Professional Documents
Culture Documents
Introduction
In our preceding papers (Torii & Iitaka, 1970; Torii &
Iitaka, 1971) we showed that the crystal structures of
L-~-amino acids having hydrocarbon side chains are
characterized by hydrogen-bonded double layers of
molecules stacked in such a way that their terminal
groups of the side chains face each other. Crystal data
for L-methionine and L-norleucine indicated that these
crystals also contain hydrogen-bonded double layers.
However, the space group of L-norleucine is different
from that of L-methionine and it was expected that the
side chains of the L-methionine molecules are packed
in a manner resembling the O_L packing of the long
chain hydrocarbons while those of the L-norleucine
molecules are packed in a TI] type. We therefore undertook the crystal structure analyses of both crystals to
see how the side chains are folded and accommodated
in the particular packing of the crystal.
Experimental
The crystals of L-methionine, in the form of thin
elongated plates, were obtained by evaporation of
ethanol-water solutions at room temperature. L-Norleucine was crystallized as thin elongated plates from a
warm saturated aqueous solution by slow cooling. The
space groups were determined by the precession photographs and the densities of the crystals were measured
by the flotation method using benzene-carbon tetrachloride mixture. The crystal data are listed in Table 1.
The crystal of methionine used for collecting the
intensity data was about 0.15 x 0.60 x 0.04 mm in size
and that of norleucine was about 0-20 x 0.50 x 0.03 mm.
The lattice constants and the intensity data were measured on a Rigaku four-circle diffractometer using Nifiltered Cu Kc~ radiation. The intensities were measured
M.W.
a (A)
L-Methionine
C5Hll NO2S
149.2
9.498 (5)
L-Norleucine
C6HI3NO2
131.2
9-550 (5)
b
c
fl ()
Space group
Z
D~ (gcm -3)
Dm
5.189 (5)
15.318 (5)
97.69 (10)
P2z
4
1.325
1"316
5.260 (5)
15-377 (5)
95.60 (5)
c2
4
1-134
1"136
2800
L-METHIONINE
AND
L-NORLEUCINE
Table 2 (cont.)
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
~~
o ~ ~0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
H(l)a
H(2)a
x
y
0"340 (10) - 0 " 2 0 1 (22)
0"426 (10) - 0 " 2 7 8 (20)
z
0"490 (6)
0"429 (6)
B B o n d e d to
4 (2)
N(1)A
2 (2)
N(1)a
H(3)a
0"406 (6)
2 (2)
H(4)a
0"422 (14)
0"104 (34)
0"393 (8)
7 (4)
C(2)a
H(5)a
0.286 (7)
6 (3)
C(3)a
N(l)a
H(6)a
0"266 (8)
8 (3)
C(3)a
H(7)a
0"424 (17)
0"216 (34)
C(4)a
H(8)a
H(9)n
H(10)n
H(ll)n
0.304
0.893
0.968
0.805
0.362
0.395
0.389
0.272
0.223
0.462
0.387
0.392
(4)
(2)
(4)
(3)
C(4)a
N(1)n
N(l)n
N(l)n
H(12)n
0.907 (10)
0.788 (21)
0.362 (6)
3 (2)
C(2)~
H(13)n
0"708 (11)
0"433 (27)
0"258 (7)
7 (3)
C(3)n
H(14)n
0.886 (12)
0.408 (26)
0.230 (7)
8 (3)
C(3)~
(16)
(10)
(15)
(13)
(32)
(24)
(32)
(28)
(9)
(7)
(9)
(8)
10
6
12
7
0 0 0 0 0 0 0 0 0 0 0 ~ 0 0 0 ~
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
~+
i ~
when
Fo < 15-0
when 1 5 . 0 < F o < 2 6 . 0
when 2 6 " 0 < F o .
]/w=Fo/(1.3
x 15.0)
V w = 1/1.3
l / w = 1/[1"3+0.0351(Fo-26.0)]
O O O O O O O O O 0 - - O O O O - - - - - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
"~
~ooooooooooOOOOOOo
6 6 6 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0
0 0 0 0 o 0 0 0 o 0 0
-.
~,.~
,
o
,..o
~,
m r-- o o ~
o,, 0o ~ 00
....
"~" e,n e~
. .e~
. e~
. ."1 "-- " ~ ."7'
o666o~6~o66OOOOooO
~ '
' ;: ';
";*"I* '
: B
~:
"?' 2
& . % *'
.~.,.'.
.'.',
2..
j,0.
.,.!
,L ,,
.!.''~ +>; r r! !,; ~ !i~ ii ~:i :~ ~ i ! i*i ! J.:. i .i:.+! .L':I'~.!),ii .i,.~.,i "i"i"i
~,~ ,i !~i ~ i ~ i i ,~ ,~ i !~,,": .~:~,! .i,.~. ~ J,.~,i -i.i. i f'i i -i.,',! .! 5 ii 7~'i "i":,"i
! ~ ii i ,~ ,~ .!,Z,~ ! ~ i i :i :i .!5.~ "hi':i -i: i -i !., ! i i "i'
"f"."~ "~.'~'~ ~:! il "!""! .!,.;, ~ i~i ~ ! i ..! ~ -,.!, ! "i"',! .V, ~ ., :,~ !.,i "~*'0~
!1! i:~i ~ I ~ i ! i~i~ ~ , ! +,',~ i'i,i .:.':.~i .!.':,'i ! ! !
'!"~ .:':0i "-)';
r:,~ "~"<,: ~'~i:i i*i i .~,.:,i i*,i:~ i ~ ! .. !, i ' ~ ! ! ....i ...::,i '!'i .,.;,i
[-
II
+'*: :':~
r~',! f'! '~ ~:i :i .;..~ ~,i ~ r~;i ~!i i! i~i i !~i :~ .;:!,~i .i.!, ~i .:~,.,;:~ .!.!. i 2 ;,,i
OOOOOOOOOOOOOOOOOO
.!,. !. ~ "i",'~ ill i~ i~; q 7",i',i i'i 'i i',~ ',i .!..:, ~! ',~i 'i .!.. :. i +2. :i !:~ :i "fi ~ :!:~i',',;
!*~! ",:. . . . ,'.', i"! ~' .~,! . i! "i",:',~ !,!i :':'! . ! : i -'..~,~: :,~ :, .!.:: "ri";
KAZUO
TORII AND
YOICHI
IITAKA
2801
Table 4 (cont.)
H(1)s
H(2)N
H(3)N
H(4)N
H(5)N
H(6)N
0 0 0 0 0 0 0 ~
0 0 0 0 0 0 0 0 0
o66od6666
III
0 0 0 0 0 0 0 ~
0 0 0 0 0 0 0 0 0
oo6o66666
',1
,-+
"-
y.
- 0 - 1 9 5 (10)
--0"307 (16)
--0.347 (16)
0"117 (14)
--0"155 (26)
--0"143 (11)
z
0-487
0-410
0.389
0"388
0"256
0"250
B Bonded to
(3) 4 (1)
N(1)N
(4) 8 (2)
N(1)s
(4) 6 (2)
N(1)N
(4) 4 (1)
C(2)N
(7) 13 (3)
C(3)N
(4) 4 (1)
C(3)r
2~
~' 1
x
0-621 (5)
0"719 (8)
0.580 (7)
0"687 (7)
0"680 (12)
0"532 (6)
..
b-,
OOZ~UUuUU
Molecular structures
Figs. 1 and 2 show the conformations of the L-methionine and L-norleucine molecules respectively. These
and Figs. 5 and 6 were drawn by the plotter program
ORTEP (Johnson, 1965). The bond lengths and angles
of the methionine and norleucine molecules are listed
in Tables 6 and 7 respectively. In these Tables the
corrected bond lengths for thermal motion by the program ORFFE (Busing, Martin & Levy, 1964) are also
given. The methionine crystal involves two independent
molecules, A and B. Except for the C~-S ~ and So-C ~
bonds, differences of the corresponding bond lengths
in A and B are smaller than 0"860"diff .. ( p = 0.39), where
O'diff" is the sum of the squares of the standard deviations of the corresponding bond lengths in A and B. It
seems that they are not significant. In the cases of
2802
L-METHIONINE
AND
L-NORLEUCINE
factors of L-norleucine
molecules*
O(1)-C(l)
I
:
:
i,.i!, ii .~,.~.:,i i":i" :i :i::,i: ! .:;,.'i,'! .!,.'i '! 91"i "i"i' 'i .!5.'i .!,. ~. i i-',;',i i" ;' 'i i'" i' 'i :';::: :i O(2)-C(1)
,.",. ;, i .!:.".'! "i'"i',~ ! ~ ! "V :' ! .!,. :, i .~,.,:," "f':,',i ~ i i ~ i 'i -~.',:, ,i ::.: :! :i::,~: !i :!:: i: :~
C(1)-C(2)
C(2)-C(3)
.,. ,l
. . ', ;
~ " ':
.t. t : .'.. ;, : .t. '
";",,' J
t I . . ',
: ; t .! .". ';
....
'~ 2, '
:
C(3)-C(4)
," i ! .(.':,'~ .i," :. ! f q ,: +' :' : .!.. :. ! ";"-": -;. :, ~ ! ! i " :' t -i :' ! i" ,', .[.. ',i -;': !
"i":"! i'i 'i .!,.:,! "i,.f,! "i":'; +.:, ; -i,.1,i .!..'. ~ "i',:',i .;,.:. .;,,:. i ZiY,! -',.:,,i :!::r::i C(4)-C(5)
:i::::::i "i":~':]-~;,.~,:J"i",i',] [[)!i'i :i::i:i-i,.'i.i-':.'i,'i i![:'. i -i,.i, i i![.il,i .!,.!,,! :i::i::! "i"i"] C(5)-C(6)
:,: ,: ":'.'; ::: ',~ ";.',:,: :': " .'...:,: .:..'. ; :: : : : : "r'.', .'.,.,,,: ~:: ";";": ";.':': C(2)-N(I)
. ,
"i",,' .'
, ,
";",;' ,I
,,,1
; 't
, ,
";'":'
,
'
, ,
";'" ,' ;
. . .
.:,. ", :
, ,
; '; '!
,,,:
: ;
,,,,
2,. t
,,,
......
1.
.:,. t, t
~ ' I
,,.1,
";'" ,' ';
, , ,
2,. :, ,I
, , ,
";" ,' 'I
:,.-;, ~ -.',.', ~ -:,.'. ! ~:; ~: "i":" i .i,.,!,.i .i,.i. ! +.:, i .:..!, i .i,.+ i "i",,i'il -i,.:.,i "f'f'! :!::~::i
"i",i' .i -',,.';..'i .!,.:!, :i "i",':' :i +.:? .i .!,. !. i 7" i' ! :!:.-!: i -'::. i. ] 2: i: ~ "i" ~' '! .!,. :, .i +. :, .! +. :, 'i
O(1)-C(1)-O(2)
O(1)-C(I
)-C(2)
O(2)-C(1)-C(2)
C(1)-C(2)-N(i)
.:,, t, I
....
.'.,, ?, |
,
";'" .' ;
,
......
";",,'
....
,~
,.
', ;
,,.,,
,;
";",
,
.:,. t, :
,
.:,. :, :
.'.,. ', d
",","t
L-Norleucine
1-247 (5)/~
1.240 (7)
1.541 (7)
1.487 (9)
1"546 (14)
1.426 (18)
1.552 (26)
1.481 (8)
125-0
116.9
118"0
108"6
112"8
110.4
112"2
113"8
109"9
C(1)-C(2)-C(3)
N(1)-C(2)-C(3)
C(2)-C(3)-C(4)
C(3)-C(4)-C(5)
C(4)-C(5)-C(6)
State of
about
about
about
rotation
C(2)-C(3)
C(3)-C(4)
C(4)-C(5)
corr.t
1.513/~
1-596
1.479
1.584
DL-Norleucine
1-20 (4)/~,
1"26
1.49
1.58
1.51
1.57
1.48
1.50
(0.5)
(0.4)
(0"5)
(0"4)
(0"5)
(0-5)
(0"7)
(1"0)
(1"3)
122 (5)
118
120
109
112
110
114
110
120
Reference
N(1)
C(1)
trans
trans
trans
n'ans
(1)
(2)
1.254 (13)
1.230 (18)
1.547 (15)
1-525 (17)
1"511 (22)
1-832 (15)
1-805 (27)
1"485 (I 8)
O(1)-C(1)-O(2)
O(1)-C(1)-C(2)
O(2)-C(1)-C(2)
C(1)-C(2)-N(I)
C(1)-C(2)-C(3)
N(1)-C(2)-C(3)
125.7
116.7
117.6
109.3
112.3
110"8
C(2)-C(3)-C(4)
111.1 (1.1)
C(3)-C(4)-S(1)
C(4)-S(1)-C(5)
107.3 (1-0)
99.8 (1.0)
State of
about
about
about
rotation
C(2)-C(3)
C(3)-C(4)
C(4)-S(1)
L-Methionine
corr.1"
(B)
1"268 (16)
1.246 (18)
1.528 (16)
1.536
1.531 (19)
1"535
1.511 (34)
1.863
1.792 (26)
1.810
1-718 (31)
1"467 (19)
(1.1)
(i-0)
(1.0)
(0-9)
(1-0)
(l'0)
124-3
116.7
118.8
110.0
110.7
107.4
117-8
113.4
101.8
corrA"
1.561
1.546
1-798
1.758
(1.2)
(1.1)
(1.1)
(1.0)
(1.1)
(l-l)
(I.5)
(1.7)
(1.4)
DL-Methionine
(~t)
(fl)
1-21 (4) 1.21 (4)
1.28
1.27
1.47
1.52
1.55
1.58
1.51
1.54
1-79
1.80
1.77
1.78
1.52
1.50
Dichloro-DLmethioninepalladium
1.205 (21)
1.295 (23)
1-536 (22)
1-506 (23)
1.493 (22)
1-827 (16)
1.800 (21)
1.472 (23)
121
119
120
112
111
110
111
111
100
123.77
113.22
123-00
107.96
107.89
111.94
113.68
117.04
100-14
122
120
118
110
108
109
113
109
100
(1-69)
(1.52)
(1.74)
(1-35)
(1.30)
(1-48)
(1.38)
(1.25)
(0.94)
N(1)
N(1)
C(1)
C(1)
C(1)
trans
trans
gauche
gauche
trans
gauche
trans
trans
gauche
gauche
(1)
(1)
(2)
(2)
(3)
Reference
* Standard deviations are shown in parentheses denoting the least significant digits of the corresponding values.
1" See footnote in Table 7.
References:
(1) Present work.
(2) Mathieson (1952).
(3) Warren, McConnell & Stephenson (1970).
KAZUO
TORII
AND
_o0),4
C(1)A
O(2)A ~
r-x
T
S(1)A
= ~ ~ ~ ~ ~ ~
C(5)A ~
~"
N(1)A
C(4)B
)
0(2)B
~
c(1)B
YOICHI
IITAKA
2803
(II)
C(2)A
0"045 A
C(3)a - 0 " 0 3 9
C(4),4 - 0 " 0 4 3
S(1)A
0"031
C(5)a
0.007
L-Norleucine
(IV)
O(1)s - 0 " 0 0 6 A
O(2)N - 0 " 0 0 6
C(1)N
0"016
C(2)N
-- 0"004
N(1)~
0.569
(V)
C(3)N
0"054 A
C(4)N --0"059
C(5)N --0"048
C(6)N
0"052
C(2)~
0.361
(III)
O(l)n --0"009 ,~,
O(2)n - 0 " 0 1 0
C(I)B
0"026
C(2)n - 0"007
N(1);
0.709
(I)
(II)
(III)
(IV)
(V)
0-3955
0.9927
0"5428
0.3730
0"9691
X + 0"3003
X - 0"0360
X+0"0841
X+0.1679
X-0"0296
Y+ 0"8680
Y+ 0"1152
Y+0.8357
Y+0.9125
Y+0.2431
Z = 5"8962
Z = 3.7270
Z=8.1419
Z=6.8135
Z=6.4564
C(5)B ~ ~
and norleucine
N(1)B
(1)N
O(2)N~
C(1)N
~ //---7
C(5)N
L-Methionine
molecule A
- 1 7 . 5 194.0 174.2
molecule B
- 34.3
194.4
73.6
~t-oL-Methionine --33.7
299.9
176.9
fl-oL-Methionine --29-4
299.0
183.6
179-7
73.6
80-5
190.4
Reference*
(1)
(l)
(2)
(2)
L-Norleucine
DL-Norleucine
188"6
195.2
(1)
(3)
--25"9
-- 35.3
194"2
303-1
166"5
182.2
or
or
~'[C(2)-C(3)-C(4)-C(5)]
r[C(3)-C(4)-C(5)-C(6)]
C(6)/~
C(--~ja,/N~
C(2)N
N(1)N
2804
L-METHIONINE
AND
bond, very short contacts of about 3.2/~, would be observed between the carbon and sulphur atoms ot
neighbouring side chains as far as the shape and dimensions of the lattice are not changed.
The conformation of L-norleucine is very similar to
that of molecule A of methionine.
Hydrogen bonds
Table 10 shows the values of short intermolecular
/ O(2)A[I(0]O)]
2"85A/"~,,."-,,~"-.,.,
...............
"- j
,...O0)B[ll(010)]/] I
3 ~
~H(I~ ~
L-NORLEUCINE
'
~,,2"'78A . . . .
2"86~"5~/"
~H(9)B
\'...
,,y"
(a)
]
//
(b)
'7 2
()
Fig. 3. Stereographic projection showing the arrangement of oxygen and hydrogen atoms around the nitrogen atom. Notation
of the symmetry operations is shown in Table 10. Direction of the C-N bond is taken as the polar axis.
KAZUO
TORII
AND
.-:;.~-"
:~. :~.
YOICHI
IITAKA
2805
[II(000)]
[ I(010)]
[ I(100)]
[ I(100)]
2"782 (13)
2"859 (16)
2"867 (1 l)
2"981 (12)
II
1 -x
+y
1 -z
where the values of x, y and z are given in Table 2.
L-Norleucine
N(1)N--O(1)N [III(000)]
N(I)N--O(2)N [ I(OTO)]
N(1)N-O(1)u [ II(0T0)]
N(1)N--O(2)N [ II(0T0)]
98.1 (3)
2"792 (6) A
2.799 (6)
2"813 (5)
3"231 (5)
l ! 8.0 (3)
121.2 (3)
81.9 (3)
1I
+x
+y
Z
III
1 -x
y
1--g
1--Z
IV
1-x
+y
where the values of x, y and z are given in Table 4.
of each atom can be seen in Figs. 1 and 2. The orientation of each principal axis of thermal ellipsoid and the
root-mean-square (r.m.s.) displacement along each
axis are given in Table 12. Within the hydrogen-bonded
layers, the amplitude of each atom in the direction
normal to the layer is larger than those in other direcTable 11. lntermolecular short contacts less than
4.2 A between side-chain carbon atoms
L-Methionine
Within single layer:
C(5)A--C(4)8 [I(000)] 4"16 (3) /~
C(4)A-C(3)A [I(010)] 4"01 (2)
C(5)A--S(1)A [I(010)] 3"65 (3)
C(4)B--S(1)A [I(010)] 4"03 (2)
S(1)n-C(3)B [I(010)] 3"91 (2)
S(1)n-C(5)n [I(010)] 4"16(3)
C(5)B--C(5)A [I(100)] 4"16(4)
S(1)B-C(3)a [1(110)] 4"10(1)
Between double layers:
C(5)A--C(5)A [II(00]')]
C(5)A--S(I)A [II(00]')]
C(4)B--C(5)A [II(00T)]
C(5)B-C(5)B [II(10T)]
L-Norleucine
Within single layer:
C(4)N--C(3)N [I(010)]
C(6)N-C(3)N [I(010)]
C(6)N-C(5)N [I(010)]
108"3 (7)
115"1 (8)
103"8 (7)
146"3 (8)
3"98 (4)
3"83 (3)
4"09 (3)
4"07 (4)
4"06(2)
4"15(2)
3"99 (2)
2806
L-METHIONINE
AND
L-NORLEUCINE
T a b l e 12
T a b l e 12.
Principal
axes (j)
L-Methionine
O(1)a
1
2
3
O(2)a
1
2
3
N(1)a
1
2
3
C(1)A
1
2
3
C(2)A
1
2
3
C(3)a
1
2
3
C(4)a
1
2
3
S(1)a
1
2
3
C(5)a
1
2
3
O(1)8
1
2
3
0(2)8
1
2
3
N(1)n
1
2
3
C(1)n
1
2
3
C(2)n
1
2
3
C(3)8
1
2
3
U(j)
102
11
20
27
13
20
25
14
18
24
9
19
21
13
15
24
12
21
29
12
18
37
21
26
46
21
36
52
13
17
29
14
17
34
9
21
24
2
21
24
12
19 A
23
16
30
34
cos ~1
0"982
-0.040
0"185
0.842
-0"472
0"261
-0"432
-0"893
-0"124
0.466
-0-843
0"270
-0"030
0"999
0"035
-0"310
-0"246
0"918
0"241
0"117
-0-963
0.444
0"088
-0.892
-0-298
-0"196
0"934
0.876
-0-407
0"259
0.549
0.831
0"091
-0.731
0-567
-0.379
0"737
-0.185
0.650
-0.864
-0.267
0.427
-0.220
0.932
0"289
cos ~2j
0"032
0.998
0.047
-0-521
-0.837
0.167
0"829
-0"340
-0"443
-0.885
-0-451
0.117
0.991
0"025
0-133
0.582
-0-813
-0.021
0"174
-0"982
-0.076
0.028
-0"996
-0.084
-0"554
0"832
-0"002
-0-453
-0-878
0.153
-0"835
0.543
0"089
0.681
0"647
-0.344
-0.570
0"347
0.745
0.168
-0.952
-0.256
-0"669
-0"360
0"650
cos ~3j
-0"187
-0'040
0"982
-0.140
0"277
0.951
-0-354
0"294
-0.888
0.023
-0.294
-0.956
-0.132
-0"039
0"990
0"751
0"528
0"395
-0"955
-0"149
-0'257
-0.896
0"012
-0.445
0"777
0"519
0"356
-0"165
0.252
0.954
0"024
-0"125
0"992
0"050
-0"510
0.859
0"363
0"919
-0"150
-0.475
0.150
-0"867
0"709
-0"050
0"703
C(5),
S(I)B
Principal
axes (j)
1
2
3
1
2
3
1
2
3
L-Norleucine
O(1)N
1
2
3
O(2)N
1
2
3
N(1)N
1
2
3
C(1)N
1
2
3
C(2)N
1
2
3
C(3)N
1
2
3
C(4)N
1
2
3
C(5)N
1
2
3
C(6)N
1
2
3
(cont.)
U(j) x
102
28 A
38
45
26
31
49
26
36
43
cos ~ j
0-830
-0-023
-0.557
- 0.437
- 0.561
0.704
0.512
0.368
- 0.776
cos ~2j
-0.308
0-814
-0.492
0.764
-0.645
-0.040
0.653
-0.754
0-074
cos ~3j
-0.464
-0-580
-0"669
0.476
0.520
0.710
- 0.558
-0.544
-0.626
15
21
29
19
21
36
14
22
28
16
20
27
16
22
28
22
29
32
27
35
46
30
37
60
28
45
64
--0.969
--0-178
0.170
-- 0-499
--0.866
0.042
0"849
--0-528
0"028
0.928
-0.371
0.019
0.978
--0.192
--0.079
-- 0"806
-- 0"007
0"592
0"337
--0"469
0"816
--0-431
-- 0"409
-0"804
0"371
--0"244
0-896
0.199
--0.973
0.117
0.866
--0.496
0.068
--0"520
--0"825
0"220
-0.372
-0.927
0.042
--0.184
--0.979
0.089
0"458
-- 0"640
0"617
0"287
0"877
0"386
--0"384
0"890
--0"247
0-482
0"875
0"039
0.145
0.147
0-978
-- 0.038
0-070
0-997
--0-093
--0-201
-- 0"975
0.003
-0.050
-0.999
--0.094
--0-072
--0.993
0-374
0"768
0"519
-- 0"897
0"105
0"430
0-817
0"202
--0"540
--0"794
0"418
0-442
Fig. 5. Stereoscopic drawing of the crystal structure of L-methionine viewed along the c* axis.
The atoms are represented by 50 % probability ellipsoids.
2807
References