Correlating DFT-Calculated Energy Barriers to Experiments in Nonheme Octahedral Fe(IV) O Species

The experimentally measured bimolecular reaction rate constant, k(2) , should in principle correlate with the theoretically calculated rate-limiting free energy barrier, ΔG(≠) , through the Eyring equation, but it fails quite often to do so due to the inability of current computational methods to account in a precise manner for all the factors contributing to ΔG(≠) . This is further aggravated by the exponential sensitivity of the Eyring equation to these factors. We have taken herein a pragmatic approach for C?H activation reactions of 1,4-cyclohexadiene with a variety of octahedral nonheme Fe(IV) O complexes. The approach consists of empirically determining two constants that would aid in predicting experimental k(2) values uniformly from theoretically calculated electronic energy (ΔE(≠) ) values. Shown in this study is the predictive power as well as insights into energy relationships in Fe(IV) O C?H activation reactions. We also find that the difference between ΔG(≠) and ΔE(≠) converges at slow reactions, in a manner suggestive of changes in the importance of the triplet spin state weight in the overall reaction.     

Effects of gamma irradiation on the yields of volatile extracts of Angelica gigas Nakai

The study was carried out to determine the effects of gamma irradiation on the volatile flavor components including essential oils, of Angelica gigas Nakai. The volatile organic compounds from non- and irradiated A. gigas Nakai at doses of 1, 3, 5, 10 and 20 kGy were extracted by a simultaneous steam distillation and extraction (SDE) method and identified by GC/MS analysis. A total of 116 compounds were identified and quantified from non- and irradiated A. gigas Nakai. The major volatile compounds were identified 2,4,6-trimethyl heptane, α-pinene, camphene, α-limonene, β-eudesmol, α-murrolene and sphatulenol. Among these compounds, the amount of essential oils in non-irradiated sample were 77.13%, and the irradiated samples at doses of 1, 3, 5, 10 and 20 kGy were 84.98%, 83.70%, 83.94%, 82.84% and 82.58%, respectively. Oxygenated terpenes such as β-eudesmol, α-eudesmol, and verbenone were increased after irradiation but did not correlate with the irradiation dose. The yields of active substances such as essential oil were increased after irradiation; however, the yields of essential oils and the irradiation dose were not correlated. Thus, the profile of composition volatiles of A. gigas Nakai did not change with irradiation.     

Silver(I) mediated folding of a molecular basket

We have investigated Ag(I) mediated folding of a tridentate compound, containing three pyridine flaps tethered to a semirigid scaffold, into a molecular basket, using both experimental and theoretical methods. The basket formation has been shown to be highly favorable in organic media (Delta G degrees = -7.2 kcal/mol), with the assembly process allowing for another ligand to bind preferentially on the outer side.     

Magnesium ion selective two-photon fluorescent probe based on a benzo[h]chromene derivative for in vivo imaging

A novel, two-photon probe for the detection of free Mg2+ ions in living cells and live tissues has been developed. The probe can be excited by 880 nm laser photons, emits strong two-photon excited fluorescence in response to Mg2+ ions, can be easily loaded into the cell and tissue, shows high photostability, and can measure the Mg2+ ion concentration without interference by Ca2+ ions in living cells. The intracellular dissociation constant (Kdi) for Mg2+ determined by the two-photon process is 2.5 mM, which is suitable for dynamic Mg2+ concentration measurement. In addition, the probe is capable of imaging endogenous stores of free Mg2+ at a few hundred micrometers depth in live tissues using two-photon microscopy (TPM).     

Drug-likeness scoring based on unsupervised learning

Drug-likeness prediction is important for the virtual screening of drug candidates. It is challenging because the drug-likeness is presumably associated with the whole set of necessary properties to pass through clinical trials, and thus no definite data for regression is available. Recently, binary classification models based on graph neural networks have been proposed but with strong dependency of their performances on the choice of the negative set for training. Here we propose a novel unsupervised learning model that requires only known drugs for training. We adopted a language model based on a recurrent neural network for unsupervised learning. It showed relatively consistent performance across different datasets, unlike such classification models. In addition, the unsupervised learning model provides drug-likeness scores that well separate distributions with increasing mean values in the order of datasets composed of molecules at a later step in a drug development process, whereas the classification model predicted a polarized distribution with two extreme values for all datasets presumably due to the overconfident prediction for unseen data. Thus, this new concept offers a pragmatic tool for drug-likeness scoring and further can be applied to other biochemical applications.

A new quantification method of drug-likeness based on unsupervised learning. The method only uses drug molecules as training set without any non-drug-like molecules.     

Hierarchical Self‐Assembly of Poly‐Pseudorotaxanes into Artificial Microtubules

Hierarchical self‐assembly of building blocks over multiple length scales is ubiquitous in living organisms. Microtubules are one of the principal cellular components formed by hierarchical self‐assembly of nanometer‐sized tubulin heterodimers into protofilaments, which then associate to form micron‐length‐scale, multi‐stranded tubes. This peculiar biological process is now mimicked with a fully synthetic molecule, which forms a 1:1 host‐guest complex with cucurbit[7]uril as a globular building block, and then polymerizes into linear poly‐pseudorotaxanes that associate laterally with each other in a self‐shape‐complementary manner to form a tubular structure with a length over tens of micrometers. Molecular dynamic simulations suggest that the tubular assembly consists of eight poly‐pseudorotaxanes that wind together to form a 4.5 nm wide multi‐stranded tubule.     

Soluble factor from tumor cells induces heme oxygenase-1 by a nitric oxide-independent mechanism in murine peritoneal macrophages

Tumor target-derived soluble secretary factor has been known to influence macrophage activation to induce nitric oxide (NO) production. Since heme oxygenase-1 (HO-1) is induced by a variety of conditions associated with oxidative stress, we questioned whether soluble factor from tumor cells induces HO-1 through NO-dependent mechanism in macrophages. We designated this factor as a tumor-derived macrophage-activating factor (TMAF), because of its ability to activate macrophages to induce iNOS. Although TMAF alone showed modest activity, TMAF in combination with IFN-gamma significantly induced iNOS expression and NO synthesis. Simultaneously, TMAF induced HO-1 and this induction was slightly augmented by IFN-gamma. Surprisingly, however, induction of HO-1 by TMAF was not inhibited by the treatment with the highly selective iNOS inhibitor, 1400 W, indicating that TMAF induces the HO-1 enzyme by a NO-independent mechanism. While rIFN-gamma alone induced iNOS, it had no effect on HO-1 induction by itself. Collectively, the current study reveals that soluble factor from tumor target cells induces HO-1 enzyme in macrophages. However, overall biological significance of this phenomenon remains to be determined.     

Emulsion of aqueous-based nonspherical droplets in aqueous solutions by single-chain surfactants: templated assembly by nonamphiphilic lyotropic liquid crystals in water

Single-chain surfactants usually emulsify and stabilize oily substances into droplets in an aqueous solution. Here, we report a coassembly system, in which single types of anionic or non-ionic surfactants emulsify a class of water-soluble nonamphiphilic organic salts with fused aromatic rings in aqueous solutions. The nonamphiphilic organic salts are in turn promoted to form droplets of water-based liquid crystals (chromonic liquid crystals) encapsulated by single-chain surfactants. The droplets, stabilized against coalescence by encapsulated in a layer (or layers) of single chain surfactants, are of both nonspherical tactoid (elongated ellipsoid with pointy ends) and spherical shapes. The tactoids have an average long axis of ～9 μm and a short axis of ～3.5 μm with the liquid crystal aligning parallel to the droplet surface. The spherical droplets are 5-10 μm in diameter and have the liquid crystal aligning perpendicular to the droplet surface and a point defect in the center. Cationic and zwitterionic surfactants studied in this work did not promote the organic salt to form droplets. These results illustrate the complex interplay of self-association and thermodynamic incompatibility of molecules in water, which can cause new assembly behavior, including potential formation of vesicles or other assemblies, from surfactants that usually form only micelles. These unprecedented tactoidal shaped droplets also provide potential for the fabrication of new soft organic microcapsules.