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We report on a novel self-driven climbing of two-dimensional (2-D) ordered monolayer crystalline colloidal arrays (CCAs). This phenomenon can be used to rapidly and efficiently prepare large area, highly ordered 2-D array monolayer CCA films on various substrates. Large area 2-D polystyrene (PS) particle CCAs were fabricated on water surfaces by a needle tip flow technique. Introduction of a wet substrate through the 2-D particle monolayer array on the water surface causes the 2-D array to flow onto the wet substrate surface due to a surface spreading pressure. This method can quickly prepare ordered 2-D particle arrays on numerous wet substrates including flat/curved glass slides, inner walls of glass tubes, hydrogels, flexible polymer films, patterned surfaces, etc. By using responsive hydrogels as substrates, we can conveniently prepare 2-D photonic crystal sensors that can be used to visually determine analyte concentrations. For example, we prepared 580 nm PS 2-D arrays on poly(2-hydroxyethyl methacrylate) hydrogels to sense ethanol in water. © 2013 The Royal Society of Chemistry.

Generalized two-dimensional correlation spectroscopy (2D-COS) can be used to enhance spectral resolution in order to help differentiate highly overlapped spectral bands. Despite the numerous extensive 2D-COS investigations, the origin of the 2D spectral resolution enhancement mechanism(s) is not completely understood. In the work here, we studied the 2D-COS of simulated spectra in order to develop new insights into the dependence of 2D-COS spectral features on the overlapping band separations, their intensities and bandwidths, and their band intensity change rates. We found that the features in the 2D-COS maps that are derived from overlapping bands were determined by the spectral normalized half-intensities and the total intensity changes of the correlated bands. We identified the conditions required to resolve overlapping bands. In particular, 2D-COS peak resolution requires that the normalized half-intensities of a correlating band have amplitudes between the maxima and minima of the normalized half-intensities of the overlapping bands. © 2013 Society for Applied Spectroscopy.

We utilize T-jump UV resonance Raman spectroscopy (UVRR) to study the impact of ion binding on the equilibrium energy landscape and on (un)folding kinetics of poly-l-lysine (PLL). We observe that the relaxation rates of the folded conformations (including π-helix (bulge), pure α-helix, and turns) of PLL are slower than those of short alanine-based peptides. The PLL pure α-helix folding time is similar to that of short alanine-based peptides. We for the first time have directly observed that turn conformations are α-helix and π-helix (bulge) unfolding intermediates. ClO 4- binding to the Lys side chain -NH3+ groups and the peptide backbone slows the α-helix unfolding rate compared to that in pure water, but little impacts the folding rate, resulting in an increased α-helix stability. ClO4- binding significantly increases the PLL unfolding activation barrier but little impacts the folding barrier. Thus, the PLL folding coordinate(s) differs from the unfolding coordinate(s). The-π helix (bulge) unfolding and folding coordinates do not directly go through the α-helix energy well. Our results clearly demonstrate that PLL (un)folding is not a two-state process. © 2012 American Chemical Society.

We utilize 198 and 204 nm excited UV resonance Raman spectroscopy (UVRR) and circular dichroism spectroscopy (CD) to monitor the backbone conformation and the Gln side chain hydrogen bonding (HB) of a short, mainly polyGln peptide with a D2Q10K2 sequence (Q10). We measured the UVRR spectra of valeramide to determine the dependence of the primary amide vibrations on amide HB. We observe that a nondisaggregated Q10 (NDQ10) solution (prepared by directly dissolving the original synthesized peptide in pure water) exists in a β-sheet conformation, where the Gln side chains form hydrogen bonds to either the backbone or other Gln side chains. At 60 °C, these solutions readily form amyloid fibrils. We used the polyGln disaggregation protocol of Wetzel et al. [Wetzel, R., et al. (2006) Methods Enzymol.413, 34-74] to dissolve the Q10 β-sheet aggregates. We observe that the disaggregated Q10 (DQ10) solutions adopt PPII-like and 2.51-helix conformations where the Gln side chains form hydrogen bonds with water. In contrast, these samples do not form fibrils. The NDQ10 β-sheet solution structure is essentially identical to that found in the NDQ10 solid formed upon evaporation of the solution. The DQ10 PPII and 2.51-helix solution structure is essentially identical to that in the DQ10 solid. Although the NDQ10 solution readily forms fibrils when heated, the DQ10 solution does not form fibrils unless seeded with the NDQ10 solution. This result demonstrates very high activation barriers between these solution conformations. The NDQ10 fibril secondary structure is essentially identical to that of the NDQ10 solution, except that the NDQ10 fibril backbone conformational distribution is narrower than in the dissolved species. The NDQ10 fibril Gln side chain geometry is more constrained than when NDQ10 is in solution. The NDQ10 fibril structure is identical to that of the DQ10 fibril seeded by the NDQ10 solution. © 2012 American Chemical Society.

Nanoparticle coating: A suspension of colloidal particles in a water/propanol solution was layered onto a water surface, where the particles self-assembled into ordered two-dimensional hexagonal crystal arrays (>280 cm 2) within two minutes. These arrays were transferred from the water surface to other substrates (see picture) and embedded in a chitosan hydrogel for visual detection of the pH value. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined low-energy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO 2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO 2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX. © 2012 American Chemical Society.

We developed a novel two-dimensional (2-D) crystalline colloidal array photonic crystal sensing material for the visual detection of amphiphilic molecules in water. A close-packed polystyrene 2-D array monolayer was embedded in a poly(N-isopropylacrylamide) (PNIPAAm)-based hydrogel film. These 2-D photonic crystals placed on a mirror show intense diffraction that enables them to be used for visual determination of analytes. Binding of surfactant molecules attaches ions to the sensor that swells the PNIPAAm-based hydrogel. The resulting increase in particle spacing red shifts the 2-D diffracted light. Incorporation of more hydrophobic monomers increases the sensitivity to surfactants. © 2012 American Chemical Society.

A study was conducted to demonstrate ultraviolet resonance Raman (UVRR) investigations of peptide and protein structure and dynamics. The tuning of the excitation wavelengths allowed the probing of different chromophoric segments of a macromolecule. Another advantage of deep UV Raman measurements was that there was no interference from molecular relaxed fluorescence, as those chromophores that had their first transition below 260 nm were highly flexible and possessed small fluorescence quantum yields. UVRR was also used in pump-probe measurements to give kinetic information on fast biological processes. It was a powerful technique for studying static protein structure and for studying protein dynamics, such as in protein folding. The rapid development of UVRR was aided by the latest advancements in lasers, optics, and detectors.

We report a refractive-index matching method to measure nonabsorbing solid ultraviolet (UV) Raman cross-sections that avoids the local field correction and interface scattering of incident light. We used refractiveindex- matched chloroform as an internal standard to determine the solidstate 995 cm -1Na 2SO 4 244 nm Raman cross-sections. The pure liquid chloroform 668 cm -1 244 nm Raman cross-section was determined by using acetonitrile as an internal standard and by calculating the local field corrections for the observed Raman intensities. Our measured 244 nm UV Raman cross-section of the solid-state 995 cm -1 SO 42- band of 1.97 ±0.07 6 10 -28 cm2/(molc.sr) is about half of its aqueous solution Raman crosssection, indicating interactions between the sulfate species in the solid that decrease the Raman polarizability. © 2012 Society for Applied Spectroscopy.

We developed a facile method to fabricate deep ultraviolet (UV) photonic crystal crystalline colloidal array (CCA) Bragg diffraction devices. The CCAs were prepared through the self-assembly of small, monodisperse, highly surface charged silica particles (∼50 nm diameter) that were synthesized by using a modified Stöber process. The particle surfaces were charged by functionalizing them with the strong acid, non-UV absorbing silane coupling agent 3-(trihydroxylsilyl)-1-propane-sulfonic acid (THOPS). These highly charged, monodisperse silica particles self assemble into a face-centered cubic CCA that efficiently Bragg diffracts light in the deep UV. The diffracted wavelength was varied between 237 nm to 227 nm by tilting the CCA orientation relative to the incident beam between glancing angles from 90° to ∼66°. Theoretical calculations predict that the silica CCA diffraction will have a full width at half-maximum (FWHM) of 2 nm with a transmission of ∼10 -11 at the band center. We demonstrate the utility of this silica CCA filter to reject the Rayleigh scattering in 229 nm deep UV Raman measurements of highly scattering Teflon. © 2012 Society for Applied Spectroscopy.

CD and UV resonance Raman measurements surprisingly find that the charge screening of even 2 M concentrations of NaCl and KCl does not alter the unfolded PPII and 2.5 1-helix conformations of poly-l-glutamate. These salts appear to be excluded from the region between the side chain charges and the peptide backbone. Furthermore, no direct ion pairing occurs between these salts and the side chain carboxylates. © 2011 Elsevier B.V. All rights reserved.

We used 204 nm excitation UV resonance Raman (UVRR) spectroscopy to examine the role of side chain electrostatic interactions in determining the conformation of poly-l-lysine (PLL). We examined the pH and ionic strength dependence of the UVRR. The pH dependence of PLL UVRR spectra between pH 7.1 and 11.7 cannot be described by a two-state model but requires at least one additional state. The AmIII3 region fitting with pH 7.1 and 11.7 basis spectra reveals a small pH-induced decrease in the relative fraction of the 2.51-helix conformation compared to the PPII conformation. We performed a 2D general correlation analysis on the PLL pH dependence UVRR spectra. The asynchronous spectrum shows enhanced spectral resolution. The 2D asynchronous spectrum reveals multiple components in the Cα-H b band and the AmII band whose origins are unclear. The cross peaks in the 2D asynchronous spectrum between the AmIII band and the other bands reveals that increasing pH induces three new structures: π-helix, α-helix, and some turn structure. We find that 2.5 M NaCl does not change the equilibrium between the PPII and 2.51-helix conformations by screening side chain electrostatic repulsion. The result indicates that NaCl does not penetrate the region between the side chain and the peptide backbone. We also compared PLL conformations induced by high pH to that induced by 0.8 M ClO4-. Both conditions induce α-helix-like conformations. ClO 4- (0.8 M) induces 6% more α-helix-like conformations than at pH 12.4. Higher pH gives rise to longer α-helices and less turn structures. © 2011 American Chemical Society.

We report the first experimental measurements of Ramachandran Ψ-angle distributions for intrinsically disordered peptides: the N-terminal peptide fragment of tumor suppressor p53 and its P27S mutant form. To provide atomically detailed views of the conformational distributions, we performed classical, explicit-solvent molecular dynamics simulations on the microsecond time scale. Upon binding its partner protein, MDM2, wild-type p53 peptide adopts an α-helical conformation. Mutation of Pro27 to serine results in the highest affinity yet observed for MDM2-binding of the p53 peptide. Both UV resonance Raman spectroscopy (UVRR) and simulations reveal that the P27S mutation decreases the extent of PPII helical content and increases the probability for conformations that are similar to the α-helical MDM2-bound conformation. In addition, UVRR measurements were performed on peptides that were isotopically labeled at the Leu26 residue preceding the Pro27 in order to determine the conformational distributions of Leu26 in the wild-type and mutant peptides. The UVRR and simulation results are in quantitative agreement in terms of the change in the population of non-PPII conformations involving Leu26 upon mutation of Pro27 to serine. Finally, our simulations reveal that the MDM2-bound conformation of the peptide is significantly populated in both the wild-type and mutant isolated peptide ensembles in their unbound states, suggesting that MDM2 binding of the p53 peptides may involve conformational selection. © 2011 American Chemical Society.

Electrostatic interactions between side chains can control the conformation and folding of peptides and proteins. We used circular dichroism (CD) and ultraviolet (UV) resonance Raman spectroscopy (UVRR) to examine the impact of side chain charge on the conformations of two 21 residue mainly polyala peptides with a few Arg and Glu residues. We expected that attractions between Arg-10 and Glu-14 side chains would stabilize the α-helix conformation compared to a peptide with an Arg-14. Surprisingly, CD suggests that the peptide with the Glu-14 is less helical. In contrast, the UVRR show that these two peptides have similar α-helix content. We conclude that the peptide with Glu-14 has the same net α-helix content as the peptide with the Arg but has two α-helices of shorter length. Thus, side chain interactions between Arg-10 and Glu-14 have a minor impact on α-helix stability. The thermal melting of these two peptides is similar. However the Glu-14 peptide pH induced melting forms type III turn structures that form α-helix-turn-α-helix conformations. © 2011 American Chemical Society.

We examined the deep UV 229 nm photochemistry of NaNO3 in solution and in the solid state. In aqueous solution excitation within the deep UV NO3- strong π → π* transition causes the photochemical reaction NO3- → NO2- + O·. We used UV resonance Raman spectroscopy to examine the photon dose dependence of the NO2- band intensities and measure a photochemical quantum yield of 0.04 at pH 6.5. We also examined the response of solid NaNO3 samples to 229 nm excitation and also observe formation of NO2-. The quantum yield is much smaller at ∼10-8. The solid state NaNO3 photochemistry phenomena appear complex by showing a significant dependence on the UV excitation flux and dose. At low flux/dose conditions NO2- resonance Raman bands appear, accompanied by perturbed NO3- bands, indicating stress in the NaNO3 lattice. Higher flux/dose conditions show less lattice perturbation but SEM shows surface eruptions that alleviate the stress induced by the photochemistry. Higher flux/dose measurements cause cratering and destruction of the NaNO3 surface as the surface layers are converted to NO2-. Modest laser excitation UV beams excavate surface layers in the solid NaNO3 samples. At the lowest incident fluxes a pressure buildup competes with effusion to reach a steady state giving rise to perturbed NO3- bands. Increased fluxes result in pressures that cause the sample to erupt, relieving the pressure. © 2011 American Chemical Society.

We measured the UV resonance Raman excitation profiles and Raman depolarization ratios of the arginine (Arg) vibrations of the amino acid monomer as well as Arg in the 21-residue predominantly alanine peptide AAAAA(AAARA)3A (AP) between 194 and 218 nm. Excitation within the π → π* peptide bond electronic transitions result in UVRR spectra dominated by amide peptide bond vibrations. The Raman cross sections and excitation profiles indicate that the Arg side chain electronic transitions mix with the AP peptide bond electronic transitions. The Arg Raman bands in AP exhibit Raman excitation profiles similar to those of the amide bands in AP which are conformation specific. These Arg excitation profiles distinctly differ from the Arg monomer. The Raman depolarization ratios ofArg in monomeric solution are quite simple with p = 0.33 indicating enhancement by a single electronic transition. In contrast, we see very complex depolarization ratios of Arg in AP that indicate that the Arg residues are resonance enhanced by multiple electronic transitions. © 2011 American Chemical Society.

UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this Perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the amide III3 band and the Cα-H band frequencies and intensities, can be used to determine Ramachandran ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π and 310 states from pure α-helices. These approaches can be used to determine the Gibbs free-energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of side chain vibrations will probe the role of side chains in determining protein secondary, tertiary, and quaternary structures. © 2011 American Chemical Society.

We developed a convenient and fast approach to preparing close-packed two-dimensional (2-D) particle arrays on mercury surfaces. Addition of cosolvents, such as alcohols, to aqueous colloidal particle suspensions induces spreading and self-assembly of the particles into 2-D arrays on top of the mercury surface. We can fabricate large-area close-packed 2-D arrays (>70 cm 2) within 30 s. We attached these 2-D arrays to functional hydrogel films such that the 2-D array spacings were altered by the hydrogel volume response to the environment. We directly observed the hydrogel volume induced 2-D array spacing changes by using confocal laser scanning microscopy to monitor the spacings of fluorescent polystyrene particle 2-D arrays in response to changes in pH, solvent composition, temperature, etc. © 2011 American Chemical Society.

Development of methods to fabricate nanoparticles is of great interest for many applications. In this paper, we developed a facile method to fabricate complex stoichiometrically defined nanoparticles by ultilizing the defined volume interstices of close-packed photonic crystals. Fabrication of small defined size nanoparticles enables measurements of resonance Raman cross sections of solid materials. We successfully ultilized this method to fabricate mixed NaNO3/Na2SO4 nanoparticles with a defined stoichiometry on the surface of the photonic crystal spherical particles. We used these stoichiometrically defined NaNO3/Na2SO 4 nanoparticles to determine the solid UV resonance Raman cross section of the NO31 symmetric stretching band (229 nm excitation wavelength) by monitoring the Raman spectrum of Na2SO4 as an internal standard. These are the first resonance Raman cross section measurements of solids that avoid the biasing of self-absorption. These NaNO3/Na2SO4 nanoparticles appear to show a more facile photolysis than is observed for normal solid NaNO3 samples. This templated photonic crystal fabrication of complex nanoparticle method will be important for many applications. © 2011 American Chemical Society.

We have developed the first high-diffraction-efficiency two-dimensional (2-D) photonic crystals for molecular recognition and chemical sensing applications. We prepared close-packed 2-D polystyrene particle arrays by self-assembly of spreading particle monolayers on mercury surfaces. The 2-D particle arrays amazingly diffract 80% of the incident light. When a 2-D array was transferred onto a hydrogel thin film showing a hydrogel volume change in response to a specific analyte, the array spacing was altered, shifting the 2-D array diffraction wavelength. These 2-D array photonic crystals exhibit ultrahigh diffraction efficiencies that enable them to be used for visual determination of analyte concentrations. © 2011 American Chemical Society.

We use UV resonance Raman spectroscopy to probe the lowest energy allowed electronic transitions of aqueous solutions containing Cl - salts. We show that the waters hydrating the Cl - are involved in charge transfer transitions that transfer electron density from Cl - to the water molecules. These charge transfer transitions cause significant change in the H-O-H bond angle in the excited state, which results in a strong enhancement of the preresonance Raman intensity of the water bending modes. Our work gives the first insight into the lowest allowed electronic transition of hydrated Cl -. © 2010 American Chemical Society.

Spectroscopic investigations of macromolecules generally attempt to interpret the measured spectra in terms of the summed contributions of the different molecular fragments. This is the basis of the local-mode approximation in vibrational spectroscopy. In the case of resonance Raman spectroscopy, independent contributions of molecular fragments require both a local-mode-like behavior and the uncoupled electronic transitions. Here, we show that the deep-UV resonance Raman spectra of aqueous solution-phase oligoglycines show independent peptide bond molecular fragment contributions, indicating that peptide bond electronic transitions and vibrational modes are uncoupled. We utilize this result to separately determine the conformational distributions of the internal and penultimate peptide bonds of oligoglycines. Our data indicate that in aqueous solution, the oligoglycine terminal residues populate conformations similar to those found in crystals (31-helices and β-strands) but with a broader distribution, while the internal peptide bond conformations are centered around the 31-helix Ramachandran angles. © 2009 American Chemical Society.

UV resonance Raman excitation profiles and Raman depolarization ratios were measured for trialanine and tetraalanine between 198 and 210 nm. Excitation within the π → π* electronic transitions of the peptide bond results in UVRR spectra dominated by amide peptide bond vibrations. In addition to the resonance enhancement of the normal amide vibrations, we find enhancement of the symmetric terminal COO- vibration. The Ala3 UVRR AmIII3 band frequencies indicate that poly-proline II and 2.5 1 helix conformations and type II turns are present in solution. We also find that the conformation of the interior peptide bond of Ala4 is predominantly poly-proline-II-like. The Raman excitation profiles of both Ala3 and Ala4 reveal a charge transfer electronic transition at 202 nm, where electron transfer occurs from the terminal nonbonding carboxylate orbital to the adjacent peptide bond π* orbital. Raman depolarization ratio measurements support this assignment. An additional electronic transition is found in Ala4 at 206 nm. © 2010 American Chemical Society.

We monitored the crystal growth kinetics of crystallization of a shear melted crystalline colloidal array (CCA). The fcc CCA heterogeneously nucleates at the flow cell wall surface. We examined the evolution of the (1. 1. 1) Bragg diffraction peak, and, for the first time, quantitatively monitored growth by measuring the temporal evolution of the Bragg diffraction interference fringes. Modeling of the evolution of the fringe patterns exposes the time dependence of the increasing crystal thickness. The initial diffusion-driven linear growth is followed by ripening-driven growth. Between 80 and 90 μM NaCl concentrations the fcc crystals first linearly grow at rates between 1.9 and 4.2 μm/s until they contact homogeneously nucleated crystals in the bulk. At lower salt concentrations interference fringes are not visible because the strong electrostatic interactions between particles result in high activation barriers, preventing defect annealing and leading to a lower crystal quality. The fcc crystals melt to a liquid phase at >90 μM NaCl concentrations. Increasing NaCl concentrations slow the fcc CCA growth rate consistent with the expectation of the classical Wilson-Frenkel growth theory. The final thickness of wall-nucleated CCA, that is determined by the competition between growth of heterogeneously and homogenously nucleated CCA, increases with higher NaCl concentrations. © 2010 Elsevier Inc.

We used CD and UV resonance Raman spectroscopy to study the impact of alcohols on the conformational equilibria and relative Gibbs free energy landscapes along the Ramachandran φ-coordinate of a mainly poly-Ala peptide, AP with an AAAAA(AAARA)3A sequence. 2,2,2-Trifluoroethanol (TFE) most stabilizes the α-helix-like conformations, followed by ethanol, methanol, and pure water. The π-bulge conformation is stabilized more than the α-helix, while the 310-helix is destabilized due to the alcohol-increased hydrophobicity. Turns are also stabilized by alcohols. We also found that while TFE induces more α-helices, it favors multiple, shorter helix segments. © 2010 American Chemical Society.

We measured the 229 nm absolute ultraviolet (UV) Raman cross-sections of the explosives trinitrotoluene (TNT), pentaerythritol tetranitrate (PETN), cyclotrimethylene-trinitramine (RDX), the chemically related nitroamine explosive HMX, and ammonium nitrate in solution. The 229 nm Raman cross-sections are 1000-fold greater than those excited in the near-infrared and visible spectral regions. Deep UV resonance Raman spectroscopy enables detection of explosives at parts-per-billion (ppb) concentrations and may prove useful for stand-off spectroscopic detection of explosives. © 2010 Society for Applied Spectroscopy.

We developed a straightforward method to form non-close-packed highly ordered fcc direct and inverse opal silica photonic crystals. We utilize an electrostatically self assembled crystalline colloidal array (CCA) template formed by monodisperse, highly charged polystyrene particles. We then polymerize a hydrogel around the CCA (PCCA) and condense silica to form a highly ordered silica impregnated (siPCCA) photonic crystal. Heating at 450 °C removes the organic polymer leaving a silica inverse opal structure. By altering the colloidal particle concentration we independently control the particle spacing and the wall thickness of the inverse opal photonic crystals. This allows us to control the optical dielectric constant modulation in order to optimize the diffraction; the dielectric constant modulation is controlled independently of the photonic crystal periodicity. These fcc photonic crystals are better ordered than typical close-packed photonic crystals because their self assembly utilizes soft electrostatic repulsive potentials. We show that colloidal particle size and charge polydispersity has modest impact on ordering, in contrast to that for close-packed crystals. © 2010 Elsevier Inc. All rights reserved.

We developed an efficient synthesis of monodisperse, highly surface charged, high refractive index ZnS spherical particles by using a gel-sol method. Concentrated solutions of zinc-ammonia-NTA (nitrilotriacetic acid) were reacted with thioacetamide in the presence of gelatin which stabilized the growing particles. We dramatically increased the particle surface charge density by condensing silica and silylated phosphonate groups on the particle surface. These monodisperse highly charged ZnS particles are somewhat porous and have a refractive index of 1.868. These are the highest refractive index, monodisperse, highly charged spherical particles to self assemble into non-close-packed crystalline colloidal arrays which Bragg diffract light. © 2010 Elsevier Inc.

Sodium perchlorate salt (NaClO4) is commonly used as an internal intensity standard in ultraviolet resonance Raman (UVRR) spectroscopy experiments. It is well known that NaClO4 can have profound effects on peptide stability. The impact of NaClO4 on protein stability in UVRR experiments has not yet been fully investigated. It is well known from experiment that protein stability is strongly affected by the solution composition (water, salts, osmolytes, etc.). Therefore, it is of the utmost importance to understand the physical basis on which the presence of salts and osmolytes in the solution impact protein structure and stability. The aim of this study is to investigate the effects of NaClO4, on the helical stability of an alanine peptide in water. Based upon replica-exchange molecular dynamics data, it was found that NaClO4 solution strongly stabilizes the helical state and that the number of pure helical conformations found at room temperature is greater than in pure water. A thorough investigation of the anion effects on the first and second solvation shells of the peptide, along with the Kirkwood-Buff theory for solutions, allows us to explain the physical mechanisms involved in the observed specific ion effects. A direct mechanism was found in which ClO4 ̄ ions are strongly attracted to the folded backbone. © 2010 by the Biophysical Society.

We used CD,UV resonance Raman spectroscopy, and molecular dynamics simulation to examine the impact of salts on the conformational equilibria and the Ramachandran Ψ angle (un)folding Gibbs free energy landscape coordinate of a mainly polyalanine α-helical peptide, AP of sequence AAAAA-(AAARA)3A. NaClO4 stabilizes α-helical-like conformations more than does NaCl, which stabilizes more than Na 2SO4 at identical ionic strengths. This α-helix stabilization ordering is the reverse of the Hofmeister series of anions in their ability to disorder water hydrogen bonding. Much of the NaClO4 α-helix stabilization results from ClO4- association with the AP terminal-NH3+ groups and Arg side chains. ClO4- stabilizes 310-helix conformations but destabilizes turn conformations. The decreased Cl- and SO 42- AP α-helix stabilization probably results from a decreased association with the Arg and terminal -NH3+ groups. Cl- is expected to have a smaller binding affinity and thus stabilizes α-helical conformations intermediately between NaClO 4 and Na2SO4. Electrostatic screening stabilizes π-bulge conformations. © 2009 American Chemical Society.

We utilized UV resonance Raman (UVRR) measurements and density functional theory (DFT) calculations to relate the AmII'p frequency to the Ψ angle. The AmII'p frequency shifts by ∼ 25 cm-1 as the Ψ angle is varied over allowed angles of the Pro peptide bond. The AmII'p frequency does not show any significant dependence on the Ψ dihedral angle. The conformation sensitivity of the AmII'p frequency derives from conformation-induced changes in the planarity of the Pro peptide bond; Ψ angle changes push the amide nitrogen out of the peptide bond plane. We use this AmII'p frequency dependence on the Ψ angle to track temperature-induced conformation changes in a polyproline peptide. The temperature-induced 7 cm -1 downshift in the AmII'p frequency of the polyproline peptide results from an ∼45° rotation of the Ψ dihedral angle from Ψ = 145° (ideal PPII conformation) to Ψ = 100° (collapsed PPII conformation). © 2009 American Chemical Society.

We used electronic circular dichroism (CD) and UV resonance Raman (UVRR) spectroscopy at 204 nm excitation to examine the temperature dependence of conformational changes in cyclic and linear elastin peptides. We utilize CD spectroscopy to study global conformation changes in elastin peptides, while UVRR is utilized to probe the local conformation and hydrogen bonding of Val and Pro peptide bonds. Our results indicate that at 20°C cyclic elastin predominantly populates distorted β-strand, β-type II and β-type III turn conformations. At 60°C, the β-type II turn population increases, while the distorted β-strand population decreases. Linear elastin predominantly adopts distorted β-strand and β-type III turn conformations with some β-type II turn population at 20°C. Increasing temperature to 60°C results in a small increase in the turn population. © 2008 Wiley Periodicals, Inc.

Angular-resolved reflection measurements suggest that higher-order Miller-index crystal planes of a fcc photonic crystal reflect specularly about the normal to the (111) planes. We suggest that this phenomenon results from a two-step diffraction process where light is first Bragg diffracted by higher-order Miller-index crystal planes and is then two-dimensionally diffracted by periodicities within the (111) planes to produce the specularly diffracted light. This phenomenon is a three-dimensional analog of the well-known Wood's anomaly. © 2009 The American Physical Society.

We developed a photonic crystal sensing method for diol containing species such as carbohydrates based on a poly(vinyl alcohol) (PVA) hydrogel containing an embedded crystalline colloidal array (CCA). The polymerized CCA (PCCA) diffracts visible light. We show that in the presence of borax the diffraction wavelength shifts as the concentration of glucose changes. The diffraction shifts result from the competitive binding of glucose to borate, which reduces the concentration of borate bound to the PVA diols. © 2009 The Royal Society of Chemistry.

We attached very small silica particles onto flexible monodisperse poly(N-isopropylacrylamide, PNIPAm) core particles synthesized by dispersion polymerization. These silica particles were attached to the partially swollen PNIPAm particles by the hydrolysis and condensation of tetraethoxysilane at 24 C. The resulting silica particle-functionalized PNIPAm core particles show reversible swelling and shrinking as the temperature is cycled. These particles form close-packedarray photonic crystals (PCs) as the solvent evaporates; the cores shrink to form a silica shell around the pure PNIPAm dry core particles as they close pack. The PNIPAm cores were removed by calcination, leaving a PC composed of essentially pure continuous silica shells. These silica shell PCs Bragg diffract UV light at 310 nm. The close packed particle interstices are continuous and are easily filled by water. In contrast, the silica shells are impervious to water because the process of making them results in a continuous shell of silica without holes.

Galectin-1 (Gal-1), a member of a family of evolutionarily conserved glycan-binding proteins, binds specifically to poly-N-acetyllactosamine-enriched glycoconjugates. Through interactions with these glycoconjugates, this protein modulates inflammatory responses and contributes to tumor progression and immune cell homeostasis. The carbohydrate recognition domain includes the single protein tryptophan (Trp68). UV resonance Raman spectroscopy and molecular dynamic simulation were used to examine the change in the environment of the Trp on ligand binding. The UV Raman spectra and the calculated water radial distribution functions show that, while no large structural changes in the protein follow lactose binding, substantial solvent reorganization occurs. These new insights into the microscopic role of water molecules in Gal-1 binding to its specific carbohydrate ligands provides a better understanding of the physicochemical properties of Gal-1 - saccharide interactions, which will be useful for the design of synthetic inhibitors for therapeutic purposes. © 2009 American Chemical Society.

The first quantitative study of how the mechanical properties of a swollen hydrogel depend upon the diameter of nonbonded embedded nanoparticles was studied. Monodisperse, highly charged polystyrene colloidal particles with diameters between 114 and 186 nm were used in the preparation of the PCCA studied. The PCCA studied were synthesized by UV initiated free radical polymerization of a hydrogel around the CCA. The CCA solutions used for the PCCA preparations were composed of identical weight percent particle dispersions in water to ensure constant overall polymer content within the corresponding pre-polymerization solutions. This linear dependence derives primarily from the contribution of slip within the system, which varies based on the surface area of the embedded particles. We also found that the increase in storage modulus upon exclusion of oxygen during polymerization is more pronounced for hydrogels without nanoparticle inclusions and that the modulus is dominated by particle inclusions as opposed to the cross-linker.

We are developing photonic crystal glucose sensing materials to continuously monitor relatively high glucose concentrations, such as found in blood. We modified our synthetic fabrication methodologies in order to increase the glucose concentration range and to increase the reproducibility of our PCCA fabrication. We have also advanced our understanding of the sensing response by developing a mechanical method to independently determine the hydrogel cross-link density. Our investigation of the sensing mechanism indicates that glucose binding depends mainly on the boronic acid concentrations and affinities. We determined the binding constant of 2-fluoro-5-aminophenyl boronic acid for glucose under physiological conditions. We have examined the dependence of glucose sensing upon interferences by other species that ligand to boronic acids, such as lactate and human serum albumin. We examined the stability of our sensors over a period of weeks at room temperature and demonstrated that we could further stabilize our sensing materials by reversibly dehydrating them for storage. © 2009 American Chemical Society.

Poly(N-isopropylacrylamide) (PNIPAM) is the premier example of a macromolecule that undergoes a hydrophobic collapse when heated above its lower critical solution temperature (LCST). Here we utilize dynamic light scattering, H-NMR, and steady-state and time-resolved UVRR measurements to determine the molecular mechanism of PNIPAM's hydrophobic collapse. Our steady-state results indicate that in the collapsed state the amide bonds of PNIPAM do not engage in interamide hydrogen bonding, but are hydrogen bonded to water molecules. At low temperatures, the amide bonds of PNIPAM are predominantly fully water hydrogen bonded, whereas, in the collapsed state one of the two normal CdO hydrogen bonds is lost. The NH-water hydrogen bonding, however, remains unperturbed by the PNIPAM collapse. Our kinetic results indicate a monoexponential collapse with t̃ 360 (±85) ns. The collapse rate indicates a persistence length of n ̃ 10. At lengths shorter than the persistence length the polymer acts as an elastic rod, whereas at lengths longer than the persistence length the polymer backbone conformation forms a random coil. On the basis of these results, we propose the following mechanism for the PNIPAM volume phase transition. At low temperatures PNIPAM adopts an extended, water-exposed conformation that is stabilized by favorable NIPAM-water solvation shell interactions which stabilize large clusters of water molecules. As the temperature increases an increasing entropic penalty occurs for the water molecules situated at the surface of the hydrophobic isopropyl groups. A cooperative transition occurs where hydrophobic collapse minimizes the exposed hydrophobic surface area. The polymer structural change forces the amide carbonyl and N-H to invaginate and the water clusters cease to be stabilized and are expelled. In this compact state, PNIPAM forms small hydrophobic nanopockets where the (i, i + 3) isopropyl groups make hydrophobic contacts. A persistent length of n ̃ 10 suggests a