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Matt Lang, MIT

Forces at the Molecular Level


Covalent Interactions
Here electrons are truly shared between atoms. To do this properly we need to know the wavefunctions describing the electron probability density around the atoms. Lets assume a model of a bond as a spring to make some approximations. Examples of typical energy of covalent bonds: Carbon Carbon single bond ~140kT Carbon Carbon double bond ~240kT Force on a spring ~ kx Fspring := k stiff x integrate to get the energy, Mathcad does this for us 1 2
Energy in a spring = Fspring dx k stiff x 2
Ebond := 140 4. units of pN*nm A reasonable dissociation distance for this bond is 0.5 angstroms 0.5 converted to nm set this value x := 10 We can now estimate an approximate stiffness for the bond: k stiff_estimate := 2 Ebond
x

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

Matt Lang, MIT

Ionic bonding/interactions
develop using the physics of the coulombic interaction charge on an electron Thermal Energy "kT" kT := 4.1 10
21 19

distance separation, "r" J r := 2.3 10


10

q 1 := 1.60 10 q 2 := q 1 0 := 8.85 10 := 1

4.1 pN*nm

typical NaCl separation is 2.3 angstroms q 1 q 2 4 0 rkT kT

12

Ecoulomb :=

epsillon for water =80, for oils, it is ~3

Ecoulomb = 244.104 units in kT q 1 q 2 4 0 80rkT

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

Coulombic force goes as 1/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

rin = 2.3 10 rin = 2.9 10

sum over the force, multiply times the distance, add these all up to get the energy. basically integrate

EFtotal :=

it

10 Fcou( rinit) 0.2 10 kT

from summation EFtotal = 254.968 units of kT

from equation Ecoulomb = 244.104

Matt Lang, MIT

Coulomb Force vs. Distance

Force (N)

4 .10

try making the boxes smaller, approach the integration limit

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

Should be about 7 angstroms in water

units of meters

Matt Lang, MIT

Hydrogen Bond Examples


:= 1 Ehydrogenbond := (0.2)(0.3) q 1 q 2

distance separation, "r" r := 3.0 10


10

put in partial charges 4 0 rkT E hydrogenbond = 11.229

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

0 Cconc := Dataconc Cconc =

concentration

1 z := Dataconc z=

charge on ion

1 10 4 4 1 10

1 1

formula for ionic strength Istr :=

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

Matt Lang, MIT


1 k screen
8

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

Ecoulomb2 = 1.871 units in kcal/mole converted to kT units C12 := 2.75 10


6 4.1

Lennard-Jones potential
(Carbon example)

repulsive term attractive terms

0.59

ELJ( x ) :=

C12 x
12

C6 x
6

C6 := 1425

4.1 0.59

conversion factor is 4.1 (kT)/0.59 (kcal/mole) ERepLJ( x := ) C12 x


12

EAttrLJ( x ) :=

C6 x
6

Ebase( x ) := x 0

EkT ( x ) := x 0 1

d := 0.001 , 0.01 .. 8

van der Walls interaction for Carbon


green is repulsive potential

Energy (units of kT)

dark blue is attractive

black is sum
0

light blue is kT level

Separation between atoms (Angstroms)

example parameters from Creighton