A C T A U N I V E R S I T A T I S L O D Z I E N S I S _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ FOLIA C H I M ICA B, 19B8
A n d r zej M. Br zo zow sk i* , Tomasz A. Olszak*, An dr z e j Stępień*, M i e c z y s ł a w J. Gr ab ows ki *, Tadeusz Wasiak**, W i to ld K o z i o ł k i e w i c z * *
S i l v ain L e c o c q * * *
THE M O L E CUL AR AND CRYSTAL S T R U C T U R E OF B E N Z Y L 0 X Y C A R 8 0 N Y L - - L , D - P H E N Y L A L A N Y L - ( a , ft d e h y d r o ) P H E N Y L A L A N I N Ę (1)****
C 2 6 H 2 4 N 2 ° 5 ’ M = 444.49, triclinic, P i , a = 6. 42 9(4)A, b = 13 . 225(9) A , c = 14.126(13)A, a = 104.68( 7) °, ft* 94 .4 4(7)°, <T = <>6.49(5)°, V = 1147(2) A 3 , Z = 2, D = 1.287 g e m - 3 , p =
-1
= 6.50 cm . D i f f r a c t o m e t e r data, room tempera tu re , A(CuKoc) = = 1.54178 A, F(000) = 468, R = 0.04 59 for 3715 r e f l e c t i o n s with I > 3 ar ( I ) , max A / O’ < 1.421 for both p o s i t i o n a l and thermal p a r a m e t e r s .
The m o l e c u l e has an e x te nde d co nf orm at io n: the angl es 0 for L-Phe are -89.5(2)°, 114. 1(1)° respect iv el y; the pe pt i d e bond exists in a trans form : (J = -179.8(1)°. The -^1 value = = 3.4(3)° for (a, ft - d e h y d r o ) P h e in di cates a cis c o n f o r m a t i o n of this amino acid wi th re sp ect to the pe pt i d e bond.
In t r o d u c t i o n
The title c o m p o u n d (1) was o b t a ine d by W a s i a k , K o z i o ł k i e w i c z (1983) [l] , as an i n t e r m e d i a t e to s y n t h e s i s of the an al ogs of the n e u r o p e p t i d e S u b s t a n c e P. The pr es ent st r u c t u r a l
De p a r t m e n t of C r y s t a l l o g r a p h y , I n s t i t u t e of Ch em istry, U n i v e r s i t y of Łódź.
** De p a r t m e n t of Ch em istry, In st itu te of B i o c h e m i s t r y and
Physiol og y, Ac ad emy of Medicine, Łódź.
* " * L a b o r a t o i r e de M i n é r a l o g i e - C r i s t a l l o g r a p h i e , as so c i é au CNRS, UA 805, U n i v e r s i t é Clau de Bernard, Lyon I, France.
**"* This work was s u p p ort ed by the pr oj e c t R.P.2.10. from the Poli sh M i ni str y of Science, T e c h nol og y and H i gh er Education.
w ork on [lj has been u n d e r t a k e n to d e t e r m i n e the s t r u c t u r e of (a, (î-dehydro)phenylalanine (APhe) and the s t r u c t u r e of d i p e p t i d e of this am ino acid with its n a t u r a l pr ec urs or .
E x p e r i m e n t a l
C o l o u rl es s, n e e d l e - s h a p e d c r y s t a l s were o b t a i n e d fr om ethanol. Cell p a r a m e t e r s and i n t e nsi ty data m e a s u r e d on Enraf N o ni us CAO-4 d i f f r a c t o m e t e r . O r i e n t a t i o n m a t r i x from 25 c a r e f u l l y c e n t e r e d r e f l e x i o n s with 8-range: 10°-56.4°; g r a p h i t e m o n o c h r o m a t i z e d CuKoc,
u / 2 6 scan; the range of h, k and 1: -7 to 7, -16 to 16, -17 to 17
r e s p e c t i v e l y ; t o t a l 4760 r e f l e x i o n s m e a s u r e d to s i n 8 / x = 0.63,data not c o r r e c t e d for a b s o r p t i o n (controls: o r i e n t a t i o n m a t r i x and i n t e n s ity 4l2 (tf(Icontrol)/Icontrol » 0.015). 3714 r e f l e x i o n s wi th I >3o'(I) used in re fi nem en t. S t r u c t u r e s o lv ed by d i re ct m e t h o d s * S H E L X 76 [2] and re fi n e d on F by f u l l - m a t r i x l e a s t - s q u a r e s ; atom ic s c a t t e r i n g fa ct ors f r o m # S H E L X 7 6 [2]. Af ter initial a n i s o t r o p i c r e f i n e m e n t a d i f f e r e n c e Fo ur i e r s y n t h e s i s at R = 0.084 r e v e a l e d p o s i tions of all h y d r o g e n atoms. In s u b s e q u e n t c y cl es of r e f i n e m e n t H atoms al lo w e d to refi ne i s o t r o p i c a l l y ; max and min A p in final d i f fere nt map are 0.17 and - 0.18 e A ” "5 r e s p e ct iv el y. Final R = 0.0459, S = 0. 4 b 4 , unit we ights. To rs i o n angl es were c a l c u l a t e d by # F F E 3 [3] .
D i s c u s s i o n
It is d i f f i c u l t to c l a s s i f y the c o n f o r m a t i o n of the b a c k b o n e of b e n z y l o x y c a r b o n y 1 - L ,D - P h e - A P h e due to only one p r op er p e p t i d e bond in the mo lecule. However, the t o r s i o n a n gl es 0 for L-Phe: -89.5(2), 11 4 . 1 ( 1 ) ° lie on the (f R a m a c h a n d r a n diagram [4] w i t h i n an al lo w e ; re gi on for /^-structure, i n d i c a t i n g rath er e x t e n d e d c o n f o r m a t i o n of the b a c k b o n e arou nd Ca(C9) of this amin o acid. These v a lu es can b ; co mp ared, for example, wi th th ose of the a n gl es for Phe in Gly-l - -Phe-Gly: -119°, 113° [5] or in N - ( H a l o a c e t y l ) - L - P h e - l - P h e - e t h y l esters: - 1 0 2 ° ( - 10 0) °, 1 0 6 ° ( 1 1 0 ) ° [6j .
The atoms fo rm ing the pe pt ide bond (C9, C7, N6, C2) are in a trans c o n f i g u ra ti on, the torsion angle u about this bond b e i n g -179.8( 1) °. The m e n t i o n e d pe pt ide gr oup and 08 and H106 atom s from this p e p t i d e bond are co-planar, the max. d i s t a n c e from the best p l an e th ro ugh these atoms is 0.02(3) A. The am ide bond b e t w e e n ben- z y l o x y c a r b o n y l - and - Phe exists in a trans co nf i g u r a t i o n : to rs ion an gle C 9 - N 1 1 - C 1 2 - 0 1 4 = 171.5(1)°. The X 1 , -><2 angl es (N 11 - C 9 - C 1 0 - - C 3 0 , C 9 - C 1 0 - C 3 0 - C 3 1 ) for L- Phe are - 1 7 7 . 7 ( 2 ) ° , 7 9 . 7 ( 3 ) ° ; it m e an s that C30(Cj-) at om is in - a p ( tra ns ) p o s i t i o n to Nll(N) atom, and
C4 4
Fig. 1. The atom n u m b e r i n g sche me
C31(C<51) is in +sc(+g) c o n f o r m a t i o n wi th re sp e c t to C9(Ca) atom. This c o n f o r m a t i o n of the L-Phe side chain, p r e d o m i n a n t in s o l u t i o n
[7], was found, among others, in 31% of ca ses for Phe, Trp, Tyr in 19 a n a l y z e d p r o t e i n structures: -^1,-^2 = 18 4° ,76 ° (the data are a v e r a g e d for Phe, Trp, Tyr) [8]. The y2 = 7 9 (3 )° valu e indicates, that the phenyl ring of Phe is trying to a c h i e v e p e r p e n d i c u l a r a r r a n g e m e n t to C9(Ca)-C10(C/i)-C30(Cj') plane, r e s u l t i n g in m i n i m u m s t er ic h i n d r a n c e b e t w e e n the a. - and 6 - c a rb on atoms.
In APhe: -^1, -^2 = 3 . 4 ( 3 ) 0 , - 1 6 4 . 2 ( 2 ) ° . The value, in d i c a t i n g a +s p( cis ) p o s i t i o n of 040(0,}-) atom, is not su pr isi ng , c o n t r a r y to y2, whos e value is rather rare in p e p t i d e s and p r o t e i n s [a]. Several s y s t e m s of 3T c o n j u g a t e d bo nds in A P h e c a us e s h o r t e n i n g of the s i n g l e bonds in this a m in o acid (see Table 2).
Fig. 2. A p r o j e c t i o n of the s t r u c t u r e al ong the x axis. D o tt ed lines i n d i cat e h y d r o g e n bonds
Each m o l e c u l e of (1) p a r t i c i p a t e s in three h y d r o g e n bonds. The 04 and H1 05 (05 ) atoms from the free c a r b oxy l t e rm ina l g r ou p of one m o l e c u l e are i n t e r a c t i n g w i th the H 1 0 6 (N6 ) and 013 atom s fr om a n e i g h b o u r i n g molecule: 0 1 3 . . H 1 0 5 = 1.78(3) A, 0 1 3 . . H 1 0 5 - 0 5 = 167(3)°, 0 . 4 . . H 1 0 6 = 2.25(2) A, 0 4 . . H 1 0 6 - N 6 = 162(2)°. Two m o l e c u l e s r e l a ted by a c e nt re of i n v e r s i o n form a h y d r o g e n bo nd b e t w e e n H l l l ( N l l ) and 08 wi th a d i s t a n c e of H i l l . . 08 = 2.12 A and an an gle 0 8 . . H 1 1 1 - N 1 1 = = 165(2)°.
The Tables (1-4) in 11> i 3 pa per are for m o l e c u l e with L - i s o m e r of p h en yla la ni ne.
T a b l e 1
Final fr ac tio na l co o r d i n a t e s ( x l O A ) and is ot r o p i c te m p e r a t u r e f actors (xlO^) wi th e . s . d . ’s in_ p a r e n t h e s e s
Atoms X y z % 1 2 3 4 5 Nil 2993(3) 5719(1) 833(1) 417( 7) N6 4952(2) 4789(1) 2671(1) 4 0 0( 7) 08 6255(2) 4435(1) 1200(1) 478( 7) 013 2185(2) 6920(1) 2174(1) 540( 7) 014 3474(2) 7406(1) 893(1) 518( 7) 04 10533(2) 5054(1) 3304(1) 606( 8) 05 8588(2) 6103(1) 2725(1) 551( 7) C9 2681(3) 4799(1) 1212(1) 397( 8) C7 4795(3) 4657(1) 1692(1 ) 382( 7) Cl 6888(3) 4149(2) 3899(1) 471( 9) Cl 5 3351(4) 8494(2) 1375(2) 604(12) C2 6818(3) 4687(2) 3223(1) 4 16( 8) C12 2831(3) 6688(1) 1367(1) 419( 8) * CIO 1816(4) 3816(2) 382(2) 487(10) C3 8828(3) 5287(2) 3083(1) 455( 9) C20 5114(4) 8966(2) 2186(2) 577(11) C21 4903(6) 9880(2) 2870(3) 917(18) C22 6558(9) 10353(3) 3614(3) 1191(24) C2'3 8354(7) 9901(3) 3663(3) 1057(22) C24 8569(5) 8990(3) 2991(2) 819(16) C25 6960(4) 8527(2) 2246(2) 667(13) C30 1373(3) 2838(1) 736(2) 476( 9) C31 -461(4) 2652(2) 1163(2) 608(12) C32 -886(5) 1737(2) 1465(2) 753(15) C33 505(5) 1012(2) 1354(3) 859(17) C34 2352(5) 1207(2) 961(3) 934(18) C35 2779(4) 2109(2) 652(2) 695(14) C40 5226(3) 3502(2) 4225(2) 464( 9)
Ta ble 1 (contd) 1 2 3 4 5 C41 5686(4) 3256(2) 5114(2) 559(10) C42 4201(5) 2679(2) 5494(2) 68 7( 13) C43 2242(5) 2338(2) 4493(2) 741(14) C44 1754(4) 2542(2) 4103(2) 741(14) C45 3232(4) 3119(2) 3713(2) 623(12) H109 1703(30) 4939 (15 ) 1709(14) 442( 53) HI 15 3390(35) 88 29(18) 801(17) 682( 70) H101 8268(34) 4196(16) 42 24(16) 561( 64) H2J.0 2829(38) 3705(18) -1 22(18) 6B2( 73) H215 1981(39) 85 75(19) 1613(18) 741( 77) HI 11 3439(35) 5681(18) 308(17) 537( 70 ) HI 10 538(36) 39 66(17) 64(16) 600( 65) H106 3912(37) 49 37(18) 2959(17) 609( 73) H145 2799(37) 3267(18) 3071(18) 695( 74) H144 361(45) 22 70(22) 37 04(20) 902( 92) H 141 6955(39) 3490(19) 54 76(18) 695( 79) H-l 31 -1 480(39) 3169(20) 1235(18) 751( 78) H143 1345(45) 1877(23) 52 21(21) 901( 97) H125 7087(44) 7825(23) 1701(21) 1001( 95) H133 230(43) 363(23) 1542(20) 949( 91) H142 4654(44) 2513(22) 6 0 B 0 ( 21) 902( 95) HI 34 3390(57) 613(29) 779(26) 14 31 (13 4) HI 22 6093(61) 10993(32) 41 11(30) 15 73 (152) H 135 41 20(50) 2252(25) 341(23) 12 14 (11 5) HI 2 3 94 54(55) 10219(27) 42 00(26) 1243(123) H10 5 99 61(57) 63 13(28) 25 79(26) 13 69 (138) HI 32 -2 074(44) 1632(22) 1735(20) 830( 95) H121 3529(55) 10181(27) . 29 07 (26 ) 12 42 (139) HI 24 99 88(56) 86 69(27) 3122(26) 12 99 (13 5)
Bond lengths [a] Cl C40 1.467(3) Cl C2 1.329(3) C2 C3 1 .492(3) C2 N6 1.418(2) C3 04 1 .211(2) C3 05 1.320(2) C7 C9 1 .524(2) C7 N6 1.343(2) C7 08 1.229(2) C9 El 0 1.529(3) C9 Nil 1.450(2) CIO C 30 1.507(3) C 12 Nil 1.332(2) C12 0.13 1.222(2) C12 014 1.340(2) Cl 5 014 1.441(2) C15 C20 1.504(3) C20 C 21 1.371(3) C20 C25 1.385(3) C21 C22 1.404(5) C22 C23 1.364(6) C23 C24 1.359(5) C24 C25 1.383(4) C 30 C31 1.391(3) C30 C35 1.384(3) C31 C3? 1.387(4) C32 C33 1.373(4) C33 C 34 I .375(5) C34 C35 .1. 377(4) C40 C41 1.394(3) C40 C45 1 . 395(3) C41 C 4 2 1.380(4) C42 C43 1 .364(4) C43 C44 1.372(4) C44 C45 1.386(4)
... ....
' 1 T a b l e 3 Bond angl es [°] C2 Cl C40 131.3(2) C3 C2 Cl 117 6(2) C3 C2 N6 117.6(2) Cl C2 N6 124 7(2) C2 C3 04 122.2(2) C2 C3 05 114 5(2) 04 C3 05 123.3(2) C9 C7 N6 116 2(2) C9 C7 08 121.1(2) N6 C7 08 122 8(2) C7 C9 CIO 110.0(2) C7 C9 Nil 108 2(1)CIO C9 Nil 110.6(2) C9 CIO C 30 113 1(2)
Nil C 12 013 126.4(2) Nil Cl 2 014 110 5(2)
013 C 12 01 4 123.1(2) 014 C 15 C20 112 6(2)
C7 N6 C2 122.8(2) C9 Nil Cl 2 122 8(2)
Cl 2 014 C 15 116.9(2) Cl 5 C20 C21 118 5 ( ¿ )
Ta ble 3 (contd) C20 C 21 C22 119 5(3) C 21 C22 C23 ' 120 3(3) C22 C23 C24 120 5(3) C23 C24 C25 119 6(3) C24 C25 C20 121 0(2) CIO C30 C 31 120 5(2) CIO C30 C35 121 1(2) C31 C30 C 3 5 118 4(2) o o C 31 C32 120 2(2) C 31 C32 C33 120 5(3) C32 C33 C34 119 6(3) C33 C34 C35 120 3(3) C34 C35 C30 120 9(3) Cl C40 C 41 117 2(2) Cl C40 C45 124 9(2) C41 C40 C45 1 17 9(2) C40 C 41 C42 121 3(2) C41 C4 2 C43 119 7(2) C42 C43 C44 120 6(3) C4 3 C44 C45 120 2(2) C44 C45 C40 120 3(2) T a b l e 4 To rs i o n angl es [°] Atoms Angle 1 2 C22 * C21 C20 Cl 5 -1 77 .9( 3) C24 C25 C20 C15 L70 .8(3) C 21 C20 C 15 014 -1 62 .8( 3) C25 C20 Cl 5 014 19.2(4) C20 Cl 5 014 Cl 2 77.7(3) Cl 5 014 C 12 Nil 178.9(2) C 15 014 C12 013 -0.8(3) 014 C12 Nil C9 17 1.5(1) Cl 2 Nil C9 CIO 14 9. 9(2 ) C 12 Nil C9 C7 -8 5.5(2) 013 C12 Nil C9 - 8.9(3) Nil C9 CIO C30 -1 77 .7( 2) Nil C9 C7 N6 114.1(1) Nil C9 C7 08 -6 5. 9(2 ) C9 CIO C30 C31 79.7(2) C9 CIO C30 C35 -9 9. 8(3 ) C9 C7 N6 C2 -179 .8(1) CIO C30 C31 C32 178.4(2) CIO C30 C35 C34 -1 78 .9( 3) CIO C9 C7 N6 -1 24 .9( 2)
Table 4 (contd) 1 2 ue C7 N6 C2 0.2(2) 08 C7 C9 CIO 55.1(2) C7 N6 C2 Cl -1 33 .7(2) C7 N6 C2 C3 50.7(2) C7 C9 CIO C30 62.8(2) N6 C2 Cl C40 3.4(3) N6 C2 C 3 04 -1 60.2(1) N6 C2 C3 05 21.5(2) C2 Cl C40 C41 -1 64.2(2) C2 Cl C40 C45 15.8(4) C3 C2 Cl C40 179.0(2) 04 C3 "2 Cl 23.8(2) 05 C3 C2 Cl -1 54.5(2) Cl C40 C 4 1 C42 178.0(2) Cl C40 C45 C44 -1 77 .9( 2) HI 06 N6 C2 Cl -47( 2) HI 06 N6 C2 C3 129( 2) H106 N6 C7 C9 1( 2) H106 N6 C7 08 -179( 2) C2 C3 04 H 1 0 6 1 -14 6( 1) 05 C3 04 H 1 0 6 1 36 ( 1) C3 04 H 1 0 6 1 N 6 1 58( 7) 04 H10'6] N 6 1 C 2 1 148( 6) 04 H 1 0 6 1 N 6 1 C 7 1 -33( 7) Hill Nil C 12 013 - 179( 2) Hill Nil C 12 014 1( 2)
Hill Nil C9 CIO 39( 2)
Hill NI 1 C9 C7 -82( 2) C9 C7 08 H i l l 2 -6 ( 1) N6 C 7 08 H i l l 2 174( 1) C7 08 H i l l 2 N i l 2 -159( 7) 08 H i l l 2 N i l 2 C 1 2 2 -94( 8) 08 H i l l 2 N i l 2 C 9 2 94( 8) HI 05 05 C3 04 -10( 2)
T a bl e 4 (contd) 1 2 H105 05 C3 C2 172( 2) Nil C2 013 X f—t 0 LTV 45( 1) 014 C12 013 H105 -134( 1) C12 013 H1053 053 73(12) 013 H1053 053 C33 -161(11) S y m m e t r y r e l a t e d atoms 1 X ’ = X - 1, y' » y, z ’ = z 2 x ’ = 1 - x, y* = 1 - y, z ’ = 2 - z
3
x > = X + 1, y ’ = y . z ’ = z R e f e r e n c e s[1] W a s i a k T . , K o z i o l k i e w i c z A., Pol. J. Chem., 57, 86 1- 869 (1983).
[2] S h e 1 d r i c k G. M . , S H EL X 76., P r o g r a m for cr ys t a l s t r u c ture d e t e r m i n a t i o n , U n i v e r s i t y of Ca m b r i d g e , E n g l a n d (1976). [3] B u s i n g W. R., M a r t i n K . G ., L e v y H . A . ORFFE,
C r y s t a l l o g r a p h i c f u n c t i o n and e r ro r pr ogram, Oak R i dg e N a ti ona l L a b o r at or y, USA (1971). [4] I U P A C-I UB C o m m i s i o n on B i o c h e m i c a l N o m e n c l a t u r e , Bi oc hem ., _9_, 3471 (1970). [5] M a r s h R. E., G l u s k e r J. P., Ac ta Cryst. 14, 1110- -1116 (1961). [6] W e i C. H., D o h e r t y D. G., E i n s t e i n J. R. ,A c t a Cryst., B28, 90 7- 9 1 5 (1972).
[7] S c h i 1 1 e r P. W., [in:] The Peptides: An al ysi s, Sy nt hesis, Biology, Vol. 6 , eds. S. Ud e n f r i e n d , J. M e i n e h o f e r , A c a d e m i c Press, New York, 219 (1984).
[8] J a n i n 3., W 0 d a k S., L e v i t t M . , M a i g r e t B., J. M o l . Biol., 121, 35 7- 3 8 9 (1978).
An dr zej M. Br zo zow sk i, Tomasz A. Olszak, A n d r zej Stępień, M i e c z y s ł a w J. Gr ab ows ki , Tadeusz Wasiak, W i t o l d K o z i o ł k i e w i c z ,
Si l v ain L e co cg S T R U K T U R A K R Y S Z T A Ł Ó W I C Z Ą S T E C Z K I B E N Z Y L O K A R B O N Y L O - L ,D- -FENYL0ALANYL0-(a,ft de hy dro ) F E N Y L O A L A N I N Y (1) C 2 6 H 2 4 N 2 ° 5 ’ M cz = 444.49, u k ł a d t r ó j s k o ś n y , PI a = 6.429(4), b = 13.225(9), c = 14 .1 26( 13 ) A, a « 104.68(7), ft = 94.44(7), r - 9 6 . 4 9 ( 5 ) ° , V = 1147(2) A 3 , Z = 2, 0 x = 1.287 g e m " 3 , jj= 6 . 5 0 c m ' 1 . Oane d y f r a k t o m e t r y c z n e , t e m p e ra tu ra po ko jowa, A(CuKoc) = 1. 54 178 A F(000) = 468, R = 0.04 59 dla 3715 r e f l e k s ó w z k r y t e r i u m ob s e r w o w a l - noici I > 3ff(I), max & / t f < 1.421 dla p a r a m e t r ó w p o z y c y j n y c h i t e m p e r a t u r o w y c h .
M o le kuł a z n a j duj e się w ko n f o r m a c j i r o zc iąg ni ęt ej: kąty 0,1)/ dla L- Fen p r z y jmu ją wa rt ośc i -8 9. 5(2 )° i 114.1(1)°. W i ą z a n i e p e p t y d o w e tworzy formę trans: « = -1 79.8(1)°. Wa rt o ś ć x 1 * 3.4(3)° dla (a, ft-Jehydro)Fen w s k a z u j e ria k o n f o r m a c j ę cis tego a m i n o k w a s u w s t o s u n ku do w i ą z ani a pe ptydowego.
