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2
5
k stiff_estimate = 4.592 10
units of pN/nm
now generate a characteristic force required to rupture a covalent bond characteristic_force_covalent := k stiff_estimatex characteristic_force_covalent = 2.296 10
4
units of pN
this = 23 nN or so
These bonds are strong you couldn't break for example with an optical trap, need more force
Ionic bonding/interactions
develop using the physics of the coulombic interaction charge on an electron Thermal Energy "kT" kT := 4.1 10
21 19
q 1 := 1.60 10 q 2 := q 1 0 := 8.85 10 := 1
4.1 pN*nm
12
Ecoulomb :=
do salt, then do salt in water, also show salt in non-polar q 1 q 2 4 0 3rkT Energy in units of kT
Ewater :=
Eoil :=
Ewater = 3.051
Eoil = 81.368
Coulombic Force
Fcoulomb := q 1 q 2 4 0 r
2
Lets add up an array of work elements N create a range of r values increasing to infinity it := 0 , 1 .. 50000 rin := r + it 0.2 10
it 0 3 10 10 10
Fcoulomb = 4.351 10
Fcou( ri) :=
q1 q2 4 0 ri
2
sum over the force, multiply times the distance, add these all up to get the energy. basically integrate
EFtotal :=
it
Force (N)
4 .10
2 .10
0 10 2 .10
3 .10
10
4 .10
10
5 .10
10
distance (m)
Instead of doing this by hand, we can do the integral in Mathcad to get the 1/r dependence: q 11q 22 4 00 11 r3
2
Fcou :=
Energy =
q 22 1 F dr3 q 11
cou 4 00 11
r3
Bjerrum length
set for water := 80
Ask: How close do ions need to be to have a stable interaction? solve coulombic interaction for a "kT" characteristic length
Lb :=
q1 q2 4 0 kT Lb = 7.018 10
10
units of meters
units of kT
Debye Length
i := 0 .. 1 Ionic Strength
The coulomb potential is normally nice and long, but ions can screen this. We can calculate an ionic strength and a screening parameter that leads to a characteristic screening length called the Debye Length. Make a table with concentrations and valency concentration Molar charge or valency
1 110-4 110-4 1 -1
Dataconc :=
0 1
concentrations in a cell ~150mM plug this in and look at the Debye length
concentration
1 z := Dataconc z=
charge on ion
1 10 4 4 1 10
1 1
the higher the ionic strength, the more things are screened
2
1 2
Cconci(z i)
i
Istr = 1 10
12
4 26
:= 78.54
2
0 = 8.85 10 2 q 1 n
o 0 kT
7
n o := 6.022 10
k screen :=
Istr
this equation is approximate, valid in a limit of dilute species screening parameter (units of inverse length) Will a charge "see" the full other charge? The ions in solution, reduce a charge, effectively the molecule "sees" less of the original charge. screening length, units of Angstroms these are short range, contact interactions
k screen = 3.289 10
Debye Length
10 k screen 1
10
= 304.021
D :=
D = 3.04 10
= 78.54 := 1
r = 3 10
10 10
r := 300 10
Ecou_debye :=
q 1 q 2 4 0 rkT
Ecoulomb2 :=
q1 q2 4 0 rkT
Ecou_debye = 0.698
Lennard-Jones potential
(Carbon example)
0.59
ELJ( x ) :=
C12 x
12
C6 x
6
C6 := 1425
4.1 0.59
EAttrLJ( x ) :=
C6 x
6
Ebase( x ) := x 0
EkT ( x ) := x 0 1
d := 0.001 , 0.01 .. 8
black is sum
0