Chemistry and Biochemistry Copyright (c) 2013 California Polytechnic State University All rights reserved. http://digitalcommons.calpoly.edu/chem_fac Recent documents in Chemistry and Biochemistry en-us Fri, 25 Jan 2013 16:53:39 PST 3600 Microfluidic paper-based analytical devices: from POCKET to paper-based ELISA http://digitalcommons.calpoly.edu/chem_fac/44 http://digitalcommons.calpoly.edu/chem_fac/44 Fri, 20 Apr 2012 15:26:52 PDT Microfluidic paper-based analytical devices (microPADs) began as a simple idea with an ambitious goal. The idea was to make microfluidic devices out of paper instead of plastic or glass. The goal was to develop low-cost and portable paper-based diagnostic devices to improve healthcare in developing countries. Over the past 6 years, many developments have been made in the emerging field of paper-based microfluidic devices. Reviewing the development of these devices in the Whitesides group at Harvard University (Cambridge, MA, USA) can provide some insight into the future of the field and encourage scientists from a variety of backgrounds to contribute their expertise toward further development of useful microPADs.

]]> Andres W. Martinez β-Casein–phospholipid monolayers as model systems to understand lipid–protein interactions in the milk fat globule membrane http://digitalcommons.calpoly.edu/chem_fac/43 http://digitalcommons.calpoly.edu/chem_fac/43 Thu, 02 Feb 2012 13:20:14 PST Phospholipid–protein monolayer films were studied as model systems to mimic the structure of the native bovine milk fat globule membrane (MFGM) and to understand lipid–protein interactions at the surface of the globule. Phospholipids extracted from bovine raw milk, raw cream, processed milk and buttermilk powder were spread onto the air–water interface of a Langmuir trough, β-casein was then added to the sub-phase, and Langmuir–Blodgett films were studied by epifluorescence microscopy and atomic force microscopy. In all films, β-casein was responsible for clustering of the sphingomyelin- and cholesterol-rich microdomains into larger platforms. This suggests that the same phenomenon may happen at the surface of the milk fat globule, where specific MFGM proteins may cause aggregation of microdomains.

]]> Sophie Gallier et al. Three-Phase Intersection Points in Monolayers http://digitalcommons.calpoly.edu/chem_fac/42 http://digitalcommons.calpoly.edu/chem_fac/42 Wed, 18 Jan 2012 14:05:54 PST Some phospholipid/dihydrocholesterol Langmuir monolayers form coexisting liquid phases. Gas domains form at the interface between the phospholipid-rich and dihydrocholesterol-rich liquid phases when these monolayers undergo expansion to low surface pressure. Analysis of the domain shapes thus formed yields the relative line tensions of the gas/phospholipid, gas/dihydrocholesterol, and phospholipid/dihydrocholesterol phase interfaces.

]]> John P. Hagen et al. Critical Pressures in Multicomponent Lipid Monolayers http://digitalcommons.calpoly.edu/chem_fac/41 http://digitalcommons.calpoly.edu/chem_fac/41 Wed, 18 Jan 2012 14:05:51 PST Epifluorescence microscopy has been used previously to study coexisting liquid phases in lipid monolayers of dihydrocholesterol and dimyristoylphosphatidylcholine at the air/water interface. This binary mixture has a critical point at room temperature (22°C), a monolayer pressure of approx. 10 mN/m, and a composition in the vicinity of 20-30 mol% dihydrocholesterol. It is reported here that this critical pressure can be lowered, raised, or maintained constant by systematically replacing molecules of this phosphatidylcholine with molecules of a phosphatidylethanolamine, or an unsaturated phosphatidylcholine, or mixtures of the two, while maintaining the dihydrocholesterol concentration at 20 mol%. Thus, even complex mixtures of lipids may be characterized by a single, well-defined second-order phase transition. In principle, such transitions might be found in biological membranes.

]]> John P. Hagen et al. Liquid-Liquid Immiscibility in Lipid Monolayers http://digitalcommons.calpoly.edu/chem_fac/40 http://digitalcommons.calpoly.edu/chem_fac/40 Wed, 18 Jan 2012 14:05:47 PST Some binary lipid mixtures form coexisting liquid phases when spread at the air/water interface. This work describes the pressure–composition phase diagrams of binary mixtures of four unsaturated phosphatidylcholines with dihydrocholesterol. These four binary mixtures have critical compositions of approximately fifty mole percent, and average critical exponents of 0.25±0.07. The data can also be approximated by a regular solution thermodynamic model, yielding parameters for the non-ideality of these mixtures.

]]> John P. Hagen et al. Molecular Engineering of Side-Chain Liquid Crystalline Polymers by Living Polymerizations http://digitalcommons.calpoly.edu/chem_fac/39 http://digitalcommons.calpoly.edu/chem_fac/39 Fri, 28 Oct 2011 08:30:48 PDT “Living” anionic, cationic, metalloporphyrin and ring-opening metathesis polymerizations have been used to prepare well-defined side-chain liquid crystalline homopolymers, block and graft copolymers and statistical copolymers. This paper analyzes their successes and failures by reviewing the mechanistic aspects and experimental conditions of each type of polymerization, and identifies other classes of mesogenic monomers that could be polymerized in a controlled manner in the future. The emerging structure/property relationships are then identified using well-defined SCLCPs in which only one structural feature is varied while all others remain constant.

The thermal transitions of liquid crystalline polymethacrylates, polynorbomenes and poly(viny1 ether)s reach their limiting values at less than 50 repeat units, which are generally equal to those of the corresponding infinite molecular weight polymers’lncreasing spacer length depresses the glass transition of SCLCPs, and consequently often uncovers mesophases that are not observed without a spacer. The crystalline melting of tactic SCLCPs also tends to decrease (with odd-even alternation) with increasing spacer length. Without additional order within the polymer backbone due to high tacticity, mesogenic side-chains generally do not crystallize until the spacer contains at least nine carbon atoms. As the flexibility of the polymer backbone increases, the glass transition temperature decreases, and the side chains are able to crystallize at shorter spacer lengths and form more ordered rr esophases. The isotropization temperature (Ti = ΔHi/ΔSi) also increases since the change in entropy decreases more rapidly than the change in enthalpy with increasing backbone flexibility. However, the mesogenic side groups of most highly tactic polymers, which are less flexible than the corresponding atactic polymers, are evidently in the proper configuration to crystallize and/or form ordered phases. If the mesogen density is taken into account, the increase in ΔHi and ΔSi per methylenic unit in the spacer are equivalent for a given mesophase, and increase as the order of the mesophase increases. The discontinuity and/or change in the slope of ΔΔHi/-CH2- and ΔΔSi/ -CH2- with a change in the type of mesophase can be used to confirm that a phase change has occurred with the addition or subtraction of one methylenic unit in the spacer of a homologous series.

Model compounds corresponding to exactly one repeat unit of the polymer, or which take into account only the (appropriately substituted) mesogen and spacer, mimic the phase behavior of the corresponding SCLCPs well. The monomers themselves, which have chemical structures very different from that of the polymer backbone, are the least appropriate model compounds for most SCLCPs. The effect of polydispersity has not been clarified yet, although it may manifest itself in broad phase transitions if the broad polydispersity is accompanied by polydispersity in molecular architecture, and the molecular architectures are immiscible.

Liquid crystalline block and graft copolymers microphase separate into classic morphologies, but with the mesogens within the liquid crystalline block organize anisotropically if the blocks are sufficiently long. Although the same mesophase is generally formed by the copolymers and homopolymer, the phase diagram is asymmetric and less ordered mesophases may result if spheres of the liquid crystalline block are dispersed in a matrix of the other block. The morphology and thermotropic behavior of diblock and ABA and BAB triblock copolymers of 2-(cholesteryloxycarbonyloxy)ethyl methacrylate and styrene are identical when the volume fraction of the blocks are equal. Statistical copolymers also require a minimum concentration of the mesogenic monomer to form a mesophase. The isotropization temperatures of statistical copolymers based on two mesogenic monomers whose homopolymers exhibit identical mesophases follow ideal solution behavior as a function of copolymer composition. Copolymers based on structural units which are not isomorphic do not exhibit their respective mesophases over the entire copolymer composition, and intermediate compositions may exhibit an entirely different phase.

]]> Coleen Pugh et al. Examination of Technologies for Student-Generated Work in a Peer-Led, Peer-Review Instructional Environment http://digitalcommons.calpoly.edu/chem_fac/38 http://digitalcommons.calpoly.edu/chem_fac/38 Fri, 28 Oct 2011 08:30:04 PDT There is a growing literature demonstrating the effectiveness of using computer environments to assist students’ in visualizing science and mathematics concepts. However, with many of these computerized learning environments, students do not have the option of manipulating the environment. Instead, they are presented with pre-made visualizations. Enabling students to display their understanding through multiple representational forms is more interesting. In our peer-led, peer-review environment, students generate a complex, literature-based, multimedia text on which their final examination is based. However, there are great time and personnel costs in this design. Collaborating with SRI Inc., we are addressing these demands via the ChemSense Studio. This second-generation tool allows students to create texts, images and animations using one simple application. Peer-review is facilitated. We have begun to develop and modify methods of visual discourse analysis in order to examine the effectiveness of the ChemSense Studio in assisting students in their development of representational competence.

]]> Brian P. Coppola et al. A natural missing link between activated and downhill protein folding scenarios http://digitalcommons.calpoly.edu/chem_fac/37 http://digitalcommons.calpoly.edu/chem_fac/37 Fri, 28 Oct 2011 08:29:58 PDT We propose protein PTB1:4W as a good candidate for engineering into a downhill folder. PTB1:4W has a probe-dependent thermal unfolding curve and sub-millisecond T-jump relaxation kinetics on more than one time scale. Its refolding rate in denaturant is a non-linear function of denaturant concentration (curved chevron plot). Yet at high denaturant concentration its unfolding is probe-independent, and the folding kinetics can be fitted to a single exponential decay. The domain appears to fold via a mechanism between downhill folding and activated folding over several small barriers, and when denaturant is added, one of these barriers greatly increases and simplifies the observed folding to apparent two-state kinetics. We predict the simplest free energy function consistent with the thermai denaturation and kinetics experiments by using the singular value Smoluchowski dynamics (SVSD) model. PTB1:4W is a natural 'missing link' between downhill and activated folding. We suggest mutations that could move the protein into the downhill folding limit.

]]> Feng Liu et al. Direct Imaging of Two-State Dynamics on the Amorphous Silicon Surface http://digitalcommons.calpoly.edu/chem_fac/36 http://digitalcommons.calpoly.edu/chem_fac/36 Fri, 28 Oct 2011 08:29:51 PDT Amorphous silicon is an important material, amidst a debate whether or not it is a glass. We produce amorphous Si surfaces by ion bombardment and vapor growth, and image discrete Si clusters which hop by two-state dynamics at 295 K. Independent of surface preparation, these clusters have an average diameter of ~5 atoms. Given prior results for metallic glasses, we suggest that this cluster size is a universal feature. The hopping activation free energy of 0.93 ± 0.15 eV is rather small, in agreement with a previously untested surface glass model. Hydrogenation quenches the two-state dynamics, apparently by increasing surface crystallinity.

]]> S. Ashtekar et al. Solving the Low Dimensional Smoluchowski Equation with a Singular Value Basis Set http://digitalcommons.calpoly.edu/chem_fac/35 http://digitalcommons.calpoly.edu/chem_fac/35 Fri, 28 Oct 2011 08:29:47 PDT Reaction kinetics on free energy surfaces with small activation barriers can be computed directly with the Smoluchowski equation. The procedure is computationally expensive even in a few dimensions. We present a propagation method that considerably reduces computational time for a particular class of problems: when the free energy surface suddenly switches by a small amount, and the probability distribution relaxes to a new equilibrium value. This case describes relaxation experiments. To achieve efficient solution, we expand the density matrix in a basis set obtained by singular value decomposition of equilibrium density matrices. Grid size during propagation is reduced from (100–1000)N to (2–4)N in N dimensions. Although the scaling with N is not improved, the smaller basis set nonetheless yields a significant speed up for low-dimensional calculations. To demonstrate the practicality of our method, we couple Smoluchowsi dynamics with a genetic algorithm to search for free energy surfaces compatible with the multiprobe thermodynamics and temperature jump experiment reported for the protein α3D.

]]> Gregory E. Scott et al. Performance of binary-encounter-Bethe (BEB) theory for electron-impact ionization cross sections of molecules containing heavy elements (<em>Z</em> > 10) http://digitalcommons.calpoly.edu/chem_fac/34 http://digitalcommons.calpoly.edu/chem_fac/34 Fri, 28 Oct 2011 08:29:43 PDT The binary-encounter-Bethe (BEB) theory developed by Kim and coworkers has been successful for computing electron-impact ionization cross sections of many molecules. However, some recent publications have stated that BEB theory performs poorly for molecules that contain heavier elements such as chlorine and sulfur. We have found that the BEB calculations in those publications were performed incorrectly. When performed correctly, BEB predictions are as good for heavy-element molecules as for light-element molecules. We recommended recently that an alternative, less-confusing procedure be used for molecules that contain heavier elements. The alternative procedure, based upon effective core potentials (ECPs), does not require explicit kinetic energy corrections. For peak cross sections of a group of 18 molecules, the root-mean-square difference between BEB predictions and experimental values is 13%. Results are presented for CCl3CN, C2Cl6, C2HCl5, C2Cl4, both isomers of C2H2Cl4, CCl4, TiCl4, CBr4, CHBr3, CH2Br2, GaCl, CS2, H2S, CH3I, Al(CH3)3, Ga(CH3)3, and hexamethyldisiloxane. Incorrect BEB calculations have been reported in the literature for several of these molecules.

]]> Gregory E. Scott et al. Better biomolecule thermodynamics from kinetics http://digitalcommons.calpoly.edu/chem_fac/33 http://digitalcommons.calpoly.edu/chem_fac/33 Fri, 28 Oct 2011 08:29:36 PDT Protein stability is measured by denaturation: When solvent conditions are changed (e.g., temperature, denaturant concentration, or pH) the protein population switches between thermodynamic states. The resulting denaturation curves have baselines. If the baselines are steep, nonlinear, or incomplete, it becomes difficult to characterize protein denaturation. Baselines arise because the chromophore probing denaturation is sensitive to solvent conditions, or because the thermodynamic states evolve structurally when solvent conditions are changed, or because the barriers are very low (downhill folding). Kinetics can largely eliminate such baselines: Relaxation of chromophores, or within thermodynamic states, is much faster than the transition over activation barriers separating states. This separation of time scales disentangles population switching between states (desired signal) from chromophore or population relaxation within states (baselines).We derive simple formulas to extract unfolding thermodynamics from kinetics. The formulas are tested with model data and with a difficult experimental test case: the apparent two-state folder PI3K SH3 domain. Its melting temperature Tm can be extracted reliably by our “thermodynamics from kinetics approach,” even when conventional fitting is unreliable.

]]> Kiran Girdhar et al. Thermal-initiated hydroxyethyl methacrylate functionalization of multiwalled carbon nanotubes http://digitalcommons.calpoly.edu/chem_fac/31 http://digitalcommons.calpoly.edu/chem_fac/31 Thu, 25 Aug 2011 15:59:58 PDT Multiwalled-carbon nanotubes (MWCNTs) were functionalized via thermoinitiated free radical polymerization of 2-hydroxyethyl methacrylate (HEMA) using benzoyl peroxide. Tip sonication was used during the polymerization reaction to separate agglomerated nanotubes. The functionalization was confirmed by control experiments and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Differential scanning calorimetry indicated that the addition of poly(HEMA)-MWCNTs to a two-component polyurethane coating will have little effect on the glass transition temperature of the coating. The poly(HEMA)-functionalized MWCNTs formed large colloidal structures of highly dispersed nanotubes in both the nonsheared and sheared coatings as determined by atomic force microscopy. This study determined a quick and easy method to functionalize MWCNTs for incorporation into a two-component polyurethane coating. A simple method for producing ordered structures of the MWCNTs via shear observed.

]]> Greg Curtzwiler et al. Millimeter-Scale Contact Printing of Aqueous Solutions Using a Stamp Made Out of Paper and Tape http://digitalcommons.calpoly.edu/chem_fac/30 http://digitalcommons.calpoly.edu/chem_fac/30 Thu, 02 Jun 2011 13:41:29 PDT This communication describes a simple method for printing aqueous solutions with millimeter-scale patterns on a variety of substrates using an easily fabricated, paper-based microfluidic device (a paper-based ―stamp‖) as a contact printing device. The device is made from inexpensive materials, and it is easily assembled by hand; this method is thus accessible to a wide range of laboratories and budgets. A single device was used to print over 2500 spots in less than three minutes at a density of 16 spots per square centimetre. This method provides a new tool to pattern biochemicals—reagents, antigens, proteins, and DNA—on planar substrates. The accuracy of the volume of fluid delivered in simple paper-to-paper printing is low, and although the pattern transfer is rapid, it is better suited for qualitative than accurate, quantitative work. By patterning the paper to which the transfer occurs using wax printing or an equivalent technique, accuracy increases substantially.

]]> Chao-Min Cheng et al. Programmable Diagnostic Devices Made from Paper and Tape http://digitalcommons.calpoly.edu/chem_fac/29 http://digitalcommons.calpoly.edu/chem_fac/29 Thu, 02 Jun 2011 13:41:25 PDT This paper describes three-dimensional microfluidic paper-based analytical devices (3-D μPADs) that can be programmed (postfabrication) by the user to generate multiple patterns of flow through them. These devices are programmed by pressing single-use ‘on’ buttons, using a stylus or a ballpoint pen. Pressing a button closes a small space (gap) between two vertically aligned microfluidic channels, and allows fluids to wick from one channel to the other. These devices are simple to fabricate, and are made entirely out of paper and double-sided adhesive tape. Programmable devices expand the capabilities of μPADs and provide a simple method for controlling the movement of fluids in paper-based channels. They are the conceptual equivalent of field-programmable gate arrays (FPGAs) widely used in electronics.

]]> Andres W. Martinez et al. Electrochemical Sensing in Paper-Based Microfluidic Devices http://digitalcommons.calpoly.edu/chem_fac/28 http://digitalcommons.calpoly.edu/chem_fac/28 Thu, 02 Jun 2011 13:41:20 PDT This paper describes the fabrication and the performance of microfluidic paper-based electrochemical sensing devices (we call the microfluidic paper-based electrochemical devices, μPEDs). The μPEDs comprise paper-based microfluidic channels patterned by photolithography or wax printing, and electrodes screen-printed from conducting inks (e.g., carbon or Ag/AgCl). We demonstrated that the μPEDs are capable of quantifying the concentrations of various analytes (e.g., heavy-metal ions and glucose) in aqueous solutions. This low-cost analytical device should be useful for applications in public health, environmental monitoring, and the developing world.

]]> Zhihong Nie et al. Three-Dimensional Microfluidic Devices Fabricated in Layered Paper and Tape http://digitalcommons.calpoly.edu/chem_fac/27 http://digitalcommons.calpoly.edu/chem_fac/27 Thu, 02 Jun 2011 13:41:14 PDT This article describes a method for fabricating 3D microfluidic devices by stacking layers of patterned paper and double-sided adhesive tape. Paper-based 3D microfluidic devices have capabilities in microfluidics that are difficult to achieve using conventional open-channel microsystems made from glass or polymers. In particular, 3D paper-based devices wick fluids and distribute microliter volumes of samples from single inlet points into arrays of detection zones (with numbers up to thousands). This capability makes it possible to carry out a range of new analytical protocols simply and inexpensively (all on a piece of paper) without external pumps. We demonstrate a prototype 3D device that tests 4 different samples for up to 4 different analytes and displays the results of the assays in a side-by-side configuration for easy comparison. Three-dimensional paper-based microfluidic devices are especially appropriate for use in distributed healthcare in the developing world and in environmental monitoring and water analysis.

]]> Andres W. Martinez et al. FLASH: A Rapid Method for Prototyping Paper-Based Microfluidic Devices http://digitalcommons.calpoly.edu/chem_fac/26 http://digitalcommons.calpoly.edu/chem_fac/26 Thu, 02 Jun 2011 13:41:08 PDT This article describes FLASH (Fast Lithographic Activation of Sheets), a rapid method for laboratory prototyping of microfluidic devices in paper. Paper-based microfluidic devices are emerging as a new technology for applications in diagnostics for the developing world, where low cost and simplicity are essential. FLASH is based on photolithography, but requires only a UV lamp and a hotplate; no clean-room or special facilities are required (FLASH patterning can even be performed in sunlight if a UV lamp and hotplate are unavailable). The method provides channels in paper with dimensions as small as 200 μm in width and 70 μm in height; the height is defined by the thickness of the paper. Photomasks for patterning paper-based microfluidic devices can be printed using an ink jet printer or photocopier, or drawn by hand using a waterproof black pen. FLASH provides a straightforward method for prototyping paper-based microfluidic devices in regions where the technological support for conventional photolithography is not available.

]]> Andres W. Martinez et al. Removal of P-Cresol Sulfate by Hemodialysis http://digitalcommons.calpoly.edu/chem_fac/25 http://digitalcommons.calpoly.edu/chem_fac/25 Thu, 02 Jun 2011 13:41:04 PDT Protein-bound solutes are poorly cleared by dialysis. Among the most extensively studied of these solutes is p-cresol, which has been shown to be toxic in vitro. This study examined the form in which p-cresol circulates and quantified its removal by hemodialysis. HPLC analysis of plasma from hemodialysis patients contained a peak whose mobility corresponded to synthetic p-cresol sulfate (PCS) but no detectable unconjugated p-cresol. Treatment with sulfatase resulted in recovery of this peak as p-cresol, confirming its identity. Subsequent studies compared the removal of PCS and another protein-bound solute, indican, to the removal of urea during clinical hemodialysis treatments. PCS and indican were 94 ± 1% and 93 ± 2% bound to plasma protein, respectively. Protein-binding caused a predictable decrease in measured dialytic clearance, which averaged 20 ± 4 ml/min for PCS and 25 ± 5 ml/min for indican as compared with 260 ± 20 ml/min for urea. Volumes of distribution for the protein-bound solutes were greater than the plasma volume, averaging 15 ± 7 L for PCS and 14 ± 3 L for indican as compared with 37 ± 7 for urea. Solute reduction ratios were 20 ± 9% for PCS, 30 ± 7% for indican, and 69 ± 5% for urea. We conclude that p-cresol circulates in the form of its sulfate conjugate, PCS. PCS is poorly removed by hemodialysis because its clearance is limited by protein binding and the ratio of its volume of distribution to its clearance is high.

]]> Andres W. Martinez et al. The Clearance of Protein-Bound Solutes by Hemofiltration and Hemodiafiltration http://digitalcommons.calpoly.edu/chem_fac/24 http://digitalcommons.calpoly.edu/chem_fac/24 Thu, 02 Jun 2011 13:41:00 PDT Background. Hemofiltration in the form of continuous venovenous hemofiltration (CVVH) is increasingly used to treat acute renal failure. Compared to hemodialysis, hemofiltration provides high clearances for large solutes but its effect on protein-bound solutes has been largely ignored.

Methods. Standard clinical systems were used to remove test solutes from a reservoir containing artificial plasma. Clearances of the protein-bound solutes phenol red (CPR) and indican (CIN) were compared to clearances of urea (CUREA) during hemofiltration and hemodiafiltration. A mathematical model was developed to predict clearances from values for plasma flow Qp, dialysate flow Qd, ultrafiltration rate Qf, filter size and the extent of solute binding to albumin.

Results. When hemofiltration was performed with Qp 150 mL/min and Qf 17 mL/min, clearance values were CPR 1.0 ± 0.1 mL/min; CIN 3.7 ± 0.5 mL/min; and CUREA 14 ± 1 mL/min. The clearance of the protein-bound solutes was approximately equal to the solute-free fraction multiplied by the ultrafiltration rate corrected for the effect of predilution. Addition of Qd 42 mL/min to provide HDF while Qp remained 150 mL/min resulted in proportional increases in the clearance of protein-bound solutes and urea. In contrast, the clearance of protein-bound solutes relative to urea increased when hemodiafiltration was performed using a larger filter and increasing Qd to 300 mL/min while Qp was lowered to 50 mL/min. The pattern of observed results was accurately predicted by mathematical modeling.

Conclusion. In vitro measurements and mathematical modeling indicate that CVVH provides very limited clearance of protein-bound solutes. Continuous venous hemodiafiltration (CVVHDF) increases the clearance of protein-bound solutes relative to urea only when dialysate flow rate and filter size are increased above values now commonly employed.

]]> Timothy W. Meyer et al.