Supramolecular Assemblies of (±-2,2''''-Dihydroxy-1,1''''-binaphthyl with 2,2''''-Bipyridine and Naphthodiazine

Introduction Optically active 1,1'-bi-2-naphthol (BINOL) and its derivatives have been widely used as chiral ligands of catalysts for asymmetric reactions and effective host compounds for the isolation or optical resolution of a wide range of organic guest molecules through the for-mation of crystalline inclusion complexes.1,2 The wide-ranging and important applications of these com-pounds in organic synthesis have stimulated great inter-est in developing efficient methods for their prepara-…     

Achieving Strong Positive Cooperativity through Activating Weak Non‐Covalent Interactions

Positive cooperativity achieved through activating weak non‐covalent interactions is common in biological assemblies but is rarely observed in synthetic complexes. Two new molecular tubes have been synthesized and the syn isomer binds DABCO‐based organic cations with high orientational selectivity. Surprisingly, the ternary complex with two hosts and one guest shows a high cooperativity factor (α=580), which is the highest reported for synthetic systems without involving ion‐pairing interactions. The X‐ray single‐crystal structure revealed that the strong positive cooperativity likely originates from eight C?H???O hydrogen bonds between the two head‐to‐head‐arranged syn tube molecules. These relatively weak hydrogen bonds were not observed in the free hosts and only emerged in the complex. Furthermore, this complex was used as a basic motif to construct a robust [2+2] cyclic assembly, thus demonstrating its potential in molecular self‐assembly.     

Chiral Encapsulation by Directional Interactions

The complexation of chiral guests in the cavity of dimeric self‐assembled chiral capsule 1 ₂ was studied by using NMR spectroscopy and X‐ray crystallography. Capsule 1 ₂ has walls composed of amino acid backbones forming numerous directional binding sites that are arranged in a chiral manner. The polar character of the interior dictates the encapsulation preferences towards hydrophilic guests and the ability of the capsule to extract guests from water into an organic phase. Chiral discrimination towards hydroxy acids was evaluated by using association constants and competition experiments, and moderate de values were observed (up to 59 %). Complexes with one or two guest molecules in the cavity were formed. For 1:1 complexes, solvent molecules are coencapsulated; this influences guest dynamics and makes the chiral recognition solvent dependent. Reversal of the preferences can be induced by coencapsulation of a nonchiral solvent in the chiral internal environment. For complexes with two guests, filling of the capsule’s internal space can be very effective and packing coefficients of up to 70 % can be reached. The X‐ray crystal structure of complex 1 ₂?((S) ‐6 )₂ with well‐resolved guest molecules reveals a recognition motif that is based on an extensive system of hydrogen bonds. The optimal arrangement of interactions with the alternating positively and negatively charged groups of the capsule’s walls is fulfilled by the guest carboxylic groups acting simultaneously as hydrogen‐bond donors and acceptors. An additional guest molecule interacting externally with the capsule reveals a possible entrance mechanism involving a polar gate. In solution, the structural features and dynamic behavior of the D₄‐symmetric homochiral capsule were analyzed by variable‐temperature NMR spectroscopy and the results were compared with those for the S₈‐symmetric heterochiral capsule.     

Ritter reactions. VI. Crystal structure of a new multicyclic hydroxy amide clathrate

The compound 9-benzamido-6,7,8,9,10,11-hexahydro-5,9:7,11-dimethano-5H-benzocyclononen-7-ol,3, has been prepared, and found to crystallise as inclusion complexes ( ₂ ·G where the guest G is ethyl acetate or carbon tetrachloride. The host molecule contains a benzo group as part of a rigid polycyclic framework, on which there are hydroxy and benzamido substituents. The crystal structure of the complex with CCl₄ contains the host molecules hydrogen-bonded in layers, with the CCl₄ molecules trapped between the layers. Two types of host-host hydrogen bonds, OH to amide carbonyl O, and amide NH to hydroxyl O, maintain the host layers. The benzo groups protrude normal to these host layers, and six such groups provide the closest surroundings of the CCl₄, which is constrained to two disordered orientations at the one location. This is a layer clathrate structure. Supplementary Data relating to this article are deposited with the British Library as supplementary publication No. SUP 82110 (13 pages).     

Chiral crystalline hosts derived from lactic acid.* X-ray crystal structures of optically resolved and racemic host compound 1,1-diphenyl-1,2-propanediol and a 2:1 complex between optically resolved host and 3-picoline

Abstract

The X-ray crystal structures of racemic (1) and S-1,1-diphenyl-1,2-propanediol (2), and of a 2:1 inclusion complex (3) of 2 with 3-picoline are reported. Three different binding schemes characterize the packing of these structures. Only one of the two hydroxy groups (that which is not related to the asymmetric carbon) is involved in O-H…O hydrogen bonds responsible for the formation of dimers and chains in 1 and 2, leaving the other OH group for stabilization of dimers through OH…phenyl interactions in 1 or free of interactions in 2. In the crystal structure of the chiral complex 3, the hydroxy groups link the two independent host molecules, A and B, the 3-picoline guest to the B host molecule, and a remaining one forms H-bonded chains along the c axis.     

Selective product amplification of thymine photodimer by recognition-directed supramolecular assistance

Two symmetric ditopic supramolecular templates (1 and 2) each presenting two hydrogen bonding recognition subunits were synthesized. Each such subunit comprises the same donor and acceptor pattern, capable of binding a substrate molecule with complementary hydrogen bonding groups to form a supramolecular complex. Substrate molecules, such as thymine or uracil derivatives, yield 2 : 1 complexes with the acceptors involving two hydrogen bonds to each subunit with ideal orientation for subsequent [2 + 2] dimerization upon photoirradiation. Selective syn photoproduct formation and concomitant suppression of the trans isomer are favored by orientation of the two guest nucleobases within the template cleft. Complementary donor and acceptor hydrogen bonding induced positioning of the two substrates and steric hindrance within the template clefts are responsible for the selective product formation.     

环双(对-蒽基-对草快)的分子识别与谱学性质

环双(对-蒽基-对草快)是一种新型的缺电子大环仿生主体, 分子识别是其最重要的应用之一. 考察主体对一系列客体分子如水、氨、醇及杂环等的识别能力, 用密度泛函理论(DFT)中的B3LYP/3-21G基组对主客体复合物的结构进行优化. 在B3LYP/6-31G(d)水平上进行单点能计算, 校正后得到复合物的结合能. 用B3LYP/3-21G方法计算13C和3He化学位移. 结果表明, 主体对客体分子的识别主要靠客体上的杂原子与主体上的氢原子之间的氢键进行. 复合物的稳定化能受氢键的数目和距离影响. 氢键的形成导致部分复合物LUMO与HOMO能隙增大, 同时导致与氢键相连的C—H键上C原子的化学位移向低场移动. 复合物的芳香性与其结合能的大小及结合方式有关. 主体的芳香性因其与客体之间的弱相互作用而提高, 但太强的相互作用及客体在主体空腔内都将影响主体的环电流, 从而削弱其芳香性.     

Crystal structures of inclusion compounds of 4-aminobenzenesulfamidine (sulfaguanidine) with two dicyclohexano-18-crown-6 isomers

The crystal structures of inclusion compounds of 4-aminobenzenesulfamidine (sulfaguanidine) (L) with two dicyclohexano-18-crown-6 (DCH-6) isomers A(cis-syn-cis) and B(cis-anti-cis) have been determined by X-ray methods. The complexes exhibit 1:2 host-guest ratios. In fact the complex of isomer A is formulated as [DCH-6^A·[L]H₂O]L (complexI), while that of isomerB is DCH-6 ^B L₂ (complex I1).In the crystals, host and guests are connected by O-H...0 and N-H...O bonds.     

Host–Guest Complexation Using Pillar[5]arene Crystals: Crystal-Structure Dependent Uptake,Release, and Molecular Dynamics of an Alkane Guest

Host–guest complexation has been mainly investigated in solution, and it is unclear how guest molecules access the assembled structures of host and dynamics of guest molecules in the crystal state. In this study, we studied the uptake, release, and molecular dynamics of n-hexane vapor in the crystal state of pillar[5]arenes bearing different substituents. Pillar[5]arene bearing 10 ethyl groups yielded a crystal structure of herringbone-type 1:1 complexes with n-hexane, whereas pillar[5]arene with 10 allyl groups formed 1:1 complexes featuring a one-dimensional (1D) channel structure. For pillar[5]arene bearing 10 benzyl groups, one molecule of n-hexane was located in the cavity of pillar[5]arene, and another n-hexane molecule was located outside of the cavity between two pillar[5]arenes. The substituent-dependent differences in molecular arrangement influenced the uptake, release, and molecular dynamics of the n-hexane guest. The substituent effects were not observed in host–guest chemistry in solution, and these features are unique for the crystal state host–guest chemistry of pillar[5]arenes.     

A novel polymeric (4-chloro-2-methylphenoxy) acetate complex of cadmium(II)

The infinite, two-dimensional polymer bis[(4-chloro-2-methylphenoxy)acetato] cadmium dihydrate was synthesized and characterized by elemental analysis and infrared spectroscopy. The crystal and molecular structure has been determined. The cadmium atom is six coordinated by four oxygen atoms from bridging carboxyl groups and two oxygen atoms from water molecules. The polymer net is stabilized by two O–H···O hydrogen bonds. Bond distances and angles within MCPA molecules are comparable to those found for the free acid and its complexes. The shortest cadmium–cadmium distance is 5.453(1) Å.     

2‐{[(3‐Fluorophenyl)amino]methylidene}‐3‐oxobutanenitrile and 5‐{[(3‐fluorophenyl)amino]methylidene}‐2,2‐dimethyl‐1,3‐dioxane‐4,6‐dione: X‐ray and DFT studies

In the crystal structures of the title compounds, C₁₁H₉FN₂O, (I), and C₁₃H₁₂FNO₄, (II), the molecules are joined pairwise via different hydrogen bonds and the constituent pairs are crosslinked by weak C—H...O hydrogen bonds. The basic structural motif in (I), which is partially disordered, comprises pairs of molecules arranged in an antiparallel fashion which enables C—H...N[triple‐bond]C interactions. The pairs of molecules are crosslinked by two weak C—H...O hydrogen bonds. The constituent pair in (II) is formed by intramolecular bifurcated C—H...O/O′ and combined inter‐ and intramolecular N—H...O hydrogen bonds. In both structures, F atoms form weak C—F...H—C interactions with the H atoms of the two neighbouring methyl groups, the H...F separations being 2.59/2.80 and 2.63/2.71 Å in (I) and (II), respectively. The bond orders in the molecules, estimated using the natural bond orbitals (NBO) formalism, correlate with the changes in bond lengths. Deviations from the ideal molecular geometry are explained by the concept of non‐equivalent hybrid orbitals. The existence of possible conformers of (I) and (II) is analysed by molecular calculations at the B3LYP/6–31+G** level of theory.     

Hydrogen bonding between aromatic H and F groups leading to a stripe structure with R‐ and S‐columns: the crystal structure of (2,7‐dimethoxynaphthalen‐1‐yl)(3‐fluorophenyl)methanone and comparison with its 1‐aroylnaphthalene analogues

In the molecule of (2,7‐dimethoxynaphthalen‐1‐yl)(3‐fluorophenyl)methanone, C₁₉H₁₅FO₃, (I), the dihedral angle between the plane of the naphthalene ring system and that of the benzene ring is 85.90 (5)°. The molecules exhibit axial chirality, with either an R‐ or an S‐stereogenic axis. In the crystal structure, each enantiomer is stacked into a columnar structure and the columns are arranged alternately to form a stripe structure. A pair of (methoxy)C—H...F hydrogen bonds and π–π interactions between the benzene rings of the aroyl groups link an R‐ and an S‐isomer to form a dimeric pair. These dimeric pairs are piled up in a columnar fashion through (benzene)C—H...O=C and (benzene)C—H...OCH₃ hydrogen bonds. The analogous 1‐benzoylated compound, namely (2,7‐dimethoxynaphthalen‐1‐yl)(phenyl)methanone [Kato et al. (2010). Acta Cryst. E 66 , o2659], (II), affords three independent molecules having slightly different dihedral angles between the benzene and naphthalene rings. The three independent molecules form separate columns and the three types of column are connected to each other via two C—H...OCH₃ hydrogen bonds and one C—H...O=C hydrogen bond. Two of the three columns are formed by the same enantiomeric isomer, whereas the remaining column consists of the counterpart isomer. In the case of the fluorinated 1‐benzoylated naphthalene analogue, namely (2,7‐dimethoxynaphthalen‐1‐yl)(4‐fluorophenyl)methanone [Watanabe et al. (2011). Acta Cryst. E 67 , o1466], (III), the molecular packing is similar to that of (I), i.e. it consists of stripes of R‐ and S‐enantiomeric columns. A pair of C—H...F hydrogen bonds between R‐ and S‐isomers, and C—H...O=C hydrogen bonds between R(or S)‐isomers, are also observed. Consequently, the stripe structure is apparently induced by the formation of R...S dimeric pairs stacked in a columnar fashion. The pair of C—H...F hydrogen bonds effectively stabilizes the dimeric pair of R‐ and S‐enantiomers. In addition, the co‐existence of C—H...F and C—H...O=C hydrogen bonds makes possible the formation of a structure with just one independent molecule.     

Dansyl-Modified γ-Cyclodextrin as a fluorescent sensor for molecular recognition

The crystal structure of thiamine iodide sesquihydrate has been determined by X-ray diffraction methods as a host-guest model for coenzyme-substrate interactions. The asymmetric unit contains two chemical units. Both the thiamine molecules A and B, which are crystallographically independent, assume the usualF conformation and have a disordered hydroxyethyl side chain. An iodide anion (or a water molecule) bridges the pyrimidine and thiazolium rings of molecule A (or B) by forming a hydrogen bond with the amino group and an electrostatic contact with the thiazolium ring to stabilize the molecular conformation. In the crystal the thiamine molecules self-associate to form a pipe-like polymeric structure, in which four thiamine hosts surround an iodide guest and hold it through C(2)-H...I hydrogen bonds and thiazolium...I electrostatic interactions. Crystal data: C₁₂H₁₇N₄OS⁺·I^– · 1.5 H₂O, monoclinic,P2₁/c, a=12.585(2), b=25.303(5), c=12.030(2) Å, =115.15(1)°,V=3468(1) ų,Z=8,D _c=1.606 g cm^–3,R=0.045 for 3328 observed reflections. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP. 82156 (13 pages).     

A novel 1:2 cucurbit[8]uril inclusion complex with N-phenylpiperazine hydrochloride

A new 1:2 inclusion complex of cucurbit[8]uril (CB[8]) and protonated N-phenylpiperazine was synthesized and characterized by ¹H NMR and X-ray crystallography. The crystal structure showed that the phenyl rings of the two equivalents of guest encapsulated in the cavity of CB[8] are parallel to one another with a mean plane separation of 3.899 Å. In contrast, the piperazinyl phenyl ammonium moieties slightly protrude from the ureidyl carbonyl lined portals in order to accommodate the ion–dipole interaction between host and guest which provides a substantial driving force for the assembly. The oxygen atoms of the carbonyl groups form hydrogen bonds with the hydrogen atoms in both bridging methylene groups of CB[8] and water molecules. There are also hydrogen bonds formed among CB[8], water, and the protonated piperazinyl rings. These hydrogen bonds are formed between the ureidyl C=O groups and hydrogens in methylenes of piperazinyl rings; through hydrogen bonding N⁺–H···O(H)–H···O=C. The protonated piperazinyl rings connect the carbonyl groups with the bridging water molecules.     

Laser Spectroscopic Study of Cold Gas‐Phase Host‐Guest Complexes of Crown Ethers

The structure, molecular recognition, and inclusion effect on the photophysics of guest species are investigated for neutral and ionic cold host‐guest complexes of crown ethers (CEs) in the gas phase. Here, the cold neutral host‐guest complexes are produced by a supersonic expansion technique and the cold ionic complexes are generated by the combination of electrospray ionization (ESI) and a cryogenically cooled ion trap. The host species are 3n‐crown‐n (3nCn; n = 4, 5, 6, 8) and (di)benzo‐3n‐crown‐n ((D)B3nCn; n = 4, 5, 6, 8). For neutral guests, we have chosen water and aromatic molecules, such as phenol and benzenediols, and as ionic species we have chosen alkali‐metal ions (M⁺). The electronic spectra and isomer‐specific vibrational spectra for the complexes are observed with various laser spectroscopic methods: laser‐induced fluorescence (LIF); ultraviolet‐ultraviolet hole‐burning (UV‐UV HB); and IR‐UV double resonance (IR‐UV DR) spectroscopy. The obtained spectra are analyzed with the aid of quantum chemical calculations. We will discuss how the host and guest species change their flexible structures for forming best‐fit stable complexes (induced fitting) and what kinds of interactions are operating for the stabilization of the complexes. For the alkali metal ion?CE complexes, we investigate the solvation effect by attaching water molecules. In addition to the ground‐state stabilization problem, we will show that the complexation leads to a drastic effect on the excited‐state electronic structure and dynamics of the guest species, which we call a “cage‐like effect”.     

Hydrogen bonding between carboxylic acids and amide-based macrocycles in their host–guest complexes

For 12- and 13-membered macrocycles in which two amide linkages are integrated in the macrocyclic ring systems, the formation of 1:1 host–guest complexes with acetic and benzoic acids has been confirmed by NMR titrations. The complex formation occurs with the formation constants of 8–27 M^? 1, under competition with the dimerisation of acid molecules. Benzoic acid tends to form more stable complexes than acetic acid. The binding force is due to a pair of hydrogen bonds, O_carboxyl–H…O = C_amide and C = O_carboxyl…H–N_amide, between the carboxyl group of a guest molecule and the amide group of a host molecule. The former bond is stronger than the latter, and defines the stability of the complexes. The formation of the pair of hydrogen bonds is accompanied by the conformational conversion of the amide group from the trans-form to the cis-form. The influence of such a conversion on the internal molecular motion is observed as a slight broadening of signal width.

For 12- and 13-membered macrocycles in which two amide linkages are integrated in the macrocyclic ring systems, the formation of 1:1 host–guest complexes with acetic and benzoic acids has been confirmed by NMR titrations. The binding force for the complex formation is due to a pair of hydrogen bonds, O_carboxyl–H…O = C_amide and C = O_carboxyl…H–N_amide. The former bond is stronger than the latter and dominates the hydrogen-bond formation. The formation of the pair of hydrogen bonds is accompanied by the conformational conversion of the amide group from the stable trans-form to the less stable cis-form.     

A New Functional Cyclophane Host. Synthesis, Complex Formation and Crystal Structures of Three Inclusion Compounds

A new macrocyclic host compound 2 having an octamethylsubstituted cyclophane structure with two intra-annular carboxylic acid functions has beensynthesized. The properties of crystalline inclusion formation are studied and X-ray crystalstructures of three inclusion complexes including acetic acid, propionic acid and acetone asthe guest molecules are reported. Inter-host channel formation with complexed guest moleculesaccommodated into the channels are typical features of the acetic acid and acetone 1 : 4 (host : guest) stoichiometric complexes being also hydrated species, while the propionicacid 1 : 2 complex is of the close packing type containing no additional water molecules.Systems of hydrogen bonds involving the host and guest functional groups are common toall structures. In the case of the acetic acid inclusion compound, a complex supramolecularhydrogen-bonded array comprising a bordering tricyclic assembly of eight molecular species exists.     

Study of H-bonded assemblies of the solvates of anthracene derivatives: guest effect on the crystal symmetry and spectroscopic properties

Two solvates of title compound 1-acetyl-3-naphthyl-5-(9-anthryl)-2-pyrazoline solvate(ANNP) (1a) with chloroform (1b) and acetic acid (1c) and a single crystal of another title compound 1-acetyl-3-(4-chloro)phenyl-5-(9-anthryl)-2-pyrazoline (ACAP) (2a) and its adduct with phenol (2b) were afforded via solution growth technique. The structure of these solids were confirmed and verified by multiple techniques such as single crystal X-ray diffraction (SCXRD) analysis, PXRD, DSC/TGA and Infrared spectroscopy. Structural analysis indicates that guest inclusion results not only in stronger hydrogen bonds, but also in a larger number of favourable C–H?π interactions between ANNP/ACAP molecules. The solvates show symmetry reduction guest effect comparing with the guest free molecules of ANNP and ACAP. Moreover, characteristic changes have been observed in the Infrared bands of the solvates owing to the formation of hydrogen bonds between host–guest.     

Effect of Guest–Host Hydrogen Bonding on the Structures and Properties of Clathrate Hydrates

To provide improved understanding of guest–host interactions in clathrate hydrates, we present some correlations between guest chemical structures and observations on the corresponding hydrate properties. From these correlations it is clear that directional interactions such as hydrogen bonding between guest and host are likely, although these have been ignored to greater or lesser degrees because there has been no direct structural evidence for such interactions. For the first time, single‐crystal X‐ray crystallography has been used to detect guest–host hydrogen bonding in structure II (sII) and structure H (sH) clathrate hydrates. The clathrates studied are the tert‐butylamine (tBA) sII clathrate with H₂S/Xe help gases and the pinacolone + H₂S binary sH clathrate. X‐ray structural analysis shows that the tBA nitrogen atom lies at a distance of 2.64 Å from the closest clathrate hydrate water oxygen atom, whereas the pinacolone oxygen atom is determined to lie at a distance of 2.96 Å from the closest water oxygen atom. These distances are compatible with guest–water hydrogen bonding. Results of molecular dynamics simulations on these systems are consistent with the X‐ray crystallographic observations. The tBA guest shows long‐lived guest–host hydrogen bonding with the nitrogen atom tethered to a water HO group that rotates towards the cage center to face the guest nitrogen atom. Pinacolone forms thermally activated guest–host hydrogen bonds with the lattice water molecules; these have been studied for temperatures in the range of 100–250 K. Guest–host hydrogen bonding leads to the formation of Bjerrum L‐defects in the clathrate water lattice between two adjacent water molecules, and these are implicated in the stabilities of the hydrate lattices, the water dynamics, and the dielectric properties. The reported stable hydrogen‐bonded guest–host structures also tend to blur the longstanding distinction between true clathrates and semiclathrates.     

Three closely related thienyl‐substituted 1,4‐epoxynaphtho[1,2‐b]azepines: hydrogen‐bonded assembly in one,two and three dimensions

(2R,4S)‐2‐(3‐Methylthiophen‐2‐yl)‐2,3,4,5‐tetrahydro‐1,4‐epoxynaphtho[1,2‐b]azepine, C₁₉H₁₇NOS, (I), crystallizes with a single enantiomer in each crystal, whereas its geometrical isomer (2RS,4SR)‐2‐(5‐methylthiophen‐2‐yl)‐2,3,4,5‐tetrahydro‐1,4‐epoxy‐naphtho[1,2‐b]azepine, (II), and (2RS,4SR)‐2‐(5‐bromothiophen‐2‐yl)‐2,3,4,5‐tetrahydro‐1,4‐epoxynaphtho[1,2‐b]azepine, C₁₈H₁₄BrNOS, (III), both crystallize as racemic mixtures. A combination of one C—H...O hydrogen bond and two C—H...π(arene) hydrogen bonds links the molecules of (I) into a three‐dimensional framework; the molecules of (II) are linked into a C(4)C(4)[R₂²(7)] chain of rings by a combination of C—H...N and C—H...O hydrogen bonds; and in (III), where Z′ = 2, a combination of four C—H...π(arene) hydrogen bonds and two C—H...π(thienyl) hydrogen bonds links the molecules into complex sheets. Comparisons are made with the assembly patterns in some aryl‐substituted 1,4‐epoxynaphtho[1,2‐b]azepines.