Mar 24, 2018 - atom existing in a square planar geometry with two disparate Pd--S bond distances of 2.3129(9) and 2.292(I) ... these suggest the predominance of a particular canonical form in the solid state. The lattice is .... lEo -> 6.0otFo)].
Journal of Chemical Crystallography, Vol. 24, No. I0. 1994
Spectroscopic, thermal, and X-ray diffraction studies of tetrakis(thiourea)palladium chloride bis(5,7dimethyl [1,2,4]triazolo[ 1,5-a] pyrimidine dihydrate Juan M. Salas, (*'u Abderrahman Rahmani, ~u Maria A. Romero, ~l) Miguel Quirbs, ~u and Edward R.T. Tiekink (*'2)
Received March 24. 1994; accepted June 5. 1994 The crystal and molecular structure of the title compound,.lPd(S=C(NH,)_,)4]Cl_,-2dmtp-2H,O, has been determined and refined to a final R = 0.034. The cation is centrosymmetric with the Pd atom existing in a square planar geometry with two disparate P d - - S bond distances of 2.3129(9) and 2.292(I),~,. lnteratomic parameters are reported for the first non-coordinated dmtp molecule: these suggest the predominance of a particular canonical form in the solid state. The lattice is stabilized via a series H-bonding contacts involving the thiourea. CI and dmtp species. Crystals of [Pd(S=C(NH2)2)4]CI2-2dmtp'2H20 are monoclinic with space group P21/c, and unit cell dimensions a = 15.129(1), b = 8.512(I), c = 12.663(I),~, /3 = 104.05(1) ~ . KEY WORDS: X-Ray diffraction studies.
is the first example o f a dmtp complex in which the dmtp molecule is not directly coordinated to a metal center.
Introduction Transition metal complexes of different purine analogs have been studied widely in order to elucidate the role of metal ions in nucleic acids biochemistry. One such example, 5,7-dimethyl [ 1,2,4]triazolo[ 1,5a]pyrimidine, hereafter dmtp, is an example of a purine mimic that has been studied in this context. ~-9 As dmtp does not have an acidic hydrogen atom, metal complexes containing this species will always involve a counteranion. In the dmtp complexes characterized thus far, coordination has been observed exclusively via the N(3) atom, except in the tetrameric copper(I) species, [Cu4(dmtp)4Cl2] 2+, in which the N(4) atom is also involved in coordination. 4 As a continuation of previous studies in this area, the synthesis, spectroscopic characterization (IR), thermal behavior and crystal structure of the title compound, [Pd(S = C(NH2)2)4]C12" 2dmtp" 2H20, is reported. This
Experimental
Instrumentation Microanalyses were determined by the Technical Services of the University of Granada using a PerkinElmer 240C microanalyzer. Palladium and water contents were determined by thermogravimetry using a Mettler TG-50 thermobalance. DSC curves were obtained on a Mettler DSC-20 differential scanning calorimeter. Infrared spectra were recorded on a Perkin-Elmer 983-G spectrophotometer in KBr discs (4000-250 c m - i ) and polyethylene (600-180 cm-~) pellets.
Synthesis of [Pd(S: C(NH2)~4ICl2"2dmtp" 2H20 (1) To an aqueous solution (15 cm 3) of dmtp (2 mmol, 0.296 g) was added [NH4]2[PdCI4] (2 mmol, 15 cm 3 water) and thiourea (2 mmol, 15 cm 3 water). After 5 days, orange crystals separated out which were washed with cold water and used without further purification. Analysis: Found C, 26.53; H, 4.42, N, 27.51, Calc.
mDepartamento de Qufmica lnorgfinica, Universidad de Granada, 18071 Granada, Spain. C2~Depanment of Chemistry, The University of Adelaide, Adelaide, S.A. 5005, Australia.
669 1074-1542/94/1000-0669S07.(~)/0 ,c~ 1994 Plenum Publishing Coqx~rJtion
670 for CIsH36CI~NjrO2S,~Pd, C, 26.55; H, 4.46; N, 27.53%. From the mother liquor, yellowish brown flakes o f the anhydrous material (2) also appeared after several days. Analysis: Found C, 27.70; H, 4.11; N, 28.79. Calc. for CtsH32CI2NIrS4Pd , C, 27.78; H, 4.15; N, 28.81%.
C~. stallography Data for the structure determination are summarized in Table 1. The scattering factors for all atoms (corrected for f ' and f " ) were as incorporated in teXsan ~~ which was installed on an Iris Indigo workstation. Final fractional atomic coordinates for the non-H atoms are listed in Table 2 and the crystallographic numbering scheme employed is shown in Figs. 1 and 2 which were drawn with O R T E P II at 50% probability ellipsoids, t
Results and Discussion The infrared spectra o f both 1 and 2 reveal that the thiourea molecules are S-bonded to the Pd atom as the u ( N - - H ) absorption bands at 3381, 3277 and 3178 cm - I are not shifted to lower frequency upon coordination thereby ruling out N-coordination. ~2-~4 In the spectrum o f 1 a new sharp band at 3484 c m - ~ can be assigned to l , ( O - - H ) o f water. One o f the u ( C - - N ) bands o f thiourea occurring at 1469 cm-~ appears to be shifted to higher frequency (1492 cm -~) in 1; whereas the band at 1412 c m - i remains unchanged. The band at 1084 c m - i for thiourea, assigned to u ( C - - S ) , splits into two bands, i.e. 1057 and 1101 c m - i . Bands due to the dmtp ligand appear,at virtually the same places in the spectra o f 1, 2, and free dmtp. The thermogravimetric curve o f 1 shows the first weight loss in the 6 0 - 9 0 ~ range, clearly corresponding to the dehydration o f the sample (experimental weight loss 4.6% cf. theoretical weight loss o f 4.43%). This process appears in the DSC diagram as a sharp endothermic effect centered at 8 0 . 3 ~ with an associated dehydration enthalpy o f 42.6 kJ/mol o f water. As expected, TG and DSC diagrams above 100~ are identical for both 1 and 2, dehalogenation taking place in the 2 0 0 - 2 8 0 ~ temperature range; this process is responsible for the endothermic effect centered at 238~ with a dehalogenation enthalpy o f 284 kJ/at-g o f CI, close to the value found in similar compounds.~5 py_ rolitic decomposition takes place from 300 to 570~ leaving PdO as the final residue. In order to fully char-
Salas, Rahmani, Romero, Quirbs, and Tiekink Table 1. Crystal data and summary of intensity data collection and structure refinement for [Pd(S=C(NH~)2h]CI2.2dmtp.2H20 Formula Form. wt. Color/Shape Space group Temp., ~ Cell constants (25 reflections > 17~ a, ,~, b. ,~ c, ,~ /3, deg. Cell vol., , ~ Formula units/unit cell D~k., g cm 3 Radiation, graphite monochromator h, .~. #~lc, cm-~ Diffractometer/scan Range of relative transm factors Max. crystal dimensions, mm Scan width, deg. Standard reflections Decay of standards, % Reflections measured 28 range, deg. Range of h, k, I Reflections observed lEo -> 6.0otFo)] Corrections applied Source of scattering factors used Structure solution Treatment of hydrogen atoms
C IsHs~,CI2NIrO2S4Pd 814.1 orange block monoclinic, P2Jc 2I 15.129(I) 8.512(1) 12.663(I) 104.05(1) 1581.9(2) 2 1.709 Mo Ka 0.71073 10.69 Rigaku AFC6R/~:20 0.935 to 19 0.13 x 0.16 x 0.19 0.39 113, 120, 320 -3 4204 3.0 - 55.0 -20 to +20, 0 to + 11, 0to +17 2687 Absorption t8 teXsan ~~
No. of parameters varied
SAPI88~9 in calculated positions (except for OH which were not included) 196
Weights
a,.(Fo)
GOF R R~ Largest feature in final diff. map, e,~.-5
1.89 0.034 0.038 0.52
1
acterize the structure o f 1, a single crystal X-ray crystal analysis was undertaken. The molecular structure of the [Pd(S----C(NH2)2)4] 2+ cation is shown in Fig. 1 and that of dmtp is shown in Fig. 2; selected interatomic parameters are collected in Table 3. The unit cell is comprised o f [Pd(S=C(NH2)2)4] 2+, C l - ions and dmtp molecules in the ratio l : 2 : 2. The Pd atom in the cation is situated
S t r u c t u r e o f [ P d ( S : C ( N H 2 ) 2 ) 4 ] C I 2 92 d m t p ' 2 H 2 0
671
Table 2. Fractionalatomic coordinatesand B~qvalues (&2) for [Pd(S= C(NH,)~h]CI2"2dmtp-2H20
L .k,
Atom
Fig. I. Crystallographic numbering scheme [Pd(S=C(NH2)2),d-'~ cation.
~
for
the
Pd CI(I) S(I) S(2) 0(I) N(I) N(3) N(4) N(8) N(ll) N(12) N(21) N(22) C(2) C(3a) C(5') C(5) C(6) C(7') C(7) C(II) C(21)
x
y
1/2 0.33880(7) 0.43817(6) 0.58850(7) 0,9442(2) -0.0215(2) -0.0826(2) 0.0553(2) 0.0437(2) 0.5147(2) 0.5957(2) 0.7517(2) 0.7337(2) -0.0938(3) 0.0059(2) 0.2002(3) 0.1439(3) 0.1845(3) 0.1677(3) 0.1348(31 0.5229(2) 0.6990(2)
z
0 0.1675(1) 0.0120(2) 0.2114(1) 0,3129(3) -0.3481(4) -0.1060(4) 0.0403(4) -0.2362(4) 0.0137(5) -0,1121(4) 0.3033(4) 0.0395(4) -0.2614(5) -0.0920(5) 0.1649(5) 0.0208(5) -0.1274(5) -0.4213(5) -0.2583(5) -0.0313(4) 0.1798(4)
Bcq"
0 0.44636(8) 0.14988(8) 0.07090(9) 0.1221(2) 0.1169(3) 0,1141(3) 0.1364(3) 0.1285(2) 0.3558(2) 0.2547(3) 0.0770(3) 0.0662(3) 0.1091(3) 0.1273(3) 0.1615(4) 0.1500(3) 0.1543(3) 0.1481(4) 0.1437(3) 0.2609(3) 0.0698(3)
1.91(1) 2.89(4) 2.90(4) 2.78(4) 3.2(1) 2.7(1) 2.8(1) 2.3(1) 2.1(1) 3.1(I) 3.3(2) 2.9(1) 2.6(1) 3.0(2) 2.1(1) 3.1(2) 2.3(1) 2.5(2) 3.5(2) 2.3(l) 2.2(1t 2.1(1)
"B~, = (87r-'/3)(U.~(aa*)-" + U22(bb*)2 + U33(cc*)-' + 2Ui2aa*bb*
3
c6
Fig. 2. Crystallographicnumberingscheme for the dmtp molecule.
on a crystallographic center of inversion and is coordinated by four S atoms which define a square planar geometry about this atom. The two independent P d - - S bond distances are not equivalent, i.e., P d - - S ( I ) 2.3129(9) and Pd - - S(2) 2,292( 1) A . Th is d isparity may be compared to the two independent P d - - S bond distances of 2.33 and 2.35 ,4, (no esd values given) found in the monoclinic form of [Pd(S=C(NH2)2)4]CI2 in which the Pd atom is situated on a crystallographic twofold axis ~6 and the range of P d - - S distances of 2.316(3) to 2.346(3)ik found in the orthorhombic form of [Pd(S=C(NH2)2)4]CI2 .17 Associated with the Pd atom are two symmetry related CI atoms, i.e., above and below the square plane, such that the P d . . . C I separation
cos 3' + 2Ur~aa*cc* cos ,8 + 2U23bb*cc* cos u).
Table 3. Selected interatomicparameters (,&, ~ for [Pd(S= C(NH_,)2h]"2dmtp'2H20 Pd--S(I) S(1)--C(II) C(II)--N(II) C(II)--N(12) N(1)--N(8) N(3)--C(2) N(4)--C(3a) N(8)-C(3a) C(5)--C(5') C(6)--C(7)
2.3129(9) 1.697(4) t.29515) 1.316(5) 1.354(4) 1.333(5) 1,341(5) 1,353(5) 1.481(5) 1.333(5)
Pd--S(2) S(2)-C(21) C(21)--N(21) C(21)--N(22) N(1)--C(2) N(3)--C(3a) N(4)--C(5) N(8)--C(7) C(5)--C(6) C(7)--C(7')
2.292(1) . 1.697(4) 1.309(51 1.309(5) 1.304(5) 1.313(4) 1.320(4) 1.357(5) 1.399(5) 1.471(6)
S(I)--Pd--S(2) Pd--S(I)--C(II) S(I)--C(II)--N(II) S(I)-C(II)--N(12) N(I1)--C(II)--N(12) N(8)--N(I)--C(2) C(3a)--N(4)-C(5) N(I)--N(8)--C(7) N(I)--C(2)--N(3) N(3)--C(3a)-N(8) N(4)-C(5)-C(5') C(5')--C(5)--C(6) N(8)--C(7)--C(6) C(6)-C(7)-C(7')
87.60(4) 107.2(I) 118.7(3) 122.6(3) t18.6(4) 100.7(3) 115.6(3) 127.2(3) 117.6(4) 109.5(3) 116.8(4) 120.4(3) 115,3(4) 127.4(4)
S(I)--Pd--S(2)'" Pd--S(2)--C(21) S(2)--C(21)--N(21) S(2)--C(21)-N(22) N(21)--C(21)--N(22) C(2)--N(31-C(3al N(I)--N(8)-C(3a) C(3a)--N(8)--C(7) N(3)--C(3a)--N(4) N(4)--C(3a)--N(8) N(4)--C(5)--C(6) C(5)--C(6)--C(7) N(8)--C(7)-C(7')
92.40(4) 110.8(I) 117.1(3) 123.3(3) 119.5(3) 102.2(3) 110.1(31 122,7(3) 128.1(4) 122.4(3) 122.8(4) 121.2(4) 117.3(4)
"Atom related by crystallographiccenter of inversion.
672
is 3 . 6 9 0 ( ! ) , ~ .
Salas, R a h m a n i , R o m e r o , Quirbs, and T i e k i n k Table 4. Hydrogen bonding contacts (A--H. 9 .B; A,) for
The two independent thiourea molecules
are p l a n a r to 0 . 0 0 9 ( 3 ) a n d 0 . 0 1 5 ( 4 ) , ~ , a n d f o r m d i h e d r a l a n g l e s o f 106.1 a n d 5 8 . 3 , r e s p e c t i v e l y , w i t h the s q u a r e p l a n e a n d 9 9 . 6 " with e a c h o t h e r . T h e s t r u c t u r e o f the d m t p m o l e c u l e is the first rep o r t e d in w h i c h the m o l e c u l e is not c o n n e c t e d to a m e t a l c e n t e r ; the s t r u c t u r e o f d m t p not h a v i n g b e e n d e t e r m i n e d . T h e m e a n d e v i a t i o n o f the a t o m s f r o m t h e / e a s t s q u a r e s p l a n e t h r o u g h the d m t p m o l e c u l e is 0 . 0 0 9 ( 4 ) , ~ . W h e r e a s the o v e r a l l p l a n a r i t y o f the d m t p m o l e c u l e w o u l d facilitate the d e l o c a l i z a t i o n o f r - e l e c t r o n d e n s i t y o v e r the fused rings, a careful c o n s i d e r a t i o n o f the derived i n t e r a t o m i c d i s t a n c e s s u g g e s t s a d o m i n a n c e o f o n e c a n o n i c a l f o r m . H e n c e , the N ( 1 ) - - C ( 2 ) b o n d d i s t a n c e o f 1.304(5),~. is s i g n i f i c a n t l y s h o r t e r t h a n the N ( 3 ) - - C ( 2 ) s e p a r a t i o n o f 1.333(5),~,. S i m i l a r l y , a n d c o n s i s t e n t with the a b o v e , is the o b s e r v a t i o n that the N ( 3 ) - - C ( 3 a ) s e p a r a t i o n o f 1 . 3 1 3 ( 4 ) , ~ is s h o r t e r than the o t h e r t w o b o n d s i n v o l v i n g the C ( 3 a ) a t o m . In the sixm e m b e r e d ring, the N ( 4 ) - - C ( 5 ) d i s t a n c e o f 1 . 3 2 0 ( 4 ) , ~ is s h o r t e r t h a n the N ( 4 ) - - C ( 3 a ) d i s t a n c e o f 1 . 3 4 1 ( 5 ) A a n d s i m i l a r l y the C ( 6 ) - - C ( 7 ) s e p a r a t i o n o f 1 . 3 3 3 ( 5 ) is s h o r t e r t h a n the C ( 5 ) - - C ( 6 ) d i s t a n c e o f 1 . 3 9 9 ( 5 ) ~,. T h e results s u g g e s t a d o m i n a n c e o f the f o l l o w i n g c a n o n i c a l f o r m to the o v e r a l l s t r u c t u r e :
[Pd(S = C(NHz),).dCI2- 2dmtp- 2H20" m
,
A
H
B
A. 9 9B
H- 9 .B
N(II) N(21)
H(lla) H(21a)
CI(I) CI(I)
3.297(3) 3.373(4)
2.37 2.41
N(22)
H(22a)
CI(1)
3.342(3)
2.43
N(I 1) N(12)
H(I Ib) H(12b)
CI(I) CI(I)
3.406(3) 3.494(3)
2.49 2.59
N(12)
H(12a)
S(I)
3.501(4)
3.28
N(I 1)
H(I la)
S(21
3.559(4)
3.16
N(I 1)
H(I la)
S(2)
3.260(4)
3.29
N(II)
H(llb)
S(2)
3.260(4)
3.33
N(II)
H(llb)
S(2)
3.559(4)
3.40
N(21) N(21) N(22) O(1) O( I ) O(1)
H(21b) H(21a) H(22b) H~' H~' Hb
O(1) O(1) N(3) N(I) N(4) N(I)
2.830(4) 2.830(4) 2.969(4) 2.935(5) 2.845(4) 3.506(4)
1.89 3.31 2.10 ----
O(1) O(1)
HI' HI'
N(I) N(3)
3.512(5) 3.553(4)
---
O(I)
H~'
N(3)
3.588(5)
--
Symmetry operation 1 -x, -y, 1 - z 1 - x, - 0 . 5 + y, 0.5 - z I - x. 0.5 + y, 0.5 - z x, y. z 1 - x, 0.5 + 3', 0.5 - z 1 - x, 0.5 + 3', 0.5 - z x, 0.5 - y, -0.5 + z 1 - x, 0.5 + y, 0.5 - z 1 - x, 0.5 + 3', 0.5 - z x, 0.5 - y, -0.5 + z x, y. z x, y, z x - 1, y, z x + 1, y. z x + 1, y, z 1 - x, 0.5 + v 0.5 - z 1 - x, - y , - z 1 - x, 0.5 + y, 0.5 - z x + I, v z
i
As w o u l d be e x p e c t e d in a s t r u c t u r e o f this t y p e t h e r e are several s i g n i f i c a n t H - b o n d i n g c o n t a c t s in the lattice. T h e unit cell is c o m p r i s e d o f layers o f d m t p a n d w a t e r m r l e c u l e s s a n d w i c h e d b e t w e e n layers o f c o m p l e x c a t i o n s a n d t h e i r a s s o c i a t e d CI a n i o n s . T h e c l o s e s t c o n tact i n v o l v e s a t h i o u r e a m o l e c u l e a n d a w a t e r m o l e c u l e a n d o c c u r s b e t w e e n the N(2 I ) - - H ( 2 1 b)- 9 9O ( 1 ) a t o m s at 1.89 A, s u c h that the a n g l e s u b t e n d e d at the H ( 2 1 b ) a t o m is 161 ~ a n d the N ( 2 1 ) . - . O ( I ) s e p a r a t i o n is 2 . 8 3 0 ( 4 ) , ~ . O t h e r c o n t a c t s o c c u r b e t w e e n the N(3) a t o m o f the d m t p m o l e c u l e a n d a t h i o u r e a H ( 2 2 b ) ' - - N ( 2 2 ) ' a t o m at 2 . 1 0 ,~. ( s y m m e t r y o p e r a t i o n x - 1, y, z, the N(3), 9 .H(22b)--N(22) angle is 149 ~ and N(3)...N(22) is 2 . 9 6 9 ( 4 ) , ~ a n d the o t h e r i n v o l v e s a CIand another thiourea molecule, i.e., CI(1)" 9 -__H(1l a ) " - - N ( l l ) " of 2.37 ~, ( s y m m e t r y operation: l x, -y, l z, the C l ( l ) " 9 - H ( l l a ) " - - N ( l 1)" angle is 159 ~ and C l ( l ) ' - . N ( l l ) " is 3 . 2 9 8 ( 3 ) , ~ ) . A listing o f h y d r o g e n b o n d i n g c o n t a c t s is g i v e n in T a b l e 4.
"H atoms were included in the model at their calculated positions, i.e., A--B 0.97 A, ~'The oxygen-bound H atoms were not located in the analysis.
Acknowledgment The Spanish Ministry of Education and Science ( D G I C Y T , P r o j e c t P B 9 1 / 0 7 3 4 ) a n d t h e A u s t r a l i a n Res e a r c h C o u n c i l are t h a n k e d for s u p p o r t .
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Structure o f [Pd(S = C(NH2)2)4]CI 2 92 d m t p - 2 H 2 0
6. Lenstm, A.T.H.; Bruins Slot, H.J.; Beurskens, P.T,: Haasnoot, J.G.; Reedijk, J. Reel. Tray. Chim. Pays-Bas 1989, 108, 133. 7. Romero, M.A.; Salas, J.M.; Quirds, M,: Williams, D.J.; Molina, J. Transition Met. Chem. 1993, 18, 595, 8. Salas, J,M.; Enrique, C.; Romero, M.A.: Takagi. K.; Aoki, K.; Miyashita, Y., Sub, I.-H. Polyhedron 1992, II, 2903. 9. Salas, J. M.; Romero, M.A.; Enrique. C.; Sirera, R.; Faure. R. Acta Cry.stallogr. 1993, C49, 1902. 10. teXsan Single crystal structure analysis sol;ware. Version I. 6. 1993, Molecular Structure Corporation: The Woodlands, TX. I 1, Johnson, C.K. ORTEPII, ORNL Report 5138, 1976, Oak Ridge National Laboratory: TN. 12. Yamaguchi, A,: Penland, R.B.: Mizushima, S.; Lane, T.J.; Curran, C.; Quagliano, J,V. J. Am. Chem. Soc. 1958, 80, 527.
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