Chemical Informatics Functionality in R

The flexibility and scope of the R programming environment has made it a popular choice for statistical modeling and scientific prototyping in a number of fields. In the field of chemistry, R provides several tools for a variety of problems related to statistical modeling of chemical information. However, one aspect common to these tools is that they do not have direct access to the information that is available from chemical structures, such as contained in molecular descriptors. We describe the rcdk package that provides the R user with access to the CDK, a Java framework for cheminformatics. As a result, it is possible to read in a variety of molecular formats, calculate molecular descriptors and evaluate fingerprints. In addition, we describe the rpubchem that will allow access to the data in PubChem, a public repository of molecular structures and associated assay data for approximately 8 million compounds. Currently, the package allows access to structural information as well as some simple molecular properties from PubChem. In addition the package allows access to bio-assay data from the PubChem FTP servers.

A Fully Differential CMOS Potentiostat

A CMOS potentiostat for chemical sensing in a noisy environment is presented. The potentiostat measures bidirectional electrochemical redox currents proportional to the concentration of a chemical down to pico-ampere range. The fully differential architecture with differential recording electrodes suppresses the common mode interference. A 200μm×200μm prototype was fabricated in a standard 0.35μm standard CMOS technology and yields a 70dB dynamic range. The in-channel analog-to-digital converter (ADC) performs 16-bit current-tofrequency quantization. The integrated potentiostat functionality is validated in electrical and electrochemical experiments

Electrochemical impedance spectroscopy as a tool for probing the functionality of ion-selective membranes

Recent success in lowering of the detection limit of ion-selective electrodes (ISEs) to part-perbillion levels have opened up the possibility for their application in environmental analysis. Its simplicity, low cost, and low power requirement coupled with excellent selectivity and sensitivity make ISEs excellent detecting system in autonomous and deployable sensing devices for routine analysis and as early warning systems. However, the necessity for calibration of detecting systems implies the use of sometimes complicated and costly systems for calibration solution and waste handling, pumps and data acquisition including the labour for system maintenance. Reducing the need for sensor calibration (or its complete elimination) would not only simplify sensing devices and reduce their costs but would allow integration of chemical sensors into the emerging area of wireless sensing networks (WSNs). It is envisioned that this integration will bring new dimensions into chemical sensing and bring benefits in many aspects of human lives. Here, we describe our attempts to address the issue of reducing the need for sensor calibration. The functionality of a typical physical transducer is probed using electrical signals testing its resistance, impedance, conductance etc. We employ a similar strategy and apply relatively simple AC signals to an ion-selective membrane in order to probe its functionality after it has been subjected to conditions that simulate in-situ long-term deployments. For example, we observe the impedance spectra of membranes that have been physically damaged, biofouled and/or have components leached out. Comparing this information with the sensor's potentiometric behaviour, we can draw conclusions regarding the functionality of the devices and their suitability to continue serving as a reliable detectors, for example, in remote locations

In Situ Nanomechanical Measurements of Interfacial Strength in Membrane-Embedded Chemically Functionalized Si Microwires for Flexible Solar Cells

Arrays of vertically aligned Si microwires embedded in polydimethylsiloxane (PDMS) have emerged as a promising candidate for use in solar energy conversion devices. Such structures are lightweight and concurrently demonstrate competitive efficiency and mechanical flexibility. To ensure reliable functioning under bending and flexing, strong interfacial adhesion between the nanowire and the matrix is needed. In situ uniaxial tensile tests of individual, chemically functionalized, Si microwires embedded in a compliant PDMS matrix reveal that chemical functionality on Si microwire surfaces is directly correlated with interfacial adhesion strength. Chemical functionalization can therefore serve as an effective methodology for accessing a wide range of interfacial adhesion between the rigid constituents and the soft polymer matrix; the adhesion can be quantified by measuring the mechanical strength of such systems

Photoactivated biological processes as quantum measurements.

We outline a framework for describing photoactivated biological reactions as generalized quantum measurements of external fields, for which the biological system takes on the role of a quantum meter. By using general arguments regarding the Hamiltonian that describes the measurement interaction, we identify the cases where it is essential for a complex chemical or biological system to exhibit nonequilibrium quantum coherent dynamics in order to achieve the requisite functionality. We illustrate the analysis by considering measurement of the solar radiation field in photosynthesis and measurement of the earth's magnetic field in avian magnetoreception

Development of a compact, IoT-enabled electronic nose for breath analysis

In this paper, we report on an in-house developed electronic nose (E-nose) for use with breath analysis. The unit consists of an array of 10 micro-electro-mechanical systems (MEMS) metal oxide (MOX) gas sensors produced by seven manufacturers. Breath sampling of end-tidal breath is achieved using a heated sample tube, capable of monitoring sampling-related parameters, such as carbon dioxide (CO2), humidity, and temperature. A simple mobile app was developed to receive real-time data from the device, using Wi-Fi communication. The system has been tested using chemical standards and exhaled breath samples from healthy volunteers, before and after taking a peppermint capsule. Results from chemical testing indicate that we can separate chemical standards (acetone, isopropanol and 1-propanol) and different concentrations of isobutylene. The analysis of exhaled breath samples demonstrate that we can distinguish between pre- and post-consumption of peppermint capsules; area under the curve (AUC): 0.81, sensitivity: 0.83 (0.59–0.96), specificity: 0.72 (0.47–0.90), p-value: <0.001. The functionality of the developed device has been demonstrated with the testing of chemical standards and a simplified breath study using peppermint capsules. It is our intention to deploy this system in a UK hospital in an upcoming breath research study

Influence of Sulfoxide Group Placement on Polypeptide Conformational Stability.

The synthesis of a homologous series containing five new nonionic sulfoxide containing polypeptides was described. Sulfoxide groups bestowed water solubility for all homologues, which allowed their use as a model for study of helix-coil transitions in water while avoiding contributions from charged groups or phase separation. Polypeptides were found to adopt chain conformations in water that were dependent on distance of sulfoxides from chain backbones, overall side-chain lengths, and solvent. These results allow preparation of polypeptide segments with different chain conformations without changing chemical functionality for potential use in structural studies and functional applications

Quorumpeps database : chemical space, microbial origin and functionality of quorum sensing peptides

Quorum-sensing (QS) peptides are biologically attractive molecules, with a wide diversity of structures and prone to modifications altering or presenting new functionalities. Therefore, the Quorumpeps database (http://quorumpeps.ugent.be) is developed to give a structured overview of the QS oligopeptides, describing their microbial origin (species), functionality (method, result and receptor), peptide links and chemical characteristics (3D-structure-derived physicochemical properties). The chemical diversity observed within this group of QS signalling molecules can be used to develop new synthetic bio-active compounds

Removal of GaAs growth substrates from II-VI semiconductor heterostructures

We report on a process that enables the removal of II-VI semiconductor epilayers from their GaAs growth substrate and their subsequent transfer to arbitrary host environments. The technique combines mechanical lapping and layer selective chemical wet etching and is generally applicable to any II-VI layer stack. We demonstrate the non-invasiveness of the method by transferring an all-II-VI magnetic resonant tunneling diode. High resolution X-ray diffraction proves that the crystal integrity of the heterostructure is preserved. Transport characterization confirms that the functionality of the device is maintained and even improved, which is ascribed to completely elastic strain relaxation of the tunnel barrier layer