Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge

Here, we test a method, called semi-explicit assembly (SEA), that computes the solvation free energies of molecules in water in the SAMPL4 blind test challenge. SEA was developed with the intention of being as accurate as explicit-solvent models, but much faster to compute. It is accurate because it uses pre-simulations of simple spheres in explicit solvent to obtain structural and thermodynamic quantities, and it is fast because it parses solute free energies into regionally additive quantities. SAMPL4 provided us the opportunity to make new tests of SEA. Our tests here lead us to the following conclusions: (1) The newest version, called Field-SEA, which gives improved predictions for highly charged ions, is shown here to perform as well as the earlier versions (dipolar and quadrupolar SEA) on this broad blind SAMPL4 test set. (2) We find that both the past and present SEA models give solvation free energies that are as accurate as TIP3P. (3) Using a new approach for force field parameter optimization, we developed improved hydroxyl parameters that ensure consistency with neat-solvent dielectric constants, and found that they led to improved solvation free energies for hydroxyl-containing compounds in SAMPL4. We also learned that these hydroxyl parameters are not just fixing solvent exposed oxygens in a general sense, and therefore do not improve predictions for carbonyl or carboxylic-acid groups. Other such functional groups will need their own independent optimizations for potential improvements. Overall, these tests in SAMPL4 indicate that SEA is an accurate, general and fast new approach to computing solvation free energies.     

Rhodium-Catalyzed Highly Diastereo- and Enantioselective Synthesis of a Configurationally Stable S-Shaped Double Helicene-Like Molecule

An S-shaped double helicene-like molecule (>99 % ee), possessing stable helical chirality, has been synthesized by the rhodium(I)/difluorphos complex-catalyzed highly diastereo- and enantioselective intramolecular double [2+2+2] cycloaddition of a 2-naphthol- and benzene-linked hexayne. The collision between two terminal naphthalene rings destabilizes the helical chirality of the S-shaped double helicene-like molecule, but the introduction of two additional fused benzene rings significantly increases the configurational stability. Thus, no epimerization and racemization were observed even at 100 °C. The enantiopure S-shaped double helicene-like molecule forms a trimer through the multiple C−H⋅⋅⋅π and C−H⋅⋅⋅O interactions in the solid-state. The trimers stack to form columnar packing structures, in which neighboring stacks have opposite dipole directions. The accumulation of helical structures in the same direction in the S-shaped double helicene-like molecule enhanced the chiroptical properties.     

Water-based Synthesis and Properties of a Scandium 1,4-Naphthalenedicarboxylate

A new scandium naphthalenedicarboxylate with the framework composition [Sc₂(1,4-NDC)₃] (H₂-1,4-NDC = 1,4-naphthalenedicarboxylic acid) was obtained under hydrothermal synthesis conditions. A structure model could be developed by a combination of 3D electron diffraction measurements and computationally assisted structure determination, which was further validated by a good agreement with the experimental powder X-ray diffraction pattern. The structure consists of isolated ScO₆ octahedra interconnected by the carboxylate groups of linker molecules to form chains. These chains are connected by the naphthalene-moieties to form a three-dimensional framework with square-shaped pores and the organic group pointing into the pores. Although very similar synthesis conditions were chosen, [Sc₂(1,4-NDC)₃] is not isostructural to aluminum naphthalenedicarboxylate [Al(OH)(1,4-NDC)], which crystallizes in a MIL-53 type structure. This can be traced back to the different inorganic building units that are observed. The compound was thoroughly characterized by elemental analysis, IR spectroscopy, sorption measurements, thermogravimetric analysis and luminescence measurements. [Sc₂(1,4-NDC)₃] exhibits a high thermal stability and a ligand-based blue luminescence in the solid state at room temperature.     

Observations and theories of quantum effects in proton transfer electrode processes

Quantum tunneling effects play an important role in a variety of chemical reactions considerably affecting the reaction rates via opening the classically forbidden paths and emerging as highly efficient or selective processes. However, in the case of electrochemical reactions, quantum tunneling effects are less investigated due to complicated nature of chemical interactions at the electrified interfaces. In this review, we summarize the experimental/theoretical concept of electrochemical quantum proton tunneling (EQPT), which is a key element in microscopic electrode processes. First, we review the experimental observations of EQPT, and next, we discuss possible theoretical pictures of the process. This review shows that a combination of a wide spectrum of scientific efforts is required to understand microscopic mechanism of EQPT including development of the precise electrochemistry-oriented experimental techniques and methodologies, formulation of the appropriate theoretical models for specific systems, and performance of the advanced computational simulations.     

Phytochemical Analysis and Habitat Suitability Mapping of Glycyrrhiza glabra L. Collected in the Hatay Region of Turkey

The growth and quality of licorice depend on various environmental factors, including the local climate and soil properties; therefore, its cultivation is often unsuccessful. The current study investigated the key factors that affect the contents of bioactive compounds of Glycyrrhiza glabra L. root and estimated suitable growth zones from collection sites in the Hatay region of Turkey. The contents of three bioactive compounds (glycyrrhizic acid, glabridin, and liquiritin), soil factors (pH, soil bearing capacity, and moisture content), and geographical information (slope, aspect, curvature, elevation, and hillshade) were measured. Meteorological data (temperature and precipitation) were also obtained. An analysis of variance (ANOVA) and multivariate analysis of variance (MANOVA) were performed on the data. The soil bearing capacity, moisture content, slope, aspect, curvature, and elevation of the study area showed statistically significant effects on the glycyrrhizic acid and liquiritin contents. A habitat suitability zone map was generated using a GIS-based frequency ratio (FR) model with spatial correlations to the soil, topographical, and meteorological data. The final map categorized the study area into four zones: very high (15.14%), high (31.50%), moderate (40.25%), and low suitability (13.11%). High suitability zones are recommended for further investigation and future cultivation of G. glabra.     

Intramolecular Benzyne–Phenolate [4+2] Cycloadditions

An intramolecular benzyne–phenolate [4+2] cycloaddition is reported. Benzyne precursors, having vicinal halogen‐sulfonate functionalities, linked with a phenol(ate) by various tether groups undergo efficient intramolecular [4+2] cycloaddition by treatment with either Ph₃MgLi or nBuLi for halogen–metal exchange to form various benzobarrelenes.     

Cyclization reaction of polyacrylonitrile and poly(styrene-co-acrylonitrile) studied by PVT measurements

Pressure, volume, temperature (PVT) measurements reveal that during the intramolecular cyclization reaction of poly(acrylonitrile) (PAN) and poly(styrene-co-acrylonitrile) (SAN) the volume decreases. This volume contraction becomes smaller with increasing styrene content in the random copolymers and should be related to the simultaneous decrease of longer acrylonitrile homo-sequences. The onset temperature of the cyclization reaction is raised with higher styrene contents in the random copolymers. Thus, it can be excluded that the cyclization reaction has a major influence on the discoloration process of SAN samples having relatively small acrylonitrile contents (less than 50 mol-%) during thermal annealing below 300°C.     

NANOMECHANICAL MAPPING OF CARBON BLACK REINFORCED NATURAL RUBBER BY ATOMIC FORCE MICROSCOPY

Atomic force microscopy （AFM） has the advantage of obtaining mechanical properties as well as topographic information at the same time. By analyzing force-distance curves measured over two-dimensional area using Hertzian contact mechanics, Young＇s modulus mapping was obtained with nanometer-scale resolution. Furthermore, the sample deformation by the force exerted was also estimated from the force-distance curve analyses. We could thus reconstruct a real topographic image by incorporating apparent topographic image with deformation image. We applied this method to carbon black reinforced natural rubber to obtain Young＇s modulus distribution image together with reconstructed real topographic image. Then we were able to recognize three regions; rubber matrix, carbon black （or bound rubber） and intermediate regions. Though the existence of these regions had been investigated by pulsed nuclear magnetic resonance, this paper would be the first to report on the quantitative evaluation of the interfacial region in real space.     

Cu-DNAzyme facilitates highly sensitive immunoassay

A simple Cu-DNAzyme system is used for signal transduction of a CuO nanoparticle-labeled immunoassay, which makes the immunoassay fast, simple, cost-effective, and sensitive, thus promising for biomedical applications and point-of-care testing.     

Functional porous coordination polymers

The chemistry of the coordination polymers has in recent years advanced extensively, affording various architectures, which are constructed from a variety of molecular building blocks with different interactions between them. The next challenge is the chemical and physical functionalization of these architectures, through the porous properties of the frameworks. This review concentrates on three aspects of coordination polymers: 1). the use of crystal engineering to construct porous frameworks from connectors and linkers ("nanospace engineering"), 2). characterizing and cataloging the porous properties by functions for storage, exchange, separation, etc., and 3). the next generation of porous functions based on dynamic crystal transformations caused by guest molecules or physical stimuli. Our aim is to present the state of the art chemistry and physics of and in the micropores of porous coordination polymers.