-
HELVETICA CHIMICA ACTA Vol. 58, Fasc. 2 (1975) - Nr. 53
432
51. The Crystal Structure of a K+ Complex of Valinornycia by Katarina Neupert-Laves and M s x Dobler Laboratorium fiir organische Chemie der Eidg. 'l'echnischen Hochschule, 8006 Ztirich
(11. X1.74) Snrmmary. A KI,/KI, complex of the cyclododecaclepsipeptjcle antibiotic valinomycin crystallizes in the spacc group C222,. a = 13.34,b = 24.65.E = 46.96 A. Thc crystal structure investigation shows that K k is coordinated octahedrally by six carbonyl oxygen atoms. The macrocyclic ring skeleton adopts non-crystallographic S, symmetry. Six hydrogen bonds involving aniidc nitrogen atoms and carbonyl oxygen atoms form a bclt around the molecule.
The cyclododccadepsipeptide antibiotic valinomycin (1) has been shown to act as an ionophorc with both biological and artificial membranes [l-31 and to exhibit a marked specificity for potassium ions. 14 C"Q
2%
13CH 1 21
N-C-CH H I
21
20
15
"\
7 4 3
19CH 3
4 -0
I
0
16
1
1
-
D Val
L-Lac
L -Val
D-HYV
(1)
The conformations of valinmnycin and its K+ complex in solution have been studied by IR., ORD., CD. and NMR. techniques c4-71. For uncomplexed valinomycin a solvent-dependent equilibrium mixture of at least three conformations with a varying number of amide hydrogen bonds .was found. Whereas in unpolar solvents all six aniide hydrogen atoms are involved in intramolecular hydrogen bonds, in polar solvents there are only three such bonds, with the other three arnide hydrogen atoms probably forming hydrogen bonds to solvent molecules. The secondary structure of the K+ complex was characterized as a series of /%turns [6] involving all amide hydrogen atoms in intramolecular hydrogen bonds. On this basis conformational energy calculations were used to determine a minimum energy model constrained to s,, symmetry of the 36-membered ring skeleton with p-carbon atoms included [S]. The calculated model seems to be in good agreement with results of an earlier crystal structure analysis of the KAuCL complex [9]. Although atomic coordinates for this structure were not published, and positions of side chains were not completely defined, it was established that the K+ ion is octahedxally coordinated
-
HELVETICA CHIMICAACTA- Vol. 58, Fasc. 2 (1975) Nr. 51.
433
to carbonyl oxygen atoms and that the six amide hydrogen atoms form a belt of hydrogen bonds around the molecule. The crystal structure of the KI,/KI, complex reported here confirms these results arid also establishes the positions of the sidc chains. Wc find that the non-crystallographic threefold rotation symmetry also holds (with the exception of C(25*)) for the side chains. If the difference between the sidc chains in L-Lac (methyl) and D-HyV (isopropyl) is ignored, the approxirnatc symmetry is raised to S,. The K+. . . 0 distances are 2.69-2.83A (mean 2.7568)and the N-H . . - 0hydrogen bond distances are 2.88-2.98A (mean 2.932A).Two types of anion, I; and ICl both on crystallographic twofold rotation axes, arc present in the crystal. A crystal structure determination of uncomplexed valinomych [lo] [ll) gave a conformation which is completely different from the one in the K+ complcx. All six amide hydrogen atoms form intramolccular hydrogen bonds but two of these involve other carbonyl oxygen atoms than in the K+ complex. Of the other six carbonyl oxygen atoms two point inwards, two outwards and two upwards. Cryyetallographlc Data. - Crystalline complexes of valinomycin appear to show a strong tendency to polymorphism. The following crystal mddifications were ob-
tained. a) with KI: (1)from chloroform/hexane; trigonal P321,a = b = 13.7,c = 25.3 A, U = 4177 A3, Z = 2. (2) from ethyl acetate; trigonal R32,a = b = 23.5, c = 74.2 8, U = 35487 A3,Z = 18. (3) from acetone/hexane; monoclinic P2,a = 14.4,b = 10.4, c = 22.9A, p = 99.5", U = 3382 As,Z = 2. b) with K1 and 1,: (4)from ethyl acetate; triclinic PI,a = 13.6,b = 13.8, c = 23.3 8, a = 92", p = 97.2", y = 118.4', U = 3824 A3,Z = 2. (5) from ethyl acetate; triclinicP1, a = 16.3,b = 15.0, c = 20.3& CL 97.1",@ ==104.7",y = 126', U = 3641 As, Z = 2. (6) from ethyl. acetate/water; orthorhombic C22Z1,a = 13.34, b = 24.65,c = 46.96 A, u = 15443 A 3 , z = 8. Several other modifications of poor quality showed either disorder or twinning. The variation in thc apparent molecular volume (1700-2100As)in the KI complexes suggests that variable amounts or kinds of solvent molecules are included in the crystals. The variation in the KI/I, complexes is less pronounced (1820-1930AS) but still considerable. Modification (6) was chosen for crystal structure analysis. KIa/K16 complex of vahomycin, C,O,,N,H,, * KI,, M. W. = 1628. Orthorliombic, a = 13.342(20), b= 24.648(37), c = 46.%1(70) A, U = 15443 As,2 I= 8. Space group C222, (DX), Dx = 1.40 g c t r S . Cell constants were obtained from 30" precession photographs (CuKa radiation) and diffractometer measurements (MoKoc radiation).
-
Data Collection. - The intensities o f the 5900 reflections in the range 8 == 23" were measured with a computer-controlled four-cjrcle diffractometer (HiZgev & Watts Y2W) using graphite-monochromatized MoKa radiation, from a crystal with dimensions 0.25 x 0.3 x 0.15 mm. The rcflectioas were processed in the usual way, giving 4656 unique reflections with F,, > 3a(F0).Corrections for absorption effects were not applied (p = 12.5 cm-l for MoKa radiation), giving rise to some errors in the measured intensities. 28
434
HELVETICA CHIMLCAACTA Vo!. 58, Pasc. 2 (1975) -1
- Nr. 51
Structure Analyeis. - Our initial attempts to solve the structure werc based on the assumption that the crystal was a K13 complex. From a sharpened Patkt-so~ map the position of a linear 1; ion with its central atom an a twofold rotation axis at (0, y, 114) was found. Further prominent vectors indicated the presence of a second I; unit MI the twofold axis at (x,0,O). Here, however, the angle at thc central atom was about 90°, which was quite incompatible with the expected linearity of the 1; anion. A F'owier map calculated with phases from the linear ion alone clearly showed the three other pcaks again, with indications of two weaker peaks on the extension of the angular triatomic unit. These peaks were first thought to be spurious, but after scverd attempts to find altcrnative interpretations of the PathwsoH and Fozdviev map had failed, we had to conclude that they were genuine, and that the angular unit was actually an 1; anion, bent at the central atom, linear at the two adjacent ones. Once this model was adopted as a ba3is for phasing cdculations, the potassium ion and all the non-hydrogen atoms in the valinomycin molecule could be placed in stages from three successive Fourier maps. Refinement was carried out by blockdiagonal least-squares calculations. After five cycles with isotropic temperature factors, a (F,-F,)-Fmvie~map showed peaks correspondingto many of the hydrogen atoms. However, the H atoms were included in the structure model at positions calculated from stereochemical assumptions (C-H, equal angles with the three attached bonds; CH, groups, staggered conformation, H-CH bond angle 109", H-Cdistance 1.09A).The (F,-F,)-maps also show residual electron density (1.3eA-a) between valinomycin molecules, which may suggest that disordered solvent mdecdes are occluded in the crystal structure. The refinement was completed with four cycles of block-diagonal least-squares calculations using anisotropic temperature factors for the K+ and iodine atoms. In the find cycle thrce atoms with scattering factors f0/2were introduced to simulate the residual electron density attributed to the disordered solvent molecules. The final R factor, based on the 4656 reflections with Fa > 3@,) was Results. - The results are summarized in Tables. Fractional atomic coordinates, vibrational parameters and calculated hydrogen atom positions are given in Tables 1, 2 and 3. Standard deviations (in parentheses) were estimated by inversion of the least-squares normal equations. Bond lengths and angles and some torsion angles relevant to the ligand conformation are given in Tables 4 and 5. The corresponding estimated standard deviations are 0.015-0.020 i$ for C-C, C-0 and C-N bonds of the ring system, 0.017-0.026 A for C-C bonds of the methyl and isopropyl substituents and 1.0-1.5" for bond angles. Discussion. - The structure of the K+ complex of valinomych is depicted in Fig.1-The conformation of the ligand i s characterized by a non-crystallographic approximate threefold rotation axis (corresponding to the threefold repetition of units in the chemical formula) and approximate S,, symmetry of the 36-membered macrocyclic ring skeleton. To test how well these approximate symmetry elements hold, the atom coordinates were first transformed to the best plane through the -.
_~
1)
A table of obscrved structure amplitudes i s available on request.
0Clf.l
CC14') CC15')
CCIJ')
CCII') cc 1 2 ' 1
OI10'>
CCA') CL9*)
CC5.J CC6'l NC7')
cc3*> 0C4*)
CC2')
KCI'I
0c 26)
CC241 CC25)
Cc231
R I ??J
C120) CC211
cc 191
CC 13) CC 14) EC 15) 0 C 16) CC17) 0C18)
CC 123
CCIII
BC 103
cc91
cca)
NC7)
CC3) 0c 4) cc 5) CC 6 )
NIL) cc 2)
5.0 6.8
7.4 4.4
.oua3 cia)
,0867 (15) -275I ( 1 1
4-2 3.4 3.4 3.5 4.2 3.8 4-1 4.3
4.0
3.8
4.0
3.9
8.6 4.3
7.3
5.0
5.3 5.4 7.7 5.9 4.3
5.6 5.0 8.2
6.2
3.5 4.4
3.6 a. I
3-9 4.5 5. I 4.7 9- 6 3.8 3.7
4.4 4. I
e
-2442 t1OJ - 2 ~ 4 4( 8 1 -2861 110) -3928 ! I l l *U5R1 ( 7 ) -5636 ( 1 1 1 . 5 9 9 7 (101 .117E (121
m
1272 ( 7 ) .L779 -3946 t l O l a 3 6 0 1
HELVETICA CHIMICA ACTA Vol. 58, Fasc. 2 (1975) - Nr. 53
432
51. The Crystal Structure of a K+ Complex of Valinornycia by Katarina Neupert-Laves and M s x Dobler Laboratorium fiir organische Chemie der Eidg. 'l'echnischen Hochschule, 8006 Ztirich
(11. X1.74) Snrmmary. A KI,/KI, complex of the cyclododecaclepsipeptjcle antibiotic valinomycin crystallizes in the spacc group C222,. a = 13.34,b = 24.65.E = 46.96 A. Thc crystal structure investigation shows that K k is coordinated octahedrally by six carbonyl oxygen atoms. The macrocyclic ring skeleton adopts non-crystallographic S, symmetry. Six hydrogen bonds involving aniidc nitrogen atoms and carbonyl oxygen atoms form a bclt around the molecule.
The cyclododccadepsipeptide antibiotic valinomycin (1) has been shown to act as an ionophorc with both biological and artificial membranes [l-31 and to exhibit a marked specificity for potassium ions. 14 C"Q
2%
13CH 1 21
N-C-CH H I
21
20
15
"\
7 4 3
19CH 3
4 -0
I
0
16
1
1
-
D Val
L-Lac
L -Val
D-HYV
(1)
The conformations of valinmnycin and its K+ complex in solution have been studied by IR., ORD., CD. and NMR. techniques c4-71. For uncomplexed valinomycin a solvent-dependent equilibrium mixture of at least three conformations with a varying number of amide hydrogen bonds .was found. Whereas in unpolar solvents all six aniide hydrogen atoms are involved in intramolecular hydrogen bonds, in polar solvents there are only three such bonds, with the other three arnide hydrogen atoms probably forming hydrogen bonds to solvent molecules. The secondary structure of the K+ complex was characterized as a series of /%turns [6] involving all amide hydrogen atoms in intramolecular hydrogen bonds. On this basis conformational energy calculations were used to determine a minimum energy model constrained to s,, symmetry of the 36-membered ring skeleton with p-carbon atoms included [S]. The calculated model seems to be in good agreement with results of an earlier crystal structure analysis of the KAuCL complex [9]. Although atomic coordinates for this structure were not published, and positions of side chains were not completely defined, it was established that the K+ ion is octahedxally coordinated
-
HELVETICA CHIMICAACTA- Vol. 58, Fasc. 2 (1975) Nr. 51.
433
to carbonyl oxygen atoms and that the six amide hydrogen atoms form a belt of hydrogen bonds around the molecule. The crystal structure of the KI,/KI, complex reported here confirms these results arid also establishes the positions of the sidc chains. Wc find that the non-crystallographic threefold rotation symmetry also holds (with the exception of C(25*)) for the side chains. If the difference between the sidc chains in L-Lac (methyl) and D-HyV (isopropyl) is ignored, the approxirnatc symmetry is raised to S,. The K+. . . 0 distances are 2.69-2.83A (mean 2.7568)and the N-H . . - 0hydrogen bond distances are 2.88-2.98A (mean 2.932A).Two types of anion, I; and ICl both on crystallographic twofold rotation axes, arc present in the crystal. A crystal structure determination of uncomplexed valinomych [lo] [ll) gave a conformation which is completely different from the one in the K+ complcx. All six amide hydrogen atoms form intramolccular hydrogen bonds but two of these involve other carbonyl oxygen atoms than in the K+ complex. Of the other six carbonyl oxygen atoms two point inwards, two outwards and two upwards. Cryyetallographlc Data. - Crystalline complexes of valinomycin appear to show a strong tendency to polymorphism. The following crystal mddifications were ob-
tained. a) with KI: (1)from chloroform/hexane; trigonal P321,a = b = 13.7,c = 25.3 A, U = 4177 A3, Z = 2. (2) from ethyl acetate; trigonal R32,a = b = 23.5, c = 74.2 8, U = 35487 A3,Z = 18. (3) from acetone/hexane; monoclinic P2,a = 14.4,b = 10.4, c = 22.9A, p = 99.5", U = 3382 As,Z = 2. b) with K1 and 1,: (4)from ethyl acetate; triclinic PI,a = 13.6,b = 13.8, c = 23.3 8, a = 92", p = 97.2", y = 118.4', U = 3824 A3,Z = 2. (5) from ethyl acetate; triclinicP1, a = 16.3,b = 15.0, c = 20.3& CL 97.1",@ ==104.7",y = 126', U = 3641 As, Z = 2. (6) from ethyl. acetate/water; orthorhombic C22Z1,a = 13.34, b = 24.65,c = 46.96 A, u = 15443 A 3 , z = 8. Several other modifications of poor quality showed either disorder or twinning. The variation in thc apparent molecular volume (1700-2100As)in the KI complexes suggests that variable amounts or kinds of solvent molecules are included in the crystals. The variation in the KI/I, complexes is less pronounced (1820-1930AS) but still considerable. Modification (6) was chosen for crystal structure analysis. KIa/K16 complex of vahomycin, C,O,,N,H,, * KI,, M. W. = 1628. Orthorliombic, a = 13.342(20), b= 24.648(37), c = 46.%1(70) A, U = 15443 As,2 I= 8. Space group C222, (DX), Dx = 1.40 g c t r S . Cell constants were obtained from 30" precession photographs (CuKa radiation) and diffractometer measurements (MoKoc radiation).
-
Data Collection. - The intensities o f the 5900 reflections in the range 8 == 23" were measured with a computer-controlled four-cjrcle diffractometer (HiZgev & Watts Y2W) using graphite-monochromatized MoKa radiation, from a crystal with dimensions 0.25 x 0.3 x 0.15 mm. The rcflectioas were processed in the usual way, giving 4656 unique reflections with F,, > 3a(F0).Corrections for absorption effects were not applied (p = 12.5 cm-l for MoKa radiation), giving rise to some errors in the measured intensities. 28
434
HELVETICA CHIMLCAACTA Vo!. 58, Pasc. 2 (1975) -1
- Nr. 51
Structure Analyeis. - Our initial attempts to solve the structure werc based on the assumption that the crystal was a K13 complex. From a sharpened Patkt-so~ map the position of a linear 1; ion with its central atom an a twofold rotation axis at (0, y, 114) was found. Further prominent vectors indicated the presence of a second I; unit MI the twofold axis at (x,0,O). Here, however, the angle at thc central atom was about 90°, which was quite incompatible with the expected linearity of the 1; anion. A F'owier map calculated with phases from the linear ion alone clearly showed the three other pcaks again, with indications of two weaker peaks on the extension of the angular triatomic unit. These peaks were first thought to be spurious, but after scverd attempts to find altcrnative interpretations of the PathwsoH and Fozdviev map had failed, we had to conclude that they were genuine, and that the angular unit was actually an 1; anion, bent at the central atom, linear at the two adjacent ones. Once this model was adopted as a ba3is for phasing cdculations, the potassium ion and all the non-hydrogen atoms in the valinomycin molecule could be placed in stages from three successive Fourier maps. Refinement was carried out by blockdiagonal least-squares calculations. After five cycles with isotropic temperature factors, a (F,-F,)-Fmvie~map showed peaks correspondingto many of the hydrogen atoms. However, the H atoms were included in the structure model at positions calculated from stereochemical assumptions (C-H, equal angles with the three attached bonds; CH, groups, staggered conformation, H-CH bond angle 109", H-Cdistance 1.09A).The (F,-F,)-maps also show residual electron density (1.3eA-a) between valinomycin molecules, which may suggest that disordered solvent mdecdes are occluded in the crystal structure. The refinement was completed with four cycles of block-diagonal least-squares calculations using anisotropic temperature factors for the K+ and iodine atoms. In the find cycle thrce atoms with scattering factors f0/2were introduced to simulate the residual electron density attributed to the disordered solvent molecules. The final R factor, based on the 4656 reflections with Fa > 3@,) was Results. - The results are summarized in Tables. Fractional atomic coordinates, vibrational parameters and calculated hydrogen atom positions are given in Tables 1, 2 and 3. Standard deviations (in parentheses) were estimated by inversion of the least-squares normal equations. Bond lengths and angles and some torsion angles relevant to the ligand conformation are given in Tables 4 and 5. The corresponding estimated standard deviations are 0.015-0.020 i$ for C-C, C-0 and C-N bonds of the ring system, 0.017-0.026 A for C-C bonds of the methyl and isopropyl substituents and 1.0-1.5" for bond angles. Discussion. - The structure of the K+ complex of valinomych is depicted in Fig.1-The conformation of the ligand i s characterized by a non-crystallographic approximate threefold rotation axis (corresponding to the threefold repetition of units in the chemical formula) and approximate S,, symmetry of the 36-membered macrocyclic ring skeleton. To test how well these approximate symmetry elements hold, the atom coordinates were first transformed to the best plane through the -.
_~
1)
A table of obscrved structure amplitudes i s available on request.
0Clf.l
CC14') CC15')
CCIJ')
CCII') cc 1 2 ' 1
OI10'>
CCA') CL9*)
CC5.J CC6'l NC7')
cc3*> 0C4*)
CC2')
KCI'I
0c 26)
CC241 CC25)
Cc231
R I ??J
C120) CC211
cc 191
CC 13) CC 14) EC 15) 0 C 16) CC17) 0C18)
CC 123
CCIII
BC 103
cc91
cca)
NC7)
CC3) 0c 4) cc 5) CC 6 )
NIL) cc 2)
5.0 6.8
7.4 4.4
.oua3 cia)
,0867 (15) -275I ( 1 1
4-2 3.4 3.4 3.5 4.2 3.8 4-1 4.3
4.0
3.8
4.0
3.9
8.6 4.3
7.3
5.0
5.3 5.4 7.7 5.9 4.3
5.6 5.0 8.2
6.2
3.5 4.4
3.6 a. I
3-9 4.5 5. I 4.7 9- 6 3.8 3.7
4.4 4. I
e
-2442 t1OJ - 2 ~ 4 4( 8 1 -2861 110) -3928 ! I l l *U5R1 ( 7 ) -5636 ( 1 1 1 . 5 9 9 7 (101 .117E (121
m
1272 ( 7 ) .L779 -3946 t l O l a 3 6 0 1
