When Does a Supramolecular Synthon Fail? Comparison of

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When does a supramolecular synthon fail? Comparison of bridgehead-functionalized adamantanes: the tri- and tetra- amides and amine hydrochlorides Ishtvan Boldog, Guido Reiss, Kostiantyn V. Domasevitch, Tomas Base, and Stefan Braese Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.9b00594 • Publication Date (Web): 12 Jul 2019 Downloaded from pubs.acs.org on July 17, 2019

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Crystal Growth & Design

When does a supramolecular synthon fail? Comparison of bridgehead-functionalized adamantanes: the tri- and tetra- amides and amine hydrochlorides Ishtvan Boldog,*,†, Guido Reiss,|| Kostiantyn V. Domasevitch,§ Tomas Base,# and Stefan Bräse†

† Institute

of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-

Weg 6, 76131 Karlsruhe, Germany

|| Institute

of Inorganic Chemistry and Structural Chemistry, Heinrich Heine University

Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany

§ Inorganic

Chemistry Department, Taras Shevchenko National University of Kiev,

Vladimirskaya Street 64, Kiev 01033, Ukraine

ACS Paragon Plus Environment

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# Institute

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of Inorganic Chemistry, The Czech Academy of Sciences, v.v.i. 250 68

Husinec-Rež, c.p. 1001, Czech Republic

E-mail: [email protected]

KEYWORDS: adamantane, crystal structure, H-bond, prediction, supramolecular synthon, violation, amide, amine, hydrochloride.

Abstract

1,3,5-trisubstituted

adamantane

carboxamide

and

amine

hydrochloride,

Ad(CONH2)3 · 2.5H2O and [Ad(NH3)3]Cl3 · H2O (Ad = adamant-n-yl) respectively, crystallized from aqueous solutions, possess crystal structures with predictable H-bonded assembly, consistent with the C3v symmetry of the building blocks. The triamide structure consists of interpenetrated hexagonal networks, sustained by the well-known cyclic Hbonded bis-amide synthon, R22(8), which ensures linear connectivity. The structure of the triamine hydrochloride, assembled through the tetrahedral {RN+H3---(Cl-)3} synthon,


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features a remarkably symmetric assembly with narrow trigonal pore-channels, hosting water molecules. The structures of the tetrahedral 1,3,5,7-tetrasubstituted Ad(CONH2)4 and [Ad(NH3)4]Cl4, obtained similarly, demonstrate a formal prediction failure of synthon based approach. Instead of the anticipated bis-amide synthon based diamond network (1.485 g cm-3) analogous to the 5-fold interpenetrated paradigmatic structure of Ad(COOH)4, a non-interpenetrated assembly, sustained by a dense network of H-bonds, is realized (1.433 g cm3). Lessened geometric regularity was also found in the tetrahydrochloride salt assembled via 5-connected nodes, {RN+H3---(Cl-)4}, which involve a bifurcated H-bond. The failures of the supramolecular synthons in these simple cases could be interpreted either in terms of symmetry and/or limitations associated with the ‘synthon-density’. A potential machine learning approach oriented on heuristic retrosupramolecular synthesis relies on such selected high-weight conceptual cases.


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Introduction

The emergence and development of crystal engineering, the field devoted to prediction and 'rational design' of crystal structure, could be traced back to a relatively small number of paradigmatic observations.1,2 One of such observations was the structure of 1,3,5,7-adamantanetetracarboxylic acid, reported by O. Ermer in 1988.3 The structure features a 5-fold interpenetrated diamond net topology (dia), in which the tetrahedral molecules are associated via H-bonded, i.e. 'supramolecular', carboxylic acid dimers. The crystal engineering of coordination polymers also found its mayor inspiration in tetrahedral building blocks and the respective diamondoid structures,4 with a focus on the underlying nets by Robson.5,6 Periodic nets are now the classificational and heuristic backbone of the rational crystal-structure ‘design’, particularly in its most important off-shoot, the field of the metal-organic frameworks.7

The tetrahedron is the most symmetric synthetically affordable molecular shape (not counting the trivial cases belonging to infinite point groups). Its role in insights is not surprising,8 taking in account the all-pervasive importance of symmetry in natural


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sciences, abstract thinking and the instinctive perception of beauty itself. Symmetric settings of a problem typically correspond to conditions of an extremum. Hence in is not rare to for tetrahedral molecules to bear ‘the most’ attributive in the area of supramolecular solids. Among them are, for example, the most porous representatives among Zr-MOFs as well as COFs9 (notably, Covalent Organic Frameworks, are covalent objects, but their synthesis at least formally involves reversible interactions). The diamond net, primarily associated with tetrahedral building blocks, is the most frequent of all observed topologies10, and also of all interpenetrated network structures.11 Tetrahedral building blocks are also proved to be important in evasion of dense lamellar packings, recently allowing the synthesis of the first truly-porous ultrastable phosphonate Zr-MOFs.12

Central notions in the 'rational design' of crystal structures are the concepts of supramolecular synthon and retro-supramolecular synthesis. The latter implies a formal dissection of the aimed periodic net to fragments, which could be embodied by molecular entities eventually undergoing self-assembly. The reversibility of the


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assembly ensures 'defect-healing' (dynamic chemistry).13 An early straightforward analysis of the Cambridge Structural Databank (CSD) gave a reassuring view on the utility of supramolecular synthons.14 The concept15 is inherently based on limiting the analysis to the strongest, most directional intermolecular interactions (i.e. coordination bonds and H-bonds16) and neglecting the weaker ones. However, it turned out that the straightforward geometric approach is not efficient.17 It is not possible simply to neglect neither the impact of the multitude of weaker interactions nor avoid the in-depth treatment of symmetry-related demands. On the one hand, this phenomenological approach is thriving in the MOF field,18,19,20 where as robust coordination-bonded clusters are viewed as dominating entities. On the other hand, the discourse related to supramolecular synthons and its utility for crystal structure prediction (CSP) of Hbonded solids has fallen in relative disuse.

The limited success of the early ‘rational design’ approach was probably predestined due to the complexity of the problem and futile focus on ab-initio predictions. Two wellknown comments on the situation are ‘A continuing scandal in physical sciences’ by J.


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Maddox21 in the editorial of Nature in 1988, and ‘Are crystal structures [at all] predictable?’ by J. Dunitz22 in 2003. Since then, the ab-initio, semi-empirical, genetic/evolutionary algorithms, and, importantly, stochastic (Monte-Carlo) CSP methods made very significant progress with a variety of methods/software available today.23,24,25 However they do not provide a final solution, being computation-hungry and easy missing local minima, which correspond to the actually existing polymorphs. It is particularly true, when the non-bonding dispersive (van der Waals) interactions represent a significant part of the total formation energy share. The DFT computational methods are considered to be the most versatile and efficient and yet faces significant challenges in precise accounting for those weak interactions in complex (supra)molecular systems.26

However, the goal of a synthon-based approach would not be the prediction of structure(s) for any given compound, but only for a predicted set of them. Currently, machine (deep) learning27 algorithms / neuronal computing trickles down to the level of everyday use, which gives the approach a second chance to actualize. How efficient


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such a system will be, is largely dependent on the parameters, used for machinecorrelations.28 The strong side of such an approach coupled with synthon-level assessment is its closeness to human reasoning, invaluable for subsequent heuristic analysis by a researcher. The optimal parameter-choice in the context of machinelearning efficiency should be strongly influenced by selected, most illustrative cases when the synthon-approach fails (cf. verifiability principle). And as usual, the most symmetric cases of concept-violations give the most insight.

CONH2 H2NOC

CONH2

CONH2

H2NOC

CONH2 CONH2

1

2

NH3+ +

H 3N

NH3+ NH3+

(Cl-)3

+

H 3N

NH3+

4(Cl-)

NH3+

3

4

Chart 1. The adamantane derivatives, whose crystal structures are reported in this work: Ad(CONH2)3, 1; Ad(CONH2)4, 2; [Ad(NH3)3]Cl3, 3; [Ad(NH3)4]Cl4, 4. Note: for the sake of simplicity, the same ‘Ad’ root in the encoded compound names is used for both adamantane-n-yl radicals, namely the adamantane-1,3,5,7-tetrayl and the adamantane-1,3,5-triyl.


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In this contribution, the structures of 1,3,5,7-tetrakis- and 1,3,5-tris bridgeheadfunctionalized adamantanes (Chart 1) are reported, namely amides and amine hydrochlorides. On a conceptual level the approach of truncation of a highly symmetric 'building-block' offers an interesting view on structure formation, especially from the point of view of the regular introduction of defects.29 The comparison of the tetrakis- and tris- functionalized structures in this work offers an exemplary case of a situation "when a supramolecular synthon fails", and the failure, curiously enough, happens with the molecule of higher symmetry. In simple terms, this paper reports some H-bonded structures of adamantanes that are important for structural chemistry of H-bonded solids due to fundamental simplicity/symmetry of the building blocks.

Results and Discussion

The structures presented in this publication were not reported earlier most probably due to not straightforward availability of the bridge-head functionalized adamantane-triand -tetra-carboxylic acids. The syntheses are not particularly complicated, but they involve non ubiquitously available steps, like oleum use of particular concentration in the


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case of the triacid or photochemical cyanodebromination in NaCN solution in DMSO (the latter reaction, reported relatively recently, greatly facilitated the route towards 1,3,5,7-adamantanetetracarboxylic acid). Further reaction sequence involving conversion to acylchloride, followed by Shotten-Bauman reaction leading to amide, and Hofmann rearrangement yielding the amine are standard (see Schemes S1, S2; the experimental details were published by us in concise form earlier;30 see chapt. 1 in SI for the related discussion and additional details).

Crystallization of the amides. The crystallization of the tri- and particularly tetraamide posed a certain problem, due to their low solubility in all solvents except the most polar ones, like DMF, DMSO. The use of such solvents was not only inconvenient but posed a significant risk of their incorporation. As particularly strong H-bond donors, these large molecules tend to enter the structure yielding crystal-solvates with ‘disturbed’ H-bonded patterns rather than the desired pure compound. After a series of experiments, a simple solution of the problem was found: concentrated aqueous ammonia, by means of concurrence with the intermolecular H-bonding, proved to be an enough good solvent


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for the triamide at room temperature and for tetraamide under hydrothermal conditions. Slow evaporation of the ammoniacal solution at room temperature, or slow cooling under solvothermal conditions, yielded crystals of 1 · 2.5H2O and 2 respectively, suitable for single crystal XRD structure determination.


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Figure 1. a) Asymmetric unit of Ad(CONH2)3 · 2.5H2O, 1 · 2.5H2O (the water molecule with partial occupancy is not shown). b) Polycatenation mode of the honeycomb underlying nets of the structure, shown completely for the medium cell-row of the red net (the color-code aims better visual differentiation; the nets are identical by symmetry). Each mesh of a given net topologically locks two other nearly parallel nets, running askew (red vs blue and grey nets on the image).

The structure of Ad(CONH2)3 · 2.5H2O. The structure of 1 · 2.5H2O fully conforms to the expectations (Fig. 1). The bis-amide synthon is realized (average d(NH···O) = 3.012 Å, N = 0.035 Å; where N is the standard error), giving rise to a honeycomb, hcb, network which is one of the most expected outcomes for a trigonal molecule (see Table 1 and the SI for more information; for three letter RCSR topology codes see ref. 18 ). While 1, possessing a C3v symmetry, is non-planar, the geometry of the layers is corrugated. However, due alternating orientation of the molecules within the net, i.e. the signs of the shifts introduced by non-planarity, the C3v molecules could behave similarly to the higher symmetry C3h/D3h prototypes at least in the case of the


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hcb net (it was already observed 30,29 that tri-substituted adamantanes have the tendency to form topologies typical or conceivable for highly symmetric trigonal building blocks).

Importantly, the water molecules, which are present in the structure do not disturb the assembly of the bis-amide synthon (they are also excluded from the topological analysis). Their presence could be interpreted as simple space-fillers in the hydrophilic regions near the amide groups. One of the water molecules forms an H-bond with an NH donor and two others with O-acceptors of amide groups, being additionally associated with each other. The partial occupancy of one water molecule is clearly suggested by the structural data: the symmetry equivalent of that molecule is located too close, disallowing a relative occupancy factor of more than 0.5.

The primary space filling factor is, nevertheless, not water, but the polycatenation31 of the honeycomb networks (Fig. 1b), which leaves only 19.1% of solvent accessible space (2.4 Å3 probe diameter32). Each mesh of a given network interlocks two other parallel networks at an angle of 2arctg(0.5) = ~53.1° (in other words each network


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crosses two unit-cells in the bc projection), i.e. the interweaving is of an ‘inclined’ type.31 Despite of the presence of water-filled cavities the 1.355 g cm-3 calculated density is remarkably high for organic compounds, reflecting the overall strength of multiple H-bond interactions (cf. with the 1.276 value for 1,3-adamantanedicarboxamide 33

).

Table 1. Topological analysis summary (see also the SI chapt. 9 for more details).

Stoichiometry Interpretation level; (connectivity, Compd.

Point

symbol;

c

nodality;

node

polycatenation or interpenetratio

connectivity a

representation

n

)b 1 · 2.5H2O

Molecular

d

uninodal; 1-c

2

level;

(3-c, 1)

Molecular level;

(12-c, 2)(16-c,

2-nodal; 12,16-c

2)

Adamantane/Amid

(4-c, Ad)(4-

e level;

c, Ad)(5-c,

4-nodal; 4,4,5,5-c

Amide)4

Amide)4(5-c,

{63}, hcb or honeycomb net; 2D+2D polycatenation, inclined

{322.436.58}{338.460.522}

{52.64}{66}{42.5.65.72}4{43.5.66}4


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Molecular level;

2-dia

(4-c, 2)

{66}, dia or diamond net;

(hypothetic) uninodal; 4-c

3 · H2O

4

Class Ia interpenetration, 5-fold

Molecular level;

(3-c,

2-nodal net; 3,9-c

Ad)

Ad , NH3+, Cl- level;

(3-c,

3-nodal; 3,3,4-c

)3

d

Cl)3(9-c,

{42.6}3{46.624.86}, IrSi3-type

Ad)(3-c,

NH3+)3(4-c, Cl- {83}{63.83}3{63}3

Molecular level;

(4-c, Cl-)2(4-c,

3-nodal; 4,4,16-c

Cl-)2(16-c, 4) (4-c,

{448.662.810}{45.6}2{46}2

Ad)(4-c,

Ad , NH3+, Cl- level;

Cl-)2(4-c,

5-nodal; 4,4,4,5,5-c

NH3+)2(5-c,

)2(5-c,

Cl{66}{42.64}2{43.63}2{42.68}2{43.67}2

NH3+)2 a

The topological interpretation level could be molecular, i.e. the molecules are taken

as nodes, or the molecular entities are subdivided further. The nodality is the number of topologically distinct nodes. The row of connectivity indices enumerates the number of bonds, made by each node. b

In the stoichiometry notation, the brackets enclose information about the nodes,

the connectivity, and the representation, i.e. the molecule or fragment. c

The point symbols34 of the node is enclosed in curly brackets and given in the

same order as in the stoichiometry notation, i.e. the n-th node in both notations corresponds to each other. d

Note that the water molecules are excluded from the topological analysis.


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Figure 2. a) The super-adamantane cage of the expected, but not observed, hypothetical dia-Ad(CONH2)4, 2-dia structure consisting of networks with the diamond underlying net.


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b) The 5-fold interpenetration of the networks with one network shown explicitly, on the level of the constituting molecules.

The expected structure of Ad(CONH2)4. If the structure of Ad(CONH2)4 were based on the bis-amide synthon, it would have a diamond underlying net (dia), designated as diaAd(CONH2)4, 2-dia. This structure should possess the same organization as in the paradigmatic structure of dia-Ad(COOH)4.3 The structure of 2-dia would, by analogue, consist of 5 interpenetrated dia networks (Fig. 2). There are no principal obstacles for the realization of 2-dia, as the geometrical difference of one added proton does not alter the molecular sterics significantly. On the other hand, the presence of an additional Hbond acceptor is a factor, which could disturb the connectivity (according to the analysis of reported structures primary amides have probabilities of realization comparable to carboxylic acids14. However, chain motifs, employing the additional H-bond donors, are also possible and could be a viable alternative, when the sterics is compliant).

Careful analysis of the shortest intermolecular distances shows that the optimal molecular geometry and the placement of the molecule in the unit cell should be very


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close to the one observed in dia-Ad(COOH)4 (see the discussion in chapter 6 of the SI; a two-parameter model were analyzed, with α being the angle of molecular turn on the particular site of the unit cell, and ω being the turn of the amide group around the C-C bond connecting it with the adamantane moiety, Fig. 29, 30). The only difference is the presence of NH···HN repulsive contacts in 2-dia, which could, nevertheless, easily brought in the desired range (>3.5 Å) by variation of the model’s parameters and/or proportional elongation of the weak-contacts (i.e. decrease of density, which is practically the third variable parameter). The geometry of dia-networks is highly adaptable as the three-parametric geometry space provides enough opportunities to minimize the unfavorable interactions. At a chosen d(NH···O) = 2.930 Å length of the amide bond, which is the average for the already described bis-amide based structures, the density of the model optimal structure is ~1.480-1.485 g cm-3, depending on the fine-tuning of the other two α and ω parameters (see the discussion in the SI; the lengths of the shortest inter-molecular contacts were chosen as the subject of optimization), which only slightly affects the density near the optimum. At the α and ω values precisely the same as in the dia-Ad(COOH)4, the densities compares as 1.481 vs


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1.652 g cm-3, i.e. the tetraacid has higher density in accordance with shorter d(OH···O) compared to d(NH···O) lengths, 2.647 vs 2.930 Å respectively (the density of diaAd(COOH)4 is anomalously high for non-aromatic organic compound consisting of elements up to oxygen,3 which also reflects the efficiency of the packing). Thus the structure of 2-dia seems to be feasible.

The experimental structure of Ad(CONH2)4. To our surprise, the observed actual structure of 2 is, however, completely different (Fig. 3). The bis-amide synthon is not realized and the obvious local difference is that the amide groups are involved more efficiently in the H-bonded network, serving as 2/2 donor/acceptor instead of the less symmetric 1+1/1+1 case in the hypothetical 2-dia. In the optimal structure of 2-dia, which is believed to be close to dia-Ad(COOH)4, the ‘side’ H-bonds, additional to the primary ones, sustaining the bis-amide synthon, is practically absent (d(N···O = 4.3 Å) and the amide is functioning as a 1/1 donor/acceptor. Even if the structure of 2-dia could, in principle be deformed in a way, to reach decrease the length of the ‘side’ bonds below 3.5 Å, the significant asymmetry would remain.


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The structure of 2 has a remarkably low P2 symmetry compared to the I41/a of 2-dia. A situation of Z´ = 20.5 takes place,35 i.e. there are two independent molecules in the structure, however, each of them is represented only by an independent half (Fig. 3a). The two molecules are the same from the point of view of immediate H-bonding connectivity (but not regarding the overall topology). The latter could be rationalized via its more salient feature, the smallest cyclic H-bonded pattern, ··(·CONH2···NH2···CONH2···O··)·, consisting of two full amide groups and two parts, represented by one NH2 donor and one O-acceptor. In ‘graph-set analysis’ notation by Bernstein et al. for H-bonded patterns,36,37 this pattern is of R34(12) type, where R stands for the cyclic (ring) type of the pattern, 3 in the superscript for the number of the three O acceptors, 4 in the subscript for the number of NH donors of the four involved NH2 groups, and 12 is the total number of H-bonds36 in the ring (formerly, it was the number of atoms including hydrogens,37 which gives the same result for rings). This cyclic pattern could be interpreted as a symmetric expansion of the bis-amide pattern by the inclusion of two moieties, representing a double donor and a double acceptor (the well-known bis-amide or bis-carboxylic acid synthons are both of R22(8)). Such, nearly symmetric expansion


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allows incorporating more available H-bond donors and acceptors. The R34(12) patterns with some additional contacts between them sustain the H-bonded layers running perpendicular to the c-axis (Fig. 3b), with precisely half of the Ad(CONH2)4 molecules involved. Thus, the layers are duplicated through the adamantane moieties, and those ‘sandwiches’ are further associated by additional H-bonds between the NH2 and O donors and acceptors, which are not involved in the formation of the cyclic pattern (Fig. 3b).

Despite the amide groups of the two crystallographically different molecules of Ad(CONH2)4 have the same H-bonding connectivity (i.e. same way, they are associated with the neighbors), the molecules as a whole, viewed themselves as nodes of a network, are topologically distinct. As the Ad(CONH2)4 molecules have very high Hbonding connectedness, the topological analysis in the case of 2 is rather of formal interest. It confirms that the network is binodal, with a 12- and 16-connected nodes, corresponding to the two independent molecules. Topological analysis on the level of 5connected amide and 4-connected adamantane moieties (i.e. the bond between the


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amide and adamantane moieties are considered as inter-nodal) give a stoichiometry of (4-c, Ad)(4-c, Ad)(5-c, Amide)4(5-c, Amide)4. Thus there are only two topologically different amides in the structure, associated with the two crystallographically independent Ad(CONH2)4 molecules. The amides belonging to the same molecule are topologically equivalent, even if crystallographically distinct. It is curious, as the symmetry breaking occurs on the level of whole molecules, but not within them: the molecules have the highest possible topological symmetry (with 1/4 of the molecule being topologically independent).

The average NH···O H-bond length in 2 is 2.934 Å (N = 0.024), i.e. practically the same as used for the modeling of 2-dia, while the density is 1.433 vs 1.481 g cm-3, i.e. considerably smaller. Nonetheless, the non-interpenetrated structure of 2 with a dense H-bonding network is the preferred polymorph, at least under preparation condition, used by us. Interesting to note the ∠OCCC torsion angle in 2 and 2-dia (in the latter case practically equivalent to the ω parameter of the model) is close to each other, 18°

vs 28-31°, so the evidently small energy difference should not be held responsible as an


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‘induction factor’ during crystallization (note, that for example in 1 · 2.5H2O the ∠OCCC torsion values are 0, 0 and -34.9°, i.e. cover a much broader range).


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Figure 3. a) Asymmetric unit of Ad(CONH2)4, 2. Z´ = 20.5. The symmetry equivalents completing the fragments to full molecules are shown semi-transparent. b) Top-view on the structure, showing the layers associated by the principal R34(12) cyclic H-bonded


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pattern, ··(·CONH2-···NH2···CONH2···O··)·, delineated with thick orange dashed lines. The additional bonds between the patterns are shown in thin dashed orange lines c) side-view of the structure with the additional ‘inter-layer’ H-bonds shown in blue.

Additional remarks regarding the structures of the amides. The second hydrate, Ad(CONH2)3 · H2O. The comparison between the structures of 1 · 2.5H2O and 2 would not be complete without mentioning some observations, which complicates the clear view, given above. Firstly, it is a short account of our alternative crystallization experiments. Initially, the use of solvothermal crystallization for Ad(CONH2)4 was conditioned by its very low solubility in an aqueous ammonia solution at room temperature. To our surprise, the crystallization of Ad(CONH2)3 under elevated temperatures in a closed vessel, i.e. under conditions of elevated pressure resembling the crystallization conditions of Ad(CONH2)4, yielded another hydrate form, 1 · H2O, with a distinctively different crystal habit (Fig. S18). The crystallizations were done repeatedly, confirming the high reliability of the procedures and the phase purity of the products (Fig. S24, 25). 1 · H2O has a denser structure than 1 · 2.5H2O (1.415 vs 1.355 g cm-3) and the water molecule ‘disturbs’ the connectivity of


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the amides, interposing between some pairs (Fig. S20) unlike the case of the latter semipentahydrate H-bonded connectivity. Hence, from the viewpoint of this contribution, the structure of 1 · H2O is of secondary importance; however, it indicates that a variety of adducts could be possibly obtained. We also attempted to crystallize Ad(CONH2)3 and Ad(CONH2)4 via sublimation. Both compounds sublime very slowly at ~130-160 °C and ~10-5 Torr, but while Ad(CONH2)3 crystallizes in distinguishable microcrystals, the Ad(CONH2)4 sublimes as a polycrystalline solid. Due to that further experiments were not pursued. The second complication, we have met, is a reliable quantum-mechanical calculation of the energy difference between the polymorphs 2 and 2-dia. The most efficient DFT methods, as it is mentioned in the introduction, needs corrections accounting for longrange dispersion forces. The addition of semi-empirical terms to the Kohn-Sham equations improves significantly the situation, but we were not able, even nearly, to estimate the precision of the calculations.26 Full optimization, including the optimization of molecular geometries using the experimental and suggested structures of 2 and 2-dia resulted in a small energy difference of a few kJ per Ad(CONH2)4 molecule. However, the


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result depended significantly on the methods / parameters used. Interestingly, the optimization of the structure of 2-dia yields a structure with even higher density compared to the suggested variant, and actualization of the 2/2 donor/acceptor mode, even if the ‘outer’ H-bonds formed by the amides remained significantly weaker compared to the ones sustaining the bis-amide synthon (see the beginning of the discussion on 2). Due to the very high role of dispersive interaction (very high density of the experimental structure of 2), and due to precision problems in accounting them, we decided to refrain from publishing the results or the quantum mechanical calculations as inconclusive.

Crystallization of the amine hydrochlorides. Interesting parallelism in low symmetry of tetra- vs tri-substituted adamantane on the level of crystal structure could be also seen in the structures of the respective aminohydrochorides. The 1,3,5-adamantanetriamine trihydrochloride, hydrate, Ad(NH2)3 · 3HCl · H2O, 3 · H2O; and 1,3,5,7adamantanetetraamine tetrahydrochloride, [Ad(NH3)4]Cl4, 4, were obtained by slow diffusion of hydrochloric acid vapors to the solutions of the respective amines in diluted hydrochloric acid (the rapid solubility decrease of polyamine chlorides with the increase


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of concentration of hydrochloric acid is a general phenomenon; it is a consequence of ample possibilities for H-bonded association).

Figure 4. a) View on the structure of 3 · H2O along the c-axis in parallel projection. b) The same view-direction on a representative fragment of the structure shown in central projection, demonstrating the tubular cavities filled by water molecules. c) An isolated H-


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bonded channel with water-molecules, purposefully depicted disproportionately large, reflecting the available space.

The structure of [Ad(NH3)3]Cl3 · H2O. In 3 · H2O both the NH3+ cation-donor and the Clanion-acceptor forms 3 H-bonds, while the arrangement of the bonds is pyramidal and geometrically close in both cases (Fig. 4). 2 out of 3 bonds formed by both the cation and anion are oriented in the plane perpendicular to the c-axis and associated in large cycles, R36(12), with a C3v symmetry (Fig. 4a). The tri-substituted adamantane possesses the same symmetry and orientation of the main axis, so the two elements are combined in an hcb-a subtopology (‘-a’ stands for augmented net is a net, where the vertices of the original net are replaced by a group of vertices with the shape of the original coordination figure of the vertex).38 Geometrically, the formed network could be imagined as a substitution of each non-neighboring node of a regular net by a hexagon (topologically by a triangle, as three of the hexagon’s vertices are non-branching), thus leaving an opening in the layer. The whole structure is a stack of these hcb-a subtopologies connected by the remaining H-bonds along the c-axis (Fig. 4b).


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The structure organization is marked by elegance, reflected also by the high P63mc symmetry (such a high-symmetry outcome could have been expected simply because the adamantane moiety, the NH3+, and Cl- all possess at least C3v symmetry, and the rigid combination of the first two moieties is compatible with it). Due to augmentation of the hexagonal sub-net, there are pore-channels in the structure, running along the caxis (Fig. 4b,c). The 11.0 % of solvent accessible space (2.4 Å probe diameter32) corresponds to 40 Å3 per one adamantane molecule, which is near-exactly the same as the volume of one water molecule in the liquid phase. Indeed, the pores are filled by water molecules, located on the main axis, but their placement is somewhat loose as it is also reflected by asymmetric disposition in relation to the neighboring Cl- anions at a distance of 3.46 and 3.98 Å, with the second distance corresponding to a very weak contact.

The structural elegance is also reflected on the topological level. If the adamantane, NH3+, and Cl- moieties are taken respectively as 3-, 4- and 4-connected nodes, the network in such interpretation has a simple and symmetric combined point symbol of


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{83}{63.83}3{63}3. On the other hand on the level of the full molecule, the 3,9-c network has a known analog, represented by the structure of IrSi3.39 As connectedness of 9 is relatively rare, and such coincidence may indicate that such topology might have an increased importance for such kind of rare building blocks.

The structure might have been an interesting prototype for an ionic conductor; however, the channels are too narrow even for free and unhindered passage of noncharged water molecules. The movement of the guest in the channel would involve a traverse of a potential barrier when the distance to the three Cl- anions lowers simultaneously to approx. ~3.0 Å3. Such barrier is prohibitive for nearly anything except gases and an unrealistic case of a naked H+ (effective chain mechanism, akin to Grotthuss mechanism, is also not possible due to the relative isolation of the small cavities along the pore-channel).


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Figure 5. a) The asymmetric unit of [Ad(NH3)4]Cl4, 4 with the covalently bound symmetry equivalents, which are shown semitransparent, and the involved H-bonds b) A view along the b-axis showing the overall H-bonding connectivity. Note the different level of the layers, which are emphasized by color saturation (i.e. ‘depth-cueing’, darker areas are closer).


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The structure of [Ad(NH3)4]Cl4. 4 crystallizes in a C2 space group of much lower symmetry compared to 3 · H2O. The asymmetric unit consists of half of the molecular formula (Fig. 5b). The NH3+ and the Cl- moieties participates in four hydrogen bonds (Fig. 5). While the regular-tetrahedral environment of Cl- is feasible and actually takes place, the environment of NH3+ cannot be symmetric with three donors and four acceptors. One NH donor participates in a bifurcated H-bond and the local symmetry at the N atom lowers from C3v to Cs (curiously, the symmetry lowering resembles another ‘failed crystal engineering attempt’ in 1:1 salts of adamantanetetracarboxylic acid and hexamethylenetetramine).40 The structure is dense, represented by a single H-bonded topology, and is dominated by small cyclic patterns of different types, R22(4), R23(6) and R24(8). This row enumerates the simplest symmetric ones (at least of Cs in max. symmetry realization), very typical for RNH3+ and RR´NH2+ hydrochlorides. Due to the high interconnectedness, it is not possible to make a simple hierarchical rationalization of the pattern. When looking along the b-axis, the undulation of the level of the molecules within a given ‘layer’ is easily distinguishable (Fig. 5b). There is a row-wise alternation, with the rows running along c-axis. Within the rows, there are only ‘fully-


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even’ patterns, namely R22(4) and R24(8). The ‘partially-odd’ R23(6) is only involved in the connection of the neighboring rows. This is how the local ‘asymmetry’ of the R-NH3+ participating in four H-bonds is accounted for. Thus, the single NH-bond donor that makes two bonds is involved in one row (the higher one in Fig. 5b), while the other two NH-bond donors, which make per one bond, are involved in the alternate row.

While there is a certain perceptible logic in the H-bonded structure of 4, the only straightforward way of description here is only topological. The point symbol of the 3,3,16-c net, when Ad(NH3)44+ and the Cl- are taken as nodes, is rather of formal/classificatory value (Table 1), due to the too high 16-c of the cationic node. Further topological subdivision to 4-c (i.e. 4-connected) adamantane moiety, 5-c NH3+ and 4-c chloride moieties as nodes is quite straightforward, as the nodes are wellseparable or represented practically by a single atom or a very small aggregate, like in the case of ammonium or chloride (this is different to 2, where the amide moiety is not so localized and not so ‘node-separable’). Within such interpretation, the topology of the structure is a 5-nodal Ad, N, N´, Cl, Cl´ net with a respective stoichiometry of (4-c)(5-


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c)2(5-c)2(4-c)2(4-c)2 and complete net point symbol of {66}{43.67}2{42.68}2{43.63}2{42.64}2. Thus, while the two NH3+ and two Cl- nodes are pairwise close within their groups structurally, this semblance does not hold the test by analysis of connectivity and the topological symmetry (i.e. node equivalence) of this structure is not higher than the crystallographic symmetry (contrary to what is observed in the structure of 2).

It is interesting to note that the difference in H-bonding, particularly the presence of bifurcation only in 4, but not in 3 · H2O, is clearly distinguishable in the otherwise very similar IR spectra (see SI, chapt. 3) in the region of H‒N‒H bending bands, ~1500-1600 cm-3. The same effect could be distinguished, albeit to a lesser degree, in the structures of 1 · 2.5H2O and 2 for the characteristic ν(CO) band, 1600-1670 cm-1, which is slightly split in the latter case. The IR spectra are provided as supplementary files for possible theoretical calculations.

A curious illustrative fact is the closeness of densities of the reported amides— 1 · 2.5H2O 1.355 g cm-3; 2 1.433—and hydrochlorides— 3 · H2O 1.407; [Ad(NH3)4]Cl4


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1.470, 4— which are all in turn dwarfed by the paradigmatic Ad(COOH)4 tetraacid with an anomalously high density of 1.652. The salts, with their potentially stronger ‘chargeassisted’ H-bonds and the heavier chloride constituent, should have had higher density (even if the loose placement of water in the cavities of 3 · H2O is a slight countering factor). However, the densities of the chlorides prevail only marginally. Both chloride structure features H-bonds of average length, 3.148- 3.159 Å in 3 · H2O, and 3.214 Å (N = 0.084) in 4 (the average RNH3+···Cl- H-bond length according to the CSD statistics is 3.207(4) Å 41). However, the H-bonds in the amide structures are shorter due to the smaller radius of Oδ- compared to Cl- and the generally efficient packing gives rise to the effect of similar densities across all compounds.

Conclusions

The structure of 1,3,5,7-adamantanetetraamide, elusive until now, is reported. Contrarily to the expectations it does not feature a diamond underlying net (I41/a, ρ ~ 1.485 g cm-3), which would form if the dimeric amide synthon had actualized, but a far less symmetric structure (P2, ρ = 1.433 g cm-3 ) with an complex binodal 12,16-


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connected underlying net having a {322.436.58}{338.460.522} point symbol. In contrary, 1,3,5-adamantanetriamide follows the expected self-assembly scenario, featuring a structure with interpenetrated hexagonal nets. Similar contraposition takes place in the chlorides of the respective amines. The structure of 1,3,5,7-adamantanetetraamine tetrahydrochoride is of low C2 symmetry and has a complex trinodal 4,4,16-c underlying net. In contrary, in the structure of 1,3,5,7-adamantanetriamine hydrochloride the (R)NH3+ and Cl- tetrahedral H-bond donors and acceptors assemble in a highly symmetric P63mc structure with a binodal 3,9-c {42.6}3{46.624.86} underlying net, found also in IrSi3. The structure features channels filled with water molecules and could serve as a prototype of an ionic-conductor. The formation of channels could also be viewed as a particular case of void generation by truncation of the tetrahedral building block.

The two pair of examples, but especially the example of amides, where symmetry considerations does not play a significant role, demonstrate the importance of the functional group density parameter, which is connected both with steric and energetic factors. The given examples could be viewed as valuable cases for a possible machine-


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learning project aiming synthon based approach for prediction, with main focus on delimitation where such prediction is possible (i.e. with computation of a figure of merit regarding the probability of actualization). While conceptually inferior to the firstprinciples prediction, a 'return to the origins' of supramolecular synthon-based 'rational design' of crystal structures and its evaluation by machine ‘deep’ learning may again make the synthon based approach viable.

Experimental The synthesis of the compounds 1-4 was concisely reported earlier.30 For the convenience of the reader, extended synthetic description with an introduction is given in the SI.

Preparation of single crystals Ad(CONH2)3 · 2.5H2O, 1 · 2.5H2O: 15 mg of the triamide was dissolved in 3 ml of conc. NH3·H2O in a 5 ml vial under prolonged stirring at ~50 °C (the vial was closed hermetically during the dissolution in order to prevent the loss of ammonia). The contents of the vial were cooled to room temperature and allowed to evaporate slowly through a non-tight plug. As the concentration of ammonia decreased during a few days, slow crystallization


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took place. Long co-grown needle-like crystals were formed with nearly quantitative yield (Fig. S18). Ad(CONH2)3 · H2O, 1 · H2O: 15 mg of Ad(CONH2)3 and 0.5 ml of conc. aqueous ammonia were sealed in a culture tube. The contents of the tube were heated at 80 °C for 3h and occasionally shaken until complete dissolution followed by linear gradient cooling to room temperature during 30h. Large block-like crystals with a size up to 2 mm and a distinct habit suggesting an S4 point group (Fig. S18) were obtained. Ad(CONH2)4, 2: 25 mg of Ad(CONH2)4 and 5 ml of conc. NH3·H2O were placed in a culture tube and sealed with a dedicated heat-resistant cap. (Caution! Some commercial culture tubes might not withstand the pressure). The sealed tube was placed in an oven and heated up to 120 °C until complete dissolution of the amide. The oven was cooled with a rate of 2 K min-1, which resulted in a formation of very small (~10 µm) single crystals. [Ad(NH3)3]Cl3 · H2O, 3 · H2O; [Ad(NH3)4]Cl4, 4: ~5 mg of the respective amine was dissolved in a solution obtained by dilution of 30 µL of conc. HCl in 1 ml of water. The vial, containing the solution, was loosely stoppered by a cotton-wool plug and placed in a


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larger vial, containing concentrated aqueous HCl. The outer vial was closed hermetically, allowing slow diffusion of HCl vapors in the inner vial. In four days block-shaped single crystals were formed and the process was stopped (the crystals were stored in a hermetically stored vial under the mother solution).

AUTHOR INFORMATION

Corresponding Author * E-mail: [email protected]

ACKNOWLEDGMENT I.B. expresses his sincere gratitude to the Alexander von Humboldt Foundation for a three-month return fellowship. We thank the Agilent Company and its representative Mr. Andy Dorn for the possibility to measure the structure of 2 (special thanks go to Dr. Alex Griffin who collected the data as well as to Dr. Fraser White for assistance). We are grateful to Prof. Aleš Růžička for collecting the diffraction data for structural


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characterization of 1 · H2O. We thank Dr. I. Baburin for discussions and his attempt to calculate the energy difference between the polymorphs of Ad(CONH2)4.

SUPPORTING INFORMATION

Description of the organic syntheses; NMR, IR (also as separate files) and MS spectra; complete single crystal XRD data; powder XRD data; discussion on the structural model of the hypothetic 2-dia structure; topological analysis output.

FOOTNOTES_AT_THE_END_OF_THE_MANUSCRIPT 1 · 2.5H2O: C13H24N3O5.50, 310.35 g mol-1, λ = 0.71073 Å, a = 15.4624(10) Å, b = 14.0002(9) Å, c = 14.0559(8) Å, 293(2) K, orthorhombic, Pbca, Z = 8, μ = 0.106 mm-1, data / restraints / parameters = 2673 / 0 / 270, R1[F2>2σ(F2)]= 0.0757, wR2 (all data) = 0.2125.

1 · H2O:

c = 16.5321(7) Å,

C13H21N3O4, 150(2) K,

283.33 g mol-1, tetragonal,

λ = 1.54178 Å,

P41,

Z = 4,

a = b=8.9689(4) Å, μ = 0.878 mm-1,

data / restraints / parameters = 2813 / 1 / 205, R1[F2>2σ(F2)]= 0.0273, wR2 (all data) = 0.0696. 2: C14H20N4O4, 308.34 g mol-1, λ = 1.54184 Å, a = 7.1028(9) Å, b = 7.1979(10) Å,

c = 13.9789(18) Å, β = 90.534(12)°, 293(2) K, monoclinic, P2, Z = 2, μ = 0.890 mm-1,


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data / restraints / parameters = 1781 / 1 / 201, R1[F2>2σ(F2)] = 0.0350, wR2 (all data) = 0.0878. 3 · H2O: C10H24Cl3N3O, 308.7 g mol-1, λ = 0.71073, a = b = 9.91190(10) Å,

c = 8.5653(2) Å,

293(2) K,

hexagonal,

P63mc,

Z = 2,

μ = 0.619 mm-1,

data / restraints / parameters = 820 / 1 / 55, R1[F2>2σ(F2)] = 0.0306, wR2 (all data) = 0.0833. 4: C10H24Cl4N4, 342.13 g mol-1, λ = 0.71073, a = 14.9094(18) Å, b = c = 7.4358(4) Å,

β = 118.741(9)°,

293(2) K,

monoclinic,

C2, Z = 2, μ = 0.756 mm-1,

data / restraints / parameters = 1798 / 1 / 132, R1[F2>2σ(F2)] = 0.0284, wR2 (all data) = 0.0775. CCDC 1908047-1908051 contains the supplementary crystallographic data that could be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/structures.

REFERENCES (1)

Desiraju, G. R. Crystal Engineering: The Design of Organic Solids; Elsevier Science, 1989.

(2)

Desiraju, G. R. Crystal Engineering: A Holistic View. Angew. Chem. Int. Ed. 2007,

46, 8342–8356.


p. 42

Page 43 of 52 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(3)

Ermer, O. Five-Fold Diamond Structure of Adamantane-1,3,5,7-Tetracarboxylic Acid. J. Am. Chem. Soc. 1988, 110, 3747–3754.

(4)

Zaworotko, M. J. Crystal Engineering of Diamondoid Networks. Chem. Soc. Rev. 1994, 23, 283.

(5)

Hoskins, B. F.; Robson, R. Infinite Polymeric Frameworks Consisting of Three Dimensionally Linked Rod-like Segments. J. Am. Chem. Soc. 1989, 111, 5962– 5964.

(6)

Hoskins, B. F.; Robson, R. Design and Construction of a New Class of Scaffoldinglike Materials Comprising Infinite Polymeric Frameworks of 3D-Linked Molecular Rods . A Reappraisal of the Zn (CN)2 and Cd (CN)2 Structures and the Synthesis and Structure of the Diamond-Related. 1990, 1546–1554.

(7)

Kaskel, S. (editor). The Chemistry of Metal-Organic Frameworks; Wiley-VCH, 2016.

(8)

Muller, T.; Bräse, S. Tetrahedral Organic Molecules as Components in Supramolecular Architectures and in Covalent Assemblies, Networks and


p. 43


Page 44 of 52

Polymers. RSC Adv. 2014, 4, 6886.

(9)

Lohse, M. S.; Bein, T. Covalent Organic Frameworks: Structures, Synthesis, and Applications. Adv. Funct. Mater. 2018, 28, 1705553.

(10) Alexandrov, E. V.; Blatov, V. A.; Kochetkov, A. V.; Proserpio, D. M. Underlying Nets in Three-Periodic Coordination Polymers: Topology, Taxonomy and Prediction from a Computer-Aided Analysis of the Cambridge Structural Database. CrystEngComm 2011, 13, 3947.

(11) Blatov, V. A.; Carlucci, L.; Ciani, G.; Proserpio, D. M. Interpenetrating Metal– Organic and Inorganic 3D Networks: A Computer-Aided Systematic Investigation. Part I. Analysis of the Cambridge Structural Database. CrystEngComm 2004, 6, 377–395.

(12) Zheng, T.; Yang, Z.; Gui, D.; Liu, Z.; Wang, X.; Dai, X.; Liu, S.; Zhang, L.; Gao, Y.; Chen, L.; et al. Overcoming the Crystallization and Designability Issues in the Ultrastable Zirconium Phosphonate Framework System. Nat. Commun. 2017, 8,


p. 44

Page 45 of 52 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


15369.

(13) Lehn, J.-M. Toward Complex Matter: Supramolecular Chemistry and SelfOrganization. Proc. Natl. Acad. Sci. 2002, 99, 4763–4768.

(14) Allen, F. H.; Samuel Motherwell, W. D.; Raithby, P. R.; Shields, G. P.; Taylor, R. Systematic Analysis of the Probabilities of Formation of Bimolecular HydrogenBonded Ring Motifs in Organic Crystal Structures. New J. Chem. 1999, 23, 25–34.

(15) Desiraju, G. R. Supramolecular Synthons in Crystal Engineering—A New Organic Synthesis. Angew. Chem. Int. Ed. 1995, 34, 2311–2327.

(16) Steiner, T. The Hydrogen Bond in the Solid State. Angew. Chem. Int. Ed. 2002, 41, 48–76.

(17) Gavezzotti, A. The Lines-of-Force Landscape of Interactions between Molecules in Crystals; Cohesive versus Tolerant and `collateral Damage’ Contact. Acta

Crystallogr. Sect. B Struct. Sci. 2010, 66, 396–406.

(18) O’Keeffe, M.; Peskov, M. A.; Ramsden, S. J.; Yaghi, O. M. The Reticular Chemistry


p. 45


Page 46 of 52

Structure Resource (RCSR) Database of, and Symbols for, Crystal Nets. Acc.

Chem. Res. 2008, 41, 1782–1789.

(19) Tranchemontagne, D. J.; Mendoza-Cortés, J. L.; O’Keeffe, M.; Yaghi, O. M. Secondary Building Units, Nets and Bonding in the Chemistry of Metal-Organic Frameworks. Chem. Soc. Rev. 2009, 38, 1257–1283.

(20) Li, M.; Li, D.; O’Keeffe, M.; Yaghi, O. M. Topological Analysis of Metal–Organic Frameworks with Polytopic Linkers and/or Multiple Building Units and the Minimal Transitivity Principle. Chem. Rev. 2014, 114, 1343–1370.

(21) Maddox, J. Crystals from First Principles. Nature 1988, 335, 201–201.

(22) Dunitz, J. D. Are Crystal Structures Predictable? Chem. Commun. 2003, No. 5, 545–548.

(23) Mellot-Draznieks, C. Computational Exploration of Metal–Organic Frameworks: Examples of Advances in Crystal Structure Predictions and Electronic Structure Tuning. Mol. Simul. 2015, 41, 1422–1437.


p. 46

Page 47 of 52 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(24) Evans, J. D.; Jelfs, K. E.; Day, G. M.; Doonan, C. J. Application of Computational Methods to the Design and Characterisation of Porous Molecular Materials. Chem.

Soc. Rev. 2017, 46, 3286–3301.

(25) Day, G. M.; Görbitz, C. H. Introduction to the Special Issue on Crystal Structure Prediction. Acta Crystallogr. Sect. B Struct. Sci. Cryst. Eng. Mater. 2016, 72, 435– 436.

(26) Ramalho, J. P. P.; Gomes, J. R. B.; Illas, F. Accounting for van Der Waals Interactions between Adsorbates and Surfaces in Density Functional Theory Based Calculations: Selected Examples. RSC Adv. 2013, 3, 13085.

(27) LeCun, Y.; Bengio, Y.; Hinton, G. Deep Learning. Nature 2015, 521, 436–444.

(28) Ryan, K.; Lengyel, J.; Shatruk, M. Crystal Structure Prediction via Deep Learning.

J. Am. Chem. Soc. 2018, 140, 10158–10168.

(29) Zhao, T.; Heering, C.; Boldog, I.; Domasevitch, K. V.; Janiak, C. A View on Systematic Truncation of Tetrahedral Ligands for Coordination Polymers.


p. 47


Page 48 of 52

CrystEngComm 2017, 19, 776–780.

(30) Senchyk, G. A.; Lysenko, A. B.; Boldog, I.; Rusanov, E. B.; Chernega, A. N.; Krautscheid, H.; Domasevitch, K. V. 1,2,4-Triazole Functionalized Adamantanes: A New Library of Polydentate Tectons for Designing Structures of Coordination Polymers. Dalt. Trans. 2012, 41, 8675–8689.

(31) Alexandrov, E. V; Blatov, V. A.; Proserpio, D. M. How 2-Periodic Coordination Networks Are Interweaved: Entanglement Isomerism and Polymorphism.

CrystEngComm 2017, 19, 1993–2006.

(32) Spek, A. L. Structure Validation in Chemical Crystallography. Acta Crystallogr.

Sect. D Biol. Crystallogr. 2009, 65, 148–155.

(33) Bridson, J. N.; Schriver, M. J.; Zhu, S. X-Ray Structure of 1,3-Adamantane Dicarbonamide. J. Chem. Crystallogr. 1995, 25, 11–14.

(34) Blatov, V. A.; O’Keeffe, M.; Proserpio, D. M. Vertex-, Face-, Point-, Schlafli-, and Delaney-Symbols in Nets, Polyhedra and Tilings: Recommended Terminology.


p. 48

Page 49 of 52 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


CrystEngComm 2010, 12, 44–48.

(35) Steed, K. M.; Steed, J. W. Packing Problems: High Z ′ Crystal Structures and Their Relationship to Cocrystals, Inclusion Compounds, and Polymorphism. Chem. Rev. 2015, 115, 2895–2933.

(36) Grell, J.; Bernstein, J.; Tinhofer, G. Investigation of Hydrogen Bond Patterns∶ A Review of Mathematical Tools For the Graph Set Approach. Crystallogr. Rev. 2002,

8, 1–56.

(37) Bernstein, J.; Davis, R. E.; Shimoni, L.; Chang, N.-L. Patterns in Hydrogen Bonding: Functionality and Graph Set Analysis in Crystals. Angew. Chem. Int. Ed. 1995, 34, 1555–1573.

(38) O’Keeffe, M.; Eddaoudi, M.; Li, H.; Reineke, T.; Yaghi, O. M. Frameworks for Extended Solids: Geometrical Design Principles. J. Solid State Chem. 2000, 152, 3–20.

(39) White, J. G.; Hockings, E. F. Crystal Structure of Iridium Trisilicide, IrSi3. Inorg.


p. 49


Page 50 of 52

Chem. 1971, 10, 1934–1935.

(40) Lemmerer, A.; Bernstein, J.; Spackman, M. A. Supramolecular Polymorphism of the

1 :

1

Molecular

Salt

(Adamantane-1-Carboxylate-3,5,7-Tricarboxylic

Acid)·(Hexamethylenetetraminium). A “Failed” Crystal Engineering Attempt. Chem.

Commun. 2012, 48, 1883–1885.

(41) Steiner, T. Hydrogen-Bond Distances to Halide Ions in Organic and Organometallic Crystal Structures : Up-to-Date Database Study. Acta Cryst. Sect. B 1998, 54, 456– 463.


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For Table of Contents Use Only

When does a supramolecular synthon fail? Comparison of bridgeheadfunctionalized adamantanes: the tri- and tetra- amides and amine hydrochlorides

Ishtvan Boldog, Guido Reiss, Kostiantyn V. Domasevitch, Tomas Base, and Stefan Bräse

TOC synopsis:

1,3,5-trisubstituted adamantane carboxamide and amine hydrochloride crystallize to yield structures based on expected patterns, while the 1,3,5,7-trisubstituted analogues


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Page 52 of 52

are not. The distinction is thought provoking, as tetrahedral molecules are paradigmatic for crystal structure ‘design’ and feature high historic importance.


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When Does a Supramolecular Synthon Fail? Comparison of

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