Atomic imaging of zeolite-confined single molecules by electron microscopy.

Single-molecule imaging with atomic resolution is a notable method to study various molecular behaviours and interactions1-5. Although low-dose electron microscopy has been proved effective in observing small molecules6-13, it has not yet helped us achieve an atomic understanding of the basic physics and chemistry of single molecules in porous materials, such as zeolites14-16. The configurations of small molecules interacting with acid sites determine the wide applications of zeolites in catalysis, adsorption, gas separation and energy storage17-21. Here we report the atomic imaging of single pyridine and thiophene confined in the channel of zeolite ZSM-5 (ref. 22). On the basis of integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM)23-25, we directly observe the adsorption and desorption behaviours of pyridines in ZSM-5 under the in situ atmosphere. The adsorption configuration of single pyridine is atomically resolved and the S atoms in thiophenes are located after comparing imaging results with calculations. The strong interactions between molecules and acid sites can be visually studied in real-space images. This work provides a general strategy to directly observe these molecular structures and interactions in both the static image and the in situ experiment, expanding the applications of electron microscopy to the further study of various single-molecule behaviours with high resolution.

A single-molecule van der Waals compass.

Single-molecule imaging is challenging but highly beneficial for investigating intermolecular interactions at the molecular level1-6. Van der Waals interactions at the sub-nanometre scale strongly influence various molecular behaviours under confinement conditions7-11. Inspired by the traditional compass12, here we use a para-xylene molecule as a rotating pointer to detect the host-guest van der Waals interactions in the straight channel of the MFI-type zeolite framework. We use integrated differential phase contrast scanning transmission electron microscopy13-15 to achieve real-space imaging of a single para-xylene molecule in each channel. A good correlation between the orientation of the single-molecule pointer and the atomic structure of the channel is established by combining the results of calculations and imaging studies. The orientations of para-xylene help us to identify changes in the van der Waals interactions, which are related to the channel geometry in both spatial and temporal dimensions. This work not only provides a visible and sensitive means to investigate host-guest van der Waals interactions in porous materials at the molecular level, but also encourages the further study of other single-molecule behaviours using electron microscopy techniques.

Single-particle cryo-EM structures from iDPC-STEM at near-atomic resolution.

In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently computationally combined into a high-resolution three-dimensional structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC-STEM to two cryo-EM test specimens, keyhole limpet hemocyanin (KLH) and tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination for KLH at 6.5 Å resolution, as well as for TMV at 3.5 Å resolution using single-particle reconstruction methods, which share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. These data show that STEM imaging in general, and in particular the iDPC-STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules.

Differential phase contrast (DPC) mapping electric fields: Optimising experimental conditions.

DPC in Scanning Transmission Electron Microscopy (STEM) is a valuable method for mapping the electric fields in semiconductor materials. However, optimising the experimental conditions can be challenging. In this paper, we test and compare critical experimental parameters, including the convergence angle, camera length, acceleration voltage, sample configuration, and orientation using a four-quadrant segmented detector and a Si specimen containing layers of different As concentrations. The DPC measurements show a roughly linear correlation with the estimated electric fields, until the field gets close to the detection limitation, which is ∼0.5 mV/nm with a sample thickness of ∼145 nm. These results can help inform which technique to use for different user cases: When the electric field at a planar junction is above ∼0.5 mV/nm, DPC with a segmented detector is practical for electric field mapping. With a planar junction, the DPC signal-to-noise ratio can be increased by increasing the specimen thickness. However, for semiconductor devices with electric fields smaller than ∼0.5 mV/nm, or for devices containing curved junctions, DPC is unreliable and techniques with higher sensitivity will need to be explored, such as 4D STEM using a pixelated detector.

Rapid Access to Encapsulated Molecular Rotors via Coordination-Driven Macrocycle Formation.

Macrocycle formation that relies upon trans metal coordination of appropriately placed pyridine ligands within an arylene ethynylene construct provides rapid and reliable access to molecular rotators encapsulated within macrocyclic stators. Showing no significant close contacts to the central rotators, X-ray crystallography of AgI -coordinated macrocycles provides plausibility for unobstructed rotation or wobbling of rotators within the central cavity. Solid-state 13 C NMR of PdII -coordinated macrocycles supports the notion of unobstructed movement of simple arenes in the crystal lattice. Solution 1 H NMR studies indicate complete and immediate macrocycle formation upon the introduction of PdII to the pyridyl-based ligand at room temperature. Moreover, the formed macrocycle is stable in solution; a lack of significant changes in the 1 H NMR spectrum upon cooling to -50 °C is consistent with the absence of dynamic behavior. The synthetic route to these macrocycles is expedient and modular, providing access to rather complex constructs in four simple steps involving Sonogashira coupling and deprotection reactions.

Complementary, Cooperative Ditopic Halogen Bonding and Electron Donor-Acceptor π-π Complexation in the Formation of Cocrystals.

This study expands and combines concepts from two of our earlier studies. One study reported the complementary halogen bonding and π-π charge transfer complexation observed between isomeric electron rich 4-N,N-dimethylaminophenylethynylpyridines and the electron poor halogen bond donor, 1-(3,5-dinitrophenylethynyl)-2,3,5,6-tetrafluoro-4-iodobenzene while the second study elaborated the ditopic halogen bonding of activated pyrimidines. Leveraging our understanding on the combination of these non-covalent interactions, we describe cocrystallization featuring ditopic halogen bonding and π-stacking. Specifically, red cocrystals are formed between the ditopic electron poor halogen bond donor 1-(3,5-dinitrophenylethynyl)-2,4,6-triflouro-3,5-diiodobenzene and each of electron rich pyrimidines 2- and 5-(4-N,N-dimethyl-aminophenylethynyl)pyrimidine. The X-ray single crystal structures of these cocrystals are described in terms of halogen bonding and electron donor-acceptor π-complexation. Computations confirm that the donor-acceptor π-stacking interactions are consistently stronger than the halogen bonding interactions and that there is cooperativity between π-stacking and halogen bonding in the crystals.

Controlling Thermal Expansion in Supramolecular Halogen-Bonded Mixed Cocrystals through Synthetic Feed and Dynamic Motion.

Control over thermal expansion (TE) behaviors in solid materials is often accomplished by modifying the molecules or intermolecular interactions within the solid. Here, we use a mixed cocrystal approach and incorporate molecules with similar chemical structures, but distinct functionalities. Development of mixed cocrystals is at a nascent stage, and here we describe the first mixed cocrystals sustained by one-dimensional halogen bonds. Within each mixed cocrystal, the halogen-bond donor is fixed, while the halogen-bond acceptor site contains two molecules in a variable ratio. X-ray diffraction demonstrates isostructurality across the series, and SEM-EDS shows equal distribution of heavy atoms and similar atomic compositions across all mixed cocrystals. The acceptor molecules differ in their ability to undergo dynamic motion in the solid state. The synthetic equivalents of motion capable and incapable molecules were systematically varied to yield direct tunabililty in TE behavior.

Controlling Topology within Halogen-Bonded Networks by Varying the Regiochemistry of the Cyclobutane-Based Nodes.

The formation of a pair of extended networks sustained by halogen bonds based upon two regioisomers of a photoproduct, namely rctt-1,3-bis(4-pyridyl)-2,4-bis(phenyl)cyclobutane (ht-PP) and rctt-1,2-bis(4-pyridyl)-3,4-bis(phenyl)cyclobutane (hh-PP), that have varied topology is reported. These networks are held together via I⋯N halogen bonds between the photoproduct and the halogen-bond donor 1,4-diiodoperchlorobenzene (C6I2Cl4). The observed topology in each solid is controlled by the regiochemical position of the halogen-bond accepting 4-pyridyl group. This paper demonstrates the ability to vary the topology of molecular networks by altering the position of the halogen bond acceptor within the cyclobutane-based node.

Triple-Pnictogen Bonding as a Tool for Supramolecular Assembly.

Supramolecular assembly utilizing simultaneous formation of three pnictogen bonds around a single antimony vertex was explored via X-ray crystallography, solution NMR, and computational chemistry. An arylethynyl (AE) ligand was designed to complement the three electrophilic regions around the Sb compound. Though solution studies reveal large binding constants for individual pyridyl units with the Sb donor, the rigidity and prearrangement of the AE acceptor proved necessary to achieve simultaneous binding of three acceptors to the Sb-centered pnictogen-bond donor. Calculations and X-ray structures suggest that negative cooperativity upon sequential binding of three acceptors to a Sb center limits the utility of triple-pnictogen bonding pyridyl acceptors. These limitations can be negated, however, when positive cooperativity is designed into a complementary acceptor ligand.

Effects of Halogen and Hydrogen Bonding on the Electronics of a Conjugated Rotor.

The electronic properties of a pyrazine-containing arylene ethynylene unit are influenced by hydrogen bond and halogen bond donors that are held in proximity of the pyrazine rotor. These interactions are evident with iodine- and bromine-centered halogen bonds and O-H- and C-H-based hydrogen bonds. Bathochromic shifts of UV-vis and fluorescence signals are the best indicators of this intramolecular attraction. The effects can be attenuated in solvents that are less favorable for intramolecular halogen or hydrogen bonding, such as 2-propanol, and amplified in solvents that are supportive, such as toluene. Intramolecular attractions promote planarity in the pyrazine ethynylene system, likely increasing the effective conjugation of the unsaturated backbone. Additionally, computations at the B3LYP and M062X levels of theory using 6-311++G(2d,p) and aug-cc-pVTZ basis sets suggest that the Lewis acidity of the halogen and hydrogen atoms influences electronic behavior even in the absence of conformational constraints.

Intramolecular halogen bonding supported by an aryldiyne linker.

Intramolecular halogen bonds between aryl halide donors and suitable acceptors, such as carbonyl or quinolinyl groups, held in proximity by 1,2-aryldiyne linkers, provide triangular structures in the solid state. Aryldiyne linkers provide a nearly ideal template for intramolecular halogen bonding as minor deviations from alkyne linearity can accommodate a variety of halogen bonding interactions, including O···Cl, O···Br, O···I, N···Br, and N···I. Halogen bond lengths for these units, observed by single crystal X-ray crystallography, range from 2.75 to 2.97 Å. Internal bond angles of the semirigid bridge between halogen bond donor and acceptor are responsive to changes in the identity of the halogen, the identity of the acceptor, and the electronic environment around the halogen, with the triangles retaining almost perfect co-planarity in even the most strained systems. Consistency between experimental results and structures predicted by M06-2X/6-31G* calculations demonstrates the efficacy of this computational method for modeling halogen-bonded structures of this type.

Role of secondary interactions in a series of 2:1 halogen-bonded cocrystals formed between 4-(dimethylamino)pyridine and ditopic halogen-bond donors.

The structures of a series of 2:1 cocrystals formed between 4-(dimethylamino)pyridine and each of 1,2,4,5-tetrachloro-3,6-diiodobenzene, 2C7H10N2·C6Cl4I2, 1,2,4,5-tetrabromo-3,6-diiodobenzene, 2C7H10N2·C6Br4I2, 1-bromo-4-iodo-2,3,5,6-tetrafluorobenzene, 2C7H10N2·C6BrF4I, and 1,2-dibromo-4,5-difluoro-3,6-diiodobenzene, 2C7H10N2·C6Br2F2I2, are reported. In all five structures, the core halogen-bonded 2:1 trimolecular units have geometrically similar parameters, with the central halogen-bond donor flanked by two pyridine halogen-bond acceptors twisted with respect to the central halogen-bond donor at angles ranging from 76 to 86°. The I...N halogen-bond separations are all short, ranging from 73.3 to 76.7% of the sum of the van der Waals radii, while the C-I...N bond angles are essentially linear. The Br...N halogen-bond separation in the cocrystal formed with 1-bromo-4-iodo-2,3,5,6-tetrafluorobenzene is 80.4% of the sum of the van der Waals radii. Subtle differences in the crystal packings are attributed to the role of secondary C-H...π and weak π-type interactions with chloro and bromo substituents. The cocrystals 2C7H10N2·C6Cl4I2 and 2C7H10N2·C6Br4I2 are isomorphous.

Halogen-Bonded Supramolecular Parallelograms: From Self-Complementary Iodoalkyne Halogen-Bonded Dimers to 1:1 and 2:2 Iodoalkyne Halogen-Bonded Cocrystals.

The formation of supramolecular parallelograms utilizing iodoalkyne-pyridine halogen bonding is described. The crystal structures of four iodoalkynyl-substituted (phenylethynyl)pyridines demonstrate the feasibility of discrete self-complementary dimer formation. These compounds 3-(2-iodoethynyl-phenylethynyl) pyridine (1), 2-(3-iodoethynyl-phenylethynyl) pyridine (2), 3-(4,5-difluoro-2-iodoethynyl-phenylethynyl) pyridine (3), and 2-(5-iodoethynyl-2,4-dimethylphenylethynyl) pyridine (4) all form parallelogram-shaped dimers with two self-complementary short N-I halogen bonds. The potential formation of iodoalkynyl halogen-bonded supramolecular macrocycles is demonstrated by the formation of a discrete halogen-bonded parallelogram-shaped complex in the 1:1 cocrystal formed from the bis iodoalkyne, 1-iodoethynyl-2-(3-iodoethynyl-phenylethynyl)-4,5-dimethoxybenzene (6), and the dipyridyl, 5-phenyl-2-(pyridin-3-ylethynyl)pyridine (7). Furthermore, discrete supramolecular parallelograms form within the 2:2 cocrystal formed between 1,2-bis(iodoethynyl)-4,5-difluorobenzene and the dipyridyl 4-(3-pyridylethynyl) pyridine (8).

π-Complexation and C-H hydrogen bonding in the formation of colored cocrystals.

The present study evaluates the potential combination of charge-transfer electron-donor-acceptor π-π complexation and C-H hydrogen bonding to form colored cocrystals. The crystal structures of the red 1:1 cocrystals formed from the isomeric pyridines 4- and 3-{2-[4-(dimethylamino)phenyl]ethynyl}pyridine with 1-[2-(3,5-dinitrophenyl)ethynyl]-2,3,5,6-tetrafluorobenzene, both C14H4F4N2O4·C15H14N2, are reported. Intermolecular interaction energy calculations confirm that π-stacking interactions dominate the intermolecular interactions within each crystal structure. The close contacts revealed by Hirshfeld surface calculations are predominantly C-H interactions with N, O, and F atoms.

Co-crystal sustained by π-type halogen-bonding inter-actions between 1,4-di-iodo-perchloro-benzene and naphthalene.

The formation and crystal structure of a co-crystal based upon 1,4-di-iodo-perchloro-benzene (C6I2Cl4) as the halogen-bond donor along with naphthalene (nap) as the acceptor is reported. The co-crystal [systematic name: 1,2,4,5-tetra-chloro-3,6-di-iodo-benzene-naphthalene, (C6I2Cl4)·(nap)] generates a chevron-like structure that is held together primarily by π-type halogen bonds (i.e. C-I⋯π contacts) between the components. In addition, C6I2Cl4 also inter-acts with the acceptor via C-Cl⋯π contacts that help stabilize the co-crystal. Within the solid, both aromatic components are found to engage in offset and homogeneous face-to-face π-π stacking inter-actions. Lastly, the halogen-bond donor C6I2Cl4 is found to engage with neighboring donors by both Type I chlorine-chlorine and Type II iodine-chlorine contacts, which generates an extended structure.

Halogen-bonded co-crystal containing 1,3-di-iodo-perchloro-benzene and the photoproduct rtct-tetra-kis-(pyridin-4-yl)cyclo-butane resulting in a zigzag topology.

The formation and crystal structure of a zigzag network held together by I⋯N halogen bonds is reported. In particular, the halogen-bond donor is 1,3-di-iodo-perchloro-benzene (C6I2Cl4 ) while the acceptor is the photoproduct rtct-tetra-kis-(pyridin-4-yl)cyclo-butane (TPCB). Curiously, within the resulting co-crystal (C6I2Cl4 )·(TPCB), the photoproduct accepts only two halogen bonds between neighbouring 4-pyridyl rings and as a result behaves as a bent two-connected node rather than the expected four-connected centre. In addition, the photoproduct, TPCB, is also found to engage in C-H⋯N hydrogen bonds, forming an extended zigzag chain.

5-{[4-(Di-methyl-amino)-phen-yl]ethyn-yl}pyrimidine-1,2,3,5-tetra-fluoro-4,6-di-iodo-benzene (1/2).

The treatment of 5-{[4-(di-methyl-amino)-phen-yl]ethyn-yl}pyrimidine with a threefold excess of 1,2,3,5-tetra-fluoro-4,6-di-iodo-benzene in di-chloro-methane solution led to the formation of the unexpected 1:2 title co-crystal, C14H13N3·2CF4I2. In the extended structure, two unique C-I⋯N halogen bonds from one of the 1,2,3,5-tetra-fluoro-4,6-di-iodo-benzene mol-ecules to the pyrimidine N atoms of the 5-{[4-(di-methyl-amino)-phen-yl]ethyn-yl}pyrimidine mol-ecule generate [110] chains and layers of these chains are π-stacked along the a-axis direction. The second 1,2,3,5-tetra-fluoro-4,6-di-iodo-benzene mol-ecule resides in channels formed parallel to the a-axis direction between stacks of 5-{[4-(di-methyl-amino)-phen-yl]ethyn-yl}pyrimidine mol-ecules and inter-acts with them via C-I⋯π(alkyne) contacts.

Co-operative halogen bonds and nonconventional sp-C-H...O hydrogen bonds in 1:1 cocrystals formed between diethynylpyridines and N-halosuccinimides.

The rapid evaporation of 1:1 solutions of diethynylpyridines and N-halosuccinimides, that react together to form haloalkynes, led to the isolation of unreacted 1:1 cocrystals of the two components. The 1:1 cocrystal formed between 2,6-diethynylpyridine and N-iodosuccinimide (C4H4INO2·C9H5N) contains an N-iodosuccinimide-pyridine I...N halogen bond and two terminal alkyne-succinimide carbonyl C-H...O hydrogen bonds. The three-dimensional extended structure features interwoven double-stranded supramolecular polymers that are interconnected through halogen bonds. The cocrystal formed between 3,5-diethynylpyridine and N-iodosuccinimide (C4H4INO2·C9H5N) also features an I...N halogen bond and two C-H...O hydrogen bonds. However, the components form essentially planar double-stranded one-dimensional zigzag supramolecular polymers. The cocrystal formed between 3,5-diethynylpyridine and N-bromosuccinimide (C4H4BrNO2·C9H5N) is isomorphous to the cocrystal formed between 3,5-diethynylpyridine and N-iodosuccinimide, with a Br...N halogen bond instead of an I...N halogen bond.

A structural and computational comparison of close contacts and related intermolecular energies of interaction in the structures of 1,3-diiodo-5-nitrobenzene, 1,3-dibromo-5-nitrobenzene, and 1,3-dichloro-5-nitrobenzene.

1,3-Diiodo-5-nitrobenzene, C6H3I2NO2, and 1,3-dibromo-5-nitrobenzene, C6H3Br2NO2, crystallize in the centrosymmetric space group P21/m, and are isostructural with 1,3-dichloro-5-nitrobenzene, C6H3Cl2NO2, that has been redetermined at 100 K for consistency. While the three-dimensional packing in all three structures is similar, the size of the halogen atom affects the nonbonded close contacts observed between molecules. Thus, the structure of 1,3-diiodo-5-nitrobenzene features a close Type 1 I...I contact, the structure of 1,3-dibromo-5-nitrobenzene features a self-complementary nitro-O...Br close contact, while the structure of 1,3-dichloro-5-nitrobenzene also has a self-complementary nitro-O...Cl interaction, as well as a bifurcated C-H...O(nitro) close contact. Notably, the major energetically attractive intermolecular interaction between adjacent molecules in each of the three structures corresponds to a π-stacked interaction. The self-complementary halogen...O(nitro) and C-H...O(nitro) interactions correspond to significant cohesive attraction between molecules in each structure, while the Type 1 halogen-halogen contact is weakly cohesive.