Multiscale Modeling Approach for the Aldol Addition Reaction in Multicompartment Micelle-Based Nanoreactor.

Water has emerged as a versatile solvent for organic chemistry in recent years due to its abundance, low cost, and environmental friendliness. However, one of the most important reactions, the aldol reaction, in the presence of excess water exhibits low yields and poor enantioselectivities. In this regard, we have employed a multiscale modeling approach to investigate the aldol addition reaction catalyzed by l-proline in the hydrophobic compartment of multicompartment micelle (MCM) nanoreactor consisting of amphiphilic bottlebrush copolymer, which minimizes the water content at the reactive site. Through performing dissipative particle dynamics (DPD) simulation, it is found that the "clover-like" morphology of the MCM is formed from multiblock copolymer with a sequence of ethylene oxide-based hydrophilic blocks, styrene lipophilic blocks, l-proline catalyst blocks, and a pentafluorostyrene fluorophilic block in aqueous media. We find that the vicinity of the catalyst in the clover-like MCM has a low dielectric environment, which could facilitate the aldol addition reaction. Our DFT calculations demonstrate that the asymmetric aldol addition of l-proline-catalyzed acetone and 4-nitrobenzaldehyde is energetically more favorable under the low dielectric environment in MCM compared with other commonly used solvents such as DMSO, water, and vacuum condition.

Association between body mass index and fitness in Korean adults according to the lump mean value and Gaussian fitting.

The aim of this study was to determine the body mass index (BMI) for the best fitness and effective exercise. This study analyzed data from the Korean national fitness assessment by the Korea Institute of Sport Science (2017). The fitness tests considered were sit-up, standing long jump (SLJ), 20-m multi-stage shuttle run (20-m MSSR), and 10-m shuttle run (10-m SR) tests. The BMIs for the best fitness and widths of the fitness distributions were calculated using the lump mean value and Gaussian fitting. The values of BMI (kg/m2) associated with the best sit-up, SLJ, 20-m MSSR, and 10-m SR scores were 23.4, 22.6, 22.2, and 22.6 for males and 19.0, 18.5, 18.6, and 18.6 for females. The widths (kg/m2) of the sit-up, SLJ, 20-m MSSR, and 10-m SR distributions were 3.65, 3.42, 3.73, and 2.86 for males and 4.84, 4.88, 4.45, and 4.35 for females. The results show that the BMI can be reduced the most and fitness can be increased effectively by the 20-m MSSR for males and the SLJ for females, which could be used to establish personal exercise aims.

Experimental and numerical evaluation of a genetically engineered M13 bacteriophage with high sensitivity and selectivity for 2,4,6-trinitrotoluene.

Selective and sensitive detection of desired targets is very critical in sensor design. Here, we report a genetically engineered M13 bacteriophage-based sensor system evaluated by quantum mechanics (QM) calculations. Phage display is a facile way to develop the desired peptide sequences, but the resulting sequences can be imperfect peptides for binding of target molecules. A TNT binding peptide (WHW) carrying phage was self-assembled to fabricate thin films and tested for the sensitive and selective surface plasmon resonance-based detection of TNT molecules at the 500 femtomole level. SPR studies performed with the WHW peptide and control peptides (WAW, WHA, AHW) were well-matched with those of the QM calculations. Our combined method between phage engineering and QM calculation will significantly enhance our ability to design selective and sensitive sensors.

The Effect of Precursor Composition on the Structural Properties of Nanocrystalline Diamond Films.

Nanocrystalline diamond (NCD) films were grown by hot filament CVD and the precursor composition dependence of the structural properties was examined. Films grown at 1 and 2 CH4 Vol% were found to be NCD layers with grain sizes of ~23-25 nm while films grown at 3-5 Vol% were identified as the mixtures of microcrystalline diamond and graphitic phase. The sp2/sp3 bonded carbon ratio in the grown films increased as the CH4 content increased up to 3 Vol% and then decreased beyond 4 Vol%. Microstructure and deposition rate were also found to be affected by the precursor composition and the NCD film grown at 1 CH4 Vol% showed a very dense microstructure and the highest deposition rate of ~3 nm/min.

Very Smooth Ultrananocrystalline Diamond Film Growth by a Novel Pretreatment Technique.

Very smooth ultrananocrystalline diamond (UNCD) film growth on SiC substrate was achieved by a novel pretreatment technique consisted of SiC surface texturing and deaggregation of nanodiamond (ND) seed particles. Texturing of SiC surfaces in Ar and SF6/02 plasmas was found to be able to provide normalized roughness values of 0.5-7.0 compared to the untreated surface. SiC surface plasma-textured and seeded with H2 heat-treated ND particles at 600 degrees C showed the highest nucleation density of ~44.2 x 10(11) cm(-2) and a highly uniform coverage of surface with very fine ND seeds. The UNCD film grown with this new pretreatment technique showed a very smooth surface morphology consisted of small and uniformly distributed grains.

Synthesis of Gold Nanoparticles with Buffer-Dependent Variations of Size and Morphology in Biological Buffers.

The demand for biologically compatible and stable noble metal nanoparticles (NPs) has increased in recent years due to their inert nature and unique optical properties. In this article, we present 11 different synthetic methods for obtaining gold nanoparticles (Au NPs) through the use of common biological buffers. The results demonstrate that the sizes, shapes, and monodispersity of the NPs could be varied depending on the type of buffer used, as these buffers acted as both a reducing agent and a stabilizer in each synthesis. Theoretical simulations and electrochemical experiments were performed to understand the buffer-dependent variations of size and morphology exhibited by these Au NPs, which revealed that surface interactions and the electrostatic energy on the (111) surface of Au were the determining factors. The long-term stability of the synthesized NPs in buffer solution was also investigated. Most NPs synthesized using buffers showed a uniquely wide range of pH stability and excellent cell viability without the need for further modifications.

Picosecond dynamics of photoexcited DNO-bound myoglobin probed by femtosecond vibrational spectroscopy.

Like nitric oxide (NO), nitroxyl (HNO), a reduced form of NO, plays many biologically important roles including neurological function and vascular regulation. Although HNO is unstable in aqueous solution, it is exceptionally stable on binding to ferrous myoglobin (Mb) to form MbHNO. Various experimental and theoretical investigations has been carried out to unveil the structure of the active site and binding characteristics of MbHNO that can explain its functioning mechanism and the origin of its unusual stability. However, the binding dynamics of HNO to Mb, as well as the photochemical and photophysical processes associated with binding, have not been fully established. Herein, femtosecond vibrational spectroscopy was used to probe the photoexcitation dynamics of excited MbDNO in D2O solution at 294 K with a 575 nm pulse. Time-resolved spectra were described by three vibrational bands near 1380 cm(-1), in the expected N-O stretching (νN-O) mode of MbDNO, and all three bands showed instantaneous bleach that decays on a picosecond time scale. The three bands were assigned based on isotope shifts upon (15)N substitution and ab initio calculation of the vibrational frequency on a DNO-bound model heme. These three bands likely arise from Fermi interactions between the strong νN-O mode and the weak overtone and combination modes of the N atom-related modes. The immediate appearance of the bleach in these bands and the picosecond decay of the bleach indicate that most of the photoexcited MbDNO undergoes picosecond geminate rebinding (GR) of DNO to Mb subsequent to its immediate deligation. Ultrafast and efficient GR of DNO likely arises from the bonding structure of the ligand and high reactivity between DNO and Mb.

Principal factors that determine the extension of detection range in molecular beacon aptamer/conjugated polyelectrolyte bioassays.

A strategy to extend the detection range of weakly-binding targets is reported that takes advantage of fluorescence resonance energy transfer (FRET)-based bioassays based on molecular beacon aptamers (MBAs) and cationic conjugated polyelectrolytes (CPEs). In comparison to other aptamer-target pairs, the aptamer-based adenosine triphosphate (ATP) detection assays are limited by the relatively weak binding between the two partners. In response, a series of MBAs were designed that have different stem stabilities while keeping the constant ATP-specific aptamer sequence in the loop part. The MBAs are labeled with a fluorophore and a quencher at both termini. In the absence of ATP, the hairpin MBAs can be opened by CPEs via a combination of electrostatic and hydrophobic interactions, showing a FRET-sensitized fluorophore signal. In the presence of ATP, the aptamer forms a G-quadruplex and the FRET signal decreases due to tighter contact between the fluorophore and quencher in the ATP/MBA/CPE triplex structure. The FRET-sensitized signal is inversely proportional to [ATP]. The extension of the detection range is determined by the competition between opening of the ATP/MBA G-quadruplex by CPEs and the composite influence by ATP/aptamer binding and the stem interactions. With increasing stem stability, the weak binding of ATP and its aptamer is successfully compensated to show the resistance to disruption by CPEs, resulting in a substantially broadened detection range (from millimolar up to nanomolar concentrations) and a remarkably improved limit of detection. From a general perspective, this strategy has the potential to be extended to other chemical- and biological-assays with low target binding affinity.

Amorphous thieno[3,2-b]thiophene and benzothiadiazole based copolymers for organic photovoltaics.

Three types of amorphous thienothiophene (TT)-benzothiadiazole (BT) based copolymers (PFTTBT) were synthesized by incorporating alkyl-substituted fluorene moieties as a third component in the polymer backbone. Their optical, electrochemical, morphological, and photovoltaic properties were examined by a comparison with those of a crystalline TT-BT derivative (PTTBT14). PTTBT14 was reported to have a high hole mobility (0.26 cm(2)/(V s)) due to the pronounced interchain ordering but poor photovoltaic power conversion efficiency (PCE) of 2.4-2.6% was reported due to excessively strong self-interactions with poor miscibility with fullerene structures. By incorporating fluorene units, the UV-vis spectra showed an increased bandgap (∼1.9 eV) with the disappearance of the packing-originated shoulder peak, and the valence band decreased compared to crystalline PTTBT14. The amorphous PFTTBT polymers showed substantially improved photovoltaic properties compared to PTTBT14, even though they showed poor hole mobility (∼10(-6) cm2/(V s)) and fill factor. The optimal devices were achieved by blending with excess PC71BM (polymer:PC71BM=1:4 by weight), showing little improvement in the thermal and additive treatments. Under simulated solar illumination of AM 1.5 G, the best PCE of 6.6% was achieved for a PFehTTBT:PC71BM device with an open-circuit voltage of 0.92 V, a short-circuit current of 15.1 mA/cm2, and a fill factor of 0.48. These results suggest that it is useful to disrupt partially the interchain organizations of excessively crystalline polymers, enabling fine-control of intermolecular ordering and the morphological properties (i.e., miscibility with fullerene derivatives, etc.) to utilize the advantages of both crystalline and amorphous materials for further improving PCE of polymer solar cells.

Efficient conventional- and inverted-type photovoltaic cells using a planar alternating polythiophene copolymer.

A low-band-gap alternating copolymer, poly{5,6-bis(octyloxy)-4-(thiophen-2-yl)benzo[c]-1,2,5-thiadiazole} (PTBT), was synthesized and investigated for photovoltaic applications. PTBT showed a minimized torsion angle in its main backbone owing to the introduction of solubilizing octyloxy groups on the electron-poor benzothiadiazole unit, thereby resulting in pronounced intermolecular ordering and a deep level of the HOMO (-5.41 eV). By blending PTBT with [6,6]phenyl-C61-butyric acid methyl ester (PC(61)BM), highly promising performance was achieved with power-conversion efficiencies (PCEs) of 5.9 and 5.3% for the conventional and inverted devices, respectively, under air mass 1.5 global (AM 1.5G, 100 mW cm(-2)) illumination. The open-circuit voltage (V(OC) ≈ 0.85-0.87 V) is one of the highest values reported thus far for thiophene-based polymers (e.g., poly(3-hexylthiophene) V(OC) ≈ 0.6 V). The inverted device also achieved a remarkable PCE compared to other devices based on low-band-gap polymers. Ideal film morphology with bicontinuous percolation pathways was expected from the atomic force microscopy (AFM) images, space-charge-limited current (SCLC) mobility, and selected-area electron-diffraction (SAED) measurements. This molecular design strategy is useful for achieving simple, processable, and planar donor-acceptor (D-A)-type low-band-gap polymers with a deep HOMO for applications in photovoltaic cells.

Solvent-assisted optical modulation of FRET-induced fluorescence for efficient conjugated polymer-based DNA detection.

The solvent effects were studied in fluorescence resonance energy transfer (FRET) from a cationic polyfluorene copolymer (FHQ, FPQ) to a fluorescein (Fl)-labelled oligonucleotide (ssDNA-Fl). Upon addition of dimethyl sulfoxide (DMSO), the optical properties of polymers and the probe dye were substantially modified and the FRET-induced PL signal was enhanced 3.8-37 times, relative to that in phosphate buffer solution (PBS). The hydrophobic interaction between polymers and ssDNA-Fl is expected to decrease in the presence of DMSO, which induces the weaker polymer/ssDNA-Fl complexation with longer intermolecular donor-acceptor separation and perturbs the competition between the FRET and PL quenching processes such as photo-induced charge transfer. The gradual decrease in Fl PL quenching with increasing the DMSO content was investigated by measuring the Stern-Volmer quenching constants (3.3-4.2 × 10(6) M(-1) in PBS, 0.56-1.1 × 10(6) M(-1) in 80 vol% DMSO) and PL lifetime of the excited Fl* in polymer/ssDNA-Fl (600 ps in PBS and 2120 ps in 80 vol% DMSO for FHQ/ssDNA-Fl) in PBS/DMSO mixtures. The substantially reduced PL quenching would amplify the resulting FRET Fl signal. The signal amplification in real DNA detection was also demonstrated with fluorescein-labelled PNA (probe PNA) in the presence of a complementary target DNA and noncomplementary DNA in aqueous DMSO solutions. This approach suggests a simple way of modifying the fine-structure of polymer/ssDNA-Fl and improving the detection sensitivity in conjugated polymer-based FRET bioassays.

Acid dissociation constants of melamine derivatives from density functional theory calculations.

Melamine and its hydrolysis products (ammeline, ammelide, and cyanuric acid) recently attracted great attention as major food contaminants. Developing analytical tools to quantify them requires exact knowledge of their acid dissociation constants (pK(a) values). Herein, we calculated the pK(a) values of these melamine derivatives in water, using a density functional theory quantum mechanical method [B3LYP/6-311++G(d,p)] in combination with the Poisson-Boltzmann continuum solvation model. The excellent agreement of the calculated values with the experimental ones shows that our method can be used to predict such properties of other food contaminants.

Counterion effects on fluorescence energy transfer in conjugated polyelectrolyte-based DNA detection.

Cationic poly[9,9'-bis[6''-(N,N,N-trimethylammonium)hexyl]fluorene-co-alt-phenylene]s with five different counterions (CIs) were synthesized and studied as fluorescence resonance energy transfer (FRET) donors (D) to dye-labeled DNA (FRET acceptor, A). The polymers with different CIs show the same pi-conjugated electronic structure with similar absorption (lambda(abs) = approximately 380 nm) and photoluminescence (lambda(PL) = approximately 420 nm) emission spectra in water. The CIs accompanying the polymer chain are expected to affect the D/A complexation and modify the D-A intermolecular separation by acting as a spacer. Polymers with different CIs function differently as FRET excitation donors to fluorescein (Fl)-labeled single-stranded DNA (ssDNA-Fl). The FRET-induced Fl emission was enhanced significantly by the larger CI-exchanged polymers. The polymers with the CIs of tetrakis(1-imidazolyl)borate (FPQ-IB) and tetraphenylborate (FPQ-PB) showed a 2-4-fold enhancement in the FRET-induced signal compared with the polymer with bromide (FPQ-BR). The delayed FRET signal saturation and low association constants (K(a)) with ssDNA-Fl (3.53 x 10(6) M(-1) for FPQ-BR and 1.80 x 10(6) M(-1) for FPQ-PB) were measured for the polymers with larger CIs. The delayed acceptor saturation strengthens the antenna effect and reduces self-quenching of Fl by increasing the polymer concentration near Fl. The weak polymer/ssDNA-Fl association reduces the amount of energy-wasting charge transfer by increasing D-A intermolecular separation. The combined effects lead to increase the overall FRET-induced signal.

Observation of an unusually facile fragmentation pathway of gas-phase peptide ions: a study on the gas-phase fragmentation mechanism and energetics of tryptic peptides modified with 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC) and their 18-crown-6 complexes.

Various peptide modifications have been explored recently to facilitate the acquisition of sequence information. N-terminal sulfonation is an interesting modification because it allows unambiguous de novo sequencing of peptides, especially in conjunction with MALDI-PSD-TOF analysis; such modified peptide ions undergo fragmentation at energies lower than those required conventionally for unmodified peptide ions. In this study, we systematically investigated the fragmentation mechanisms of N-terminal sulfonated peptide ions prepared using two different N-terminal sulfonation reagents: 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC). Collision-induced dissociation (CID) of the SPC-modified peptide ions produced a set of y-series ions that were more evenly distributed relative to those observed for the SPITC-modified peptides; y(n-1) ion peaks were consistently and significantly larger than the signals of the other y-ions. We experimentally investigated the differences between the dissociation energies of the SPITC- and SPC-modified peptide ions by comparing the MS/MS spectra of the complexes formed between the crown ether 18-crown-6 (CE) and the modified peptides. Upon CID, the complexes formed between 18-crown-6 ether and the protonated amino groups of C-terminal lysine residues underwent either peptide backbone fragmentation or complex dissociation. Although the crown ether complexes of the unmodified ([M + CE + 2H]2+) and SPC-modified ([M* + CE + 2H]2+) peptides underwent predominantly noncovalent complex dissociation upon CID, the low-energy dissociations of the crown ether complexes of the SPITC-modified peptides ([M' + CE + 2H]2+) unexpectedly resulted in peptide backbone fragmentations, along with a degree of complex dissociation. We performed quantum mechanical calculations to address the energetics of fragmentations observed for the modified peptides.

Density functional theory studies of the [2]rotaxane component of the Stoddart-heath molecular switch.

The central component of the programmable molecular switch recently demonstrated by Stoddart and Heath is [2]rotaxane, which consists of a cyclobis(paraquat-p-phenylene) shuttle (CBPQT(4+))(PF(6)(-))(4) (the ring) encircling a finger and moving between two stations, tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP). As a step toward understanding the mechanism of this switch, we report here its electronic structure using two flavors of density functional theory (DFT): B3LYP/6-31G and PBE/6-31G. We find that the electronic structure of composite [2]rotaxane can be constructed reasonably well from its parts by combining the states of separate stations (TTF and DNP) with or without the (CBPQT)(PF(6))(4) shuttle around them. That is, the "CBPQT@TTF" state, (TTF)(CBPQT)(PF(6))(4)-(DNP), is described well as a combination of the (TTF)(CBPQT)(PF(6))(4) complex and free DNP, and the "CBPQT@DNP" state, (TTF)-(DNP)(CBPQT)(PF(6))(4), is described well as a combination of free TTF and the (DNP)(CBPQT)(PF(6))(4) complex. This allows an aufbau or a "bottom-up" approach to predict the complicated [n]rotaxanes in terms of their components. This should be useful in designing new components to lead to improved properties of the switches. A critical function of the (CBPQT(4+))(PF(6)(-))(4) shuttle in switching is that it induces a downshift of the frontier orbital energy levels of the station it is on (TTF or DNP). This occurs because of the net positive electrostatic potential exerted by the CBPQT(4+) ring, which is located closer to the active station than the four PF(6)(-)'s. This downshift alters the relative position of energy levels between TTF and DNP, which in turn alters the electron tunneling rate between them, even when the shuttle is not involved directly in the actual tunneling process. Based on this switching mechanism, the "CBPQT@TTF" state is expected to be a better conductor since it has better aligned levels between the two stations. A second potential role of the (CBPQT(4+))(PF(6)(-))(4) shuttle in switching is to provide low-lying LUMO levels. If the shuttle is involved in the actual tunneling process, the reduced HOMO-LUMO gap (from 3.6 eV for the isolated finger to 1.1 eV for "CBPQT@TTF" or to 0.6 eV for "CBPQT@DNP" using B3LYP) would significantly facilitate the electron tunneling through the system. This might occur in a folded conformation where a direct contact between free station and the shuttle on the other station is possible. When this becomes the main switching mechanism, we expect the "CBPQT@DNP" state to become a better conductor because its HOMO-LUMO gap is smaller and because its HOMO and LUMO are localized at different stations (HOMO exclusively at TTF and LUMO at CBPQT encircling DNP) so that the HOMO-to-LUMO tunneling would be through the entire molecule of [2]rotaxane. Thus an essential element in designing these switches is to determine the configuration of the molecules (e.g., through self-assembled monolayers or incorporation of conformation stabilizing units).

Binding of aromatic isocyanides on gold nanoparticle surfaces investigated by surface-enhanced Raman scattering.

The adsorption structure and binding of phenyl isocyanide (PNC), 2,6-dimethyl phenyl isocyanide (DMPNC), and benzyl isocyanide (BZI) on gold nanoparticle surfaces have been studied by means of surface-enhanced Raman scattering (SERS). PNC, DMPNC, and BZI have been found to adsorb on gold assuming a standing geometry with respect to the surfaces. The presence of the nu(CH) band in the SERS spectra denotes a vertical orientation of the phenyl ring of PNC, DMPNC, and BZI on Au. The lack of a substantial red shift and significant band broadening of the ring breathing modes implied that a direct ring pi orbital interaction with metal substrates should be quite low. For PNC, the band ascribed to the C-NC stretching vibration was found to almost disappear after adsorption on Au. On the other hand, the C-NC band remained quite strong for DMPNC after adsorption. This result suggests a rather bent angle of C-N[triple bond]C: for the nitrogen atom of the NC binding group on the surfaces, whereas a linear angle of C-N[triple bond]C: should be more favorable on gold surfaces due to an intramolecular steric hindrance of its two methyl groups. SERS of BZI on gold nanoparticles also supports a bent angle of :C[triple bond]N-CH2 for its nitrogen atom, suggesting a preference of sp3 (or sp2) hybridization for the nitrogen atom.

Bowl-shaped C(3)-symmetric receptor with concave phosphine oxide with a remarkable selectivity for asparagine derivatives.

A bowl-shaped C(3)-symmetric receptor (1a) that has a phosphine oxide functionality in the interior of a "molecular bowl" shows remarkable selectivity for Asn derivatives. [structure: see text]

First principles calculations of the tautomers and pK(a) values of 8-oxoguanine: implications for mutagenicity and repair.

8-Oxoguanine is a mutagenic oxidative damage product of guanine that has been the subject of many experimental studies. Despite numerous references to this damaged base, its precise configuration or population of configurations in equilibrium are unknown, as it can be drawn in over 100 potential neutral and ionized tautomeric forms. The structural uncertainty surrounding 8-oxoguanine complicates mechanistic studies of its mutagenicity and capacity to be recognized for repair. Experimental measurements on the tautomeric equilibria and pK(a) values of 8-oxoguanine are complicated by its insolubility in water. Therefore, we used first principles quantum mechanics (density functional theory, B3LYP, in combination with the Poisson-Boltzmann continuum-solvation model) to investigate the relative stabilities and site-specific pK(a) values of various neutral and ionized tautomers of 8-oxoguanine. We show that the major tautomer of neutral 8-oxoguanine in aqueous solution is the 6,8-diketo form 2, and that 8-oxoguanine has increased acidity at N1 relative to guanine. Our calculations on 2'-deoxyguanosine-3',5'-bisphosphate and its 8-oxo analogue support the accepted conclusion that repulsion between the O8 of 8-oxoguanine and O5' of the backbone sugar promote 8-oxoguanine:adenine pairings in the syn:anti conformation. Further, we show that the N7 proton of 8-oxoguanine is difficult to remove either through tautomerization or ionization, consistent with its involvement as an important landmark in distinguishing guanine from 8-oxoguanine. The possibility of additional structural landmarks that distinguish 8-oxoguanine from guanine, and a possible mechanism for glycosylase removal of 8-oxoguanine are discussed.