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Minute Papers Due 12/07/2012

Please post this week's minute papers as "comments" to this post. Minute papers should be posted by 5 pm on Friday. Feel free to read your classmate's posts.


Minute Paper # 10 Joseph DeWilde

Title: Evolution of carbonaceous deposits on H-mordenite and Pt-doped H-mordenite during n-butane conversion


By: Wulfers et al.

Journal: Journal of Catalysis

Methyl, ethyl, and tert-butyl ethers are industrial relevant chemical feedstocks capable of being synthesized from isobutane. Thus, the isomerization of n-butane into isobutane over acidic zeolites, such as H-mordenite is an area of active research. Previous investigations have demonstrated that these catalysts deactivate during n-butane isomerization which is mitigated with by loading of the catalyst with a small amount of Pt and co-feeding H2.1 To gain an understanding of the deactivation process, the authors used kinetic measurements and in situ diffuse reflectance ultraviolet–visible–near infrared (UV-vis-NIR) spectroscopy to investigate mechanism of and relevant surface species present during the deactivation of n-butane isomerization over H-mordenite and Pt/H-mordenite catalysts.
In this work, the authors investigated n-butane isomerization over both H-mordenite and Pt/H-mordenite catalyst samples with H2 co-feed using UV-vis-NIR spectroscopy and a gas chromatograph equipped with a flame ionization detector. To investigate the role of H2 in preventing catalyst deactivation, H2 was co-fed for 3 h, the co-fed gas was then switched to He for an additional 3 h before returning to the initial H2 co-feed. The isomerization rates of n-butane were found to be stable in the initial H2 feed for both catalyst samples. Upon switching the co-fed gas to He, deactivation was measured for n-butane isomerization over both catalyst systems. This reduction in the rate of n-butane isomerization corresponded with the growth of bands attributed to the formation conjugated surface species such as aromatics or polyenes (286, 335, 395, and 458 nm with increasing conjugation) and the evolution of butenes in the vapor phase. The isomerization rate of n-butane on the H-mordenite sample did not recover upon returning to a H2 co-feed while the bands at 286, 335, and 395 nm diminished and the band at 458 nm increased in size, suggesting the further growth of the conjugated species and coke formation. Conversely, isomerization rates regenerated slowly on the Pt/H-mordenite sample upon returning to a H2 co-feed while all of the bands corresponding to conjugated surface species reduced in intensity over time. These observations caused the authors to conclude the butenes that form from the dehydrogenation of n-butane in absence of H2 adsorb onto the H-mordenite active sites and grow into large conjugated compounds, causing deactivation. This conclusion was supported by observation of bands attributed to conjugated species on 1-butene doused H-mordenite. The Pt was postulated to hydrogenate these deactivating species in presence of H2.
The authors successfully found a correlation between conjugated surface species and isomerization deactivation. The mechanism for the formation of these surface species from butenes and hydrogenation of these species by the Pt, however, is still unknown. Analysis of the effects of H2, Pt loading, and temperature on the transient behavior of the UV-vis-NIR bands associated with the conjugated surface species under a 1-butene feed could potentially help elucidate the kinetic mechanism of deactivation. Ultimately, this understanding will provide a basis for the development of catalysts and conditions for the efficient and stable isomerization of n-butane.

[1] Liu, H.; Adeeva, V.; Lei, G.D.; Sachtler, W.M.H. J. Mol. Catal. A: Chem. 1995, 100, 35-48.

Title: Attomole Sensitivity of Staphylococcal Enterotoxin B Detection Using an Aptamer-Modified Surface-Enhanced Raman Scattering Probe

By: Temur et al.

Journal: Analytical Chemistry

Staphylococcus aureus, a Gram-positive bacterium, is a known human health hazard as it secretes toxins (staphylococcal enterotoxin B or SEB) which are associated with gastrointestinal poisoning and toxic shock syndrome. S. aureus poses significant risk to humans, because its most common infection route is via food and water sources. The motivation behind this work was to develop an effective SEB detection probe that may be utilized in complex media.

Surface-Enhanced Raman Spectroscopy (SERS) was the analytical technique featured in this work. The authors used multi-tiered SERS platforms that included magnetic gold nanorods (Fe3O4-Au) as a SEB capture probe, plain gold nanorods as a SERS reporter tag, and gold slides as a secondary option for SEB capture. The authors used two different approaches, a “heterogeneous sandwich” and a “homogeneous sandwich,” for effectively binding SEB to plasmonically active gold surfaces.

The heterogeneous method included self-assembled monolayer (SAM) modified gold slides. The SAMs were then functionalized with peptide aptamers and subsequently treated with SEB. In addition to surface functionalized gold slides, gold nanorods were treated with activated SERS reporter molecules, which were in turn modified with the peptide aptamer. Adding the aptamer functionalized gold nanorods to the gold slides bound with SEB formed a heterogeneous “sandwich” with SEB packed between the gold slide and nanorods.

The homogeneous platform differed from the heterogeneous method in that magnetic gold nanorods were functionalized with SAMs and then peptide aptamers. After treatment with SEB, magnetic gold nanorods were separated via a magnet and treated by gold nanorods functionalized with SERS reporter molecules and peptide aptamers. These modified gold rods then homogenously “sandwiched” SEB between the magnetic rods.

SERS detection of SEB via reporter Raman shift was best obtained from the homogeneous approach, which provided limits of detection (LOD) in the attomolar range. In addition, SEB sensing was accomplished in complex media such as artificially contaminated milk, blood, and urine.

Although these heterogeneous and homogeneous “sandwiches” provided a SERS platform capable of low LOD in complex media, the authors’ materials did not seem optimized and therefore expensive to make. The authors required the SAMs and reporter molecules themselves to be functionalized with peptide aptamers. This suggested the compatibility between the peptide aptamers and the gold surfaces was minimal. Integrating SAMs or reporters between the gold surface and the aptamer likely reduced the amount of attainable LSPR. I imagine if the aptamers or reporters could bind more specifically to SEB, even higher signal and LOD could be acquired.

Despite the authors’ intent to develop a platform capable of sensing SEB in vitro, the term “sandwich” implied agglomeration of gold nanorods. Furthermore, no biocompatible gold surface modifications were used. These points severely limit any potential for in vivo use of this SERS platform. Biocompatible surface modification schemes should be employed, as this could increase the diversity of applications for this sensor.

Minute Paper #10
Tian Qiu 4651092
Title: A Droplet-Based, Optofluidic Device for High-Throughput, Quantitative Bioanalysis
Authors: Feng Guo, et al.
Journal: Analytical Chemistry

In this article, the authors demonstrated an simple and integrated optofluidic device for high-throughput, real-time, quantitative analysis of droplet contents. The contents in individual droplets were accurately analyzed with a frequency up to 2000 per second. Optical fiber, instead of conventional CCD camera or confocal fluorescence microscopy, lowered the cost of the device. The detection of the abnormality on the BRCA1 gene, related with breast and ovarian cancer, was used to demonstrate the performance of this optofluidic device, indicating the capability of this device for single nucleotide polymorphism (SNP) analysis.
The droplet-based optofluidic device was fabricated with PDMS using standard soft-lithography and mold-replica techniques. The device was composed of a droplet generation unit, a mixing region for probes and analytes, and an optical fiber-based detection unit using photomultiplier tubes (PMTs). A modified T-junction droplets generation inlet was used. Buffers, noted as Chem1, buffer and Chem 2, were loaded from the three-forked inlet under the oil flow with surfactant in oil to generate water-in-oil droplets. In the long curved serpentine-like mixing channel, reagents were mixed and delivered to the detection unit. An input fiber and a detection fiber were used in the detection region. The input fiber was aligned perpendicular to the microfluidic channel, and the detection fiber was fixed at an angle of 27 from the input fiber to capture maximal fluorescent signals.
After device fabrication, a characterization of droplet-based fluorescence detection was carried out for device evaluation, using the commercial Alexa Fluor 488 dye. The fluorescent solution was injected at different concentrations to form droplets. A calibration curve was obtained, presenting a linear relationship between the fluorescent dye concentration and the detection voltage in the PMTs. Furthermore, to test the detection throughput, the highest droplet production frequency and minimal interdroplet distance were obtained, showing a detection throughput as high as 2000 droplets per second with reliable results. These characterization showed the reproducibility and consistency of the device to perform high-throughput, real-time and quantitative analysis.
Furthermore, a DNA analysis of BRCA1 gene using molecular beacon on this device was performed. Wild-type single-strain DNA (WT), single-mutation single-strain DNA (SM), control single-strain DNA (CON), and molecular beacon (MB) were prepared for the test. Four experiments were performed sequentially with WT, SM, CON, or MB as Chem 1 and MB solution as Chem 2. The size of the droplets was controlled as 7.5 nL in volume with the rate of 4 droplets per second. Results showed that the BRCA1 DNA and its mutation were clearly identified by the difference in their response voltages. Signal to noise ratio was also calculated.
I think they still left many questions unsolved in this paper. First, they didn't demonstrate if the intensity of signal is size-dependent of droplets or not. If the intensity of signal not only depends on the concentration of fluorescence within the droplets but also on the size of droplets, then the size of droplets have to be controlled the same among every single test to ensure the consistency, which is very hard, or an internal standard method is needed. Secondly, pure solution was used in the paper, while there are always huge background signals from complex biological samples in real tests. More experiments should be done to explore the background signals and how to eliminate them. Finally, when it comes to a real test, kinetic issues must be taken into account, which can be another area to further work on.

Title: High-Throughput Multiplexed Competitive Immunoassay for Pollutants Sensing in Water
Author: Cloe Desmet, Loic J. Blum, and Christophe A. Marquette
From: Analytical Chemistry

In this paper, the authors presented a multiplexed competitive immunosensor for simultaneous detection of five pollutants in water. Target analytes including okadaic acid (OA), 2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine (atrazine), 2,4-dichlorophenoxy-acetic acid (2,4-D), 2,4,6-trinitrotoluene (TNT) and 11,3,5-trinitroperhydro-1,3,5-triazine (RDX) were chosen due to their potential threat to human health. The sensor produced easily observable Colorimetric signal change and semi-quantitative analysis could be achieved by ordinary flatbed scanner.

As to the mechanism, the five haptens were conjugated to a high molecular weight carrier and immobilized on a solid surface. Antibodies towards specific analyte and sample solution containing these haptens were added to the system. Competitive binding reaction took place and antibodies that bound to the haptens in the solution were washed away while those bound to the immobilized haptens stayed on the surface. Secondary enzyme labeled IgG antibodies were then introduced to the system, which would bind to the hapten antibodies on the surface. After that, alkaline phosphatase substrate was added to the system, generating colorimetric signals. A color change from transparent to purple indicated low concentration of haptens while no color change meant high concentration of haptens.

For the experiment, in order to run multiplexed test, an optical clear pressure sensitive adhesive was utilized and the hapten-carrier conjugates were spotted on the adhesive by using a piezoelectric spotter. The adhesive was then coupled to a bottomless 96-well plate. To optimize detection conditions, three different carriers, including latex-amino, dextran-amino and bovine serum albumin (BSA) were conjugated to the haptens separately. Cross-reactivity tests were run by testing the response of each hapten-carrier to all the antibodies for all five haptens. Only the ones with minimal response to other non-specific antibodies were chosen. Then concentration of antibodies for each hapten was also optimized to minimize the effect of cross-reactivity. However, after modification, RDX and atrazine still suffered from cross-reactivity to non-specific antibodies. Subsequent performance test were run to build calibration curve for each hapten and test spiked water samples. The results showed that limit of detection for all the haptens was comparable to EU and U.S. regulations, in spite of the abnormal signal for RDX and atrazine in high concentrations. Spiked water test also revealed an 82.5 % average recovery.

The biggest advantage of the method demonstrated in this paper is the multiplexed detection ability and the usage of a 96-well plate to maximize detection efficiency. Although cross-reactivity can’t be avoided entirely, the assay still achieves a high sensitivity. As an improvement of the method, a reversed color change as signal output can make the detection more straightforward. To make it possible, a non competitive mechanism with sandwich format can be used. In short, antibodies for haptens can be first immobilized on the surface. After incubating with the sample solution, secondary enzyme labeled antibody can be introduced to the system, followed by enzyme substrate to give signal readout. In terms of the cross-reactivity, incubation time can be optimized since reducing the time might decrease non-specific binding, although it may need to sacrifice the sensitivity.

Title: Catalytic Conversion of Carbon Dioxide to Methane on Ruthenium − Cobalt Bimetallic Nanocatalysts and Correlation between Surface Chemistry of Catalysts under Reaction Conditions and Catalytic Performances
By: F. Tao et al.
Journal: ACS Catalysis

In this paper, the group studied the carbon dioxide to methane reaction on ruthenium-cobalt bimetallic nanorods. They compare the bimetallic catalyst to monometallic catalysts, Co and Ru. They said that there was structural change on the surface of bimetallic catalyst at reaction condition. Because of global warming, they said the utilization of carbon dioxide has been becoming important. They mentioned that the conversion of carbon dioxide to methane will be a good solution because of two aspects, usage of carbon dioxide and production of energy. For this study, they used transmission electron microscopy(TEM), gas chromatography(GC), and ambient pressure - X-ray photoelectron spectroscopy.

They compared reactivity of catalysts, Co-Ru bimetallic catalyst((Co0.95Ru0.05)3O4), Co only catalyst(Co3O4), and Ru only catalyst(Ru-silica). Bimetallic catalyst showed higher conversion and selectivity and higher activity at lower temperature than other two catalysts. It means bimetallic catalyst have different surface characters. They studied surface structure of catalysts during reaction using in-house AP-XPS. They said fully reduced Co metal, Ru metal, and Co-Ru metal alloy were formed at 220˚C. For monometal catalysts, they need higher temperature to form metal, 300˚C for Co catalyst. They confirmed existence of metal alloy by energy dispersive spectroscopy(EDS) using TEM. They said Ru metal covers surface of bimetallic catalyst, so its reactivity increases.

In conclusion, they said bimetallic catalyst is better than monometallic catalysts. In my opinion, I would study more about reaction mechanism on surface. They can study how carbon dioxide and hydrogen bonded on surface of catalyst. They can see difference between bimetallic and monometallic catalyst. They can use IR to study surface interaction. Also, they can study kinetics of each catalyst. They can get reaction constant and activation energy of the reaction. Then, they can prove bimetallic catalyst is more efficient with specific numbers. In addition, they can check the whole ratio of Ru and Co, not the ratio on surface by EDS, by using ICP-MS.

Title: Nanoclustered gold honeycombs for surface-enhanced Raman scattering
Authors: Leng, W.; Vikesland, P. J.
Journal: Analytical Chemistry

The authors developed a honeycomb-shaped substrate made of clusters of 50-70 nm gold nanoparticles for surface-enhanced Raman imaging (SERI). This substrate was produced by the Langmuir-Blodgett (LB) method, followed by sputter-coating with gold and removing the silica spheres. This produced large surface area nanoparticle substrates with a high degree of uniformity. Images of trace analytes on the substrate were collected at thousands of analysis points in order to measure the spatial variability of the surface enhancement. The XY-surface-enhanced imaging minimized thermal and photo degradation of the analytes, and low power and short exposure times helped to ensure that the focused laser beam did not heat the sample too much or cause conformational changes to the substrate.

The morphology of the substrate was evaluated by atomic force microscopy over three different 100x100 µm2 scan areas to measure the difference between 3-dimensional surface area and the 2-dimensional footprint of the scan. This gave an estimate of the gold surface coverage throughout the substrate. The thickness of the gold film over the substrate was controlled by sputter time, applied current and working distance, producing thicknesses between 20 and 60 nm. The sputtered gold was transported through the gaps between the silica particles, resulting in the honeycomb shape on the glass substrate which the silica particles covered. The silica particles were then removed through sonication. The absorbance of the gold film was studied in the visible-IR range, showing a LSPR band around 580 nm that varied only slightly by film thickness. The atomic force microscopy analysis of gold coverage of the substrate determined that 62% of the glass substrate was covered by gold nanoparticles.

The SERS performance of the honeycomb substrate was compared to those of a simple gold film, a honeycomb substrate before silica particle removal, and a substrate with gold triangular footprints made by thermal vacuum gold deposition instead of sputter coating. Despite the fact that the honeycomb substrates have lower surface coverage, they produced Raman intensities 2.5 times higher than the triangular footprint substrate, leading the authors to suggest that the honeycomb matrix structure is partially responsible for the SERS enhancement.

The detection limit of malachite green isothiocyanate (MGITC) deposited on the substrate after solvent evaporation was found by large area Raman image scanning. The MGITC was not uniformly distributed across the substrate, so the authors averaged the total MGITC SERS contribution over reach sample region. This led to a detection limit of ~10 nM and a linear dynamic range over four orders of magnitude.

The authors concluded that they successfully produced a substrate with high SERS sensitivity and signal reproducibility. The relatively simple and cost-effective fabrication of the substrate led the authors to suggest that the substrate would have utility for using SERS in quantitative diagnoses and analyte detections.

The authors could next attempt to find a method for producing honeycomb substrates with higher coverage, or examine the effect of the ‘hot spot’ shape on the SERS enhancement.

Title: Clean and efficient transfer of CVD-grown graphene by electrochemical etching of metal substrate
Author: Xiwen Yang et al.
Journal: Journal of Electroanalytical Chemistry

In this publication, Yang et al. develops a technique to transfer large surface sections of grapheme grown from copper foils by wet etching method. These films are characterized with various methods including UV-Vis and Raman spectroscopy.

The most common existing way to generate graphene is by the recent chemical vapor deposition technique on a copper surface, but transferring to another surface is a big problem. Usually done by a polymer cast and back-etching the metal substrate (i.e. iron (III) nitrate iron (III) chloride), you usually end up with metal doping of the graphene or defect creation.

Experiments were performed by spin-coating PMMA onto graphene layer on 25um copper foil, and 0.5M H2SO4 buffer solution was used for supporting electrolyte. As a control FeCl3 was also used to dissolve the copper backing. The PMMA/graphene/copper stack was submerged in H2SO4 as the working electrode and etched for 10min at 0.5V room temp. Lastly the PMMA (on graphene) was removed by acetone after transfer to Si/SiO2.

In the results Yang et al. uses SEM/AFM images to confirm graphene smoothness and quality after electrochemical transfer is done. XPS results show few metal contaminations. The UV-Vis measurements show a highly transparent film (95% nominal), and raman measurements show monolayer and bilayer regions can be identified by width of raman peaks. The D bands at 1350 cm-1 (show defect and disorder level) are negligible which he claims points to high quality film. A comparison is made to control films etched with FeCl3, and raman red/blue shifts in the D bands indicate significant extrinsic p-doping.

Lastly, a comparison was done of copper removal vs. oxidation potentials during etching. Raman results show defects in graphene at 2volts, but none below 1volt.

The proposed method of graphene transfer shows promising results.
I would be interested in focusing more effort on the removal of PMMA from graphene after transfer. I know groups that have to deal with this issue and there are many processing problems such as polymer becoming trapped in the monolayer due to PMMA “stickiness”. Also, PMMA can show up in the raman signal with an increase in background noise because the high power of the laser burns some of the PMMA. This generates small particles which scatter more light but the author did not talk about this.
I would have a before and after comparison of the raman spectra with the PMMA etched to see if the signal/noise ratio changes, because this could explain some of his shifts in peak strength/broadness. He could repeat the raman measurements with different raman laser power to try and identify a point where burning the PMMA is not much of an issue.

A key issue that was not discussed here was quantification of the largest obtainable graphene surface area with acceptable defect levels. This is a crucial roadblock today where many groups are forced to run multiple parallel experiments and pick out a tiny spot that works. The author only shows a 200x200um SEM image and points out some structures without quantification.

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