SpecPad: device‐independent NMR data visualization and processing based on the novel DART programming language and Html5 Web technology

SpecPad is a new device‐independent software program for the visualization and processing of one‐dimensional and two‐dimensional nuclear magnetic resonance (NMR) time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks. Another topic of interest is whether this technique also effectively supports the required sophisticated graphical and computational algorithms. SpecPad is device‐independent because DART's compiled executable code is JavaScript and can, therefore, be run by the browsers of PCs and tablets. Because of Html5 browser cache technology, SpecPad may be operated off‐line. Network access is only required during data import or export, e.g. via a Cloud service, or for software updates. A professional and easy to use graphical user interface consistent across all hardware platforms supports touch screen features on mobile devices for zooming and panning and for NMR‐related interactive operations such as phasing, integration, peak picking, or atom assignment. Copyright © 2017 John Wiley & Sons, Ltd.     

JGromacs: a Java package for analyzing protein simulations

In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .     

Developing adaptive QM/MM computer simulations for electrochemistry

We report the development of adaptive QM/MM computer simulations for electrochemistry, providing public access to all sources via the free and open source software development model. We present a modular workflow‐based MD simulation code as a platform for algorithms for partitioning space into different regions, which can be treated at different levels of theory on a per‐timestep basis. Currently implemented algorithms focus on targeting molecules and their solvation layers relevant to electrochemistry. Instead of using built‐in forcefields and quantum mechanical methods, the code features a universal interface, which allows for extension to a range of external forcefield programs and programs for quantum mechanical calculations, thus enabling the user to readily implement interfaces to those programs. The purpose of this article is to describe our codes and illustrate its usage. © 2016 Wiley Periodicals, Inc.     

Implementation and performance of the artificial force induced reaction method in the GRRM17 program

This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC‐AFIR), single‐component algorithm (SC‐AFIR), and double‐sphere algorithm (DS‐AFIR), are available, where the MC‐AFIR was the only algorithm which has been available in the previous 2014 version. The MC‐AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC‐AFIR performs automated generation of global or semiglobal reaction path network. The DS‐AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

JACOB: An enterprise framework for computational chemistry

Here, we present just a collection of beans (JACOB): an integrated batch‐based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user‐specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application‐programming interface provides a set of generic tools for processing large‐scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob . © 2013 Wiley Periodicals, Inc.     

Zherlock: an open source data analysis software

Zherlock is an open source software that provides state-of-the-art data analysis tools to the user in an intuitive and flexible way. It is a front-end to different numerical "engines" to produce a seamless integration of algorithms written in different computer languages. Of particular interest is creating an interface to high-level scientific languages such as Octave (a Matlab clone) and R (an S-PLUS clone) to enable efficient porting of new data analytical methods. Zherlock uses advanced scientific visualization tools in 2-D and 3-D and has been extended to work on virtual reality (VR) systems. Central to Zherlock is a visual programming environment (VPE) which enables diagram based programming. These diagrams consist of nodes and connection lines where each node is an operator or a method and lines describe the flow of data between nodes. A VPE is chosen for Zherlock because it forms an effective way to control the processing pipeline in complex data analyses. The VPE is similar in functionality to other programs such as IRIS Explorer, AVS or LabVIEW.     

PSI3: an open-source Ab Initio electronic structure package

PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis‐set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file‐system‐sizes), especially multi‐index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree‐Fock, multiconfigurational self‐consistent‐field, second‐order Møller‐Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second‐order perturbation theory; coupled cluster frequency‐dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born‐Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open‐source, GNU General Public License. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007     

Metal–Organic Frameworks: From Molecules/Metal Ions to Crystals to Superstructures

Metal–organic frameworks (MOFs) are among the most attractive porous materials known today, exhibiting very high surface areas, tuneable pore sizes and shapes, adjustable surface functionality, and flexible structures. Advances in the formation of MOF crystals, and in their subsequent assembly into more complex and/or composite superstructures, should expand the scope of these materials in many applications (e.g., drug delivery, chemical sensors, selective reactors and removal devices, etc.) and facilitate their integration onto surfaces and into devices. This Concept article aims to showcase recently developed synthetic strategies to control the one‐, two‐ and three‐dimensional (1‐, 2‐ and 3D) organisation of MOF crystals.     

Organic nanodielectrics for low voltage carbon nanotube thin film transistors and complementary logic gates

We report the implementation of three dimensionally cross-linked, organic nanodielectric multilayers as ultrathin gate dielectrics for a type of thin film transistor device that uses networks of single-walled carbon nanotubes as effective semiconductor thin films. Unipolar n- and p-channel devices are demonstrated by use of polymer coatings to control the behavior of the networks. Monolithically integrating these devices yields complementary logic gates. The organic multilayers provide exceptionally good gate dielectrics for these systems and allow for low voltage, low hysteresis operation. The excellent performance characteristics suggest that organic dielectrics of this general type could provide a promising path to SWNT-based thin film electronics.     

lipID—a software tool for automated assignment of lipids in mass spectra

A new software tool called lipID is reported, which supports the identification of glycerophospholipids, glycosphingolipids, fatty acids and small oligosaccharides in mass spectra. The user‐extendable software is a Microsoft (MS) Excel Add‐In developed using Visual Basic for Applications and is compatible with all Versions of MS Excel since MS Excel 97. It processes singly given mass‐to‐charge values as well as mass lists considering a number of user‐defined options. The software's mode of operation, usage and options are explained and the benefits and limitations of the tool are illustrated by means of three typical analytical examples of lipid analyses. Copyright © 2009 John Wiley & Sons, Ltd.     

Liquid‐Crystalline Ordering as a Concept in Materials Science: From Semiconductors to Stimuli‐Responsive Devices

While the unique optical properties of liquid crystals (LCs) are already well exploited for flat‐panel displays, their intrinsic ability to self‐organize into ordered mesophases, which are intermediate states between crystal and liquid, gives rise to a broad variety of additional applications. The high degree of molecular order, the possibility for large scale orientation, and the structural motif of the aromatic subunits recommend liquid‐crystalline materials as organic semiconductors, which are solvent‐processable and can easily be deposited on a substrate. The anisotropy of liquid crystals can further cause a stimuli‐responsive macroscopic shape change of cross‐linked polymer networks, which act as reversibly contracting artificial muscles. After illustrating the concept of liquid‐crystalline order in this Review, emphasis will be placed on synthetic strategies for novel classes of LC materials, and the design and fabrication of active devices.     

Challenges and prospects of ambient hybrid solar cell applications

The impending implementation of billions of Internet of Things and wireless sensor network devices has the potential to be the next digital revolution, if energy consumption and sustainability constraints can be overcome. Ambient photovoltaics provide vast universal energy that can be used to realise near-perpetual intelligent IoT devices which can directly transform diffused light energy into computational inferences based on artificial neural networks and machine learning. At the same time, a new architecture and energy model needs to be developed for IoT devices to optimize their ability to sense, interact, and anticipate. We address the state-of-the-art materials for indoor photovoltaics, with a particular focus on dye-sensitized solar cells, and their effect on the architecture of next generation IoT devices and sensor networks.

The impending implementation of billions of Internet of Things and wireless sensor network devices has the potential to be the next digital revolution, if energy consumption and sustainability constraints can be overcome.     

Microreactors as Tools for Synthetic Chemists—The Chemists' Round‐Bottomed Flask of the 21st Century?

Will microreactors replace the round‐bottomed flask to perform chemical reactions in the near future? Recent developments in the construction of microstructured reaction devices and their wide‐ranging applications in many different areas of chemistry suggest that they can have a significant impact on the way chemists conduct their experiments. Miniaturizing reactions offers many advantages for the synthetic organic chemist: high‐throughput scanning of reaction conditions, precise control of reaction variables, the use of small quantities of reagents, increased safety parameters, and ready scale‐up of synthetic procedures. A wide range of single‐ and multiphase reactions have now been performed in microfluidic‐based devices. Certainly, microreactors cannot be applied to all chemistries yet and microfluidic systems also have disadvantages. Limited reaction‐time range, high sensitivity to precipitating products, and new physical, chemical, and analytical challenges have to be overcome. This concept article presents an overview of microfluidic devices available for chemical synthesis and evaluates the potential of microreactor technology in organic synthesis.     

开发面向分析化学的复杂方程绘图求解软件

化学平衡的精确解析会涉及复杂方程的求解,而分析化学专业人员通常不完全具备相关算法和编程知识。所以,尽管当前硬件发达、编程语言丰富,精确解析仍然难以在分析化学课程中大规模推广。为此,基于Matlab语言,开发了具有针对性的方程求解软件。该软件以简洁的界面、直观的图像和自然的人机交互,实现方程的高效求解;对用户的编程要求非常低。期望通过这种方式,显著降低化学平衡精确解析中的软件使用成本,从而为大规模推广提供进一步的支持。本文介绍了该软件的基本原理和主要特点;通过3个复杂化学平衡实例,详细说明软件的使用方法以及注意事项。另外提供Android系统版本,免费使用。     

Piezoelectric Crystal Membrane Chemical Sensors Based on Fullerene and Macrocyclic Polyethers

Various reusable and sensitive piezoelectric (PZ) quartz crystal membrane sensors with home‐made computer interfaces for signal acquisition and data processing were developed to detect organic/inorganic vapors and organic/inorganic/biologic species in solutions, respectively. Fullerene(C60), fullerene derivatives and artificial macrocyclic polyethers, e.g., crown ethers and cryptands, were synthesized and applied as coating materials on quartz crystals of the PZ crystal sensors. The oscillating frequency of the quartz crystal decreased due to the adsorption of organic or inorganic species onto coating material molecules on the crystal surface. The crown ether‐coated PZ crystal gas detector exhibited high sensitivity with a frequency shift range of 10–340 Hz/(mg/L) for polar organic gases, a short response time (< 2.0 min.), good selectivity, and good reproducibility. The Ag(I)/crptand22 and Ru(III) / crptand22 coated PZ gas detectors were also prepared for nonpolar organic vapors, e.g., alkynes and alkenes. The frequency shifts of the nonpolar PZ sensors were in the order: alkynes > alkenes > alkanes. A Ti(IV)/Cryptand22‐coated PZ crystal sensor was also developed to detect the inorganic air pollutants, e.g., CO and NO₂. A piezoelectric gas sensor for both polar/nonpolar organic vapors based on C60‐cryptand22 was also prepared. The cryptand22‐coated PZ gas sensor was also employed as a GC detector for organic molecules. The cryptand22‐coated piezoelectric GC detectors compared well with the commercial thermal conductivity detector (TCD). The interaction between fullerene C60 and organic molecules was studied with a fullerene coated PZ gas detector. A multi‐channel PZ organic gas detector with PCA(Principal Component Analysis) and BPN (Back Propagation Neural) analysis methods was developed. Various liquid piezoelectric crystal sensors based on long‐chain macrocyclic polyethers, e.g., C₁₀H₂₁‐dibenzo‐16‐crown‐5, C₁₈H₃₇‐benzo‐15‐crown‐5, (C₁₇CO)₂‐cyptand22 and fullerene derivatives, e.g., C60‐NH‐cryptand22 and dibenzo‐16‐crown‐5‐C60, were also developed as HPLC detectors for metal ions, anions, and various organic compounds in solutions. The sensitive and highly selective PZ bio‐sensors based on enzymes, polyvinylaldehyde, polycinnaldehyde‐C60 and C60‐cryptand22 were developed to detect various biologic species, e.g., proteins, glucose, and urea. A quite sensitive EQCM (Electrochemical Quartz Crystal Micro‐balance) detection system was also developed for detection of trace heavy metal ions.     

Transforming Ionene Polymers into Efficient Cathode Interlayers with Pendent Fullerenes

A new and highly efficient cathode interlayer material for organic photovoltaics (OPVs) was produced by integrating C₆₀ fullerene monomers into ionene polymers. The power of these novel “C₆₀‐ionenes” for interface modification enables the use of numerous high work‐function metals (e.g., silver, copper, and gold) as the cathode in efficient OPV devices. C₆₀‐ionene boosted power conversion efficiencies (PCEs) of solar cells, fabricated with silver cathodes, from 2.79 % to 10.51 % for devices with a fullerene acceptor in the active layer, and from 3.89 % to 11.04 % for devices with a non‐fullerene acceptor in the active layer, demonstrating the versatility of this interfacial layer. The introduction of fullerene moieties dramatically improved the conductivity of ionene polymers, affording devices with high efficiency by reducing charge accumulation at the cathode/active layer interface. The power of C₆₀‐ionene to improve electron injection and extraction between metal electrodes and organic semiconductors highlights its promise to overcome energy barriers at the hard‐soft materials interface to the benefit of organic electronics.     

NMR data visualization,processing, and analysis on mobile devices

Touch‐screen computers are emerging as a popular platform for many applications, including those in chemistry and analytical sciences. In this work, we present our implementation of a new NMR ‘app’ designed for hand‐held and portable touch‐controlled devices, such as smartphones and tablets. It features a flexible architecture formed by a powerful NMR processing and analysis kernel and an intuitive user interface that makes full use of the smart devices haptic capabilities. Routine 1D and 2D NMR spectra acquired in most NMR instruments can be processed in a fully unattended way. More advanced experiments such as non‐uniform sampled NMR spectra are also supported through a very efficient parallelized Modified Iterative Soft Thresholding algorithm. Specific technical development features as well as the overall feasibility of using NMR software apps will also be discussed. All aspects considered the functionalities of the app allowing it to work as a stand‐alone tool or as a ‘companion’ to more advanced desktop applications such as Mnova NMR. Copyright © 2015 John Wiley & Sons, Ltd.     

A general-purpose minicomputer system for electrochemical studies

A software system (SYS) is described for a 16-bit minicomputer interfaced to a potentiostat and electrochemical cells, as well as various display and signal devices. The software controls the functions common to all electrochemical experiments, such as applying cell voltage, timing, sampling signals, displaying these on graphic devices, and smoothing data; it also loads specific user programs into core, for experiments requiring these functions. In this way, a new experiment can quickly be programmed and running; the software also contains some debugging aids. While the system described is specific to the minicomputer used, its general structure should be capable of implementation on any mini- or micro-computer.     

Molecular Materials That Can Both Emit Light and Conduct Charges: Strategies and Perspectives

Molecular materials with concomitant light‐emissive and semiconducting properties have received increasing attention in recent years. Such dual functional materials ensure the development of multifunctional devices (e.g., organic light‐emitting transistors) and the emergence of new technologies. However, owing to the fact that intermolecular interactions and dense packing have opposite effects on photoluminescence and charge‐carrier mobility, it is still rather challenging to rationally design high‐performance molecular materials that exhibit both semiconducting and light‐emissive properties. In fact, only a limited number of such dual functional materials are available, and most of their performances need to be further improved. In this concept article we discuss the design strategies and perspectives of this challenging area with the introduction of representative examples of such dual functional materials reported in recent years.