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X-ray study of spermine tetrahydrochloride
J. Mol. Biol. (1965) 11,438-440
LETTERS TO THE EDITOR
X-ray Study of Spermine Tetrahydrochloride Spermine and spermidine, as well as other aliphatic polyamines, are natural compounds of considerable biological interest. They are known to be present in several kinds of living cells. Recently the antibacterial activity of these compounds (Guirard & Snell, 1962) has been studied and a stabilizing effect in vitro of spermine on DNA has been reported (Mandel, 1962). Structure analysis of salts of spermine and spermidine was undertaken in this laboratory in order to determine the effect of the interactions between protonated amino groups and anions on the molecular conformation. In this letter the preliminary results of an accurate X-ray crystal structure determination of spermine tetrahydrochloride +
+
+
+
NHa-(CH2la-NH2-(CH2)4-NH2-(CH2la-NHa·40lare reported. Crystals were prepared by cooling a warm solution of the free base in a 4 : 1 mixture of ethanol and concentrated hydrochloric acid. Using copper K(J.. radiation, the following cell dimensions were obtained from precession photographs:
± 0·01 A;
±
c = 15·26 ± 0'02 A {3 = 121 ± 12' The space group is P2 1 !c, since hOl reflexions occur only with l even and OkO only with k even. With two formula units (01oN4H26,4H OI) per unit cell, the calculated density is 1·318 gem-a. The density measured by flotation is 1·321 g cm- 3 • The symmetry of the space group requires that the molecular chains be centrosymmetric and that their centres be situated at 0,0,0; O,!,!. The structure, in projection on (010) and on (100), was determined by the interpretation of Patterson functions and application of HarkerKasper inequalities. A preliminary refinement of the structure was then carried out through cycles of structure factors and Fourier projection calculations. After three cycles of calculations for the (010) and two cycles for the (100) projections, the agreement indices for the 116 hOl and 122 Okl observed reflexions were 0·16 and 0·15 respectively. An average isotropic temperature factor of 2·9 A2 was used. The Fourier projections of the electron density on (010) and (100) are shown in Figs 1 and 2. At this stage the atomic co-ordinates were considered to be accurate enough to start a. three-dimensional refinement, which is in progress. The conformation of the molecular chain represents the most interesting feature of the structure. Unexpectedly, the chain is not zig-zag planar, the bond 02-Nl being in gauche conformation. a = 8·60
b = 7·88
030'
438
0·01 A;
LETTERS TO THE EDITOR
439
cf4
FIG. 1. Fourier projection of the electron density on (010). Contour lines are drawn at arbitrary intervals.
440
A. DAMIANI ET AL.
{ sinfl
FIG. 2. Fourier projection of the electron nensrty on (100). Contour lines are drawn at arbitrary intervals.
The close approaches between chloride ions and protonated amino groups indicate the formation of hydrogen bonds N-H ... 01-. These strong interactions between anions and protonated molecules might be responsible for the deviation from planarity of the molecular chains. The results ofthe three-dimensional analysis and a detailed description of the structure will be published shortly. This investigation was supported by the Consiglio Nazionale delle Rieerche, Rome, Italy.
A. DAMIANI A. M. LIQUORI
Istituto Chimico Universita' di Napoli Napoli, Italy
R.PULITI A. RIPAMONTI
Centro Nazionale di Ohimica delle Macromolecole (CNR) Sez. III, Napoli Italy Received 5 August 1964 REFERENCES
Ouirard, B. M. &: Snell, E. E. (1962). In Bacteria, ed, by I. C. Gunsalus &: R. Y. Stranier. vol. 4, p. 73. New York: Academic Preas. Mandel, M. (1962). J. Mol. Biol. 5, 435.
LETTERS TO THE EDITOR
X-ray Study of Spermine Tetrahydrochloride Spermine and spermidine, as well as other aliphatic polyamines, are natural compounds of considerable biological interest. They are known to be present in several kinds of living cells. Recently the antibacterial activity of these compounds (Guirard & Snell, 1962) has been studied and a stabilizing effect in vitro of spermine on DNA has been reported (Mandel, 1962). Structure analysis of salts of spermine and spermidine was undertaken in this laboratory in order to determine the effect of the interactions between protonated amino groups and anions on the molecular conformation. In this letter the preliminary results of an accurate X-ray crystal structure determination of spermine tetrahydrochloride +
+
+
+
NHa-(CH2la-NH2-(CH2)4-NH2-(CH2la-NHa·40lare reported. Crystals were prepared by cooling a warm solution of the free base in a 4 : 1 mixture of ethanol and concentrated hydrochloric acid. Using copper K(J.. radiation, the following cell dimensions were obtained from precession photographs:
± 0·01 A;
±
c = 15·26 ± 0'02 A {3 = 121 ± 12' The space group is P2 1 !c, since hOl reflexions occur only with l even and OkO only with k even. With two formula units (01oN4H26,4H OI) per unit cell, the calculated density is 1·318 gem-a. The density measured by flotation is 1·321 g cm- 3 • The symmetry of the space group requires that the molecular chains be centrosymmetric and that their centres be situated at 0,0,0; O,!,!. The structure, in projection on (010) and on (100), was determined by the interpretation of Patterson functions and application of HarkerKasper inequalities. A preliminary refinement of the structure was then carried out through cycles of structure factors and Fourier projection calculations. After three cycles of calculations for the (010) and two cycles for the (100) projections, the agreement indices for the 116 hOl and 122 Okl observed reflexions were 0·16 and 0·15 respectively. An average isotropic temperature factor of 2·9 A2 was used. The Fourier projections of the electron density on (010) and (100) are shown in Figs 1 and 2. At this stage the atomic co-ordinates were considered to be accurate enough to start a. three-dimensional refinement, which is in progress. The conformation of the molecular chain represents the most interesting feature of the structure. Unexpectedly, the chain is not zig-zag planar, the bond 02-Nl being in gauche conformation. a = 8·60
b = 7·88
030'
438
0·01 A;
LETTERS TO THE EDITOR
439
cf4
FIG. 1. Fourier projection of the electron density on (010). Contour lines are drawn at arbitrary intervals.
440
A. DAMIANI ET AL.
{ sinfl
FIG. 2. Fourier projection of the electron nensrty on (100). Contour lines are drawn at arbitrary intervals.
The close approaches between chloride ions and protonated amino groups indicate the formation of hydrogen bonds N-H ... 01-. These strong interactions between anions and protonated molecules might be responsible for the deviation from planarity of the molecular chains. The results ofthe three-dimensional analysis and a detailed description of the structure will be published shortly. This investigation was supported by the Consiglio Nazionale delle Rieerche, Rome, Italy.
A. DAMIANI A. M. LIQUORI
Istituto Chimico Universita' di Napoli Napoli, Italy
R.PULITI A. RIPAMONTI
Centro Nazionale di Ohimica delle Macromolecole (CNR) Sez. III, Napoli Italy Received 5 August 1964 REFERENCES
Ouirard, B. M. &: Snell, E. E. (1962). In Bacteria, ed, by I. C. Gunsalus &: R. Y. Stranier. vol. 4, p. 73. New York: Academic Preas. Mandel, M. (1962). J. Mol. Biol. 5, 435.