Gas-Induced Electrical and Magnetic Modulation of Two-Dimensional Conductive Metal-Organic Framework.

Controlled modulation of electronic and magnetic properties in stimuli-responsive materials provides valuable insights for the design of magnetoelectric or multiferroic devices. This paper demonstrates the modulation of electrical and magnetic properties of a semiconductive, paramagnetic metal-organic framework (MOF) Cu3(C6O6)2 with small gaseous molecules, NH3, H2S, and NO. This study merges chemiresistive and magnetic tests to reveal that the MOF undergoes simultaneous changes in electrical conductance and magnetization that are uniquely modulated by each gas. The features of response, including direction, magnitude, and kinetics, are modulated by the physicochemical properties of the gaseous molecules. This study advances the design of multifunctional materials capable of undergoing simultaneous changes in electrical and magnetic properties in response to chemical stimuli.

Fabrication of Multifunctional Electronic Textiles Using Oxidative Restructuring of Copper into a Cu-Based Metal-Organic Framework.

This paper describes a novel synthetic approach for the conversion of zero-valent copper metal into a conductive two-dimensional layered metal-organic framework (MOF) based on 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) to form Cu3(HHTP)2. This process enables patterning of Cu3(HHTP)2 onto a variety of flexible and porous woven (cotton, silk, nylon, nylon/cotton blend, and polyester) and non-woven (weighing paper and filter paper) substrates with microscale spatial resolution. The method produces conductive textiles with sheet resistances of 0.1-10.1 MΩ/cm2, depending on the substrate, and uniform conformal coatings of MOFs on textile swatches with strong interfacial contact capable of withstanding chemical and physical stresses, such as detergent washes and abrasion. These conductive textiles enable simultaneous detection and detoxification of nitric oxide and hydrogen sulfide, achieving part per million limits of detection in dry and humid conditions. The Cu3(HHTP)2 MOF also demonstrated filtration capabilities of H2S, with uptake capacity up to 4.6 mol/kgMOF. X-ray photoelectron spectroscopy and diffuse reflectance infrared spectroscopy show that the detection of NO and H2S with Cu3(HHTP)2 is accompanied by the transformation of these species to less toxic forms, such as nitrite and/or nitrate and copper sulfide and Sx species, respectively. These results pave the way for using conductive MOFs to construct extremely robust electronic textiles with multifunctional performance characteristics.

Epitaxial Self-Assembly of Interfaces of 2D Metal-Organic Frameworks for Electroanalytical Detection of Neurotransmitters.

This paper identifies the electrochemical properties of individual facets of anisotropic layered conductive metal-organic frameworks (MOFs) based on M3(2,3,6,7,10,11-hexahydroxytriphenylene)2 (M3(HHTP)2) (M = Co, Ni). The electroanalytical advantages of each facet are then applied toward the electrochemical detection of neurochemicals. By employing epitaxially controlled deposition of M3(HHTP)2 MOFs on electrodes, the contribution of the basal plane ({001} facets) and edge sites ({100} facets) of these MOFs can be individually determined using electrochemical characterization techniques. Despite having a lower observed heterogeneous electron transfer rate constant, the {001} facets of the M3(HHTP)2 systems prove more selective and sensitive for the detection of dopamine than the {100} facets of the same MOF, with the limit of detection (LOD) of 9.9 ± 2 nM in phosphate-buffered saline and 214 ± 48 nM in a simulated cerebrospinal fluid. Langmuir isotherm studies accompanied by all-atom MD simulations suggested that the observed improvement in performance and selectivity is related to the adsorption characteristics of analytes on the basal plane versus edge sites of the MOF interfaces. This work establishes that the distinct crystallographic facets of 2D MOFs can be used to control the fundamental interactions between analyte and electrode, leading to tunable electrochemical properties by controlling their preferential orientation through self-assembly.

Bimetallic Two-Dimensional Metal-Organic Frameworks for the Chemiresistive Detection of Carbon Monoxide.

This paper describes the demonstration of a series of heterobimetallic, isoreticular 2D conductive metal-organic frameworks (MOFs) with metallophthalocyanine (MPc, M=Co and Ni) units interconnected by Cu nodes towards low-power chemiresistive sensing of ppm levels of carbon monoxide (CO). Devices achieve a sub-part-per-million (ppm) limit of detection (LOD) of 0.53 ppm toward CO at a low driving voltage of 0.1 V. MPc-based Cu-linked MOFs can continuously detect CO at 50 ppm, the permissible exposure limit required by the Occupational Safety and Health Administration (OSHA), for multiple exposures, and realize CO detection in air and in humid environment. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), density functional theory (DFT) calculations, and comparison experiments suggest the contribution of Cu nodes to CO binding and the essential role of MPc units in tuning and amplifying the sensing response.

Conductive Stimuli-Responsive Coordination Network Linked with Bismuth for Chemiresistive Gas Sensing.

This paper describes the design, synthesis, characterization, and performance of a novel semiconductive crystalline coordination network, synthesized using 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) ligands interconnected with bismuth ions, toward chemiresistive gas sensing. Bi(HHTP) exhibits two distinct structures upon hydration and dehydration of the pores within the network, Bi(HHTP)-α and Bi(HHTP)-ß, respectively, both with unprecedented network topology (2,3-c and 3,4,4,5-c nodal net stoichiometry, respectively) and unique corrugated coordination geometries of HHTP molecules held together by bismuth ions, as revealed by a crystal structure resolved via microelectron diffraction (MicroED) (1.00 Å resolution). Good electrical conductivity (5.3 × 10-3 S·cm-1) promotes the utility of this material in the chemical sensing of gases (NH3 and NO) and volatile organic compounds (VOCs: acetone, ethanol, methanol, and isopropanol). The chemiresistive sensing of NO and NH3 using Bi(HHTP) exhibits limits of detection 0.15 and 0.29 parts per million (ppm), respectively, at low driving voltages (0.1-1.0 V) and operation at room temperature. This material is also capable of exhibiting unique and distinct responses to VOCs at ppm concentrations. Spectroscopic assessment via X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopic methods (i.e., attenuated total reflectance-infrared spectroscopy (ATR-IR) and diffuse reflectance infrared Fourier transformed spectroscopy (DRIFTS)), suggests that the sensing mechanisms of Bi(HHTP) to VOCs, NO, and NH3 comprise a complex combination of steric, electronic, and protic properties of the targeted analytes.

Employing Conductive Metal-Organic Frameworks for Voltammetric Detection of Neurochemicals.

This paper describes the first implementation of an array of two-dimensional (2D) layered conductive metal-organic frameworks (MOFs) as drop-casted film electrodes that facilitate voltammetric detection of redox active neurochemicals in a multianalyte solution. The device configuration comprises a glassy carbon electrode modified with a film of conductive MOF (M3HXTP2; M = Ni, Cu; and X = NH, 2,3,6,7,10,11-hexaiminotriphenylene (HITP) or O, 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP)). The utility of 2D MOFs in voltammetric sensing is measured by the detection of ascorbic acid (AA), dopamine (DA), uric acid (UA), and serotonin (5-HT) in 0.1 M PBS (pH = 7.4). In particular, Ni3HHTP2 MOFs demonstrated nanomolar detection limits of 63 ± 11 nM for DA and 40 ± 17 nM for 5-HT through a wide concentration range (40 nM-200 µM). The applicability in biologically relevant detection was further demonstrated in simulated urine using Ni3HHTP2 MOFs for the detection of 5-HT with a nanomolar detection limit of 63 ± 11 nM for 5-HT through a wide concentration range (63 nM-200 µM) in the presence of a constant background of DA. The implementation of conductive MOFs in voltammetric detection holds promise for further development of highly modular, sensitive, selective, and stable electroanalytical devices.

The effectiveness of a novel cable-driven gait trainer (Robowalk) combined with conventional physiotherapy compared to conventional physiotherapy alone following stroke: a randomised controlled trial.

There is increasing interest in gait training devices to improve walking ability in people following stroke. This randomised controlled trial aimed to compare the effectiveness of the Robowalk, a novel cable-driven gait trainer combined with conventional physiotherapy to conventional physiotherapy alone in improving walking speed, endurance, balance, functional outcomes, and quality of life in people following stroke. Rehabilitation inpatients within 3 months following stroke (n = 40) were randomised to standard care with conventional physiotherapy ('control,' n = 20) and cable-driven gait trainer combined with conventional physiotherapy ('intervention,' n = 20). All participants received 1 hour of physiotherapy a day, 5 days a week. The control group received conventional physiotherapy only; the intervention group received a combination of 30 minutes of conventional physiotherapy and 30 minutes of cable-driven gait trainer consecutively. Outcome measures were 10-metre walk test (primary outcome), 6-minute walk test, timed up and go, step test, Functional Independence Measure, and EuroQol five-dimension scale. Evaluation timepoints were on admission (T0), discharge (T1), and 4 weeks post discharge (T2). There were no differences between groups at T0, T1, and T2 in all outcome measures although there was a trend towards a larger and more sustained improvement in 10-metre walk test in favour of the intervention group and in Functional Independence Measure motor and self-care in favour of the control group, both at T2. The combination of cable-driven gait trainer with conventional physiotherapy appears as effective as conventional physiotherapy alone in improving gait outcomes in people following a recent stroke. Further studies are required to confirm these findings and determine optimal dosing regimens and long-term outcomes.

Dendritic architectures by orthogonal thiol-maleimide "click" and furan-maleimide dynamic covalent chemistries.

A set of dendrons and dendrimers is synthesized divergently using an orthogonal combination of kinetically-driven thiol-maleimide "click" chemistry and thermodynamically reversible furan-maleimide cycloaddition/retrocycloaddition reactions. Growth is controlled by taking advantage of the selective thiol-ene addition of thiols to the electron withdrawn alkene of maleimide in the presence of electron rich alkene of oxanorbornene. Subsequent activation of growing dendrons/dendrimers requires only heat to induce the dynamic covalent liberation of peripheral furan protecting groups. The methodology introduced provides a new route to multifunctional dendrimers that could, in principle, be synthesized by introducing different branched monomers at any stage of dendrimer growth, allowing dendrimer architectures and properties to be better tailored to their intended applications.

Two-Dimensional Chemiresistive Covalent Organic Framework with High Intrinsic Conductivity.

This paper describes the synthesis of a novel intrinsically conductive two-dimensional (2D) covalent organic framework (COF) through the aromatic annulation of 2,3,9,10,16,17,23,24-octa-aminophthalocyanine nickel(II) and pyrene-4,5,9,10-tetraone. The intrinsic bulk conductivity of the COF material (termed COF-DC-8) reached 2.51 × 10-3 S/m, and increased by 3 orders of magnitude with I2 doping. Electronic calculations revealed an anisotropic band structure, with the possibility for significant contribution from out-of-plane charge-transport to the intrinsic bulk conductivity. Upon integration into chemiresistive devices, this conductive COF showed excellent responses to various reducing and oxidizing gases, including NH3, H2S, NO, and NO2, with parts-per-billion (ppb) limits of detection (for NH3 = 70 ppb, for H2S = 204 ppb, for NO = 5 ppb, and for NO2 = 16 ppb based on 1.5 min exposure). Electron paramagnetic resonance spectroscopy and X-ray photoelectron spectroscopy studies suggested that the chemiresistive response of the COF-DC-8 involves charge transfer interactions between the analyte and nickelphthalocyanine component of the framework.

Interplay between DNA sequence and negative superhelicity drives R-loop structures.

R-loops are abundant three-stranded nucleic-acid structures that form in cis during transcription. Experimental evidence suggests that R-loop formation is affected by DNA sequence and topology. However, the exact manner by which these factors interact to determine R-loop susceptibility is unclear. To investigate this, we developed a statistical mechanical equilibrium model of R-loop formation in superhelical DNA. In this model, the energy involved in forming an R-loop includes four terms-junctional and base-pairing energies and energies associated with superhelicity and with the torsional winding of the displaced DNA single strand around the RNA:DNA hybrid. This model shows that the significant energy barrier imposed by the formation of junctions can be overcome in two ways. First, base-pairing energy can favor RNA:DNA over DNA:DNA duplexes in favorable sequences. Second, R-loops, by absorbing negative superhelicity, partially or fully relax the rest of the DNA domain, thereby returning it to a lower energy state. In vitro transcription assays confirmed that R-loops cause plasmid relaxation and that negative superhelicity is required for R-loops to form, even in a favorable region. Single-molecule R-loop footprinting following in vitro transcription showed a strong agreement between theoretical predictions and experimental mapping of stable R-loop positions and further revealed the impact of DNA topology on the R-loop distribution landscape. Our results clarify the interplay between base sequence and DNA superhelicity in controlling R-loop stability. They also reveal R-loops as powerful and reversible topology sinks that cells may use to nonenzymatically relieve superhelical stress during transcription.

Electrically-Transduced Chemical Sensors Based on Two-Dimensional Nanomaterials.

Electrically-transduced sensors, with their simplicity and compatibility with standard electronic technologies, produce signals that can be efficiently acquired, processed, stored, and analyzed. Two dimensional (2D) nanomaterials, including graphene, phosphorene (BP), transition metal dichalcogenides (TMDCs), and others, have proven to be attractive for the fabrication of high-performance electrically-transduced chemical sensors due to their remarkable electronic and physical properties originating from their 2D structure. This review highlights the advances in electrically-transduced chemical sensing that rely on 2D materials. The structural components of such sensors are described, and the underlying operating principles for different types of architectures are discussed. The structural features, electronic properties, and surface chemistry of 2D nanostructures that dictate their sensing performance are reviewed. Key advances in the application of 2D materials, from both a historical and analytical perspective, are summarized for four different groups of analytes: gases, volatile compounds, ions, and biomolecules. The sensing performance is discussed in the context of the molecular design, structure-property relationships, and device fabrication technology. The outlook of challenges and opportunities for 2D nanomaterials for the future development of electrically-transduced sensors is also presented.

Pathways of DNA unlinking: A story of stepwise simplification.

In Escherichia coli DNA replication yields interlinked chromosomes. Controlling topological changes associated with replication and returning the newly replicated chromosomes to an unlinked monomeric state is essential to cell survival. In the absence of the topoisomerase topoIV, the site-specific recombination complex XerCD- dif-FtsK can remove replication links by local reconnection. We previously showed mathematically that there is a unique minimal pathway of unlinking replication links by reconnection while stepwise reducing the topological complexity. However, the possibility that reconnection preserves or increases topological complexity is biologically plausible. In this case, are there other unlinking pathways? Which is the most probable? We consider these questions in an analytical and numerical study of minimal unlinking pathways. We use a Markov Chain Monte Carlo algorithm with Multiple Markov Chain sampling to model local reconnection on 491 different substrate topologies, 166 knots and 325 links, and distinguish between pathways connecting a total of 881 different topologies. We conclude that the minimal pathway of unlinking replication links that was found under more stringent assumptions is the most probable. We also present exact results on unlinking a 6-crossing replication link. These results point to a general process of topology simplification by local reconnection, with applications going beyond DNA.

Current theoretical models fail to predict the topological complexity of the human genome.

Understanding the folding of the human genome is a key challenge of modern structural biology. The emergence of chromatin conformation capture assays (e.g., Hi-C) has revolutionized chromosome biology and provided new insights into the three dimensional structure of the genome. The experimental data are highly complex and need to be analyzed with quantitative tools. It has been argued that the data obtained from Hi-C assays are consistent with a fractal organization of the genome. A key characteristic of the fractal globule is the lack of topological complexity (knotting or inter-linking). However, the absence of topological complexity contradicts results from polymer physics showing that the entanglement of long linear polymers in a confined volume increases rapidly with the length and with decreasing volume. In vivo and in vitro assays support this claim in some biological systems. We simulate knotted lattice polygons confined inside a sphere and demonstrate that their contact frequencies agree with the human Hi-C data. We conclude that the topological complexity of the human genome cannot be inferred from current Hi-C data.

Experimental and theoretical studies of selective thiol-ene and thiol-yne click reactions involving N-substituted maleimides.

A combination of experimental and computational methods has been used to understand the reactivity and selectivity of orthogonal thiol-ene and thiol-yne ″click″ reactions involving N-allyl maleimide (1) and N-propargyl maleimide (2). Representative thiols methyl-3-mercaptopropionate and ß-mercaptoethanol are shown to add exclusively and quantitatively to the electron poor maleimide alkene of 1 and 2 under base (Et3N) initiated thiol-Michael conditions. Subsequent radical-mediated thiol-ene or thiol-yne reactions can be carried out to further functionalize the remaining allyl or propargyl moieties in near quantitative yields (>95%). Selectivity, however, can only be achieved when base-initiated thiol-Michael reactions are carried out first, as radical-mediated reactions between equimolar amounts of thiol and N-substituted maleimides give complex mixtures of products. CBS-QB3 calculations have been used to investigate the energetics and kinetics of reactions between a representative thiol (methyl mercaptan) with N-allyl and N-propargyl maleimide under both base-initiated and radical-mediated conditions. Calculations help elucidate the factors that underlie the selective base-initiated and nonselective radical-mediated thiol-ene/yne reactions. The results provide additional insights into how to design selective radical-mediated thiol-ene/yne reactions.

Automated analysis of protein subcellular location in time series images.

MOTIVATION: Image analysis, machine learning and statistical modeling have become well established for the automatic recognition and comparison of the subcellular locations of proteins in microscope images. By using a comprehensive set of features describing static images, major subcellular patterns can be distinguished with near perfect accuracy. We now extend this work to time series images, which contain both spatial and temporal information. The goal is to use temporal features to improve recognition of protein patterns that are not fully distinguishable by their static features alone. RESULTS: We have adopted and designed five sets of features for capturing temporal behavior in 2D time series images, based on object tracking, temporal texture, normal flow, Fourier transforms and autoregression. Classification accuracy on an image collection for 12 fluorescently tagged proteins was increased when temporal features were used in addition to static features. Temporal texture, normal flow and Fourier transform features were most effective at increasing classification accuracy. We therefore extended these three feature sets to 3D time series images, but observed no significant improvement over results for 2D images. The methods for 2D and 3D temporal pattern analysis do not require segmentation of images into single cell regions, and are suitable for automated high-throughput microscopy applications. AVAILABILITY: Images, source code and results will be available upon publication at http://murphylab.web.cmu.edu/software CONTACT: murphy@cmu.edu.