Indian Journal of Chemistry Vol. 398, March 2000, pp. 177 -182
The crystal and molecular structure of 2-aminocyclopentene-l-dithiocarboxy-S- acetic acid and its methyl ester.
V Garcia-Montalvo, M A Santana-Valdes, S Hernandez-Gonzalez, G Espinosa-Perez & R Cea-Olivares*.
Institute of Chemistry, National Autonomous University of Mexico (UN AM).
Circuito Exterior, Ciudad Universitaria, Mexico 04510, D F, Mexico.
Received 25 September 1998; accepted 29 February 1999
e-mail: cea@servidor.unam.mx
The crystal and molecular structure of 2-aminocyclopentene-l-dithiocarboxy-S-acetic acid (ACDASA) and its methyl ester (ACDASAME) have been obtained. The ACDASA structure confirms that the CH2COOH group is bonded to one of the sulphur atoms· instead to the nitrogen atom. ACDASA exists as a dimer through the interaction between the carboxylate groups and exhibits additional inter and intramolecular hydrogen bonds. ACDASAMe is monomeric with secondary bonds.
With the formation of the Me ester in ACDASAMe the early dimeric interaction is destroyed, but there is a new N-H ... O intermolecular secondary bond, while the N-H ... S intramolecular hydrogen band is still present.
Main Group and transition metal complexes of 2- aminocyclopentene-l-dithiocarboxylic acid (ACDA) and its derivatives have been extensively studied from the synthetic and structural points of view and also as models for metal sulphur proteins '-J. Some years ago, Nag et.
at
reported the synthesis of a very interesting ligand (2-aminocyclopentene-I-dithiocarboxy)-S- acetic acid (ACDASA) and some of its transition metal derivatives. ACDASA was obtained by the_ reaction between ACDA and monochloroacetic acid.The spectroscopic data, JR, MS, PMR indicate that the attack is on the sulphur atoms instead of the nitrogen atom. Besides, the IR spectrum suggests the presence of a dimeric structure, formed by an intramolecular hydrogen bonding between two COOH groupS4.
It is interesting to note that in the same article Nag et al. pointed out that an X-ray crystallographic study of the ACDASA ligand confirmed the proposed structure4, however the corresponding reference indicates a personal communication5. Hitherto, we were unable to find in the literature the reported structure of such ligand. As part of our interest in the main group complexes of ACDA and its derivatives6-7
, we considered that it would be useful to report the full crystal and molecular structure of ACDASA in order to confirm that the CH2COOR group (R = H or Me) is bonded to one of the sulphur atoms and also to identify which are the intermolecular interactions present in the dimeric
structure proposed for ACDSA. In addition, we report the structure of its methyl ester derivative (ACDASAMe) in order to compare both structures and try to understand the coordination chemistry of these two ligands. Both compounds have been characterized by melting points, IR, PMR, mass spectra and X-Ray diffractometry.
Experimental Section
General. All the chemicals used were of reagent grade. ACDA was obtained according to the described methods8, ACDASA as reported by Nag el a! FT-IR spectra were obtained on a Nicolet FT-IR Magna 7650 spectrophotometer \Ising KBr pellets, elemental analyses in a commercial laboratory, while mass spectra on a lEOL lMS-5X I 02A instrument using the technique of EI.
Preparation of ACDASAMe
ACDASA (73g, 3.3 mmoles) was dissolved in MeOH, and a catalytic amount of HC) was added to it. After 20 min, the yellow precipitated was filtered washed several times with water and MeOH, dried in the air and recrystallized from ethanol, yield 0.46 g (70%), mp 119-120. (Found C, 46.00%; H 5.45%; N 5.99%. C9H13N02S2 requires C 46.73%; H 5.66%; N 6.05%; M 231). 1R (KBr) 3324 s, 1735s, 1617s, 1467 vs., 1159s em-I; I H NMR 8 (CDCl,): CH2(4) q 1.8-2.0;
CH2 (3 a"d 5) t 2.6-2.70 and III 2.8-3.0; CI-I3(9) s 3.7;
CH2(7) s 4.2; NI-I(free) bs 6.0; NH(chelatcd) bs 11.2. IJC(I)
178 INDIAN J CHEM, SEC B, MARCH 2000
118; C(2) 168.1; C(J) 32.6; C(4) 20.6; C(5) 35.4; C(o) 200.0; C(7) 36.6; C(8) 169.8; C(9) 52.7. MS (EI) mle 231(52%) M+, 158(40%), 126 (iOO%).
R-X determination:
Suitable crystals for X-ray single crystal structural determination were obtained by careful layering of a solution of both ACDASA or ACDASAMe in CH2CI2
with n-hexane at room temperature. ;\CDASA and ACDASAMe crystals cell parameters were obtained from 40 reflections in the range 5.07 < 28 < 24.249 and 45 reflections in the rangc 8.42 < 28 < 25.12.
respectively. Data collections were carried on a SIEMENS P4 diffractometer at room temperature, with graphite-monochromated Mo-Kn radiation ("-=0.71073). Intensity data were corrected for background and Lorentz-polarization effects, an absorption correction was applied for ACDASAMe (face-indexed numerical, min.lmax. transmission factors 0.8923/ 0.9448). The structures were solved by direct methods and full matrix least squares refinement using the program SIEMENS-PLUS (PC version( Non-hydrogen atoms refinement anisotropically; the hydrogen atoms included in idealized positions, except for the hydrogen atom bonded to oxygen. Final difference Fourier maps were
0.27 and -0.25 eA-3 and 0.25 and -·0.22 eA-3 for ACDASA and ACDSAMe, respectively. A summary of crystallographic and structure solution data for ACDASA and ACDASAMe is presented in Table I.
Fractional coordinates and thermal parameters have been assembled in Tables II and III for ACDASA and ACDASAMe, respectively.
Results and Discussion
The spectroscopic and analytical data confiml the synthesis of ACDASAMe, the close res~mblance in IR and 'H NMR spectra with other ACDA derivatives leads to the conclusion that there exist an intnmolecular hydrogen bonding between -NH2 and C=S groups in this molecule.
ACDASA and ACDASAMe Were amenable to the study by single crystal X-ray diffraction. Tables IV and V show the corresponding bond distances and angles for ACDASA and ACDASAMe and Figures 1 and II the molecular structure with the atom numbering scheme. Figures III and IV show the inter and intramolecular hydrogen bonds existing in both compounds.
The five-membered rings in ACDASA and ACDASAMe are quite similar with such reported for ACDA'O or other ACDA derivativeso,7. The C(l )-C(2)
Table I-Crystallographic data for ACDASA and ACDASMe
Compound HACDASA ACDASMe
Formula CxHIIN02S2 CqHuN02S2
Formula weight 217.3 231.3
Crystal size mm !lAO x 020 x O.I() 0.34 x 0.24 x 0.14
Crystal color, habit Yellow, prism Colorless, prism
Crystal system Monoclillic Orthorombic
Space group P2/n P212121
A.A 7806(2) 7.844(2)
B,A I 1.991 (2) 8.388(3 )
c, A I 1.074(2) 17.488(6)
~: 101.:14(2) ---
Volume, A \ 1016.20(11) 1150.5( I)
Dgcalcd, cm·3 4 4
Radiation wavelength. A 0.71073 0.71073
Temperature, K 293 293
11, CIll ·1 4.91 4.38
Number of unique reflections 2341 2375
Number of observed reflections 1256 1442
Range of Ilk! O~II~ I() -I ~ II ~ II
o
~ k ~ 15 -I ~ k ~ II-14s!~ 14 -I ~! ~ 24
R % (Obs. data) 4.97 406
R %( 9.92 6.62
GOF 1.14 1.02
F(OOO) 456 4g8
GARCIA-MONT AL VO et al.: STRUCTURE OF 2-AMINOCYCLOPENTENE-I-DITHIOCARBOXY -S-ACETIC ACID 179
Table II-Atomic coordinates (x 104) and equivalent isotropic displacement coefficients
(A
x 103) for ACDASA.C(I) C(2) N(I) C(3) C(4) C(5) C(6) S(I) S(2) C(7) C(8) 0(1) 0(2)
x 2401(5) 2764(6) 2863(7) 3049(8) 2950(8) 2367(7) 2065(5) 1537(2) 2138(2) 1251 (7) 2921(7) 2681 (5) 4336(5)
y 259(3) -506(3) -321(3) -1650(4) -1521(4) -328(4) 1402(3) 2065( I) 2100(1 ) 3496(4) 4127(4) 5074(3) 3817(3)
Equivalent isotropic U defined as one third of the trace of the orthogonalized Uij tensor.
Z 5044(4) 6000(4) 7186(4) 5551 (5) 4179(5) 3865(4) 5156(4) 3 712( I) 6482( I) 4090(5) 4512(4) 5028(4) 4344(4)
U(eq) 39( I) 42( I) 57(2) 60(2) 65(2) 55(2) 39( I) 53( I) 57( I) 54(2) 52(2) 71 (2) 65( I)
Table III-Atomic coordinates (x 104) and equivalent isotropic displacement coefficientes (A x 103) for ACDASAMe.
x Y
C(\) 1573(5) 1344(5)
C(2) -87(5) 727(5)
N(I) -976(4) -206(5)
C(3) -790(6) 1299(6)
C(4) 750(7) 1969(7)
C(5) 2066(6) 2377(6)
C(6) 2589(5) 1130(4)
SCI) 4527(\) 2222(1)
S(2) 2086(2) 23(2)
C(7) 5610(5) 1780(5)
C(8) 5029(5) 2718(5)
0(\) 5838(4) 2219(4)
0(2) 4029(4) 3798(4)
C(9) 5463(9) 3069(7)
Z 8313(2) 8433(2) 7977(2) 9187(2) 9608(3) 8993(2) 7654(2) 7719(1 ) 6880( 1)9 6840(2) 6165(2) 5534(2) 6154(2) 4834(3) Equivalent isotropic U defined as one third of the trace of the orthogonalized Uii tensor.
Table IV-Interatomic distances (A) and angles (0) for ACDASA.
Interatomic distances A
C( I )-C(2) C(2)-C(3) C(3)-C(4) C(4)-C(5) C( I )-C(5) C(2)-N(I ) C( I )-C(6) C(6)-S( I) C(6)-S(2) S( I )-C(7) C(7)-C(8) C(8)-0( I) C(8)-0(2)
Hidrogen Bonds A····H-D
1.387(6) 1.492(6) 1.513(8) 1.527(7) 1.509(6) 1.319(6) 1.405(6) 1.761(4) 1.681(4) 1.790(5) 1.500(7) 1.30 I (6) 1.214(7)
System A···H-D Distance A-H 0(2) ····H-O(IA) 1.963(64)
C(2)-C( I )-C(5) C( I )-C(2)-C(3) C(2)-C(3)-C(4) C(3 )-C(4)-C(5) C( I )-C(5)-C( 4) C(2)-C( 1 )-C(6) C(5)-C( 1 )-C(6) C( I )-C(2)-N( I) C(3 )-C(2)-N( I) C( 1 )-C(6)-S( I) C( 1 )-C(6)-S(2) S( I )-C(6)-S(2) C(6)-S( 1 )-C(7) S( I )-C(7)-C(8) C(7)-C(8)-0( I ) C(7)-C(8)-0(2) O( 1 )-C(8)-0(2)
Bond angles (0)
Symmetry I-x, I-y. I-z
U(eq) 48( I) 50(1 ) 66( I) 66(2) 93(2) 71 (2) 47( I) 58( I) 62(1 ) 61 (I) 54( I) 81 (I) 70(1) 105(3)
109.5(4) 112.1(4) 105.0(4) 107.5(4) 105.3(4) 126.2(4) 124.2(4) 127.7(4) 120.2(4) 112.0(3) 126.0(3 ) 122.0(2) 103.7(2) 114.6(4) 112.7(5) 124.0(4) 123.2(5)
S(2) ······H-N( 1 A) 2.626(57)
Distance D-A 2.653(5) 3.427(4) 3.029(4)
Angle DHA 166.1(7.5) 149.7(4.4) 139.4(5.2)
0.5-x, -0.5 + y, 1.5 -z S(2) ····H-N( I) 2.292(59)
180 fNDIAN J CHEM, SEC B, MARCH 2000
Table V-Interatomic distances (A) and angles CO) for compounds ACDASAMe.
Interatomic distances A Bond angles CO)
C( I )-C(2) C(2)-C(3) C(3)-C(4) C(4)-C(5) C( I )-C(5) C(2)-N(I ) C(1)-C(6) C(6)-S( I) C(6)-S(2) S( I )-C(7) C(7)-C(8) C(8)-0( I) C(8)-0(2) C(9)-0(1)
Hydrogen Bonds A ·····H-D System A H-D
0(2) ····H-N(IA )
S(2) " H-N( I)
1.415(5) 1.5 I 0(6) 1.521 (7) 1.529(7) 1.523(6) 1.3 I 5(5) 1.412(5) 1.778(4) 1.689(4) 1.795(4) 1.493(6) 1.341 (5) 1.196(5) 1.446(6)
Distance H-A 2.09(2»
2.38(4)
NllI
Distance D-A 2.955(2) 3.081(4)
C(2)-C( I )-C(5) C( I )-C(2)-C(3) C(2)-C(3)-C(4) C(3 )-C( 4 )-C(5) C( I )-C(5)-C(4) C(2)-C( I )-C(6) C(5)-C( I )-C(6) C( I )-C(2)-N( I ) C(3 )-C(2)-N( 1 ) C( I )-C( 6)-S( I ) C( I )-C(6)-S(2) S( I )-C(6)-S(2) C( 6 )-S( I )-C(7) S( I )-C(7)-C(8) C(7)-C(8)-0( I ) C(7)-C(8)-0(2) O( I )-C(8)-0(2) C(8)-0( 1 )-C(9) Angle DHA
162 134(2)
Symmetry
Figure I--ORTEP view of ACDASA with the atom numbering squeme.
~----
C2
52
109.0(3) 110.5(3) 104.4(4) 106.3(4) 104.4(4) 126.4(3) 124.4(4) 128.0( 4) 121.5(4) 111.5(3) 126.2(3) 122.3(2) 104.1(2) 115.1 (3) 109.8(3) 127.7(4) 122.4(4) 116.4(4)
-x, 0.5 + y, 1.5 -z
~C9
C8
~
Figure 2---ORTEP view uf ACDASAMe with the atom numbering squeme.
GARCIA-MONTALVO el al.: STRUCTURE OF 2-AMINOCYCLOPENTENE-I-DITHIOCARBOXY-S-ACETIC ACID 181
Figure 3----Structure of ACDASA showing the intra and intermolecular secondary bonds.
y
Figure 4--Stru:;ture of ACDASAMe showing the intra and intermolecular secondary bonds.
bond shows a double bond character, as well as C(2)- C(3) and C(1)-C(5) bonds. This is due to the hyperconjugation of the pi bond system. The short distance C(2)-N(l) in both compounds is indicative of the double bond character, also bond angles S(2)- C(6)-C(J), C(2)-C(J)-C(6) and C(J)-C(2)-N(J) are bigger than the expected 1200 for an Sp2 hybridization.
It may be due to the presence of a hydrogen bond, which forms a six-membered ring. All other distances an angles show a normal behavior.
The main feature of the study is the confirmation that -CH2COOR (R = H, Me) is bonded to one of the sulphur atoms of the dithio portion, and the possibility of the N- bond is discarded. ACDASA forms a dimeric planar ring by intramolecular hydrogen bonding with other ACDASA molecule, as usually seen in organic carboxylic acids, and in agreement with the structure indicated by Nag4, however the situation with other secondary bonds is more complex. Also Nag pointed to the presence of an intramolecular N-H ... S bond, nevertheless in the structural determination reported here we found two N-H ... S interactions, one intramolecular and the other intermolecular (Figure 3). As expected, with the formation of Me ester in ACDASAMe, the early dimeric interaction was destroyed, but there appears a new N-H ... O intermolecular secondary bond, while the N-H ... S intramolecular hydrogen bond is still present (Figure 4).
Acknowledgment
This work was supported by a CONACYT Grant (OJ09P-E).
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182 rNDIAN J CHEM, SEC B, MARCH 2000
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