Molecular compasses and gyroscopes with polar rotors: synthesis and characterization of crystalline forms

We report the highly convergent synthesis and solid-state characterization of six crystalline "molecular compasses" consisting of a central phenylene rotor with polar substituents, or compass needle, and two trityl groups axially connected by acetylene linkages to the 1,4-positions. Compounds with fluoro-, cyano-, nitro-, amino-, diamino-, and nitroamino substituents are expected to emulate the parent compound which was shown to form crystals where the central phenylene can rotate about its 1,4-axis with rate constants in the 10(3) -10(6) s(-)(1) dynamic ranges near ambient temperature, depending on crystal morphology. With data from single-crystal X-ray diffraction analysis, solid-state CPMAS (13)C NMR, differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA), it is shown that a relatively small structural perturbation by a single polar group (F, CN, NO(2), NH(2)) results in isomorphous structures with analogous properties. In analogy to the parent compound, crystals grown from benzene formed clathrate structures in the space group Ponemacr; with one molecular compass and two benzene molecules per unit cell. Solvent-free crystals with the same space group obtained by a first-order phase transition between 60 and 130 degrees C were shown to be spectroscopically identical to those obtained by slow solvent evaporation from a mixture of CH(2)Cl(2) and hexanes. A qualitative analysis of the positionally disordered phenylene groups in terms of the expected solid-state rotational dynamics suggests a nonsymmetric, 2-fold rotational potential, or a process involving full 360 degrees turns.     

Molecular crystals with moving parts: synthesis, characterization, and crystal packing of molecular gyroscopes with methyl-substituted triptycyl frames

We report a highly convergent synthesis for the preparation of molecular gyroscopes consisting of para-phenylene rotors linked by triple bonds to methyl-substituted triptycenes acting as pivots and encapsulating frames. The desired 1,4-bis[2-(2,3,6,7,12,13-hexamethyl-10-alkyl-9-triptycyl)ethynyl]benzenes were prepared from 2,3-dimethyl-1,3-butadiene using Diels-Alder cycloadditions and Pd(0)-catalyzed coupling as the key reactions. The main challenge in the synthesis came about in the preparation of 9-alkynyl-triptycenes by Diels-Alder reaction of benzynes and 9-alkynyl-2,3,6,7-tetramethylanthracenes. These reactions occurred with chemical yields and regioselectivities that were strongly influenced by steric and electronic effects of substituents at C10 of the anthracene core. Anthracenes with methyl, propyl, and phenyl substituents were utilized to complete the synthesis of their corresponding molecular gyroscopes, and their solid-state structures were determined by single-crystal X-ray diffraction analysis. Examination of these results indicated that, as expected, the bulky triptycyl groups encourage crystallization motifs that create more free volume around the phenylene rotor, as needed to facilitate fast gyroscopic motion in the solid state.     

Molecular methods to measure intestinal bacteria: a review

The intestine is an exceptionally rich ecosystem encompassing a complex interaction among microorganisms, influenced by host factors, ingested food, and liquid. Characterizing the intestinal microbiota is currently an active area of research. Various molecular-based methods are available to characterize the intestinal microbiota, but all methods possess relative strengths, as well as salient weaknesses. It is important that researchers are cognizant of the limitations of these methods, and that they take the appropriate steps to mitigate weaknesses. Here, we discuss methodologies used to monitor intestinal bacteria including: (i) traditional clone libraries; (ii) direct sequencing using next-generation parallel sequencing technology; (iii) denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis; (iv) terminal restriction fragment length polymorphism analysis; (v) fluorescent in situ hybridization; and (vi) quantitative PCR. In addition, we also discuss experimental design, sample collection and storage, DNA extraction, gene targets, PCR bias, and methods to reduce PCR bias.     

Efficient intramolecular general acid catalysis: a preview from a crystal structure

The crystal structure of acetal acid 5 reveals changes in geometry representing progress along the reaction coordinate for acetal cleavage.     

Physical,hydrochemical and isotopic characteristics of springs in Beijing,China, compared to historical properties

A physical, hydrochemical and isotopic evaluation of springs in Beijing was conducted in 2009 to reveal apparent changes in the properties of those springs. The results showed that most of the 2nd class springs and more than 50 % of the 1st class springs recorded in the early 1980s were depleted, while the discharges of existing springs have also decreased sharply. In addition, the majority of springs were of the HCO₃–Ca–Mg type and good water quality, with the quality indices changing slightly compared to those recorded 30 years ago. The abundances of ²H, ¹⁸O, and ³H in the springs indicated that most of the springs were of meteoric origin with a relatively close connection to modern atmospheric precipitation. As a result, the springs have a relatively strong renewability within a shallow circulation.     

Molecular contrast optical coherence tomography: a review

This article reviews the current state of research on the use of molecular contrast agents in optical coherence tomography (OCT) imaging techniques. After a brief discussion of the basic principle of OCT and the importance of incorporating molecular contrast agent usage into this imaging modality, we shall present an overview of the different molecular contrast OCT (MCOCT) methods that have been developed thus far. We will then discuss several important practical issues that define the possible range of contrast agent choice, the design criteria for engineered molecular contrast agent and the implementability of a given MCOCT method for clinical or biological applications. We will conclude by outlining a few areas of pursuit that deserve a greater degree of research and development.     

Molecular absorption spectrometry in flames and furnaces: A review

Molecular absorption spectrometry (MAS), originally developed in the 1970s, is a technique to determine non-metals in flames and graphite furnaces by monitoring the absorbance of diatomic molecules. Early studies employed low resolution instruments designed for line source atomic absorption, which provided a limited choice of analytical wavelengths, insufficient spectral resolution, and spectral interferences. However, the development of high-resolution continuum source atomic absorption spectrometry (HR-CS AAS) instrumentation has allowed the analysis of challenging samples for non-metals as well as some difficult elements to determine by AAS, such as aluminum and phosphorus. In this review, theory and analytical considerations for MAS are discussed. The principles and limitations of low resolution MAS are described, along with its applications. HR-CS AAS instrumentation is reviewed, emphasizing performance characteristics most relevant for MAS. Applications of flame and HR-CS GFMAS are reviewed, highlighting the most significant work to date. The paper concludes with an evaluation of the enhanced analytical capabilities provided by HR-CS MAS.     

Radon measurements in water samples from the thermal springs of Yalova basin, Turkey

The radon concentration has been measured in thermal waters used for medical therapy and drinking purposes in Yalova basin, Turkey. Radon activity measurements in water samples were performed using RAD 7 radon detector equipped with RAD H₂O (radon in water) accessory and following a protocol proposed by the manufacturer. The results show that the concentration of ²²²Rn in thermal waters ranges from 0.21 to 5.82 Bql^?1 with an average value of 2.4 Bql^?1. In addition to radon concentration, physicochemical parameters of water such as temperature (T), electrical conductivity, pH and redox potential (E_h) were also measured. The annual effective doses from radon in water due to its ingestion and inhalation were also estimated. The annual effective doses range from 0.2 to 0.75 μSvy^?1 for ingestion of radon in water and from 2.44 to 9 μSvy^?1 for inhalation of radon released from the water.     

Molecular organic crystals: from barely porous to really porous

Holey suitable crystals: A trisbenzimidazolone molecule self-assembles by hydrogen bonding to form a permanently porous crystal with an apparent surface area, SA(BET) , of 2796?m(2) g(-1) , demonstrating that extrinsic, intermolecular porosity is a viable strategy for highly porous materials.     

Molecular modeling and photovoltaic applications of porphyrin-based dyes: A review

In this review, the introduction of solar cells is presented. Old and new generation solar cells are briefly described. Quantum dot solar cells (QDSCs), perovskite solar cells, and dye-sensitized solar cells (DSSCs) are concisely introduced. The sensitization mechanism in DSSCs is discussed in detail concerning the spectral and electron injection properties of different dyes. An analysis of the intramolecular charge transfer process in the excited dye molecule is also provided. The use of porphyrin-based dyes as sensitizers in DSSCs is then reviewed. The design, synthesis, and photovoltaic application of a wide variety of porphyrin-based dyes as well as porphyrin dyads are presented and discussed. Theoretical studies of the spectral and electronic properties of different porphyrin-based dyes using DFT and TD-DFT methods are described. The different possibilities for improving the light-to-electrical energy conversion performance are discussed, such as structural modifications through introducing push-pull moieties, which in turn tunes the HOMO-LUMO energy gap of the sensitizing dye used in the DSSC. Experimental, as well as theoretical calculations of adsorption energies of the sensitizing dyes, are crucial for predicting the relative performance and efficiency of the dyes.     

Molecular scale simulations on thermoset polymers: A review

This article reviews the field of molecular simulations of thermoset polymers. This class of polymers is of interest in applications ranging from structural components for aerospace to electronics packaging and predictive simulations of their response is playing an increasing role in understanding the molecular origin of their properties and complementing experiments in the search for tailored materials for specific applications. It focuses on modeling and simulation of the process of curing to predict the molecular structure of these polymers and their thermomechanical response by all-atom molecular dynamics simulations. Results from Monte Carlo and coarse-grained simulations are briefly summarized. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 103–122     

Quantification, 2DE analysis and identification of enriched glycosylated proteins from mouse muscles: Difficulties and alternatives

One of the problems with 2DE is that proteins present in low amounts in a sample are usually not detected, since their signals are masked by the predominant proteins. The elimination of these abundant proteins is not a guaranteed solution to achieve the desired results. The main objective of this study was the comparison of common and simple methodologies employed for 2DE analysis followed by MS identification, focusing on a pre‐purified sample using a wheat germ agglutinin (WGA) column. Adult male C57Black/Crj6 (C57BL/6) mice were chosen as the model animal in this study; the gastrocnemius muscles were collected and processed for the experiments. The initial fractionation with succinylated WGA was successful for the elimination of the most abundant proteins. Two quantification methods were employed for the purified samples, and bicinchoninic acid (BCA) was proven to be most reliable for the quantification of glycoproteins. The gel staining method, however, was found to be decisive for the detection of specific proteins, since their structures affect the interaction of the dye with the peptide backbone. The Coomassie Blue R‐250 dye very weakly stained the gel with the WGA purified sample. When the same gel was stained with silver nitrate, however, MS could positively assign 12 new spots. The structure of the referred proteins was not found to be prone to interaction with Coomassie blue.     

Molecular Recognition and Catalysis: from Macrocyclic Receptors to Molecularly Imprinted Metal Complexes

Summary: The results of studying a number of reactions catalyzed by several types of soluble macromolecular catalytic systems capable of selectively binding organic substrates, namely, modified cyclodextrins, calixarenes and dendrimers are presented. The use of modified cyclodextrins as components of a catalytic system in the phenol and benzene hydroxylation by hydrogen peroxide allows one both to increase the catalytic activity and to change significantly the chemical selectivity. Phosphorilated calixarene – Rh catalytic systems was found to be catalytically active in hydroformylation of linear alkenes C₇–C₁₂. The results of experiments on the oxidation of C₇–C₁₆ alkenes show that, when the ligand is the dendrimer molecule, the fraction of forming methyl ketones substantially increases for the substrates C₇–C₉. For the higher alkenes, this effect is not observed.     

Molecular dynamics simulations of proteins and peptides: from folding to drug design

Computer simulations of proteins, lipids and nucleic acids at equilibrium have become essentially routine. However, the fact remains that complete sampling of conformational space continues to be a bottle-neck in the field. The challenge for the future is to overcome such problems and use computational approaches to understand recognition and spontaneous self-organization in biomolecular systems (folding, aggregation and assembly of complexes), processes that cannot be directly observed experimentally. In this review, examples illustrating the extent to which simulations can be used to understand these phenomena in biomolecular systems will be presented along with examples of methodological developments to increase our physical understanding of the processes. The study cases will cover the problems of peptide-receptor recognition and the use of the information obtained for the design of new non-peptidic ligands; the study of the folding mechanism of small proteins and finally the study of the initial stages of peptide self-aggregation.     

Molecular simulations for energy, environmental and pharmaceutical applications of nanoporous materials: from zeolites, metal-organic frameworks to protein crystals

Nanoporous materials have widespread applications in chemical industry, but the pathway from laboratory synthesis and testing to practical utilization of nanoporous materials is substantially challenging and requires fundamental understanding from the bottom up. With ever-growing computational resources, molecular simulations have become an indispensable tool for material characterization, screening and design. This tutorial review summarizes the recent simulation studies in zeolites, metal-organic frameworks and protein crystals, and provides a molecular overview for energy, environmental and pharmaceutical applications of nanoporous materials with increasing degree of complexity in building blocks. It is demonstrated that molecular-level studies can bridge the gap between physical and engineering sciences, unravel microscopic insights that are otherwise experimentally inaccessible, and assist in the rational design of new materials. The review is concluded with major challenges in future simulation exploration of novel nanoporous materials for emerging applications.     

2D Inorganic Materials: from Atomic Crystals to Molecular Crystals

rof.Zhai Tianyou and co-workers introduce the concept of 2D inorganic molecular crystals,which are different from traditional 2D atomic crystals,such as graphene,MoS2,black phosphorus,MXene,etc.The materials system is unique,and completely new to the community.Another research boom on 2D molecular materials may thus be drawn in the scope of electronics,energy and environment.This work has been published online in the Nature Communications in October 17,2019.     

Molecular recognition: from solution science to nano/materials technology

In the 25 years since its Nobel Prize in chemistry, supramolecular chemistry based on molecular recognition has been paid much attention in scientific and technological fields. Nanotechnology and the related areas seek breakthrough methods of nanofabrication based on rational organization through assembly of constituent molecules. Advanced biochemistry, medical applications, and environmental and energy technologies also depend on the importance of specific interactions between molecules. In those current fields, molecular recognition is now being re-evaluated. In this review, we re-examine current trends in molecular recognition from the viewpoint of the surrounding media, that is (i) the solution phase for development of basic science and molecular design advances; (ii) at nano/materials interfaces for emerging technologies and applications. The first section of this review includes molecular recognition frontiers, receptor design based on combinatorial approaches, organic capsule receptors, metallo-capsule receptors, helical receptors, dendrimer receptors, and the future design of receptor architectures. The following section summarizes topics related to molecular recognition at interfaces including fundamentals of molecular recognition, sensing and detection, structure formation, molecular machines, molecular recognition involving polymers and related materials, and molecular recognition processes in nanostructured materials.     

Molecular tectonics: from molecular recognition of anions to molecular networks

One may apply concepts developed in the context of molecular recognition of anions by synthetic receptors in solution to the design of molecular tectons capable of generating molecular networks with anionic species in the crystalline phase. With respect to that, bis-cyclic amidinium dications are interesting tectons because they offer two positive charges allowing strong electrostatic charge–charge interactions with anions and four acidic protons divergently oriented and capable of forming two sets of two H-bond chelates. The latter characteristic is of interest for the generation of supramolecular chirality taking place within the second coordination sphere around anionic metal complexes adopting an octahedral coordination geometry.