Institute for Molecular Science

Covalent organic frameworks (COFs) are a class of crystalline porous polymers that allow the atomically precise integration of organic units to create predesigned skeletons and nanopores. They have recently emerged as a new molecular platform for designing promising organic materials for gas storage, catalysis, and optoelectronic applications. The reversibility of dynamic covalent reactions, diversity of building blocks, and geometry retention are three key factors involved in the reticular design and synthesis of COFs. This tutorial review describes the basic design concepts, the recent synthetic advancements and structural studies, and the frontiers of functional exploration.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure and dynamics of hydrated ionsHitoshi. Ohtaki and Tamas. RadnaiCite this: Chem. Rev. 1993, 93, 3, 1157–1204Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/cr00019a014https://doi.org/10.1021/cr00019a014research-articleACS PublicationsRequest reuse permissionsArticle Views10177Altmetric-Citations1976LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts

Single wall carbon nanotubes (SWNTs) that are found as close-packed arrays in crystalline ropes have been studied by using Raman scattering techniques with laser excitation wavelengths in the range from 514.5 to 1320 nanometers. Numerous Raman peaks were observed and identified with vibrational modes of armchair symmetry (n, n) SWNTs. The Raman spectra are in good agreement with lattice dynamics calculations based on C-C force constants used to fit the two-dimensional, experimental phonon dispersion of a single graphene sheet. Calculated intensities from a nonresonant, bond polarizability model optimized for sp2 carbon are also in qualitative agreement with the Raman data, although a resonant Raman scattering process is also taking place. This resonance results from the one-dimensional quantum confinement of the electrons in the nanotube.

Conjugated microporous polymers (CMPs) are a class of organic porous polymers that combine π-conjugated skeletons with permanent nanopores, in sharp contrast to other porous materials that are not π-conjugated and with conventional conjugated polymers that are nonporous. As an emerging material platform, CMPs offer a high flexibility for the molecular design of conjugated skeletons and nanopores. Various chemical reactions, building blocks and synthetic methods have been developed and a broad variety of CMPs with different structures and specific properties have been synthesized, driving the rapid growth of the field. CMPs are unique in that they allow the complementary utilization of π-conjugated skeletons and nanopores for functional exploration; they have shown great potential for challenging energy and environmental issues, as exemplified by their excellent performance in gas adsorption, heterogeneous catalysis, light emitting, light harvesting and electrical energy storage. This review describes the molecular design principles of CMPs, advancements in synthetic and structural studies and the frontiers of functional exploration and potential applications.

Small gold clusters (approximately 1 nm) protected by molecules of a tripeptide, glutathione (GSH), were prepared by reductive decomposition of Au(I)-SG polymers at a low temperature and separated into a number of fractions by polyacrylamide gel electrophoresis (PAGE). Chemical compositions of the fractionated clusters determined previously by electrospray ionization (ESI) mass spectrometry (Negishi, Y. et al. J.Am. Chem. Soc. 2004, 126, 6518) were reassessed by taking advantage of freshly prepared samples, higher mass resolution, and more accurate mass calibration; the nine smallest components are reassigned to Au10(SG)10, Au15(SG)13, Au18(SG)14, Au22(SG)16, Au22(SG)17, Au25(SG)18, Au29(SG)20, Au33(SG)22, and Au39(SG)24. These assignments were further confirmed by measuring the mass spectra of the isolated Au:S(h-G) clusters, where h-GSH is a homoglutathione. It is proposed that a series of the isolated Au:SG clusters corresponds to kinetically trapped intermediates of the growing Au cores. The relative abundance of the isolated clusters was correlated well with the thermodynamic stabilities against unimolecular decomposition. The electronic structures of the isolated Au:SG clusters were probed by X-ray photoelectron spectroscopy (XPS) and optical spectroscopy. The Au(4f) XPS spectra illustrate substantial electron donation from the gold cores to the GS ligands in the Au:SG clusters. The optical absorption and photoluminescence spectra indicate that the electronic structures of the Au:SG clusters are well quantized; embryos of the sp band of the bulk gold evolve remarkably depending on the number of the gold atoms and GS ligands. The comparison of these spectral data with those of sodium Au(I) thiomalate and 1.8 nm Au:SG nanocrystals (NCs) reveals that the subnanometer-sized Au clusters thiolated constitute a distinct class of binary system which lies between the Au(I)-thiolate complexes and thiolate-protected Au NCs.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTDiradicalsManabu Abe*View Author Information Department of Chemistry, Graduate School of Science, Hiroshima University (HIRODAI), 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan Institute for Molecular Science (IMS), Okazaki, Aichi 444-8787, Japan JST-CREST, 5 Sanbancho, Chiyodaku, Tokyo 102-0075, Japan*E-mail: [email protected]Cite this: Chem. Rev. 2013, 113, 9, 7011–7088Publication Date (Web):July 24, 2013Publication History Received31 January 2013Published online24 July 2013Published inissue 11 September 2013https://pubs.acs.org/doi/10.1021/cr400056ahttps://doi.org/10.1021/cr400056areview-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views27957Altmetric-Citations1130LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Electrical energy,Energy,Molecules,Quantum mechanics,Reaction products Get e-Alerts

Conjugated covalent networks Although graphene and related materials are two-dimensional (2D) fully conjugated networks, similar covalent organic frameworks (COFs) could offer tailored electronic and magnetic properties. Jin et al. synthesized a fully π-conjugated COF through condensation reactions of tetrakis(4-formylphenyl)pyrene and 1,4-phenylenediacetonitrile. The reactions were reversible, which provides the self-healing needed to form a crystalline material of stacked, π-bonded 2D sheets. Chemical oxidation of this semiconductor with iodine greatly enhanced its conductivity, and the radicals formed on the pyrene centers imparted a high spin density and paramagnetism. Science , this issue p. 673

We present possible observing scenarios for the Advanced LIGO, Advanced Virgo and KAGRA gravitational-wave detectors over the next decade, with the intention of providing information to the astronomy community to facilitate planning for multi-messenger astronomy with gravitational waves. We estimate the sensitivity of the network to transient gravitational-wave signals, and study the capability of the network to determine the sky location of the source. We report our findings for gravitational-wave transients, with particular focus on gravitational-wave signals from the inspiral of binary neutron star systems, which are the most promising targets for multi-messenger astronomy. The ability to localize the sources of the detected signals depends on the geographical distribution of the detectors and their relative sensitivity, and [Formula: see text] credible regions can be as large as thousands of square degrees when only two sensitive detectors are operational. Determining the sky position of a significant fraction of detected signals to areas of 5-[Formula: see text] requires at least three detectors of sensitivity within a factor of [Formula: see text] of each other and with a broad frequency bandwidth. When all detectors, including KAGRA and the third LIGO detector in India, reach design sensitivity, a significant fraction of gravitational-wave signals will be localized to a few square degrees by gravitational-wave observations alone.

The density functional theory method (M05-2X/6-31G(d)) was used to investigate reaction mechanisms for deoxygenation of graphene oxides (GOs) with hydrazine or heat treatment. Three mechanisms were identified as reducing epoxide groups of GO with hydrazine as a reducing agent. No reaction path was found for the hydrazine-mediated reductions of the hydroxyl, carbonyl, and carboxyl groups of GO. We instead discovered the mechanisms for dehydroxylation, decarbonylation, and decarboxylation using heat treatment. The hydrazine de-epoxidation and thermal dehydroxylation of GO have opposite dependencies on the reaction temperature. In both reduction types, the oxygen functionalities attached to the interior of an aromatic domain in GO are removed more easily, both kinetically and thermodynamically, than those attached at the edges of an aromatic domain. The hydrazine-mediated reductions of epoxide groups at the edges are suspended by forming hydrazino alcohols. We provide atomic-level elucidation for the deoxygenation of GO, characterize the product structures, and suggest how to optimize the reaction conditions further.

Applications of the discrete variational (DV) Xα molecular orbital method based on the self-consistent Hartree-Fock-Slater model to metal clusters are presented. Numerical basis functions are utilized in the present calculations. Variations of orbital energies and populations with exchange scaling parameter α are investigated. It is proved that the self-consistent-charge (SCC) approximation to the SCF method gives accurate orbital energies. The numerical basis SCC-DV-Xα method is shown to be very efficient for studies of rather large metal clusters such as Ni 13 .

Condensation of hydrazine with 1,3,6,8-tetrakis(4-formylphenyl)pyrene under solvothermal conditions yields highly crystalline two-dimensional covalent organic frameworks. The pyrene units occupy the vertices and the diazabutadiene (-C═N-N═C-) linkers locate the edges of rohmbic-shaped polygon sheets, which further stack in an AA-stacking mode to constitute periodically ordered pyrene columns and one-dimensional microporous channels. The azine-linked frameworks feature permanent porosity with high surface area and exhibit outstanding chemical stability. By virtue of the pyrene columnar ordering, the azine-linked frameworks are highly luminescent, whereas the azine units serve as open docking sites for hydrogen-bonding interactions. These synergestic functions of the vertices and edge units endow the azine-linked pyrene frameworks with extremely high sensitivity and selectivity in chemosensing, for example, the selective detection of 2,4,6-trinitrophenol explosive. We anticipate that the extension of the present azine-linked strategy would not only increase the structural diversity but also expand the scope of functions based on this highly stable class of covalent organic frameworks.

Three mammalian hyaluronan synthase genes, HAS1, HAS2, and HAS3, have recently been cloned. In this study, we characterized and compared the enzymatic properties of these three HAS proteins. Expression of any of these genes in COS-1 cells or rat 3Y1 fibroblasts yielded de novo formation of a hyaluronan coat. The pericellular coats formed by HAS1 transfectants were significantly smaller than those formed by HAS2 or HAS3 transfectants. Kinetic studies of these enzymes in the membrane fractions isolated from HAS transfectants demonstrated that HAS proteins are distinct from each other in enzyme stability, elongation rate of HA, and apparent K(m) values for the two substrates UDP-GlcNAc and UDP-GlcUA. Analysis of the size distributions of hyaluronan generated in vitro by the recombinant proteins demonstrated that HAS3 synthesized hyaluronan with a molecular mass of 1 x 10(5) to 1 x 10(6) Da, shorter than those synthesized by HAS1 and HAS2 which have molecular masses of 2 x 10(5) to approximately 2 x 10(6) Da. Furthermore, comparisons of hyaluronan secreted into the culture media by stable HAS transfectants showed that HAS1 and HAS3 generated hyaluronan with broad size distributions (molecular masses of 2 x 10(5) to approximately 2 x 10(6) Da), whereas HAS2 generated hyaluronan with a broad but extremely large size (average molecular mass of >2 x 10(6) Da). The occurrence of three HAS isoforms with such distinct enzymatic characteristics may provide the cells with flexibility in the control of hyaluronan biosynthesis and functions.

Gold nanoclusters (phi = 1.3 nm) stabilized by poly(N-vinyl-2-pyrrolidone) (Au:PVP NCs) readily oxidize benzylic alcohols to the corresponding aldehydes and/or carboxylic acids under ambient temperature in water. Kinetic measurement revealed that smaller Au:PVP NCs exhibit higher catalytic activity than larger (9.5 nm) homologues and, more surprisingly, than Pd:PVP NCs of comparable size (1.5 and 2.2 nm). On the basis of the marked difference in the kinetic isotope effect and activation energy between Au:PVP and Pd:PVP NCs, a reaction mechanism for alcohol oxidation catalyzed by Au:PVP NCs is proposed in which a superoxo-like molecular oxygen species adsorbed on the surface of the small Au NCs abstracts a hydrogen atom from the alkoxide.

Blue belt: Condensation polymerization of pyrene (blue) and triphenylene (green) monomers leads to the formation of a hexagonal mesoporous covalent organic framework (see picture). This material exists in a belt shape, absorbs photons over a wide wavelength range to emit them as blue luminescence, and is semiconducting, as well as being capable of repetitive on–off switching. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.

Prediction of chemical bioactivity and physical properties has been one of the most important applications of statistical and more recently, machine learning and artificial intelligence methods in chemical sciences. This field of research, broadly known as quantitative structure-activity relationships (QSAR) modeling, has developed many important algorithms and has found a broad range of applications in physical organic and medicinal chemistry in the past 55+ years. This Perspective summarizes recent technological advances in QSAR modeling but it also highlights the applicability of algorithms, modeling methods, and validation practices developed in QSAR to a wide range of research areas outside of traditional QSAR boundaries including synthesis planning, nanotechnology, materials science, biomaterials, and clinical informatics. As modern research methods generate rapidly increasing amounts of data, the knowledge of robust data-driven modelling methods professed within the QSAR field can become essential for scientists working both within and outside of chemical research. We hope that this contribution highlighting the generalizable components of QSAR modeling will serve to address this challenge.

Pulsed laser vaporization of a heated, Fe/Ni or Co/Ni catalyzed, carbon target in argon gas has been used to synthesize single-wall carbon nanotubes (SWNTs). Electron microscopy, x-ray diffraction, and Raman spectroscopy were all used to study the effect of the catalyst on the tube yield, and the evolution of the tube diameter distribution with increasing growth environment temperature $T$. By controlling the temperature in the range $780<T<1050\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$, we have been able to tune the diameter of the tubules from $\ensuremath{\sim}0.81$ to $\ensuremath{\sim}1.51\mathrm{nm}$. The threshold temperature for significant SWNT production was found to be $\ensuremath{\sim}850\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$.

One of the keys to highly efficient phosphorescent emission in organic light-emitting devices is to confine triplet excitons generated within the emitting layer. We employ “starburst” perfluorinated phenylenes (C60F42) as a both hole- and exciton-block layer, and a hole-transport material 4,4′,4″-tri(N-carbazolyl) triphenylamine as a host for the phosphorescent dopant dye in the emitting layer. A maximum external quantum efficiency reaches to 19.2%, and keeps over 15% even at high current densities of 10–20 mA/cm2, providing several times the brightness of fluorescent tubes for lighting. The onset voltage of the electroluminescence is as low as 2.4 V and the peak power efficiency is 70–72 lm/W, promising for low-power display devices.

In complex systems with many degrees of freedom such as peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present three new generalized-ensemble algorithms that combine the merits of the above methods. The effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems.

Ordered open channels found in two-dimensional covalent organic frameworks (2D COFs) could enable them to adsorb carbon dioxide. However, the frameworks' dense layer architecture results in low porosity that has thus far restricted their potential for carbon dioxide adsorption. Here we report a strategy for converting a conventional 2D COF into an outstanding platform for carbon dioxide capture through channel-wall functionalization. The dense layer structure enables the dense integration of functional groups on the channel walls, creating a new version of COFs with high capacity, reusability, selectivity, and separation productivity for flue gas. These results suggest that channel-wall functional engineering could be a facile and powerful strategy to develop 2D COFs for high-performance gas storage and separation.