Stereochemistry of Molecules in Crystals (part 1, 2)
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Stereochemistry of Molecules in Crystals (part 1, 2) Fumio Toda Okayama University of Science, Okayama, Japan key word: solid state, host-guest complex part 1: statistic aspect part 2: dynamic aspect
Transcript of Stereochemistry of Molecules in Crystals (part 1, 2)
Stereochemistry of Molecules in Crystals (part 1, 2)
Fumio TodaOkayama University of Science, Okayama, Japan
key word: solid state, host-guest complex
part 1: statistic aspectpart 2: dynamic aspect
ROH OH
RPhPh
Br
Br
Ph
RR
Ph
∆BrPh
RPh
R
Br
Ph
R BrPh
R
Br
Br
Br
Ph
R
PhR
in, out
meso
Br
Br
Ph
RPh
R
∆BrPh
RR
Ph
Br
Ph
R BrR
Ph
Br
Br
Br
R
Ph
PhR
in, in
rac
Br
Br
Ph
R
RPh
+
out, out
HBr, W-H rule (conrotatory)
R = Me
part 2: dynamic aspect(I) Thermal cyclization of diallenes in own crystals
Angew. Chem. Int. Ed. 1988, 2724.
1) dimethylenecyclobutene
Ph
Ph
tButBu
PhPh
rac
colorless prisms
∆140 º
solid Ph
PhtBu
tBu
Ph
Ph
Ph
Ph
PhtBu
PhtButBu
tBuPh
PhPh
Ph
green prisms
2) benzodicyclobutadiene
Ph
Ph
tButBu
PhPh
rac
∆140 º
solidPh
PhtBu
tBu
Ph
Ph
Ph
Ph
PhtBu
PhtBu tBu
tBuPh
PhPh
Ph
tBu
tBuPh
PhPh
Ph 1.407
1.540
1.414
1.471
1.401
1.413
Chem. Commun. 1999, 319.Eur. J. Org. Chem. 2000, 1377.
Table 1. Calculated (B3LYP/6-31G* and MP2/6-31G*) geometries and relative energies of the isomeres of 2.
R1
R2
R3
R4
Isomer
2a
2b
2c
2d
Level
MP2/6-31G*
MP2/6-31G*
B3LYP/6-31G*
B3LYP/6-31G*
R1 R2 R3 R4 ∆E/kcal mol-1
00
-3.7
0
-2.4
1.3943
1.3898
1.3944
1.3888 1.5461
1.4026
1.5545
1.4082 1.5361
1.3921
1.5430
1.3916
1.3456
1.4587
1.3456
1.4583
tBu
tBuPh
PhPh
Ph
1 2a 2b
2c 2d3
Br
Br
Ph2COH
C CH
PdII
CPh2
CPh2
OH
OH
SOCl2
C
C C C
C CPh
PhPh
Ph
Cl
Cl
∆Ph
Ph
PhPh
Cl
Cl
3) naphthocyclobutenes
Angew. Chem. Int. Ed. 1994, 1757.
C
C C C
C CPh
PhPh
Ph
Cl
ClC
C
CC
CC
Ph
Ph
Ph
Ph
Cl
Cl Me
MePh
Ph
PhPh
Cl
Cl
PhPh
PhPh
Cl
Cl Me
Mesolid
∆
180 ºC, 30 min
PhPh
PhPh
I
I
Cl
Cl
PhPh
PhPh Exptl. 1.720 Å
1.710 Å at 90 K
B3YLP/613G* 1.732 Å
B3YLP/613G* 1.731 Å
M. Kertesz 1997
P. v. R. Schleyer 1998
through bond interaction
B3YLP/dz(2d, p) 1.708 Å
J. S. Siegel 1998
(II) Phase transitions in crystals1) photodimerizatin of 2-pyridones
O
N
OP
O
O
HN
N
MeNH
Me
HO OH
O
O
O
O
O O
hν
O
OP
O
O
HN
N
NH
HO OH
O
O
O
O O
Me Me
12
3 456 O
H HN
NH
O12
3
4
56
thymine in DNA
HNNH
O
O
HN
HN
O
O
[4+4]
HNNH
O
O
HN NH
OO
HN
NH
HN
HNO O O
O
[2+2]
(3.4)
(5.6)
syn/anti
syn/anti
O
Cl
Cl
O
NN
O
O
NN
O
O
Cl
Cl
N
N O
ONN
[2+2]
complex complex
cis-anti dimer cis-anti dimer
COOHHOOC
NH
O
X hν
NH
HN
O
O
H X
HX
X=Cl, Me cis-anti dimer
O
O
O
O
N
N N
N
Cl
Cl
Cl
Cl
[4+4]
Chem. Commun., 2005, 643; Mendeleev Commun., 2004, 247; Heterocycles, 2004, 383.
NH
O
ClCOOH
COOH
HOOC
HOOC NH
NHCl
O
Cl
O4hν ∆
NH
NH
O O
Cl Cl
HH
meso-cis-syn dimer
MeOH hν
NH O
Me
NH
OMe
NH O
Me
NH
OMe
HN
OMe
NH
OMe
NH
NH
OMe
NH O
Me
NH
OMe
∆ or
MeOHsolvent
- MeOH
MeOHvapor
∆
grinding
hν
MeO
MeOHvapor
8 9 10
13 14
MeOHvapor
CH3CNvapor
COOH
HOOC COOH
NH O
Me
HN
HN
Me
O
Me
O
6meso-cis-syn dimer
HNNH
5
MeMe
O
Orac-trans-anti dimer
Scheme 1. Reversible phase transition between photochemically nonreactive and reactive complexes. For clarity host is omitted
A reversible phase transition between photochemically nonreactive and reactive complexes
O
O
O OH
HO
OH
OH
N
Me
HO
O
O OH
O
OH
OH
N
Me
HO
Me
OH Me
COOH
HOOC COOHNH
O
Me
MeOH··
8
Fig. X-ray structure of 8 (top view)
Fig. X-ray structure of the 1:1:1 complex of host:5-methyl-2-pyridone:MeOH (8).
MeOH
NH O
Me
NH
OMe
COOH
HOOC COOH
Fig. Packing diagram of 10.
Fig. Packing diagram of 10.
Fig. Distances between 5-methyl-2-pyridone molecules in 10.
2) succinamide
N
O
O
Me
Ph
Ph
Ph
PhMeOH
vapor
∆
Achiral
Brac
Crac
260 ºC
Achiral
B Crac rac
orange hexagonalsmp 260 ºC
orange plates302 ºC
yellow plates297 ºC
P21Pbcn P21/n
3) tetraphenyletheneBr
Br Br
Br
1
solvent vaporcomplex with
Br
Br Br
Br Br
Br Br
Br
P-1 M-1
and / or
rac or chiral
Table 1. Inclusion complexation of 1 with some guest compounds
Inclusion complex
By recrystallization By gas-solid reaction
host : guestGuest host : guest t/h
Acetone chiral 1 : 2 a a 168
Cyclohexanone rac 1 : 1 a a 168
rac 1 : 2
chiral 1 : 1
chiral 1 : 1
rac 1 : 1
chiral 1 : 1
rac 1 : 1
chiral 1 : 2
chiral 1 : 1
chiral 1 : 1a a
chiral 1 : 1
chiral 1 : 1
2
24
24
168
24
168
THF
1,4-Dioxane
Benzene
Toluene
p-Xylene
β-Picolinea No complexation occurred.
Chem. Comm. 2000, 413.
O
O
Ph2C
Ph2C
O
O
(R, R)-(-)-
CH3OH
H
H
O
O
Ph2C
Ph2C
O
O
(R, R)-(-)- H
H
NO Et
MeOMePh
(-)-
O
O
Ph2C
Ph2C
O
O
(R, R)-(-)- H
H
NO Et
MeOPhMe
(+)-
NO Et
HOPh
MeMe(+)-
76% ee
hν
4 h 5 h
4) oxoamide
Chem. Lett. 1995, 809.
OHOH
3aracemate
OHOH Me4NCl
conglomerate complex
Me4NCl
MeOH
(S)-(−)-BNO Me4NCl
5) BNO
OHOH
Me4N Cl
racemic complex conglomerate complex
3b Me4NCl + 3c Me4NCl3a Me4NClMeOHMeOH
3a7 ml 15 ml
1.43 g
0.55 g
OHOH
Me4N Cl
racemic complex conglomerate complex
3b Me4NCl + 3c Me4NCl3a Me4NClMeOH vaporsolid-state
3a
rac-
rt, 170 h rt, 1 h
phase transition
Tetrahedron. 2004, 7767; Chem. Comm. 2004, 1844.
racemate complex
OHOH Me4N Cl
or MeOH vaporconglomerate complex
30 min
160 C, 5 min
MeOH vapor
guest host : guest ratio[a] decomp. (°C)
Me2C=O
O
O
O
COMe
O O
1 : 1
1 : 1
1 : 1
1 : 2
1 : 2
1 : 2
70-98
79-107
87-117
94-121
97-141
87-128
νOH (cm-1) [b]
3036, 3404
3321, 3419
3264, 3417
3199
3198
3366
Table 1. Data of inclusion complexes of 3a with various liquid guests.
Et2O
OMe
THF
O O
3 : 1
1 : 2
1 : 2
2 : 3
2 : 3
Et2O
87-108
40-61
37-74
48-106
61-116
3419, 3459, 3489
3198
3198
3173, 3519
3248
AcOMe
AcOEt
3 : 1
3 : 1
83-108
75-105
3403, 3463, 3491
3413, 3464, 3490
(CPME)
complex
[a] The ratio was determined by 1H NMR spectra and TG analysis.[b] IR spectra were measured by using the ATR (Attenuated total reflection) method.
OHOHrac-
3a
(III) Seed crystals in the solid state
OHOH
3a (0.2 g)
3:1 complex (5) 1:2 complex (4)3 ml 5 ml
Et2O Et2O
4 mlEt2O
4 or 5
Scheme 1. Inclusion complexation of 3a and Et2O by recrystallization of 3a from Et2O solutions of different concentration.
rac-
can be controlled bya seed crystal
a b
c
Figure 1. Crystal structure of the 1:2 complexof 3a and Et2O (4).
Figure 2. Crystal structure of the 3:1 complexof 3a and Et2O (5).
(S)-(−)-form
(R)-(+)-form
Scheme 1. Memory of inclusion pattern.
OHOH
rac- · 2Et2O
4
-Et2O, ∆ / vacuo
Et2O vaporEt2O - free BNO
OHOH
rac- ·
5
-Et2O, ∆ / vacuo
Et2O vapor
Et2O - free BNO3 Et2O
3a
3a
3a
4, Et 2O
5, Et2 O
4
5
−Et2O
−Et2O
Et2O
3a
3a
Scheme 2. Seed crystal experiments in the inclusion complexationbetween solid host and gaseous Et2O guest.
Et2O
5, Et 2O
4, Et2 O
OHOHrac-
1 : 2
3 : 1
Angew. Chem. Int. Ed. 2005, in press.
guest (3a:guest ratio)in seed crystal
reactiontime (h)
guest (3a:guest ratio)in product
gaseousguest
AcOMe (3 : 1) Et2O 3
AcOEt (3 : 1) Et2O 3
AcOMe (3 : 1) CPME 12
CPME (1 : 2) Et2O 12
Et2O (3 : 1) CPME 12
AcOMe (3 : 1) AcOEt 3
AcOE t (3 : 1) AcOMe 3
Et2O (3 : 1) AcOMe 3
Et2O (1 : 2) CPME 12
Et2O (3 : 1)
Et2O (3 : 1)
Et2O (1 : 2)
AcOEt (3 : 1)
AcOMe (3 : 1)
AcOMe (3 : 1)
CPME (1 : 2)
Table . Inclusion complexation of powdered rac-BNO (3a) andgaseous guest in the presence of pseudo seed crystal.
