A computational model for predicting RNA nearest neighbor free energy rankings has been expanded to include the nonstandard nucleotide inosine. The model uses average fiber diffraction data and molecular dynamic simulations to generate input geometries for Quantum mechanic calculations. This resulted in calculated intrastrand stacking, interstrand stacking, and hydrogen bonding energies that were combined to give total binding energies. Total binding energies for RNA dimer duplexes containing inosine were ranked and compared to experimentally determined free energy ranks for RNA duplexes containing inosine. Statistical analysis showed significant agreement between the computationally determined ranks and the experimentally determined ranks.
MD simulations; nonstandard nucleotide; RNA; QM calculations; inosine; base stacking
Environmentally persistent free radicals (EPFRs) are toxic organic/metal oxide composite particles that have been discovered to form from substituted benzenes chemisorbed to metal oxides. Here, we perform photoelectron spectroscopy, electron energy loss spectroscopy, and low energy electron diffraction of phenol chemisorbed to ZnO(1 0 1̱ 0) and (0 0 0 1̱)-Zn to observe electronic structure changes and charge transfer as a function adsorption temperature. We show direct evidence of charge transfer from the ZnO surfaces to the phenol. This evidence can help gain a better understanding of EPFRs and be used to develop possible future remediation strategies.
•Solid-electrolyte interfaces (SEI) are polymers derived from solvent reduction.•SEI properties depend on the degree of solvent polymerization.•Slow reduction rates yield electronically insulating, ion-conducting, solvent-impermeable SEI films.
Understanding the mechanism of formation of solid-electrolyte interphases (SEI) is key to the prospects of lithium metal batteries (LMB). Here, we investigate via cyclic voltammetry, impedance spectroscopy and chronoamperometry the role of kinetics in controlling the properties of the SEI generated from the reduction of propylene carbonate (PC, a typical solvent in LMB). Our observations are consistent with the operation of a radical chain PC electropolymerization into polymer units whose complexity increases at lower initiation rates. As proof-of-concept, we show that slow initiation rates via one-electron PC reduction at underpotentials consistently yields compact, electronically insulating, Li+-conducting, PC-impermeable SEI films.
Solid electrolyte interphase; Electropolymerization; Lithium metal batteries; Dendrite inhibition; Organic carbonates
Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.
Crystal Structure Prediction; DFT-D; polymorphs; glycine
To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data.
In this short letter, we have synthesized the BSA protected Au25 nanoclusters and studied their two photon luminescence behavior. We demonstrate that BSA Au25 nanoclusters can be used as a probe with two photon excitation capability. Our results show a quadratic relation between excitation power and emission intensity whereas with one photon excitation shows a linear dependence. The emission spectrum of BSA Au25 nanoclusters with one photon and two photon excitation shows no appreciable change. Due to its long wavelength emission (650 nm) and two photon excitation, BSA Au25 can be potentially used as a probe for deep tissue imaging.
Gold clusters; One and two photon excitation; Luminescence; BSA
A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design.
The discharge of a platinum parallel-plate capacitor filled with ultrapure water has been measured. The observed discharge trend can be described by a Modified Poisson-Boltzmann Equation (MPB) only when the voltage is very low. Increasing the applied voltage creates an “exclusion zone,” in which the MPB equation no longer fits, and the system capacitance shows a dependence on the spacing between the two platinum plates. The permittivity of water, calculated considering the system as a plane capacitor, appears to be very high. This implies that the exclusion zone could have extraordinary dielectric properties.
Knowledge of water-water potential is important for an accurate description of water. Potential between two molecules depends upon the distance, relative orientation of each molecule and local environment. In simulation, water-water hydrogen bonds are handled by point-charge water potentials and by polarizable models. These models produce good results for bulk water being parameterized for such environment. Water around surfaces and in channels, however is different from bulk water. Using quantum-mechanical methods, hydrogen bond strength was calculated in the vicinity of different monoions. A simple empirical relationship was discovered between the maximum hydrogen bond and the electric field produced by ion.
The nonlinear optical properties of a series of pyrrolic compounds consisting of BODIPY and aza-BODIPY systems are investigated using 532 nm nanosecond laser and the Z-scan technique. Results show that 3,5-distyryl extension of BODIPY to the red shifted MeO2BODIPY dye has a dramatic impact on its nonlinear absorption properties changing it from a saturable absorber to an efficient reverse saturable absorbing material with a nonlinear absorption coefficient of 4.64 × 10−10 m/W. When plotted on a concentration scale per mole of dye in solution MeO2BODIPY far outperforms the recognized zinc(II) phthalocyanine dye and is comparable to that of zinc(II) tetraphenylporphyrin.
C29-peridinin is a synthetic analogue of the important, naturally-occurring carotenoid, peridinin, found in several marine algal species. C29-peridinin has five conjugated carbon-carbon double bonds compared to eight possessed by peridinin and also lacks the methyl group functionalities typically present along the polyene chain of carotenoids. These structural modifications lead to unique excited state properties and important insights regarding the factors controlling the photophysics of peridinin and other carbonyl-containing carotenoids, which are critical components of the light-harvesting systems of many photosynthetic organisms.
We describe a novel approach to enhance the sensitivity of a grating-based surface plasmon-coupled emission (SPCE) sensor by increasing the thickness of the metal film used in this system. The calculated optical properties of grating-based SPR spectra were significantly affected by both grating depth and by gold thickness. Higher angular sensitivity could be achieved at short wavelengths and under in situ measurement (analysis under aqueous condition). We confirmed the predicated enhancements of SPCE response using Alexa Fluor 647-labeled anti-mouse IgG immobilized on the SPCE sensor chips. Grating-coupled SPCE sensor chips can be used as a useful tool for high contents analysis of chemical and biomolecular interactions.
Bone minerals possess two primary hydrogen sources: hydroxide ions in the nanocrystalline core and structural water in the amorphous surface layer. In order to accurately measure their concentrations using hydrogen to phosphorus cross polarization NMR spectroscopy, it is necessary to analyze the dependence of signal intensities on serial contact times, namely, cross polarization kinetics. A reliable protocol is developed to iteratively decompose the severely overlapped spectra and to analyze the cross-polarization kinetics, leading to measurement of hydroxyl and structural water concentrations. Structural water concentration is used to estimate mineral specific surface area and nanocrystal thickness for intact bone.
bone; biominerals; cross-polarization; CP kinetics; spectral deconvolution; solid-state NMR; magic-angle spinning
Peptide hydrogels are promising candidates for a wide range of medical and biotechnological applications. To further expand the potential utility of peptide hydrogels, herein we demonstrate a simple yet effective strategy to render peptide hydrogels photodegradable, making controlled disassembly of the gel structure of interest feasible. In addition, we find that the high-frequency amide I′ component (i.e., the peak at ~1685 cm−1) of the photodegradable peptide hydrogel studied shows an unusually large enhancement, in comparison to that of other peptide fibrils consisting of antiparallel β-sheets, making it a good model system for further study of the coupling-structure relationship.
We used Surface Enhanced Raman Spectroscopy (SERS) to detect binding events between streptavidin and biotinylated lipid bilayers. The binding events took place at the surface between microfluidic channels and anodized aluminum oxide (AAO) with the latter serving as substrates. The bilayers were incorporated in the substrate pores. It was revealed that non-bound molecules were easily washed away and that large suspended cells (Salmonella enterica) are less likely to interfere with the monitoring process: when focusing to the lower surface of the channel, one may resolve mostly the bound molecules.
Many aspects of biology depend on the ability of DNA-binding proteins to locate specific binding sites within the genome. Interest in this target search problem has been reinvigorated through the recent development of microscopy-based technologies capable of tracking individual proteins in real-time as they search for binding sites. In this review we discuss how two different proteins, lac repressor and RNA polymerase, have solved the target search problem through seemingly different mechanisms, with an emphasis on how recent in vitro single-molecule studies have influenced our understanding of these reactions.
To expand the spectroscopic utility of the non-natural amino acid p-cyanophenylalanine (PheCN), we examine the quenching efficiencies of a series of commonly encountered anions toward its fluorescence. We find that iodide exhibits an unusually large Stern-Volmer quenching constant, making it a convenient choice in PheCN fluorescence quenching studies. Indeed, using the villin headpiece subdomain as a testbed we demonstrate that iodide quenching of PheCN fluorescence offers a convenient means to reveal protein conformational heterogeneity. Furthermore, we show that the amino group of PheCN strongly quenches its fluorescence, suggesting that PheCN could be used as a local pH sensor.
Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.
membrane proteins; continuum membrane model; Poisson-Boltzmann; implicit solvation
•Water confined in cylindrical silica channels is studied with neutron scattering and computer simulation.•Density distribution across the pore is not uniform and peaks near the surface.•At low temperatures the distribution becomes less uniform, possibly resembling disordered ice.•Significant penetration into silica surface.•Methods can be applied to many other instances of fluids at surfaces.
The structure of water confined in MCM41 silica cylindrical pores is studied to determine whether confined water is simply a version of the bulk liquid which can be substantially supercooled without crystallisation. A combination of total neutron scattering from the porous silica, both wet and dry, and computer simulation using a realistic model of the scattering substrate is used. The water in the pore is divided into three regions: core, interfacial and overlap. The average local densities of water in these simulations are found to be about 20% lower than bulk water density, while the density in the core region is below, but closer to, the bulk density. There is a decrease in both local and core densities when the temperature is lowered from 298 K to 210 K. The radical proposal is made here that water in hydrophilic confinement is under significant tension, around −100 MPa, inside the pore.
As nanotechnology field continues to develop, assessing nanoparticle toxicity is very important for advancing nanoparticles for daily life application. In this Letter, we report the effect of surface coating on cyto, geno and photo-toxicity of silver nanomaterials of different shapes on human skin HaCaT keratinocytes. We found that the citrate coated colloidal silver nanoparticles at 100 µg/mL level are not geno-, cyto- and phtotoxic. On the other hand, citrate coated powder form of the silver nanoparticles are toxic. We have demonstrated that coating of the silver nanoparticles with a biodegradable polymer prevents the toxicity of the powder. Toxicity mechanism has been discussed.
Femtosecond photodynamics of the reverse (15EPfr→15ZPr) reaction of the red/far-red phytochrome Cph1 from Synechocystis were resolved with visible broadband transient absorption spectroscopy. Multi-phasic dynamics were resolved and separated via global target analysis into a fast-decaying (260 fs) excited-state population that bifurcates to generate the isomerized Lumi-F primary photoproduct and a non-isomerizing vibrationally excited ground state that relaxes back into the 15EPfr ground state on a 2.8-ps time scale. Relaxation on a 1-ms timescale results in the loss of red absorbing region, but not blue region, of Lumi-F, which indicates that formation of 15ZPr occurs on slower timescales.
In the present work, we have synthesized water soluble Ag nanoclusters using PMAA as a template with different Ag+: COO-ratios, to optimize it for highest brightness using less UV exposure time. Fluorescence polarization was 0.30 for and was found to vary with excitation and emission wavelength with few hundred picoseconds average fluorescence lifetime. Fluorescence Correlation Spectroscopy data depicts slower diffusion at red excitation compared to blue excitation in confocal volume than conventionally synthesized colloids proving presence of multiple sizes. The optical properties of the particles are dependent upon the excitation wavelength used and the emission wavelength collected.
Metal Nanoclusters; Fluorescent Ag Nanoclusters; Polymethylacrylic Acid; Polarization; FCS
Dynamics of the chemical transformation of dicyclopentadiene into cyclopentadiene in a supersonic molecular beam is elucidated using femtosecond time-resolved degenerate pump–probe mass spectrometry. Control of this ultrafast chemical reaction is achieved by using linearly chirped frequency modulated pulses. We show that negatively chirped femtosecond laser pulses enhance the cyclopentadiene photo-product yield by an order of magnitude as compared to that of the unmodulated or the positively chirped pulses. This demonstrates that the phase structure of femtosecond laser pulse plays an important role in determining the outcome of a chemical reaction.
We investigated the feasibility of using platinum nanostructures to accomplish the metal-enhanced fluorescence (MEF) in the UV spectral region. We examine the possibility for detection of the intrinsic fluorescence from nucleotides and G-quadruplex DNA on platinum nanoparticles. Guanosine monophosphate (GMP) showed significant increases (~20-fold) in fluorescence intensities in the presence of platinum nanostructures when compared to quartz controls. G-quadruplex DNA demonstrated ~5-fold increase in fluorescence intensity and higher photostability in the presence of Pt nanostructures. We performed finite element method simulations to explore how Pt nanoparticles interact with plane waves and conformed that the Pt nanostructures are promising for enhancing the fluorescence emission in the UV region.
Intrinsic fluorescence of nucleotides; metal-enhanced fluorescence (MEF); plasmonics; metallic nanoparticles; finite element calculations
As the nanotechnology field continues to develop, assessing nanoparticle toxicity is very important for advancing nanoparticles for biomedical application. Here we report cytotoxicity of gold nanomaterial of different size and shape using MTT test, absorption spectroscopy and TEM. Spherical gold nanoparticles with different sizes are not inherently toxic to human skin cells, but gold nanorods are highly toxic due to the presence of CTAB as coating material. Due to CTAB toxicity, and aggregation of gold nanomaterials in the presence of cell media, it is a real challenge to study the cytotoxicity of gold nanomaterials individually.