van der waals forces and hydrogen bonds j. israelichvili, „intermolecular and surface forces”,...
TRANSCRIPT
![Page 1: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/1.jpg)
Van der Waals forces and hydrogen bonds
J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997
![Page 2: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/2.jpg)
Types of „weak” interactions
![Page 3: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/3.jpg)
Types of „weak” interactions (continued)
![Page 4: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/4.jpg)
![Page 5: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/5.jpg)
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
![Page 6: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/6.jpg)
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
![Page 7: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/7.jpg)
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.
![Page 8: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/8.jpg)
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
![Page 9: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/9.jpg)
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
![Page 10: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/10.jpg)
Repulsive potentials
0
exp
0
rcrw
rrw
r
rrw
n
![Page 11: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/11.jpg)
![Page 12: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/12.jpg)
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-
![Page 13: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/13.jpg)
rVDW(O)=1.52 ArVDW(H)=1.09 A
![Page 14: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/14.jpg)
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.
![Page 15: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/15.jpg)
Examples
weak
moderately strong
strong
![Page 16: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/16.jpg)
H-bonds in proteins
• backbone-backbone• backbone-sidechain• sidechain-sidechain• backbone-solvent• sidechain-solvent
![Page 17: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/17.jpg)
Examples
![Page 18: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/18.jpg)
Hydrogen bonding and proton transfer
X H Y
X-H…Y X-…H-Y+
polarity
![Page 19: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/19.jpg)
Symmetric hydrogen bonds
Kojić-Prodić & Molcanov, Acta Chim. Slov., 2008, 55, 692-708
![Page 20: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/20.jpg)
H-bonding energy surfaces are reflected in structural structures
H.B. Burgi, J.D. Dunitz, Acc. Chem. Res., 1983, 16, 153-161
![Page 21: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/21.jpg)
Energy decompositionE=ESX+EPOL+ECT+EDISP
E=EES+EXC+EPOL+ECT
Singh and Kollman, J. Chem. Phys., 1985, 83, 4033-4040
![Page 22: Van der Waals forces and hydrogen bonds J. Israelichvili, „Intermolecular and Surface Forces”, Academic Press, London, 1997](https://reader035.vdocuments.us/reader035/viewer/2022062308/56649dc55503460f94ab904d/html5/thumbnails/22.jpg)
Korochowiec et al., J. Chem. Phys., 2000, 112, 1623-1632