Probing the structure of single-molecule surface-enhanced Raman scattering hot spots

We present here a detailed study of the specific nanoparticle structures that give rise to single-molecule surface-enhanced Raman scattering (SMSERS). A variety of structures are observed, but the simplest are dimers of Ag nanocrystals. We chose one of these structures for detailed study using electrodynamics calculations and found that the electromagnetic SERS enhancement factors of 10(9) are easily obtained and are consistent with single-molecule SERS activity.     

Diverse fragment clustering and water exclusion identify protein hot spots

Simulated annealing of chemical potential located the highest affinity positions of eight organic probes and water on eight static structures of hen egg white lysozyme (HEWL) in various conformational states. In all HELW conformations, a diverse set of organic probes clustered in the known binding site (hot spot). Fragment clusters at other locations were excluded by tightly-bound waters so that only the hot-spot cluster remained in each case. The location of the hot spot was correctly predicted irrespective of the protein conformation and without accounting for protein flexibility during the simulations. Any one of the static structures could have been used to locate the hot spot. A site on a protein where a diversity of organic probes is calculated to cluster, but where water specifically does not bind, identifies a potential small-molecule binding site or protein-protein interaction hot spot.     

Preparation and dynamics of vibrational hot spots in polyatomics via raman scttering

We exploit a recent time dependent formulation of resonance Raman scattering to examine vibrational hot spot production in molecules which have dissociative excited states. The excited-state dynamics are described by a Raman wavefunction which is used to obtain the resonance Raman (RR) spectrum. The RR spectrum will contain the spectral signature of the subsequent dynamics and decay of the hot spot initial condition.     

Porous polyurethanes synthesized within high internal phase emulsions

PolyHIPE are highly porous, emulsion‐templated polymers typically synthesized via free‐radical polymerization within a water‐in‐oil (W/O) high internal phase emulsion (HIPE) whose dispersed, aqueous phase occupies more than 74% of the volume. The synthesis of a polyHIPE containing biodegradable polymers is not straightforward because the presence of both an organic phase and an aqueous phase within the HIPE limits the type of polymerization reactions that can be used. This article describes the synthesis of polyHIPE containing biodegradable poly(ε‐caprolactone) (PCL) groups through the step‐growth reaction of a diisocyanate with a flexible PCL triol to form a crosslinked polyurethane. The reaction of the diisocyanate with the water in the HIPE produced urea groups and large bubbles from the generation of CO₂. The polymer walls between these bubbles consisted of a porous, emulsion‐templated structure. Polymerization with an excess of diisocyanate produced a significant enhancement in the amounts of urea and CO₂. The reduction in the flexible PCL content and the enhancement in the rigid urea content produced an increase in wall modulus that was over 20‐fold. The ability to synthesize polyHIPE through such step‐growth reactions is an important advance in the adaptation of polyHIPE for such applications as tissue engineering. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5806–5814, 2009     

Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes

"Hot spots" are residues accounting for the majority of the protein-protein binding free energy (BFE) despite that they comprise only a small fraction of the protein-protein interface. A hot spot can be found experimentally by measuring the BFE change upon mutating it to alanine: the mutation gives rise to a significantly large increase in the BFE. Theoretical prediction of hot spots is an enthusiastic subject in biophysics, biochemistry, and bioinformatics. For the development of a reliable prediction method, it is essential to understand the physical origin of hot spots. To this end, we calculate the water-entropy gains upon binding both for a wild-type complex and for its mutant complex using a hybrid method of the angle-dependent integral equation theory applied to a molecular model for water and the morphometric approach. We note that this type of calculation has never been employed in the previously reported methods. The BFE change due to alanine mutation is evaluated only from the change in the water-entropy gain with no parameters fitted to the experimental data. It is shown that the overall performance of predicting hot spots in our method is higher than that in Robetta, a standard free-energy-based method using fitting parameters, when the most widely used criterion for defining an actual hot spot is adopted. This result strongly suggests that the water-entropy effect we calculate is the key factor governing basic physics of hot spots.     

Self-assembled nanodisks with targetlike multirings aggregated at the air-water interface

In this communication, we report the self-assembly of zirconia by mixing its precursor with another solution containing surfactant as well as gelatin. The resulting zirconia product consists of many disks with a range of diameter from approximately 100 nm to approximately 2 mum. These disks can be assembled inside aqueous systems. Meanwhile the disks rise gradually and eventually form a visible film at the air-water interface. Remarkably, the structure of zirconia disks templated by surfactant has been found to be targetlike multirings with a d spacing of approximately 3.3 nm. We propose that a successful multirings self-assembly depends on two different template-functions from the same surfactant, excellent tenacity of the zirconia layers and the strong ability of the gelatin to stabilize and disperse the disks.     

The influences of particle number on hot spots in strongly coupled metal nanoparticles chain

In understanding of the hot spot phenomenon in single-molecule surface enhanced Raman scattering (SM-SERS), the electromagnetic field within the gaps of dimers (i.e., two particle systems) has attracted much interest as it provides significant field amplification over single isolated nanoparticles. In addition to the existing understanding of the dimer systems, we show in this paper that field enhancement within the gaps of a particle chain could maximize at a particle number N>2, due to the near-field coupled plasmon resonance of the chain. This particle number effect was theoretically observed for the gold (Au) nanoparticles chain but not for the silver (Ag) chain. We attribute the reason to the different behaviors of the dissipative damping of gold and silver in the visible wavelength range. The reported effect can be utilized to design effective gold substrate for SM-SERS applications.     

Two-dimensional LDH nanodisks modified with hyaluronidase enable enhanced tumor penetration and augmented chemotherapy

The condensed tumor extracellular matrix(ECM) consisting of cross-linked hyaluronic acid(HA) is one of the key factors that result in the aberrant tumor microenvironment and severely impair drug delivery and tumor penetration. Herein, we report a simple design of a hyaluronidase(HAase)-modified layered double hydroxide(LDH) nanoplatform loaded with anticancer drug doxorubicin(DOX) for enhanced tumor penetration and augmented chemotherapy. In our approach, LDH nanodisks were synthesized via a co-precipitation method, modified with HAase by electrostatic attraction, and finally physically loaded with DOX. The formulated DOX/LDH-HAase complexes show a high DOX loading percentage of 34.2% with good colloidal stability, retain 86.1% of the enzyme activity, and release DOX in a pH-responsive manner having a faster release rate under slightly acidic tumor microenvironment than that under a physiological condition. With the catalytic activity of HAase to digest the HA nearby the cancer cells, the developed DOX/LDH-HAase complexes enable more significant uptake by cancer cells and penetration in 3-dimensional tumor spheroids than enzyme-free DOX/LDH complexes, thus displaying much better antitumor efficacy in vitro than the latter. The more significant tumor penetration and inhibition of the DOX/LDH-HAase complexes than that of the DOX/LDH complexes was further demonstrated by in vivo tumor imaging and therapeutic activity assessments. Our study suggests a unique nanomedicine platform combined with both anticancer drug and enzyme for improved tumor penetration and chemotherapy, which is promising for effective chemotherapy of different types of stroma-rich tumors.     

Aromatic and antiaromatic gold(III) hexaphyrins with multiple gold-carbon bonds

Au(III) metalation of hexakis(pentafluorophenyl) [26]hexaphyrin led to formation of aromatic mono-Au(III) hexaphyrin and bis-Au(III) hexaphyrin, in which the inner pyrrolic beta-protons are activated to form gold-carbon bonds, hence accommodating Au(III) ion with a NNCC core in a square planar manner. Two-electron reductions of these complexes with NaBH4 provided the corresponding [28]hexaphyrin complexes which exhibit distinct paratropic ring currents.     

Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme

Binding hot spots, protein regions with high binding affinity, can be identified by using X-ray crystallography or NMR spectroscopy to screen libraries of small organic molecules that tend to cluster at such hot spots. FTMap, a direct computational analogue of the experimental screening approaches, uses 16 different probe molecules for global sampling of the surface of a target protein on a dense grid and evaluates the energy of interaction using an empirical energy function that includes a continuum electrostatic term. Energy evaluation is based on the fast Fourier transform correlation approach, which allows for the sampling of billions of probe positions. The grid sampling is followed by off-grid minimization that uses a more detailed energy expression with a continuum electrostatics term. FTMap identifies the hot spots as consensus clusters formed by overlapping clusters of several probes. The hot spots are ranked on the basis of the number of probe clusters, which predicts their binding propensity. We applied FTMap to nine structures of hen egg-white lysozyme (HEWL), whose hot spots have been extensively studied by both experimental and computational methods. FTMap found the primary hot spot in site C of all nine structures, in spite of conformational differences. In addition, secondary hot spots in sites B and D that are known to be important for the binding of polysaccharide substrates were found. The predicted probe-protein interactions agree well with those seen in the complexes of HEWL with various ligands and also agree with an NMR-based study of HEWL in aqueous solutions of eight organic solvents. We argue that FTMap provides more complete information on the HEWL binding site than previous computational methods and yields fewer false-positive binding locations than the X-ray structures of HEWL from crystals soaked in organic solvents.     

Transient cage formation around hot gold colloids dispersed in polymer solutions

Gold colloids dispersed in dilute to concentrated polymer solutions can efficiently be heated by laser irradiation and act as almost pointlike heat sources. In systems with positive Soret coefficients S(T) of the polymer, such as solutions of polystyrene in toluene, the polymer can almost entirely be removed from the particle surface. The colloid attracts the solvent and a transient cage of low viscosity and dramatically enhanced mobility is formed, which follows the motion of the particle with a certain retardation. Based on a complete parameterization of S(T)(M, c, T), we analyze in detail the stationary temperature, concentration, and viscosity profiles. Depending on the polymer molar mass and concentration on the distance to the glass transition temperature, the negative or positive feedback-loops are established that lead to either attenuation or self-amplification of the polymer depletion.     

3D aluminum/silver hierarchical nanostructure with large areas of dense hot spots for surface‐enhanced raman scattering

Plasmonic nanomaterials possessing large‐volume, high‐density hot spots with high field enhancement are highly desirable for ultrasensitive surface‐enhanced Raman scattering (SERS) sensing. However, many as‐prepared plasmonic nanomaterials are limited in available dense hot spots and in sample size, which greatly hinder their wide applications in SERS devices. Here, we develop a two‐step physical deposition protocol and successfully fabricate 3D hierarchical nanostructures with highly dense hot spots across a large scale (6 × 6 cm²). The nanopatterned aluminum film was first prepared by thermal evaporation process, which can provide 3D quasi‐periodic cloud‐like nanostructure arrays suitable for noble metal deposition; then a large number of silver nanoparticles with controllable shape and size were decorated onto the alumina layer surfaces by laser molecular beam epitaxy, which can realize large‐area accessible dense hot spots. The optimized 3D‐structured SERS substrate exhibits high‐quality detection performance with excellent reproducibility (13.1 and 17.1%), whose LOD of rhodamine 6G molecules was 10^?9 M. Furthermore, the as‐prepared 3D aluminum/silver SERS substrate was applied in detection of melamine with the concentration down to 10^?7 M and direct detection of melamine in infant formula solution with the concentration as low 10 mg/L. Such method to realize large‐area hierarchical nanostructures can greatly simplify the fabrication procedure for 3D SERS platforms, and should be of technological significance in mass production of SERS‐based sensors.     

A study of internal standardization in the analysis of fine gold with the glow-discharge source

Methods of internal standardization in the glow-discharge spectrometric analysis of gold are discussed. The method recommended by Jäger, based on the amount of material sputtered from the sample, gives less precise results for the gold content than when results are calculated by a simple difference method. The Jäger method is also shown to give a false impression of sensitivity where this does not exist at high concentrations. Results obtained by difference with a direct-reading spectrometer and glowdischarge source compare well with fire-assay results.     

Ultrafast investigations of vibrationally hot molecules after internal conversion in solution

The creation of vibrationally very hot molecules after internal conversion is seen for the first time in a liquid environment. Cooling of the excited molecules occurs within several 10⁻¹¹ s. Excitation of azulene with photons of 19000 cm⁻¹ leads to a transient internal temperature of 1200 K. The excess population of vibrational modes of 700 cm⁻¹ decays with a time constant of 40 ps.     

Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy

Journal of Computer-Aided Molecular Design - Assessment of target druggability guided by search and characterization of hot spots is a pivotal step in early stages of drug-discovery. The raw output...     

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

The identification of hot spots, i.e., binding regions that contribute substantially to the free energy of ligand binding, is a critical step for structure-based drug design. Here we present the application of two fragment-based methods to the detection of hot spots for DJ-1 and glucocerebrosidase (GCase), targets for the development of therapeutics for Parkinson’s and Gaucher’s diseases, respectively. While the structures of these two proteins are known, binding information is lacking. In this study we employ the experimental multiple solvent crystal structures (MSCS) method and computational fragment mapping (FTMap) to identify regions suitable for the development of pharmacological chaperones for DJ-1 and GCase. Comparison of data derived via MSCS and FTMap also shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult crystallographic experiments.