Il Seung Youn

Selective fluorescent detection of RNA in living cells by using imidazolium-based cyclophane

A water-soluble imidazolium-based fluorescent chemosensor senses RNA selectively through fluorescence enhancement over other biologically relevant biomolecules in aqueous solution at physiological pH 7.4. Fluorescence image detection of RNA in living cells such as onion cells, HeLa cells, and animal model cells was successfully demonstrated which displays a chelation-enhanced fluorescence effect. These affinities can be attributed to the strong electrostatic (C-H)(+)···A(-) ionic H-bonding and the aromatic moiety driven π-stacking of imidazolium-based cyclophane with the size-complementary major groove of RNA.

A highly selective fluorescent chemosensor for guanosine-5?-triphosphate via excimer formation in aqueous solution of physiological pH

A new water-soluble and fluorescent imidazolium-anthracene cyclophane 1 effectively recognizes and differentiates the biologically important GTP and ATP in 100% aqueous solution of physiological pH 7.4. Fluorescence, (1)H-NMR spectra and ab initio calculations demonstrate that excimer formation and fluorescence enhancement occur upon GTP and ATP binding, respectively, through (C-H)(+)···A(-) hydrogen bond interactions.

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.

Precise tuning of cationic cyclophanes toward highly selective fluorogenic recognition of specific biophosphate anions

Cationic cyclophanes with bridging and spacer groups possess well-organized semirigid cavities and are able to encapsulate and stabilize anionic species through diverse molecular interactions. We highlight the precise tuning of functionalized cyclophanes toward selective recognition of AMP, GTP, and pyrophosphate (PPi) using fluorescence, NMR spectroscopy, and density functional theory (DFT).

Intercalation of Transition Metals into Stacked Benzene Rings: A Model Study of the Intercalation of Transition Metals into Bilayered Graphene.

Structures of neutral metal-dibenzene complexes, M(C6H6)2 (M = Sc-Zn), are investigated by using Møller-Plesset second order perturbation theory (MP2). The benzene molecules change their conformation and shape upon complexation with the transition metals. We find two types of structures: (i) stacked forms for early transition metal complexes and (ii) distorted forms for late transition metal ones. The benzene molecules and the metal atom are bound together by δ bonds which originate from the interaction of π-MOs and d orbitals. The binding energy shows a maximum for Cr(C6H6)2, which obeys the 18-electron rule. It is noticeable that Mn(C6H6)2, a 19-electron complex, manages to have a stacked structure with an excess electron delocalized. For other late transition metal complexes having more than 19 electrons, the benzene molecules are bent or stray away from each other to reduce the electron density around a metal atom. For the early transition metals, the M(C6H6) complexes are found to be more weakly bound than M(C6H6)2. This is because the M(C6H6) complexes do not have enough electrons to satisfy the 18-electron rule, and so the M(C6H6)2 complexes generally tend to have tighter binding with a shorter benzene-metal length than the M(C6H6) complexes, which is quite unusual. The present results could provide a possible explanation of why on the Ni surface graphene tends to grow in a few layers, while on the Cu surface the weak interaction between the copper surface and graphene allows for the formation of a single layer of graphene, in agreement with chemical vapor deposition experiments.

Selective detection of guanosine-5′-triphosphate and iodide by fluorescent benzimidazolium-based cyclophanes

New fluorescent benzimidazolium-based receptors selectively display the effective fluorescence quenching effect for biologically important anions, GTP and I(-), in aqueous solution of physiological pH 7.4. These affinities can be attributed to the strong ionic H-bonding along with additional interactions of fluorophore moieties with the nucleic base of GTP and I(-).

An imidazolium-based fluorescent cyclophane for the selective recognition of iodide.

For your Is only: A new imidazolium-based fluorescent cyclophane 1 was designed and synthesized that was quenched selectively in the presence of iodide but not other anions, as assessed by fluorimetry. In addition, fluorescence titration experiments, 1H NMR spectroscopic data, and theoretical calculations provide evidence that 1 encapsulates two iodides inside its cavity.

Turn‐On Ratiometric Fluorescent Probe for Selective Discrimination of Cr3+ from Fe3+ in Aqueous Media for Living Cell Imaging

Pyrene-based turn-on ratiometric fluorescent probe 1 demonstrates high sensitivity and exceptional selectivity toward Cr(3+) in the presence of other metals, including Fe(3+) in aqueous media. Interaction of Cr(3+) with probe 1 brings pyrene moieties close enough to have better aligned π-π stacking, thus enhancing the excimer peak many fold. On the other hand, the interaction of Fe(3+) with probe 1 brings forth a negligible difference in stacking, resulting in an insignificant change in fluorescence intensity. Exceptional selectivity of probe 1 with Cr(3+) over Fe(3+) and other metals has been confirmed by theoretical studies in addition to experimental results. Imaging of HeLa cells observed by confocal fluorescence microscopy reveals that probe 1 can be used to monitor Cr(3+) in live cells to map its subcellular distribution.

An efficient non-reaction based colorimetric and fluorescent probe for the highly selective discrimination of Pd0 and Pd2+ in aqueous media

A novel anthraquinone-imidazole based colorimetric and fluorogenic probe 1 is synthesized, which can discriminate the oxidation states of palladium (Pd0 and Pd2+) by naked eye with high selectivity in aqueous media owing to the difference in coordination within the right sized pocket of the probe molecule. The experimental results (fluorescence, UV/Vis and 1H NMR spectroscopy) aided by density functional theory (DFT) calculations reveal that charge transfer (CT) is the main cause of the selective detection of the oxidation states of palladium. In the 1–Pd2+ complex, which is deficient in electrons, all the electron transitions represent electron transfers from the probe molecule to the central metal atom i.e. partial ligand-to-metal transition excitation while electronically filled Pd0 shows electron transfers from the metal atom to the probe ligand i.e. partial metal-to-ligand transition excitation.

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.