Molecular Solids Formed by the Self-Organisation of Dialcohols into Hydrogen-Bonded Ladders

Stereoselective preparation of mono- and bis-derivatives of pentacyclo[6.3.0.02,6.03,10.05,9] undecane (D 3-trishomocubane)

The rearrangement of easily accessible Cookson’s diketone with chlorosulfonic acid in chloroform followed by the acidic hydrolysis gave 6-chloro-7-hydroxy-dichloropentacyclo[6.3.0.02,6.03,10.05,9]undecane-4-one, whose syn-stereochemistry was assigned through the X-ray crystal structure analysis. This key structure was used for the stereoselective synthesis of the D 3-trishomocubane derivatives as well as for the preparation of potential drugs bearing hydroxy- and amino-functional groups. A new multigram preparative synthesis of D 3-trishomocubane was developed.

Synthesis and characterisation of selected group 14 derivatives of the 2,5-(CF3)2C6H3 (Ar) ligand

Selected group 14 tetrahalides EX(4) (E = Si, Ge or Sn; X = Cl or Br) have been reacted in various molar ratios with ArLi, where Ar = 2,5-(CF(3))(2)C(6)H(3). The compounds Ar(2)SiCl(2)1, Ar(3)SiF 3, Ar(2)Si(OH)(2)4, Ar(2)GeCl(2)7, Ar(2)Ge(Br)Ge(Br)Ar(2)8, Ar(3)SnCl 10, Ar(4)Sn 11 and Ar(3)SnBr 12 have been isolated, and characterised by single-crystal X-ray diffraction, elemental analysis and (19)F solution-state NMR spectroscopy.

(1R*,2R*,4S*,5R*,6R*,8S*)-4,8-Dimethyl-2,6-diphenyl-bicyclo-[3.3.1]nonane-2,6-diol

The racemic title compound, C₂₃H₂₈O₂, crystallizes in the space group C2/c as a layered structure in which a centrosymmetric three hydrogen bond sequence links four molecules. Both hydroxy groups are involved in this arrangement, but they differ in that one participates in two hydrogen bonds while the other takes part in only one. Between layers, the aromatic rings take part in edge-face interactions [shortest C—H⋯C distances 3.04, 3.10 and 3.12 Å and angle between normal to planes 86.7(2)°], forming a centrosymmetric dimer. The lattice is further stabilized by C—H⋯π interactions involving both methyl (shortest C⋯C 3.82 and 3.97 Å) and methylene (shortest C⋯C 3.60 Å) groups.

Helical tubuland diols: a synthetic and crystal engineering quest

Despite many advances in recent years, crystal engineering remains a risky venture. A successful outcome requires manipulation of the noncovalent bonding and properties such as size, shape, repulsion, attraction, polarity, and chirality. In this Account, we describe the interplay of crystal engineering and synthetic organic chemistry required to develop the family of helical tubuland diol hosts, the members of which exhibit a wide range of tube dimensions and inclusion properties. Certain alicyclic dialcohols crystallize with a hydrogen-bonded network structure, termed the helical tubuland lattice, in space group P3(1)21 (or its enantiomorph P3(2)21). Double helices of diol molecules surround parallel tubes that contain guest molecules, which are included on the basis of size and shape rather than functional group. The crystal structure of (diol)(3).(chloroacetic acid)(1.2) is illustrative. These chiral helical tubulate lattice inclusion compounds are formed when the racemic host diol is allowed to crystallize from solution. Complete enantiomer separation occurs during this process, producing a 1:1 mixture of pure (+)- and pure (-)-crystals (a conglomerate). The challenge of creating this family of compounds required the development of much synthetic chemistry, in particular new pathways to alicyclic ring systems with specific substitution patterns. It was also necessary to understand and control the supramolecular properties of the diol molecules. What makes the original compound tick, and why did it behave in this remarkable manner, when most of its structural neighbors crystallize totally differently? The synthesis of new helical tubuland diols requires not just preparation of a new molecular structure but also a transplant of the original unchanged hydrogen-bonding supramolecular synthon. Synthesis of the specific crystal space group is necessary. This was achieved by defining structural characteristics, termed molecular determinants, which are essential for the helical tubuland structure to occur. If these requirements were met, then the target molecule had a high probability of success. This investigation has close conceptual parallels with the search for pharmacophore properties of bioactive molecules. In both situations, parts of a molecule with little or no chemical reactivity may actually play vital supramolecular roles. The review illustrates how crystal engineering is based on specific supramolecular properties that can be uncovered and then exploited by synthetic chemists.

Syntheses and Properties of Enantiomerically Pure Higher (n ≥ 7) [n−2]Triangulanedimethanols and σ-[n]Helicenes

(P)-(+)-Hexaspiro[2.0.0.0. 0.0.2.1.1.1.1.1]pentadecane [(P)-17] as well as (M)-(-)- and (P)-(+)-octaspiro[2.0.0.0.0.0.0.0.2.1.1.1.1.1.1.1]nonadecanes [(M)- and (P)-25]-enantiomerically pure unbranched [7]- and [9]triangulanes-have been prepared starting from racemic THP-protected (methylenecyclopropyl)methanol 6. The relative configurations of all important intermediates as well as the absolute configurations of the key intermediates were established by X-ray crystal structure analyses. This new convergent approach to enantiomerically pure linear [n]triangulanes for n=7, 9 was also tested in two variants towards [15]triangulane. Some of the most prominent and unexpected features of the newly prepared compounds are the remarkable modes of self-assembly of the diols (P)-14, (E)-(3S,3'S,4S,4'S,5R,5'R)-21, (P)-(+)-22, and (E)-31 in the solid state through frameworks of intermolecular hydrogen bonds leading to, depending on the respective structure, nanotube- [(P)-14, (P)-(+)-22, and (E)-31], honeycomb-like structures [(E)-(3S,3'S,4S,4'S,5R,5'R)-21] or a supramolecular double helix [(P)-(+)- and (M)-(-)-22]. Liquid crystalline properties of the esters and ethers of the diols (P)-14, (P)-, and (M)-22 have also been tested. Although all of these [n]triangulanes have no chromophore which would lead to significant absorptions above 200 nm, they exhibit surprisingly high specific rotations even at 589 nm with [alpha](20)(D)=+672.9 (c=0.814 in CHCl(3)) for (P)-(+)-17, +909.9 (c=0.96 in CHCl(3)) for (P)-(+)-25, -890.5 (c=1.01 in CHCl(3)) for (M)-(-)-25, and -1302.5 (c=0.36 in CHCl(3)) for (M)-(-)-39, and the specific rotations increase drastically on going to shorter wavelengths. This outstanding rotatory power is in line with their rather rigid helical arrangement of sigma bonds, and accordingly these helically shaped unbranched [n]triangulanes may be termed "sigma-[n]helicenes", as they represent the sigma-bond analogues of the aromatic pi-[n]helicenes. Density functional theory (DFT) computations at the B3 LYP/6-31+G(d,p) level of theory for the geometry optimization and time-dependent DFT for determining optical rotations with a triplet-zeta basis set (B3 LYP/TZVP) reproduce the optical rotatory dispersions (ORD) very well for the lower members (n=4, 5) of the sigma-[n]helicenes. For the higher ones (n=7, 9, 15) the computed specific rotations turn out increasingly larger than the experimental values. The remarkable increase of the specific rotation with an increasing number of three-membered rings is proportional neither to the molecular weight nor to the number of cyclopropane rings in these sigma-[n]helicenes.

Crystal engineering of analogous and homologous organic compounds: hydrogen bonding patterns in trimethoprim hydrogen phthalate and trimethoprim hydrogen adipate

BACKGROUND

Trimethoprim [2,4-diamino-5-(3',4',5'-trimethoxybenzyl)pyrimidine] is an antifolate drug. It selectively inhibits the bacterial dihydrofolate reductase (DHFR) enzyme.

RESULTS

In the crystal structures of trimethoprim (TMP)-hydrogen phthalate (1) and trimethoprim-hydrogen adipate (2), one of the N atoms of the pyrimidine ring is protonated and it interacts with the deprotonated carboxylate oxygens through a pair of nearly parallel N-H...O hydrogen bonds to form a fork-like interaction. In the compound 1, the pyrimidine moieties of the TMP cations are centrosymmetrically paired through a pair of N-H...N hydrogen bonds involving 4-amino group and the N (N3) atom of the pyrimidine rings to form a 8-membered hydrogen bonded ring [R2(2)(8)]. The 4-amino group of one TMP moiety and 2-amino group of another TMP moiety (both moieties are members of a base pair) are bridged by the carbonyl oxygen of the phthalate moiety through N-H...O hydrogen bonds forming 8-membered hydrogen-bonded ring [R2(2)(8)]. The characteristic hydrogen-bonded rings observed in the structure aggregate into a supramolecular ladder consisting of a pair of chains, each of which is built up of alternate TMP and hydrogen phthalate ions. In the compound 2, two TMP cations and two hydrogen adipate anions are arranged about an inversion center so that the complementary DDAA (D = donor, A = acceptor) arrays of quadruple hydrogen-bonding patterns are formed. The head-to-tail arrangement of the hydrogen adipate ions leads to a hydrogen-bonded supramolecular chain. From crystal engineering point of view, it is interesting to note that the compound 1 has a hydrogen-bonded network remarkably identical with its aliphatic analogue, trimethoprim hydrogen maleate. Similarly the compound 2, resembles its homolog trimethoprim hydrogen glutarate.

CONCLUSION

In the crystal structure of trimethoprim hydrogen phthalate, the hydrogen-bonded network is remarkably identical with its aliphatic analogue, trimethoprim hydrogen maleate. Similarly in the crystal structure of trimethoprim hydrogen adipate the hydrogen bonded network resembles its homolog trimethoprim hydrogen glutarate.

The World of Non-Covalent Interactions: 2006

The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.

Guest-Induced Supramolecular Isomerism in Inclusion Complexes of T-Shaped Host 4,4-Bis(4′-hydroxyphenyl)cyclohexanone

The T-shaped host molecule 4,4-bis(4'-hydroxyphenyl)cyclohexanone (1) has an equatorial phenol group and a cyclohexanone group along the arms and an axial phenol ring as the stem. The equatorial phenyl ring adopts a "shut" or "open" conformation, like a windowpane, depending on the size of the guest (phenol or o/m-cresol), for the rectangular voids of the hydrogen-bonded ladder host framework. The adaptable cavity of host 1 expands to 11x15-18 A through the inclusion of water with the larger cresol and halophenol guests (o-cresol, m-cresol, o-chlorophenol, and m-bromophenol) compared with a size of 10x13 A for phenol and aniline inclusion. The ladder host framework of 1 is chiral (P2(1)) with phenol, whereas the inclusion of isosteric o- and m-fluorophenol results in a novel polar brick-wall assembly (7x11 A voids) as a result of auxiliary C-H...F interactions. The conformational flexibility of strong O-H...O hydrogen-bonding groups (host 1, phenol guest), the role of guest size (phenol versus cresol), and weak but specific intermolecular interactions (herringbone T-motif, C-H...F interactions) drive the crystallization of T-host 1 towards 1D ladder and 2D brick-wall structures, that is, supramolecular isomerism. Host 1 exhibits selectivity for the inclusion of aniline in preference to phenol as confirmed by X-ray diffraction, 1H NMR spectroscopy, and thermogravimetry-infrared (TG-IR) analysis. The T(onset) value (140 degrees C) of aniline in the TGA is higher than those of phenol and the higher-boiling cresol guests (T(onset)=90-110 degrees C) because the former structure has more O-H...N/N-H...O hydrogen bonds than the clathrate of 1 with phenol which has O-H...O hydrogen bonds. Guest-binding selectivity for same-sized phenol/aniline molecules as a result of differences in hydrogen-bonding motifs is a notable property of host 1. Host-guest clathrates of 1 provide an example of spontaneous chirality evolution during crystallization and a two-in-one host-guest crystal (phenol and aniline), and show how weak C-H...F interactions (o- and m-fluorophenol) can change the molecular arrangement in strongly hydrogen-bonded crystal structures.