The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net
 .

/pdf/avogadro-an-advanced-semantic-chemical-editor-visualization-2imnj3h9vl.pdf

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Organic compounds offer new possibilities for high energy/power density, cost-effective, environmentally friendly, and functional rechargeable lithium batteries. For a long time, they have not constituted an important class of electrode materials, partly because of the large success and rapid development of inorganic intercalation compounds. In recent years, however, exciting progress has been made, bringing organic electrodes to the attention of the energy storage community. Herein thirty years' research efforts in the field of organic compounds for rechargeable lithium batteries are summarized. The working principles, development history, and design strategies of these materials, including organosulfur compounds, organic free radical compounds, organic carbonyl compounds, conducting polymers, non-conjugated redox polymers, and layered organic compounds are presented. The cell performances of these materials are compared, providing a comprehensive overview of the area, and straightforwardly revealing the advantages/disadvantages of each class of materials.

Organic Electrode Materials for Rechargeable Lithium Batteries

Organic electrode materials are very attractive for electrochemical energy storage devices because they can be flexible, lightweight, low cost, benign to the environment, and used in a variety of device architectures. They are not mere alternatives to more traditional energy storage materials, rather, they have the potential to lead to disruptive technologies. Although organic electrode materials for energy storage have progressed in recent years, there are still significant challenges to overcome before reaching large-scale commercialization. This review provides an overview of energy storage systems as a whole, the metrics that are used to quantify the performance of electrodes, recent strategies that have been investigated to overcome the challenges associated with organic electrode materials, and the use of computational chemistry to design and study new materials and their properties. Design strategies are examined to overcome issues with capacity/capacitance, device voltage, rate capability, and cycling stability in order to guide future work in the area. The use of low cost materials is highlighted as a direction towards commercial realization.

/pdf/the-rise-of-organic-electrode-materials-for-energy-storage-28pg8f2130.pdf

The rise of organic electrode materials for energy storage

Research on redox-flow batteries (RFBs) is currently experiencing a significant upturn, stimulated by the growing need to store increasing quantities of sustainably generated electrical energy. RFBs are promising candidates for the creation of smart grids, particularly when combined with photovoltaics and wind farms. To achieve the goal of "green", safe, and cost-efficient energy storage, research has shifted from metal-based materials to organic active materials in recent years. This Review presents an overview of various flow-battery systems. Relevant studies concerning their history are discussed as well as their development over the last few years from the classical inorganic, to organic/inorganic, to RFBs with organic redox-active cathode and anode materials. Available technologies are analyzed in terms of their technical, economic, and environmental aspects; the advantages and limitations of these systems are also discussed. Further technological challenges and prospective research possibilities are highlighted.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201604925

Redox-Flow Batteries: From Metals to Organic Redox-Active Materials

Heterocyclic pyrrole molecules are in situ aligned and polymerized in the -absence of an oxidant between layers of the 2D Ti3C2Tx (MXene), resulting in high volumetric and gravimetric capacitances with capacitance retention of 92% after 25,000 cycles at a 100 mV s(-1) scan rate.

Pseudocapacitive Electrodes Produced By Oxidant-Free Polymerization of Pyrrole Between the Layers of 2D Titanium Carbide (MXene)

https://iopscience.iop.org/article/10.1149/2.0971602jes/pdf

On the Benefits of a Symmetric Redox Flow Battery

The financial support from Lockheed Martin and the KAUST-Cornell Center for Energy and Sustainability (KAUST-CU) are greatly appreciated. MAL is supported by a National Defense Science and Engineering Graduate Fellowship. This work is based upon research conducted at the Cornell high energy synchrotron source (CHESS) which is supported by the National Science Foundation and the National Institutes of Health/National Institute of General Medical Sciences under NSF award DMR-0936384. The authors gratefully acknowledge assistance from CHESS staff scientist Dr. Darren Dale, and prior synthesis of the BMTTD molecule by Dr. Jay C. Henderson.

Poly(2,5-dimercapto-1,3,4-thiadiazole) as a cathode for rechargeable lithium batteries with dramatically improved performance.

Synthesis and Characterization of Poly-3,4-ethylenedioxythiophene/2,5-Dimercapto-1,3,4-thiadiazole (PEDOT-DMcT) Hybrids

Electrical energy storage devices will play a key role in the development of sustainable energy production and usage, and for integrating intermittent and renewable sources into the energy landscape. One strategy for developing improved energy storage materials and devices is to take advantage of capacitive and pseudocapacitive electrodes such as activated carbons or conducting polymers. However, these materials generally suffer from low energy densities. Functionalization of these materials with pendant redox units has been proposed as a method to improve the energy densities while maintaining the high rate capability. In this report, we present the synthesis and thorough characterization of one such candidate pendant molecule, 2,5-bis(methylthio)thieno[3,2-b]thiophene, and assess its potential use as a cathode material. Electrochemical, spectroelectrochemical and computational data suggest that bis(methylthio)thieno[3,2-b]thiophene is a lightweight molecule, capable of undergoing multiple reversible redox processes, and a good candidate for improving the energy density of cathode materials while still offering high rate (power) capability.

http://www.rsc.org/suppdata/jm/c1/c1jm10664c/c1jm10664c.pdf

Towards organic energy storage: characterization of 2,5-bis(methylthio)thieno[3,2-b]thiophene

Over the past decade, there has been a great deal of interest in graphene with regards to its electrochemical behavior. Previous studies have focused on understanding fundamental processes such as charge transfer and molecular transport at the graphene–electrolyte interface as well as on applications of graphene in electronic, optical, and mechanical systems. We present illustrative examples of large area, single layer graphene platforms for applications such as optical and sensing devices as well as microfluidic systems. Three examples of graphene modified with thin polymer films are discussed. We have explored the use of graphene as an electrochemical platform for surface-generated electrogenerated chemiluminescence (ECL) using poly-[Ru(v-bpy)3]2+, where v-bpy is 4-vinyl, 4′-methyl 2,2′-bipyridine, as a model system. We found that while graphene can sustain ECL conditions, there was film degradation during ECL, as demonstrated by a decrease in ECL intensity upon potential cycling even in the presence of a graphene coating (“graphene blanket”). Using poly 3,4-ethylenedioxythiophene (EDOT), we demonstrate a facile method of fabricating electrochromic electrodes from large area graphene. The oxidation of NADH at graphene was catalyzed using an electrodeposited layer of 3,4-dihydroxybenzaldehyde as an effective redox mediator. In addition, we describe the fabrication and characterization of a microfluidic device based on a solution-gated field effect transistor which was able to detect changes of 60 mV per pH unit change in an inverted cell design. On the other hand, a 29 mV shift in the Dirac point per unit pH change was measured with our microfluidic devices, and a ca. 10% FET conductance change was measured when we continuously changed the pH in solution from 6.91 to 7.64 in the microfluidic channel, demonstrating local microfluidic pH sensing (albeit non-Nerstian) in real time.

Single layer graphene as an electrochemical platform

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