Supramolecular Synthesis and Experimental and Theoretical Studies

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Supramolecular synthesis and experimental and theoretical studies of co-crystal systems based on resorcinolthiosemicarbazones and N,N'-divergent dipyridines Ara Nuñez-Montenegro, Saray Argibay-Otero, Rosa Carballo, Ana Graña, and Ezequiel M. Vazquez-Lopez Cryst. Growth Des., Just Accepted Manuscript • Publication Date (Web): 02 May 2017 Downloaded from http://pubs.acs.org on May 4, 2017

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Crystal Growth & Design

Supramolecular synthesis and experimental and theoretical studies of co-crystal systems based on resorcinol-thiosemicarbazones and N,N'-divergent dipyridines Ara Núñez-Montenegro,a Saray Argibay-Otero,a Rosa Carballo,a Ana Graña,b Ezequiel M. Vázquez-López,a,* a

Departamento de Química Inorgánica, Facultade de Química, Instituto de Investigación

Sanitaria Galicia Sur – Universidade de Vigo, Campus Universitario, E-36310 Vigo, Galicia, Spain b

Departamento de Química Física, Facultade de Química, Universidade de Vigo, Campus

Universitario, E-36310 Vigo, Galicia, Spain KEYWORDS. Co-crystal, thiosemicarbazone, bipyridine, hydrogen bond, resorcinol.

ACS Paragon Plus Environment

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ABSTRACT: A supramolecular synthesis process in methanol of a combination of several resorcinol-thiosemicarbazones (TSC) and two N,N'-divergent bipyridines (BP) led to the isolation of 14 co-crystals, some of which contained solvent in the crystal lattice. The main hydrogen bonded motifs have been identified and some key structural factors have been analyzed by theoretical calculations. Structurally, the 14 co-crystals can be grouped into two main types. The first type is characterized by the formation of TSC:BP cyclic arrangements involving a solvent and also by the absence of the intramolecular O–H...N, (6), interaction in the TSC component. The second type is characterized by TSC:BP acyclic associations, in most cases without the inclusion of solvent, and the usual intramolecular O–H...N, (6), interaction is maintained in the TSC component.

INTRODUCTION Diffractometric studies and theoretical calculations have recently shown the robustness of the thiourea and thioamide groups in molecular associations and highlighted both groups as suitable candidates for crystal engineering.1-3 The higher capacity of these groups for association when compared to urea and amide groups is attributed to the higher acidity of the N–H when oxygen is replaced by sulfur. Under these conditions, and despite the weaker acceptor character of the thiocarbonyl moiety when compared to the carbonyl group,4 the molecular association continues to be based on H-bonding and on a pair of recognizable motifs: (8) and (4) (Scheme 1). This behavior was recently highlighted by Desiraju5 and it means that the H-bond has a greater dependence on the H-donor acidity/activity than the acceptor basicity. A similar conclusion was reported for more complex groups, but based on the thioureido group, in salicylaldehyde


2

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thiosemicarbazone4 and Jawaria et al. studied the effect of the thioamide-thioamide synthon (8) in different ferrocene-based thiosemicarbazones (TSCs).6

Scheme 1 In cases where the resorcinol group faces 4,4'-bipyridine-like molecules (BP, Scheme 2), the ability to organize O–H...N hydrogen bonds in the heterosynthon results in [2+2] molecular associations. The resulting material can be used for solid state reactions between these units, for example in the photodimerization process of olefins.7 Although deviations from the resorcinol group-based design (and thus the formation of extensive associations of the two elements) have been attributed to the unwanted occurrence of intramolecular hydrogen bonds involving one of the OH groups,8 behavioral studies that consider the presence of other H-bonding donors are scarce. In previous work we showed that TSCs can be used as elements to design molecules with interesting properties based on the H-bond. For example, resorcinol thiosemicarbazone complexes show some ability to interact with the estrogen receptor.9 We have also experienced that the thioamide group is a very active element in the molecular association in these compounds because it is usually involved in the intermolecular interaction with other equivalent molecules or solvents trapped in the crystal.10


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The aim of the work described here was to analyze the associations resulting from the crystallization of several thiosemicarbazones derived from resorcinol in conjunction with 4,4'dipyridine molecules (Scheme 2). It was borne in mind that complex compositions are possible, as observed by Ng.11 An effort was made to identify the factors that allow the intervention of the different groups in the association of the TSC, an area that has important applications not only in Crystal Engineering (including the design of dosage forms based on co-crystals) but in other fields such as the design of drugs.

Scheme 2. Thiosemicarbazone derived from resorcinol and 4,4-dipyridine molecules used in this paper (atomic numbering scheme is also included). RESULTS AND DISCUSSION Synthesis Initial attempts to monitor the reactions between the TSC compounds shown in Scheme 2 and the dipyridine derivative (BP) by NMR (by chemical displacement of the OH protons) were hampered by the solubility of the TSC and / or the deuteration groups OH.. In most cases, the best conditions involved heating a methanolic solution of TSC:BP (1:2) under reflux followed by the addition of several drops of diethyl ether drops after vacuum concentration to reduce the


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volume to around 2/3 of the initial volume. Nevertheless, different three-component co-crystals (due to the inclusion of solvent molecules) were also obtained by crystallization from other solvents at room temperature and under different conditions. In some cases, products resulting from hydrolysis of the C=N bond of the TSC were isolated as crystalline solids but the most relevant finding was the formation of oxidized species of TSC under aerobic conditions and in the presence of BP (Scheme 3, see supplementary material). Reactions in an argon atmosphere exclusively yielded products that were a combination of TSC/BP. Although the formation of this type of disulfide derivative from TSC is not unknown,12 the formation usually seems to be mediated by redox active metals such as Cu(II)/Cu(I). In our case, the presence of BP is necessary to observe the oxidation process, since the disulfide derivatives of 1b and 2b were not detected when air was bubbled for several hours through saturated methanol solutions of the TSCs. Although the role of BP in the process may vary (for instance, its basic character may be important in the deprotonation process of TSC), the easy crystallization of TSC-TSC/BP is probably a factor to take into account. A more detailed study of these reactions and the product formed will be published elsewhere.

Scheme 3


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Identification of the association patterns Prior to the analysis of the structures of co-crystals formed by TSC-BP, we set out to identify the association paths of the different elements. A search was performed on the CSD databank (version 5.37 updates Nov 2015)13 for TSC (uncoordinated) structures derived from phenyl carbaldehyde thiosemicabazone. The same database was subsequently used to review the effect of the inclusion of substituents on the phenyl group.

A)

D)

B)

E)

C)

F)

Figure 1. Ilustration of the association patterns (A–E) observed in the X-ray structures based on the phenylcarbaldehyde thiosemicarbazone (F) moiety (color scheme used for atoms grey: C, light blue: N, red: O and, yellow). Identification of the association patterns in thiosemicarbazones The association patterns observed in the X-ray structures based on the phenylcarbaldehyde thiosemicarbazone moiety are shown in Figure 1 along with the graph-set proposed by Etter14 to identify the corresponding interactions. The observed patterns for each structure are included in


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Table S1 along with relevant aspects such as the nature of the R1 and R2 groups (as defined in Scheme 2) and a description of the configuration/conformation around the bonds of the thiosemicarbazone arm.

A)

B)

C)

E) D) Figure 2. Additional association patterns (A–D) observed in the X-ray structures based on the salicylaldehyde thiosemicarbazone moiety (E) involving the OH group (color scheme used for atoms grey: C, light blue: N, red: O and, yellow). The results of the CSD search suggest that, as observed in other thioureido derivatives,1-3 the main way in which phenylcarbaldehyde thiosemicarbazone associates, in the absence of other donor and acceptor groups, is through the (8) ring (Figure 1A) because this motif is observed in all of the structures (most often as the only relevant intermolecular interaction) except for YODRUF15 and PANJAQ.16 This pattern involves the hydrazinic N(2)–H group and the sulfur atom of a neighboring molecule. The resulting association forms dimers that are usually centrosymmetric units and this can eventually be distorted, probably due to steric hindrance, when the hydrogen atom on the C(2) carbon is replaced, for instance, by a CH3 group. In this case, as observed in PANJAQ,16 the ring size can be expanded to (14) and the methyl C–H groups act as H-donors towards the S-thioamide group. When the N(1)–H is not substituted (R1 = H) other motifs, such as the ring (8)′ also forming centrosymmetric rings, can coexist with


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the predominant (8). If water molecules are included in the crystal, the N(2)–H group interacts with the oxygen water atom and the association of the TSC molecules in chains ( (4), Figure 1C) can be observed. The inclusion of an –OH group in the ortho-position of the phenyl ring gives rise to the presence of an additional acceptor group in the molecule because its H-bonding activity is always involved in the intramolecular interaction with the N(3) group. The formation of the sixmembered (6) ring is strongly favored14 and this also fixes the E configuration around the C(2)–N(3) bond. In any case, the acceptor capacity seems rather poor because the predominance of the (8) ring is again observed in the cases studied by X-ray diffraction (Table S2), although the chelating motif (6) (Figure 2D) involving the unusual Z conformation of the C(1)–N(1) bond is observed in two structures (Table S2).

A)

B)

C)

Figure 3. Association patterns (A, B) observed in the X-ray structures based on the 4-hydroxyphenylaldehyde thiosemicarbazone moiety (C) involving the OH group (color scheme used for atoms grey: C, light blue: N, red: O and, yellow). Unfortunately, the number of reported crystal structures (two) in which the –OH group is in the para-position is hardly representative. Despite the availability of the free –OH group, the


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association involving the N(2)–H group and sulfur continues to be present in the (8) or (8) motifs. However, the thioamide group also acts as an acceptor in other intermolecular interactions involving the –OH group and this results in the chains (11)and (6), both of which are included in Figure 3. The combination of both OH groups in the resorcinol group (Figure 4) is represented in a single pattern, (6) (Figure 4A), which associates the molecules in chains. Three of the six structures included in Table S4 have the (8) motif. Furthermore, other cyclic arrangements can be identified as a consequence of the simultaneous presence of other

(44) (not included in Figure 4) formed by a combination of single synthons, such as the ring

(6) and (6) motifs.

A)

B)

C) Figure 4. Association patterns (A, B) observed in the X-ray structures based on the resorcinol aldehyde thiosemicarbazone moiety (C) involving at least one of the OH groups (color scheme used for atoms grey: C, light blue: N, red: O and, yellow).


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2.2.2 The effect of the solvent Solvents are two faces of the same coin in the (co)crystallization process. Solvents are essential agents in the most widely used crystallization solution process and they were the first alternative synthons (i.e., rivals) because they carry additional functional groups. However, it can be considered as experimental proof for the robustness of a particular heterosynthon when it remains intact after interaction with solvent.17 In the hydrate YODRUF,15 and in the absence of any substituent on the phenyl group, the interaction pattern (8) observed in the non-hydrate crystal changes to (4) involving a thioamide N(1)–H group and the sulfur atom of a neighboring molecule (Figure 1C, Table S1). This change is probably due to the better acceptor character of the water oxygen, which should interact with a better H-donor such as the N(2)–H hydrazinic group, a situation in agreement with Etter’s rules.14 The inclusion of water in the structure of the salicylaldehyde TSC derivative does not seem to modify substantially the intermolecular association pattern. As reported by Janiak et al., the inclusion of different stoichiometric amounts of water (UJIPIN, UJIPOT and UJIPUZ18) can be described in the non-solvated structure (GEXKID19 and GEXKID012,4) with the water molecule trapped between two S-groups ((4) interaction, Figure 5A). Similar considerations can be applied to the non-hydrated and hydrated forms of the corresponding acetylsalicylaldehyde derivatives (GEYRAD20 and VEBREZ,21 respectively, Figure 5B). In contrast, methanol does seem to be able to modify the original association mode observed in GEYRAD22 and in the corresponding structure (DUXXOK22) the contacts between the TSC molecules are negligible


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but they are bridged by a methanol molecule through acceptor and donor interactions with the ring (6) and the chain (6), respectively (Figure 5C).

A)

B)

C) Figure 5. Intermolecular interactions observed in the crystal structures of solvates of TSC molecules (color scheme used for atoms grey: C, light blue: N, red: O and, yellow). 2.2.3 Theoretical calculations The Quantum Theory of Atoms in Molecules (QTAIM)23 was applied in an effort to gain an insight into the factors that play a role in the intermolecular interactions – besides the predominance of some of the possible conformational isomers in the TSC chain. The theory concerns a topological analysis of the electron density function, ρ(r), and it has been widely used to identify and describe the nature of intra- and intermolecular interactions in molecular systems. Under the QTAIM formalism two atoms are considered to be bonded if there is a bond path between them with a saddle point with two negative eigenvalues of the Hessian matrix of ρ(r). These points are called bond critical points (BCP). In this paper we relate the strength of hydrogen bonds with the value of the electron density at the bond critical points, ρ(rc). Furthermore, in order to confirm the nature of these interactions the Interacting Quantum Atoms


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(IQA)24 energy decomposition technique was employed. This method allows the interaction energies as well as their components, the electrostatic term (Vc) and the exchange-correlation term (Vxc), to be calculated. Table 1. Values of ρ(rc) at the bond critical points of hydrogen bonds and the interaction energy between hydrogen bonded atoms (Eint) and its components, the electrostatic term (Vc) and the exchange-correlation term (Vxc). D…A distance (Å) Molecule 1a

c

Conformer Z

b

interaction O(1)-H…N(3) N(1)-H…N(3)

Ef 1b

Z

N(1)-H…N(3) O(1)-H…N(3) N(1)-H…N(3)

Ef 2a

Z

E 2b

2b

f

Z

E

f

N(1)-H…N(3)

experimen tal 2.683d 2.731e 2.683d 2.690e -g

2.695 2.699h 2.715g 2.708h --

a

a

a

theoret ical 2.706

ρ(rc)a

Vc

0.0352

-99.79

-12.54

2.680

--

--

--

112.33 --

2.639

--

--

--

--

2.713

0.0349

-99.66

-12.46

2.688

--

--

--

112.12 --

Vxc

Eint

2.643

--

--

--

--

O(1)-H…N(3)

2.600

i

2.597

0.0490

-108.82

-17.08

N(1)-H…N(3)

2.642i

2.666

--

--

--

125.90 --

N(1)-H…N(3)

--

2.630

0.0192

-47.12

-4.78

-51.89

O(1)-H…N(3)

2.615(3)

j

--

0.0498

-109.55

-17.38

N(1)-H…N(3)

2.620(3)j

--

--

--

--

126.93 --

N(1)-H…N(3)

--

2.643

0.0211

-47.23

-5.92

-53.15

a

ρ(rc) in au and energies in kcal mol–1. b Conformational isomers defined with respect to the C(2)–C(3) bond:

c

Wavefunctions were obtained for the optimized geometries in the gas state. dMonoclinic C2/c polymorph, reference 25. eTriclinic P-1 polymorph, reference this paper. f Bond critical points were not found in this conformer. g Monoclinic Cc polymorph, reference 26. iData obtained from reference 22 j This paper.


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This method was applied to the TSC molecules 1a, 1b, 2a and 2b, the X-ray diffraction structures of which have been reported before22,25,26 or studied by us, on wavefunctions optimized in the gas state and a summary of the results is provided in Table 1. As can be observed, in the conformer present in the crystal structure the only relevant intramolecular interaction is that involving the O(1) and N(3) atoms. In agreement with the X-ray results, the preponderance of electrostatic character for the interaction and Eint suggests a moderate hydrogen bond in the (6) motif. Bond paths were not observed connecting N(1) and N(3) atoms, which suggests that there is no relevant interaction between the two groups. An interesting aspect is the higher Eint value in compounds 2a,b with respect to 1a,b. Comparison between the compounds shows that it is the electrostatic component that contributes most to the final difference (in both cases by more than 10 kcal.mol–1). Although some contribution from inductive effects of the methyl group at the C(2) position cannot be ruled out, the crowding effect on the C(2) atom of the methyl substituent is probably responsible for the closure of the N(3)–C(2)–C(3) angle and, consequently, for bringing the groups involved in the formation of the (6) ring closer together. The competitive effect between the O(1)–H and N(1)–H groups for N(3) was evaluated by calculating the structures of the conformational isomer E with respect to the C(2)–C(3) bond. Frequency calculations on the geometries obtained gave real values, thus confirming that they are minima on the potential energy surface. In this case only the corresponding conformers of 2a and 2b showed BCP values and the results are included in Table 1. The energy values correspond to a much weaker interaction that cannot be defined as a ‘normal’ hydrogen bond, although the electrostatic contribution is proportionally greater (around ten-fold) than in the Z conformer.


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A)

B)

C)

E) E = N, O, P, S, Se, Si D) Figure 6. Association modes observed in structures of resorcinol cocrystallized with mono- and dipyridines (A–D) and representation of the substructure (E) used in the search (color scheme used for atoms grey: C, light blue: N, red: O and, yellow). Identification of the association patterns between the resorcinol fragment and BP The search conditions in the CSD database for resorcinol derivatives where an H-bond acceptor (E) is located on a suitable position to interact with the –OH group are shown in Figure 6E. An additional search condition was the involvement at least of one OH group in an H-bond with an aromatic amine. Although several possible values were allowed for substituent E (Figure 6E) and any value for the distance C–E was allowed, only aldehydes or methyl ketones seem to have been characterized (except for the thiosemicarbazone DUCSAW,11 which is discussed in the following section). As one would expect, the formation of an OH…Npyridine interaction is a competitive process against the (6) intramolecular interaction with the carbonyl group.8 When this interaction is broken, both OH groups are able to interact with two aromatic amine nitrogen atoms and when the imine selected is an analog of 4,4'-bipyridine, the formation of 2+2 rings


14

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( ()) is observed. The process has been used in the synthesis of paracyclophanes using the topochemical postulate [see reference 27] because it was able to align parallel and be separated by distances within 4.2 Å to allow different diene diamines to undergo [2+2] photoaddition.28,29 The photoaddition process of AJOGAI (Figure 6A) could be observed by X-ray diffraction after irradiation of crystalline samples (in the crystal by irradiation of samples of AJOGAI and the structural changes at molecular level during the reaction: AJOHEN and HUHFUM).8 The unsuccessful reaction with 1,2-di-(4-pyridyl)ethane was attributed to the difficulty of the intramolecular interaction (6) in the resorcinol derivative in the crystal. Amongst the possible causes for this finding, the presence of bulky CH2–CH2 linkages that hinder stacking of dipyridines in the () interaction was proposed.8 The interactions that form the motifs (12) and work to achieve an infinite chain by intercalation of the resorcinol derivative and dipyridine molecules. Summary of the identification patterns In summary, the study of the X-ray crystal structures shows the predominance of the (8) ring based on the N(2)–H…S interaction. This fact was observed in other thioureido derivatives4 and the comparable strength of this interaction with N–H...O in ureido derivatives was recently reported.1 The few cases where this interaction is absent (with the formation of enchained (4) or (7)) seem to be more related to existence of active H-donor solvents than with the presence of –OH substituents in the benzene moiety.


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Thiosemicarbazone – bipyridine co-crystals The main results of the structural studies on the crystals obtained from reaction mixtures of TSC and BP are summarized in Table 2.

Scheme 4 Structures in which the () intramolecular interaction is absent The different structures can be grouped according the presence of certain synthons and stoichiometric relationships. The first group consists of structures where the interaction between the BP and TSC forms cyclic arrangements (entries 1–7 in Table 2, Scheme 4). Regardless of the final cyclic structure, all cases have three common aspects: (i) The (6) intramolecular interaction between the atoms O(1)–H…N(2), which is observed in the free thiosemicarbazone, is broken because both –OH groups are involved in H-donor interactions (note, Scheme 3 right, that both OH groups are not necessarily involved in H-bonds with BP); (ii) all of the thiosemicarbazones are aldehyde derivatives (R1 = H), (iii) they are obtained from a reaction ratio of 1:2 (TSC:BP) although the stoichiometry in the crystals is 1:1, (iv) solvent molecules are always included in the crystals.


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Figure 7. A) Representation of the crystal structure of entry 2 showing the H-bonding interactions with the solvent. B) Intermolecular interactions in the structure for entry 1 – the (8) rings (Figure 1A) are omitted for clarity. C) 2D association in the structure for entry 4. Color scheme used for atoms grey: C, light blue: N, red: O and, yellow, except the solvent molecule in A (ethyl ether) and B (acetone) which were light green and, TSC molecules and methanol are yellow and purple, respectively). The solvent included in the crystals was usually the methanol used in the synthesis, although in some cases the solvents used in the crystallization process were included. This group can be divided according to the kind of cyclic arrangement. The structures corresponding to entries 1–4


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have a centrosymmetric ring involving two BP molecules that interact with two TSC molecules through the resorcinol group (Scheme 3, left). Depending on the BP these can be identified as (30) or (34) for bpy or bpe, respectively. The calculated KPI30 values suggest an inefficient packing ranging between 65–68%.

Figure 8. Molecular association in the structures in entries 5 (A), 6 (B) and 7 (C). Color scheme used for atoms grey: C, light blue: N, red: O and, yellow, except the solvent molecule, methanol, is pale green.


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These [2+2] units are associated in the crystal by other intermolecular interactions involving the solvent. Depending on the nature of the solvent, it is possible to distinguish two different groups. When the solvent is an H-bond acceptor exclusively (entries 1–3, i.e., acetone, dmso or diethyl ether), the [2+2] units are chained by only (4) (entries 2 and 3) interactions or jointly with the (8) interaction (entry 1) involving the thiosemicarbazide arm (Figures 7A and 7B, respectively). The combination of these intermolecular elements results in a 2D (entries 2 and 3) or 3D (entry 1) distribution of the TSC and BP. The solvents in the structures corresponding to entries 2 and 3 play a relevant role because their interaction with two molecules of TSC, through the N(2)–H group, yields 2D arrangements. However, this is not the case in the structure for entry 1. The acetone does not seem to play an important role in the molecular packing because relevant interactions with the H-donor groups are not observed. In this case the N(2)–H group is not involved in interactions with the solvent and it is able to contribute to the final 3D arrangement through the (8) ring (Figure7B). The two supramolecular roles of the MeOH, i.e., donor and acceptor in H-bonding, promote structures such as that shown in entry 4 by association of the molecules in the (34) ring (Figure7C) through donor interactions between the methanol and one of the resorcinol OH groups and accepting the H-donating interaction with the N(2)–H group. In the structures in entries 5–7, the donor/acceptor character of MeOH, which involves interaction with N(1)–H or N(2)–H, also allows cyclic associations of TSC-BP-MeOH (Figure 8). The association is depicted in Scheme 4, right. It is worth noting that, with the exception of the structure in entry 7, the stoichiometry in the crystals is 1:2 (TSC:BP).


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In the compound in entry 5, a combination of (28) involving methanol and (8) rings leads to ribbons whereas for the compound in entry 6 the role of methanol in (28) is assumed by an OH group of the TSC molecule. The resulting centrosymmetric (22) ring (Figure 8B) was not observed in the structures of para-phenol-thiosemicarbazone (section 2.2.2). However, the structure may be described as ribbons that are formed by the association of these dimers through the interleaving of three bpe molecules by hydrogen bonds involving N (1)–H and the two resorcinol O–H groups. The ribbons are associated by intercalation of MeOH…bpe…HOMe units, which interact with the N(2)–H of the TSC through the oxygen of each MeOH (BPbridge in Table 2).

Scheme 4. Interactions involving the BP molecule in entries 8–14. Similar units, which contain three BP molecules for two TSC molecules, are observed in the structure shown in entry 7 (Figure 8C) but in this case the bulky phenyl groups on the N(1) atom probably hinder the formation of the (22) unit and the TSCs are enchained by N(1)–H…O(2) interactions ( (11)). The O(2)–H and N(2)–H establish interactions with the bpy and MeOH leading to a 3D packing of the molecules.


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Structures in which the () intramolecular interaction remains The structures in entries 8–16 cannot be described as being formed by cyclic units. Furthermore, all of these compounds retain the (6) interaction observed in the free TSC. In general, the crystals consist of structures in which one BP molecule bridges between two TSCs and this unit interacts with other TSC molecules. Thus, the stoichiometric TSC:BP ratio is usually 2:1 (except for entry 14 and DUCSAW, which was previously reported by Ng11). Note that the packing of the groups (except for entry 14 and DUCSAW without the need for the intervention of solvents) is more effective because the KPI is greater than 68%. It is possible to distinguish a first group of structures in which the BP molecule interacts with two O(2)–H resorcinol groups to form dimers -1 (Scheme 4), which are associated through the motifs observed in the free TSCs to give chains as (4) (Figure 1C) or salicylaldehyde TSCs involving the acceptor O(1)–H as (11) (Figure 2B). In this way, tapes are generated as shown in Figures 9A–C. The final arrangement is also a ribbon-like (Figure 9A-C) but, unlike previous structures, the BP rings are far from coplanar. Thus, this packing is not useful for solid state photoaddition reactions, following the topochemical criterion, because the BP molecules are not in a parallel arrangement. The structure of entry 11 is interesting because in the thiosemicarbazide chain the N(1)–C(1) and C(1)–N(2) bonds have E and Z conformations, respectively, and this is opposite to those observed in the other structures. The (8)′ motif can be observed despite the fact that R1 is a CH3 group. Both motifs form a 1D arrangement involving the two molecules (Figure 9C).


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It is noteworthy that entries 9 and 10 are polymorphs of the co-crystal 1b:bpe and the main difference is the relative orientation of the ethylene group of bpe with respect to the linked O(2)– H group.

Figure 9. A) Association in entry 8, B) and C) correspond to entries 9 and 10, which are polymorphs with a 2:1 1b:bpe ratio, D) Representation of the 1D-association in entry 11. Color scheme used for atoms grey: C, light blue: N, red: O and, yellow. In contrast to the above, in the structures in entries 12 and 13 the association of TSC and BP involves at least one N–H in addition to the interaction with O(2)–H. These interactions are identified as (22) and (20) in Scheme 4 depending on whether the interaction is only based


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on the N(1)–H or also on the N(2)–H, respectively. Two chains formed by (22) in 12 are paired by the TSC (8) motif (Figure 10A).

Figure 10. Molecular association in 12 (A) and 13 (B). Color scheme used for atoms grey: C, light blue: N, red: O and, yellow. In structure 13 the chelating H-bond between the two N–H groups of TSC with an N atom of BP (a motif identified as (6)) involves the unusual Z configuration around the C(1)–N(2) bond. The bpe molecule is not planar and the angle between the pyridine rings is 43.2°. The final arrangement of the molecules is a zig-zag chain (Figure 10B). Note that structures 13 and 11 are also polymorphs and that the significant differences between their structures are due to the different conformations of the C(1)–N(1) bond. Structure 14 is the only solvated crystal observed in this group. The stoichiometric ratio of its constituents is also different, with a larger amount of bpy to give a 1:3:2 (TSC:bpy:H2O) ratio. The structure can be described as chains formed by bpy molecules H-bonded to water molecules and a TSC molecule through the O(2)–H group. The water molecule is involved as an acceptor in


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a chelating H-bond with the TSC molecule. A second water molecule bridges the TSC and an additional bpy molecule (Figure 11A). The chains are linked by H-interactions mediated by the water molecules (Figure 11B). It is interesting that there is another bpy molecule trapped in the crystal, but this is not involved in H-bonding interactions. Furthermore, the bpy molecules are packed in parallel; in fact, an additional bpy molecule (not involved in hydrogen bonding) is trapped between the aforementioned chains. The shortest distance with the bpy neighbor is 3.81 Å (between centroids).

A)

B) Figure 11. Molecular association in the structure in entry 14

Theoretical calculations To obtain information on the factors that affect the formation of cyclic or polymeric structures, QTAIM calculations were performed on structural units formed by crystallization. Two structural units chosen for their greater structural simplicity were used directly in the calculations and these are represented in Figure 12.


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Figure 12. Structural units used for QTAIM calculations. When the structure shown in Figure 12A with the (30) motif is formed, the two intramolecular hydrogen bonds ((6)) (ρ(rc) = 0.0349 au in Table 1) break and four new stronger hydrogen bonds are formed that connect the TSC molecules and bpy by O(1/2)– H…Npyr (ρ(rc) between 0.0419 and 0.0483 au). Nevertheless, the four original O(1)–H…N(3) hydrogen bonds remain from the original TSC structure when the association represented in Figure 12B is adopted, although the ρ(rc) values (between 0.0252 and 0.0271 au) suggest a marked weakening of these interactions. In addition, six new interactions appear, four of which bind the TSC molecules to bpy by O(2)–H…Npyr (ρ(rc) between 0.0237 and 0.0317 au) and two weaker N(1)–H…S interactions (ρ(rc) = 0.006 au). The arrangement shown in Figure 12B could therefore be stabilized by a greater number of weaker hydrogen-bonding interactions than that shown in Figure 12A. CONCLUSIONS The main objective of the work described here was to identify the factors that affect the association of resorcinol-derived TSCs with H-bonding active groups towards N,N’-divergent


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aromatic diamines. Our previous analysis of the structures reported before suggested that the thioamide-thioamide (8) motif, as observed by Jawaria et al.,6 is strong enough to remain in the presence of other H-bonding acceptor groups and only when additional donor groups (such as methanol) are included is the system actually affected. Our theoretical calculations suggest that the N(1)–H…N(3) interaction must be very weak – a situation that is consistent with rather unsuitable structural parameters (for example the angle N(1)–H–N(3)). Consequently, it is not reasonable to attribute a relevant role to this interaction in the TSC associations included in this work. This is not the case for the O(1)–H…N(3) interaction, where structural parameters and QTAIM calculations agree with the moderate/strong character of this H-bond. It is difficult to know whether the observed strengthening effect of the methyl group on this interaction may be important enough to limit the behavior of the TSC/BP system but it should be noted that we did not observe any structure where this interaction was disrupted by an interaction with BP. Although the structures obtained by combining TSC and BP proved to be very varied, two main types can be established. In the first type the resorcinol fragment seems to lead to association through the (30/32) motif to yield discrete 2TSC:2BP units, which are mainly associated by TSC-solvent interactions. The other extreme structure is that in which the intramolecular O(1)–H…N(3) bond is not broken and the BP bridges between two TSC molecules by O(2)–H…Npyr interactions ( − 1 motif). The resulting TSC-BP-TSC units are associated by the interactions observed in the free TSC (mainly (8) and (4) motifs). The QTAIM calculations on 1b structures with bpy


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suggest that, although the energy of each interaction in (30) is greater than in − 1, the overall sum of weaker interactions is energetically favorable for the latter motif. Finally, all structures associated with the motif (30/34) have a KPI below those associated with − 1. This finding is even more relevant if one takes into account that the former always crystallize with solvent (in the case of the structure for entry 1 in Table 2, this is simply trapped in the crystalline lattice without any relevant interaction with the rest of the elements), thus suggesting a rather inefficient packing capacity. It is evident that this factor must also direct the formation of the product from the reaction medium. EXPERIMENTAL SECTION Synthesis Thiosemicarbazone derivatives of 2,4-dihydroxybenzaldehyde (1a, 1b, 1c) or 2,4dihydroxyacetophenone (2a, 2b, 2c) were obtained as reported previously.10 4,4’-bipyridine (bpy) and 1,2-bis(4-pyridyl)ethane (bpe) from Aldrich were used without purification. The co-crystals of TSC-BP were generally obtained as follows: the TSC was suspended in dry methanol (20 mL) and the corresponding (BP) was added (details of the ratios employed are included in Table 2). The reaction mixture was heated under reflux (65ºC) for 3 hours and this resulted in the formation of a clear yellow solution. The addition of few drops of diethyl ether after reduction of the solvent volume to approximately to 5 mL in a rotary evaporator, led to the formation of yellow crystals/powders or a mixture of both.


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X-ray crystallography Crystallographic data were collected on a Bruker SMART CCD-1000 diffractometer at 293 K using graphite monochromated Mo-Kα radiation (λ = 0.71073 Å) and were corrected for Lorentz, polarization and absorption effects.31,32 The structures were solved by direct methods using the program SHELXS. All non-hydrogen atoms were refined on F2 with anisotropic thermal parameters using SHELXL.33 Hydrogen atoms were inserted at calculated positions and refined as riders. Graphics were produced with MERCURY.34 Theoretical calculation methods All calculations were performed by using the M062X method in Gaussian0935 with the 6311++G** basis set. The wavefunctions were obtained for the optimized geometries of two conformers of the TSC molecules 1a, 2a, 1b and 2b. On these wavefunctions we performed QTAIM topological electron density analysis by using the AIMAll package36 in order to obtain bond properties for the hydrogen bonds and atomic properties for the atoms involved in the hydrogen bonds. The electron density at the bond critical points, ρ(rc), was employed as an indicator for hydrogen bond strength. IQA analyses were also performed to obtain interaction energies as well as their components, namely the electrostatic term (Vc) and the exchangecorrelation term (Vxc). Vc represents the electrostatic term and it is related to the ionic contribution to bonding. Vxc represents the non-classical component and it is related to pairs of electrons that are delocalized or shared between atoms. The M062X/6-311++G** wavefunctions were also obtained for the experimental geometries of co-crystals in entries 1 and 8 in order to calculate the strength of the bond critical points for the hydrogen bonds formed upon complexation.


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ASSOCIATED CONTENT Supporting Information. The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.cgd.XXXXXX Association patterns observed in crystal structures, crystal data and structure refinement and hydrogen bond data (PDF) Accession Codes CCDC 1534914-1534925 and CCDC 1535464-1535466 contain the supplementary crystallographic data for this paper (see Table 2 for details). These data can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif, or by emailing [email protected], or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033.

AUTHOR INFORMATION Corresponding Author *Phone: +34 986812319. Fax: +34 986 812556. E-mail: [email protected]. Web: http://angus.uvigo.es ORCID Ezequiel M. Vázquez-López: 0000-0002-6012-0931 Rosa Carballo: 0000-0002-9094-8238 Funding Ministry of Economy, Industry and Competitiveness (Spain) and European Regional Development Fund (EU) (CTQ2015-71211-REDT and CTQ2015-7091-R) for financial support. ACKNOWLEDGMENTS


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We thank the Structural Determination Service of the Universidade de Vigo – CACTI for X-ray diffraction measurements.


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Table 2. Main results of the structural studies on the crystals obtained from reaction mixtures of TSC and BP. Stoichiometry

M.p.(ºC)

Composition 1b/bpy/acetone 1b/bpe/ether 1b/bpe/DMSO 1c/bpe/MeOH 1a/bpy/MeOH 1a/bpe/MeOH 1c/bpy/MeOH 1b/bpy 1b/bpe

CCDC number 1534915 1534916 1535464 1534917 1534918 1534919 1534920 1534921 1534922

reaction crystal synthesis T 1:1:1 1:2 reflux 1:1:1 1:2 reflux 1:1:1 1:2 r.t. 1:1:1 1:2 reflux 1:2:1 1:2 reflux 1:2:1 1:2 reflux 2:3:4 1:2 reflux 2:1 1:1 r.t. 2:1 1:1.5 reflux

10

1b/bpe

1535465

2:1

1:2

r.t.

11 12 13 14 15c

2b/bpe 2a/bpe 2b/bpe 2b/bpy/H2O DUCSAW/bpy/H2O

1535466 1534923 1534924 1534925 ----

2:1 2:1 2:1 1:3:2 4:7:2

1:2 1:2 1:1.5 1:2 2:1

reflux r.t. reflux reflux r.t.

Entry 1 2 3 4 5 6 7 8 9

128 168d >300 250 215 265 104-6 220 246 (215d) 247 (217d) 201 222 212 137-141 --

Space group P21/c C2/c C2/c P21/c P-1 P-1 P21/c P-1 P-1

Vcell 2344.54 4614.29 4576.91 2593.78 1427.12 1548.15 3088.13 1426.34 755.03

KPI 65 67 66 66 66 68 66 70 70

Interactions Intermolecular BP TSC Intra R44(30) R22(8), C(4) R44(34) C(4) R44(34) C(4) R44(34) R55(28) R22(8) 5 R5 (32) R22(22), BPbridgeb R66(35) S(6) D-1 C(4), R33(C11) S(6) D-1 C(4), R33(C11)

P21/c

1535.37

69

S(6)

D-1

C(4), R33(C11)

Z/E

P-1 P-1 P21/n P-1 P-1

804.064 1006.23 2121.75 1885.96 2615.16

69 69 68 68

S(6) S(6) S(6) S(6)

D-1 C(22) C(20)

R22(8)’ R22(8)

E/Z -/E Z/Z Z/Z Z/E

a

R44(30) R55(27)

R21(6)

Others Sbridgea Sbridgea C(11)-B

C(11)-A

R21(6) R77(50)

Conformation N1-C1/C1-N2 Z/ E Z/E Z/E Z/E -/E -/E Z/E Z/E Z/E

Bridge solvent between two TSC molecules by H-bonding. The oxygen atom of the solvent molecules is the acceptor group for two interactions.

b

The BP molecule bridges between two methanol molecules by two O–H…N interactions.

c

Structure reported in reference 11.


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REFERENCES 1 Phukan, N.; Baruah, J.B. CrysEngComm 2016, 18, 7753-7763. 2 Paisner, K.; Zakharov, L.N.; Doxsee, K.M. Cryst. Growth & Des. 2010, 10, 3757-3672. 3 Eccles, K.S.; Morrison, R.E.; Maguire, A.R.; Lawrence, S.E. Cryst.Growth & Des. 2014, 14, 2753-2762. 4 Novakovic, S.B.; Fraisse, B.; Bogdanovic, G.A.; Biré, A. S. Cryst. Growth & Des. 2007, 7, 191-195. 5 Mukherjee, A.; Tothadi, S.; Desiraju, G.R. Acc. Chem. Res. 2014, 47, 2514-2524. 6 Jawaria, R.; Hussain, M.;Shafiq, Z.; Ahmad, H.B.; Tahir, M.N.; Shad, H.A.; Naseer, M.M. CrystEngComm. 2015, 17, 2553-61. 7 Gao, X.; Friscis, T.; MacGillivray, L.R. Angew. Chem. Int. Ed. 2004, 43, 232-6. 8 Khan, M.; Enkelmann, V.; Brunklaus, G. Cryst. Growth& Des.2009, 9, 2354-2362. 9 Nuñez-Montenegro, A.; Carballo, R.; Vázquez-López, E.M.J. Inorg. Biochem. 2014, 140, 5363. 10 Núñez-Montenegro, A.; Carballo, R.; Abram, U.; Vázquez-López, E.M. Polyhedron 2013, 65, 221-8. 11 Ng, S.W. Acta Crystallogr. 2009, E65, o2129. 12 Pedrido, R.; Romero, M.J.; Bermejo, M.R.; González-Noya, A.M.; García-Lema, I.; Zaragoza, G. Chem. Eur. J. 2008, 14, 500-512. 13 Groom, C. R.; Bruno, I. J.; Lightfoot, M. P.; Ward, S. C. Acta Cryst. 2016, B72, 171-179. 14 Etter, M.C. Acc. Chem. Res 1990, 23, 120-6. 15 Gu, S.-J.; Zhu, K.-M. Acta Crystallogr. 2008, E64, 64, o1597. 16 Jian, F.; Li, Y.; Xiao, H. Acta Crystallogr. 2005, E61, o2219. 17 Almarsson, Ö; Zaworotko, M.J. Chem. Commun. 2005, 1889-1896. 18 Monfared, H. H.; Chamayou, A.-C.; Khajeh, S.; Janiak, C. CrystEngComm 2010, 12, 35263530. 19 Chattopadhyay, D.; Mazumdar, S. K.; Banerjee, T.; Ghosh, S.; Mak, T. C. W. Acta Crystallogr. 1988, C44, 1025-1028. 20 Soriano-García, M.; Valdés-Martínez, J.; Toscano, R. A. Acta Crystallogr. 1988, C44, 12471249. 21 Ng, S. W.; Das, V.G. K.; Skelton, B. W.; White, A. H. J. Organomet. Chem.1989, 377, 211220 22 Xu, S.-P.; Feng, L.Z. Kristallogr.-New Cryst.Struct. 2013, 228, 213-214. 23 Bader, R. F. W. Atoms in Molecules: A Quantum Theory, Oxford University Press, Oxford (U.K.) 1990. 24 Martin Pendas, A.; Francisco, E.; Blanco, M.A. J. Chem. Phys., 2006, 125, 184112. 25 Yildiz, M.; Unver, H.; Erdener, D.; Kiraz, A.; Iskeleli, N.O. J.Mol.Struct.2009, 919, 227-234. 26 Tan, K. W.; Ng, C. H.; Maah, M.J.; Ng, S.W. Acta Crystallogr. 2008, E64, o2224. 27 MacGillivray, L.R.; Papaefstathion, G.S.in Encyclopedia of Supramolecular Chemistry, Marcel Dekker Inc. Ed. New York (USA), 2004, 1316. 28 MacGillivray, L.R.; Reid, J.L.; Ripmeester, J.A. J. Am. Chem. Soc. 2000, 122, 7817-7818. 29 Papaefstathion, G.S.; Kipp, A.J.; MacGillivray, L.R. Chem. Comm. 2001, 2462-2463. 30 Kitaigorodskii, A. I. Molecular Crystals and Molecules; Academic Press, New York, 1973.


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31 Siemens SAINT, Version 4, Software Reference Manual, Siemens Analytical X-Ray Systems, Inc., Madison, WI, USA, 1996. 32 Sheldrick, G. M. SADABS, Program for Empirical Absorption Correction of Area Detector Data; University of Göttingen, Germany, 1996. 33 Sheldrick, G.M. Acta Crystallogr. 2015, A71, 3-8. 34 Bruno,I.J. ; Cole, J.C.; Edgington, P.R.; Kessler, M.K.; Macrae, C.F.; McCabe, P.; Pearson, J.; Taylor, R. Acta Crystallogr. 2002, B58, 389-397. 35 Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, Ö.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian, Inc., Wallingford CT, 2009. 36 Keith, T.A. IMAll (Version 16.10.31), TK Gristmill Software (aim.tkgristmill.com) Overland Park KS, USA, 2016.


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For Table of Contents Use Only

Supramolecular synthesis and experimental and theoretical studies of co-crystal systems based on resorcinol-thiosemicarbazones and N,N'-divergent dipyridines Ara Núñez-Montenegro, Saray Argibay-Otero, Rosa Carballo, Ana Graña, Ezequiel M. Vázquez-López

A supramolecular synthesis process in methanol of a combination of several resorcinolthiosemicarbazones (TSC) and two N,N'-divergent bipyridines (BP) led to the isolation of cocrystals which can be grouped into TSC:BP cyclic arrangements by the absence of the intramolecular O–H...N, (6), interaction in the TSC component and, TSC:BP acyclic associations where this interaction remains.


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Supramolecular Synthesis and Experimental and Theoretical Studies

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