Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2–3 bright states and all the close by dark states, for a total of 6–9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.     

Lead–carbon hybrid ultracapacitors fabricated by using sulfur,nitrogen-doped reduced graphene oxide as anode material derived from spent lithium-ion batteries

Journal of Solid State Electrochemistry - The electrochemical-grade natural graphite flake prices are increasing day by day. Reusing and recycling graphite materials from the spent lithium-ion...     

Influence of the electrical interface properties on the rheological behavior of sonicated soy lecithin dispersions

A significant effect, on the rheological behavior, due to the electrical properties of vesicles formed from concentrated soy lecithin dispersions have been studied in this work. The rheopectic behavior of concentrated soy lecithin dispersions (120, 150, 180, 210 and 240 g L-1) prepared by swelling-light sonication-freezing-unfreezing procedure is studied and it is specially emphasized on the transition under steady shear from lamellar phase of planar sheets to closed structures as multilamellar vesicles. Samples have been exposed to a different number of sonication cycles (from 0 to 100) and the changes in the hysteresis loop area, the apparent viscosity and the electrophoretic mobility have been studied. When the number of sonication cycles increases, the size and number of bilayers of these multilamellar vesicles decrease and therefore the total number of the vesicles and the volume fraction occupied by them show an increase.     

Establishing the feasibility of coupled solid-phase extraction-solid-phase derivatization for acidic herbicides

The significance of this research is that it improves analytical methodology used for organic chemicals in aqueous solutions by establishing the feasibility of heterogeneous chemical derivatization at the liquid-solid interface (i.e., solid-phase reaction or solid-phase derivatization). A solid-phase derivatization method for determining chlorinated herbicide acids was developed. Solid-phase extraction was used to concentrate and retain analytes on sorbents for subsequent solid-phase derivatization. Background interferences were removed from the chromatograms by electronically subtracting the responses of blank, nonfortified analyses from spiked samples. Two extraction sorbents (octadecyl bonded silica and polystyrene-divinylbenzene) and two derivatizing reagents (BF3-MeOH and trimethylsilyldiazomethane) were investigated. Recovery of 13 chlorinated herbicide acids--including pentachlorophenol, dinoseb, and bentazon (having a derivatizable functional group, -OH or -NH, bonded directly to a phenyl group); dicamba, picloram, acifluorfen, 3,5-dichlorobenzoic acid, and dacthal (having a derivatizable functional group, -COOH, bonded directly to a phenyl group); and 2,4-D, 2,4,5-T, dichlorprop, 2,4,5-TP, and 2,4-DB (having a derivatizable functional group, -COOH, bonded directly to a sp3 carbon atom)--was tested. The analytical method developed was proven successful for determining acidic herbicides, except for the dacthal diacid metabolite, in aqueous samples.     

Separations of hydrophobic synthetic peptides in counter-current chromatography

Synthetic peptides with many aromatic, aliphatic and especially acidic amino acid residues are not very soluble and require strong solvents for useful partitioning. A chloroform-methanol-acidic solvent system fractionates neutral and basically charged 26-mers to provide high yields. An insoluble 15-mer with 5 Trp residues and 60% overall hydrophobic amino acid content was purified in pyridine-acetic acid and in another basic t-butyl methyl ether-n-butanol-acetonitrile solvent system with high recovery. Two instruments were used, the eccentric-multi-layer hybrid coil planet centrifuge and the new spiral disk planet centrifuge that were able to retain the stationary phase of these solvent systems, some of which have low interfacial tension.     

Structural confirmation of the dihydrosphinganine and fatty acid constituents of the dental pathogen Porphyromonas gingivalis

Porphyromonas gingivalis, a recognized periodontal pathogen, is a source of sphinganine bases, fatty acids, free ceramides as well as complex lipids that potentiate interleukin-1b-mediated secretory responses in gingival fibroblasts. The purpose of this study is the structural verification of the sphinganine bases and fatty acids that had been proposed as major components of the complex lipids found in P. gingivalis. The putative C17, C18, and C19 sphinganine bases were prepared from Garner's aldehyde (1) or from a protected serine Weinreb's amide (2). We confirmed that isobranched sphinganine bases are the major structural feature of the ceramides observed from P. gingivalis. We also prepared a C17 unsaturated fatty acid, along with an isobranched C17 3-hydroxy fatty acid, and determined that the major component of the active lipids was the latter.     

Microfluidic devices for culturing primary mammalian neurons at low densities

Microfluidic devices have been used to study high-density cultures of many cell types. Because cell-to-cell signaling is local, however, there exists a need to develop culture systems that sustain small numbers of neurons and enable analyses of the microenvironments. Such cultures are hard to maintain in stable form, and it is difficult to prevent cell death when using primary mammalian neurons. We demonstrate that postnatal primary hippocampal neurons from rat can be cultured at low densities within nanoliter-volume microdevices fabricated using polydimethylsiloxane (PDMS). Doing so requires an additional fabrication step, serial extractions/washes of PDMS with several solvents, which removes uncrosslinked oligomers, solvent and residues of the platinum catalyst used to cure the polymer. We found this step improves the biocompatibility of the PDMS devices significantly. Whereas neurons survive for > or = 7 days in open channel microdevices, the ability to culture neurons in closed-channel devices made of untreated, native PDMS is limited to < or = 2 days. When the closed-channel PDMS devices are extracted, biocompatibility improves allowing for reliable neuron cultures at low densities for > or = 7 days. Comparisons made to autoclaved PDMS and native, untreated PDMS reveal that the solvent-treated polymer is superior in sustaining low densities of primary neurons in culture. When neuronal affinity for local substrates is observed directly, we find that axons localize to channel corners and prefer PDMS surfaces to glass in hybrid devices. When perfusing the channels with media by gravity flow, cultured hippocampal neurons survive for > or = 11 days. Extracting PDMS improves biocompatibility of microfluidic devices and thus enables the study of differentiation of identifiable neurons and the characterization of local extracellular signals.     

Simple, general, and efficient synthesis of meso-substituted borondipyrromethenes from a single platform

An unprecedented synthesis of 8-substituted-borondipyrromethenes is described starting from 8-thiomethylbodipy 1. Aryl, heteroaryl, alkenyl, and organometallic boronic acids smoothly reacted with 1 in the presence of a catalytic amount of Pd(0) and a stoichiometric amount of Cu(I)-2-thienylcarboxylate under neutral conditions to give the corresponding Bodipy analogues in good to quantitative yields (20 examples). A remarkable reactivity was observed in some cases, e.g., ferrocenylboronic acid gave the product in 98% isolated yield after only 10 min at 55 degrees C.     

Validation studies of the site-directed docking program LibDock

The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, G. L.; Andrews, W. C.; Capelli, A.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Walls, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. J. Med. Chem. 2006, 49, 5912-5931). Docking experiments were performed to assess both the accuracy in reproducing the binding mode of the ligand and the retrieval of active compounds in a virtual screening protocol using both the DJD (Diller, D. J.; Merz, K. M., Jr. Proteins 2001, 43, 113-124) and LigScore2 (Krammer, A. K.; Kirchoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. J. Mol. Graphics Modell. 2005, 23, 395-407) scoring functions. This study was conducted using DJD scoring, and poses were rescored using all available scoring functions in the Accelrys LigandFit module, including LigScore2. For six out of eight targets at least 30% of the ligands were docked within a root-mean-square difference (RMSD) of 2.0 A for the crystallographic poses when the LigScore2 scoring function was used. LibDock retrieved at least 20% of active compounds in the top 10% of screened ligands for four of the eight targets in the virtual screening protocol. In both studies the LigScore2 scoring function enhanced the retrieval of crystallographic poses or active compounds in comparison with the results obtained using the DJD scoring function. The results for LibDock accuracy and ligand retrieval in virtual screening are compared to 10 other docking and scoring programs. These studies demonstrate the utility of the LigScore2 scoring function and that LibDock as a feature directed docking method performs as well as docking programs that use genetic/growing and Monte Carlo driven algorithms.     

Interaction of hydrogen chloride with ice surfaces: the effects of grain size, surface roughness, and surface disorder

Characterization of the interaction of hydrogen chloride (HCl) with polar stratospheric cloud (PSC) ice particles is essential to understanding the processes responsible for ozone depletion. The interaction of HCl with ice was studied using a coated-wall flow tube with chemical ionization mass spectrometry (CIMS) between 5x10(-8) and 10(-4) Torr HCl and between 186 and 223 K, including conditions recently shown to induce quasi-liquid layer (QLL) formation on single crystalline ice samples. Measurements were performed on smooth and rough (vapor-deposited) polycrystalline ice films. A numerical model of the coated-wall flow reactor was used to interpret these results and results of studies on zone-refined ice cylinders with grain sizes on the order of several millimeters (reported elsewhere). We found that HCl adsorption on polycrystalline ice films typically used in laboratory studies under conditions not known to induce surface disordering consists of two modes: one relatively strong mode leading to irreversible adsorption, and one relatively weak binding mode leading to reversible adsorption. We have indirect experimental evidence that these two modes of adsorption correspond to adsorption to sites at crystal faces and those at grain boundaries, but there is not enough information to enable us to conclusively assign each adsorption mode to a type of site. Unlike what was observed in the zone-refined ice study, there was no strong qualitative contrast found between the HCl uptake curves under QLL versus non-QLL conditions for adsorption on smooth and vapor-deposited ices. We also found indirect evidence that HCl hexahydrate formation on ice between 3x10(-7) and 2x10(-6) Torr HCl and between 186 and 190 K is a process involving hydrate nucleation and propagation on the crystal surface, rather than one originating in grain boundaries, as has been suggested for ice formed at lower temperatures. These results underscore the dependence of the HCl-ice interaction on the characteristics of the ice substrate.