High-temperature in situ crystallographic observation of reversible gas sorption in impermeable organic cages.

Crystallographic observation of adsorbed gas molecules is a highly difficult task due to their rapid motion. Here, we report the in situ single-crystal and synchrotron powder X-ray observations of reversible CO2 sorption processes in an apparently nonporous organic crystal under varying pressures at high temperatures. The host material is formed by hydrogen bond network between 1,3,5-tris-(4-carboxyphenyl)benzene (H3BTB) and N,N-dimethylformamide (DMF) and by π-π stacking between the H3BTB moieties. The material can be viewed as a well-ordered array of cages, which are tight packed with each other so that the cages are inaccessible from outside. Thus, the host is practically nonporous. Despite the absence of permanent pathways connecting the empty cages, they are permeable to CO2 at high temperatures due to thermally activated molecular gating, and the weakly confined CO2 molecules in the cages allow direct detection by in situ single-crystal X-ray diffraction at 323 K. Variable-temperature in situ synchrotron powder X-ray diffraction studies also show that the CO2 sorption is reversible and driven by temperature increase. Solid-state magic angle spinning NMR defines the interactions of CO2 with the organic framework and dynamic motion of CO2 in cages. The reversible sorption is attributed to the dynamic motion of the DMF molecules combined with the axial motions/angular fluctuations of CO2 (a series of transient opening/closing of compartments enabling CO2 molecule passage), as revealed from NMR and simulations. This temperature-driven transient molecular gating can store gaseous molecules in ordered arrays toward unique collective properties and release them for ready use.

Effects of an electric field on interaction of aromatic systems.

The effect of uniform external electric field on the interactions between small aromatic compounds and an argon atom is investigated using post-HF (MP2, SCS-MP2, and CCSD(T)) and density functional (PBE0-D3, PBE0-TS, and vdW-DF2) methods. The electric field effect is quantified by the difference of interaction energy calculated in the presence and absence of the electric field. All the post-HF methods describe electric field effects accurately although the interaction energy itself is overestimated by MP2. The electric field effect is explained by classical electrostatic models, where the permanent dipole moment from mutual polarization mainly determines its sign. The size of π-conjugated system does not have significant effect on the electric field dependence. We found out that PBE0-based methods give reasonable interaction energies and electric field response in every case, while vdW-DF2 sometimes shows spurious artifact owing to its sensitivity toward the real space electron density.

Halogen-π Interactions between Benzene and X2/CX4 (X = Cl, Br): Assessment of Various Density Functionals with Respect to CCSD(T).

Various types of interactions between halogen (X) and π moiety (X-π interaction) including halogen bonding play important roles in forming the structures of biological, supramolecular, and nanomaterial systems containing halogens and aromatic rings. Furthermore, halogen molecules such as X2 and CX4 (X = Cl/Br) can be intercalated in graphite and bilayer graphene for doping and graphene functionalization/modification. Due to the X-π interactions, though recently highly studied, their structures are still hardly predictable. Here, using the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)), the Møller-Plesset second-order perturbation theory (MP2), and various flavors of density functional theory (DFT) methods, we study complexes of benzene (Bz) with halogen-containing molecules X2 and CX4 (X = Cl/Br) and analyze various components of the interaction energy using symmetry adapted perturbation theory (SAPT). As for the lowest energy conformers (S1), X2-Bz is found to have the T-shaped structure where the electropositive X atom-end of X2 is pointing to the electronegative midpoint of CC bond of the Bz ring, and CX4-Bz has the stacked structure. In addition to this CX4-Bz (S1), other low energy conformers of X2-Bz (S2/S3) and CX4-Bz (S2) are stabilized primarily by the dispersion interaction, whereas the electrostatic interaction is substantial. Most of the density functionals show noticeable deviations from the CCSD(T) complete basis set (CBS) limit binding energies, especially in the case of strongly halogen-bonded conformers of X2-Bz (S1), whereas the deviations are relatively small for CX4-Bz where the dispersion is more important. The halogen bond shows highly anisotropic electron density around halogen atoms and the DFT results are very sensitive to basis set. The unsatisfactory performance of many density functionals could be mainly due to less accurate exchange. This is evidenced from the good performance by the dispersion corrected hybrid and double hybrid functionals. B2GP-PLYP-D3 and PBE0-TS(Tkatchenko-Scheffler)/D3 are well suited to describe the X-π interactions adequately, close to the CCSD(T)/CBS binding energies (within ∼1 kJ/mol). This understanding would be useful to study diverse X-π interaction driven structures such as halogen containing compounds intercalated between 2-dimensional layers.

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Limit of metastability for liquid and vapor phases of water.

We report the limits of superheating of water and supercooling of vapor from Monte Carlo simulations using microscopic models with configurational enthalpy as the order parameter. The superheating limit is well reproduced. The vapor is predicted to undergo spinodal decomposition at a temperature of Tspvap=46±10 °C (0 °C≪Tspvap≪100 °C) under 1 atm. The water-water network begins to form at the supercooling limit of the vapor. Three-dimensional water-water and cavity-cavity unbroken networks are interwoven at critically superheated liquid water; if either network breaks, the metastable state changes to liquid or vapor.

Association between cancer genes and germ layer specificity.

Cancer signaling pathways defining cell fates are related to differentiation. During the developmental process, three germ layers (endoderm, mesoderm, and ectoderm) are formed during embryonic development that differentiate into organs via the epigenetic regulation of specific genes. To examine the relationship, the specificities of cancer gene mutations that depend on the germ layers are studied. The major organs affected by cancer were determined based on statistics from the National Cancer Information Center of Korea, and were grouped according to their germ layer origins. Then, the gene mutation frequencies were evaluated to identify any bias based on the differentiation group using the Catalogue of Somatic Mutations in Cancer (COSMIC) database. The chi-square test showed that the p-value of 152 of 166 genes was less than 0.05, and 151 genes showed p-values of less than 0.05 even after adjusting for the false discovery rate (FDR). The germ layer-specific genes were evaluated using visualization based on basic statistics, and the results matched the top ranking genes depending on organs in the COSMIC database.The current study confirmed the germ layer specificity of major cancer genes. The germ layer specificity of mutated driver genes is possibly important in cancer treatments because each mutated gene may react differently depending on the germ layer of origin. By understanding the mechanism of gene mutation in the development and progression of cancer in the context of cell-fate pathways, a more effective therapeutic strategy for cancer can be established.

Chromium porphyrin arrays as spintronic devices.

Spintronic devices are very important for futuristic information technology. Suitable materials for such devices should have half-metallic properties so that only one spin passes through the device. In particular, organic half metals have the advantage that they may be used for flexible devices and have a long spin-coherence length. We predict that the one-dimensional infinite chromium porphyrin array, which we call Cr-PA(∞), shows half-metallic behavior when the spins on the chromium atoms are in a parallel alignment. Since the chromium atoms are separated by a large distance (>8 Å), the coupling between spins is small and thus their directions can be readily controlled by an external magnetic field. In the ferromagnetic state, the band gap for major spin electrons is 0.30 eV, while there is no band gap for the minor spin electrons, thus reflecting the half-metallic property. This unique property originates from the high spin state of Cr which results in the spin asymmetry of the conduction band in Cr-PA(∞). Electron transport of Cr-PA(1,2,3) is calculated with the nonequilibrium Green function technique in the presence of Au electrodes. It turned out that the spin-filtering ability appears from the dimeric Cr-PA(2). Thus, a new organometallic framework for designing a spin filter is proposed. Though many others have designed novel spintronic devices, none of them are realized due to the lack of a practical fabrication method at present. However, the porphyrin-based spintronic device provides a synthesizable framework.

Spectromicroscopic observation of a live single cell in a biocompatible liquid-enclosing graphene system.

On-the-spot visualization of biochemical responses of intact live cells is vital for a clear understanding of cell biology. The main obstacles for instant visualization of biochemical responses of living cells arise from the lack of a sophisticated detecting technique which can simultaneously provide chemical analysis tools and the biocompatible wet conditions. Here we introduce scanning transmission X-ray microscopy (STXM) combined with a liquid-enclosing graphene system (LGS), offering biocompatible conditions and improved X-ray absorption spectra to probe the chemical responses of live cells under wet conditions. This set-up enables us to probe a subtle change in absorption spectra depending on the oxidation state of a miniscule amount of oxygen in the functional groups present in each cell and its surroundings containing a minimal amount of liquid water. As an example of in situ biochemical responses of wet cells, chemical responses of a single Colo 205 cell are visualized and analyzed using X-ray absorption near the oxygen K-edge. This spectromicroscopic method using LGS can be applied to diverse biological samples under wet conditions for the analysis of their biochemical responses.

Efficient CO Oxidation by 50-Facet Cu2O Nanocrystals Coated with CuO Nanoparticles.

As carbon monoxide oxidation is widely used for various chemical processes (such as methanol synthesis and water-gas shift reactions H2O + CO ⇄ CO2 + H2) as well as in industry, it is essential to develop highly energy efficient, inexpensive, and eco-friendly catalysts for CO oxidation. Here we report green synthesis of ∼10 nm sized CuO nanoparticles (NPs) aggregated on ∼400 nm sized 50-facet Cu2O polyhedral nanocrystals. This CuO-NPs/50-facet Cu2O shows remarkable CO oxidation reactivity with very high specific CO oxidation activity (4.5 µmolCO m-2 s-1 at 130 °C) and near-complete 99.5% CO conversion efficiency at ∼175 °C. This outstanding catalytic performance by CuO NPs over the pristine multifaceted Cu2O nanocrystals is attributed to the surface oxygen defects present in CuO NPs which facilitate binding of CO and O2 on their surfaces. This new material opens up new possibilities of replacing the usage of expensive CO oxidation materials.

Minor Structural Variations of Small Molecules Tune Regulatory Activities toward Pathological Factors in Alzheimer's Disease.

Chemical tools have been valuable for establishing a better understanding of the relationships between metal ion dyshomeostasis, the abnormal aggregation and accumulation of amyloid-ß (Aß), and oxidative stress in Alzheimer's disease (AD). Still, very little information is available to correlate the structures of chemical tools with specific reactivities used to uncover such relationships. Recently, slight structural variations to the framework of a chemical tool were found to drastically determine the tool's reactivities toward multiple pathological facets to various extents. Herein, we report our rational design and characterization of a structural series to illustrate the extent to which the reactivities of small molecules vary toward different targets as a result of minor structural modifications. These compounds were rationally and systematically modified based on consideration of properties, including ionization potentials and metal binding, to afford their desired reactivities with metal-free or metal-bound Aß, reactive oxygen species (ROS), and free organic radicals. Our results show that although small molecules are structurally similar, they can interact with multiple factors associated with AD pathogenesis and alleviate their reactivities to different degrees. Together, our studies demonstrate the rational structure-directed design that can be used to develop chemical tools capable of regulating individual or interrelated pathological features in AD.

Accelerated Bone Regeneration by Two-Photon Photoactivated Carbon Nitride Nanosheets.

Human bone marrow-derived mesenchymal stem cells (hBMSCs) present promising opportunities for therapeutic medicine. Carbon derivatives showed only marginal enhancement in stem cell differentiation toward bone formation. Here we report that red-light absorbing carbon nitride (C3N4) sheets lead to remarkable proliferation and osteogenic differentiation by runt-related transcription factor 2 (Runx2) activation, a key transcription factor associated with osteoblast differentiation. Accordingly, highly effective hBMSCs-driven mice bone regeneration under red light is achieved (91% recovery after 4 weeks compared to 36% recovery in the standard control group in phosphate-buffered saline without red light). This fast bone regeneration is attributed to the deep penetration strength of red light into cellular membranes via tissue and the resulting efficient cell stimulation by enhanced photocurrent upon two-photon excitation of C3N4 sheets near cells. Given that the photoinduced charge transfer can increase cytosolic Ca2+ accumulation, this increase would promote nucleotide synthesis and cellular proliferation/differentiation. The cell stimulation enhances hBMSC differentiation toward bone formation, demonstrating the therapeutic potential of near-infrared two-photon absorption of C3N4 sheets in bone regeneration and fracture healing.

Halides with Fifteen Aliphatic C-H···Anion Interaction Sites.

Since the aliphatic C-H···anion interaction is relatively weak, anion binding using hydrophobic aliphatic C-H (Cali-H) groups has generally been considered not possible without the presence of additional binding sites that contain stronger interactions to the anion. Herein, we report X-ray structures of organic crystals that feature a chloride anion bound exclusively by hydrophobic Cali-H groups. An X-ray structure of imidazolium-based scaffolds using Cali-H···A(-) interactions (A(-) = anion) shows that a halide anion is directly interacting with fifteen Cali-H groups (involving eleven hydrogen bonds, two bidentate hydrogen-bond-type binding interactions and two weakly hydrogen-bonding-like binding interactions). Additional supporting interactions and/or other binding sites are not observed. We note that such types of complexes may not be rare since such high numbers of binding sites for an anion are also found in analogous tetraalkylammonium complexes. The Cali-H···A(-) interactions are driven by the formation of a near-spherical dipole layer shell structure around the anion. The alternating layers of electrostatic charge around the anion arise because the repulsions between weakly positively charged H atoms are reduced by the presence of the weakly negatively charged C atoms connected to H atoms.

Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease.

The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-ß (Aß), metal-Aß, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

Intriguing Electrostatic Potential of CO: Negative Bond-ends and Positive Bond-cylindrical-surface.

The strong electronegativity of O dictates that the ground state of singlet CO has positively charged C and negatively charged O, in agreement with ab initio charge analysis, but in disagreement with the dipole direction. Though this unusual phenomenon has been fairly studied, the study of electrostatic potential (EP) for noncovalent interactions of CO is essential for better understanding. Here we illustrate that both C and O atom-ends show negative EP (where the C end gives more negative EP), favoring positively charged species, whereas the cylindrical surface of the CO bond shows positive EP, favoring negatively charged ones. This is demonstrated from the interactions of CO with Na(+), Cl(-), H2O, CO and benzene. It can be explained by the quadrupole driven electrostatic nature of CO (like N2) with very weak dipole moment. The EP is properly described by the tripole model taking into account the electrostatic multipole moments, which has a large negative charge at a certain distance protruded from C, a large positive charge on C, and a small negative charge on O. We also discuss the EP of the first excited triplet CO.

Graphene edges and beyond: temperature-driven structures and electromagnetic properties.

The atomic configuration of graphene edges significantly influences the various properties of graphene nanostructures, and realistic device fabrication requires precise engineering of graphene edges. However, the imaging and analysis of the intrinsic nature of graphene edges can be illusive due to contamination problems and measurement-induced structural changes to graphene edges. In this issue of ACS Nano, He et al. report an in situ heating experiment in aberration-corrected transmission electron microscopy to elucidate the temperature dependence of graphene edge termination at the atomic scale. They revealed that graphene edges predominantly have zigzag terminations below 400 °C, while above 600 °C, the edges are dominated by armchair and reconstructed zigzag edges. This report brings us one step closer to the true nature of graphene edges. In this Perspective, we outline the present understanding, issues, and future challenges faced in the field of graphene-edge-based nanodevices.

Anisotropic charge distribution and anisotropic van der Waals radius leading to intriguing anisotropic noncovalent interactions.

Although group (IV-VII) nonmetallic elements do not favor interacting with anionic species, there are counterexamples including the halogen bond. Such binding is known to be related to the charge deficiency because of the adjacent atom's electron withdrawing effect, which creates σ/π-holes at the bond-ends. However, a completely opposite behavior is exhibited by N2 and O2, which have electrostatically positive/negative character around cylindrical-bond-surface/bond-ends. Inspired by this, here we elucidate the unusual features and origin of the anisotropic noncovalent interactions in the ground and excited states of the 2(nd) and 3(rd) row elements belonging to groups IV-VII. The anisotropy in charge distributions and van der Waals radii of atoms in such molecular systems are scrutinized. This provides an understanding of their unusual molecular configuration, binding and recognition modes involved in new types of molecular assembling and engineering. This work would lead to the design of intriguing molecular systems exploiting anisotropic noncovalent interactions.

Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition.

Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.