An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Journal of the American Chemical Society, Nov 12, 2009
We report herein the synthesis and metal complexation properties of two macrocyclic hosts that co... more We report herein the synthesis and metal complexation properties of two macrocyclic hosts that contain two 2,2'-bipyridines and two urea groups. These hosts take advantage of the conformationally mobile 5,5'-positions of the bipyridines to give metal binding sites that are dynamic. By simple bond rotation, these hosts can exchange an interior (endo) situated metal binding site for an exterior (exo) binding site. We examine the solid-state structures of the two free hosts and two coordination complexes ([Cd(host 1)(H(2)O)(NO(3))(2)] and [Ag(2)(host 2)](SO(3)CF(3))(2)) using X-ray crystallography. Analysis of these crystal structures suggests that the bipyridine groups within the hosts are able to rotate to access multiple conformations including the desired exo and endo conformations. We also investigate the binding affinity of these new ligands in solution by UV-vis titrations with…
A methylene urea bridged di-iodo triphenylamine dimer and its corresponding methylene di-iodo tri... more A methylene urea bridged di-iodo triphenylamine dimer and its corresponding methylene di-iodo triphenylamine monomer are crystallized to correlate their structures with properties. In addition, their conductivity is compared against Spiro-OMeTAD.
The reaction of cis-bis(2,2'-bipyridine)dichlororuthenium(II) hydrate with a conformationally mob... more The reaction of cis-bis(2,2'-bipyridine)dichlororuthenium(II) hydrate with a conformationally mobile bipyridyl macrocycle afforded [(bpy) 2 Ru(µ-L)Ru(bpy) 2 ]Cl 4 •6H 2 O, a bridged di-Ru complex. Single crystal X-ray diffraction showed the macrocyclic ligand adopting a bowl-like structure with the exo-coordinated Ru(II) centers separated by 7.29 Å. Photophysical characterization showed that the complex absorbs in the visible region (λ max = 451 nm) with an emission maximum at 610 nm (τ = 706 ns, Φ PL = 0.021). Electrochemical studies indicate the di-Ru complex undergoes three one-electron reversible reductions and a reversible one-electron oxidation process. This electrochemical reversibility is a key characteristic for its use as an electron transfer agents. The complex was evaluated as a photocatalyst for the electronically mismatched Diels-Alder reaction of isoprene and trans-anethole using visible light. It afforded the expected product in good conversion (69%) and selectivity (dr > 10 : 1) at low loadings (0.5-5.0 mol%) and the sensitizer/catalyst was readily recycled. These results suggest that the bipyridyl macrocycle could be widely applied as a bridging ligand for the generation of chromophore-catalyst assemblies.
Here, we compare structures determined by X-ray diffraction and subsequent Hirshfeld surface anal... more Here, we compare structures determined by X-ray diffraction and subsequent Hirshfeld surface analysis to identify and understand the non-covalent interactions within the lattices of chromone, 6-methylchromone, 6-methoxychromone, 6-fluorochromone, and 6-chlorochromone with reported 6-bromochromone. In chromone, H-bonds and CH–л interactions predominate. H-bonds and aryl-stacking interactions are distinct in 6-methylchromone and 6-methoxychromone. The 6-fluorochromone, showed two types of H-bonds with O···H bonds having a greater contribution than F···H. In contrast, 6-chlorochromone and 6-bromochromone, the halogen contributes the larger percentage of stabilizing H-bonding with Cl···H and Br···H predominating over the O···H bonds. Compound 1 crystallizes in the monoclinic space group P21/n with a = 8.1546(8) Å, b = 7.8364(7) Å, c = 11.1424(11) Å, β = 108.506(2)° and Z = 4. Compound 2 crystallizes in the triclinic space group P-1 with a = 7.0461(3) Å, b = 10.2108(5) Å, c = 10.7083(5) Å, α = 89.884(2)°, β = 77.679(2)°, γ = 87.367(2)° and Z = 4. Compound 3 crystallizes in the monoclinic space group P21/n with a = 8.1923(4) Å, b = 7.0431(3) Å, c = 15.3943(8) Å, β = 92.819(2)° and Z = 4. Compound 4 crystallizes in the triclinic space group P1 with a = 3.7059(2) Å, b = 6.1265(4) Å, c = 7.6161(5) Å, α = 84.085(3)°, β = 87.070(3)°, γ = 83.390(3)° and Z = 1. Compound 5 crystallizes in the monoclinic space group P21 with a = 3.8220(2) Å, b = 5.6985(2) Å, c = 16.9107(7) Å, β = 95.8256(18)° and Z = 2.Graphical AbstractThe effect of substituents at the 6-position on chromone on their crystal structures using Hirshfeld surface and fingerprint analysis.
Abstract Herein, we investigate co-crystallization of three linear co-formers that contain urea a... more Abstract Herein, we investigate co-crystallization of three linear co-formers that contain urea and pyridyl groups with three regioisomers of diiodotetrafluorobenzene (DITFB) to afford eleven co-crystals. The linear o-, m-, and p- dipyridylureas vary distance and geometry between the urea carbonyl oxygen and two pyridyl nitrogen acceptors, while the donors consist of urea NH groups and the activated halides in DITFB. Electrostatic potential calculations suggest that the o-dipyridylurea co-former presents two significantly different acceptors. In comparison, the acceptors in the m- and p-dipyridylurea co-formers display electrostatic potentials within 5–6 kJ/mol and should be competitive, potentially leading to altered assembly motifs. Overall, ten of the co-crystals consistently display the urea assembly motif as the best acceptor/donor pair. Seven structures were obtained as the predicted 1:1 ratio with halogen bonding interactions linking ditopic halogen bond donors and the pyridyl units through N···I interactions ranging from 78.4 to 83.1% of the van der Waals radii. Modified structures were more likely when there was a structural mismatch with the geometrically challenging o-DITFB donor and m- or p-dipyridylurea co-former. The majority of the co-crystal structures (10/11) demonstrated fully satisfied hydrogen and halogen bonding interactions suggesting that these synthons can be used synergistically to generate complex solid-state structures.
Urea is a versatile building block that can be modified to selfassemble into a multitude of struc... more Urea is a versatile building block that can be modified to selfassemble into a multitude of structures. One-dimensional nanochannels with zigzag architecture and cross-sectional dimensions of only ∼3.7 Å Â 4.8 Å are formed by the columnar assembly of phenyl ether bis-urea macrocycles. Nanochannels formed by phenylethynylene bis-urea macrocycles have a round cross-section with a diameter of ∼9.0 Å. This work compares the Xe atom packing and diffusion inside the crystalline channels of these two bis-ureas using hyperpolarized Xe-129 NMR. The elliptical channel structure of the phenyl ether bis-urea macrocycle produces a Xe-129 powder pattern line shape characteristic of an asymmetric chemical shift tensor with shifts extending to well over 300 ppm with respect to the bulk gas, reflecting extreme confinement of the Xe atom. The wider channels formed by phenylethynylene bis-urea, in contrast, present an isotropic dynamically average electronic environment. Completely different diffusion dynamics are revealed in the two bis-ureas using hyperpolarized spin-tracer exchange NMR. Thus, a simple replacement of phenyl ether with phenylethynylene as the rigid linker unit results in a transition from single-file to Fickian diffusion dynamics. Selfassembled bis-urea macrocycles are found to be highly suitable materials for fundamental molecular transport studies on micrometer length scales.
Supporting Information Table of Contents General Procedure S2 Reaction Scheme for Macrocycle 2-6 ... more Supporting Information Table of Contents General Procedure S2 Reaction Scheme for Macrocycle 2-6 S4 Characterization Data for Macrocycle 3-6 S5 1 H NMR of Macrocycle 2 S7 13 C NMR of Macrocycle 2 S8 1 H NMR of Macrocycle 3 S9 1 H NMR Titration of Macrocycle 4 S46 Determine the Diffusion Coefficients by NMR S48 FT-IR study of Self-association of Macrocycle 2, 3 and 4 in Solutions S49 References S53 b = 16.1503(6) Å β= 90°. c = 8.5508(3) Å γ = 90°. Volume 2255.14(14) Å 3 Z 4 Density (calculated) 1.215 Mg/m 3 Absorption coefficient 0.091 mm-1 F(000) 888 Crystal size 0.54 x 0.40 x 0.30 mm 3 Theta range for data collection 2.49 to 26.40°.
Journal of the American Chemical Society, Dec 21, 2007
... Mark D. Smith, † Youyong Li, ‡ and Linda S. Shimizu* †. Department of Chemistry and Biochemis... more ... Mark D. Smith, † Youyong Li, ‡ and Linda S. Shimizu* †. Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, Materials and Process Simulation Center, California Institute of Technology, California 91125. J. Am. Chem. ...
CONSPECTUS: This Account highlights the work from our laboratories on bisurea macrocycles constru... more CONSPECTUS: This Account highlights the work from our laboratories on bisurea macrocycles constructed from two C-shaped spacers and two urea groups. These simple molecular units assembled with high fidelity into columnar structures guided by the three-centered urea hydrogen bonding motif and aryl stacking interactions. Individual columns are aligned and closely packed together to afford functional and homogeneous microporous crystals. This approach allows for precise and rational control over the dimensions of the columnar structure simply by changing the small molecular unit. When the macrocyclic unit lacks a cavity, columnar assembly gives strong pillars. Strong pillars with external functional groups such as basic lone pairs can expand like clays to accept guests between the pillars. Macrocycles that contain sizable interior cavities assemble into porous molecular crystals with aligned, well-defined columnar pores that are accessible to gases and guests. Herein, we examine the optimal design of the macrocyclic unit that leads to columnar assembly in high fidelity and probe the feasibility of incorporating a second functional group within the macrocycles. The porous molecular crystals prepared through the self-assembly of bis-urea macrocycles display surface areas similar to zeolites but lower than MOFs. Their simple one-dimensional channels are well-suited for studying binding, investigating transport, diffusion and exchange, and monitoring the effects of encapsulation on reaction mechanism and product distribution. Guests that complement the size, shape, and polarity of the channels can be absorbed into these porous crystals with repeatable stoichiometry to form solid host−guest complexes. Heating or extraction with an organic solvent enables desorption or removal of the guest and subsequent recovery of the solid host. Further, these porous crystals can be used as containers for the selective [2 + 2] cycloadditions of small enones such as 2-cyclohexenone or 3-methyl-cyclopentenone, while larger hosts bind and facilitate the photodimerization of coumarin. When the host framework incorporates benzophenone, a triplet sensitizer, UVirradiation in the presence of oxygen efficiently generates singlet oxygen. Complexes of this host were employed to influence the selectivity of photooxidations of 2-methyl-2-butene and cumene with singlet oxygen. Small systematic changes in the channel and bound reactants should enable systematic evaluation of the effects of channel dimensions, guest dimensions, and channel−guest interactions on the processes of absorption, diffusion, and reaction of guests within these nanochannels. Such studies could help in the development of new materials for separations, gas storage, and catalysis.
Materials and Methods Characterization of Compounds: All DPOA ligands were synthesized by the Dan... more Materials and Methods Characterization of Compounds: All DPOA ligands were synthesized by the Daniel Reger group and used as received. All TFDIB isomers and solvents were purchased from Oak Ridge Chemical®, Thermo Fisher Scientific®, VWR®, or TCI America® and were used as received without further. 1 HNMR spectra were recorded on a Bruker Avance III-HD spectrometer (300 MHz). Chemical shifts are reported as (δ ppm) with the corresponding integration values. High-resolution mass spectrum data was recorded using a direct exposure probe (DEP) in electron ionization (EI) mode on a Waters QTOF-I quadrupole time-of-flight mass spectrometer. FT-IR data was acquired. FT-IR spectra were obtained using a Perkin Elmer Spectrum 100 FT-IR Spectrometer. Background spectra were recorded from 650 to 4000 cm-1 and taken in 4 scans. The crystalline sample was then added to the sample stage until transmittance was less than 85%. 32 scans were then taken from 650 to 4000 cm-1 to obtain spectra. Crystal Growth. To obtain crystals of the parent ligands, the DPOA ligands (20 mg) were dissolved in a minimal volume of solvent, the solution was filtered, and left to slowly evaporate for 3-5 days until crystals formed. The co-crystals were synthesized by grinding 1:1 stoichiometric ratio of the TFDIB co-formers (29.6 mg, 0.07 mmol) and DPOA ligands (20 mg, 0.07 mmol) for approximately 2 min with 3-5 drops of CHCl3. Half of this mixture was added to a vial, and gently heated (when needed) in a minimal amount of solvent until completely dissolved. The samples were then allowed to slowly evaporate for 4-6 days until crystals were formed. The other half of the ground mixture dissolved in DMSO, and water was allowed to vapor diffuse into the solution for approximately 5 days until crystals formed. Both methods were repeated with multiple solvents until co-crystals were obtained. Crystal Structure Determination: X-ray intensity data was collected at 100(2) K using a Bruker D8 QUEST diffractometer equipped with a PHOTON-100 CMOS area detector and an Incoatec microfocus source (Mo Kα radiation, λ = 0.71073 Å). The raw area detector data frames were reduced and corrected for absorption effects using the Bruker APEX3, SAINT+ and SADABS programs. 1,2 Final unit cell parameters were determined by least-squares refinement of reflections taken from the data set. The structures were solved with SHELXT. 3 Subsequent difference Fourier calculations and full-matrix least-squares refinement against F 2 were performed with SHELXL-2016 3 using OLEX2. 4 Electrostatic Potential Calculations. Electrostatic potentials were calculated using Spartan 10' software package. The crystal structure files (CIFs) of the DPOA compounds were imported and energetically optimized. The energies were then calculated using DFT B3YLP level of theory, using a 6-311++G** basis set under vacuum. Electrostatic potentials for best donor and acceptor were determined using the electrostatic potential map (0.002 e a.u. isovalue) as automatically calculated by the Spartan 10' software. Electrostatic potentials of other donors and acceptors were obtained by manually searching the atom of interest until the value with the largest absolute value was found.
This thesis describes the use of polarized fluorescence microscopy to directly probe guest molecu... more This thesis describes the use of polarized fluorescence microscopy to directly probe guest molecule orientation in bis-urea macrocycle crystals. These macrocycles assemble to afford one-dimensional (1D) microchannels ∼9 Å in diameter that have previously been shown to exhibit normal Fickian diffusion and induce selective reactivity among the confined guest molecules. In the present work, we take advantage of the quasi-1D morphology of fiber-like microcrystals with the extended dimension corresponding to the channel axis to measure excitation and emission polarization values for a bithiophene guest. Guest fluorescence is shown to be polarized along the fiber axis with emission polarization values up to 0.729, indicating a high degree of orientational order within the 1D channels. The observed behavior is consistent with calculated results for the guest orientation and electronic transition dipole moment. The results indicate the value of functional fluorescent probes as a measure of guest confinement in low-dimensional environments. vi
Changing an ether to a ketone within the framework of a bisurea macrocycle has little effect on t... more Changing an ether to a ketone within the framework of a bisurea macrocycle has little effect on the supramolecular assembly of this building block into porous crystals but introduces a triplet sensitizer into the framework that dramatically alters the photochemical reactions of included guests.
Journal of the American Chemical Society, Jun 1, 2006
We report a highly selective 2 + 2 cycloaddition of 2-cyclohexenone in the presence of self-assem... more We report a highly selective 2 + 2 cycloaddition of 2-cyclohexenone in the presence of self-assembled bisurea macrocycles that yields the head-to-tail photodimer. The reaction proceeds with high conversion and with decreased incidence of secondary photorearrangement. Furthermore, the product can be extracted from the assembly, and the solid assembly is readily recovered and reused, much like a zeolite.
Journal of the American Chemical Society, Mar 25, 2010
Conjugated polymers have demonstrated utility in organic solar cells, 1 chemical sensors, 2 and o... more Conjugated polymers have demonstrated utility in organic solar cells, 1 chemical sensors, 2 and optoelectronics. 3 Microporous materials such as metal organic frameworks (MOFs) and zeolites show practical applications in gas storage, 4 separation, 5 catalysis, 6 and as confined environments for reactions. 7 MOFs and covalently linked organic frameworks 8 utilize transition metal ions or organic monomeric units to afford porous materials with high surface areas and excellent thermal stabilities. An alternate strategy for forming porous materials relies on the columnar assembly of molecular building blocks directed by noncovalent interactions. We sought to combine the attributes of a conjugated polymer with porous materials. Herein, we report a diacetylene macrocycle that was readily synthesized and self-assembled into columns to afford porous crystals (Figure 1). Heating initiated a topochemical polymerization of the preorganized diacetylene units to give covalent conjugated polydiacetylenes (PDAs). These stable conjugated materials maintained permanent porosity as evidenced by their type I gas adsorption isotherms with CO 2 (g). Conjugated porous PDAs could have applications for sensing and in electronics.
Intentional design of crystalline frameworks requires a good understanding of how inter-and intra... more Intentional design of crystalline frameworks requires a good understanding of how inter-and intramolecular forces act together to afford solid-state structures. Herein, we synthesize and crystallize bis-thiourea and bissquaramide m-xylene macrocycles and compare the conformational preferences of these functional groups as well as their assembled structures to their bis-urea counterpart. Four new crystal structures of the bis-thiourea macrocycle and the bissquaramide macrocycle are reported. The m-xylene macrocycles of urea, thiourea, and squaramide each display trans− trans conformers in their pure crystal forms. The thiourea macrocycles show edge to face interactions driven by sulfur bonding to afford 2D sheets. This macrocycle also shows an ethylene diamine solvate that displays both trans−trans and cis−trans conformers in the same structure. Solution 2D EXSY NMR studies suggest that these and additional conformations interconvert at room temperature. Squaramide macrocycles display 2D hydrogen bonding networks forming interdigitated cycles using only one of the two available carbonyls for hydrogen bonding. Additionally, the bis-squaramide macrocycle can crystallize as a solvate, where it maintains its original 2D framework with propylene carbonate imbedded in-between its layers. Overall, these findings help build a foundation for predicting how assembly motifs are modulated by macrocyclic building units.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Journal of the American Chemical Society, Nov 12, 2009
We report herein the synthesis and metal complexation properties of two macrocyclic hosts that co... more We report herein the synthesis and metal complexation properties of two macrocyclic hosts that contain two 2,2'-bipyridines and two urea groups. These hosts take advantage of the conformationally mobile 5,5'-positions of the bipyridines to give metal binding sites that are dynamic. By simple bond rotation, these hosts can exchange an interior (endo) situated metal binding site for an exterior (exo) binding site. We examine the solid-state structures of the two free hosts and two coordination complexes ([Cd(host 1)(H(2)O)(NO(3))(2)] and [Ag(2)(host 2)](SO(3)CF(3))(2)) using X-ray crystallography. Analysis of these crystal structures suggests that the bipyridine groups within the hosts are able to rotate to access multiple conformations including the desired exo and endo conformations. We also investigate the binding affinity of these new ligands in solution by UV-vis titrations with…
A methylene urea bridged di-iodo triphenylamine dimer and its corresponding methylene di-iodo tri... more A methylene urea bridged di-iodo triphenylamine dimer and its corresponding methylene di-iodo triphenylamine monomer are crystallized to correlate their structures with properties. In addition, their conductivity is compared against Spiro-OMeTAD.
The reaction of cis-bis(2,2'-bipyridine)dichlororuthenium(II) hydrate with a conformationally mob... more The reaction of cis-bis(2,2'-bipyridine)dichlororuthenium(II) hydrate with a conformationally mobile bipyridyl macrocycle afforded [(bpy) 2 Ru(µ-L)Ru(bpy) 2 ]Cl 4 •6H 2 O, a bridged di-Ru complex. Single crystal X-ray diffraction showed the macrocyclic ligand adopting a bowl-like structure with the exo-coordinated Ru(II) centers separated by 7.29 Å. Photophysical characterization showed that the complex absorbs in the visible region (λ max = 451 nm) with an emission maximum at 610 nm (τ = 706 ns, Φ PL = 0.021). Electrochemical studies indicate the di-Ru complex undergoes three one-electron reversible reductions and a reversible one-electron oxidation process. This electrochemical reversibility is a key characteristic for its use as an electron transfer agents. The complex was evaluated as a photocatalyst for the electronically mismatched Diels-Alder reaction of isoprene and trans-anethole using visible light. It afforded the expected product in good conversion (69%) and selectivity (dr > 10 : 1) at low loadings (0.5-5.0 mol%) and the sensitizer/catalyst was readily recycled. These results suggest that the bipyridyl macrocycle could be widely applied as a bridging ligand for the generation of chromophore-catalyst assemblies.
Here, we compare structures determined by X-ray diffraction and subsequent Hirshfeld surface anal... more Here, we compare structures determined by X-ray diffraction and subsequent Hirshfeld surface analysis to identify and understand the non-covalent interactions within the lattices of chromone, 6-methylchromone, 6-methoxychromone, 6-fluorochromone, and 6-chlorochromone with reported 6-bromochromone. In chromone, H-bonds and CH–л interactions predominate. H-bonds and aryl-stacking interactions are distinct in 6-methylchromone and 6-methoxychromone. The 6-fluorochromone, showed two types of H-bonds with O···H bonds having a greater contribution than F···H. In contrast, 6-chlorochromone and 6-bromochromone, the halogen contributes the larger percentage of stabilizing H-bonding with Cl···H and Br···H predominating over the O···H bonds. Compound 1 crystallizes in the monoclinic space group P21/n with a = 8.1546(8) Å, b = 7.8364(7) Å, c = 11.1424(11) Å, β = 108.506(2)° and Z = 4. Compound 2 crystallizes in the triclinic space group P-1 with a = 7.0461(3) Å, b = 10.2108(5) Å, c = 10.7083(5) Å, α = 89.884(2)°, β = 77.679(2)°, γ = 87.367(2)° and Z = 4. Compound 3 crystallizes in the monoclinic space group P21/n with a = 8.1923(4) Å, b = 7.0431(3) Å, c = 15.3943(8) Å, β = 92.819(2)° and Z = 4. Compound 4 crystallizes in the triclinic space group P1 with a = 3.7059(2) Å, b = 6.1265(4) Å, c = 7.6161(5) Å, α = 84.085(3)°, β = 87.070(3)°, γ = 83.390(3)° and Z = 1. Compound 5 crystallizes in the monoclinic space group P21 with a = 3.8220(2) Å, b = 5.6985(2) Å, c = 16.9107(7) Å, β = 95.8256(18)° and Z = 2.Graphical AbstractThe effect of substituents at the 6-position on chromone on their crystal structures using Hirshfeld surface and fingerprint analysis.
Abstract Herein, we investigate co-crystallization of three linear co-formers that contain urea a... more Abstract Herein, we investigate co-crystallization of three linear co-formers that contain urea and pyridyl groups with three regioisomers of diiodotetrafluorobenzene (DITFB) to afford eleven co-crystals. The linear o-, m-, and p- dipyridylureas vary distance and geometry between the urea carbonyl oxygen and two pyridyl nitrogen acceptors, while the donors consist of urea NH groups and the activated halides in DITFB. Electrostatic potential calculations suggest that the o-dipyridylurea co-former presents two significantly different acceptors. In comparison, the acceptors in the m- and p-dipyridylurea co-formers display electrostatic potentials within 5–6 kJ/mol and should be competitive, potentially leading to altered assembly motifs. Overall, ten of the co-crystals consistently display the urea assembly motif as the best acceptor/donor pair. Seven structures were obtained as the predicted 1:1 ratio with halogen bonding interactions linking ditopic halogen bond donors and the pyridyl units through N···I interactions ranging from 78.4 to 83.1% of the van der Waals radii. Modified structures were more likely when there was a structural mismatch with the geometrically challenging o-DITFB donor and m- or p-dipyridylurea co-former. The majority of the co-crystal structures (10/11) demonstrated fully satisfied hydrogen and halogen bonding interactions suggesting that these synthons can be used synergistically to generate complex solid-state structures.
Urea is a versatile building block that can be modified to selfassemble into a multitude of struc... more Urea is a versatile building block that can be modified to selfassemble into a multitude of structures. One-dimensional nanochannels with zigzag architecture and cross-sectional dimensions of only ∼3.7 Å Â 4.8 Å are formed by the columnar assembly of phenyl ether bis-urea macrocycles. Nanochannels formed by phenylethynylene bis-urea macrocycles have a round cross-section with a diameter of ∼9.0 Å. This work compares the Xe atom packing and diffusion inside the crystalline channels of these two bis-ureas using hyperpolarized Xe-129 NMR. The elliptical channel structure of the phenyl ether bis-urea macrocycle produces a Xe-129 powder pattern line shape characteristic of an asymmetric chemical shift tensor with shifts extending to well over 300 ppm with respect to the bulk gas, reflecting extreme confinement of the Xe atom. The wider channels formed by phenylethynylene bis-urea, in contrast, present an isotropic dynamically average electronic environment. Completely different diffusion dynamics are revealed in the two bis-ureas using hyperpolarized spin-tracer exchange NMR. Thus, a simple replacement of phenyl ether with phenylethynylene as the rigid linker unit results in a transition from single-file to Fickian diffusion dynamics. Selfassembled bis-urea macrocycles are found to be highly suitable materials for fundamental molecular transport studies on micrometer length scales.
Supporting Information Table of Contents General Procedure S2 Reaction Scheme for Macrocycle 2-6 ... more Supporting Information Table of Contents General Procedure S2 Reaction Scheme for Macrocycle 2-6 S4 Characterization Data for Macrocycle 3-6 S5 1 H NMR of Macrocycle 2 S7 13 C NMR of Macrocycle 2 S8 1 H NMR of Macrocycle 3 S9 1 H NMR Titration of Macrocycle 4 S46 Determine the Diffusion Coefficients by NMR S48 FT-IR study of Self-association of Macrocycle 2, 3 and 4 in Solutions S49 References S53 b = 16.1503(6) Å β= 90°. c = 8.5508(3) Å γ = 90°. Volume 2255.14(14) Å 3 Z 4 Density (calculated) 1.215 Mg/m 3 Absorption coefficient 0.091 mm-1 F(000) 888 Crystal size 0.54 x 0.40 x 0.30 mm 3 Theta range for data collection 2.49 to 26.40°.
Journal of the American Chemical Society, Dec 21, 2007
... Mark D. Smith, † Youyong Li, ‡ and Linda S. Shimizu* †. Department of Chemistry and Biochemis... more ... Mark D. Smith, † Youyong Li, ‡ and Linda S. Shimizu* †. Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, Materials and Process Simulation Center, California Institute of Technology, California 91125. J. Am. Chem. ...
CONSPECTUS: This Account highlights the work from our laboratories on bisurea macrocycles constru... more CONSPECTUS: This Account highlights the work from our laboratories on bisurea macrocycles constructed from two C-shaped spacers and two urea groups. These simple molecular units assembled with high fidelity into columnar structures guided by the three-centered urea hydrogen bonding motif and aryl stacking interactions. Individual columns are aligned and closely packed together to afford functional and homogeneous microporous crystals. This approach allows for precise and rational control over the dimensions of the columnar structure simply by changing the small molecular unit. When the macrocyclic unit lacks a cavity, columnar assembly gives strong pillars. Strong pillars with external functional groups such as basic lone pairs can expand like clays to accept guests between the pillars. Macrocycles that contain sizable interior cavities assemble into porous molecular crystals with aligned, well-defined columnar pores that are accessible to gases and guests. Herein, we examine the optimal design of the macrocyclic unit that leads to columnar assembly in high fidelity and probe the feasibility of incorporating a second functional group within the macrocycles. The porous molecular crystals prepared through the self-assembly of bis-urea macrocycles display surface areas similar to zeolites but lower than MOFs. Their simple one-dimensional channels are well-suited for studying binding, investigating transport, diffusion and exchange, and monitoring the effects of encapsulation on reaction mechanism and product distribution. Guests that complement the size, shape, and polarity of the channels can be absorbed into these porous crystals with repeatable stoichiometry to form solid host−guest complexes. Heating or extraction with an organic solvent enables desorption or removal of the guest and subsequent recovery of the solid host. Further, these porous crystals can be used as containers for the selective [2 + 2] cycloadditions of small enones such as 2-cyclohexenone or 3-methyl-cyclopentenone, while larger hosts bind and facilitate the photodimerization of coumarin. When the host framework incorporates benzophenone, a triplet sensitizer, UVirradiation in the presence of oxygen efficiently generates singlet oxygen. Complexes of this host were employed to influence the selectivity of photooxidations of 2-methyl-2-butene and cumene with singlet oxygen. Small systematic changes in the channel and bound reactants should enable systematic evaluation of the effects of channel dimensions, guest dimensions, and channel−guest interactions on the processes of absorption, diffusion, and reaction of guests within these nanochannels. Such studies could help in the development of new materials for separations, gas storage, and catalysis.
Materials and Methods Characterization of Compounds: All DPOA ligands were synthesized by the Dan... more Materials and Methods Characterization of Compounds: All DPOA ligands were synthesized by the Daniel Reger group and used as received. All TFDIB isomers and solvents were purchased from Oak Ridge Chemical®, Thermo Fisher Scientific®, VWR®, or TCI America® and were used as received without further. 1 HNMR spectra were recorded on a Bruker Avance III-HD spectrometer (300 MHz). Chemical shifts are reported as (δ ppm) with the corresponding integration values. High-resolution mass spectrum data was recorded using a direct exposure probe (DEP) in electron ionization (EI) mode on a Waters QTOF-I quadrupole time-of-flight mass spectrometer. FT-IR data was acquired. FT-IR spectra were obtained using a Perkin Elmer Spectrum 100 FT-IR Spectrometer. Background spectra were recorded from 650 to 4000 cm-1 and taken in 4 scans. The crystalline sample was then added to the sample stage until transmittance was less than 85%. 32 scans were then taken from 650 to 4000 cm-1 to obtain spectra. Crystal Growth. To obtain crystals of the parent ligands, the DPOA ligands (20 mg) were dissolved in a minimal volume of solvent, the solution was filtered, and left to slowly evaporate for 3-5 days until crystals formed. The co-crystals were synthesized by grinding 1:1 stoichiometric ratio of the TFDIB co-formers (29.6 mg, 0.07 mmol) and DPOA ligands (20 mg, 0.07 mmol) for approximately 2 min with 3-5 drops of CHCl3. Half of this mixture was added to a vial, and gently heated (when needed) in a minimal amount of solvent until completely dissolved. The samples were then allowed to slowly evaporate for 4-6 days until crystals were formed. The other half of the ground mixture dissolved in DMSO, and water was allowed to vapor diffuse into the solution for approximately 5 days until crystals formed. Both methods were repeated with multiple solvents until co-crystals were obtained. Crystal Structure Determination: X-ray intensity data was collected at 100(2) K using a Bruker D8 QUEST diffractometer equipped with a PHOTON-100 CMOS area detector and an Incoatec microfocus source (Mo Kα radiation, λ = 0.71073 Å). The raw area detector data frames were reduced and corrected for absorption effects using the Bruker APEX3, SAINT+ and SADABS programs. 1,2 Final unit cell parameters were determined by least-squares refinement of reflections taken from the data set. The structures were solved with SHELXT. 3 Subsequent difference Fourier calculations and full-matrix least-squares refinement against F 2 were performed with SHELXL-2016 3 using OLEX2. 4 Electrostatic Potential Calculations. Electrostatic potentials were calculated using Spartan 10' software package. The crystal structure files (CIFs) of the DPOA compounds were imported and energetically optimized. The energies were then calculated using DFT B3YLP level of theory, using a 6-311++G** basis set under vacuum. Electrostatic potentials for best donor and acceptor were determined using the electrostatic potential map (0.002 e a.u. isovalue) as automatically calculated by the Spartan 10' software. Electrostatic potentials of other donors and acceptors were obtained by manually searching the atom of interest until the value with the largest absolute value was found.
This thesis describes the use of polarized fluorescence microscopy to directly probe guest molecu... more This thesis describes the use of polarized fluorescence microscopy to directly probe guest molecule orientation in bis-urea macrocycle crystals. These macrocycles assemble to afford one-dimensional (1D) microchannels ∼9 Å in diameter that have previously been shown to exhibit normal Fickian diffusion and induce selective reactivity among the confined guest molecules. In the present work, we take advantage of the quasi-1D morphology of fiber-like microcrystals with the extended dimension corresponding to the channel axis to measure excitation and emission polarization values for a bithiophene guest. Guest fluorescence is shown to be polarized along the fiber axis with emission polarization values up to 0.729, indicating a high degree of orientational order within the 1D channels. The observed behavior is consistent with calculated results for the guest orientation and electronic transition dipole moment. The results indicate the value of functional fluorescent probes as a measure of guest confinement in low-dimensional environments. vi
Changing an ether to a ketone within the framework of a bisurea macrocycle has little effect on t... more Changing an ether to a ketone within the framework of a bisurea macrocycle has little effect on the supramolecular assembly of this building block into porous crystals but introduces a triplet sensitizer into the framework that dramatically alters the photochemical reactions of included guests.
Journal of the American Chemical Society, Jun 1, 2006
We report a highly selective 2 + 2 cycloaddition of 2-cyclohexenone in the presence of self-assem... more We report a highly selective 2 + 2 cycloaddition of 2-cyclohexenone in the presence of self-assembled bisurea macrocycles that yields the head-to-tail photodimer. The reaction proceeds with high conversion and with decreased incidence of secondary photorearrangement. Furthermore, the product can be extracted from the assembly, and the solid assembly is readily recovered and reused, much like a zeolite.
Journal of the American Chemical Society, Mar 25, 2010
Conjugated polymers have demonstrated utility in organic solar cells, 1 chemical sensors, 2 and o... more Conjugated polymers have demonstrated utility in organic solar cells, 1 chemical sensors, 2 and optoelectronics. 3 Microporous materials such as metal organic frameworks (MOFs) and zeolites show practical applications in gas storage, 4 separation, 5 catalysis, 6 and as confined environments for reactions. 7 MOFs and covalently linked organic frameworks 8 utilize transition metal ions or organic monomeric units to afford porous materials with high surface areas and excellent thermal stabilities. An alternate strategy for forming porous materials relies on the columnar assembly of molecular building blocks directed by noncovalent interactions. We sought to combine the attributes of a conjugated polymer with porous materials. Herein, we report a diacetylene macrocycle that was readily synthesized and self-assembled into columns to afford porous crystals (Figure 1). Heating initiated a topochemical polymerization of the preorganized diacetylene units to give covalent conjugated polydiacetylenes (PDAs). These stable conjugated materials maintained permanent porosity as evidenced by their type I gas adsorption isotherms with CO 2 (g). Conjugated porous PDAs could have applications for sensing and in electronics.
Intentional design of crystalline frameworks requires a good understanding of how inter-and intra... more Intentional design of crystalline frameworks requires a good understanding of how inter-and intramolecular forces act together to afford solid-state structures. Herein, we synthesize and crystallize bis-thiourea and bissquaramide m-xylene macrocycles and compare the conformational preferences of these functional groups as well as their assembled structures to their bis-urea counterpart. Four new crystal structures of the bis-thiourea macrocycle and the bissquaramide macrocycle are reported. The m-xylene macrocycles of urea, thiourea, and squaramide each display trans− trans conformers in their pure crystal forms. The thiourea macrocycles show edge to face interactions driven by sulfur bonding to afford 2D sheets. This macrocycle also shows an ethylene diamine solvate that displays both trans−trans and cis−trans conformers in the same structure. Solution 2D EXSY NMR studies suggest that these and additional conformations interconvert at room temperature. Squaramide macrocycles display 2D hydrogen bonding networks forming interdigitated cycles using only one of the two available carbonyls for hydrogen bonding. Additionally, the bis-squaramide macrocycle can crystallize as a solvate, where it maintains its original 2D framework with propylene carbonate imbedded in-between its layers. Overall, these findings help build a foundation for predicting how assembly motifs are modulated by macrocyclic building units.
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Papers by Linda Shimizu