Crystal-Packing-Driven Enrichment of Atropoisomers

Crystal-packing forces can have a significant impact on the relative stabilities of different molecules and their conformations. The magnitude of such effects is, however, not yet well understood. Herein we show, that crystal packing can completely overrule the relative stabilities of different stereoisomers in solution. Heating of atropoisomers (i.e. “frozen-out” conformational isomers) in solution leads to complex mixtures. In contrast, solid-state heating selectively amplifies minor (<25 mole %) components of these solution-phase mixtures. We show that this heating strategy is successful for compounds with up to four rotationally hindered σ bonds, for which a single stereoisomer out of seven can be amplified selectively. Our results demonstrate that common supramolecular interactions—for example, [methyl⋅⋅⋅π] coordination and [C−H⋅⋅⋅O] hydrogen bonding—can readily invert the relative thermodynamic stabilities of different molecular conformations. These findings open up potential new avenues to control the folding of macromolecules.     

Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins

Protein structure and function is dependent on myriad noncovalent interactions. Direct detection and characterization of these weak interactions in large biomolecules, such as proteins, is experimentally challenging. Herein, we report the first observation and measurement of long‐range “through‐space” scalar couplings between methyl and backbone carbonyl groups in proteins. These J couplings are indicative of the presence of noncovalent C−H⋅⋅⋅π hydrogen‐bond‐like interactions involving the amide π network. Experimentally detected scalar couplings were corroborated by a natural bond orbital analysis, which revealed the orbital nature of the interaction and the origins of the through‐space J couplings. The experimental observation of this type of CH⋅⋅⋅π interaction adds a new dimension to the study of protein structure, function, and dynamics by NMR spectroscopy.     

Synthesis and characterization of a novel long‐alkyl‐chain ester‐substituted benzimidazole gelator and its octan‐1‐ol solvate

The synthesis of a novel benzimidazole derivative with a long‐chain‐ester substituent, namely methyl 8‐[4‐(1H‐benzimidazol‐2‐yl)phenoxy]octanoate, (3), is reported. Ester (3) shows evidence of aggregation in solution and weak gelation ability with toluene. The octan‐1‐ol solvate, methyl 8‐[4‐(1H‐benzimidazol‐2‐yl)phenoxy]octanoate octan‐1‐ol monosolvate, C₂₂H₂₆N₂O₃·C₈H₁₈O, (4), exhibits a four‐molecule hydrogen‐bonded motif in the solid state, with N—H…O hydrogen bonds between benzimidazole molecules and O—H…N hydrogen bonds between the octan‐1‐ol solvent molecules and the benzimidazole unit. The alkyl chains of the ester and the octan‐1‐ol molecules are in unfolded conformations. The phenylene ring is canted by 10.27 (6)° from the plane of the benzimidazole ring system. H…C contacts make up 20.7% of the Hirshfeld surface coverage. Weak C—H…π interactions involving the benzimidazole alkyl chain and three aromatic rings are observed.     

Effect of Intermolecular Interactions on Metal‐to‐Metal Charge Transfer: A Combined Experimental and Theoretical Investigation

Understanding the effects of intermolecular interactions on metal‐to‐metal charge transfer (MMCT) is crucial to develop molecular devices by grafting MMCT‐based molecular arrays. Herein, we report a series of solvent‐free {Fe₂Co₂} compounds sharing the same cationic tetranuclear {[Fe(PzTp)(CN)₃]₂[Co(dpq)₂]₂}²⁺ (PzTp^?=tetrakis(pyrazolyl)borate, dpq=dipyrido[3,2‐d:2′,3′‐f]quinoxaline) square units but having anions with different size, including BF₄^?, PF₆^?, OTf^?, and [Fe(PzTp)(CN)₃]^?. Intermolecular π???π interactions between dpq ligands, which coordinate to cobalt ions in the {[Fe(PzTp)(CN)₃]₂[Co(dpq)₂]₂}²⁺ units, can be modulated by introducing different counterions, regulating the distortion of the CoN₆ octahedron and ligand field around the cobalt ions. This change results in different MMCT behavior. Computational analyzes reveal the substantial role of the intermolecular interactions tuned by the presence of different counteranions on the MMCT behavior.     

Barrier heights of hydrogen‐transfer reactions with diffusion quantum monte carlo method

Hydrogen‐transfer reactions are an important class of reactions in many chemical and biological processes. Barrier heights of H‐transfer reactions are underestimated significantly by popular exchange–correlation functional with density functional theory (DFT), while coupled‐cluster (CC) method is quite expensive and can be applied only to rather small systems. Quantum Monte‐Carlo method can usually provide reliable results for large systems. Performance of fixed‐node diffusion quantum Monte‐Carlo method (FN‐DMC) on barrier heights of the 19 H‐transfer reactions in the HTBH38/08 database is investigated in this study with the trial wavefunctions of the single‐Slater–Jastrow form and orbitals from DFT using local density approximation. Our results show that barrier heights of these reactions can be calculated rather accurately using FN‐DMC and the mean absolute error is 1.0 kcal/mol in all‐electron calculations. Introduction of pseudopotentials (PP) in FN‐DMC calculations improves efficiency pronouncedly. According to our results, error of the employed PPs is smaller than that of the present CCSD(T) and FN‐DMC calculations. FN‐DMC using PPs can thus be applied to investigate H‐transfer reactions involving larger molecules reliably. In addition, bond dissociation energies of the involved molecules using FN‐DMC are in excellent agreement with reference values and they are even better than results of the employed CCSD(T) calculations using the aug‐cc‐pVQZ basis set. © 2017 Wiley Periodicals, Inc.     

Selective Sensing of Phosphates by a New Bis‐heteroleptic RuII Complex through Halogen Bonding: A Superior Sensor over Its Hydrogen‐Bonding Analogue

The selective phosphate‐sensing property of a bis‐heteroleptic Ru^II complex, 1 [PF₆]₂, which has a halogen‐bonding iodotriazole unit, is demonstrated and is shown to be superior to its hydrogen‐bonding analogue, 2 [PF₆]₂. Complex 1 [PF₆]₂, exploiting halogen‐bonding interactions, shows enhanced phosphate recognition in both acetonitrile and aqueous acetonitrile compared with its hydrogen‐bonding analogue, owing to considerable amplification of the Ru^II‐center‐based metal‐to‐ligand charge transfer (MLCT) emission response and luminescence lifetime. Detailed solution‐state studies reveal a higher association constant, lower limit of detection, and greater change in lifetime for complex 1 in the presence of phosphates compared with its hydrogen‐bonding analogue, complex 2 . The ¹H NMR titration study with H₂PO₄^? ascertains that the binding of H₂PO₄^? occurs exclusively through halogen‐bonding or hydrogen‐bonding interactions in complexes 1 [PF₆]₂ and 2 [PF₆]₂, respectively. Importantly, the single‐crystal X‐ray structure confirms the first ever report on metal‐assisted second‐sphere recognition of H₂PO₄^? and H₂P₂O₇^2? with 1 through a solitary C?I???anion halogen‐bonding interaction.     

Vinylene‐Linked Covalent Organic Frameworks by Base‐Catalyzed Aldol Condensation

Two 2D covalent organic frameworks (COFs) linked by vinylene (?CH=CH?) groups (V‐COF‐1 and V‐COF‐2) are synthesized by exploiting the electron deficient nature of the aromatic s‐triazine unit of C₃‐symmetric 2,4,6‐trimethyl‐s‐triazine (TMT). The acidic terminal methyl hydrogens of TMT can easily be abstracted by a base, resulting in a stabilized carbanion, which further undergoes aldol condensation with multitopic aryl aldehydes to be reticulated into extended crystalline frameworks (V‐COFs). Both V‐COF‐1 (with terepthalaldehyde (TA)) and V‐COF‐2 (with 1,3,5‐tris(p‐formylphenyl)benzene (TFPB)) are polycrystalline and exhibit permanent porosity and BET surface areas of 1341 m² g^?1 and 627 m² g^?1, respectively. Owing to the close proximity (3.52 Å) of the pre‐organized vinylene linkages within adjacent 2D layers stacked in eclipsed fashion, [2+2] photo‐cycloadditon in V‐COF‐1 formed covalent crosslinks between the COF layers.     

C 5 and C7 intramolecular hydrogen bonds stabilize the structure of N‐pyrazinoyl‐gabapentin (Pyr‐Gpn‐OH)

2‐{1‐[(Pyrazin‐2‐ylformamido)methyl]cyclohexyl}acetic acid (Pyr‐Gpn‐OH), C₁₄H₁₉N₃O₃, is an N‐protected derivative of gabapentin (Gpn). The compound crystallizes in the triclinic space group P and the molecular conformation is stabilized by intramolecular five‐ (C₅) and seven‐membered (C₇) hydrogen‐bonded rings. The packing of the molecules reveals intermolecular O—H...O and C—H...N hydrogen bonds, together with π–π interactions.     

Syntheses and structures of three macrocyclic supramolecular complexes and one ZnII‐containing coordination polymer generated from a semi‐rigid multidentate N‐containing ligand

Semirigid organic ligands can adopt different conformations to construct coordination polymers with more diverse structures when compared to those constructed from rigid ligands. A new asymmetric semirigid organic ligand, 4‐{2‐[(pyridin‐3‐yl)methyl]‐2H‐tetrazol‐5‐yl}pyridine ( L ), has been prepared and used to synthesize three bimetallic macrocyclic complexes and one coordination polymer, namely, bis(μ‐4‐{2‐[(pyridin‐3‐yl)methyl]‐2H‐tetrazol‐5‐yl}pyridine)bis[dichloridozinc(II)] dichloromethane disolvate, [Zn₂Cl₄(C₁₂H₁₀N₆)₂]·2CH₂Cl₂, ( I ), the analogous chloroform monosolvate, [Zn₂Cl₄(C₁₂H₁₀N₆)₂]·CHCl₃, ( II ), bis(μ‐4‐{2‐[(pyridin‐3‐yl)methyl]‐2H‐tetrazol‐5‐yl}pyridine)bis[diiodidozinc(II)] dichloromethane disolvate, [Zn₂I₄(C₁₂H₁₀N₆)₂]·2CH₂Cl₂, ( III ), and catena‐poly[[[diiodidozinc(II)]‐μ‐4‐{2‐[(pyridin‐3‐yl)methyl]‐2H‐tetrazol‐5‐yl}pyridine] chloroform monosolvate], {[ZnI₂(C₁₂H₁₀N₆)]·CHCl₃}_n, ( IV ), by solution reaction with ZnX₂ (X = Cl and I) in a CH₂Cl₂/CH₃OH or CHCl₃/CH₃OH mixed solvent system at room temperature. Complex ( I ) is isomorphic with complex ( III ) and has a bimetallic ring possessing similar coordination environments for both of the Zn^II cations. Although complex ( II ) also contains a bimetallic ring, the two Zn^II cations have different coordination environments. Under the influence of the I^? anion and guest CHCl₃ molecule, complex ( IV ) displays a significantly different structure with respect to complexes ( I )–( III ). C—H…Cl and C—H…N hydrogen bonds, and π–π stacking or C—Cl…π interactions exist in complexes ( I )–( IV ), and these weak interactions play an important role in the three‐dimensional structures of ( I )–( IV ) in the solid state. In addition, the fluorescence properties of L and complexes ( I )–( IV ) were investigated.     

Three structures of dispirooxindole derivatives generated in situ through a three‐component one‐pot strategy with complete regio‐ and stereoselectivity

The challenging molecular architecture of spirooxindoles is appealing to chemists because it evokes novel synthetic strategies that address configurational demands and provides platforms for further reaction development. The [3+2] cycloaddition of the carbonyl ylide with arylideneoxindole via a five‐membered cyclic transition state gave a novel class of dispirooxindole derivatives, namely tert‐butyl 4′‐(4‐bromophenyl)‐1′′‐methyl‐2,2′′‐dioxo‐5′‐phenyl‐4′,5′‐dihydrodispiro[indoline‐3,2′‐furan‐3′,3′′‐indoline]‐1‐carboxylate, C₃₆H₃₁BrN₂O, (Ia), 5′‐(4‐bromophenyl)‐1,1′′‐dimethyl‐4′‐phenyl‐4′,5′‐dihydrodispiro[indoline‐3,2′‐furan‐3′,3′′‐indoline]‐2,2′′‐dione, C₃₂H₂₅BrN₂O₃, (Ib), and tert‐butyl 1′′‐methyl‐2,2′′‐dioxo‐4′‐phenyl‐5′‐(p‐tolyl)‐4′,5′‐dihydrodispiro[indoline‐3,2′‐furan‐3′,3′′‐indoline]‐1‐carboxylate, C₃₇H₃₄N₂O₅, (Ic). Crystal structure analyses of these dispirooxindoles revealed the formation of two diastereoisomers selectively and confirmed their relative stereochemistry (SSSR and RRRS). In all three structures, intramolecular C—H...O and π–π interactions between oxindole and dihydrofuran rings are the key factors governing the regio‐ and stereoselectivity, and in the absence of conventional hydrogen bonds, their crystal packings are strengthened by intermolecular C—H...π interactions.     

Two New Solvent‐modulated Zinc(II) Metal‐Organic Hybrid Materials based on Rigid Tripodal Carboxylate Ligand and 2,2′‐Bipy Co‐ligand: Crystal Structures and Luminescent Properties

The zinc(II) coordination polymers [Zn(Htatb)(2,2′‐bipy) · (NMP) · H₂O] ( 1 ) and [Zn₃(tatb)₂(2,2′‐bipy)₃ · H₂O] ( 2 ) (H₃tatb = 4,4′,4′′‐s‐triazine‐2,4,6‐triyl‐tribenzoic acid; 2,2′‐bipy = 2,2′‐bipyridyl, NMP = N‐methyl‐2‐pyrrolidon), were synthesized hydrothermally, and characterized by infrared spectroscopy (IR), powder X‐ray diffraction (PXRD), and single‐crystal X‐ray diffraction. Both compounds 1 and 2 possess expectant low dimensional coordination structures, which further connected into interesting 3D networks by hydrogen bond and strong π–π interactions. Moreover, the thermal stabilities and fluorescent properties of 1 and 2 were investigated.     

Tiara[5]arenes: Synthesis,Solid‐State Conformational Studies,Host–Guest Properties,and Application as Nonporous Adaptive Crystals

Tiara[5]arenes (T[5]s), a new class of five‐fold symmetric oligophenolic macrocycles that are not accessible from the addition of formaldehyde to phenol, were synthesized for the first time. These pillar[5]arene‐derived structures display both unique conformational freedom, differing from that of pillararenes, with a rich blend of solid‐state conformations and excellent host–guest interactions in solution. Finally we show how this novel macrocyclic scaffold can be functionalized in a variety of ways and used as functional crystalline materials to distinguish uniquely between benzene and cyclohexane.     

Highly accurate benchmark calculations of the interaction energies in the complexes C6H6···C6X6 (X = F,Cl, Br,and I)

Different from the case of the benzene dimer, the differences between the interaction energies are always less than 0.50 kcal/mol for face‐to‐face eclipsed, face‐to‐face staggered, and parallel‐displaced configurations of all investigated complexes C₆H₆···C₆X₆ (X = F, Cl, Br, and I). Hence, it is a great challenge for quantum chemists to accurately calculate the interaction energies for the three configurations of the complexes C₆H₆···C₆X₆. This work demonstrates that results obtained with the PBE0 density functional combined with the D3 dispersion correction (PBE0‐D3) and the basis set def2‐TZVPP are in excellent agreement with the estimates of the coupled‐cluster singles, doubles, and perturbative triples [CCSD(T)] complete basis set (CBS) limit. The other finding in this study is that, in comparison with the gold‐standard CCSD(T)/CBS benchmark, the spin‐component scaled (SCS) zeroth‐order symmetry‐adapted perturbation theory (SAPT0), when paired with the basis set aug‐cc‐pVDZ, performs also very well, and its performance is even better than that of the PBE0‐D3/def2‐TZVPP method or the conventional SAPT/aug‐cc‐pVQZ method. The findings of this study are very significant because both PBE0‐D3/def2‐TZVPP and SCS‐SAPT0/aug‐cc‐pVDZ can deal with the systems with more than 200 atoms.     

An unusual conformation of gabapentin (Gpn) in Pyr‐Gpn‐NH‐NH‐Pyr stabilized by weak interactions

The crystal structure of N‐[(1‐{2‐oxo‐2‐[2‐(pyrazin‐2‐ylcarbonyl)hydrazin‐1‐yl]ethyl}cyclohexyl)methyl]pyrazine‐2‐carboxamide monohydrate (Pyr‐Gpn‐NN‐NH‐Pyr·H₂O), C₁₉H₂₃N₇O₃·H₂O, reveals an unusual trans–gauche (tg⁻) conformation for the gabapentin (Gpn) residue around the C^γ—C^β (θ₁) and C^β—C^α (θ₂) bonds. The molecular conformation is stabilized by intramolecular N—H...N hydrogen bonds and weak C—H...O interactions. The packing of the molecules in the crystal lattice shows a network of strong N—H...O and O—H...O hydrogen bonds together with weak C—H...O and π–π inteactions.     

Tuning the π‐π stacking distance and J‐aggregation of DPP‐based conjugated polymer via introducing insulating polymer

The close π–π stacking and the high J‐aggregation during the formation of fibrillar morphology in films of the poly[[2,5‐bis(2‐octyldodecyl)?2,3,5,6‐tetrahydro‐3,6‐dioxopyrrolo[3,4‐c]pyrrole‐1,4‐diyl]‐alt–[[2,2′‐(2,5‐thiophene)bis‐thieno[3,2‐b]thiophen]‐5,5′‐diyl]] (PDPPTT‐T) are demonstrated via blending with polystyrene (PS). The hydrodynamic radius (R_h) of PDPPTT‐T is decreased from 16.7 nm in the neat solution to 12.7 nm in the blend solution at the ratio of 1/20(PDPPTT‐T/PS). This phenomenon suggests that blending PS is beneficial for the disentanglement of PDPPTT‐T. The disentanglement of PDPPTT‐T facilitates the formation of fibrillar morphology. The growth of the fibrils occurs along the molecular backbones and the width of the fibrils is parallel to the π–π stacking direction. The disentanglement of PDPPTT‐T helps the molecules adjust conformation to improve J‐aggregation and decrease the π–π stacking distance. The maximum absorption is red‐shifted from 825 nm to 849 nm and the relative intensity of J‐aggregation (the 0‐0/0‐1 ratio) is increased from 1.19 to 1.60. The π–π stacking distance decreases from 3.57 to 3.52 Å. The charge‐carrier mobility will be improved in the fibrillar morphology with close π–π stacking and high J‐aggregation. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 838–847     

Construction of Hetero‐Four‐Layered Tripalladium(II) Cyclophanes by Transannular π⋅⋅⋅π Interactions

A synthetic strategy for the generation of new molecular species utilizing a provision of nature is presented. Nano‐dimensional (23(2)×21(1)×16(1) ų) hetero‐four‐layered trimetallacyclophanes were constructed by proof‐of‐concept experiments that utilize a suitable combination of π???π interactions between the central aromatic rings, tailor‐made short/long spacer tridentate donors, and the combined helicity. The behavior of the unprecedented four‐layered metallacyclophane system offers a landmark in the development of new molecular systems.     

A new two‐dimensional anionic cadmium(II) polymer constructed through thiocyanate coordination bridges

A new cadmium–thiocyanate complex, poly[4‐(dimethylamino)pyridin‐1‐ium [di‐μ‐thiocyanato‐κ²N:S;κ²S:N‐thiocyanato‐κN‐cadmium(II)]], {(C₇H₁₁N₂)[Cd(NCS)₃]}_n, was synthesized by the reaction of cadmium thiocyanate and 4‐(dimethylamino)pyridine hydrochloride in aqueous solution. In the crystal structure, each Cd^II ion is square‐pyramidally coordinated by three N and two S atoms from five different thiocyanate ligands, four of which are bridging. The thiocyanate ligands play different roles in the build up of the structure; one role results in the formation of [Cd₂(NCS)₂] building blocks, while the other links the building blocks and cations via N—H...S hydrogen bonds. The N—H...S hydrogen bonds and weak π–π stacking interactions are involved in the formation of both a two‐dimensional network structure and the supramolecular network.     

Synthesis,Crystal Structure and Properties of [Cu(phen)3][Cu(pheida)2]·10H2O and [(phen)2Cu(μ‐BAAP)Cu(μ‐BAAP)Cu(phen)2][Cu(BAAP)2]·8.5H2O (H2pheida = N‐phenetyl‐iminodiacetic acid,H2BAAP = N‐benzylaminoacetic‐2‐propionic acid)

The salts [Cu(phen)₃][Cu(pheida)₂]·10H₂O ( 1 ) and [(phen)₂Cu(μ‐BAAP)Cu(μ‐BAAP)Cu(phen)₂][Cu(BAAP)₂]·8.5H₂O ( 2 ) (H₂pheida = N‐phenetyl‐iminodiacetic acid, H₂BAAP = N‐benzylaminoacetic‐2‐propionic acid, phen = 1, 10‐phenanthroline) have been prepared and studied by thermal, spectroscopic and X‐ray diffraction methods. 1 has the rather unusual [Cu(phen)₃]²⁺ cation and two non‐equivalent [Cu(pheida)₂]^2— anions with a coordination type 4+2 but quite different tetragonality (T = 0.848 and 0.703 for anions 1 and 2, respectively). The crystal consists of multi‐π, π‐stacked chains (…anion 2 — cation — cation — anion 2…) connected by hydrophobic interactions; these chains build channels which are partially filled by anions 1 and water molecules. In contrast, compound 2 has a mixed‐ligand trinuclear cation with a bridging central moiety close similar to the counter anion. The formation of such a trinuclear cation is discussed as a consequence of the most advantageous molecular recognition process between [Cu(phen)₂(H₂O)_{1 or 2}]²⁺ and [Cu(BAAP)₂]^2— in solution. In the crystal of 2, multi‐π, π‐stacked arrays of C₆‐rings from phen and (BAAP)^2— ligands of trinuclear cations generate channels where counter anions and water molecules are located.     

1,4,4‐Tri­methyl‐9‐phenyl‐8‐oxa‐9‐aza­bi­cyclo­[3.2.2]­non‐6‐en‐2‐one

The structure of the adduct of eucarvone with nitro­so­benzene, C₁₆H₁₉NO₂, is reported. The [3.2.2] bicyclic system corresponds to two seven‐membered rings in boat and distorted chair conformations and a six‐membered ring that adopts a distorted boat conformation. No conjugation is observed between the phenyl group and the N—O system. The packing is directed mainly by a C?O hydrogen bond, C—H?O‐(1 ? x, ?y, z) and by intermolecular C—H?π interactions.     

Photocycloaddition of Cyclohex‐2‐enones to Penta‐1,2,4‐triene

Dihydrothiinone 9a undergoes photocycloaddition regioselectively to all three C?C bonds of penta‐1,2,4‐triene ( 10 ), the relative stabilities of the biradical intermediates determining the product distribution. In contrast, cyclohexenone 9b and dihydropyranone 9c afford more complex mixtures of bicyclo[4.2.0]octanones, which also turn out to be less stable on chromatographic workup, reflecting the higher strain due to the shorter bond lengths (C? O and C? C vs. C? S) in the six‐membered rings, respectively.