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Current fluorescent probes for lysosomes have practical limits due to their pH sensitivity, which makes them unsuitable for long-term tracking of lysosomes in live cell imaging. In addition, viscosity probes are also responsive to polarity, which imposes considerable challenges in cellular imaging. Here, we report IQ-LVs, which can serve as viscosity sensors at the lysosomal pH. In contrast to the majority of current molecular rotors that exhibit blue and green emission, IQ-LVs showed red-shifted emission (∼95 nm) upon increasing the viscosity at pH 4.5. Among the synthesized viscosity sensors, IQ-LV57 and IQ-LV70 lacking an aromatic ring at R1 displayed 15-fold and 116-fold enhancement of red-shifted emission, respectively, upon changes in viscosity. They showed negligible polarity dependency, while the pH sensitivity was minimized by tuning R2 as we envisioned. Our 1D 1H-NMR titrations along with TCSPC analysis revealed that IQ-LVs exhibit two emissions in lysosomes, viscosity-insensitive green emission (+HA’-IQH+) and viscosity-sensitive red-shifted emission (A’-IQH+), which enabled live cell imaging for tracking lysosomes during the autophagy process. In fluorescence confocal imaging, the red emission was enhanced upon the increase in lysosomal viscosity in HeLa and MCF7 cells, and the observed emission from IQ-LV57 and IQ-LV70 had a longer duration than that of LysoTracker™ Deep Red in time-lapse images of live MCF7 cells. Furthermore, treatment of IQ-LV37 in MCF7 cells resulted in increased autophagosomes and autolysosomes during the autophagy process. Further western blot analysis revealed that IQ-LV37 and IQ-LV57 block the degradation of autophagosomes, serving as autophagy inhibitors.

The design and synthesis of the first asymmetrically “two-walled” meso-substituted calix[4]pyrrole tethered by a fluorophore and its subsequent implication as an archetype sequential ‘on–off–on–off’ fluorescent single-molecular switch are reported. The current system permits us to extend the sensitivity up to sub-nanomolar levels with the detection limit as low as 0.4 nM.

Three novel BODIPY-based heterodinuclear complexes, [salen(3,5-(t)Bu)2Al-(OC6H4-BODIPY)] (6), [salen(3,5-(t)Bu)2Al-(OC6F2H2-BODIPY)] (7), and [(mq)2Al-(OC6H4-BODIPY)] (8) (salen = N,N'-bis(salicylidene)ethylenediamine, BODIPY = 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene, and mq = methyl-8-quinolinolato) were prepared and characterized by multinuclear NMR spectroscopy. The specific structures of 6-8 were also determined by single crystal X-ray analysis. In particular, the salen-based heterodinuclear complexes 6 and 7 exhibited higher thermal stability (Td5 = 309 and 306 °C, respectively) than that of the closely related mononuclear aluminum or BODIPY compounds, except for 8. The UV/vis absorption and PL spectra for 6 and 7 indicated a significant photoinduced energy transfer from the aluminum-salen moiety to the BODIPY group in an intramolecular manner. Theoretical calculations revealed independent transition states of the aluminum-salen moiety or the BODIPY group in the Al(III)-BODIPY dyads, further supporting these experimental results.

Novel salen-Al/triarylborane dyad complexes were prepared and characterized with their corresponding mononuclear compounds. The UV–vis and photoluminescence experiments for dyads exhibited photoinduced energy transfer from borane to the salen-Al moiety in an intramolecular manner. Theoretical calculation and fluoride titration results further supported these intramolecular energy-transfer features.

In this study, the thermal denaturation mechanism and secondary structures of two types of human insulin nanoparticles produced by a process of solution-enhanced dispersion by supercritical fluids using dimethyl sulfoxide (DMSO) and ethanol (EtOH) solutions of insulin are investigated using spectroscopic approaches and molecular dynamics calculations. First, the temperature-dependent IR spectra of spherical and rod-shaped insulin nanoparticles prepared from DMSO and EtOH solution, respectively, are analyzed using principal component analysis (PCA) and 2D correlation spectroscopy to obtain a deeper understanding of the molecular structures and thermal behavior of the two insulin particle shapes. All-atom molecular dynamics (AAMD) calculations are performed to investigate the influence of the solvent molecules on the production of the insulin nanoparticles and to elucidate the geometric differences between the two types of nanoparticles. The results of the PCA, the 2D correlation spectroscopic analysis, and the AAMD calculations clearly reveal that the thermal denaturation mechanisms and the degrees of hydrogen bonding in the spherical and rod-shaped insulin nanoparticles are different. The polarity of the solvent might not alter the structure or function of the insulin produced, but the solvent polarity does influence the synthesis of different shapes of insulin nanoparticles.

Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na

transition by time-dependent density functional theory calculations. Potential energy surfacesof both the ground and electronically excited states were obtained employing quantum chemical calculations.It was suggested that the dissociation of OH from propiolic acid excited at 212 nm should take place along theS

Mass-analyzed threshold ionization (MATI) time-of-flight mass spectrometer using coherent vacuum ultraviolet (VUV) laser generated by four-wave difference frequency mixing (FWDFM) in Kr has been constructed and utilized to obtain the accurate ionization energy of acetone. From the MATI onsets measured from various applied pulsed fields, the ionization energy to the ionic ground state of acetone has been determined to be 9.7074 ± 0.0019 eV.

Pulsed lasers at the 613 nm and 1064 nm wavelengths on nanoseconds have been utilized to characterize the damage on Si photodiode exposed to intense illumination. Morphological damages and structural changes at sites on the photodiode irradiated during microseconds of laser pulses were analyzed by FE-SEM images and XRD patterns, respectively. The removal of oxide coating, ripple, melting marks, ridges, and crater on photodiodes were definitely observed in order of increasing the pulse intensities generated above the damage threshold. Then, the degradation in photosensitivity of the Si photodiode irradiated by high power density pulses was measured as a function of laser irradiation time at the various wavelengths. The free charge carrier and thermal diffusion mechanisms could have been invoked to characterize the damage. The relative photosensitivity data calculated using the thermal diffusion model proposed in this paper have been compared with the experimental data irradiated above the damage threshold.

the dehydration freeenergy barriers are not eliminated by an interaction between the anion and the peptide nanotube, leading to thehigh free energy barriers in the PMF profile. Calculations of the coordination numbers of the ions with oxygenatoms pertaining to either water molecules or carbonyl groups in the peptide nanotube reveal that thestabilization of the cations in the midplane regions of the nanotube arises from the favorable interaction of thecations with the negatively charged carbonyl oxygens.Key Words : Cyclic peptide nanotube, Ion selectivity, Molecular dynamics simulation, Potential of meanforce, Umbrella samplingIntroductionIon channels, which is a class of transmembrane proteins,have drawn great attention because they play a significantrole in nerve and muscle excitation, sensory transduction,and hormone secretion.

A supramolecular host-guest complex stimulated by lithium cation and fluoride anion, functioning as reliable fluorescence "Off-On-Off" switching system has been developed. Nonfluorescent, receptor-bound fluorophore is exclusively displaced by second guest, fluoride anion to release the fluorophore that becomes highly fluorescent in guest concentration dependent way. Again, this process is completely reversed upon exposure to Li + . The entire process is an excellent model for fluorescence-based logic system.

Photodissociation dynamics of allyl alcohol (H2C=CH-CH2OH) has been investigated at 205 - 213 nm along the UV absorption band by measuring rotationally-resolved laser-induced fluorescence spectra of OH radicals. Observed energy partitioning of the available energy among products at all photon energies investigated was similar and the barrier energy for OH production is about 574.7 kJ/mol from the OH yield measurements. The potential energy surfaces for the S0, T1, and S1 excited states along the dissociation coordinate were obtained by ab initio quantum chemical calculations. The observed energy partitioning was successfully modeled by the "barrier-impulsive model" with the reverse barrier and the geometry obtained by the calculated potential energy surfaces. The dissociation takes place on the T1 excited state potential energy surface with an energy barrier in the exit channel and a large portion of the photon energy is distributed in the internal degrees of freedom of the polyatomic products.

A series of nonequilibrium molecular dynamics(NEMD) simulations are performed to investigate the kinetic energy and velocity distributions of molecules in shock waves. In the simulations, argon molecules are used as a medium gas through which shock waves are propagating. The kinetic energy distribution profiles reveals that as a strong shock wave whose Mach number is 27.1 is applied, 39.6% of argon molecules inside the shock wave have larger kinetic energy than molecular ionization energy. This indicates that an application of a strong shock wave to argon gas can give rise to an intense light. The velocity distribution profiles in z direction along which shock waves propagate clearly represent two Maxwell-Boltzmann distributions of molecular velocities in two equilibrium regions and one bimodal velocity distribution profile that is attributed to a nonequilibrium region. The peak appearing in the directional temperature in z direction is discussed on a basis of the bimodal velocity distribution in the nonequilibrium region.

Three dithienosilole (DTS) derivatives bearing naphthyl segments, 5,5′-dinaphthyl-1,1-dimethyldithienosilol (1), 5,5′-dinaphthyl-1-methyl-1-phenyldithienosilole (2), and 5,5′-dinaphthyl-1,1-diphenyldithienosilol (3), are prepared through Pd(II)-catalyzed cross-coupling using an organoindium reagent as a nucleophile. The molecular structure of 3 is confirmed by single-crystal X-ray analysis. In addition, thermal, photophysical, and electrochemical properties for all three compounds are systematically investigated. The introduction of naphthyl segments into the DTS framework leads to an excellent enhancement of thermal stability with relatively high glass transition (Tg: 87 °C) and decomposition temperatures (Td: 320−380 °C). A red shift in both absorption and emission is observed in the DTS series as the 1,1-substituents on the ring silicon atom become more electronegative. On the basis of absorption spectra and DFT/TDDFT calculations, intense green photoluminescence observed for all compounds can be attri...

Photodissociation dynamics of propargyl alcohol (HC identical withC-CH(2)OH) at 212 nm in the gas phase was investigated by measuring rotationally resolved laser-induced fluorescence spectra of OH ((2)Pi) radicals exclusively produced in the ground electronic state. From the spectra, internal energies of OH and translational energy releases to products were determined. The electronic transition at 212 nm responsible for the OH dissociation was assigned as the pi(C[triple bond]C) --> pi*(C[triple bond]C) transition by time-dependent density functional theory calculations. In addition, an energy barrier at the exit channel along the reaction coordinate on the excited electronic potential energy surface was identified by ab initio calculations. The observed energy partitioning among the fragments was successfully modeled by the so-called "barrier-impulsive model".

CN) at 193 nm has been investigated by measuring rotationallyresolved laser induced fluorescence sp ectra of CN fragments, from which rotational population distributions ofCN as well as translational energy releases in the products were obtained. From quantum chemical molecularorbital calculations, a mixture of the n →π

Principal component analysis-based two-dimensional (PCA2D) correlation spectroscopy combined with the eigenvalue manipulating transformation (EMT) technique by lowering the power of a set of eigenvalues associated with the original data was applied to the temperature-dependent infrared-reflection absorption (IRRAS) spectra of spin-coated films of biodegradable P(HB-co-HHx) (HHx = 3.8, 7.2, and 10.0 mol%) copolymers. The PCA2D correlation spectra for P(HB-co-HHx) (HHx = 10.0 mol%) copolymer is completely different from those for P(HB-co-HHx) (HHx = 3.8 and 7.2 mol%) copolymers. In the synchronous PCA2D correlation spectra, the intensity changes of the bands at 1136 and 1282 cm−1 changed greatly as HHx mol% of P(HB-co-HHx) copolymers increases. Furthermore, EMT technique accentuates the contribution of intensity of band enhanced the minor PCs, seems to preferentially emphasizes the behavior of amorphous components of during the heating process.

Generic synthesis, identification of structural identity, unique prototropy and spectroscopic properties of meso-alkylidenyl-thia(m-benzi)porphyrinoid containing one exocyclic double bond at the meso-position were presented.

Mixed quantum-classical atomistic simulations have been carried out to investigate the mechanistic details of excited state intramolecular electron transfer in a betaine-30 molecule in acetonitrile. The key electronic degrees of freedom of the solute molecule are treated quantum mechanically using the semiempirical Pariser-Parr-Pople Hamiltonian, including the solvent influence on electronic structure. The intramolecular vibrational modes are also treated explicitly at a quantum level, with the remaining elements treated classically using empirical potentials. The electron-transfer rate, corresponding to S1 --S0 relaxation, is evaluated via time-dependent perturbation theory with the explicit inclusion of the dynamics of solvation and intramolecular conformation. The calculations reveal that, while solvation dynamics is critical to the rate, the intramolecular torsional dynamics also plays an important role. The importance of the use of multiple high-frequency quantum modes is also discussed.

In order to develop a more complete understanding of the limitations of mixed quantum-classical simulation methods, the origins of electronic dephasing are analyzed in a simple model of the condensed phase, namely, the spin-boson model with an ohmic spectral density. We focus on the decay of the thermally averaged nuclear overlap/phase function (NOPF). Considering the strong coupling/high temperature limit, a relationship is obtained at short time between the rate of electronic coherence loss and the electronic dephasing rate characteristic of a classical bath. Using this relationship, we clarify the origin of the decay of the NOPF. In the same limit, we also reproduce an earlier relationship between the electronic decoherence time and a solvation relaxation time. Finally, we point out that, for the spin-boson model, the exact quantum mechanical description of electronic dephasing is reproduced by mixed quantum/classical methods if a Gaussian distribution of quantum fluctuations around each classical phase space point is introduced. That spatial distribution of quantum fluctuations is functionally the same as that appearing in the Feynman-Kleinert variational local harmonic approximation, and also that implemented in existing classical trajectory-based estimates of coherence dissipation times.

Franck−Condon (FC) factors and the FC density associated with an electron transfer reaction are calculated for a betaine molecule, pyridinium-N-phenoxide betaine (4-(1-pyridinio)phenolate) in its S1 excited state. FC factors and density functions for harmonic vibrational modes are computed first by modifying the three level-fixed binary tree algorithm (Ruhoff, P. T.; Ratner, M. A. Int. J. Quant. Chem. 2000, 1, 383), a sum-over-states method based on recursion relations. This modified method allows the calculation of FC factors for 60 vibrational modes and avoids memory problems due to the large number of modes. The effects on the FC density of frequency shifts and mode mixing (Duschinky rotation) are included. For comparison, the more efficient time-dependent alternative is also employed for the calculation of the FC density function for the harmonic motion. In all cases, for a torsional motion which cannot be described by a harmonic potential, the FC density function is computed through the time-dependen...

E-mail: hlkim@kangwon.ac.krReceived November 14, 2011, Accepted December 2, 2011Key Words : Formic acid, Photodissociation dynamics, Laser induced fluorescence, H atomsChemistry of formic acid (HCOOH) is of fundamentalinterest because it is an important intermediate in oxidationof unsaturated hydrocarbons in combustion and the mostabundant organic pollutant in Earth's atmosphere. Structuresand dynamics of formic acid in the excited electronic statesare of special importance in understanding atmosphericchemistry. In UV, the absorption spectrum shows somevibrational structures superimposed by continuous absorp-tion starting from about 250 nm, which is assigned as the n→ π

A covalently coupled, dimeric tetra-cationic calix[4]pyrrolehomodimer bearing anthracene linkers displayed distinctive cooperativity and fluoride selectivity with positive allosterism. The exclusive and successive binding of fluoride anions is accompanied by large ‘turn-on’ fluorescence (K2/K1 = 311).

The impact of electronic decoherence on electronic dynamics, and electron transfer (ET) reactions in particular, in condensed phase environments is discussed. Analytical expressions are considered for a common model system in which ET occurs between relatively displaced harmonic surfaces. We identify a relationship in the semi-classical Marcus limit between electronic decoherence and the Wigner distribution of nuclear configurations. Generalization to more complex surfaces is discussed. Additionally, we discuss electronic decoherence for ET via so-called bridge sites in materials, for both direct (superexchange) mechanisms and sequential mechanisms of ET. Quantitative simulation studies of factors affecting characteristic decoherence times for ET in solution are also presented and discussed.

The vibrational spectrum of a pyrimidine cation in the ground electronic state was obtained using vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy. Accurate ionization energy of pyrimidine was determined from the 0-0 band position in the VUV-MATI spectrum and was measured by varying the PFI field to the zero field limit, which is 75,258 ± 7 cm(-1) (9.3308 eV). The spectrum displayed a large number of vibrational peaks, which could be nearly completely assigned through Franck-Condon analysis performed with variations of geometrical parameters at the B3LYP/cc-pVTZ level. Based on the excellent agreement between experimental and calculated results, the definite geometry of the pyrimidine cation in the ground electronic state was determined to be a planar structure with C2v symmetry with a decreased N-N distance in the ring.

In this study, we demonstrate the potentials and pitfalls of using various waterfall plots, such as conventional waterfall plots, two-dimensional (2D) gradient maps, moving window two-dimensional analysis (MW2D), perturbation-correlation moving window two-dimensional analysis (PCMW2D), and moving window principal component analysis two-dimensional correlation analysis (MWPCA2D), in the detection of the existence of band position shifts. Waterfall plots of the simulated spectral datasets are compared with conventional 2D correlation spectra. Different waterfall plots give different features in differentiating the behaviors of frequency shift versus two overlapped bands. Two-dimensional correlation spectra clearly show the very characteristic cluster pattern for both band position shifts and two overlapped bands. The vivid pattern differences are readily detectable in various waterfalls plots. Various types of waterfall plots of temperature-dependent infrared (IR) spectra of ethylene glycol, which does not have the actual band shift but only two overlapped bands, and of Fourier transform infrared (FT-IR) spectra of 2 wt% acetone in a mixed solvent of CHCl(3)/CCl(4) demonstrate that waterfall plots are not able to unambiguously detect the difference between real band shift and two overlapped bands. Thus, the presence or lack of the asynchronous 2D butterfly pattern seems like the most effective diagnostic tool for band shift detection.

Pd-catalyzed cross-coupling reactions of aryl iodides containing not only an electron-donating group but also an electron-withdrawing group on the aryl ring with organoindium reagents generated in situ from indium and ethyl 4-bromo-2-alkynoates produced selectively ethyl 2-aryl-2,3-alkadienoates in good yield.

E-mail: dkan@kangwon.ac.krReceived August 18, 2008Key Words : Diisobutylaluminum hydride (DIBALH), Aldehyde, Nitrile, Partial reduction, ChemoselectivityRecently, we have reported that a new class of reducingagents, metal diisobutyl-t-butoxyaluminum hydrides such aslithium diisobutyl-t-butoxyaluminum hydride (LDBBA)

Coarse-grained (CG) molecular dynamics (MD) simulations are performed to study the insertion of cyclic peptide nanotubes into cell membranes and to examine whether cyclic peptide nanotubes can function as an ion channel and thereby as an antibacterial agent. To do so, the two coarse-grained (CG) models for lipid molecules and for proteins developed by Marrink et al. (J. Phys. Chem. B 2004, 108, 750) and by Shih et al. (J. Phys. Chem. B 2006, 110, 3674), respectively, were extended and modified. These CG models were verified by performing CG MD and all-atom (AA) MD simulations for a cyclic peptide nanotube, 8 x cyclo[(-d-Ala-l-Glu-d-Ala-l-Gln-)2], in water and by comparing the results from the two simulations. Comparison between static and dynamic (water transport) properties obtained from both simulations shows good agreement. To study nanotube insertion, a CG cyclic peptide nanotube, 8 x cyclo[(-Trp-d-Leu-)4], was prepared above the surface of a CG DPPC lipid bilayer, restrained with constraints, and equilibrated, and then a series of CG MD simulations were carried out by lifting the constraints imposed on the nanotube. The CG MD simulations show that the cyclic peptide nanotube spontaneously inserts into and reorients inside the lipid bilayer. After insertion, the long axis of the cyclic peptide nanotube is aligned approximately perpendicular to the bilayer plane indicating that the nanotube can function as an ion channel and as an antibacterial agent. Tilt structures of the cyclic peptide nanotubes inside the lipid bilayer are found to be in agreement with experiment and earlier AA simulations. Lipid flip-flop, a migration of lipid molecules from one leaflet to the other leaflet of the lipid bilayer, is also observed from the CG MD simulations. Finally, the CG MD simulations reveal that a lipid headgroup can be inserted into the cyclic peptide nanotube. This process is confirmed by an AA MD simulation.

Ion current calculations based on Poisson-Nernst-Planck (PNP) theory are performed for a synthetic cyclic peptide nanotube that consists of eight or ten cyclo[(-L-Trp-D-Leu-)4] embedded in a lipid bilayer membrane to investigate the ion transport properties of the nanotube. To explore systems with arbitrary geometries, three-dimensional PNP theory is implemented using a finite difference method. The influence of dipolar lipid molecules on the ion currents is also examined by turning on or off the charges of the lipid dipoles in dipalmitoylphosphatidylcholine (DPPC). Comparisons between the calculated and experimentally measured ion currents show that the PNP approach agrees well with the measurements at low ion concentrations but overestimates the currents at higher concentrations. Concentration profiles reveal the selectivity of the peptide nanotube to cations, which is attributed to the negatively charged carbonyl oxygens inside the nanotube. The dominant cation and the minimum anion concentrations inside the cyclic peptide nanotube suggest that these cyclic peptide nanotubes can be employed as ion sensors. In the case of the polar DPPC bilayer, smaller currents are obtained in the calculation. The variation of current with polarity of the lipids implies that both polar and nonpolar lipid bilayer membranes can be utilized to regulate ion currents in the peptide nanotube and other ion channels. Strengths and limitations of the PNP theory are also discussed.

E-mail: dkan@kangwon.ac.krReceived August 18, 2008Key Words : Diisobutylaluminum hydride (DIBALH), Aldehyde, Nitrile, Partial reduction, ChemoselectivityRecently, we have reported that a new class of reducingagents, metal diisobutyl-t-butoxyaluminum hydrides such aslithium diisobutyl-t-butoxyaluminum hydride (LDBBA)

A new bis-pyridinium calix[4]pyrrole derivative is reported. This system forms a non-fluorescent complex upon exposure to the chromenolate anion. The resulting supramolecular ensemble binds the pyrophosphate anion with high affinity (Ka = (2.55 ± 0.12) × 107 M−1) in acetonitrile. It exhibits sensitive “turn-on” fluorescence when exposed to tetrabutylammonium pyrophosphate, and does so in preference to other anions, including the fluoride and phosphate anions.

Three new organic dyes that contain the dithienosilole (DTS) moiety as spacer have been synthesized and their photophysical/electrochemical properties, theoretical calculation and dye-sensitized solar cell (DSSC) performance have been investigated. The overall conversion efficiencies for DSSCs based on these dyes range from 6.73 to 7.50%, comparable to a (3–5′-[N,N-bis(9,9-dimethylfluorene-2-yl)phenyl]2,2′-bithiophene-5-yl}-2-cyanoacrylic acid (JK-2)-sensitized device (7.63%), fabricated and measured under the same experimental conditions. The DSSC constructed from one of the three compounds shows a higher open-circuit voltage (VOC) compared to those of the other two dye sensitized solar cells due to an increased electron lifetime (τe) in the conduction band of TiO2.

One of the most fundamental challenges in biochemistry and biophysics is describing the function of ion channels, proteins that control ion transport across cell membranes. One approach to this problem is the application of Poisson�Nernst�Planck (PNP) theory. In practice, applying PNP theory involves creating a computational model of the ion channel and generating a numerical solution of differential equations that describes ion transport and electrostatic interactions. The PNP Cyclic Peptide Ion Channel Model is a simulation tool designed to offer an integrated approach to this important problem in bionanotechnology by demonstrating and explaining the application of PNP theory in a way that is accessible to students at an upper undergraduate level. The program interface was made using the free Rapid Application Infrastructure (Rappture) software made available by the Network for Computational Nanotechnology (NCN). Rappture is designed specifically for Web-based applications. Here we introduce a free version of the PNP Cyclic Peptide Ion Channel Model for use in the simulation of ion transport properties for a model ion channel structure that has been the subject of recent experiments.