermodynamics/H2ODissociation.doc

pH calculation in solutions of acids, bases and salts

Strong acid

H2SO4 => 2 H+ + SO42-, where z = 2eq, strong acid H+ ions concentration [H+] = zCdis,

[H+] = CM•α•z or, since CM•z = CN, [H+] = CN•α

Taking logarithm from both sides and changing signs we obtain pH expression:

pH = -log [H+] = -logCM•α•z or pH=-logCN•α .

Weak acid concentration as Ostwald’s dilution law side product [H+] = .

Taking a logarithm from both sides with minus pH = -log [H+] = - =

Strong base

Ca(OH)2 => Ca2+ + 2 OH- , where z = 2eq, strong base concentration of OH- ions [OH-] = zCdis,

[OH-] = α•z•CM or, since CM•z = CN, [OH-] = CN•α Taking logarithm from both sides and changing signs we obtain pOH expression:

pOH= -log [OH-]= -logCM•α•z=-logCN•α or pH=14-pOH=14+logCM•α•z

CKa

2

log CKa

2

log CpK a

Weak base concentration as Ostwald’s dilution law side product [OH-] = .

Taking a logarithm from both sides with minus pOH = -log [OH-] = - =

or pH= 14 - pOH =14 -

CKb

2

log CKb

2

log CpK b

2

log CpK b

Strong acid and strong base concentration for dissociated molecules Cdis = α•CM .

4th page : http://aris.gusc.lv/BioThermodynamics/H2ODissociation.doc

Hydrolysis of salts Brensted protolytic reaction with water

1. Strong acid and base salts are not hydrolyzed.

Strong acid anion is very weak base 0< Kb <1.

Strong base cation is very weak acid 0< Ka <1.

Na2SO4 is not hydrolyzed, as SO42- anion is a very weak base and Na+ cation is a very weak acid..

2. Weak acid and strong base salt Na2CO3 give CO32- anion is strong base Kb >> 1, but Na+

cation is a very weak acid. The CO32- reacts with water-weak acid - hydrolysis just in 1 stage:

stage 1 CO32- + H2O => HCO3

- + OH-.

Salt solution of weak acid and strong base due to OH- ions environment in is basic pH > 7.

stage 2: HCO3- + H2O => H2CO3 + OH- not happen without acid addition.

For this reason, if we have to write the hydrolysis reaction in molecular form according 1st stage:

Na2CO3 + H2O => NaHCO3 + NaOH

Hydrolysis will be increased by adding acid to solution and oppressed by adding base.

3. Weak base and strong acid salt NH4Cl give NH4+ cation strong acid Ka >> 1, but Cl- anion is

very weak base react with water-weak base. The NH4+ cation hydrolysed in one stage:

NH4+ + H2O => NH4OH + H+

Due to H+ ions environment in weak base salt solution is strong acid. As pH < 7 is acidic.

Hydrolysis reaction in molecular form is: NH4Cl + H2O => NH4OH + HCl

acid a H+ + b base

If acid a is weak

coupled salt is strong base b

Ka = ]a[

]b[]H[ Kb =

]b[]H[

]a[

; Ka = ; bK

1 b base + H+ acid a

If base b is weak

coupled salt is strong acid a

1st page : http://aris.gusc.lv/BioThermodynamics/H2ODissociation.doc

4. Hydrolysis of a weak acid and weak base salt CH3COONH4. Anion CH3COO- is strong base

and cation NH4+ is strong acid, which react with water weak acid and weak base:

CH3COO- + H2O => CH3COOH+OH- ; NH4+ + H2O => NH4OH + H+ .

Hydrolysis in great extent as H+ and OH- ions form water: H++OH- =>H2O

Weak acid its salt protolytic Equilibrium

BUFFER SOLUTIONS Brønsted Acid Base protolytic pair

Ka = = = ]a[

]b[]H[

acid

salt

C

C]H[

pH=pKa+log ; acid

salt

n

n

acid

salt

C

CpH=pKa+log

Vbuf

n acid

n salt

Vbuf

Cacid

Csalt

A BUFFER SOLUTION always consists

of both protolytic pair forms ratio b / a

of the same protolytic pair,

or, in other words, of an salt base b and

its conjugated weak acid a

ratio b / a.

Amount ratio of acid

[a]acid, Cacid , nacid and

its conjugated base

[b]salt, Csalt , nsalt

is amount in common

buffer solution volume

Vbuf.

since 1908 publicated Henderson Haselbalh expressions for pH calculation

weak acid a H+ + b salt (base)

Concentration of weak acid [a]

Concentration of hydrogen [H+] ion

Concentration of conjugated base [b] salt

pH=pKa+log ;

acid

salt

n

nH ][

Vbuf

a acid

b salt[ ]

[ ]

acid

salt

a

b

][

][

a H+ + b acid H+ + salt

nacid = Cacid * Vbuf

nsalt = Csalt * Vbuf

3rd page : http://aris.gusc.lv/BioThermodynamics/BufferSolution.doc

Factors, that affect the pH value of a buffer system

The pH value, that is kept constant by a buffer, depends :

1) on weak acid strength, included in buffer system (Ka is the measure of acid strength) and

2) on the ratio between salt and acid amount nsalt/nacid of buffer solution Vbuf.

3) not on dilution of buffer solution. Drinking the water leave safe the blood pH=7.36 constant.

4) Fourth factor, that affects pH of a buffer system, is temperature

for weak acids;

- temperature growth increase the Ka value and this shifts pH to lower values

(as pKa = -log Ka, the greater is acid Ka, the smaller is pKa);

- temperature decrease this shifts pH to greater values as Ka value decreases and

(as pKa = -log Ka greater is, the smaller is acid Ka).

for weak base;

- temperature growth increase the Kb value and this shifts pH to higher values

(as pKb = -log Kb, the greater is base Kb, the smaller is pKb);

- temperature decrease this shifts pH to smaller values as Kb value decreases and

(as pKb = -log Kb greater is, the smaller is base Kb).

Phosphate BUFFER SOLUTION

H2P

HPO4

O4

2 -

-[ ]

[ ]

acid H2PO4- H+ + salt HPO4

2- (base)

pH=pKa+log ][

][

42

24

POH

HPO

if [H2PO4-]= [HPO4

2-] ratio is 1 log1=0

pH=pKa+ 0= 7.2 is middle point of buffer solution as over inflection point

Protolytical pair a H+ + b

weak acid H2PO4- concentration [H2PO4

-] as anion

concentration of hydrogen [H+] ion

salt HPO42- (conjugated base) concentration [HPO4

2-]

=1 ][

][

42

24

POH

HPOBuffer region

pH interval:

8.2 > pH >6.2

Buffer plateau region pH values

around over inflection point

pH = pKa± 1= 7.2 ± 1

8.2 > pH >6.2

is around middle point

pH =7.2 value

plus-minus one pH unit.

1st page : http://aris.gusc.lv/BioThermodynamics/BufferSolution.doc

Mechanism of BUFFER action Ostwald’s dilution law

Acetate BUFFER solution: weak acid salt (base) equilibrium

CH3COOH H+ + CH3COO-

Sodium acetate as a salt (strong electrolyte) dissociates completely:

CH3COONa => CH3COO- + Na+ α = 1

If strong acid H3O+ ions are added to the buffer solution, strong acid react with weak base

form of buffer (with the acetate ion) : H3O+ + CH3COO- => CH3COOH + H2O

The concentration C of acetic acid is increasing, grows, its dissociation degree is adjusted to be

smaller and therefore the concentration of H+ ions and pH remain practically constant.

If strong base OH- ions is added to acetate buffer solution, strong base react with weak acid

form of buffer (acetic acid) : OH- + CH3COOH => CH3COO- + H2O

The concentration C of acetic acid decreases, its dissociation degree α grows, hence, H+

concentration and pH remains constant.

α= C

KProtolytical pair a b + H+

2nd page : http://aris.gusc.lv/BioThermodynamics/BufferSolution.doc

Weak base and its salt Ostwald’s dilution law

Ammonium BUFFER solution: weak base salt (acid) equilibrium

NH4OH NH4+ + OH- ; Kb = = ; pOH=pKb+log

Ammonium chloride as a salt (strong electrolyte) dissociates completely:

NH4Cl => NH4++ Cl- α = 1

nondis4

4

]OHNH[

]NH[]OH[

base

salt

C

COH ][

base

salt

C

C

pOH=pKb+log base

salt

n

npOH=pKb+log pOH=pKb+log

pOH=pKb+log

Vn

Vn

base

salt

/

/

''

''

basebase

saltsalt

VC

VC

acbase

acsalt

nn

nn

pOH=pKb+log

bbase

bsalt

nn

nn

If strong acid H3O+ ions are added to buffer solution strong acid is transformed to a salt (NH4

+):

H3O+ + NH4OH => NH4

+ + 2 H2O

The concentration C of weak base decreases, its dissociation degree α grows, hence,

OH- concentration remains constant and pH=const.

If strong base is added to buffer solution, the OH- ions are transformed into weak base NH4OH:

OH- + NH4+ => NH4OH

The concentration C of this weak base is increasing, grows, its dissociation degree is adjusted to

be smaller and therefore

the concentration of OH- ions remain practically constant and pH=const.

α= C

K

2nd page : http://aris.gusc.lv/BioThermodynamics/BufferSolution.doc

DIFFERENT FORMS OF pH Henderson Haselbalh EQUATION

=

pH=pKa+log acid

salt

C

CpH=pKa+log

acid

salt

n

n pH=pKa+log V/n

V/n

acid

salt pH=pKa+log ''

''

acidacid

saltsalt

VC

VC

pHac=pKa+log

acacid

acsalt

nn

nn

pHb=pKa+log

bacid

bsalt

nn

nn

The Δnac=Cas•Vac is number of strong acid moles, for example HCl, added to buffer

solution, which decreases the buffer system salt as Brensted base amount nsalt - Δnac and

increases the buffer system weak acid amount nacid + Δnac, thus change the buffer

system pH value about ΔpH= pH - pHac to decrease that.

The Δnb=Cb•Vb is number of strong base moles, for example NaOH, added to buffer

solution, which increases the buffer system salt as Brensted base amount nsalt + Δnb and

decreases the buffer system acid amount nacid - Δnb, thus change the buffer system pH

value about ΔpH= pHb - pH to increase that.

3rd page : http://aris.gusc.lv/BioThermodynamics/BufferSolution.doc

Buffer system middle point pH= pKa = 7,199

Buffer capacity β

Buffer capacity β shows, how much mol numbers of strong

acid Δnac or strong base Δnb can be added to 1 liter Vbuffer

of buffer solution to shift its pH value for 1 pH unit

bufferVpH

n

Liter

molβ = =

The buffer capacity is affected by four reasons:

1.the total concentration of buffer solution Csalt’ and Cacid’.

The buffer solution C’ is proportional to buffer capacity β.

2. the ratio between buffer components =1

on middle point of buffer solution :

2. a) maximal value βac= βb=0.55·C’ buffer capacity have on middle point - over

inflection point solution have symmetric equal values βac= βb=0.55 C’;

2. b) as soon as the ratio between buffer components deviates from middle point value

nsalt/nacid=1, both buffer capacities βac and βb becomes fast smaller as 0.55·C;

2. c) as soon as the salt/acid ratio in buffer solution deviates from middle point

nsalt/nacid=1, buffer capacity becomes asymmetric

(βac and βb differ from each other).

acid

salt

n

n

5th page : http://aris.gusc.lv/BioThermodynamics/BufferSolution.doc

1 Buffer solution dilution dose no change value pH=constant as ratio logarithm log1/1=0

the same for ten times diluted buffer 0.1 M concentration as ratio logarithm log0.1/0.1=0!

1.a Water drinking in human organism physiologic pH=7,36 value do not change and not intact!

2. β~C Buffer capacity β is proportional to buffer concentration Cbuffer

as Cbuffer=1 M β=0.55 and Cbuffer=0.1 M β=0.055!

β , mol/l H3PO4/H2PO4- H2PO4

-/HPO42- HPO4

2-/PO43-

red Concentration of Buffer solution Cbuffer=1.0 M

blue Concentration of Buffer solution Cbuffer=0.5 M

green Concentration of Buffer solution Cbuffer=0.1 M

3. Buffer solution Middle point pH=pKa=7.199 Buffer capacity has maximal value βmax!

4. Buffer capacity at middle point is βmax = 0.55•Cbuffer as β=0.55•1 = 0.55 mol / l and

β'=0.55•0.1= 0.055 mol / l !

5. Buffer solution Middle point Buffer capacity against

strong acid and strong base is symmetrically equal βac=0.55=βb, β’ac=0.055=β’b!

1 Buffer solution Dilution dose no change value pH=constant as ratio logarithm log1/1=0

the same for ten times diluted buffer 0.1 M concentration as ratio logarithm log0.1/0.1=0!

1.a Water drinking in human organism physiologic pH=7,36 value do not change and not intact!

2. β~C Buffer capacity β is proportional to buffer concentration Cbuffer

as Cbuffer=1 M β=0.55 and Cbuffer=0.1 M β=0.055!

β , mol/l CH3COOH/CH3COO-

red Concentration of Buffer solution Cbuffer=1.0 M

blue Concentration of Buffer solution Cbuffer=0.5 M

green Concentration of Buffer solution Cbuffer=0.1 M

3. Buffer solution Middle point pH=pKa=4.76 buffer capacity has maximal value βmax!

4. Buffer capacity at middle point is βmax = 0.55•Cbuffer as β=0.55•1 = 0.55 mol / l and

β'=0.55•0.1 = 0.055 mol / l !

5. Buffer solution Middle point Buffer capacity against

strong acid and strong base is symmetrically equal βac=0.55=βb, β’ac=0.055=β’b!

1) First of four human buffer systems is enzyme CA carbonic anhydrase made Brønsted

Acid/Base endothermic equilibrium combined with shuttle hemoglobin mechanism:

Q+CO2aqua+2H2O ←CA→H3O++HCO3

- ,

which consume heat Q of Krebs cycle complex enzymes driven exothermic reactions.

4 human buffer systems

2) Second buffer system, that is present in blood, are proteins containing two type protolytic

functional groups -NH2 amine

weak base and weak acid -COOH

carboxylic group:

Shuttle molecule hemoglobin for HCO3-, H+ and O2 stabilize physiologic pH=7.36 .

Deoxy hemoglobin in venous blood (H+His63,58)4HbT link bicarbonate by salt bridge

HCO3- H3

+N and captures proton equal amount produced protons by Krebs cycle

[CO2Krebs]=0,0275=[HCO3-]=[H+] instead oxygen and its lungs antagonist oxy hemoglobin

(O2His63,58)4HbR is deprotonated by adsorbed oxygen molecule, but still protein with buffer 2).

4) Biological ubiquities exist besides the inorganic phosphate buffer system,

buffer systems of the organic R-groups phosphate esters so as ATP (adenosine tri phosphate),

ADP (adenosine di phosphate), CTP, CDP, GTP, GDP, TTP, TDP, UTP, UDP, NADH B3 vitamin,

FADH2 B2 vitamin, phospho proteins, glucose phosphate, fructose phosphate, etc.

proteinNH

C

2

OO_

+ H+

+ H+ protein

NH

C

+

OO

3

H

acid base + H+ salt

weak acid salt

weak base

3) Biological important inorganic phosphate buffer system NaH2PO4/Na2HPO4 pKa=7,199.

O

O

O

P ORH

HO

O

O

P ORH

weak acid H+ + salt

acid H+ + base - salt

11th page : http://aris.gusc.lv/BioThermodynamics/BufferSolution.doc

020010

,,

4 6 7.0512=pKa 9 10 11→pH

7.36 = pH = pK+log =7.0512+log

]CO[

]HCO[

aqua2

3

]CO[

]HCO[

aqua2

3

β, mol/L buffer capacity

0.6

0.5

0.4

0.3

0.2

0.1

0

10

9

8

7

6

5

4

3

2

HCO3-0% 50% 100%

CO2+ 2H2O 100% 50% 0%

Human blood pH=7,36 Henderson Haselbalh CA equation - Shuttle hemoglobin

Main buffer system CA uses hemoglobin Shuttle stabilized pH=7,36 from tissues capturing

[H+]=0,02754 M instead desorbed oxygen for Krebs cycle use keeping venous [O2aqua] =1.85·10-5 M

but in lungs arteries adsorbed oxygen releases H+ keeping concentration [O2aqua] =6·10-5 M by

sensitive deoxy hemoglobin Tense state - oxy hemoglobin Relax state Shuttle equilibrium:

in lungs=> 4O2aqua + (H+His63,58)4HbT <= [O2aqua] =>(O2His63,58)4HbR +4 H+ <= tissues

Q+CO2aqua+2H2O ←CA→H3O++HCO3

- Alkaline reserve is

10(pH-pK)= 10(7.36-7.0512)= 100.3088 = = ][

][

2

3

aquaCO

HCO

1

2.0361

acidose alkalose

acidose alkalose

15th page : http://aris.gusc.lv/BioThermodynamics/BufferSolution.doc

Building Atoms – nucleus (proton p+, neutron n), electron e- orbital

Electron staying wave atomic orbital .

Atomic nucleus

Nucleus is small, dense region consisting of protons p+ and neutrons n at atom center.

All atom mass is located in nucleus, with a very small contribution from the electron orbital cloud.

Electrons exist negatively charged (–) as staying waves clouds,

what sciences designated as electron orbitals,

due to central symmetry of electron filled atom space

symetry relating to central positive charge (+) on nucleus.

Electrons in atoms staying wave energy level determines frequency times Plank constant f•h=E .

Periodic table of elements has seven periods 1,2,3,4,5,6,7

with seven ground tones orbitals s1,s2,s3,s4, s5, s6, s7

physically as seven quantum numbers n =1,2,3,4,5,6,7 to determine electrons energy levels.

2

4

He helium

1

1

0

1

1

0

0.62 Å+

+

nucleus

electron cloud orbitalsize

Atomic size determines electron

orbital cloud.

Smallest size atom in universe is

helium atom.

Atomic size unit angstrom

1 Ǻ =0.1 nm = 10-8 cm =10-10 m

Electron cloud

atomic mas

Z atomic number

Electron staying wave ground tone s orbitals have three overtones p, d, f orbitals

s orbital – Geeks sphaira – ground tone, l =0

p sub orbital – Geeks protos – first, one node plane l =1,

d sub orbital – Geeks deitos – second, two node planes l =2,

f sub orbital–Latin finēre, last one finite, three node planes l =3.

Sub orbitals have node planes number or orbital quantum number l

Magnetic quantum number ml shows the possible spatial

orientation of orbitals having the azimuthal quantum number ml

can take values from the interval:

– l, , 0 , , + l magnetic quantum numbers.

One electron orbital can occupy two electrons

with opposite magnetic moments spins and .

Spin is the magnetic moment what create electron orbital.

Electron having opposite spin attracts with anti parallel spin

in one orbital together.

two node planes l =2

N

S

S

N

N

S

S

N

three node planes l =3

l =0 one node planes l =1

2nd page : http://aris.gusc.lv/BioThermodynamics/ 34AtomaUzbuveSAngl.doc

1

2

3

4

5

6

7

Energy included in atomic orbital of electron

He0.62 Å +

+

Atomic size

Hund’s law

energy minimum principle of

electron state:

electron orbitals occupying

sequence from lowest energy

level orbitals 1s to ascending

electron orbital energy increase.

Chemical element atoms in periodic table have

the label color last occupied orbital.

That is outer shell energy level valence electron

orbital color.

s orbitals blue colors,

p orbitals yellow color,

d orbitals red color and

f orbitals green colors

s orbital spherical – Geeks sphaira – ground tone, l =0

p sub orbital – Geeks protos – first, one node plane l =1,

d sub orbital – Geeks deitos – second, two node planes l =2,

f sub orbital–Latin finēre, last one finite, three node planes l =3.

Electrons energy level E=f•h determines frequency times plank constant

Plank constant times frequency is

Energy E= h×f of green photon

f= 540×1012 Hz; = 555 nm

E= 3.58×10−19 J/photon

Avogadro NA=6.022×1023 mol−1

number for one mol green light

Emol=215.6 kJ/mol

4th page : http://aris.gusc.lv/BioThermodynamics/ 34AtomaUzbuveSAngl.doc

Chemical element atoms in periodic table have

the label color last occupied orbital.

That is outer shell energy level valence electron

orbital color.

s orbitals blue colors,

p orbitals yellow color,

d orbitals red color and

f orbitals green colors

1. Covalent electron pair Covalent bond

VSEPR

2. Overlapping electron orbitals Cl Cl

3. negative charge () density between positive charged (+) nucleus

4. Covalent bond is saturated

5. Covalent bond has symmetric geometry in space

C O :

O

O

C OO

C

H

HH

H

N

HH

H

..

O

H

H..:

O :H

:O H

:O H

:O HO :H

Al3+

O :H

linear trigonal

planar

trigonal

pyramidal bent tetragonal

tetrahedral hexagonal

octahedral

*

**

**

*

*

*

*

*

*

*

*

*

*

*

*..:*

*

*

*

*

..* *

*

*

* * *

O

O

O

:O

Al

:O

:O

H

H

H

HH

H

2nd page : http://aris.gusc.lv/BioThermodynamics/4KimiskaSaiteAngl.doc

Sigma bond -C-C- and paired bond >C=C<

=>

node planes node planes node planes are parallel

symmetry axes align

=>=>=>=> on one line

Paired bond formed molecular orbital double bond >C=C< has energy from -100 to -150 kJ/mol

=> on node plane

lie both

carbon atom nuclei

Sigma bond first formed single bond -C-C- ranges energy from -200 kJ/mol up to -350 kJ/mol

3rd page : http://aris.gusc.lv/BioThermodynamics/4KimiskaSaiteAngl.doc

symmetry axes are parallel

Liquid water tetramer structure no free water molecules present

Hydrogen bond polar water molecule attraction force

H

H

O HH

H

OH

O

H

H

O0.98 A

1.6 A

104.8

104.7

-0.8+0.4

-0.8 1.6 A

104.7

+0.4

-0.8 1.6 A

104.7

+0.4

-0.8

-30 kJ/mol -30 kJ/mol -30 kJ/mol

0.98 A

0.98 A

OH( )42

Three hydrogen bonds as polar water interaction resulting in tetramer (H2O)4 three hydrogen

bonds energies sum ΔG= - 90 kJ/mol

Ice water molecules

hydrogen bonding hexagonal structure

Pure hydrogen bonding crystalline lattice

type structure OH

H

OHH

OH

H

OHH

OHH

OHH

O

H

H

O

H

H

OHH

O

H

H

OHH

OH

H

OHH

OH

H

OH

H

OH

H

0.96 Å

1.76 Å109,47°

MW 288.25 g/mol16 OH2

-0.8

+0.4+0.4

1st page : http://aris.gusc.lv/BioThermodynamics/4HydrogenBond.doc

O

H

H

..:2.61 A

-0.8 +0.8q= q=

Serine acceptor and asparagine amide

hydrogen donor Ser-C-O•••H-NHC=O-Asn

Hydrogen bond

-30 kJ/mol

Tyrosine acceptor and glutamine amide

hydrogen donor Tyr-C-O•••H-NHC=O-Gln

O

HCO

NH

CHCH

2N H

C O

CHCH

2

CH

2

C

O

H

NHTyr Gln

1st page : http://aris.gusc.lv/BioThermodynamics/4HydrogenBond.pdf

O HNH

CO

CH

CH

2

H N

N CHCH

2

C

C OO

HH

Ser

Asn

threonine acceptor and serine hydrogen

donor Thr-C-O•••H-O-C-Ser

CO

NH

CH CH

O

CH3

H

NH

CO

CH

CH

2

OH

Thr Ser

guanine G with ciytosine C three hydrogen bonds

G=O•••H-NHC; G=N-H•••N≡C; GHN-H•••O=C;

adenine A with thimine T two hydrogen bonds

AHN-H•••O=T; A≡N-H•••N=T;

H

O

O

N

N

CH3

N

N

N N

N

H

H

AT

NH

H

O

N

N

N

N H

N HH

O

N

N

CG

adenine A with uracil U two hydrogen bonds

AHN-H•••O=U; A≡N-H•••N=U;

H

O

O

N

N

H

N

N

N N

N

H

H

AU

DNA, RNA

G ≡ C

DNA

A = T

RNA

A = U

alpha1 Arg141 C-terminusCOO-...H3+N Lys127 alpha2

alpha2 Arg141 C-terminusCOO-...H3+N Lys127 alpha1

Salt bridge - deoxy hemoglobine

-10 kJ/mol

OC

O

N H

CH

2HC

2HC

2HC

NCN

+

N HHH

H H

N+

H

H

H

CH

C

O

CH

CH3 CH

3Arg

Val

N H

N+

H

CH2HC

2HC

C O

2HC

2HC

H

H

OC

O

N H

CH

2HC

2HC

2HC

NCN

+

N HHH

H HLys

Arg

NH

CO

CH C

H2

CO

ON H

C ON

H

N+

CHCH

2

H

Asp His

1. lapas puse : http://aris.gusc.lv/BioThermodynamics/4HydrogenBond.doc

3. lapas puse : http://aris.gusc.lv/NutritionBioChem/38Olbalt10311Eng.doc

7. lapas puse : http://aris.gusc.lv/NutritionBioChem/32ProteinsC.doc

alpha1 Arg141 C-terminusCOO-...H3+N Val1 alpha2

alpha2 Arg141 C-terminusCOO-...H3+N Val1 alpha1

beta1 Asp94COO-...H3+NHis146 beta1

beta2 Asp94COO-...H3+NHis146 beta2

OC

ON

+

H

N

CH

N

CH

2H

HN H

N+

H

CH2HC

2HC

C O

2HC

2HC

H

HLysHis

beta1 His146 C-terminusCOO-...H3+NLys40 alpha2

beta2 His146 C-terminusCOO-...H3+NLys40 alpha1 N H

C O

CHC

H2

CO

OCO

NH

CH2HC

2HC

CH2

N C

N+

NH

H H

H

H

AspArg

alpha1 Arg141N+H3...-OOCAsp125 beta1

alpha2 Arg141N+H3...-OOCAsp125 beta2

Two bensene rings in water structure

Hydrophobic bond in water structure

(H2O)4→← (H2O)4 -10 kJ/mol

CH CH

2HC CH

3

CH3

CO

NH

CH

C O

N H

CH

2

(H ) O 2 4

(H ) O 2 4

Ile

Phe

CH

CO

NH

CH

2

CH

C O

N H

CH

2

(H ) O 2 4

(H ) O 2 4

Phe

Phe CHCH

CH3

CH3

C O

N H

CH3

CH

CO

NH

(H ) O 2 4

(H ) O 2 4

Val

Ala

Isoleucine and benzene ring

contact in water structure

Alanine and valine contact in water structure

CH CH CH

3

CH3CO

NH

CHCH

3

CH3

CH

2HC

C O

N H

(H ) O 2 4

(H ) O 2 4Val

Leu

Valine and leucine contact

in water structure

CHCH

CH3

CH3

C O

N H

CH2HC S

CH3

CO

NH

(H ) O 2 4

(H ) O 2 4

Val

Met

(H ) O 2 4

Methionine and valine contact in water structure

DNA doubule helix base pair tabletes in

water structure pressed together

(H ) O 2 4(H ) O 2 4

1. lapas puse : http://aris.gusc.lv/BioThermodynamics/4HydrogenBond.doc

3. lapas puse : http://aris.gusc.lv/NutritionBioChem/38Olbalt10311Eng.doc

7. lapas puse : http://aris.gusc.lv/NutritionBioChem/32ProteinsC.doc

Disulfide bond forms at milde oxidation conditions between two protein strands,

joning adjacend chain cysteines (Cys[C]), via oxidation sulf-hydril groups

of amin acids as removing hydrogen atoms.

Disulfide bond CysSSCys

-200 kJ/mol

C

O

CH

H N

CH2

CO

CH

HN

CH2

HS

H S+

Cys

CysS

S

C O

CH

H N

CH2

CO

CH

HN

CH2

H H+ +

Cys

Cys

Oxidation is hydrogen atoms removing

- 2 H

=================================>

Coordinative bond forms complex makers (A .Rauhvarger, General Chemistry, p. 3 in 12th part:

http://aris.gusc.lv/GenChem93/12_ComplexComp.pdf) metal ions are acceptors:

iron(II) ion Fe2+, iron(III) ioni Fe3+, calcium ion Ca2+,

magnesium ion Mg2+ zink ion Zn2+ or cooper ion Cu2+ e.c.

Coordinative bond donor atom O:→□Fe2+ acceptor metal ion

NH

CO

CH C

H2

C

O

O

Ca2+ N H

C O

CHCH

2

C:O

:O-

N H

CO

CHCH

2

C

:O

O

N H

CO

CHC

H2

C

:O

O

Asp

Asp

Asp

Asp

N

:N

Fe2+

CH3

OO

N

CH3

CH2

CH3

CH2

:N

CH3

O

O

N

:N

CH2

H

NH

:N

2HC

OO

His93

His92beta

His87alpha

His63beta

His58alpha

His64 oxy

proximal

distal

hexagonal

octahedral

bipyramidal

*

**

**

*

*

1. lapas puse : http://aris.gusc.lv/BioThermodynamics/4HydrogenBond.doc

3. lapas puse : http://aris.gusc.lv/NutritionBioChem/38Olbalt10311Eng.doc

7. lapas puse : http://aris.gusc.lv/NutritionBioChem/32ProteinsC.doc

Ca2+

N+

HH

H

CAsn

O

N H

H

Asp

Ser

C

O

O

Lys

Phe

Glu

Phe

C

O

O

Cys

Glu

Cys S S

C

O

O

O

H(H ) O 2 4

(H ) O 2 4

1. Hydrogen bonds of

O and N atoms between

hydrogen atom H acceptor

and other side H donor

2. Salt bridge

5. Disulphide bonds

3. Hydrophobic bonds

4. Coordinative bonds AspCOO-...+H3NLys

N

:N

CH2

H

N

:N

Fe2+

CH3

OO

N

CH3

CH2

CH3

CH2

:N

CH3

O

O

NH

:NCH

2

OO

globinoxy

globin

CysSSCys

hydrogen acceptor

O

O

H

N

O

H

O

O

H

O

NH

N

NH

O

NH

hydrogen donor

coordinative donor acceptor bond calcium ion

with carboxyl groups -COO→□Ca2+ □←OOC-

or iron(II) ion on center of hem → □Fe2+ □←

(H2O)4→← (H2O)4

water press together

nonpolar residues

of amino acids or

base pairing tablets

in DNA and RNA

molecules

5 Intermolecular forces (intermolecular bonds) biomolecules

1st page : http://aris.gusc.lv/BioThermodynamics/4HydrogenBond.doc

London Force (Wan der Walls) Bonding Energy in contact point between hydrogen atoms H-H is weak -2

kJ/mol. Investigations shows great number of contact points 84. Total energy EII=-2*84= -168 kJ/mol. Water

molecules green atoms absolutely isolate both saide of membrane double layer. Phosphatidyl Choline

molecules MW=760.10 g/mol in close packing doubule layer membrane touthe at

contact in 7 points with methylene groups >CH2:H2C< .

Close packing

Total energy for one phosphatidyl choline molecle is Esumma = -168 +(-30)= -198 kJ/mol.

2) Non polar fatty acid tayles with two methyl groups –CH3░H3C= in membranes interier close

contakt three hydrogen atoms of methyl groups between ajacent layers.

Each hydrophobic bond force energy is -10 kJ/mol on one contact point. Six contact points of

hydrophobic bonds Energy=6*-10= -60kJ/mol. So two times smaler for one double layer molecule

each side Ehydrophob=-60/2= -30kJ/mol.

Van der Walls–London dispersion force in phospholipid-cholesterol membranes

1.,2. Lapas puses : http://aris.gusc.lv/06Daugavpils/Engl/LipdBiLayerMembran.doc

C

H H

HH

H H

HH

H H

HH

H H

H H

H H

HH

H H

HH

HH

H H

HH

HH

H

C

HH

H H

HH

H H

HH

HH

H H

HH

H H

HH

H H

HH

H H

H H

HH

H

C

H

HN+

CH3

CH3

CH3

CH2

CH2

O P

O

O

O CHH

CH

O

O

O

O

Palmitate

1

2

3Oleateester of glycerol C1,C2

of Choline ester & of Phosphate - glycerol C3

7

CH

H H

C

HHH

CH

HH

CH

HH

(H ) O 2 4

(H ) O 2 4

(H ) O 2 4

(H ) O 2 4

hidrofoba- saistiba-

membranas vidu- -

udens struktura- - -

udens struktura- - -

Close packing

56 Å

↑↑↑↑

56 Å

↓↓↓↓

56 Å

Double layer membranes of phospho lipids 1.,2. Lapas puses : http://aris.gusc.lv/06Daugavpils/Engl/LipdBiLayerMembran.doc

Phosphatidyl cholin double layer membrane isolate two water compartments of solutions and

has electric double layer on surface with positive charged nitrogen N+ atoms blue and negative

charged phosphate groups PO4-. The average thickness mesurement value of membrane is

d =56Å or 5,6 nm. The size of water molecule 1,4 Å cover membrane thickness 56/1,4=40 times.

If wall thickness would be 40 man 1,7 m tall size, then wall thickness between rooms would be

68 m and home doures would be 68 m long tunnels in walls.

N+

PO4-

PO4-

N+

Waterless interier in membranes

are impermeable isolate cell membrane wall for water medium components molecules and

solutions: saļs and organic compound molecules. As the home walls separate rooms. That

entrance the rooms we use doores, but membranes equiped with transport and signaling

enzymes–proteins: aquaporins H2O,O2,CO,NO,C3H8O3, proton H+ channals, bicarbonate chanals

HCO3-, sodium Na+, potasium K+, magnesium Mg2+, calcium Ca2+, chloride Cl- ions, sugares Glc,

Gal, Man, 21 amino acids and other biologic water solutes. Destiny of studies is organic regulate

opened thermodynamics systemes, which through cell membranes organize the life organisms.

Composition of double layer membranes with Phospho lipids and Cholesterol 1.,2. Lapas puses : http://aris.gusc.lv/06Daugavpils/Engl/LipdBiLayerMembran.doc

1/3 mass fraction of cell and organell membranes constitute Phospho lipids as Phosphatidyl

choline. Binding energy Ebound=-198 kJ/mol make membranes liquid therefore can be mechanic

disordered, as liquids with pressure, gravitation and mechanic movement impact. Cholesterol

content makes membranes stronger and flexible evoid its destruction and following cell content

leaking which water solution contains salts and organic compounds molecules.

Second third part of membranes mass constitutes

hydrocarbon 27 carbon steric frame steroid

molecule: four rings are labeled A, B, C and D.

Angular methyl –CH3 groups 18 and 19 as well

tail fork, rod, splinter are good clutch fixing close

hydrocarbon chains. Double bond between carbon

atoms >C=C< 5 and 6. Alcohol HO- at C 3 forms

hydrogen bond >C=O...HO- with fatty acid

H HH

HHH

H

HH

H HH

H

O

H HH

O

C

H H

HH

H H

HH

H H

HH

H H

H H

H H

HH

H H

HH

HH

H H

HH

H H

H

C

HH

H H

HH

H H

HH

HH

H H

HH

H H

HH

H H

HH

H H

H H

HH

H

C

H

HN+

CH3

CH3

CH3

CH2

CH2

O P

O

O

O CHH

CH

O

O

O

1

2

3 18

19

abas angularas metil grupas

H HH

H

HH

H

HH

H HH

H HH

H

O

O

CO both angular methyl groups18

19

HH

H

H

H HH

H HH

H HH

HO

HH

Cholesterol

10

4

912

675

8

1211 13

14 1516

A

17

18

3B

C D

19

202122

23

24

2526

27

Oleate

carboxyl oxygen >C=O.

Cholesterol as Steroid

makes membranes unbroken, flexible and

so prevent following leaking of water molecules and of water solution components:

salts and water soluble organic molecules. The Cholesterol/Phospho Lipid C/PL mole ratio of human red blood cell membranes ranges from a normal value of 0.9–1.0

(since 1978 first publication as refference in Journal of Cellular Biochemistry 2004 V8, 4, p 413-430).

If Cholesterol amount decreases up to 0,5= C/PL , then membranes leak cell content out, but

If Cholesterol amount increases up to 1,5= C/PL , then membrane becomes solid, inflexible and

squeeze channels, aquaporins, but receptors becomes inactive due to absence conformational flexibility.

When a molecule is subjected to an outer electrical field,

the dipole momentum of the molecule is changed : = μo + μind, where

μ o is the dipole momentum of the molecule itself as well

μo = 0 for a non-polar molecule or μo > 0 for a polar one and

μ ind is the dipole momentum, induced by the outer field.

Non-polar molecules become polar and polar molecules

become more polar.

Polarization of molecules in outer electric field

Orientation forces can be established between two polar molecules.

Dispersion forces act between two non-polar molecules: :Aδ-Bδ+A:BA δ+Bδ-:

the common pair of electrons is shown as a pair of two dots :

Intra molecular polarization, when a hydrogen atom is replaced by a more

electro negative (EN) atoms (O, N, Cl). The Cl atom attracts electrons and

therefore shifts the electron density of the entire molecule:

As a result, the O-H bond in the carboxyl group becomes more polar and

therefore chloroacetic acid appears to be a much stronger acid than acetic

acid. Compare the acetic acid dissociation constant K = 1.75 • 10-5 and

chloroacetic acid K = 1.4 • 10-3 . If all the three hydrogen atoms in the methyl

group are substituted by Cl atoms, forming trichloro acetic acid one gets an

acid, the strength of which can be compared to hydrochloric acid.

Van der Waals’s interaction forces of biomolecules–London dispersion forces

4th page : http://aris.gusc.lv/BioThermodynamics/4HydrogenBond.doc

He

- +++

nucleus

electrons

outer electric field

Cl

Cl

Cl C C

O

O H

Cl C C

O

O H

H

H

C C

O

O H

H

H

H

- +

- +

- +

temperature

- +

He

-+ ++

nucleus

electrons

-+ -+ Induction forces exist between a polar and a non-polar molecules.

= q•l dipol H2O =0.8 el•2.61 Å=2.088 el•Å.

O

H

H

..:2.61 A

-0.8 +0.8q= q=