van der waals forces and hydrogen bonds j. israelichvili, „intermolecular and surface forces”,...
TRANSCRIPT
Van der Waals forces and hydrogen bonds
J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997
Types of „weak” interactions
Types of „weak” interactions (continued)
Interactions between backbone peptide groups
mj
mi
ji
jiijijijijpp
ijijijijij ddRT
rERTrf ji
,;,,,exp
2
1ln,,,
)2()1(
2)2()1()1(
pi
pj
sin
cos
)ˆˆ3(
)()(),;(
,;,;
3
u
ΩTrrIA
uΩAuΩ
ΩΩ
ijijTijij
ij
jiij
jijijT
ijiijel
ijnbjiijeljiijpp
Dr
pp
E
rEEEji
lj
li)1(
ij
)2(ij
ij
Cai Ca
i+1
Caj
Caj+1
antinsignific
222
22)1(
||||||||
2
1
...2
1
jijijijiji
jijijiji
EEERT
EE
EERT
EEf
VDWpp
VDWppij
C
C
NC
O
H
||
jiijijijijiij
ijijijijijij
ij
ijijijij
ij
ij
ij
ij
ijijij
r
B
r
A
r
r
r
rf
uururu ˆˆ,ˆˆ,ˆˆ
334
32
)12(2
)2()1(
2)2(2)1(2)2()1()12(6
)2()1()12(3
60120)1(
)1(ij
)2(ij
ijr̂
)1(ˆ iju
)2(ˆ iju
insignificant
PMF
)1(ij
)2(ij
0ij
2ele captures the orientation dependence of backbone hydrogen bonding interactions
Liwo et al., Prot. Sci., 2, 1697 (1993); J. Phys. Chem. B 108, 9421 (2004)
ijr̂
)1(ˆ iju
)2(ˆ iju
oij 90)1(
ij)2(
ij
ijr̂
)1(ˆ iju
)2(ˆ iju
PMF
Approx.
Dispersion forces
62
0
20
3000
620
02
062
0
02
0
2
0
0
4
4
44
53.0)4(2
r
hrw
a
r
ea
rrw
Ah
ea
ea
6
0
20
620
20
6 44
3
44
3
r
I
r
h
r
Crw disp
QM (London, 1930)
21
2162
0
0201
21
2162
0
0201
21
2162
0
0201
42
3
42
3
42
3
II
II
r
h
r
h
rrw
Different atoms
Repulsive potentials
0
exp
0
rcrw
rrw
r
rrw
n
What are hydrogen bonds?
• X, Y are usualy (99% or so) electronegative atoms• q is usually close to 180o • d(X …Y) < rVDW(X)+rVDW(Y); d(H…Y)<rVDW(H)+rVDW(Y)• d(X-H) is greater than in the free X-H molecule• d+H and d-Y are pronounced wrt non-interacting molecules
HX Yq
d+
d-
rVDW(O)=1.52 ArVDW(H)=1.09 A
Types of hydrogen bonds
• Weak (DH<1 kcal/mol) usually involve non-polar or weakly polar groups.
• Moderately strong (1<DH<20 kcal/mol) involve polar groups.
• Strong (DH>20 kcal/mol) involve ions.
Examples
weak
moderately strong
strong
H-bonds in proteins
• backbone-backbone• backbone-sidechain• sidechain-sidechain• backbone-solvent• sidechain-solvent
Examples
Hydrogen bonding and proton transfer
X H Y
X-H…Y X-…H-Y+
polarity
Symmetric hydrogen bonds
Kojić-Prodić & Molcanov, Acta Chim. Slov., 2008, 55, 692-708
H-bonding energy surfaces are reflected in structural structures
H.B. Burgi, J.D. Dunitz, Acc. Chem. Res., 1983, 16, 153-161
Energy decompositionE=ESX+EPOL+ECT+EDISP
E=EES+EXC+EPOL+ECT
Singh and Kollman, J. Chem. Phys., 1985, 83, 4033-4040
Korochowiec et al., J. Chem. Phys., 2000, 112, 1623-1632