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Supramolecular Signatures of AdenineContaining Organostannoxane Assemblies Vadapalli Chandrasekhar, Subrata Kundu, Jitendra Kumar, Sandeep Verma, Kandasamy Gopal, Amaresh Chaturvedi, and K Subramaniam Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/cg3018776 • Publication Date (Web): 15 Feb 2013 Downloaded from http://pubs.acs.org on February 27, 2013

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Crystal Growth & Design

Supramolecular Signatures of Adenine-Containing Organostannoxane Assemblies Vadapalli Chandrasekhar*a,b, Subrata Kundua, Jitendra Kumara, Sandeep Vermaa,c, Kandasamy Gopala, Amaresh Chaturbedid, Kuppuswamy Subramaniamd a

Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur – 208016, India. Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, 21, Brindavan Colony, Narsingi, Hyderabad- 500 075 c DST Thematic Unit of Excellence on Soft Nanofabrication, Indian Institute of Technology Kanpur, Kanpur – 208016, India. d Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur – 208016, India. b

RECEIVED DATE (to be automatically inserted after your manuscript is accepted if required according to the journal that you are submitting your paper)

CORRESPONDING AUTHOR FOOTNOTE: * To whom correspondence should be addressed. E-mail: [email protected]. Phone: (+91) 512-259-7259. Fax: (+91) 521-259-0007 / 7436.

ACS Paragon Plus Environment


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Abstract

The reaction of 3-(N9-adeninyl) propanoic acid (LH) with various di- and triorganotin oxides have been investigated. Thus, the reaction of di-tert-butyltin oxide (t-Bu2SnO)3 in a 3:1 ratio afforded the dinuclear derivative

[t-Bu2Sn(µ-OH)L]2 ·7H2O (1). A similar reaction

involving bis(tri-n-butyltin)oxide, (n-Bu3Sn)2O, in a 2:1 ratio afforded the one-dimensional coordination polymer [n-Bu3SnL· 0.33H2O]n ( 2). Similarly the reaction with (n-Bu2SnO)n in a 2:1 ratio afforded the tetranuclear [{n-Bu2Sn}2(µ3-O)(µ2-OH)L]2 (3). On the other hand a similar reaction in a 1:1 ratio also gave the tetranuclear product [{n-Bu2Sn}2(µ3-O) L2]2 (4). The molecular structure of 1 reveals a central dinuclear Sn2O2 motif where the two tin centers are bridged by two µ-OH groups. Each tin is bound with a mono dentate carboxylate group; the C=O unit of these carboxylates are involved in an intramolecular hydrogen bonding with the bridging OH unit. The supramolecular structure of 1 reveals the formation of a 1D-zig-zag chain mediated by intermolecular hydrogen bonding interaction through the Watson-Crick or the Hoogsteen faces. 2 is a 1D-coordination polymer formed by the successive bridging of triorganotin units by the carboxylate ligand, L. The supramolecular structure of 2 reveals that two 1D coordination polymers interact to generate novel adenine homotrimers formed as a result of alternating Watson-Crick-Watson-Crick and Hoogsteen-Watson-Crick interactions.

The molecular

structures of 3 and 4 reveal them to be tetranuclear possessing a ladder-like structure. The essential difference between their molecular structures is that in the 4 there are four carboxylate ligands while in 3 there are only two. Both of these complexes reveal intramolecular and intermolecular hydrogen bonding and π…π stacking interactions. The nematicidal activity of 1-3 was examined against Caenorhabditis elegans. Compound 2 was found to be highly active, effecting a high mortality even at very low concentrations such as 25 or 10 ppm.

Keywords Adenine, organostannoxane, supramolecular assembly, 3-(N9-adeninyl) propanoic acid, organotin carboxylate, nematicidal activity


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Introduction Organotin compounds have been of importance for a variety of reasons including their biological and catalytic activity.1A number of organotin compounds have shown considerable promise, as anti-neoplastic agents.2 Many triorganotin compounds have biocidal activity and many anti-fouling paints were formulated using trialkyltin compounds which were particularly effective against molluscs.3 In recent years, however, the environmental concerns regarding organotin compounds have dampened this utility to some extent.4 The use of triorganotin hydrides in organic synthesis is well documented.5 There have also been several reports on the use of organooxotin compounds as catalysts particularly in esterification reactions.6 Among organotin compounds, organostannoxanes, prepared from the reactions of organotin oxides, -hydroxides and -oxide-hydroxides with protic reagents such as carboxylic acids, phosphinic acids, phosphonic acids or sulfonic acids have received special attention particularly in view of the immense structural diversity that is present in this family of compounds.7Another aspect of interest is the ability of some of these compounds to serve as scaffolds for supporting a functional periphery that is electrochemically, photochemically or catalytically active.8 Also, a number of supramolecular frameworks have been found in the crystal structures of organostannoxanes which were formed with the help of noncovalent interactions such as H-bonding, C–H···π and π···π interactions.9 One of the most aesthetically pleasing supramolecular architecture realized in these systems is the Rangoli pattern in the hexaferrocenyl derivative, [n-[BuSn(O)(OCH2C5H4FeC5H5)]6.10 In view of the structural diversity of organostannoxanes, we were intrigued by the possibility of decorating them with nucleobases to investigate the supramolecular signatures that can detected in such systems. In particular, we were interested in capturing rare or unique nucleobase supramolecular motifs. To test this concept we chose to assemble different types of organostannoxanes that contained adenine units. Adenine and its derivatives are well-known to participate in a variety of hydrogenbonding interactions.11 Among the most important of these are the Watson-Crick interaction as observed in DNA12 or the Hoogsteen interactions that dominate the complexes of adenine with Rebek imides.13In addition, adenine and its derivatives can also be involved in hydrogen bonding to afford homodimers.14 Furthermore, adenine also possesses a delocalized π-electron system which allows the possibility of π…π / C-H...π interactions.15 Many novel supramolecular



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structures based on adenine-metal coordination as well as other non covalent interactions have been reported recently.16 In view of this interest, in this paper, we report our findings on the synthesis and structural characterization of [t-Bu2Sn(µ-OH)L]2 ·7H2O (1), [(n-Bu3Sn)3L3·H2O]n (2), [{n-Bu2Sn}2(µ-O)(µ-OH)L]2 (3) and [{n-Bu2Sn}2(µ3-O) L2]2 (4) [LH = 3-(N9-adeninyl) propanoic acid]. Interestingly, the coordination polymer 2 displays a unique adenine homotrimer which to the best of our knowledge is an unprecedented supramolecular motif. Experimental Section Reagents and General Procedure All the reactions were performed under a dry nitrogen atmosphere by employing standard Schlenk techniques. Solvents were stored over appropriate reagents and distilled under nitrogen prior to use. [n-Bu2SnO]n, [(n-Bu3Sn)2O] were purchased from Aldrich and used as supplied. 3-(N9-adeninyl) propanoic acid, LH,17 and [t-Bu2SnO]318 were prepared according to literature procedures. Instrumentation 1

H and

119

Sn NMR spectra were recorded on a JEOL JNM Lambda spectrometer

operating at 500.0 and 150.0 MHz respectively. The chemical shifts are referenced with respect to tetramethylsilane (for 1H) and tetramethyltin (for 119Sn). High resolution ESI-MS spectra were recorded on a MICROMASS QUATTRO II triple quadrupole mass spectrometer. Methanol was used as the solvent for the ESI-MS studies. IR spectra were recorded as KBr pellets on a Bruker Vector 22 FT IR spectrophotometer operating from 400 to 4000 cm-1. Elemental analyses were carried out using a thermoquest CE instruments model EA/110 CHNS-O elemental analyzer. Melting points were recorded using a JSGW melting point apparatus and are uncorrected. TGA measurements were carried out using a Perkin-Elmer Pyris6 thermogravimetric analyzer at a heating rate of 10 °C/min under an argon atmosphere. Synthesis of various organostannoxanes A stoichiometric mixture of the organotin oxide precursor and LH in toluene (70 mL) was heated under reflux for 6 h. The water formed in the reaction was removed by using a DeanStark apparatus. The reaction mixture was evaporated to afford the corresponding products. Specific details of each reaction are given below. [t-Bu2Sn(µ-OH)L]2 ·7H2O (1)


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[t-Bu2SnO]3 (0.23 g, 0.32 mmol); HL (0.186 g, 0.90 mmol). Yield: 0.365 g (78.29 %). M.p.: 144 °C. Elemental Analysis: Calcd (%) for C64H122N20O19Sn4: C, 39.41; H, 6.30; N, 14.36. Found: C 39.11; H, 6.60; N, 14.11. 1H NMR (500 MHz, CD3OD, 25 °C) (δ, ppm): 1.38 (s, 36H, t-butyl CH3), 2.91 (t, 4H, CH2), 4.49 (t, 4H, N-CH2), 8.12 (s, 2H, C8-H), 8.18 (s, 2H, C2-H). 119

Sn NMR (δ, ppm): –262.12 (s). IR (KBr, ν/cm-1): 3104.19 (m, br), 2923 (m), 2832 (m, br),

1705 (s), 1622 (m), 1505 (m), 1440 (s), 866 (s, br), 715 (s), 644 (s). ESI-MS: m/z (%) 954.2167 [{(t-Bu2Sn)2(OH)L}2(1) + CH3CN + H]+ (30). Colorless crystals of 1 were obtained by a slow evaporation of its 1:1 methanol/dichloromethane solution. Synthesis of [n-Bu3SnL· 0.33H2O]n ( 2) [n-Bu3Sn]2O (0.36 g, 0.6 mmol); HL (0.25 g, 1.2 mmol). Yield: 0.56 g (92.7 %). M.p.: 97 °C. Analysis. Calcd (%) for C20H35N5O2Sn: C, 48.41; H, 7.11; N, 14.11. Found: C, 48.26; H, 7.18; N, 13.89. 1H NMR (500 MHz, CD3OD, 25 °C) (δ, ppm): 0.86(t, 9H, n-butyl CH3), 1.081.52 (m, 18H, n-butyl CH2), 2.83 (t, 2H, CH2), 4.42 (t, 2H, N-CH2), 8.06 (s, 1H, C8-H), 8.17 (s, 1H, C2-H). 119Sn NMR (δ, ppm): 123.6 (s). IR (KBr, ν/cm-1): 3477 (m), 3331 (m, br), 3160 (m, br), 2955 (s), 2921 (s), 2853 (m), 1655 (s), 1587 (s), 1417 (s), 1306 (s), 1250 (m), 877 (m), 846 (m), 666 (s), 607 (s), 537 (m). ESI-MS: m/z (%) 291.1218 [n-Bu3Sn]+ (100), 498.2063 [nBu3SnLH]+ (8), 625.2427 [(n-Bu3Sn)2(HCOO)]+ (95), 786.3177 [(n-Bu3Sn)2L]+ (2), 1015.3819 [(n-Bu3Sn)2 (L)2Na]+ (2). Colorless crystals of 2 were obtained from slow evaporation of a chloroform solution of 2. [{n-Bu2Sn}2(µ3-O)(µ2-OH)L]2 (3) [n-Bu2SnO]n (0.38 g, 1.5 mmol); HL (0.157 g, 0.76 mmol). Yield: 0.451 g (84.3 %). M.p.: 210 °C. Elemental Analysis: calcd. (%) for C48H90N10O8Sn4: C, 40.88; H, 6.43; N, 9.93; found: C, 41.13; H, 6.56; N, 9.65. 1H NMR (500 MHz, DMSO-d6, 25 °C) (δ, ppm): 0.78 (t, 24H, n-butyl CH3), 1.06-1.96 (m, 48H, n-butyl CH2’s), 2.89 (t, 4H, CH2), 4.34 (t, 4H, N-CH2), 8.06 (s, 2H, C8-H), 8.10 (s, 2H, C2-H). IR (KBr, ν/cm-1): 3314 (m, br), 3330 (m, br), 2956 (s), 2924 (s), 2855 (m), 1618 (s), 1414 (m), 1361 (s), 1302 (m) 1019 (m), 944 (m), 681 (s), 606 (m, br). ESIMS: m/z (%) 279.0543 [n-Bu2Sn(OOCH)]+ (50), 440.1256 [n-Bu2SnL]+ (6), 688.1673 [(nBu2Sn)2(µ-O)L]+ (5), 821.1776 [(n-Bu2Sn)3(µ-O)2(HCOO)2]+ (30). Colorless crystals of 3 were obtained by a slow evaporation of its 1:1 methanol/acetonitrile solution. [{n-Bu2Sn}2(µ3-O) L2]2 (4)



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[n-Bu2SnO]n (0.19 g, 0.76 mmol); HL (0.157 g, 0.76 mmol). This reaction afforded an insoluble product. Attempts to grow crystals by dissolving in many solvents did not succeed. However, the product could be solubilized in a mixture of triethylamine/methanol/chloroform (v/v/v: 0.1:1:1) and kept for crystallization affording crystals of 4. Yield: 0.29 g (81 %). M.p.: 225 °C. Elemental Analysis: Calcd. (%) for C64H104N20O10Sn4: C, 42.98; H, 5.86; N, 15.66; found: C, 42.87; H, 5.97; N, 15.55. IR (KBr, ν/cm-1): 3358 (m, br), 3275 (m, br), 3143 (m, br), 2952 (s), 2928 (s), 2866 (m), 1678 (s), 1661 (s), 1643 (s), 1603 (s), 1575 (s), 1420 (m), 1304 (s), 1242 (m), 1082 (m), 727 (m), 635 (m, br), 609 (s).

Single crystal X-ray crystallography Suitable crystals for single crystal X-ray diffraction studies were loaded on a Bruker AXS Smart Apex CCD diffractometer using a MoKα (λ = 0.71073 Å) sealed tube. All the structures were solved by direct methods using SHELXS-9719a and refined by full-matrix least squares on F2 using SHELXL-97. The program SMART19b was used for collecting frames of data, indexing reflections, and determining lattice parameters, SAINT19c for integration of the intensity of reflections and scaling, SADABS19d for absorption correction, and SHELXTL19e for space group and structure determination and least-squares refinements on F2. Hydrogen atoms were fixed at calculated positions and their positions were refined by a riding model. The N-H and O-H proton ware included from the electron density map and refined isotopically. Non-hydrogen atoms were refined with anisotropic displacement parameters. Details of the data collection and refinement parameters are given in Table 1. The crystallographic figures have been generated using Diamond 3.2g 19f and ORTEP softwares.19g Results and Discussion Synthesis Although the reactions of organotin oxides with carboxylic acids afford various types of products, an excellent control on product formation is often achieved by the nature and number of organic substituents present on tin.20 Accordingly we chose (n-Bu3Sn)2O, [n-Bu2SnO]n, and [t-Bu2SnO]3 as the organotin oxide precursors. In order to introduce the adenine motif on the stannoxane platform, we have chosen the adenine-appended carboxylic acid, 3-(N9-adeninyl) propanoic acid, as a convenient precursor.21


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The reaction of (t-Bu2SnO)3 with LH in toluene in a 1:3 ratio afforded the hydroxidebridged dimer, [t-Bu2Sn(µ-OH)L]2 ·7H2O (1) (Scheme 1).

Scheme 1: General synthetic procedure for the complexes 1-4; R and R′ represent n-butyl and t-butyl group respectively. In contrast, the reaction of [n-Bu2SnO]n with LH in a 1:1 molar ratio afforded an intractable product. Upon reducing the stoichiometric ratio between [n-Bu2SnO]n and LH (1:0.5) we obtained the tetranuclear derivative [{n-Bu2Sn}2(µ-O) (µ-OH)L]2 (3) (Scheme 1).

As

anticipated, the reaction of [n-Bu3Sn]2O with two equivalents of LH in toluene resulted in the carboxylate-bridged coordination polymer [n-Bu3SnL]n (2) (Scheme 1). The intractable product obtained

in

the

1:1

reaction

as

described

above

was

treated

dissolved

in

a

triethylamine/methanol/chloroform mixture (v/v/v: 0.1:1:1) and kept for crystallization affording 4. However, the latter was found to be insoluble in many solvents/solvent mixtures and hence we could not carry out its characterization in solution. While 1 and 2 are soluble in polar solvents such as CHCl3 and CH3OH, 3 has very poor solubility.

119

Sn {1H} NMR spectra of 1 and 2

shows singlets at –262.1 (s) and 123.6 (s) ppm respectively. ESI-MS of 1 under positive ion



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ionization mode showed a peak at

m/z (%) 954.2167

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which corresponds to [{(t-

Bu2Sn)2(OH)L}2(1) + CH3CN + H]+ (Figure 4 and Figure S1) indicating that the structural integrity of 1 is retained in solution. The ESI-MS of 2 reveals, as anticipated, a breakdown of the coordination polymer and shows peaks at

498.2063 [n-Bu3SnLH]+, 625.2427 [(n-

Bu3Sn)2(HCOO)]+, 786.3177 [(n-Bu3Sn)2L]+ (2) and 1015.3819 [(n-Bu3Sn)2 (L)2Na]+ (Figure S2). Similarly the ESI-MS of 3 also reveals a breakdown of the tetranuclear derivative in solution: m/z (%) 279.0543 [n-Bu2Sn(OOCH)]+, 440.1256 [n-Bu2SnL]+ (6), 688.1673 [(nBu2Sn)2(µ-O)L]+, 821.1776 [(n-Bu2Sn)3(µ-O)2(HCOO)2]+ (Figure S3). We have also carried out the thermogravimetric analysis of 1-4; these data are given in the Supporting Information (Figure S4). Nematicidal activity In view of the known biological activity of oragnotin compounds22 we were interested in knowing if the organotin adenine carboxylates would be show nematicidal activity. The summary of results is given in Table S1. These indicate that compound 2, containing the trioragnotin motif is the most active compound, effecting a high mortality on Caenorhabditis elegans even at very low concentrations such as 25 or 10 ppm (Table S1, Supporting Information). Crystal structure of [t-Bu2Sn(µ-OH)L]2 ·7H2O (1) The molecular structure of 1 is depicted in Figure 1 and its crystal structure refinement parameters have been provided in Table 1. Complex 1 crystallized as a discrete dimer where the two tin atoms are bridged by two hydroxide ligands to generate a four-membered Sn2O2 ring. Additionally, seven different non-coordinated water molecules are also encountered in the lattice as solvent of crystallization. The asymmetric unit of 1 consists of two crystallographically unique [t-Bu2Sn(µ-OH)L] units and each unit is self- replicating on a centre of inversion to form two unique dimeric species [Figure 1(a)]. Both the tin centers are five-coordinate in a distorted trigonal bipyramidal geometry (τ = 0.511; cf. the τ values for the idealized geometries are: τ = 0, rectangular pyramidal; τ = 1, trigonal-bipyramidal)23 [Figure 1(b)] possessing two t-butyl groups, two hydroxides and one monodentate carboxylate ligand with slight variation in their bond length and angles (Table S2).


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Figure 1: (a) Molecular structure of complex 1 as an ORTEP diagram drawn at 25 % probability level with unique atoms labeled, (H atoms, part of the t-butyl group and lattice water molecules are omitted for clarity). (b) Coordination environment around Sn1 (distorted trigonal bipyramid), for other tin similar environment is there. Selected bond parameters for one of the molecules of 1 are as follows. Bond distances (Å):Sn(1)-O(4), 2.031(4); Sn(1)-O(4)*, 2.160(4); Sn(1)-O(1b), 2.205(4); Sn(1)-C(26), 2.159(7); Sn(1)-C(22), 2.168(7); Bond angles (º): Sn(1)-O(4)-Sn(1)*, 110.0(2);

O(4)-Sn(1)-O(4)*, 70.0(2); O(4)*-Sn(1)-O(1b), 154.48(17); C(18)-Sn(2)-O(1A),

94.0(2); O(4)-Sn(1)-C(26), 115.2(2); C(26)-Sn(1)-O(4)*, 98.0(2); O(4)-Sn(1)-C(22), 116.3(2); C(26)-Sn(1)-C(22), 128.5(3); O(4)*-Sn(1)-C(22), 98.9(2); O(4)-Sn(1)-O(1b), 84.50(17); C(26)Sn(1)-O(1B), 92.3(2); C(22)-Sn(1)-O(1b), 92.7(2).

The average Sn-O bond distance found in the Sn2O2 core is 2.096 (5) Å (Figure 1). The average O-Sn-O bond angle is 70.2˚ (2). The average Sn-O-Sn bond angles within the Sn2O2 core is 109. 85˚(2). The four-membered Sn2O2 ring is planar (Figure S5). The Sn-Ocarboxylate distance is 2.202(4) Å. On the other hand the Sn-O distance involving the C=O unit of the carboxylate is long 3.459(4) Å. The Sn-C bond distances 2.164 (7) Å. The bond parameters found in the present instance are comparable to literature precedents [t-Bu2Sn(O2CCH3)(µOH)]224and [t-Bu2Sn(µ-OH)L]2, (L = 1-fluorenecarboxylic acid)8e. Several hydrogen bonding interactions and other non-covalent interactions are present in the crystal structure of 1. The various hydrogen bonding parameters found in this compound are



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summarized in Table 2. The bridging hydroxide ligands are involved in an intramolecular hydrogen bonding with the C=O unit of the carboxylate ligands (Figure S6) to generate a sixmembered ring on either side of the four-membered Sn2O2 ring. Two hydrogen bonding interactions between the Watson-Crick face of the adenine unit of one entity with the Hoogsteen face of another entity allow the formation of a one-dimensional tape (Figure 2). Crystallographically different adenine units offer different faces for these interactions; as a result in a given molecule both the adenine units offer either the Watson-Crick or the Hoogsteen faces for hydrogen bonding interactions (Figure 2). In addition, one of the CH2 (C11-H2) groups of the tether that links the adenine with the carboxylate is involved in hydrogen bonding with the lattice water (C-H---O). Also, a similar hydrogen bonding is present between the NH2 unit of the adenine and the lattice water (Figure 3, Figure S7). Further, intermolecular interactions (π-π, and CH-π) between two counter-running 1D chains strengthen the supramolecular network found in 1 (Figure 2).

Figure 2: 1D zig-zag chain structure in 1 as a result of intermolecular hydrogen bonding between adenine units; π… π and C-H… π interactions are also depicted, (some of H atoms, the t-butyl groups and lattice water molecules are omitted for clarity)


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Figure 3: Partial view of the involvement of lattice water molecule in hydrogen bonding (t-Bu groups are omitted for clarity).

(a)

(b)

Figure 4: ESI-MS of 1 (a) experimental (b) theoretical Crystal structure of [(n-Bu3Sn)L]n (2) Complex 2 consists of 1D polymeric chains propagating along the crystallographic baxis, as a result of isobidentate carboxylate coordination to tin ions (η1:µ2 mode). Although, the asymmetric unit consists of three crystallographically unique tin ions namely Sn1, Sn2 and Sn3 along with three different L anions, the binding modes of the carboxylate groups are almost similar with only a slight variation in the bond length and bond angles [Table S2]. Selected bond parameters are summarized in the caption of Figure 5. Each tin is five-coordinate in a distorted trigonal bipyramidal geometry (τ = 0.732) with the oxygen atoms occupying the axial positions



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[Figure 4(b)]. The Sn-O distances are 2.387(4)Å, and 2.216(4)Å. The average Sn-C distance is 2.216(4)Å. The O-Sn-O bond angle is 171.58(15)º. The C-Sn-C bond angle is 119.4(3)º. The long bond distance between Sn and the C=O unit is 3.169Å. This distance is shorter than the sum of Van der Waals radii between the Sn and O atoms (3.69Å).25 The adenine nucleobases of the two coordination polymers interact to generate adenine homotrimers. The formation of an unprecedented trimeric adenine homotrimer motif which is formed as a result of alternating Watson-Crick-Watson-Crick and Hoogsteen-Watson-Crick interactions Figure 6). As can be seen from Figure 6, the distances between alternate adenine residues differ significantly, although they are held together with almost similar Sn-carboxylate interaction. Consequently, a peculiar scenario emerges where three crystallographically unique adenine moieties, contributed by two 1D polymeric chains, interact with each other exploiting their Watson Crick and Hoogsteen faces for hydrogen bonding to form an adenine trimer (Figure 6). Here, it can be seen that one adenine residue utilizes both its faces for H-bonding with the other two adenine residues whereas the latter two adenine units offer only one face for homoadenine trimerization. This variation in distances as a result of crystallographically dissimilar adenine residues allow lattice water molecule to occupy spaces between such trimeric species. The water molecule (O1W) interconnects such adenine trimers by behaving as a donor for N1B and N7A nitrogen atoms of terminal adenine residues from two trimeric species and as an acceptor for the exocyclic amino group N6A as shown in Figure 6. In view of the surprising discovery of the homo-adenine trimeric motif in the present instance it would be interesting to examine the possibility of the existence of such trimeric motifs in a biological mileu.


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(a)

(b)

Figure 5: (a) Asymmetric unit of 2 as ORTEP diagram drawn at 25% probability level. (H atoms, part of the n-butyl group are omitted for clarity). (b) The coordination environment around Sn1 (distorted trigonal bipyramid), for other tin similar environment is there. Selected bond parameters. Distances(Å): Sn(1)-O(1a), 2.387(4); Sn(1)-O(2C), 2.216(4); Sn(1)C(5), 2.133(6); Sn(1)-C(1), 2.155(6); Sn(1)-C(9), 2.140(6); Sn(1)-O(1c), 3.093(4).Angles(º): O(2c)-Sn(1)-O(1a), 171.58(15); C(5)-Sn(1)-C(9), 112.9(3); C(5)-Sn(1)-C(1), 117.7(3); C(9)Sn(1)-C(1), 127.6(3); C(5)-Sn(1)-O(2c), 89.7(2); C(9)-Sn(1)-O(2c), 96.5(2); C(1)-Sn(1)-O(2c), 96.27(19); C(5)-Sn(1)-O(1a), 83.9(2); C(9)-Sn(1)-O(1a), 91.0(2); C(1)-Sn(1)-O(1a), 82.04(19);.



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Figure 6: Hydrogen bonding in 2 with adenine trimers highlighted in the inset rectangle; inset shows the adenine trimer with the number scheme. Fragmented bonds indicate hydrogen bonding interactions. (n-Bu groups have been omitted for clarity) The other crystal stabilizing interaction comes from face-to-face C-H…π interactions (2.605 Å, 2.666 Å and 2.826 Å) (Figure 7) between the adjacent 2D hydrogen bonded sheets as shown with fragmented bonds to form the 3-D supramolecular structure (Figure S8).

Figure 7: C-H…π interaction between adjacent layers in 2 (n-Bu groups have been omitted for clarity)


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Crystal structure of [{n-Bu2Sn}2(µ-O)(µ-OH)L]2 (3) The molecular structure of the hydroxide-bridged tetrameric organostannoxane ladder 3 is shown in Figure 8(a). This reveals that there are two distannoxane motifs which are fused to each other to form a ladder like structure. Apart from the two hydroxide bridges (O3 and O3*) in the two stannoxane units, there are two capping (µ3-O) oxygen atoms O4 and O4* which also serve to bridge the stannoxane units.

The selected bond parameters corresponding to the

tetrameric stannoxane core are summarized in the caption of Figure 8. Details of other bond parameters are given in Table S2. The molecular structure of 3 shows that the two adenine moieties, related by a center of inversion, are supported by a planar Sn4O2(OH)2 core( Figure S9). The adenine carboxylate binds to the terminal tin atoms in an anisobidentate chelating mode as can be seen by the difference the corresponding Sn-O bond lengths: Sn1-O1, 2.164(6) and Sn1-O2, 2.837(7) Å. (Table S2). The terminal tin atoms (Sn1 and Sn1*) in complex 3 are six- coordinate [Figure 8(b)] while the central tin atoms (Sn2 and Sn2*) are five-coordinate [Figure 8(c)].



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Figure 8: (a) Molecular structure of 3 as ORTEP representation drawn at 25% probability level. (H atoms, part of the n-butyl group are omitted for clarity). (b) Coordination environment around Sn1 (Sn1*), distorted trigonal prism (c) coordination environment Sn2 (Sn2*), distorted trigonal bipyramid. Selected bond Parameters. Distances: O(1)-Sn(1), 2.164(6); Sn(1)-O(2), 2.838(65); O(3)-Sn(1), 2.268(5); O(4)-Sn(1), 2.013(5); Sn(2)-O(4)*, 2.129(6); O(3)-Sn(2), 2.153(5); O(4)Sn(2), 2.042(5). Angles:

Sn(2)-O(3)-Sn(1), 98.6(2); Sn(1)-O(4)-Sn(2),111.6(3); Sn(1)-O(4)-

Sn(2)*, 141.2(3); Sn(2)-O(4)-Sn(2)*,

107.1(2); O(4)-Sn(1)-O(1), 81.8(2); O(4)-Sn(1)-O(3),

73.9(2); O(1)-Sn(1)-O(3), 155.5(2); O(4)-Sn(2)-C(25), 114.6(5); O(4)-Sn(2)-O(4)*, 72.9(2); O(4)-Sn(2)-O(3), 75.9(2); O(4)*-Sn(2)-O(3), 148.7(2).

The crystal structure of 3 reveals the formation of a one-dimensional tape as a result of intermolecular adenine interactions to form a homodimer through the Watson-Crick faces [Figure 9(a)]. Such one-dimensional tapes are joined together by the interaction of the Hoogsteen face of the adenine units of one chain with the bridging OH groups of the stannoxane core of the other chain [Figure 9(a)]. Interestingly, in this interaction, the hydroxide ligand (O3-H3) behaves as a hydrogen bond donor to the N7 nitrogen while at the same time acting as a hydrogen bond acceptor from the exocyclic amino group. The adenine units present in different 2D sheets are further involved in π… π stacking interactions [Figure 9(b)] which promote the 2D-chain formation (Figure S10).


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Figure 9: (a) Different types of intermolecular hydrogen bonding interactions present in 3 (b) Interlayer π… π staking interaction of the ladder 3 (some H atoms, part of the n-butyl group are omitted for clarity). Crystal structure of [{n-Bu2Sn}2(µ3-O) L2]2 (4) The molecular structure of the tetrameric organostannoxane ladder 4 is shown in Figure 10(a). The selected bond parameters corresponding to the tetrameric stannoxane core are summarized in the caption of Figure 10. Details of other bond parameters are given in Table S2. The essential difference between the molecular structure of 4 and that of 3 is that in the former there are four carboxylate ligands. The oxygen atom of a carboxylate ligand (O1 and O1*) serves to bridge a pair of tin atoms. In 3 this function was carried out by a µ-OH. The terminal tin atoms (Sn1 and Sn1*) in complex 4 are five- coordinate (τ = 0.50) [Figure 10(b)] while the central tin atoms (Sn2 and Sn2*) are six-coordinate [Figure 10(c)]. Several hydrogen bonding interactions along with other non-covalent interactions are present in the crystal structure of 4. Selected hydrogen bonding parameters found in 4 have been summarized in Table 2. The C8-H8 of each adenine moiety is involved in a strong intramolecular hydrogen bonding with the carboxylate oxygen atom (O2, O4) (Figure S11) to generate a seven-membered ring. The Hoogsteen face of



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an adenine moiety intramolecularly interacts with N3 of another adenine motif along with C11H11B of the tether.

Figure 10: (a) Molecular structure of 4 as ORTEP diagram drawn at 25% probability level. (H atoms, part of the n-butyl group are omitted for clarity). (b) Coordination environment around Sn1 (Sn1*), is distorted trigonal bipyramid. (c) Coordination environment Sn2 (Sn2*), are distorted octahedral. Selected bond parameters. Distances (Å): Sn(1)-O(1), 2.188(2); Sn(1)-O(3), 2.228(2);

Sn(1)-O(5), 2.028(2); Sn(2)-O(1), 2.625(28); Sn(2)-O(5), 2.055(2); Sn(2)*-O(5),

2.145(2); Sn(2)-O(4), 2.342(2); Sn(1)-O(2), 3.174(25). Angles (º) O(1)-Sn(1)-O(3), 165.85(7); 135.66(11); O(5)-Sn(1)-O(1), 75.80(8); O(5)-Sn(1)-O(3), 90.81(8); O(5)-Sn(2)-O(4), 85.76(7); O(5)*-Sn(2)-O(4), 159.99(7); O(5)-Sn(2)-C(25), 104.41(10); O(5)-Sn(2)-C(21), 108.54(10); O(5)-Sn(2)-O(5)*1, 75.49(8);

Sn(1)-O(5)-Sn(2), 134.95(10); Sn(1)-O(5)-Sn(2)*, 119.47(9);

Sn(2)-O(5)-Sn(2)*, 104.51(8). Further, the crystal structure of 4 reveals the formation of a two-dimensional hydrogen bonding framework as a result of intermolecular hydrogen bonding interactions [Figure 11].


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Here, it can be seen that while two adenine residues utilize both Watson-Crick as well as Hoogsteen faces the other two use only their Watson-Crick faces (along with N3). Finally, intermolecular π… π stacking interactions (Figure S12) between adenine moieties leads to the formation a 3D-supramolecular framework (Figure S13).

Figure 11: 2-D, Hydrogen bonding in 4 highlighted with circle; inset shows the adenine units with number scheme. Fragmented bonds indicate hydrogen bonding interactions. (n-Bu groups have been omitted for clarity).

Summary The use of organotin motifs to support adenine peripheries has been succesful. All the compounds 1-4 reveal rich supramolecular structures as a result of intermolecular adenineadenine interactions. Most remarkably we have observed a new trimeric supramolecular signature for adenine in the form of a trimeric motif made up of alternating Watson-CrickWatson-Crick and Hoogsteen-Watson-Crick interactions. It would be interesting to investigate the effect of mixing organotin coordination polymers containing adenine and cytosine units to check if supramolecular recognition can occur between such organometallic polymers. Such studies are underway.



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Table 1. Crystal data collection and refinement parameters for 1-4. Complex

1

Empirical

2

4

3

C32H68N10O13Sn2 C60H107N15O7Sn3 C48H90N10O8Sn4

formula Formula weight (g) Temperature (K) Crystal system,

1038.34

1506.68

1410.06

100(2)

100(2)

100(2)

Triclinic, P-1

Monoclinic, P

Space group

C64H104N20 O10Sn4 1868.4

100(2)

Triclinic, P-1

Triclinic, P-1

21/n a (Å): 10.877(5)

a (Å): 13.880(5)

a (Å): 10.903(5)

a (Å): 11.648(5)

b (Å): 13.682(5)

b (Å): 30.531(6)

b (Å): 11.744(5)

b (Å):12.780(5)

Unit cell

c (Å): 16.048(6)

c (Å): 16.747(5)

c (Å): 12.783(6)

c (Å): 14.126(5)

dimensions

α (°): 79.096(5)

α (°): 90

α (°): 104.306(6)

α (°): 73.159(5)

β (°): 74.690(5)

β (°): 101.941(5)

β (°): 102.130(5)

β (°): 69.017(5)

γ (°): 85.081(6)

γ (°): 90

γ (°): 101.758(5)

γ (°): 78.508(5)

Volume (Å ), Z

2260.3(15), 2

6943(4), 4

1493.1(11), 1

1868.4(13), 1

F(000)

1068

3112

712

908.0

Crystal size

0.20 x 0.20 x

0.20 x 0.20 x

0.20 x 0.20 x

0.17 x 0.16x 0.13

(mm3)

0.20

0.20

0.20

4.12 to 25.02

4.14 to 25.03

3.42 to 25.68

-12 ≤ h ≤12

-16 ≤ h ≤ 16

-13 ≤ h ≤ 12

-13 ≤ h ≤ 14

-16 ≤k ≤ 14

-36 ≤ k ≤ 31

-13 ≤ k ≤ 14

-14 ≤ k ≤ 15

-19 ≤ l ≤ 19

-19 ≤ l ≤ 19

-11 ≤ l ≤ 15

-17≤ l ≤ 17

11618 / 7790

35858 / 12194

8155 / 5537

3

θ collection

2.02 to 25.50

range (°) Limiting indices Reflections collected / unique

[R(int) = 0.0312] [R(int) = 0.0761] [R(int) = 0.0182]

12761 /6870 [R(int) = 0.0181]

Completeness to θ (%) Absorption correction Data / Restrains / Parameters Goodness-of-fit on F2

97.8

99.4

98.0

98.8

Psi-scan

Psi-scan

Psi-scan

Empirical

7790/ 23 /550

12194 / 156/ 774

5537/ 134/ 320

6870/ 0 /446

1.108

1.014

1.047

1.061

Final R indices

R1 = 0.0571

R1 = 0.0556,

R1 = 0.0636,

[I > 2σ(I)]

wR2 = 0.1501

wR2 = 0.1238

wR2 = 0.1723

R indices (all

R1 = 0.0753,

R1 = 0.0873,

R1 = 0.0755,


R1 = 0.0288, wR2 = 0.0766

R1 = 0.0334,

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data)

wR2 = 0.1818

wR2 = 0.1424

wR2 = 0.1858

wR2 = 0.0801

1.786 and -0.935

2.146 and -0.821

2.109 and -2.065

1.639 and -0.833

Largest diff. Peak and hole (e. Å-3) R = ΣF0–Fc/ΣF0; wR = {[Σw(F02Fc2)2]/[Σw(F02)2]}1/2

Table 2. Hydrogen bonding parameters found in 1- 4 D-H···A

Symmetry of A

D-H

H···A

D-A

∠ D-H···A

Complex 1 N6A-H6A2···N1B

1-x, 2-y, -z

0.860(6)

2.164(6)

2.992(8)

161.69(47)

N6A-H6A1···O4W

1+x, y, z

0.859 (7)

2.221 (7)

3.080(1)

177.11(56)

N6B-H6B1···N7A

1-x, 2-y, -z

0.860(6)

2.260(6)

3.105 (8)

167.49(46)

N6B-H6B2···O6W

-x, 2-y, 1-z

0.859(7)

2.190 (8)

2.946(1)

146.57(48)

O3-H3···O2A

1-x, 2-y, -z

0.818(6)

1.780(8)

2.562(6)

159.40(66)

O4-H4···O2B

-x, 2-y, -z

0.813 (4)

1.797(5)

2.571 (6)

159.40(66)

0.859(5)

2.189(5)

3.047(7)

176.16(38)

0.859(6)

1.972(6)

2.811(8)

165.11(41)

Complex 2 N6A-H6A1···N7C

[ x+1, y, z ]

N6A-H6A2···O1W N6B-H6B2···N1C

[ x+1, y, z ]

0.860(6)

2.086(6)

2.888(8)

154.85(42)

N6C-H6C1··· N7B

[ x-1, y, z ]

0.859(5)

2.378(5)

3.234(7)

174.70(38)

N6C-H6C2···N1A

x-1, y, z

0.859(6)

2.212(5)

3.050(8)

165.24(39)

0.826(5)

2.015(6)

2.809(8)

161.06(46)

0.818(4)

2.030(5)

2.802(8)

157.22(49)

-x+3/2, y-1/2, O1W-H1W···N1B z+3/2 ] O1W-H2W···N7A

Complex 3 N6-H6A···N1

-x-1, -y+1, -z+2

0.861(7)

2.148(8)

3.005(1)

173.45(57)

O3-H3···N7

[x, y, -1+z]

0.824(5)

2.100(7)

2.832(8)

147.84(39)

N6-H6B···O3

[-x, -y, 1-z]

0.860(6)

2.170(4)

2.999(7)

161.66(51)

2.220(30)

3.006(42)

151.63(2)

Complex 4 N6A-H6A2···N3

1-x, 1-y, 1-z

0.861(27)



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N6A-H6A1···N1

-1+x, 1+ y, -1+ z

0.861 (24)

2.181 (25)

3.031(35)

169.5(2)

N6-H6B···N7

1-x, 1-y, 1-z

0.859(28)

2.137(29)

2.964 (41)

161.46(2)

C2A-H2A···O2

-1+x, y, -1+z

0.929(27)

2.560 (26)

3.787(35)

171.42(19)

Acknowledgments VC is thankful to the Department of Science and Technology, New Delhi, for the award of the National J. C. Bose Fellowship.SK is thankful to the Council of Scientific and Industrial Research, New Delhi, for the award of a Junior Research Fellowship. ASSOCIATED CONTENT: Supporting Information. It includes crystallographic data in CIF format, some structural diagrams and bond parameters. This information is available free of charge via the Internet at http://pubs.acs.org/

References 1. (a) Davies, A. G. Organotin Chemistry; Wiley-VCH, Verlag/GmbH &Co., KgaA, Weinheim, 2004.(b) Davies, A. G.; Gielen, M.; Pannell, K. H.; Tiekink E. R. T. Tin Chemistry: Fundamental, Frontiers and Applications; Wiley-VCH, Weinheim, 2008. 2. (a)Hadjikakou, S. K.; Hadjiliadis, N.Coord. Chem. Rev. 2009, 253, 235. (b) Alama, A.; Tasso, B.; Novelli, F.; Sparatore, F. Drug Discovery Today, 2009, 14. (c) de Vos, D.; Wiiiem, R.; Gielen, M.; van Wingerden, K. E.; Nooter, K. Met Basd Drugs 1988, 5, 179. 3. (a)Evans, C. J. In: Smith, P. J. (Ed); Chemistry of Tin, Blackie Academic and Professional,

London, 1998, 442. (b) Thodupunoori, S. K.; Alamudun, I. A.; Cervantes-Lee. F.; Gomez, F. D.; Carrasco, Y.P.; Pannell, K. H. J. Organomet. Chem. 2006, 691, 1790. 4. (a) Hoch, M. Applied Geomistry 2001, 16, 719. (b) Kimbrough, R. D. Environmental Health Perspecives 1976, 14, 51.


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toc 12x7mm (300 x 300 DPI)


Supramolecular Signatures of Adenine-Containing ... - ACS Publications

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